Genome analysis of Endomicrobium proavitum suggests loss and gain of relevant functions during the evolution of intracellular symbionts.   
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Genome analysis of Endomicrobium proavitum suggests loss and gain of relevant functions during the evolution of intracellular symbionts.

Appl Environ Microbiol. 2017 Jun 23;:

Authors: Zheng H, Dietrich C, Brune A

Abstract
Bacterial endosymbionts of eukaryotes show progressive genome erosion, but detailed investigations of the evolutionary processes involved in the transition to an intracellular lifestyle are generally hampered by the lack of extant free-living lineages. Here, we characterize the genome of the recently isolated, free-living Endomicrobium proavitum, the second member of the Elusimicrobia phylum brought into pure culture, and compare it to the closely related "Candidatus Endomicrobium trichonymphae" strain Rs-D17, a previously described but uncultured endosymbiont of termite gut flagellates. A reconstruction of the metabolic pathways of E. proavitum matched the fermentation products formed in pure culture and underscored its restriction to glucose as substrate. However, several pathways present in the free-living strain, e.g., for uptake and activation of glucose and its subsequent fermentation, ammonium assimilation, and outer-membrane biogenesis, were absent or disrupted in the endosymbiont, probably lost during the massive genome rearrangements that occurred during symbiogenesis. While the majority of the genes in strain Rs-D17 have orthologs in E. proavitum, the endosymbiont also possesses a number of functions that are absent from the free-living strain and may represent adaptations to the intracellular lifestyle. Phylogenetic analysis revealed that the genes encoding glucose 6-phosphate and amino acid transporters, acetaldehyde/alcohol dehydrogenase, and the pathways of glucuronic acid catabolism and thiamine pyrophosphate biosynthesis were either acquired by horizontal gene transfer or may represent ancestral traits that were lost in the free-living strain. The polyphyletic origin of Endomicrobia in different flagellate hosts makes them excellent models for future studies of convergent and parallel evolution during symbiogenesis.Importance The isolation of a free-living relative of intracellular symbionts provides the rare opportunity to identify the evolutionary processes that occur in the course of symbiogenesis. Our study documents that the genome of "Candidatus Endomicrobium trichonymphae", which represents a clade of endosymbionts that have coevolved with termite gut flagellates for more than 40 million years, is not simply a subset of the genes present in Endomicrobium proavitum, a member of the ancestral, free-living lineage. Rather, comparative genomics revealed that the endosymbionts possess several relevant functions that were either prerequisites for colonization of the intracellular habitat or might have served to compensate for genes losses that occurred during genome erosion. Some gene sets found only in the endosymbiont were apparently acquired by horizontal transfer from other gut bacteria, which suggests that the intracellular bacteria of flagellates are not entirely cut off from gene flow.

PMID: 28646115 [PubMed - as supplied by publisher]


           Genetic biomarkers in uveal melanoma: an exploration using high-resolution array comparative genomic hy-bridization    
Alshammari, Nawal (2017) Genetic biomarkers in uveal melanoma: an exploration using high-resolution array comparative genomic hy-bridization. PhD thesis, University of Sheffield.
           Identification of Subtype-specific Pathogenetic Aberrations in Soft Tissue Sarcoma utilising High-resolution Genomic Copy Number Analysis    
Salawu, Abdulazeez (2014) Identification of Subtype-specific Pathogenetic Aberrations in Soft Tissue Sarcoma utilising High-resolution Genomic Copy Number Analysis. PhD thesis, University of Sheffield.
          Effects of Antenatal Maternal Depressive Symptoms and Socio-Economic Status on Neonatal Brain Development are Modulated by Genetic Risk   
<span class="paragraphSection"><div class="boxTitle">Abstract</div>This study included 168 and 85 mother–infant dyads from Asian and United States of America cohorts to examine whether a genomic profile risk score for major depressive disorder (GPRS<sub>MDD</sub>) moderates the association between antenatal maternal depressive symptoms (or socio-economic status, SES) and fetal neurodevelopment, and to identify candidate biological processes underlying such association. Both cohorts showed a significant interaction between antenatal maternal depressive symptoms and infant GPRS<sub>MDD</sub> on the right amygdala volume. The Asian cohort also showed such interaction on the right hippocampal volume and shape, thickness of the orbitofrontal and ventromedial prefrontal cortex. Likewise, a significant interaction between SES and infant GPRS<sub>MDD</sub> was on the right amygdala and hippocampal volumes and shapes. After controlling for each other, the interaction effect of antenatal maternal depressive symptoms and GPRS<sub>MDD</sub> was mainly shown on the right amygdala, while the interaction effect of SES and GPRS<sub>MDD</sub> was mainly shown on the right hippocampus. Bioinformatic analyses suggested neurotransmitter/neurotrophic signaling, SNAp REceptor complex, and glutamate receptor activity as common biological processes underlying the influence of antenatal maternal depressive symptoms on fetal cortico-limbic development. These findings suggest gene–environment interdependence in the fetal development of brain regions implicated in cognitive–emotional function. Candidate biological mechanisms involve a range of brain region-specific signaling pathways that converge on common processes of synaptic development.</span>
          CareDx to Purchase HLA Typing Assets From Conexio Genomics   
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          Immucor Acquires Sirona Genomics   
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          The use of antibiotics can lead to weight gain   

The study, published in the journal Gut Microbes also shows a link between the metabolic activity of intestinal bacteria with body mass index, fasting glucose and insulin resistance.

The intestine is inhabited by billions of bacteria that interact with each other and are known as microbiota or gut flora. "These bacteria can provide activities and molecules could not acquire for ourselves and are essential for the proper development of human beings. The age, geographic origin and other factors such as obesity and diet, pregnancy, or the use of antibiotics, can significantly alter intestinal microbial diversity, "explains Manuel Ferrer CSIC researcher who works at the Institute of Catalysis and Petroleoquímica.

The researchers first analyzed the metabolic activity of enzymes of intestinal bacteria present in stool samples of obese and thin and treated or not with antibiotics. For the first author Ester Hernandez, the study shows that obese people or a high body mass index and those treated with antibiotics have a similar metabolic behavior, which would impact on the ability to metabolize dietary sugars.

"The study suggests that the development of obesity and prolonged antibiotic treatment modifies the intestinal flora so that the enzymes become more active, which favors rapid and uneven absorption of carbohydrate and, in turn, develop obesity, eating disorders, and ultimately diabetes, "explains Ferrer.

The study lays the groundwork for future research that ultimately may enable the design of customized diets based on polysaccharides potential digestibility of the diet in terms of intestinal activity profiles to regulate weight gain. This would suggest, in particular, define the set enzimotipos or intestinal enzymes of each person and prebiotics design that ensure healthy intestinal microbiota.

"In addition, these cocktails could become part of standard treatment guidelines on antibiotic treatment in order to minimize side effects. Only through a comprehensive and detailed analysis of different antibiotics and people of different geographical origin, age or health status can develop personalized therapies and surgical interventions, "write the researchers.

The research, which has had the collaboration of the University of Granada, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, and the Centre of Public Health Research, is part of a series of projects funded by the Ministry of Science and Innovation, the Ministry of Health, Social Services and Equality, the Instituto Carlos III and the Generalitat Valenciana. Researchers have also been supported Eranet PathoGenoMics2 program promoted by the European Union. Some of the scientists are part of the Biomedical Research Centre Network for Epidemiology and Public Health.

 

  • Hernández E, Bargiela R, Diez MS, Friedrichs A, Pérez-Cobas AE, Gosalbes MJ, Knecht H, Martínez-Martínez M, Seifert J, von Bergen M, Artacho A, Ruiz A, Campoy C, Latorre A, Ott SJ, Moya A, Suárez A, Martins Dos Santos VA, Ferrer M. Functional consequences of microbial shifts in the human gastrointestinal tract linked to antibiotic treatment and obesity. Gut Microbes. 4: 306-3015
  • Fotografía: Vicente Segarra taken with a Galaxy SII on July 31, 2013

          Discovered new therapeutic target   

Scientists have analyzed in mice genomic profiles of various epigenetic marks of chromatin, the set of DNA and proteins found in the nucleus of eukaryotic cells in response to a family of drugs, inhibitors of histone deacetylase enzymes ( HDACi), which could represent an effective tool for the treatment of diseases affecting the nervous system.

The study describes the impact of the genomic level profiles HDACi in histone acetylation, a process related to the regulation of gene transcription or expression. "Taken together, our results illuminate both the relationship between gene expression and histone acetylation, as the mechanisms of action of these drugs neuropsychiatric" CSIC researchers say Angel Boat and Jose Lopez, who work at the Institute of Neuroscience ( joint CSIC and the University Miguel Hernández).

In a second study published in The Journal of Neuroscience, researchers have determined first genome-wide epigenetic alterations associated with Huntington's disease and its relationship failures genome expression also observed in this disease hereditary degenerative disease of the brain.

"The result of these experiments has revealed that defects in transcription and histone acetylation are two independent manifestations of the disease affecting a large number of genes, but that converge in a small number ofgenes," says CSIC researcher Luis Miguel value.

"These genes altered in both processes are particularly important to the development of the disease and therefore represent new targets for the development of drugs or therapies" adds Angel Barco. The study also provides new clues to understanding the mechanism of action of HDACi drugs in the treatment of Huntington's disease allowing therefore improve its specificity.

 

 

  • Jose P. Lopez-Atalaya, Satomi Ito, Luis M. Valor, Eva Benito, y Ángel Barco. Genomic targets, and histone acetylation and gene expression profiling of neural HDAC inhibition. Nucl. Acids Res. DOI:10.1093/nar/gkt590.
  • Valor LM, Guiretti D, López-Atalaya JP, Barco A. Genomic landscape of transcriptional and epigenetic dysregulation in early onset polyglutamine disease. Journal of Neuroscience. DOI: 33(25):10471-10482.

Fotografía: This work has been released into the public domain by its author, brian0918. This applies worldwide.


          Discovered the «anchor» of bifidobacteria that promotes digestio   

This microorganism, known for its probiotic properties, uses these appendages to colonize the intestine, as demonstrated by an international investigation in which participated the National Research Council (CSIC).

The study, published this week in the journal PNAS, reveals that B. bifidum uses these protein appendages known as pili, to interact with their host. A more specific level, these appendages that decorate the surface of the bacteria are those that are joined to human intestinal cells.

Through functional genomic techniques, the team has identified further that B. bifidum possess pili three different types, each with a particular function and different expression patterns depending on environmental conditions.

According to the CSIC researcher at the Institute of Asturias Dairy Borja Sánchez, who collaborated on the research, "so far, there is little information on the mechanisms used by this bacterium to colonize the intestine". His presence there, however, it is well known to improve the balance of intestinal flora.

For his part, CSIC researcher at the center and has also contributed to the work, Abelardo Margolles, believes that this is one of the few studies that show that some probiotic bacteria are capable of using pili as intestinal colonization factors. The finding could encourage research and development of other organisms and probiotic products.

The research was led from the University of Parma (Italy) and has had the participation of researchers from the Universities of Cork (Ireland), Milan and Verona (both in Italy).

Francesca Turroni et al. The role of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in modulating bacterium-host interactions. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1303897110

Francesca Turroni et al. The role of sortase-dependent pili of Bifidobacterium bifidum PRL2010 in modulating bacterium-host interactions. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1303897110


Photo By Y tambe (Y tambe's file) [GFDL, CC-BY-SA-3.0 or CC-BY-SA-2.5-2.0-1.0], via Wikimedia Commons


          Experimental Therapy reduces lung metastases of melanoma   

The results tested in mice, show the therapeutic potential of PARP inhibitors, a key molecule in the repair of DNA damage induced on. The research has been published in the journal PLoS Genetics.

"Metastasis is the spread of invasive tumor cells from where it originates to other parts of the body, and causes the vast majority of mortality associated with solid tumors," said CSIC researcher Javier Oliver, the Institute Parasitology and Biomedicine López Neyra.

This work describes the PARP enzyme capacity to regulate the expression of factors such as vimentin and VE-cadherin, the dynamic key proteins in vascular cells located around the tumor and malignant transformation processes, such as vascular and mimicry acquiring invasive properties.

The investigation also involved researchers from the Research Institute of Biopathology and Regenerative Medicine, University of Granada, the Center for Genomics and Oncological Research and Pompeu Fabra University.


    Mª Isabel Rodríguez*, Andreína Peralta-Leal, Francisco O’Valle, José Manuel Rodriguez-Vargas, Ariannys Gonzalez-Flores, Jara Majuelos-Melguizo, Laura López, Santiago Serrano, Antonio García de Herreros, Juan Carlos Rodríguez-Manzaneque, Rubén Fernández, Raimundo G. del Moral, Mariano Ruiz de Almodóvar, F. Javier Oliver. PARP-1 regulates metastatic melanoma through modulation of vimentininduced malignant transformation. PLOS Genetics. DOI: 10.1371/journal.pgen.1003531


          Brooke Greenberg, baby forever   

Brooke, who was born on January 8, 1993, has already served 20 years and is 73 cm, having not grown at all since I was 4 or 5 years. His story is a medical mystery that has baffled some of the best specialists worldwide.

Brooke's pediatrician, Dr. Lawrence Pakula from the Johns Hopkins School of Medicine in Baltimore, says the source of his sudden illness remains a mystery.



Because no doctor has been able to provide an official diagnosis Brooke's disease, his condition has been termed "Syndrome X". Brooke weighs about 7 kilos and is estimated to have the intellectual capacity of a 1 year old baby.

According to Dr. Eric Schadt, director of the Institute for Genomic Biology and multiscale Icahn at Mount Sinai Medical Center in New York, Brooke has no apparent abnormality in the endocrine system, chromosomal abnormalities or serious, or any other known disease that may cause developmental problems.

The enigmatic character of Brooke's disease has led some researchers to believe that its unique genetic code could help understand the aging process. Dr. Schadt is sequencing the genome of Brooke with the hope that someday I can help discover new treatments for age-related disorders such as Parkinson's disease.


          Medieval Historians Taking Genomics into Account   
At the International Congress on Medieval Studies at Kalamazoo (Kzoo) last month, I couldn’t help feeling that we have reached a turning point. I went to four sessions that engaged in genomics, human and/or bacterial, in some way. Granted, these are a tiny proportion of the 500+ sessions offered, but I have learned that if you … Continue reading Medieval Historians Taking Genomics into Account
          Protein data takes significant step forward in medicine   
PNNL-OHSU team part of NCI effort to bring proteogenomics to cancer patients The Department of Energy’s Pacific Northwest
          Open science: a future shaped by shared experience   
Mapping the human genome showed how the internet can play a vital part in collective scientific research. Now more scientists are collaborating – and inviting amateurs and colleagues from other disciplines to get involved


http://www.guardian.co.uk/education/2011/may/22/open-science-shared-research-internet?CMP=twt_gu

S
BioCurious: Joseph Jackson at his community lab in Menlo Park, California. Photograph: Robert Yager for the Observer
On the surface, it looked as if there was nothing in mathematics that Timothy Gowers couldn't achieve. He held a prestigious professorship at Cambridge. He had been a recipient of the Fields Medal, the highest honour in mathematics. He had even acted as a scientific consultant on Hollywood movies. Yet there were a few complex mathematical problems that he had struggled to solve. "In most cases, I just ran out of steam," he explains.

So one day he took one of these – finding a mathematical proof about the properties of multidimensional objects – and put his thoughts on his blog. How would other people go about solving this conundrum? Would somebody else have any useful insights? Would mathematicians, notoriously competitive, be prepared to collaborate? "It was an experiment," he admits. "I thought it would be interesting to try."

He called it the Polymath Project and it rapidly took on a life of its own. Within days, readers, including high-ranking academics, had chipped in vital pieces of information or new ideas. In just a few weeks, the number of contributors had reached more than 40 and a result was on the horizon. Since then, the joint effort has led to several papers published in journals under the collective pseudonym DHJ Polymath. It was an astonishing and unexpected result.

"If you set out to solve a problem, there's no guarantee you will succeed," says Gowers. "But different people have different aptitudes and they know different tricks… it turned out their combined efforts can be much quicker."

This ability to collaborate quickly and transparently online is just one facet of a growing movement in research known as open science.

There are many interpretations of what open science means, with different motivations across different disciplines. Some are driven by the backlash against corporate-funded science, with its profit-driven research agenda. Others are internet radicals who take the "information wants to be free" slogan literally. Others want to make important discoveries more likely to happen. But for all their differences, the ambition remains roughly the same: to try and revolutionise the way research is performed by unlocking it and making it more public.

"What we try to do is get people to organise differently," says Joseph Jackson, the organiser of the Open Science Summit, a meeting of advocates that was held for the first time last summer at the University of California, Berkeley.

Jackson is a young bioscientist who, like many others, has discovered that the technologies used in genetics and molecular biology, once the preserve of only the most well-funded labs, are now cheap enough to allow experimental work to take place in their garages. For many, this means that they can conduct genetic experiments in a new way, adopting the so-called "hacker ethic" – the desire to tinker, deconstruct, rebuild.

The rise of this group is entertainingly documented in a new book by science writer Marcus Wohlsen, Biopunk (Current £18.99), which describes the parallels between today's generation of biological innovators and the rise of computer software pioneers of the 1980s and 1990s. Indeed, Bill Gates has said that if he were a teenager today, he would be working on biotechnology, not computer software.

Spurred on by the new-found ability to work outside the system, these rebel biologists believe that the traditional way of doing science is not the most efficient and could even be holding back important developments.

"Institutions, typically, are the slowest and have the most amount of inertia lagging behind the technology," says Jackson. "We have a lot of things that made sense once, or never made sense, that are clogging up the works."

Those sound like fighting words to a traditional scientist. After all, ask any lab director and they'll tell you the same thing – doing real science is tough. It takes time, energy and money to conduct serious research. Institutes manage vast budgets, operate huge, hi-tech labs and call upon armies of graduate students to sift for evidence in great oceans of data. Real science is a slow, expensive process that has been hewn into shape over centuries of experimentation, false starts and the occasional success.

But open scientists suggest that it doesn't have to be that way. Their arguments are propelled by a number of different factors that are making transparency more viable than ever.

The first and most powerful change has been the use of the web to connect people and collect information. The internet, now an indelible part of our lives, allows like-minded individuals to seek one another out and share vast amounts of raw data. Researchers can lay claim to an idea not by publishing first in a journal (a process that can take many months) but by sharing their work online in an instant.

And while the rapidly decreasing cost of previously expensive technical procedures has opened up new directions for research, there is also increasing pressure for researchers to cut costs and deliver results. The economic crisis left many budgets in tatters and governments around the world are cutting back on investment in science as they try to balance the books. Open science can, sometimes, make the process faster and cheaper, showing what one advocate, Cameron Neylon, calls "an obligation and responsibility to the public purse".

At the same time, moves are afoot to disrupt the closed world of academic journals and make high-level teaching materials available to the public. The Public Library of Science, based in San Francisco, is working to make journals more freely accessible, while the Massachusetts Institute of Technology currently boasts that material for almost 2,000 courses is now available on the web.

"The litmus test of openness is whether you can have access to the data," says Dr Rufus Pollock, a co-founder of the Open Knowledge Foundation, a group that promotes broader access to information and data. "If you have access to the data, then anyone can get it, use it, reuse it and redistribute it… we've always built on the work of others, stood on the shoulders of giants and learned from those who have gone before."

In the seven years since he started the organisation, Pollock, now in his early 30s, has helped build communities and tools around everything from economics data to Shakespeare's sonnets. He says that it is increasingly vital for many scientists to adopt an open approach.

"We have found ourselves in a weird dead end," he says – where publicly funded science does not produce publicly accessible information. That leads to all kinds of problems, not least controversies such as the leaked climate change emails from the University of East Anglia, which led to claims of bias among the research team.

But it's more than just politics at stake – it's also a fundamental right to share knowledge, rather than hide it. The best example of open science in action, he suggests, is the Human Genome Project, which successfully mapped our DNA and then made the data public. In doing so, it outflanked J Craig Venter's proprietary attempt to patent the human genome, opening up the very essence of human life for science, rather than handing our biological information over to corporate interests.

"It was a very large project in one of the most organised and information-rich areas of science, but it faced genuine competition from a closed model," says Dr Pollock. "It is basically an extraordinary example and it could have gone in a very different way."

Unsurprisingly, the rise of open science does not please everyone. Critics have argued that while it benefits those at either end of the scientific chain – the well-established at the top of the academic tree or the outsiders who have nothing to lose – it hurts those in the middle. Most professional scientists rely on the current system for funding and reputation. Others suggest it is throwing out some of the most important elements of science and making deep, long-term research more difficult.

Open science proponents say that they do not want to make the current system a thing of the past, but that it shouldn't be seen as immutable either. In fact, they say, the way most people conceive of science – as a highly specialised academic discipline conducted by white-coated professionals in universities or commercial laboratories – is a very modern construction.

It is only over the last century that scientific disciplines became industrialised and compartmentalised. Some of history's most influential scientists and polymaths – people such as Robert Hooke, Charles Darwin and Benjamin Franklin – started as gentleman scholars and helped pioneer the foundations for modern inquiry at a time when the line between citizen and scientist was blurred.

In attempting to recapture some of this feeling, open scientists say they don't want to throw scientists to the wolves: they just want to help answer questions that, in many cases, are seen as insurmountable. This means breaking down barriers by using the tools at our disposal – whether it's abundant biological data, inexpensive lab equipment or the internet. It might not be the way we think of science, but it is still science.

"Some people are naturally sympathetic to this sort of idea," says Professor Gowers. "Some people, very straightforwardly, said that they didn't like the idea because it undermined the concept of the romantic, lone genius." Even the most dedicated open scientists understand that appeal. "I do plan to keep going at them," he says of collaborative projects. "But I haven't given up on solitary thinking about problems entirely."

In favour of spreading the word

Melanie Swan

"As a society, we don't understand biology yet," says Melanie Swan, a genomics researcher and principle at MS Futures Group in Palo Alto, California. As she sees it, there are all sorts of problems with the way we conduct biological research en masse. Individuals can gain huge amounts of information about their own genetic makeup, yet new drugs and treatments are developed very slowly because, in part, they have to be adapted for general use.

As a non-traditional scientist — she studied French, economics and finance before heading into the world of genes — Swan has decided to take a non-traditional approach. The answer, she suggests, is to push forward with studies where self-elected individuals who have already got their genomic data join in, acting as both subjects and participants. It allows those taking part, including Swan herself, to understand and monitor exactly what is happening, and massively reduces time and cost.

Swan's projects have started small, with a seven-person pilot to explore the effects of vitamin B on the MTHFR gene, which has been linked to cancer and vascular diseases. But she has more than 40 possible studies outlined. "The traditional model is very slow: every different private research organisation builds its own data store of samples and it's painstaking and expensive. It takes years and they don't share it with each other or with the public. How can we move forward in a 2.0 kind of way?"

Joseph Jackson

Describing himself as a "philosopher, entrepreneur and activist", 28-year-old Joseph Jackson is one of the leading figures in a precocious movement of DIY biologists. He's co-founder of BioCurious, a community lab based in the San Francisco Bay area, and organiser of the annual Open Science Summit. But while he envisions a world where amateurs and self-educated scientists co-exist and help one another improve, he understands that there's going to be resistance along the way.

"I think that it's already coming to a head, and that conflict is going to intensify," he explains. "It's going to be a challenge to integrate the effort of amateurs and the professional canon," he explains. "We've seen these conflicts already — whether Wikipedia can be treated as authoritative – but with a carefully chosen set of experiments, we can bridge the gap."

Although there is plenty of pain today, he suggests that in hindsight we may see the breaking down of boundaries between public and academe was inevitable. "It's obvious where the trends are going and I hope we'll look back 20 years from now and say that this was a turning point."

Cameron Neylon

For biophysicist Cameron Neylon, the conversion to open science came when he was working at the University of Southampton. He started publishing his lab notebook online, a radical step, considering most researchers keep their work under lock and key.

"Once you see how the web connects people and makes them more effective, it's a given," he says. "We can make research more efficient by making parts of the process more public."

Neylon recognises this approach isn't for everyone and that it won't have the same sort of impact in every field. But the more pressing issue is trying to work this way in a professional system that is weighted towards secrecy.

"Some people are worried they'll be scooped if they put their research into the open," he points out. "The bottom line is that the reward structures we have don't really reward anything apart from getting a peer-reviewed paper published in a high-ranking journal.

"The sooner we can get to a point where people are rewarded for making more public their ideas, concepts, materials and data, the better off we'll be."
          Join the hunt to feed the world's hungry through broadband Internet   
[Another good example of citizen science. Excerpts from NY Times article -- BSA]

http://bits.blogs.nytimes.com/2008/05/14/join-the-hunt-for-super-rice/?ref=technology

Join the Hunt for Super-Rice

There is no quick fix to the world food crisis, but a project getting underway Wednesday could make a difference in the long run. Rice

A team of researchers at the University of Washington are putting a genomics project on the World Community Grid in the computational search for strains of rice that have traits like higher yields, disease resistance and a wider range of nutrients.

The purpose is to hasten the pace of modern rice genetics, which since the 1960s has delivered a series of new strains, starting with higher-yielding semidwarf varieties, a breakthrough that was hailed as the Green Revolution.

But the demand — all those mouths to feed — keeps rising. Rice is the main staple food for more than half the world’s population. In Asia alone, more than two billion people get up to 70 percent of their dietary energy from rice.

The World Community Grid, begun in 2004, gives selected humanitarian scientific projects access to massive computing resources. It taps the unused computing cycles of nearly one million computers around the world — much like SETI@home, the best-known distributed computing effort, which claims it has harnessed more than 3 million PCs in the search for extraterrestrial life.

The World Community Grid places a small piece of software on your PC that taps your unused computing cycles and combines them with others to create a virtual supercomputer. Its equivalent computing power would make it the world’s third-largest supercomputer, according to I.B.M., which has donated the hardware, software and technical expertise for the project.

The grid will run a three-dimensional modeling program created by the computational biologists at the University of Washington to study the structures of the proteins that make up the building blocks of rice. Understanding the structures provides clues to their functions, interactions between the molecular parts and how certain desired traits are expressed.

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          This is what phylodiversity looks like   

Following on from earlier posts exploring how to map DNA barcodes and putting barcodes into GBIF it's time to think about taking advantage of what makes barcodes different from typical occurrence data. At present GBIF displays data as dots on a map (as do I in http://iphylo.org/~rpage/bold-map/). But barcodes come with a lot more information than that. I'm interested in exploring how we might measure and visualise biodiversity using just sequences.

Based on a talk by Zachary Tong (Going Organic - Genomic sequencing in Elasticsearch) I've started to play with n-gram searches on DNA barcodes using Elasticsearch, an open source search engine. The idea is that we break the DNA sequence into every possible "word" of length n (also called a k-mer or k-tuple, where k = n).

For example, for n = 5, the sequence GTATCGGTAACGAACTT would look like this:


GTATCGGTAACGAACTT

GTATC
TATCG
ATCGG
TCGGT
CGGTA
GGTAA
GTAAC
TAACG
AACGAA
ACGAAC
CGAACT
GAACTT

The sequence GTATCGGTAACGAACTT comes from Hajibabaei and Singer (2009) who discussed "Googling" DNA sequences using search engines (see also Kuksa and Pavlovic, 2009). If we index sequences in this way then we can do BLAST-like searches very quickly using Elasticsearch. This means it's feasible to take a DNA barcode and ask "what sequences look like this?" and return an answer qucikly enoigh for a user not to get bored waiting.

Another nice feature of Elasticsearch is that it supports geospatial queries, so we can ask for, say, all the barcodes in a particular region. Having got such a list, what we really want is not a list of sequences but a phylogenetic tree. Traditionally this can be a time consuming operation, we have to take the sequences, align them, then input that alignment into a tree building algorithm. Or do we?

There's growing interest in "alignment-free" phylogenetics, a phrase I'd heard but not really followed up. Yang and Zhang (2008) described an approach where every sequences is encoded as a vector of all possible k-tuples. For DNA sequences k = 5 there are 45 = 1024 possible combinations of the bases A, C, G, and T, so a sequence is represented as a vector with 1024 elements, each one is the frequency of the corresponding 5-tuple. The "distance" between two sequences is the mathematical distance between these vectors for the two sequences. Hence we no longer need to align the sequences being comapred, we simply chunk them into all "words" of 5 bases in length, and compare the frequencies of the 1024 different possible "words".

In their study Yang and Zhang (2008) found that:

We compared tuples of different sizes and found that tuple size 5 combines both performance speed and accuracy; tuples of shorter lengths contain less information and include more randomness; tuples of longer lengths contain more information and less random- ness, but the vector size expands exponentially and gets too large and computationally inefficient.

So we can use the same word size for both Elasticsearch indexing and for computing the distance matrix. We still need to create a tree, for which we could use something quick like neighbour-joining (NJ). This method is sufficiently quick to be available in Javascript and hence can be computed by a web browser (e.g., biosustain/neighbor-joining).

Putting this all together, I've built a rough-and-ready demo that takes some DNA barcodes, puts them on a map, then enables you to draw a box on a map and the demo will retrieve the DNA barcodes in that area, compute a distance matrix using 5-tuples, then build a NJ tree, all on the fly in your web browser.

Phylodiversity on the fly from Roderic Page on Vimeo.

This is all very crude, and I need to explore scalability (at the moment I limit the results to the first 200 DNA sequences found), but it's encouraging. I like the idea that, in principle, we could go to any part of the globe, ask "what's there?" and get back a phylogenetic tree for the DNA barcodes in that area.

This also means that we could start exploring phylogenetic diversity using DNA barcodes, as Faith & Baker (2006) wanted a decade ago:

...PD has been advocated as a way to make the best-possible use of the wealth of new data expected from large-scale DNA “barcoding” programs. This prospect raises interesting bio-informatics issues (discussed below), including how to link multiple sources of evidence for phylogenetic inference, and how to create a web-based linking of PD assessments to the barcode–of-life database (BoLD).

The phylogenetic diversity of an area is essentially the length of the tree of DNA barcodes, so if we build a tree we have a measure of diversity. Note that this contrasts with other approaches, such as Miraldo et al.'s "An Anthropocene map of genetic diversity" which measured genetic diversity within species but not between (!).

Practical issues

There are a bunch of practical issues to work through, such as how scalable it is to compute phylogenies using Javascript on the fly. For example, could we do something like generate a one degree by one degree grid of the Earth, take all the barcodes in each cell and compute a phylogeny for each cell? Could we do this in CouchDB? What about sampling, should we be taking a finite, random sample of sequences so that we try and avoid sampling bias?

There are also data management issues. I'm exploring downloading DNA barcodes, creating a Darwin Core Archive file using the Global Genome Biodiversity Network (GGBN) data standard, then converting the Darwin Core Archive into JSON and sending that to Elasticsearch. The reason for the intermediate step of creating the archive is so that we can edit the data, add missing geospatial informations, etc. I envisage having a set of archives, hosted say on GitHub. These archives could also be directly imported into GBIF, ready for the time that GBIF can handle genomic data.

References

  • Faith, D. P., & Baker, A. M. (2006). Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinform Online. 2006; 2: 121–128. PMC2674678
  • Hajibabaei, M., & Singer, G. A. (2009). Googling DNA sequences on the World Wide Web. BMC Bioinformatics. Springer Nature. https://doi.org/10.1186/1471-2105-10-s14-s4
  • Kuksa, P., & Pavlovic, V. (2009). Efficient alignment-free DNA barcode analytics. BMC Bioinformatics. Springer Nature. https://doi.org/10.1186/1471-2105-10-s14-s9
  • Miraldo, A., Li, S., Borregaard, M. K., Florez-Rodriguez, A., Gopalakrishnan, S., Rizvanovic, M., … Nogues-Bravo, D. (2016, September 29). An Anthropocene map of genetic diversity. Science. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aaf4381
  • Yang, K., & Zhang, L. (2008, January 10). Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Research. Oxford University Press (OUP). https://doi.org/10.1093/nar/gkn075

          iBOL DNA barcodes in GBIF   

I've uploaded all the COI barcodes in the iBOL public data dumps into GBIF. This is an update of an earlier project that uploaded a small subset. Now that dataset doi:10.15468/inygc6 has been expanded to include some 2.7 million barcodes. In the new GBIF portal (work in progress) the map for these barcodes looks like this:

Screenshot 2016 12 07 22 58 43

Many of these records have images of the specimens that were sequenced, and the new GBIF "gallery" feature displays these nicely, e.g.:

Screenshot 2016 12 08 10 04 00

Having done this, I've a few thoughts.

Why did I do this?

Why did I do this, or, put another why didn't iBOL do this already? In an ideal world, iBOL would be an active contributor to GBIF and would be routinely uploading barcodes. Since this isn't happening, I've gone ahead and uploaded the barcodes myself. From my perspective, I want as much data to be as discoverable and as accessible as possible, hence if need be I'll grab data from wherever it lives and add it to GBIF (for an earlier example see The Zika virus, GBIF, and the missing mosquitoes). A downside of this is that, long term, the relationship between data provider and GBIF may be as valuable to GBIF as the data, and simply grabbing and reformatting data doesn't, by itself, form that relationship. But in the absence of a working relationship I still need the data.

Where are the taxonomic names

Lots of barcodes lack formal scientific names, even though in many cases BOLD has them. The data in the public dumps often lacks this information. A next logical step would be to harvest data from the BOLD API and add taxonomic names as "identifications".

Where are the sequences?

The sequences themselves aren't in GBIF, which on the one hand is not surprising as GBIF isn't a sequence databases. However, I think it should be, in the sense that for a lot of biodiversity sequences are going to be the only way forward. This includes the eukaryote barcodes, bacterial sequences, and metabarcodes. Fundamentally sequences are just strings of letters, and GBIF already handles those (e.g., taxonomic names, geographic places, etc.). Furthermore, the following paper by Bittner et al. makes a strong case that rather than knowing "what is there?" it's more important to know "what are they doing?"

Bittner, L., Halary, S., Payri, C., Cruaud, C., de Reviers, B., Lopez, P., & Bapteste, E. (2010). Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biology Direct. Springer Nature. https://doi.org/10.1186/1745-6150-5-47

In other words, a functional approach may matter more than a purely taxonomic approach to diversity. For a big chunk of biology this is going to depend on analysing sequences. Even if we restrict ourselves to just taxonomic diversity, there is scope for expanding our notion of what we display once we have sequences and evolutionary trees, e.g. Notes on next steps for the million DNA barcodes map.


          EOL Traitbank JSON-LD is broken   

Follow eol on twitterOne of the most interesting aspects of EOL is "TraitBank", which has been described in a recent paper:

Cynthia S. Parr, Katja S. Schulz, Jennifer Hammock, Nathan Wilson, Patrick Leary, Jeremy Rice, & Robert J. Corrigan. (2016). TraitBank: Practical semantics for organism attribute data. Semantic Web, 7(6), 577–588. https://doi.org/10.3233/SW-150190

TraitBank is available in JSON-LD, and so is potentially part of the Semantic Web. Unfortunately, the JSON-LD provided by TraitBank is broken, to the point that it's hard to believe that anyone's actually consuming the JSON-LD. I know that Google is using EOL data for their knowledge panels, but anyone using TraitBank JSON-LD in a semantic web client is going to run into problems.

First off, let's look at the example provided in the above paper, http://eol.org/api/traits/328067 which returns data for Potos flavus.

{ "@context": { "@vocab": "http://schema.org/", "dwc:taxonID": { "@type": "@id" }, "dwc:resourceID": { "@type": "@id" }, "dwc:relatedResourceID": { "@type": "@id" }, "dwc:relationshipOfResource": { "@type": "@id" }, "dwc:vernacularName": { "@container": "@language" }, "eol:associationType": { "@type": "@id" }, "rdfs:label": { "@container": "@language" }, "dc": "http://purl.org/dc/terms/", "dwc": "http://rs.tdwg.org/dwc/terms/", "eolterms": "http://eol.org/schema/terms/", "eol": "http://eol.org/schema/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "gbif": "http://rs.gbif.org/terms/1.0/", "foaf": "http://xmlns.com/foaf/0.1/" }, "@type": "DataFeedItem", "dateModified": "2016-09-30", "item": { "@id": 328067, "@type": "dwc:Taxon", "scientificName": "Potos flavus (Schreber, 1774)", "dwc:taxonRank": "species", "dwc:parentNameUsageID": "http://eol.org/pages/14191", "potentialAction": { "@type": "EntryPoint", "target": { "@type": "Related", "url": "http://eol.org/pages/328067", "actionPlatform": [ "http://schema.org/DesktopWebPlatform", "http://schema.org/IOSPlatform", "http://schema.org/AndroidPlatform" ] } }, "sameAs": [ "http://www.iucnredlist.org/details/41679", "http://genomics.senescence.info/species/entry.php?species=Potos_flavus", "http://commons.wikimedia.org/wiki/Potos_flavus", "http://www.biolib.cz/en/taxon/id1790/", "http://www.iucnredlist.org/apps/redlist/details/41679", "http://www.discoverlife.org/mp/20q?search=Potos+flavus", "http://www.eco-index.org/search/keyword_complete.cfm?keyword=Potos flavus", "http://calphotos.berkeley.edu/cgi/img_query?seq_num=31541&one=T", "http://www.conabio.gob.mx/conocimiento/ise/fichasnom/Potosflavus00.pdf", "http://darnis.inbio.ac.cr/ubis/FMPro?-DB=UBIPUB.fp3&-lay=WebAll&-error=norec.html&-Format=detail.html&-Op=eq&-Find=&id=1689", "http://lod.taxonconcept.org/ses/2mOvV.html", "http://neotropnathistory.lifedesks.org/pages/45271", "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=73392", "http://www.catalogueoflife.org/annual-checklist/details/species/id/6902599", "http://www.catalogueoflife.org/annual-checklist/details/species/id/6902599", "http://genomics.senescence.info/species/entry.php?species=Potos_flavus", "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=621964", "http://en.wikipedia.org/w/index.php?title=Kinkajou", "http://www.iucnredlist.org/apps/redlist/details/41679", "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=29067", "http://eol.org/pages/328067", "http://animaldiversity.ummz.umich.edu/accounts/Potos_flavus/" ], "vernacularNames": [ { "@language": "af", "@value": "rolbeer", "gbif:isPreferredName": true }, { "@language": "af", "@value": "rolstaartbeer" }, { "@language": "de", "@value": "wickelbär", "gbif:isPreferredName": true }, { "@language": "en", "@value": "Kinkajou", "gbif:isPreferredName": true }, { "@language": "en", "@value": "honey bear" }, { "@language": "es", "@value": "Ak' a' mash", "gbif:isPreferredName": true }, { "@language": "es", "@value": "Chosna" }, { "@language": "es", "@value": "Cusu" }, { "@language": "es", "@value": "Martilla" }, { "@language": "es", "@value": "Martucha" }, { "@language": "es", "@value": "Mico de noche" }, { "@language": "es", "@value": "Mico león" }, { "@language": "es", "@value": "Mono michi" }, { "@language": "es", "@value": "Perro de monte" }, { "@language": "fi", "@value": "Kinkaju", "gbif:isPreferredName": true }, { "@language": "fr", "@value": "Kinkajou, Singe de nuit", "gbif:isPreferredName": true }, { "@language": "nl", "@value": "rolstaartbeer", "gbif:isPreferredName": true }, { "@language": "nl", "@value": "nachtaap" }, { "@language": "pt-BR", "@value": "Jupará", "gbif:isPreferredName": true } ], "traits": [ { "@id": "http://eol.org/pages/328067/data#data_point_949469", "eol:traitUri": "http://eol.org/resources/704/measurements/basalmetrate113", "@type": "dwc:MeasurementOrFact", "predicate": "metabolic rate", "dwc:measurementType": "http://www.owl-ontologies.com/unnamed.owl#Metabolic_rate", "value": "731.33", "units": "mL/hr O2", "eol:dataPointId": 949469, "http://purl.obolibrary.org/obo/VT_0001259": "http://eol.org/resources/704/measurements/metratemass113", "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Basal metabolic rate was measured when individual(s) were experiencing neither heat nor cold stress (i.e. are in their thermoneutral zone); are resting and calm; and are post–absorptive (are not digesting or absorbing a meal) and data were only accepted where there was also a measure of body mass for the same individual(s). Based on information from primary and secondary literature sources. This value represents a single measure of central tendency for this species. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "731.33", "dwc:measurementUnit": "http://eol.org/schema/terms/mlO2perhour", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_46140963", "eol:traitUri": "http://eol.org/resources/737/measurements/e5775a49cc4bbe3f3ae5c391776a467a", "@type": "dwc:MeasurementOrFact", "predicate": "population trend", "dwc:measurementType": "http://iucn.org/population_trend", "value": "Decreasing", "eol:dataPointId": 46140963, "dc:source": "http://eol.org/resources/737", "dwc:measurementValue": "Decreasing", "dwc:scientificName": "Potos flavus (Schreber, 1774)", "eolterms:resource": "http://eol.org/resources/737" }, { "@id": "http://eol.org/pages/328067/data#data_point_46140962", "eol:traitUri": "http://eol.org/resources/737/measurements/25c8b74374d04260b047bd57570e094b", "@type": "dwc:MeasurementOrFact", "predicate": "habitat", "dwc:measurementType": "http://rs.tdwg.org/dwc/terms/habitat", "value": "terrestrial habitat", "eol:dataPointId": 46140962, "dc:source": "http://eol.org/resources/737", "dwc:measurementValue": "http://purl.obolibrary.org/obo/ENVO_00002009", "dwc:scientificName": "Potos flavus (Schreber, 1774)", "eolterms:resource": "http://eol.org/resources/737" }, { "@id": "http://eol.org/pages/328067/data#data_point_949459", "eol:traitUri": "http://eol.org/resources/704/measurements/maxlongevity138", "@type": "dwc:MeasurementOrFact", "predicate": "total life span", "dwc:measurementType": "http://purl.obolibrary.org/obo/VT_0001661", "value": "348", "units": "months", "eol:dataPointId": 949459, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Maximum adult age measured either through direct observation, capture-recapture estimates, projected from physical wear or unspecified, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; in all localities. See source for details.", "eolterms:statisticalMethod": "http://semanticscience.org/resource/SIO_001114", "dwc:measurementValue": "348", "dwc:measurementUnit": "http://purl.obolibrary.org/obo/UO_0000035", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_949460", "eol:traitUri": "http://eol.org/resources/704/measurements/littersperyear728", "@type": "dwc:MeasurementOrFact", "predicate": "litters per year", "dwc:measurementType": "http://eol.org/schema/terms/LittersPerYear", "value": "1", "eol:dataPointId": 949460, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Number of litters per female per year using non-captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "1", "dwc:scientificName": "Potos flavus", "dwc:sex": "http://purl.obolibrary.org/obo/PATO_0000383" }, { "@id": "http://eol.org/pages/328067/data#data_point_949461", "eol:traitUri": "http://eol.org/resources/704/measurements/littersize1554", "@type": "dwc:MeasurementOrFact", "predicate": "clutch/brood/litter size", "dwc:measurementType": "http://purl.obolibrary.org/obo/VT_0001933", "value": "1.11", "eol:dataPointId": 949461, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Number of offspring born per litter per female, either counted before birth, at birth or after birth, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "1.11", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_949462", "eol:traitUri": "http://eol.org/resources/704/measurements/interbirthinterval291", "@type": "dwc:MeasurementOrFact", "predicate": "inter-birth interval", "dwc:measurementType": "http://eol.org/schema/terms/InterBirthInterval", "value": "365", "units": "days", "eol:dataPointId": 949462, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "The length of time between successive births of the same female(s) after a successful or unspecified litter using non-captive, wild, provisioned, or unspecified populations; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "365", "dwc:measurementUnit": "http://purl.obolibrary.org/obo/UO_0000033", "dwc:scientificName": "Potos flavus", "dwc:sex": "http://purl.obolibrary.org/obo/PATO_0000383" }, { "@id": "http://eol.org/pages/328067/data#data_point_949463", "eol:traitUri": "http://eol.org/resources/704/measurements/grmaxlat1392", "@type": "dwc:MeasurementOrFact", "predicate": "latitude", "dwc:measurementType": "http://semanticscience.org/resource/SIO_000319", "value": "23.72", "units": "decimal degrees", "eol:dataPointId": 949463, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Digital geographic range maps of all extant, non-marine mammals from Sechrest (2003) were converted to the Wilson and Reeder (2005) taxonomy. These ranges were used to generate measures of geographic range extent and occupancy. Spatial analyses were performed using ArcGIS (version 9.0) (ESRI 2005) for areas and R (R Development Core Team 2005) for geographic coordinates. Value calculated using a global geographic projection.", "eolterms:statisticalMethod": "http://semanticscience.org/resource/SIO_001114", "dwc:measurementValue": "23.72", "dwc:measurementUnit": "http://eol.org/schema/terms/decimaldegrees", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_949464", "eol:traitUri": "http://eol.org/resources/704/measurements/midrangelong3692", "@type": "dwc:MeasurementOrFact", "predicate": "longitude", "dwc:measurementType": "http://semanticscience.org/resource/SIO_000318", "value": "-68.67", "units": "decimal degrees", "eol:dataPointId": 949464, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Digital geographic range maps of all extant, non-marine mammals from Sechrest (2003) were converted to the Wilson and Reeder (2005) taxonomy. These ranges were used to generate measures of geographic range extent and occupancy. Spatial analyses were performed using ArcGIS (version 9.0) (ESRI 2005) for areas and R (R Development Core Team 2005) for geographic coordinates. Value calculated using a global geographic projection.", "eolterms:statisticalMethod": "http://semanticscience.org/resource/SIO_001110", "dwc:measurementValue": "-68.67", "dwc:measurementUnit": "http://eol.org/schema/terms/decimaldegrees", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_949465", "eol:traitUri": "http://eol.org/resources/704/measurements/grminlong4209", "@type": "dwc:MeasurementOrFact", "predicate": "longitude", "dwc:measurementType": "http://semanticscience.org/resource/SIO_000318", "value": "-102.55", "units": "decimal degrees", "eol:dataPointId": 949465, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Digital geographic range maps of all extant, non-marine mammals from Sechrest (2003) were converted to the Wilson and Reeder (2005) taxonomy. These ranges were used to generate measures of geographic range extent and occupancy. Spatial analyses were performed using ArcGIS (version 9.0) (ESRI 2005) for areas and R (R Development Core Team 2005) for geographic coordinates. Value calculated using a global geographic projection.", "eolterms:statisticalMethod": "http://semanticscience.org/resource/SIO_001113", "dwc:measurementValue": "-102.55", "dwc:measurementUnit": "http://eol.org/schema/terms/decimaldegrees", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346815", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269876", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Southern Mesoamerican Pacific mangroves", "eol:dataPointId": 45346815, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Southern_Mesoamerican_Pacific_mangroves", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Mangroves

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346814", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269875", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Southern Atlantic mangroves", "eol:dataPointId": 45346814, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Southern_Atlantic_mangroves", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Mangroves

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Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346795", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269856", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Beni savanna", "eol:dataPointId": 45346795, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Beni_savanna", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and subtropical grasslands, savannas, and shrublands

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346794", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269855", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Trans-Mexican Volcanic Belt pine-oak forests", "eol:dataPointId": 45346794, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Trans-Mexican_Volcanic_Belt_pine-oak_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Coniferous Forests

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Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346792", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269853", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Sierra Madre de Oaxaca pine-oak forests", "eol:dataPointId": 45346792, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Sierra_Madre_de_Oaxaca_pine-oak_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Coniferous Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346791", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269852", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Miskito pine forests", "eol:dataPointId": 45346791, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Miskito_pine_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Coniferous Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346790", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269851", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Central American pine-oak forests", "eol:dataPointId": 45346790, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Central_American_pine-oak_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Coniferous Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346789", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269850", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Belizean pine forests", "eol:dataPointId": 45346789, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Belizean_pine_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Coniferous Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346788", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269849", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Yucatán dry forests", "eol:dataPointId": 45346788, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Yucatan_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346787", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269848", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Veracruz dry forests", "eol:dataPointId": 45346787, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Veracruz_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346786", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269847", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Southern Pacific dry forests", "eol:dataPointId": 45346786, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Southern_Pacific_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346785", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269846", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Sinú Valley dry forests", "eol:dataPointId": 45346785, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Sinu_Valley_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346784", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269845", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Patía Valley dry forests", "eol:dataPointId": 45346784, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Patia_Valley_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346783", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269844", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Panamanian dry forests", "eol:dataPointId": 45346783, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Panamanian_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346782", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269843", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Maracaibo dry forests", "eol:dataPointId": 45346782, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Maracaibo_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346781", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269842", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Magdalena Valley dry forests", "eol:dataPointId": 45346781, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Magdalena_Valley_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346780", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269841", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Lara-Falcón dry forests", "eol:dataPointId": 45346780, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Lara-Falcon_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346779", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269840", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Ecuadorian dry forests", "eol:dataPointId": 45346779, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Ecuadorian_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346778", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269839", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Chiquitano dry forests", "eol:dataPointId": 45346778, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Chiquitano_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346777", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269838", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Chiapas Depression dry forests", "eol:dataPointId": 45346777, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Chiapas_Depression_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346776", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269837", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Central American dry forests", "eol:dataPointId": 45346776, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Central_American_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346775", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269836", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Cauca Valley dry forests", "eol:dataPointId": 45346775, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitation": "World Wildlife Fund. 2006. WildFinder: Online database of species distributions, ver. Jan-06. www.worldwildlife.org/WildFinder", "dwc:measurementValue": "http://eol.org/schema/terms/Cauca_Valley_dry_forests", "dwc:scientificName": "Potos flavus", "dc:contributor": "Compiler: Sarah Miller", "dwc:measurementRemarks": "Biome: Tropical and Subtropical Dry Broadleaf Forests

Realm: Neotropical", "eolterms:resource": "http://eol.org/resources/976" }, { "@id": "http://eol.org/pages/328067/data#data_point_45346774", "eol:traitUri": "http://eol.org/resources/976/measurements/m_00269835", "@type": "dwc:MeasurementOrFact", "predicate": "geographic distribution includes", "dwc:measurementType": "http://eol.org/schema/terms/Present", "value": "Balsas dry forests", "eol:dataPointId": 45346774, "dc:source": "http://www.worldwildlife.org/publications/wildfinder-database", "dc:bibliographicCitati

          On asking for access to data   

In between complaining about the lack of open data in biodiversity (especially taxonomy), and scraping data from various web sites to build stuff I'm interested in, I occasionally end up having interesting conversations with the people whose data I've been scraping, cleaning, cross-linking, and otherwise messing with.

Yesterday I had one of those conversations at Kew Gardens. Kew is a large institution that is adjusting to a reduced budget, a changing ditigal landscape, and a rethinking of it's science priorities. Much of Kew's data has not been easily accessible to the outside world, but this is changing. Part of the reason for this is that Defra, which part-funds Kew, is itself opening up (see Ellen Broad's fascinating post Lasers, hedgehogs and the rise of the Age of Yoghurt: reflections on #OpenDefra).

During this conversation I was asked "Why didn't you just ask for the data instead of scraping it? We would most likely have given it to you." My response to this was "well, you might have said no". In my experience saying "no" is easy because it is almost always the less risky approach. And I want a world where we don't have to ask for data, in the same way that we don't ask to get source code for open source software, and we don't ask to download genomic data from GenBank. We just do it and, hopefully, do cool things with it. Just as importantly, if things don't work out and we fail to make cool things, we haven't wasted time negotiating access for something that ultimately didn't work out. The time I lose is simply the time I've spent playing with the data, not any time negotiating access. The more obstacles you put in front of people playing with your data, the fewer innovative uses of that data you're likely to get.

But it was pointed out to me that a consequence of just going ahead and getting the data anyway is that it doesn't necessarily help people within an organisation make the case for being open. The more requests for access to data that are made, the easier it might be to say "people want this data, lets work to make it open". Put another way, by getting the data I want regardless, I sidestep the challenge of convincing people to open up their data. It solves my problem (I want the data now) but doesn't solve it for the wider community (enabling everyone to have access).

I think this is a fair point, but I'm going to try and wiggle away from it. From a purely selfish perspective, my time is limited, there are only so many things I can do, and making the political case for opening up specific data sets is not something I really want to be doing. In a sense, I'm more interested in what happens when the data is open. In other words, let's assume the battle for open has been won, what do we then? So, I'm essentially operating as if the data is already open because I'm betting that it will be at some point in time.

Without wishing to be too self-serving, I think there are ways that treating closed data as effectively open can help make the case that the data should (genuinely) open. For example, one argument for being open is that people will come along and do cool things with the data. In my case, "cool" means cross linking taxonomic names with the primary literature, eventually to original decsriptions and fundamental data about the organisms tagged with the taxonomic names (you may feel that this stretches the definitoon of "cool" somewhat). But adding value to data is hard work, and takes time (in some cases I've invested years in cleaning and linking the data). The benefits from being open may take time, especially if the data is messy, or relatively niche so that few people are prepared to invest the time necessary to do the work.

Some data, such as the examples given in Lasers, hedgehogs and the rise of the Age of Yoghurt: reflections on #OpenDefra will likely be snapped up and give rise to nice visualisations, but a lot of data won't. So, imagine that you're making the case for data to be open, and one of your arguments is "people will do cool things with it", eventually you win that argument, the data is opened up... and nothing happens. Wouldn't it be better if once the data is open, those of us who have been beavering away with "illicit" copies of the data can come out of the woodwork and say "by the way, here are some cool things we've been doing with that data"? OK, this is a fairly self-serving argument, but my point is that while internal arguments about being open are going on I have three choices:

  1. Wait until you open the data (which stops me doing the work I want to do)
  2. Help make the case for being open (which means I engage in politics, an area in which I have zero aptitude)
  3. Assume you will be open eventually, and do the work I want to do so that when you're open I can share that work with you, and everyone else
Call me selfish, but I choose option 3.


          Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome   

The synonymous substitution rate varies widely among species, but it is generally quite stable within a genome due to the absence of strong selective pressures. In plants, plastid genes tend to evolve faster than mitochondrial genes, rate variation among species generally correlates between the mitochondrial and plastid genomes, and few examples of intragenomic rate heterogeneity exist. To study the extent of substitution rate variation between and within plant organellar genomes, we sequenced the complete mitochondrial and plastid genomes from the bugleweed, Ajuga reptans, which was previously shown to exhibit rate heterogeneity for several mitochondrial genes. Substitution rates were accelerated specifically in the mitochondrial genome, which contrasts with correlated plastid and mitochondrial rate changes in most other angiosperms. Strikingly, we uncovered a 340-fold range of synonymous substitution rate variation among Ajuga mitochondrial genes. This is by far the largest amount of synonymous rate heterogeneity ever reported for a genome, but the evolutionary forces driving this phenomenon are unclear. Selective effects on synonymous sites in plant mitochondria are generally weak and thus unlikely to generate such unprecedented intragenomic rate heterogeneity. Quickly evolving genes are not clustered in the genome, arguing against localized hypermutation, although it is possible that they were clustered ancestrally given the high rate of genomic rearrangement in plant mitochondria. Mutagenic retroprocessing, involving error-prone reverse transcription and genomic integration of mature transcripts, is hypothesized as another potential explanation.


          Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae   

In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae. Comparative mitogenomic analysis revealed minimal gene loss among the seven Orobanchaceae species, indicating the retention of typical mitochondrial function among Orobanchaceae species. Phylogenetic analysis demonstrated that the mobile cox1 intron was acquired vertically from a nonparasitic ancestor, arguing against a role for Orobanchaceae parasites in the horizontal acquisition or distribution of this intron. The C. paramensis plastome has retained nearly all genes except for the recent pseudogenization of four subunits of the NAD(P)H dehydrogenase complex, indicating a very early stage of plastome degradation. These results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.


          ΙΑΣΩ: Με μεγάλη επιτυχία διεξήχθη η ομιλία του Καθηγητή Γενετικής κ. Στυλιανού Αντωναράκη   
Ο Καθηγητής ανέπτυξε το θέμα "The renaissance of genomic medicine", σε ομιλία που παρέθεσε την Παρασκευή 20 Ιανουαρίου 2017, στην Αίθουσα Εκδηλώσεων του ΙΑΣΩ.
          Lunch & Learn: Clickers in the Classroom with Janet Temos   

At OIT’s Lunch ‘n Learn seminar on February 7, Janet Temos, the Director of OIT’s Educational Technologies Center and Joshua Rabinowitz, Assistant Professor of Chemistry and the Lewis-Sigler Institute for Integrative Genomics, demonstrated the use of clickers (also known as … Continue reading


          80-year-old 'viable' anthrax strain debunked using advanced genomic sequencing   
A team of international researchers has found that a strain of anthrax-causing bacterium thought to have been viable 80 years after a thwarted World War I espionage attack, was, in reality, a much...
          Bioinformatics Specialist-Metagenomics/Proteomics - Signature Science, LLC - Austin, TX   
Travel to project and business development meetings as needed. Familiarity with machine learning, Git, and agile software development is a plus;... $90,000 a year
From Signature Science, LLC - Tue, 06 Jun 2017 09:05:50 GMT - View all Austin, TX jobs
           Az indvidualizált farmakoterápia lehetőségének kidolgozása - súlyos bőrgyógyászati mellékhatásokkal is járó adverz gyógyszerreakciók farmakogenomikai és etiológiai vizsgálata, genetikai megelőzése, preventív rendszerek, tesztek fejlesztése = Working towards the realization of personalized medicine - pahrmacogenomic and etiological study of adverse drug reactions with severe cutan involvement, developing preventive systems and assays    
Kárpáti, Sarolta and Bércesné Novák, Ágnes and Blazsek, Antal and Erős, Nóra and Hársing, Judit and Hatvani, Zsófia and Klausz, Gabriella and Lukács, Andrea and Marschalkó, Márta and Medvecz, Márta and Pónyai, Györgyi and Pónyai, Katinka and Preisz, Klaudia and Róna, Kálmán and Silló, Pálma and Soós, Gyöngyvér and Szathmáry, Zsuzsanna and Temesvári, Erzsébet and Tulassay, Zsolt (2013) Az indvidualizált farmakoterápia lehetőségének kidolgozása - súlyos bőrgyógyászati mellékhatásokkal is járó adverz gyógyszerreakciók farmakogenomikai és etiológiai vizsgálata, genetikai megelőzése, preventív rendszerek, tesztek fejlesztése = Working towards the realization of personalized medicine - pahrmacogenomic and etiological study of adverse drug reactions with severe cutan involvement, developing preventive systems and assays. Project Report. OTKA.
          LECTURE ANNOUNCEMENT: The Genetic Basis of Disease   
Please share with interested parties: Join us today for the third lecture in the Genomics and the Era of Personalized Medicine seminar series. Dr. Susan Dutcher,  Professor of Genetics, Cell Biology and Physiology at Washington University will present, “The Genetic Basis of Disease.” WHEN: Monday, September 16th, 4-p.m. WHAT: The Genetic Basis of Disease WHERE: Wohl Auditorium HOW […]
          Genomics and the Era of Personalized Medicine Seminar Series, starts August 26   
Genomics play in increasingly large role in 21st century research and clinical practice.  Washington University School of Medicine is at the forefront of this evolving field.  To continue to meet this challenge, a new cadre of investigators will need comprehensive training in topics related to genomic medicine. This series introduces principles of genomics in medicine […]
          JAMA Special Issue on Genomics in Medicine   
The Journal of the American Medical Association released a special issue on genomic medicine today. The issue provides some useful perspectives and content in this field of increasing importance. JAMA – April 10, 2013, Vol 309, No. 14 Other related resources of interest: Genetic Alliance: http://www.geneticalliance.org/ Genetics Home Reference: http://ghr.nlm.nih.gov/ National Coalition for Health Professional […]
          Introduction to the Analysis of Deep Sequencing Data using CLC bio’s Genomics Workbench and Genomics Server   
An Introduction to the Analysis of Deep Sequencing Data using CLC bio’s Genomics Workbench and Genomics Server Presented by Rob Mervis, Field Applications Scientist at CLC bio March 20th at 10am in Holden Auditorium This will be an interactive demonstration and discussion of the various applications and work-flows that can be performed on deep sequencing […]
           Complete genomic sequence of Pepper vein banding virus (PVBV): a distinct member of the genus Potyvirus    
Anindya, R and Joseph, J and Gowri, TDS and Savithri, HS (2004) Complete genomic sequence of Pepper vein banding virus (PVBV): a distinct member of the genus Potyvirus. In: Archives of Virology, 149 (3). pp. 625-632.
          Dispatch from HIMSS 2017   
As I wrote last week, I expected 2017 HIMSS to be filled with Wearables, Big Data, Social Networking concepts from other industries, Telemedicine, and Artificial Intelligence.

I was not disappointed.   42,000 of my closest friends each walked an average of 5 miles per day through the Orlando Convention Center.  One journalist told me “It’s overwhelming.  You do your best to look professional and wear comfy shoes!”

After 50 meetings, and 12 meals in 3 days, here’s my impression of the experience

1.  Wearables, while still relevant have gone from the peak of the hype curve to the trough of disillusionment.   Google Glass, smartwatches, and innovative fitness trackers have not quite achieved their promised potential in healthcare and no one is quite sure how to integrate their data into the workflow.    That being said, Internet of Things is bigger than in previous years, with home scales, glucometers, and blood pressure cuffs becoming more connected than ever before.  Middleware like Apple Healthkit has significantly reduced the interfacing burden.

2.  Big Data has morphed into Care Management and Population Health.   We’re at a point in history when healthcare data has become digital but few are sure how to turn that data into wisdom.   Decision support services that analyze problem lists, medications and genomic data, producing customized care plans are emerging.  The challenge is connecting them to the EHR workflow.   The Argonaut work group met for a few hours to decide on the next interoperability capabilities for FHIR and chose scheduling workflow and clinical decision support integration.  This means that any third party developer will be able to integrate their analytic functionality into EHR workflow, generating alerts and reminders and scheduling services (appointments, surgery, infusions/therapy, referrals, and even post acute care) with limited effort and cost.      To me the most important theme at HIMSS 2017 was that FHIR/APIs, cloud hosted services, and EHRs will come together in 2018 similar to the way the iPhone spawned the app store.   Assume every EHR company will have a curated app store and sandbox for developer education/pilot testing within a year.

3.  Value-based purchasing has generated an interest in customer relationship management - the patient as partner and consumer.  As reimbursement moves from fee for service to quality/outcomes driven risk contracts, incentives are aligned to provide wellness services, “care traffic control”, and loop closure.    EHRs are not optimized for these functions, so third parties are offering cloud-hosted customer relationship management for healthcare.

4.  Telemedicine and Telehealth continues to grow as efforts to reduce total medical expense move care from downtown academic tertiary referral facilities to lower cost, more convenient alternatives in the home.  Telemedicine means many things and ranges from on demand virtual urgent care visits to store/forward second opinions to expert staff augmentation from a distance.   Products are evolving that enable telemedicine record keeping, billing, and mobile device secure communications.

5.  Artificial Intelligence/Machine learning is the new “plastics”   .   There is no question that AI is the peak of the hype curve this year.  We need to be measured about our expectations for this technology.   Computers do not “think”,  they use pattern matching to focus the attention of humans, separating signal from noise.    There are great use cases for machine learning - automating sorting of paper medical records for scanning by predicting metadata, scrubbing personal identifiers from unstructured data, and suggesting reasonable ICD10 codes for episodes of care.    It’s not likely that an AI system is going to read the Merck Manual tonight and replace your doctor tomorrow.

Although my voice is nearly gone, I’m leaving HIMSS with optimism for the industry.   EHR vendors will increasingly share data with each other and with third party developers.  Usability will improve as new applications and analytics reduce clinician burden.   Patients will increasingly be equal members of the care team providing objective and subjective data from devices and mobile apps in their home.  

As I’ve said before, I believe the next phase of history belongs to the private sector, so for all of the developers, customers, and experts at HIMSS, it’s all up to you.
          Preparing for HIMSS 2017   
Next week, 50000 of our closest friends will gather together in Orlando to learn about the latest trends in the healthcare IT industry.

What can we expect?

I’ll be giving a few keynote addresses, trying to predict what the Trump administration will bring, identify those technologies that will move from hype to reality, and highlighting which products are only “compiled” in Powerpoint - a powerful development language that is really easy to modify!

Here are a few themes

1.  The Trump administration is likely to reduce regulatory burden but is unlikely to radically change the course of value-based purchasing.    This means that interoperability, analytics, and workflow products that help improve outcomes while reducing costs will still be important.   Fee for service medicine will diminish over time, so focusing on quality healthcare will be more important than increasing the quantity of tests, procedures, and visits.   Novel products and services will be needed since the existing EHR is not designed for optimizing wellness, it’s designed for documenting/billing encounters.

2.  Precision Medicine that tailors care plans and therapeutics based on the unique characteristics of each individual will continue to be important.    Although there is much discussion of genomic medicine but even simple innovations can make an impact.  For example, my wife needs to take 3.75mg of Methimazole every day but the medication is packaged as a 5mg tablet she needs to cut into quarters.  Why not offer a 3D printer that simply “prints” the tablets you need each day?

3.  Care Management solutions that treat the patient as customer will continue to be important.   Sharing care plans, monitoring progress on those plans, and engaging patients/families as a shared decision maker will require innovation.

4.  Artificial intelligence/machine learning will be at the peak of the hype curve this year.   IBM Watson will not replace clinicians, but the notion of using software for pattern matching does work well.

5.  Internet of things, patient generated healthcare data, and telemedicine/telehealth will be increasingly important tools as we strive to reduce total medical expense, address the needs of an aging society, and enable our clinicians to practice at the top of their license.  

I’ll be running from venue to venue Sunday-Wednesday.   See you there.
          Glenmark Pharma in-licenses novel anti-TrkA antibody from Lay Line Genomics   
Glenmark Pharmaceuticals SA (GPSA), a wholly owned subsidiary of Glenmark Pharmaceuticals Ltd (GPL), has been granted by Lay Line Genomics (LLG) an exclusive worldwide license to LLG’s entire intellectual property portfolio in the TrkA field.

The licensed assets include BXL1H5, which is a novel monoclonal antibody that binds to TrkA receptors. This represents another first-in-class opportunity for Glenmark. The deal is of specific significance because Glenmark has not only in-licensed a preclinical, unique monoclonal antibody, but also has the sole and exclusive license to commercialise monoclonal antibodies against TrkA receptor for pain.

The pain market generated sales in excess of $25 billion and more than 102 million individuals suffered from chronic pain across the seven major markets. Less than 30 percent of patients with chronic pain obtain adequate pain relief and efficacy remains the largest unmet need in chronic pain treatment.

Anti-TrkA is a novel class of pain therapeutics and has a central role in the pain mechanism, with the potential to address the unmet needs in pain therapy. Glenmark has gained significant expertise in developing monoclonal antibodies and also has rich experience in the pain therapeutic area. The development of this novel biologic entity (NBE) will be done by Glenmark’s biologic R&D centre in Switzerland, which is focused on discovering and developing NBEs.

Commenting on this deal, Glenn Saldanha, Chief Executive Officer and Managing Director, Glenmark Pharmaceuticals mentioned, “We are excited to have been granted the sole and exclusive license to commercialise monoclonal antibodies against the TrkA receptor for pain. We are enthusiastic about the addition of BXL1H5 to the Glenmark discovery pipeline. Glenmark will leverage its expertise in monoclonal antibodies to progress BXL1H5 rapidly into clinical development.”

"We are extremely pleased that Glenmark Pharmaceuticals shares our excitement for the anti-TrkA project and look forward to the next stages of development with great enthusiasm," said Ennio Esposito, Sole Director at LLG. Glenmark will undertake further development and commercialisation of BXL1H5 in exchange for an undisclosed upfront and milestone payments to LLG .

reff:
http://www.expresspharmaonline.com/20101031/market05.shtml
          Community Members Aid Cutting-Edge Research in ‘BioBlitz’ Project   
April 26, 2017

When scientists at UC Merced seek to better understand California’s biodiversity, they turn to cutting-edge genomics. They also turn to their neighbors.

On a sunny Saturday in April, scientists joined forces with members of the local community to take part in UC Merced’s inaugural eDNA BioBlitz.Citizen scientists head to vernal pool sites.

Under the guidance of Professor Michael Dawson and a team of conservation biologists from UC Merced, UCLA, and Cal State Los Angeles, community members trained as citizen scientists and spent the day collecting and cataloging environmental DNA (eDNA) from the Merced Vernal Pools and Grassland Reserve.

What is eDNA? It’s a really new science,” reserve director Mo Kolster explained to the nearly two dozen participants, anticipating the crowd’s most pressing question.

Plants and animals are constantly shedding cells, leaving behind what amounts to a molecular footprint. As Kolster explains, “The DNA in those cells becomes part of the environment. By collecting water or soil samples, we collect the DNA of those species.”

As soon as they’re collected, eDNA samples are sent to UCLA laboratories for genetic analysis. The resulting data will aid researchers in assembling a catalog of plant and animal species that interact with the vernal pools.

Importantly, eDNA provides a molecular tool that can reveal what the eye can’t see, including vernal pool species that have managed to elude observation. Some are too small to be seen with the naked eye. Others are transient, finding their way to vernal pools at irregular intervals and staying only a short while.

Whatever the reason, eDNA offers a way to remedy these oversights. By giving scientists the ability to identify species on the basis of their unique genetic signature, eDNA allows scientists to detect members of the vernal pool community as yet unaccounted for.

It complements observation,” said Rachel Meyer, executive director of the UC Conservation Genomics Consortium. “eDNA is the visible and the invisible.”

Citizen scientists collect eDNA from reserve.Ultimately, the eDNA samples collected by citizen scientists at BioBlitzes held in Merced and throughout California will supply conservation researchers with a more thorough catalog of regional biodiversity in the state’s many unique habitats. It will also provide a deeper understanding of how California’s changing environment affects the flora and fauna occupying these habitats.

The BioBlitz was organized as part of the University of California’s CALeDNA project, a trailblazing conservation research program that utilizes the tools of genomics to track biodiversity throughout California. The project falls under the umbrella of the University of California Conservation Genomics Consortium, a collaborative effort that brings together experts from six UC campuses to monitor the health of ecosystems statewide and find solutions to pressing issues related to conservation and biodiversity. The consortium is funded by a three-year, $1.76 million Catalyst Award from the UC Office of the President.

Dawson serves as the primary investigator for the UC Merced arm of the consortium. He’s joined by Professor Jay Sexton, whose research focuses on species endemic to the vernal pool reserve.

Asked about the consortium’s scientific significance, Dawson explained, “It uses the power of the UC system to bring campuses together,” adding that the group’s innovative efforts “bring genomic techniques into broad use for conservation biology.”

Citizen scientists who missed the April BioBlitz will have another opportunity to participate in October, with additional details to come. For more information about becoming a citizen scientist and participating in future BioBlitzes, visit ucedna.com/participate.

Jason
Alvarez
Science and Health Writer
(209) 228-4483

          Postdoc, Student: Evolutionary Genomics Plant Pathogens   
POSITIONS IN EVOLUTIONARY GENOMICS OF FUNGAL PLANT PATHOGENS We are seeking talented and motivated postdoc (research associate) and PhD student (research assistant) candidates in the Fungal Genomics and Evolution Lab within the Synthetic and Systems Biology Unit of the Biological Research Center, with experience in molecular biology, microbiology, light microscopy or bioinformatics. The successful candidate(s) … Continue reading Postdoc, Student: Evolutionary Genomics Plant Pathogens
          Faculty Jobs in Microbial/Genomics fields   
Here are some links to a few faculty positions University of Texas at Arlington Two Assistant or Associate Professor positions with a research focus in Microbiology in Dept of Biology. UTArlington microbiologist Virgina Tech Evolutionary Biologist (Assistant Professor Level) Bioinformatics and Microbiome Systems Biologist (Assistant Professor Level) Dartmouth University Microbial Computational and Systems Biology  Dartmouth MCSB Apply: https://apply.interfolio.com/37550 … Continue reading Faculty Jobs in Microbial/Genomics fields
          Postdoc: UMichigan Fungal Genomics   
The lab of Tim James in the Department of Ecology and Evolutionary Biology at the University of Michigan is looking to hire a postdoctoral fellow in the area of single cell and comparative genomics. The research is centered on understanding the phylogeny and molecular evolution of uncultured and poorly known fungi, including the Cryptomycetes, Zygomycetes, … Continue reading Postdoc: UMichigan Fungal Genomics
          Postdoc: Population Genetics/Genomics of Fungal Plant Pathogens   
The Department of Plant Pathology at the University of Nebraska-Lincoln is pleased to accept applications for a Post-Doctoral Research Associate position in Population Genetics/Genomics of Fungal Plant Pathogens. This is a 12-month, non-tenure leading position established for a period of one year. This position is available immediately. Continuation of the position beyond one year is dependent upon satisfactory … Continue reading Postdoc: Population Genetics/Genomics of Fungal Plant Pathogens
          Postdoc: Computational Fungal Genomics (Univ of New Zealand)   
Postdoctoral Fellow in Computational Fungal Genomics I am looking for a motivated and productive postdoctoral fellow to explore the evolutionary implications of interactions between genome structure, epigenetic modification and gene expression, with a particular focus on the 3D arrangement of unraveled chromosomes in the nucleus. Using a fungal model system with direct agricultural applications (Epichloe festucae), the postdoc … Continue reading Postdoc: Computational Fungal Genomics (Univ of New Zealand)
          Postdoc: Plant-fungal symbiosis and evolution   
The Vilgalys Mycology Lab at Duke University seeks a postdoctoral researcher in the area of plant-fungal symbiosis and evolution.  The selected candidate will contribute to ongoing studies on ecology and evolution of forest soil fungi and their interactions with trees including Populus, Pinus and other species.  We are especially interested in metagenomic approaches for studying fungal interactions with … Continue reading Postdoc: Plant-fungal symbiosis and evolution
          QUANTUM GENOMICS : Quantum Genomics announces the design of its next Phase II trial in arterial hypertension, NEW-HOPE   
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          QUANTUM GENOMICS : Quantum Genomics annonce le design de sa prochaine étude NEW HOPE de phase II dans l'hypertension artérielle   
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© Copyright Actusnews Wire
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          Characterization of the pheromone gene family of an antarctic and arctic protozoan ciliate, Euplotes nobilii   
Vallesi, Adriana and Alimenti, Claudio and La Terza, Antonietta and Di Giuseppe, Graziano and Dini, Fernando and Luporini, Pierangelo (2009) Characterization of the pheromone gene family of an antarctic and arctic protozoan ciliate, Euplotes nobilii. Marine Genomics, 2/2009 (1). pp. 27-32. ISSN 1874-7787
          Obama Comes To The UN’s Rescue   

Like a good lap dog, the U.S. is dedicating $36.5 million to help Africa train doctors because the famously corrupt United Nations determined that the continent has a terrible shortage of medical personnel and faculty. That means Uncle Sam must come to the rescue. The latest Africa allocation is in addition to the eye-popping $654,778,938 that American taxpayers gave the U.N. general fund in 2015 and billions more to the peacekeeping budget and other U.N. organizations. The U.S. has always been the single largest contributor to the world body, which is well known as a pillar of fraud and mismanagement. Even the U.N.’s Human Rights Council, also funded primarily by American taxpayers, is a huge joke. A few years ago Judicial Watch reported that the U.N. awarded a genocidal warlord indicted by an international court for crimes against humanity a seat on its laughable human rights council. Last year President Obama committed an astounding $3 billion to a new U.N. Climate fund run by communist and terrorist nations. Now the World Health Organization (WHO), the U.N.’s public health arm, has determined that sub-Saharan Africa is in desperate need of medical personnel. The region bears almost a quarter of the global disease burden yet has only 3% of the world’s health workforce, according to WHO. So this week, the National Institutes of Health (NIH), the nation’s medical research agency, kicked in the $36.5 million to train Africans. The NIH doles out north of $31 billion annually to hundreds of thousands of researchers at thousands of universities and institutions around the globe. A few years ago President Obama launched an NIH program to boost the number of minorities in biomedical research and he appointed the nation’s first ever Chief Officer for Scientific Workforce Diversity to mastermind a multi-million-dollar effort. The new Africa allocation will help the region strengthen medical school curricula, upgrade community-based training sites and expand communications technology, according to an NIH announcement. “Research must play an integral part in generating sustainable, quality health care in sub-Saharan Africa, which is the ultimate goal,” NIH Director Francis Collins said. “It is critical that we increase research capacity so Africans can carry out locally relevant investigations themselves, and develop the necessary expertise in areas such as bioethics, informatics, environmental science, and genomics. That will empower their participation in international collaborations.” This is all based on the WHO’s assessment. Here’s an example of how the U.N. health agency works; a few years ago it determined that 180,000 obesity-related deaths worldwide were linked to sugary drinks. The figure included about 25,000 Americans and the U.N. study made headlines because it supported a preposterous effort by the former mayor of New York, Michael Bloomberg, to ban sugary drinks. Bloomberg’s ridiculous legislation eventually got struck down by a court. This year the WHO became an even bigger joke for trying to ban disease names, such as swine flu, bird flu and monkey pox, that create a stigma. The effort includes banning the term German measles and Spanish flu because it might upset Germans and Spaniards. A British newspaper called it “an astonishing example of political correctness.”

The post Obama Comes To The UN’s Rescue appeared first on Liberty News Now.


          Healthcare IT startups to watch: Running list of big news   
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Healthcare IT startups to watch in 2016: Running list of big news
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From virtual care platforms to precision medicine, data analytics to interoperability, the healthcare IT landscape is constantly changing thanks to new approaches driven by entrepreneurs making waves in the sector.

 

 

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Mark Nathan, co-found and CEO of Zipari

Health insurance tech startup Zipari, nabbed $7 million in its first round of funding led by Vertical Venture Partners. The company will use the cash to meet the expanding demand for its suite of customer relationship management-centered software as a service for the health insurance industry.

Read the article.

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Google Glass startup Augmedix scores $23 million from McKesson Ventures, others
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The San Francisco company's focus is a smartglass-powered remote scribe tool to assist physicians with charting and documentation. Augmedix co-founders Ian Shakil, left, and Pelu Tran.

Read the most recent article.

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Cybersecurity companyAttackIQ lands $8.8 million in Series A funding
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AttackIQ will use the $8.8 million garnered in its first round of funding to expand its partner, sales and marketing initiatives, and build out its strategic services and engineering teams.

Read the article.

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Telehealth startup Avizia to expand engineering team, market reach with new funding
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Avizia client New York Presbyterian, which has been a leader in video consults and telehealth, participated in this most recent $6 million investment that adds to the $11 million Avizia raised back in July.  As Avizia CEO Mike Baird sees it, telehealth is a proven way for hospitals to close gaps in care and reduce unnecessary ER visits.

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Moxe Health promotes data sharing between payers and providers
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"The rules of healthcare are quickly being re-written, as technology presents an opportunity to facilitate more meaningful interactions between payers and providers," Moxe founder and CEO Dan Wilson says, "We enable workflows that are beneficial to both sides of the equation and focus on delivering patient health insights to providers while reducing administrative excess."

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Welltok grabs $33 million to advance CafeWell population health tool
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Welltok pulled in $33.7 million in a new round of funding and said it plans to use the investment to build out its CafeWell Health Optimization Platform. CaféWell enables population health managers to coach and inspire their clients to get healthier. The enterprise-level platform curates and connects consumers with benefits, resources and rewards, and it provides personalized action plans for each individual.

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RXAnte gets UPMC boost
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UPMC Enterprises, the commercialization arm of UPMC, has purchased all of Millennium Health’s interest in Portland, Maine-based RxAnte. The investment will go toward product development with in-house clinical expertise and accelerating growth. Founded in 2011, RxAnte manages medication use for nearly 7 million people on behalf of health insurers, providers and other stakeholders working to improve safe and effective prescription drug use. Josh Benner wil continue as CEO.

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ReadCoor spins from Harvard after a $23M first round of funding

ReadCoor will commercialize the Wyss Institute’s FISSEQ – fluorescent in situ sequencing – technology. The startup has developed an imaging platformthat provides insight into cancer, infectious diseases, cognitive disorders and more. A team headed by Wyss core faculty member and ReadCoor co-founder George Church, invented and developed the platform.

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Klara lands $3M in funding to further develop its HIPAA-compliant messaging platform for medical teams to centralize all patient-related communication in one place

Klara co-founders Simon Lorenz, left, and Simon Bolz, launched the company in 2014, They describe the technology as a "WhatsApp" for medicine.

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Catalyze, a HITRUST certified cloud provider, has raised $6.5 million in a Series B funding round. "Customers have our team the unique opportunity to solve a multitude of data exchange challenges that fall outside of traditional standards," says Catalyze CEO Travis Good, MD, pictured above.

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Cernostics CEO Mike Hoerres

Oncology diagnostics company Cernostics has pulled in a $5 million round of funding led by UPMC Enterprises, the commercial arm of UPMC. The funding will go toward growing and accelerating a new diagnostic test for people with Barrett’s Esophagus, a condition that can lead to cancer.

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J. Patrick Bewley, CEO of Big Cloud Analytics

The startup’s COVALENCE Analytics Platform is designed to simplify healthcare and help enterprises better manage population health. The Atlanta-based startup, which offers real-time predictive analytics technology for the Internet of Things, has raised $4.5 million in first round fo funding.

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CareSkore co-founders CEO Jaspinder Grewal and Puneet Dhillon Grewal, MD, chief medical  officer

CareSkore, a population health management technology vendor, has raised $4.3 million in its initial round of funding. And former San Francisco 49ers quarterback Joe Montana is part of the team of investors backing the upstart.

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Manoj Saxena, CognitiveScale executive chairman

CognitiveScale revealed a $21.8 million round of financing to advance its industry-specific machine intelligence software. “This funding will accelerate our mission to bring scalable, practical AI to the enterprise,” Saxena said.

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Accolade CEO Rajeev Singh

Seattle-based Accolade, an on-demand healthcare concierge offering for employers, health plans and health systems, has raised $71.1 million to ramp up its technology platform. Accolade’s model combines personalized service with clinical support and consumer engagement technologies to uncover inefficient healthcare utilization and its impact on healthcare costs and outcomes. Cost savings range from 5-15 percent, Accolade said.

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Redox
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Luke Bonney Niko Skievaski and James Lloyd founded Redox in 2014. The Epic alumni who run Redox are aggressive about interoperability, and they claim it's easier to achieve than it seems. They call it "turnkey interoperability." Most recently Redox has integrated its health apps with Epic, Cerner and eClinicalWorks, among others.

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Aledade founder Farzad Mostashari, MD

Aledade, former ONC chief and physician Farzad Mostashari’s accountable care organization startup, is 'steady as she goes' as it enters its third year.

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Omicia CEO Matt Tindall
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Omicia will expand HIPAA-compliant, cloud-enabled platform for research, population health, clinical trials. The startup landed $23 million in its Series B financing round, completed on June 8. UPMC led the funding.

Read the full story.

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Tom Dorsett, CEO of ePatientFinder
Slideshow Description: 

ePatientFinder announced on June 9, it had raised $8.2 million tto build out its Clinical Trial Exchange platform. The EHR agnostic cloud-based service enables doctors to locate new treatment options, preventative procedures and clinical trials for their patients.

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Elad Benjamin, CEO of Zebra
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Intermountain led a $12 million funding round that Zebra said it will use to build out its analytics engine with machine learning algorithms for diagnosing imaging scans.

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Practice Fusion veterans announce IBeat wearable-as-a-service
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The forthcoming cloud service will monitor a user’s heart activity around the clock, according to CEO Ryan Howard.

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Apixio CEO Darren Schulte raises $19 million venture capital to advance cognitive computing
Slideshow Description: 

The data science company said it will use the investment money to develop applications for care and quality measurement. 

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Decisio Health introduces clinical platform, draws $4.5M in Series A round
Slideshow Description: 

Decisio Health, a startup that aims to help acute-care provider organizations continually improve their clinical processes, launched the Decisio Health Clinical Intelligence Platform on May 17 and also announced $4.5M in Series A funding. The new platform is based on  technology developed at the University of Texas Health Center. Read full story.

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Andrew Kress, left, cofounder and CEO of HealthVerity and Andrew Goldberg co-founder and COO

HealthVerity’s technology enables customers to rapidly discover, license and assemble patient data from a wide range of traditional and emerging healthcare data sources that can aid pharmaceutical, hospital and payer organizations seeking to enhance patient insights from existing and new data sources. The startup has landed $7.1 million in its first round of funding.

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Ruben Amarasingham, MD

Pieces Technologies landed $21.6 million in its first round of funding in March 2016. The investment will help the fledgling company advance its cloud-based population health management tools, said CEO and founder Ruben Amarasingham, MD. Pieces Tech’s software platform, incubated at the Parkland Center for Clinical Innovation, provides integrated monitoring, prediction, workflow optimization and organizational learning services specifically for hospitals and health systems.

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Alejandro Foung, Lantern co-founder and CEO

Lantern, a San Francisco-based startup, with 17 employees, is working with UPMC Enterprises, the commercialization arm of the Pittsburgh-based healthcare giant, to further develop the company’s online mental health wellness services and products.

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Health Catalyst CEO Dan Burton

Health Catalyst has raised $70 million in its fifth round of funding, bringing the total of venture capital it has attracted to $235 million.

Norwest Venture Partners, the lead investor in three previous rounds of funding, and UPMC Enterprises, the commercialization arm of UPMC, co-led the round. UPMC is also a Health Catalyst customer and technology development partner.

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Zipnosis CEO Jon Pearce

Zipnosis, a startup that provides virtual care platforms, has raised $17 million in its Series A financing round to speed product development. Zipnosis describes its offering as a platform that empowers health systems to launch proprietary branded virtual care service lines staffed with their own clinicians. The goal is to maximize the clinician's time and ensure clinically appropriate patient outcomes.

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Nat Turner and Zach Weinberg, co-founders of Flatiron Health

In recent months New York-based Flatiron Health opened an office in San Francisco, completed a second round of funding – $130 million – in May 2014, and doubled down on using data to work on eradicating cancer. The company also joined forces with another oncology company to work on the next generation of cloud-based, electronic health record, data analytics and decision support software for cancer care providers around the world.

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Patrick Soon-Shiong, founder and CEO of NantHealth

Patrick Soon-Shiong, businessman, surgeon, scientist and founder of health IT company NantHealth announced back in July 2015 that he planned to take the company public by the end of the year. "We feel we have one or two transactions to accomplish, then we will initiate the public offering that we anticipate will happen probably within this year," Soon-Shiong, was quoted in the Los Angeles Times. The health IT company aims to solve the interoperability crisis and also promises to take genomics and clinical decision support to a new level. We’re still watching for an IPO in 2016.

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Teaser: 

From virtual care platforms to precision medicine, data analytics to interoperability, the healthcare IT landscape is constantly changing thanks to new approaches driven by entrepreneurs making waves in the sector.

The following gallery highlights some of those emerging companies and people who made news in 2016. Check back often as we will be updating the collection regularly.

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Health IT startups watch
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Subheader: 
From virtual care platforms to precision medicine, data analytics to interoperability, the healthcare IT landscape is constantly changing thanks to new approaches driven by entrepreneurs making waves in the sector.
Specific Terms: 

           Genomic organization and chromosomal localization of the murine 2 P domain potassium channel gene Kcnk8: conservation of gene structure in 2 P domain potassium channels    
Bockenhauer, D; Nimmakayalu, MA; Ward, DC; Goldstein, SAN; Gallagher, PG; (2000) Genomic organization and chromosomal localization of the murine 2 P domain potassium channel gene Kcnk8: conservation of gene structure in 2 P domain potassium channels. GENE , 261 (2) 365 - 372.
           Genomic organization and amplification of the human desmosomal cadherin genes DSC1 and DSC3, encoding desmocollin types 1 and 3    
Whittock, NV; Hunt, DM; Rickman, L; Malhi, S; Vogazianou, AP; Dawson, LF; Eady, RAJ; Whittock, NV; Hunt, DM; Rickman, L; Malhi, S; Vogazianou, AP; Dawson, LF; Eady, RAJ; Buxton, RS; McGrath, JA; - view fewer <#> (2000) Genomic organization and amplification of the human desmosomal cadherin genes DSC1 and DSC3, encoding desmocollin types 1 and 3. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS , 276 (2) pp. 454-460. 10.1006/bbrc.2000.3500 .
           Large-scale analysis of gene expression changes during acute and chronic exposure to Delta(9)-THC in rats    
Kittler, JT; Grigorenko, EV; Clayton, C; Zhuang, SY; Bundey, SC; Trower, MM; Wallace, D; Kittler, JT; Grigorenko, EV; Clayton, C; Zhuang, SY; Bundey, SC; Trower, MM; Wallace, D; Hampson, R; Deadwyler, S; - view fewer <#> (2000) Large-scale analysis of gene expression changes during acute and chronic exposure to Delta(9)-THC in rats. PHYSIOL GENOMICS , 3 (3) 175 - 185.
           Identification of Ankrd2, a novel skeletal muscle gene coding for a stretch-responsive ankyrin-repeat protein    
Kemp, TJ; Sadusky, TJ; Saltisi, F; Carey, N; Moss, J; Yang, SY; Sassoon, DA; Kemp, TJ; Sadusky, TJ; Saltisi, F; Carey, N; Moss, J; Yang, SY; Sassoon, DA; Goldspink, G; Coulton, GR; - view fewer <#> (2000) Identification of Ankrd2, a novel skeletal muscle gene coding for a stretch-responsive ankyrin-repeat protein. GENOMICS , 66 (3) 229 - 241. 10.1006/geno.2000.6213 .
           Cytogenetics of the chronic myeloid leukemia-derived cell line K562: Karyotype clarification by multicolor fluorescence in situ hybridization, comparative genomic hybridization, and locus-specific fluorescence in situ hybridization    
Gribble, SM; Roberts, I; Grace, C; Andrews, KM; Green, AR; Nacheva, EP; (2000) Cytogenetics of the chronic myeloid leukemia-derived cell line K562: Karyotype clarification by multicolor fluorescence in situ hybridization, comparative genomic hybridization, and locus-specific fluorescence in situ hybridization. In: CANCER GENET CYTOGEN. (pp. 1 - 8). ELSEVIER SCIENCE INC
           Characterization of the Human NMO-1 gene at 1q43 and genomic organisation of the region. NMO-1.    
Halford, S; Bellingham, J; Freedman, MS; Inglis, SL; Poopalasundaram, S; Foster, R; Hunt, DM; (2000) Characterization of the Human NMO-1 gene at 1q43 and genomic organisation of the region. NMO-1. AM J HUM GENET , 67 (4) 187 - 187.
           Genomic typing of minor histocompatibility antigen HA-1 by reference strand mediated conformation analysis (RSCA)    
Arostegui, JI; Gallardo, D; Rodriguez-Luaces, M; Querol, S; Madrigal, JA; Garcia-Lopez, J; Granena, A; (2000) Genomic typing of minor histocompatibility antigen HA-1 by reference strand mediated conformation analysis (RSCA). Tissue Antigens , 56 pp. 69-76.
          Therapy of lymphoma inspired by functional and structural genomics   
Therapy of lymphoma inspired by functional and structural genomics
Presented by: Louis M. Staudt, M.D., Ph.D., Director, Center for Cancer Genomics, National Cancer Institute, NIH
Category: WALS - Wednesday Afternoon Lectures
Aired date: 02/01/2017
          Rapid Spread and Genetic Diversification of HIV Type 1 Subtype C in a Rural Area of Southern Mozambique   
In this study, we analyzed the human immunodeficiency type 1 (HIV-1) viruses circulating between 1999 and 2004 in antiretroviral-naive women from a rural area of southern Mozambique. Nucleotide sequencing of the HIV-1 long terminal repeat (LTR) U3, envelope (env) C2V3C3, and protease (pr) genomic regions was performed from women sera samples collected in 1999 and 2004. Phylogenetic analysis revealed that all amplified sequences belonged to subtype C. Although env sequences were predominantly CCR5-tropic (R5), CXCR4-tropic (X4) variants were also identified (13%). Both 1999 and 2004 sequences were widely dispersed across multiple clusters and were related to different reference sequences from neighboring countries. Sequences from 2004 showed significantly more nucleotide genetic diversity than sequences from 1999. Importantly, genetic diversification was also observed at the pr and env amino acid level, suggesting that positive selection forces were implicated in the viral diversification. These results indicate the rapid spread and diversification of subtype C virus in Mozambique where HIV-1 prevalence in the Manhiça antenatal clinic reached 23% in 2004.
          Discriminative topological features reveal biological network mechanisms   
Background: Recent genomic and bioinformatic advances have motivated the development of numerous network models intending to describe graphs of biological, technological, and sociological origin. In most cases the success of a model has been evaluated by how well it reproduces a few key features of the real-world data, such as degree distributions, mean geodesic lengths, and clustering coefficients. Often pairs of models can reproduce these features with indistinguishable fidelity despite being generated by vastly different mechanisms. In such cases, these few target features are insufficient to distinguish which of the different models best describes real world networks of interest; moreover, it is not clear a priori that any of the presently-existing algorithms for network generation offers a predictive description of the networks inspiring them. Results: We present a method to assess systematically which of a set of proposed network generation algorithms gives the most accurate description of a given biological network. To derive discriminative classifiers, we construct a mapping from the set of all graphs to a high-dimensional (in principle infinite-dimensional) "word space". This map defines an input space for classification schemes which allow us to state unambiguously which models are most descriptive of a given network of interest. Our training sets include networks generated from 17 models either drawn from the literature or introduced in this work. We show that different duplication-mutation schemes best describe the E. coli genetic network, the S. cerevisiae protein interaction network, and the C. elegans neuronal network, out of a set of network models including a linear preferential attachment model and a small-world model. Conclusions: Our method is a first step towards systematizing network models and assessing their predictability, and we anticipate its usefulness for a number of communities.
           Chromosomal localization, gene structure, and expression pattern of DDAH1: comparison with DDAH2 and implications for evolutionary origins    
Tran, CT; Fox, MF; Vallance, P; Leiper, JM; (2000) Chromosomal localization, gene structure, and expression pattern of DDAH1: comparison with DDAH2 and implications for evolutionary origins. Genomics , 68 (1) pp. 101-105.
           Host-pathogen studies in the post-genomic era    
Kellam, P; (2000) Host-pathogen studies in the post-genomic era. [Review]. Genome Biology , 1 , Article reviews1009-reviews1009.4. 10.1186/gb-2000-1-2-reviews1009 .
          Dana-Farber Oncologists Differ Widely on the Use of Multiplex Tumor Genomic Testing   
A new study by researchers at the Dana-Farber Cancer Institute suggests that not all doctors are ready to embrace tests that may identify hundreds of genomic changes in a patient’s tumor sample for the purpose of determining appropriate treatment. Many cancer researchers believe that cutting-edge advances in genomics will pave the way for personalized or “precision” cancer […]

          Genomics 101 | Barry Schuler   
What is genomics? How will it affect our lives? In this intriguing primer on the genomics revolution, entrepreneur Barry Schuler says we can at least expect healthier, tastier food. He suggests we start with the pinot noir grape, to build better wines.
          Half the DNA on the NYC Subway Matches No Known Organism   
Mapping the Bacteria in New York's Subways Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics (pdf)
          The pigeon gets what it deserves   
Guest Contributor:  American Richard Resnick is CEO of genomic software company GenomeQuest, a TED speaker and a regular business visitor to Paris.  The day before the incident below, one of Paris’s bountiful pigeon population emptied its guts on Richard’s suit and shirt while he was on his way to a meeting. Work is over for […]
          HudsonAlpha Innovates on IT for Research-Driven Education, Genomic Medicine and Entrepreneurship   
The next BriefingsDirect Voice of the Customer IT innovation case study explores how the HudsonAlpha Institute for Biotechnology engages in digital transformation for genomic research and healthcare...

Learn more about BriefingsDirect, Dana Gardner's blog, and other Interarbor Solutions services by visiting www.interarbor-solutions.com.

          4º BIMESTRE - GENÉTICA   
GREGORIO MENDEL

Nace en Heinzendorf (Austria) el 20 de Julio de 1822 y falleció el 6 de enero de 1884 en Brünn. Es bautizado con el nombre de Johann Mendel, pro al ingresar como padre agustino en el convento de Brünn. se cambio el nombre a Gregorio (09/10/1834). Se ordena sacerdote en 1847. Fundó la Asociación Meteorológica Austriaca, miembro de la Real e Imperial Sociedad Morava y Silesia para la Mejora de la Agricultura, Ciencias Naturales y Conocimientos del País.

Mendel presenta sus trabajos en las reuniones de la Sociedad de Historia Natural de Brünn (Brno), el 8 de febrero y el 8 de marzo de 1865, publicándolos posteriormente como Experimentos sobre híbridos de plantas (Versuche über Pflanzenhybriden). Se ignoro su trabajo por que no se entendía y tuvieron que pasar más de treinta años para ser reconocidos.

Mendel realizó una serie de cruzamientos con guisantes durante generaciones sucesivas y se dedicó a la observación de determinados caracteres aparentes (rugosidad de la piel o el color amarillo o verde).

El representó las características fenotípicas (apariencia externa) de los guisantes las llamó «caracteres» y para referirse a las entidades hereditarias separadas uso la palabra «elemento».




Cromosomas


Portadores de la mayor parte del material genético y establecen la organización de la vida y las características hereditarias de cada especie. Conformados por un par de cadenas de ADN que se espiralizan y se mantienen unidas.

Estructura de un cromosoma: visto así a derecha e izquierda son las cromátidas, y arriba y abajo del centrómero son los brazos.

http://recursos.cnice.mec.es/biosfera/alumno/4ESO/genetica1/imagenes/cariotipo.gif

CARACTERÍSTICA MORFOLÓGICAS DE LOS CROMOSOMAS:

Las cromátidas:

- Estructuras idénticas en morfología e información que están unidas por el centrómero.
-Contienen cada una molécula de ADN.
- Dos cromatinas conforman un cromosoma y genéticamente cada cromátida tiene el valor de un cromosoma.
- Constituida por un esqueleto proteico, situado en el interior, alrededor del cual se disponen muy apelotonados el ADN y las proteínas que forman el cromosoma.

El centrómero:
- Región que se fija al huso acromático durante la mitosis.
- Ubicado en un estrechamiento llamado constricción primaria, que divide a cada cromátida del cromosoma en dos brazos.

Los telómeros:
- Es el extremo de cada brazo del cromosoma.
- El ADN de los telómeros no se transcribe y en cada proceso de división celular se acorta.
- Cuando los telómeros desaparecen el cromosoma sigue acortándose y la célula pierde información genética útil y degenera, entonces podemos decir que ellos determinan el número de ciclos celulares que puede tener una célula. En las células cancerosas, una enzima, la telomerasa, regenera los telómeros; esta es la razón, al parecer, de que estas células puedan dividirse indefinidamente.

El organizador nucleolar.
- Solo se halla en algunos cromosomas.
- En ella se sitúan los genes que se transcriben como ARN, con lo que se promueve la formación del nucléolo y de los ribosomas.
- Esta zona no se espiraliza tanto y por eso se ve más clara.

El satélite (SAT): Es el segmento del cromosoma entre el organizador nucleolar y el telómero correspondiente. Sólo poseen satélite aquellos cromososmas que tienen NOR.

DIVISIÓN DE LOS CROMOSOMAS

1. Metacéntricos: presenta brazos de longitud aproximadamente igual con el centrómero en el medio. En el humano los cromosomas 1, el 3, el 19, 20 y el X presentan una estructura metacéntrica.


2. Submetacéntricos: presenta brazos de longitud desigual y el centrómero muy cerca de uno de los extremos. En el humano la mayor parte de cromosomas son submetacéntricos excepto los cromosomas 1, 3, 19, 20 y el X (c. metacéntricos).


No se puede mostrar la imagen “http://img223.imageshack.us/img223/907/c1eg6.png” porque contiene errores.



3. Acrocéntricos: el centrómero está próximo a un extremo del cromosoma y un brazo pequeño y muy corto. En el humano los cromosomas 13, el 14, el 15, el 21 y el 22 son acrocéntricos y actúan como organizadores nucleolares.

No se puede mostrar la imagen “http://img80.imageshack.us/img80/619/c2gp2.png” porque contiene errores.



4.- Telocéntrico: el centrómero está en uno de los extremos, un brazo es muy corto y el otro largo.

Leyes de Mendel

Primera ley, o ley de segregación: nos dice que en un cruce monohíbrido (una sola característica) un individuo que es diploide tiene dos alelos para una misma característica, y que estos alelos se separan (se segregan) al formarse los gametos; un alelo para cada gameto formado.

Segunda ley, o de distribución independiente: En un cruce dihíbrido (dos características) dos alelos de una característica se separan y su separación es independiente a la separación de los alelos del otro locus o característica.

Tercera ley, o ley de la combinación de los genes (transmisión independiente de los genes): Cada una de las características puras de cada variedad (color, rugosidad de la piel, etc.) se transmiten a la siguiente generación de forma independiente entre sí, siguiendo las dos primeras leyes.











Ejemplos:



Diagrama de los resultados obtenidos por Mendel al cruzar razas puras considerando el carácter 'color de la semilla


Diagrama del cruzamiento entre ratones que presentan diferente alternativa (negro y café) para el color de su pelaje (razas puras en la nomenclatura de Mendel)


Diagrama del cruzamiento realizado por Mendel al cruzar razas puras de plantas de arveja considerando simultáneamente el carácter 'color de la semilla' y 'textura de la testa de la semilla'

Diagrama del 'cruzamiento control' de los experimentos de Mendel en que se consideran 2 caracteres simultáneamente


Diagrama del cruzamiento entre ratones en que se considera el 'color del pelaje' (negro y café) y la 'longitud del pelo' (corto y largo)



ANEXOS


1.- Factores que determinaron el éxito de las experiencias de Mendel.

1.1.- La selección de las plantas utilizadas como la arbeja: tiene un cultivo sencillo y un crecimiento a corto tiempo.

1.2.- El registro de datos de cada experiencia fue minucioso y preciso: esto permitió precisar el tipo de descendientes en cada generación y llegar a conclusiones válidas hasta hoy.

1.3.- Selección de caracteres sencillos: se tomo uno o dos de los caracteres para mejor precisión.

1.4.- El empleo de las matemáticas: especialmente en las probabilidades el análisis combinatorio para analizar sus observaciones formular una hipótesis explicatoria de cada experiencia.


2.- ¿CÓMO SE DA LA HERENCIA DEL SEXO?

Lo determina un par de cromosomas sexuales que son diferentes en el varón y la mujer. En el hombre son 46 cromosomas. 44 son conocidos como autosomas los cuales se distribuyen en 22 pares, los dos restantes son conocidos como cromosomas sexuales por ser los que determina el sexo.

En la mujer son iguales y se les conoce como XX, en el varón son distintos, a un cromosoma se le conoce como X y a otro como Y. Al formarse dos gametos, los dos cromosomas se dividen. De tal manera que la mitad de los espermatozoides llevan el cromosoma X, y la otra mitad lleva el cromosomas Y. En cambio los óvulos solo llevan los cromosomas X.

La fecundación se realiza al asar, es decir, pueden efectuarla el espermatozoide de los dos tipos. Cuando se tienen descendientes, las probabilidades de que se procree varón y mujer son iguales, por consiguiente, el se varón o mujer, es un simple asar.

3.- HERENCIA DEL FACTOR “RH”

Un individuo se considera que es RH + si presenta un componente llamado aglutinógeno, y si no lo posee en RH - . Por estudio científicos se a comprobado que las razas de color negra son 100% RH +, mientras que en la población blanca el 85% es RH+ y solo el 15% es RH-. Es muy importante saber que el factor RH+ es siempre dominante, y el RH- es recesivo.

Tipos de sangre: Los grupos sanguíneos están basados en específicas proteínas conocidas como antígenos, que se encuentran en la superficie de los glóbulos rojos, y en los anticuerpos que se encuentran en el plasma.


Distribución de los diferentes grupos de sangre en Estados Unidos

Existen cuatro grupos sanguíneos básicos:

1.- Grupo A con antígenos A en las células rojas y anticuerpos anti-B en el plasma.

2.- Grupo B con antígenos B en las células rojas y anticuerpos anti-A en el plasma.

3.- Grupo AB con antígenos A y B en las células rojas y sin los anticuerpos anti-A ni anti-B en el plasma.

4.- Grupo O sin antígenos A ni B en las células rojas y con los anticuerpos anti-A y anti-B en el plasma.

* Si tú tienes sangre del grupo A, no tienes anticuerpos contra los marcadores A. Pero tienes anticuerpos contra la sangre del grupo B.

* Si tu grupo sanguíneo es el B, tienes anticuerpos contra las células de la sangre A.

* Y si tienes sangre del grupo O, tienes anticuerpos contra la sangre A y la B.

4.- PROBLEMAS GENÉICOS HUMANOs

4.1.- Caracteres patológicos ligados al cromosoma X: el cromosoma X puede ser también portador de algunos genes que van ha orientan caracteres patológicos hereditarios en el nuevo individuó. Como la hemofilia, el daltonismo, la miopía y el astigmatismo

4.1.1.- La hemofilias: es una enfermedad hereditaria que se entiende por la falta de coagulación de la sangre. Esta se hereda como un carácter recesivo ligado al sexo, quien transmite esta enfermedad es la madre, pero ella no la padece. Los varones enfermos de hemofilia rara vez tienen descendencia.

4.1.2.- El Daltonismo: consiste en confundir los colores, especialmente el rojo por el verde y viceversa

4.1.3.- La Miopía: defecto visual de refracción. La persona miope tiene dificultad para ver claramente a menos que el objeto esté cerca. A menudo





La causa del error es que durante la infancia el ojo se vuelve demasiado largo y los rayos de luz provenientes de un objeto distante hacen foco delante de la retina en lugar de hacerlo sobre ella, como ocurre en una visión normal. Seda tanto en hombres como en mujeres y se presenta en los primeros grados de la escuela.

Causas:
- Factores hereditarios
- Influencias ambientales
- Combinación de ambos procesos.

Síntomas:

-Entornar los ojos
- Incapacidad de distinguir los rasgos faciales de una persona a larga distancia
- Leer sólo con el libro muy cerca de la cara
- Sentarse en las primeras filas en la clase o en el cine




4.1.4.- El Astigmatismo: condición óptica en la cual, los rayos de luz paralelos que inciden en el ojo no son refractados igualmente en todos los meridianos del mismo.

Causado por una curvatura distinta de la superficie de la córnea. Esta cornea astigmática es ovalada como la superficie de un huevo. El resultado es la falta de foco, produciendo visión borrosa En un ojo astigmático, la córnea será achatada, tórica (o sea como un trozo de balón de rugby, o un trozo de balón de baloncesto aplastado) La dirección de ese aplastamiento determina el eje del astigmatismo.

De origen hereditario, pero también se origina por culpa de complicaciones en intervenciones quirúrgicas, traumatismos o enfermedades.



5.- HERENCIA DE LOS RASGOS FÍSICOS:

RASGOS

DOMINATE

RECESIVO

1.- Color de pelo

Negro

Cero

CABELLO

Rizado

No Puede

Mechón blanco frontal

Si

No Catadores

Color de los ojos

Negro

Finos

Color de la piel

Varios genes determinan el color

Adherido

Astigmatismo

Padece

Visión normal

Pabellón de la oreja

Desprendido

Albino

Labios

Gruesos

Azul

Desarrollo del sabor

Catadores

No

Enrollamiento de la lengua

Si Puede

Liso

Grupo sanguíneo

A-B AD

Rubio



Algunas Animaciones




















PAGINAS CONSULTADAS:

http://www.geocities.com/ResearchTriangle/Lab/2513/mendel.htm

http://es.wikipedia.org/wiki/Gregor_Mendel

http://web.educastur.princast.es/proyectos/biogeo_ov/2BCH/B4_INFORMACION/T407_CROMOSOMAS/informacion.htm

http://www2.uah.es/biomodel/citogene/horwitz/cytogen1.htm

http://html.rincondelvago.com/materia-viva_2.html

http://www.galeon.com/laujomu/genetica.htm
http://bioinformatica.uab.es/genomica/swf/genotipo.swf

http://www.biotech.bioetica.org/ap1.htm

http://www.puc.cl/sw_educ/biologia/bio100/html/portadaMIval4.1.2.2.html

www.elmundo.es/especiales/2003/02/salud/genetica/descifrar_la_vida.html

www.iessuel.org/ccnn/flash/genoma[1].swf

www.80.38.220.13/~lourdes/genetica/genemendel/leyesdemendel.swf

http://bioinformatica.uab.es/genomica/swf/cromosomas.swf

http://www.tusalud.com.mx/121304.htm

http://www.tarso.com/Astig.html

http://www.pasteur.cl/cont/lasik.html





          Fast and inexpensive C. elegans genomic DNA preparation using Sigma’s Extract-N-Amp kit   
[insert_php]strip_tagsBhoomi Madhu-1 and Tina L. Gumienny-1[/insert_php]

          Metagenomics, Lyme Disease, and the Tyrolean Iceman’s Tattoos   
When the genetic analysis of the 5,300 year old Tyrolean Iceman, better known as Ötzi, was published in February, most of the attention was naturally focused on his genomic DNA. His genomic DNA produced some interesting results: he had brown eyes, blood type O+, was probably lactose intolerant and from a southern European gene pool. … Continue reading Metagenomics, Lyme Disease, and the Tyrolean Iceman’s Tattoos
          ‘Biological Teleportation’ Edges Closer With Craig Venter’s Digital-to-Biological Converter   
The year is 2030. In a high-security containment lab, scientists gathered around a towering machine, eagerly awaiting the first look at a newly discovered bacterium on Mars. With a series of beeps, the machine—a digital-to-biological converter, or DBC—signaled that it had successfully received the bacterium’s digitized genomic file. Using a chemical cocktail comprised of the […]
          Ecco l'inizio della «vita artificiale» Costruita la prima cellula   

È stata costruita in laboratorio la prima cellula artificiale, controllata da un Dna sintetico e in grado di dividersi e moltiplicarsi proprio come qualsiasi altra cellula vivente. Il risultato, pubblicato su Science, è stato ottenuto negli Stati Uniti, nell'istituto di Craig Venter. Si tratta di una svolta epocale nella ricerca.

BATTERI SALVA-AMBIENTE - Con questo nuovo passo il traguardo della vita artificiale è ormai più vicino che mai e si comincia a intravedere la realizzazione di uno dei sogni di Venter: costruire batteri salva-ambiente con un Dna programmato per produrre biocarburanti o per pulire acque e terreni contaminati. Dopo avere ottenuto il primo cromosoma artificiale, la sfida è riuscire ad attivarlo, aveva detto Venter appena due anni fa. Adesso ha raggiunto il suo obiettivo e lo ha fatto unendo, come tessere di un puzzle, i risultati ottenuti negli ultimi cinque anni. Il primo passo, nel 2007, era stato la costruzione di un Dna sintetico; quindi nel 2009 sempre il gruppo di Venter ha eseguito il primo trapianto di genoma da un batterio a un altro. Adesso è ancora lo stesso gruppo, coordinato da Daniel Gibson, ad aver combinato i due risultati e aver assemblato la prima cellula sintetica.

«COMINCIA L'ERA POST-GENOMICA» - «Si tratta di un traguardo fondamentale dell'ingegneria genetica, non solo per possibili risvolti applicativi, ma anche perché segna la tappa iniziale dell'era post-genomica» commenta il genetista Giuseppe Novelli, preside della facoltà di Medicina dell'Università di Tor Vergata di Roma. «Di fatto Venter ha creato qualcosa che prima non c'era, un batterio prima inesistente, perché il genoma artificiale che ha costruito con una macchina in laboratorio contiene dei pezzetti di Dna che non esistono nel genoma del batterio presente in natura». Venter ha fatto tutto con una macchina, spiega ancora Novelli. «Prima ha letto la sequenza genomica del batterio in un database genetico, poi con un macchinario ha ricostruito chimicamente il genoma, aggiungendovi però nuove sequenze. Ha fatto pezzetti, ciascuno di 10 mila lettere di codice, poi li ha assemblati insieme fino a creare un genoma di oltre un milione di paia di basi. Poi ha inserito il genoma artificiale in un batterio svuotato del suo Dna e ha costruito una nuova forma di vita che funziona e si riproduce. La cellula così creata, infatti, prima non esisteva, e il suo genoma porta i segni distintivi della sua differenza dal batterio esistente in natura». «In futuro - conclude Novelli - si potranno creare nuove forme di vita capaci di produrre farmaci o di aiutarci contro l'inquinamento, per esempio batteri mangia-petrolio». (Fonte: agenzia Ansa)

Da Corriere.it
          Latifa Jackson   
Institution/Organization: Howard University Department: Human Genome Center Academic Status: Postdoctoral Fellow What conference theme areas are you interested in (check all that apply): Data Analytics and Visualization Data-Driven Modeling and Prediction Interests: I have academic training in biomedical science systems biology related to human disease genomics and human evolutionary genetics training as well as a […]
          The New Living DNA Test: A Review of My Results    

I mailed in my complimentary Living DNA kit at the end of October. The test is performed using the Illumina Global Screening Array Chip. I took some photos of the kit, so testers will know what to expect. 

The Kit



Living DNA uses a swab for sample collection, as shown here. There are two in each kit. The collection process is relatively easy and involves no liquid. Although Living DNA is a British company, the mailing address for my kit was Eurofins Genomics in Louisville, Kentucky. (Eurofins is one of their partners according to the website, and the testing is done in Denmark.) The decision to use swabs for DNA collection instead of saliva, undoubtedly, makes shipping the samples to the lab from the United States, and internationally within Europe, simpler.


I received my results on February 7th, just as I was leaving for RootsTech. Now that I am home, I have had a chance to finally look them over.

Results
My results include an admixture prediction (percentages of overall ancestral origins based on autosomal DNA) and my mtDNA haplogroup (which was correct - U5b1b2). Males will also receive their Y-DNA haplogroup. 

Currently, there is no relative matching feature, but it is expected to be added in the near future, which will be essential for genealogical and unknown parentage applications. This will be a terrific addition to the U.S.-based databases we already use in our research, since it will have a unique British, and presumably, European market. 


I was excited to receive these results since I have recent English ancestry and they promised to provide a very detailed breakdown of ancestral origins within the British Isles, with 21 separate categories. You can see the descriptions of those categories here

Reportedly, this test is only looking back to where your ancestors were about four to five generations ago, but the What you are made of section on the site states, "A typical profile provides your genetic ancestry going back about six generations." Either way, this is not a deep ancestry analysis and should reflect what we know about our recent ancestors. (Edit: The site has been updated to reflect a ten generation reach, which makes more sense to me.)

Like 23andMe's former version of Ancestry Composition, the admixture results are presented at three different levels: Global, Regional and Sub-Regions. 

Here are mine. 

Global

At 23andMe, I am 100% European. 
At AncestryDNA, I am 99% European.
At Family Tree DNA, I am 97% European.

Regional

At 23andMe, I am 24.8% British/Irish and 22% Finnish. 
At AncestryDNA, I am 0% Great Britain, 10% Irish and 21% Finland/Northwest Russia.
At Family Tree DNA, I am 27% British Isles and 23% Finland and Northern Siberian.

It is immediately obvious that something is off with the Living DNA estimate, since my grandmother was of full Finnish ancestry and all three of the other companies accurately detect that (21% - 23%). Conversely, Living DNA only estimates 12.6% in their Europe East category for me, which includes Finnish DNA.  (On a side note, I consider this a misnomer. Finland is generally not considered to be part of Eastern Europe.) 

 Results Map


On the "Your Family Ancestry" page, in the How the Science Works section, Living DNA states this:
I do not accept that explanation and I hope their other customers will not be misled by it either. It is absurd to claim that it is realistically possible to inherit 0% of a grandparent's DNA. 

LivingDNA estimates that 81.7% of my DNA comes from Great Britain and Ireland. That is a significant overestimate. I have one great grandfather of full British ancestry (~12.5%) and one second great grandmother of full British ancestry (~6.25%). All of the rest of my known British ancestry, with the exception of two possible Irish 5th great grandparents, is Colonial American.  I do have some genealogical brick walls, but my matches on those lines do not indicate that behind any of them is a recent British ancestor. The other reputable companies estimate I am between 10% - 27% British/Irish. 

CeCe's Family Tree, British Ancestors in Red
Click on Image to Enlarge

I also have a great grandparent of full Norwegian ancestry as well as a significant amount of German ancestry. 

So, let's look at my Sub-regional estimates:

Sub Regions
Click on Image to Enlarge


According to these results, my ancestors came from many different areas of England, which is certainly possible if you look very deep into my pedigree, back to my immigrant ancestors in the 1600's. Focusing on my more recent English ancestors, let's see if these estimates are consistent with their known origins.

My great grandfather, George Henry Allen was born in Australia, but both of his parents, George Allen (b.1851) and Flora Chitts (b.1849) were born in Gloucestershire, England, as were their known ancestors. So, I should have inherited about 12.5% of my DNA from this area. According to this page, Gloucestershire ancestry would fall into the South Central England sub-region. I have an estimated 8% from this category. So, a little low, but not impossible when taking into account the randomness of recombination. 

My third great grandfather Thomas Armstrong was born 1801 in Cumberland (as were his known ancestors). I would have inherited approximately 3.125% of my DNA from him. The area that was once Cumberland is now part of Cumbria. According to Living DNA I have 6.4% in the Cumbria category. 

My third great grandmother Dorothy Hudspith was born 1811 in Northumberland (as were her known ancestors). I would carry about 3.125% of her DNA. Northumberland would be in the Northumbria category. 0% of my DNA is predicted to have originated in Northumbria.  

As I mentioned, I have two unconfirmed fifth great grandparents from Ireland (on different lines). One of them was reportedly born in County Armagh. If this is accurate, then I would expect to have about 1.56% of Irish DNA. I have 2.1% in the Southwest Scotland and Northern Ireland category, so this appears to be roughly consistent. 

What does that leave?
14.5% South Wales Border - no known recent ancestry from this area
14.1% Central England - no known recent ancestry from this area
12.4% Southeast England - This category could be representative of my German ancestry. The site states this about it: 

5.8% Cornwall - no known recent ancestry from this area
5.1% South Yorkshire - no known recent ancestry from this area
1.3% Northwest England - no known recent ancestry from this area
1.1% Devon - no known recent ancestry from this area
11.5% Unassigned Great Britain and Ireland 

12.6% Finland and Western Russia - expected ~25%
4.2% Scandinavia - expected ~12.5%

Conclusions
Due to my large amount of distant Colonial American ancestry, my overall British DNA is likely a challenge to specifically categorize. Focusing on my last six generations, these results were not consistent with my known ancestry. Failing to recognize half of my Finnish ancestry and significantly underestimating my Norwegian/Scandinavian ancestry does not inspire confidence. The site explained that German ancestry could be included in the Southeast England category, so that may explain why none of mine showed up elsewhere. Even with this caveat, however, this does not accurately portray my ancestral origins. 

I suspect that I am not the only one who will see over-inflated British percentages, but that remains to be seen when more results are delivered and reviews published.  

This test's launch has been highly anticipated and has definitely been getting a lot of buzz, but I think it is important to recognize that any time a company is claiming to provide very specific sub-regional percentages, we must take it with a big dose of salt. As always, I support and appreciate the efforts to advance our field. It has to start somewhere and we can't expect perfection. I look forward to improvements and the future of this exciting company. 

If you are interested in seeing what Living DNA will predict for you, you can order your kit here


          Is Ancestry.com Getting Into the Health Business?    
The following is a guest post by Angie Bush, my partner in The DNA Detectives:

Today, I received in my email inbox a questionnaire from Ancestry.com asking about my thoughts in using my family tree to study family health history. I recently wrote an article that touched on the use of genealogical data in conjunction with genetic studies for the APG Quarterly. In this article, I talked about how the Utah Population database was started as the result of a joint collaboration between the LDS Church and scientists at the University of Utah. This database is unique in that it links detailed family history information with genetic data to allow scientists to study the inheritance of many diseases. Many significant genetic discoveries have been made as a result of this database, including the famous (or infamous) BRCA1 and 2 genes. It is a significant resource for those interested in studying the inheritance of genetic disease. More about the Utah Population Database and the role of genealogical information can be found here: http://learn.genetics.utah.edu/content/science/utah/

Just as in genealogical research, DNA is of little value without a paper trail. Significant value and power lies in combining detailed family health histories with genetic data. In my opinion, 23andMe has missed a significant opportunity to link family histories with genetic data and make ground-breaking discoveries. From this survey, it appears that Ancestry.com/AncestryDNA recognizes the value of this information and that they may be considering getting into the business of supplying their customers with heath related information the way 23andMe did prior to November 2013. It would appear that they are constructing a database very similar to the Utah Population Database with SNP data generated from the Illumina Chip they currently use. 


I have a few questions about this:
  • Will AncestryDNA now be subject to the same FDA guidelines that are currently prohibiting health information from 23andMe, and if so, will Ancestry join the effort with 23andMe to allow this type of information to be provided to consumers? 
  • Or, will they ride 23andMe's coat-tails into the health side of the personal genomics market? Will Ancestry re-sell this data to large pharmaceutical companies?
  • How can we participate in this research, and should we as customers be participating?

There are many other questions I could ask, and in the end, I do believe that health care needs a serious overhaul and the revolution that Anne Wojcicki started with 23andMe cannot be stopped now. I believe one of the best ways to revolutionize health care is to understand what our individual genetic code is telling us about future disease risk, how to manage that risk and prevent disease if possible. It appears from the questions on the Ancestry survey, that they recognize the power of this information as well, and that they plan to move into the space currently occupied only by 23andMe.

 Screen shots of the email and survey follow:














Thanks to Angie for sharing this update and important information with my readers!

           Comparative genomics of serotype Asia 1 foot-and-mouth disease virus isolates from India sampled over the last two decades    
Mohapatra, Jajati K. and Sanyal, Aniket and Hemadri, Divakar and Tosh, Chakradhar and Biswas, Subhajit and Knowles, Nick J. and Rasool, Thaha J. and Bandyopadhyay, Santanu K. and Pattnaik, Bramhadev (2008) Comparative genomics of serotype Asia 1 foot-and-mouth disease virus isolates from India sampled over the last two decades. Virus Research, 136 (1-2). pp. 16-29. ISSN 0168-1702
          Integrative Physiology in the Proteomics and Post-Genomics Age   
Integrative Physiology in the Proteomics and Post-Genomics Age
Editor: Wolfgang Walz
Release: 2005-03-22
Edition: 1
Publisher: Humana Press
Format: Hardcover 280 pages
ISBN: 1588293157 (1-58829-315-7)
ISBN 13: 9781588293152

Download
Version 1

          Better medicine, brought to you by big data — Cloud Computing News   
Some concrete examples of how ‘big data’ is improving medicine and healthcare: Genomics Business intelligence for doctors to analyse hospital-wide data Semantic search to improve search results (more plain language search) Hadoop (?) for everything – identifying unsuspected adverse side effects from multi-drug combinations, or analysing medical images IMB’s Watson diagnostic tool Getting ahead of […]
          Rick Perry’s Educational Background: How Well-Educated Is He?   
  Why They’ve Earned Our Notice: On March 2nd, of 2017, James Richard “Rick” Perry become our newest Secretary of Energy. Nominated to his position by the ever-controversial Donald Trump, Perry takes the seat formerly held by Obama’s Ernest Monis.  In his new role, he’s responsible for US policies regarding energy, energy conservation, genomics, and […]
          NantHealth starts building pediatric brain tumor database   
Dr. Patrick Soon-Shiong’s NantHealth and collaborators have begun a pediatric brain tumor sequencing project. The $20 million initiative will generate genomic, transcriptomic and proteomic data from 1,600 children with brain tumors and share the data publicly.
          NCI picks Amazon, Microsoft for cloud data project    
The National Cancer Institute is teaming up with Amazon and Microsoft to work on genomic data platforms. The idea is to tap into the tech giants’ cloud computing knowledge and capabilities to create a sustainable model for sharing cancer genomic data with researchers.
          Days after scrapping crowdfunding campaign, Tute accepts PierianDx buyout bid    
PierianDx has bought Tute Genomics for an undisclosed amount. The deal gives PierianDx the genomics platform Kai Wang’s Tute built up over its four years of operation and through the buyout of former trailblazer Knome.
          PHG Foundation to speak on genomic data sharing in Washington   
PHG Foundation's Alison Hall, ​will be speaking on the UK perspective on data sharing at Curating the Clinical Genome conference in Washington this Thursday.Commencing tomorrow, this three-day conference on the pertinent topic of genomic data sharing, will bring together initiatives to develop c ...
          Making sense of genomic variants   
The aim of clinical genome analysis is to identify variants in the genome that relate to and potentially diagnose a patient’s condition. Given that the average human genome varies at more than 3 million locations, getting this analysis right is no easy task. Variant interpretation and cl ...
          PHG Foundation speaking at World Precision Medicine Congress   
PHG Foundation will be speaking on mainstreaming genomics and big data at the World Precision Medicine Congress on Thursday.The three day Precision Medicine Congress in London tomorrow will focus on a multitude of omics and disease areas; including cancer, rare diseases, infectious diseases and ot ...
          Genome editing in medicine - where are we?   
As we discussed in a recent blog, the House of Commons Science and Technology Committee's ambitious and wide-reaching inquiry into genomics and genome editing is examining the role that genomic technologies can play in health, agriculture and the environment. The PHG Foundation's written response to ...
          Data Diversity In Precision Medicine   

Bio-IT World | Why diverse datasets are needed to enhance genomic interpretation and speed the progress of precision medicine.


 
 
 
 

          Rady Children's Ambitious Genomics Expansion To Start In Orange County   
The San Diego Union-Tribune | Rady Children's Institute for Genomic Medicine announced last week that it has made a pact with Children's Hospital of Orange County, offering quick-turnaround service for infants in that facility's intensive care units who need the speed.
          The Extended Evolutionary Synthesis - a moderate step in the right direction    

A discontent grows among the practitioners of evolution theory.

Research results keep outrunning the theory’s capacity to herd them—the results, that is, but the practitioners, too—and corral them inside the Modern Synthesis.

Evidence of discontent keeps piling up. For example, in July 2008 researchers from various fields of biological science convened in Altenberg, Switzerland, to formalize a so-called Extended Synthesis of evolutionary theory. MIT Press published the conference papers as a sourcebook, Evolution - the Extended Synthesis.

The book's contributors reassure readers that the findings presented pose no fundamental threat to the Darwinian model. The collective attitude seems to be that new discoveries in genomics, epigenetics, ecology and related fields merely complicate—without undermining—the natural selection model of evolution. These reassurances reek of cover, of maneuvering to avoid the label, “fringe” or the academic equivalent. Maybe, “Traitor.”

More recently, some of the Altenberg attendees, among others, launched a web site, The Third Way, as an organizing tool for scientists working on a model of evolution that accommodates the research findings that are stretching the Modern Synthesis. More recently the The John Templeton Foundation has awarded a major grant (£5.7m or $8m) to an international team of leading researchers for a three-year research program “to put the predictions of the extended evolutionary synthesis to the test.” The Royal Society in 2015 published an article, The extended evolutionary synthesis: its structure, assumptions and predictions that provides additional background information. And in November 2016 the Society hosted a scientific meeting on the topic, entitled, “New trends in evolutionary biology: biological, philosophical and social science perspectives”.

A discontent among those working in the evolution biz is brewing if not already boiling over. 

 It seems that the evolution theory we learned in school is getting an earnest retooling. The breadth and depth of that retooling divides scientific opinion. It might involve tightening a few knobs, or it might involve a fundamental rebuild—a Kuhnian paradigm shift. Which way things shake out remains to be seen.

Whichever way things do shake out for mainstream evolution theory, the new developments embolden the star larvae hypothesis. The new developments describe a convergence of development and evolution, insofar as the new ideas describe development and evolution as sharing a common set of internal mechanics, of endogenous formative processes. In aggregate, the new discoveries make development and evolution seem to be processes of differentiation, or descent with modification, distinguished primarily by their spatial and temporal scales, not by their causal mechanisms. The following table summarizes the congruence of processes.

DiscoveryEvolution of species in ecologies Development of cell types in organisms
Conservation of DNA Much less genomic variability across species than phenotypic variability suggests Much less genotypic variability across cell types than phenotypic variability suggests
Epigenetic regulatory networks Conserved DNA produces diverse phenotypes via epigenetic regulation of gene expression Conserved DNA produces diverse phenotypes via epigenetic regulation of gene expression
Genomic mosaicism Despite a general conservation of DNA across species, organisms in an ecology exhibit a degree of genetic variance Despite a general conservation of DNA across tissues, cells in a complex organism exhibit a degree of genetic variance.
Pre-Adaptation, or "Anticipatory" Genes Some unexpressed sequences code for tissues needed by descendant species. Unexpressed sequences code for proteins needed by descendant cell types.


As these parallels (and perhaps others, such as might involve “junk” DNA) dovetail into a developmental model of evolution, the star larvae hypothesis stands ready as a paradigm within which the seemingly anomalous data—the coincidences and incommensurabilities—can reside. They can live comfortably as neighbors, having been reconciled. That contention is more fully developed at http://www.starlarvae.org/Star_Larvae_Ontophylogeny.

A recent paper, cited earlier, elaborates on this contention, incidentally to the intentions of its authors. The paper, The extended evolutionary synthesis: its structure, assumptions and predictions, includes a comparison of the core assumptions held by the Modern Synthesis and by the upstart Extended Synthesis [Table 1]. Each of the six observations to which the authors call attention happens also to make evolution, in its mechanical operations, resemble a process of development. Here are the points to which the authors call attention:

1) Unlike the Modern Synthesis, which assumes the pre-eminence of natural selection, the Extended Synthesis assumes that “Developmental processes, operating through developmental bias and niche construction, share with natural selection some responsibility for the direction and rate of evolution and contribute to organism–environment complementarity.”

That is, natural selection gets marginalized as endogenous processes and niche construction in the Extended Synthesis get a (perhaps equal?) slice of the credit for originating species. Niche construction has to do with organisms altering their environments in ways that have evolutionary consequences. An ontogenetic parallel occurs when cells in an embryo release morphogens, which influence the forms and functions of descendant cells as those cells differentiate, a case of ontogenetic niche construction.

2) Unlike the Modern Synthesis, which assumes that inheritance is genetic only, the Extended Synthesis assumes that “Inheritance extends beyond genes to encompass (transgenerational) epigenetic inheritance, physiological inheritance, ecological inheritance, social (behavioural) transmission and cultural inheritance.”

It’s not clear how literally “cultural inheritance” applies to evolution broadly, but the other considerations apply as much to cells differentiating in a body as they do to species differentiating in an ecology (at least if chemical communication among cells can be considered a social behavior). Inclusiveness in the context of cellular differentiation includes inheritance of cytoplasm and organelles, in addition to genes and epigenetic markers.

3) Unlike the Modern Synthesis, which assumes that genetic variation is random, the Extended Synthesis assumes that variation is non-random, “which means that some phenotypic variants are more likely than others.”

This also is the case with cell phenotypes as cells differentiate in a body.

4) Unlike the Modern Synthesis, which assumes that evolutionary change is gradual, the Extended Synthesis assumes that rates of change vary, depending on actions of regulatory systems or when “coordinated suites of traits” are managed by developmental processes.

This also is the case when cells in a body differentiate; e.g., some stem cells remain stem cells and some mature into their fully specialized (adult?) form. Rates of change can be very variable.

5) Unlike the Modern Synthesis, which assumes a gene-centric perspective; i.e., evolution is about changes in gene frequencies, the Extended Synthesis assumes an organism-centered perspective; i.e., evolution is about changes in phenotypic trait frequencies—whatever is going on with the genes.

This is the perspective assumed with regard to cellular differentiation in a developing organism. (That said, some degree of change in gene frequencies characterizes both the descent of species and that of cell types in a body, the latter, somewhat recent, discovery taking the name, “genomic mosaicism.”)

6) Unlike the Modern Synthesis, which assumes that macroevolution reduces to microevolution; i.e., selection, drift, mutation, and gene flow, the Extended Synthesis assumes that “Additional evolutionary processes, including developmental bias and ecological inheritance, help explain macro-evolutionary patterns and contribute to evolvability.”

Cellular differentiation during development also incorporates these circumstances / mechanisms.

What but spatial and temporal scale is left to distinguish evolution from development—the origin of species in an ecology from the origin of cell types in an organism?

 

The paper’s authors also compare the ways in which the Modern Synthesis and Extended Synthesis interpret various factors that impinge on the evolutionary process [Table 2.]

These factors are developmental bias, phenotypic plasticity, inclusive inheritance, and niche construction. The Modern Synthesis downplays the significance of these factors in shaping evolutionary outcomes. By contrast, by assigning a considerable significance to these factors as shapers of evolutionary outcomes, the Extended Synthesis funnels the dynamics of the evolutionary process into channels already recognized as facilitators and directors of cellular differentiation during development. Developmental bias, phenotypic plasticity, inclusive inheritance, and niche construction all factor into cellular differentiation.

This analysis of this particular paper might be applied to any number of publications that explicate the Extended Synthesis. The new data always point in the same direction: Evolution is a developmental process. That observation invites teleological assessments, because development is teleological—the outcomes are inherent in the process. If the process is spared meddling from disruptive outside influences and endogenous pathologies, then it can complete its life cycle, the life cycle of an organism, in the case of evolution that would be the stellar organism. But that recognition should cause no discontent.


          The Twin Phantoms: Genes and Information   
Ongoing research in molecular biology has delivered to the world the peculiar finding that the term gene refers to no determinable thing at all. Gene is an idea. It grew from an assumption. The assumption, implied by the prevailing scientific philosophy of reductionism, is that there must be a smallest unit of biological expression. And a smallest unit of biological inheritance. And that atomic entity was called a gene.

Despite gene losing its power to denote, the science of genomics continues to advance and looks determined to keep doing so. And this is also despite reductionism’s shortcomings increasingly becoming apparent, as research reveals the seemingly intractable interwovenness of the processes and subprocesses of biological metabolism.

Reductionism fails because everything that goes on inside a living cell depends on—is caused by, directly or indirectly–everything else that goes on inside the cell. And then, adding more complication, there are exogenous influences. And above it all, no locus of control. There is a lacuna of control. The cell has no brain. The sequencing of the human genome, that recent triumph of reductionism, like the cataloging of elementary particles, provides a compendium, but it resides far from the macrostructure, far from an accounting of gross outcomes. Structures and processes that define the macro world do not map readily onto elementary bits.


Once causality is recognized as a two-way street (or a multidimensional interchange), then neither top-down nor bottom-up models of nature will suffice. And whatever somethings we want to denote by gene they cannot be point origins of causal chains but only links in such chains. And what vital essence ensures that the cellular machinery runs smoothly? Somebody’s got to manage the store.

Enter then the latest applicant for the position of deus ex machina, that magical, mystical sort-of-something called information.

Arrange the atoms just right, and . . . presto! A (kind of) causal agent arrives, the untouchable information.

This property or characteristic or emergent attribute of variously arranged bits of matter (or is it just another name for the geometrical arrangement itself of the atoms in space and the distribution of electrical charges among them?) supposedly explains why at least some events occur as they do and not in some other way. Such explanations of natural forms, those that invoke information and its affiliates, the codes and programs, compose a fine metaphorical stuff, but in the world of databases and information management, what corresponds to a nucleotide or a codon or a gene? Information is just today's phlogiston.

Nonetheless, we probably should expect information talk to enjoy a resilience comparable to that wielded by gene talk. Information is a secular god of the gaps, shoveled in to smooth over the reductionist model of biology.
          Gene Regulatory Networks (GRNs): Major Collision at the Intersection of Evolution and Development   

Q:        How does a fertilized egg cell give rise to such a variety of cell types as compose the body of a complex organism?

A:        That fertilized egg cell’s DNA arrived pre-loaded with the genetic information needed to craft the specialized cell types that compose the body of that complex organism.

Although each cell in that body inherits all of the fertilized egg cell’s genes, specific genes get switched on and off by other genes that produce regulatory molecules, and those genes are switched on and off by other genes and the molecules they produce according to what is needed for each type of cell. And all of this biochemical management occurs by feedback loops. The biochemistry that oversees the differentiation (and stabilization) of cell types in the developing organism is organized into gene regulatory networks (GRNs), very elaborate chemical feedback loops. 


The point to be made about GRNs is that, by regulating gene expression, the cellular machinery can coax from a highly conserved set of genes (those of the original fertilized egg) a liberal diversity of cell types (skin, muscle, nerve, etc.).

So far so good. But one noteworthy development is the increasing significance that evolutionary theorists ascribe to GRNs. Gene regulatory networks, not the acquisition of new genes, manage the differentiation of species from their common ancestors in much the same way as they manage the differentiation of cells in a body from their common ancestor, the fertilized egg cell. Diverse descendant phenotypes lurk within the DNA of ancestral genomes and genotypes alike, waiting to be switched on. 

The science of comparative genomics confirms a fundamental conservation of DNA across species, a finding that came as a surprise to everyone. The genetic similarities seen across species are too striking to sweep under the rug, and at least some researchers are candid about the new data’s impact on evolutionary theory. 


Charles R. Marshall, a biological science professor at the University of California, Berkeley, observes in a book review in the September 20, 2013 issue of Science,
"In fact, our present understanding of morphogenesis indicates that new phyla were not made by new genes but largely emerged through the rewiring of the gene regulatory networks (GRNs) of already existing genes"
This observation does double duty, because it also describes how a fertilized egg cell gives rise to descendant cell types. The descendant cell types emerge through the rewiring of gene regulatory networks.
  

Evidently, we can say that the genes for descendant species were there already in remote ancestors, or that the GRNs for descendant species were there already, or both were there already. In any case, what were they doing there? If they functioned one way, or were silent, in ancestors, how is it that they just happened to be re-wirable to produce highly dissimilar, yet “adapted,” descendants? That seems far fetched. But it makes sense and is to be expected if evolution is a case of development. It looks like GRNs manage the differentiation of species in an ecology in some manner similar to that in which such networks regulate the differentiation of cells in a body, namely by rearranging patterns of development.
 
Consider this adaptation of the quote above, "In fact, our present understanding of cellular differentiation in developing organisms indicates that new cell types are not made by new genes but largely emerge through the rewiring of the gene regulatory networks (GRNs) of already existing genes."
  
In Universal Genome in the Origin of Metazoa (Cell Cycle 6:15, August 2007) researcher Michael Sherman also argues that diverse species develop from a common, conserved, genome. His case rests largely on the presence of anomalous genes in ancestral species that are needed by descendant species, a circumstance called, pre-adaptation. He summarizes,
“In thinking about metazoan evolution, one should realize that any evolutionary event represents changes in developmental programs, rather than changes in a developed organism. [. . . .] This hypothesis postulates that (1) shortly (in geological terms) before [the] Cambrian period a Universal Genome that encodes all major developmental programs essential for every phylum of Metazoa emerged in a unicellular or a primitive multicellular organism; (2) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs. In other words, in spite of a high similarity of the genomes in phyla X and Y, an organism belonging to phylum X expresses a specific set of active developmental programs, while an organism belonging to a different phylum Y has a distinct set of “working” programs specific for phyla Y. This seemingly trivial statement changes the whole perception of evolution, claiming that the placement of an organism to a particular taxon depends on expression of a specific set of pre-existing developmental programs, rather than on difference in the genetic information per se. Therefore, within the Universal Genome model, what we perceive as a sequential evolution is actually a reflection of expression of one or another combination of programs from the Universal Genome. These postulates explain a simultaneous emergence of Metazoan phyla during [the] Cambrian period, as well as similarities of genomes and a dramatic increase in genome complexity in Metazoan phyla. [emphasis added]”
On just how it happened that the major developmental programs essential for every phylum of Metazoa emerged in a unicellular or a primitive multicellular organism the author does not speculate. But their presence there is to be expected, if evolution is an instance of development. The author’s characterization, elsewhere in the article, of developmental algorithms that wait in the wings as harboring “excessive” genetic information might be rendered more accurately as their harboring anticipatory genetic information.

Already in 1999, researcher W. H. Holland in an article that appeared in Nature (Vol 402, Supplement, December 2, 1999) titled The Future of Evolutionary Developmental Biology recognized a common genome across species. He writes,

"So many examples of [DNA] conservation have now been found that it is no longer considered surprising. We can now state with confidence that most animal phyla possess essentially the same genes, and that some (but not all) of these genes change their developmental roles infrequently in evolution [emphasis added]."

When and where ecological conditions become hospitable, the highly conserved nucleotide sequences of the animal kingdom launch into existence new species, as needed, via the rewiring of developmental patterns. This is the developmental model of evolution proposed by the star larvae hypothesis. Evolution (phylogeny) shares with development (ontogeny) raw materials (a highly conserved set of nucleotides), operating mechanisms (gene regulatory networks), and outputs (highly diverse phenotypes).

Whether we’re talking cells in a body or species in an ecology, phenotypes diversify, or differentiate, from variously regulated but shared genes. Natural selection can cull the herd in an ecology, filtering from the pool genes that lead to reproductive incompetence, just as it can with cells in a body. As philosopher Jerry Fodor summarized it, natural selection can at most tune the piano. It cannot compose the melody.

The role of composer, or at least of conductor, seems to fall to endogenous gene regulatory networks.


But if evolution is an instance of development, then what strange creature is developing?
           Reconceptualizing Evolution as an Instance of Development - Phylogeny is its own Ontogeny; Start with the Zygote.   

During the development of a complex organism, a fertilized ovum, or zygote, divides in two, then again into twice as many cells and eventually into all the cells that compose the organism's body. As the cells proliferate, they differentiate in form and function into the various cell types of that particular kind of body. This differentiation into skin, stomach, nerve, and other cell types occurs even though the cells of a developing body all share a common genotype, that of the original zygote. The paradox of one genotype yielding many cellular phenotypes has been resolved, in a general sense, through the mechanisms of epigenetics. A relatively new branch of molecular biology, epigenetics addresses issues related to gene regulation and gene regulatory networks. The new discipline aims to explain how, during development, genes get turned on and off and when (as in larval or adult forms of organisms) and where (as in spleen or kidney) they do.

The new discipline is an upstart. Epigenetics would seem to demote DNA from being the cell's chief executive to its merely utilitarian, dumb server. DNA includes an archive of messenger-RNA templates (and the messenger RNA molecules transcribed from the templates still pass through an editing suite before being escorted to the ribosome, where they get translated into proteins). The molecular machinery of epigenetics, through normal chemical bonding, excites or inhibits DNA "expression" or "action." The countless combinations of sections of DNA that can be expressed and repressed here and there in sequence or in tandem produce multiform cellular phenotypes from the highly conserved DNA of the original zygote.

From a complex database a skilled operator can extract many kinds of reports, by slicing the data this way then that. DNA is such a complex database, responding to many and diverse calls for data. The creatures of the Earth are reports summoned from DNA, not expressions of any executive talent that resides in the DNA. This is the new view of things from the world of epigenetics.

But epigenetic mechanisms do more than regulate cellular differentiation during development. What is particularly significant, from the perspective of the star larvae hypothesis, is that epigenetic mechanisms also are implicated, increasingly, in the diversification of species from a conserved genome during evolution.

"Conserved genome" is taking a liberty, admittedly, but how much of one? As statistical genomics continues to reveal, the conservation of DNA across species is far more extensive than anyone had expected. Because genomes differ among species far less than had been anticipated, some commenters even have coined the phrase, "universal genome" to underscore the striking commonalities among genomes shared by diverse species. Evolution increasingly seems to be an instance of development, the two processes of development and evolution sharing a reliance on epigenetic mechanisms to pull forth diverse forms from a shared database. Even though development and evolution differ markedly in scale, they grow increasingly mechanically similar as research proceeds. The star larvae hypothesis suggests the term ontophylogeny to designate biology's generic process of differentiation/diversification (an appropriation from J-J. Kupiec).

Let the chips fall, but the star larvae hypothesis continues find encouragement in new discoveries in molecular biology that pertain to "descent with modification," whether the descent is of tissues during development or of species during evolution. The hypothesis watches for new breakthroughs in this area, because the trend line continues to dovetail with its prediction that evolution will come to be recognized as an instance of development.

That's when things get interesting. That's when the hypothesis directs attention to an elephant in the room. Namely, if evolution becomes mechanically indistinguishable from development, or at least so dependent on the same mechanisms that issues of spatial and temporal scale become the last refuge of defenders of the old paradigm, then potentially troubling issues arise for normal science. (These troubles don't pertain in the context of the star larvae hypothesis, however. Just saying.)

One: Development proceeds in a preferred direction. Given an accommodating environment, an adult chicken, and not an adult penguin, will be called forth from a chick embryo. Development has a teleological character. If evolution is an instance of development, then it, too, must have a teleological character, a preferred direction. This will be a tough pill for science to swallow.

Evolution coming to be seen as a process that depends on endogenous factors as much as does development raises the challenge of applying the new understanding. What might it say about evolution on exoplanets? Theorists of evolution should have something predictive to say about questions such as these: Given an Earth-size planet in some solar system's "habitable zone," i.e., at the requisite distance from the system's central star, or sun, and which planet finds itself steward of viruses and bacteria, what exogenous contingencies will influence the descent of phenotypes and to what extent and in which directions? And to what extent will endogenous physiology influence the descent of phenotypes and to what extent and in which directions? Although, such predictions might soon be forthcoming.

For its part, the star larvae hypothesis predicts that endogenous gene regulatory networks will generate phenotypes along the lines of the types of body plans that have evolved on Earth. The "tree of life" on exoplanets that bear complex life will include essentially the same major divisions, classes, orders, and phyla as those seen on Earth and probably a few platypus-like oddball assemblies as well. Incorporating the assertions of panspermia, the star larvae hypothesis assumes that diverse planets will share in the "universal genome."

>Two: Development, or ontogeny, typically is characterized as advancing through the stages of a life cycle, with the post-reproductive adult occupying the terminal stage. If evolution is an instance of development, then what is the adult form of the organism that's developing? And what events constitute a complete reproductive life-cycle of that organism?

Conceiving of life on Earth as being engaged in a process of development, a planetary ontogeny, might seem less crazy if the sceptic appreciates that the bodies of complex organisms are themselves ecologies. Most cells in a human body, for example, are bacterial cells. Each human body is a constantly evolving ecosystem of microbial symbionts, parasites and stowaways. The fellow travelers constitute the "microbiomes" that compose human bodies. Development is ecological and evolution is developmental. The same relationships seem to pertain at all scales.

The strain that humankind is putting on the Earth—particularly in light of nuclear mishaps, geoengineering, weaponized microbes, and the seemingly suicidal sociopathy of the various factions of would-be global oligarchs—might tempt observers to render a harsh verdict against humankind, to liken humans to a deadly, havoc-wreaking, ecosystem-wrecking, cancer. But such a condemnation would be misguided.

Humankind doesn't represent a global cancer that needs to be treated, but a burgeoning new life, one, however, that can distinguish itself from a cancer only by engineering its own delivery into the weightless environment of outer space.


          Evolution as Development and the Demise of Darwin's Natural Selection Theory   
The inhumanities of the Holocaust swept from public view the until-then popular cause of eugenics. But before World War II eugenics thrived as a civic cause in the United States and the United Kingdom. Improving human stock through selective breeding and the sterilizing, or even the euthanizing, of the "unfit" had come to be regarded widely as scientifically sound public policy. The Wikipedia entry for "eugenics"  provides an introduction to this mostly forgotten fashion of the times, which Nazi ideology took to extremes of horror and which today is banished, at least in its overt forms, from policy discussion, though social critics continue to uncover its covert forms & see embedded video below:
Advocacy of eugenics continues under the banner of population control and similar euphemisms.

The Anglo-American eugenicists of the early 20th century invoked Darwinian natural-selection theory to gird their ideological bent. But, according to the arguments and evidence that Alan Bennett presents in "Evolution Revolution", these social engineers did not hijack Darwinism, nor twist it into service in a way to which Darwin would have objected. On the contrary, Darwin embraced the eugenicist agenda from the outset. Not only did Darwin himself promote eugenics, but the agenda's advocates also included Darwin's half-cousin, Francis Galton, who formalized the concept and propounded it as civic duty; Thomas Henry Huxley ("Darwin's Bulldog"); and Huxley's grandsons, Julian and Aldous Huxley, Julian serving for a time as president of the British Eugenics Society and Aldous sketching a blueprint for a caste society in his "Brave New World."

The objective of the Darwinian offensive was twofold, as Bennett summarizes:
  1. Cast the working class in the role of the unfit. 
  2. Denigrate religion. 
This history, the dark heart of Darwinian theory, presented in thoroughly referenced detail, makes up the first major portion of the book.

But the anti-Darwinian angle of Bennett's argument unwinds in a complicated way and extends beyond discrediting the motives of Darwin and his acolytes. That is, the attack is not merely ad hominem. Bennett establishes it as a point of historical fact that the concept of "descent with modification" had been around for some time prior to Darwin. Victorian society was not hostile to the idea of evolution, which it saw as evidence of God's wisdom, in His having crafted natural law so as to give rise to the diversity of life.

Neither was the mechanism of natural selection original with Darwin. It too was a concept familiar to Victorian scientists. But natural selection failed to gain traction as a scientific idea, before Darwin and his propagandists took up the cause, because the scientists of the day perceived that it was inadequate to account for the diversity of life. Under the influence of an optimizing mechanism, such as natural selection, they reasoned, phenotypes should converge, not diverge, with the passing of generations.

Natural selection theory never has rested on solid scientific evidence or reasoning. Although, by appealing to statistics and common prejudice, Darwinians grafted onto natural selection theory the trappings of a science. As a result, the sequentially amended theory became almost infinitely elastic in its capacity to absorb anomalous findings. It managed consistently to re-describe "how nature works" in ways contrived to preserve a niche for itself in the explanatory scheme. From the time Charles Darwin foisted it upon the world, natural selection theory effectively served the ideological ends of diverse brands of racists and elitists, despite its lack of scientific rigor.

However, if we follow Bennett in rejecting natural selection as the primary engine of evolution, then we are left with a process minus any explanation as to how it works. We still have to account for evolution's particular outcomes. Bennett proposes to fill the void, but the mechanism that he nominates to serve as evolution's centerpiece arrives with its own baggage.


One thrust of Bennett's revision of evolution theory borrows from ideas that competed early on with Darwin's own. The author combines the structuralist approach of Darwin's contemporary and rival, Richard Owen, with the "Lamarckian" approach of Jean-Baptiste Lamarck. This hybrid model has much to recommend it.

Naturalist Richard Owen ascribed the particulars of evolutionary change to natural laws (endogenous factors); whereas Lamarck ascribed the particulars to heritable changes in an organism that are caused by environmental stresses (exogenous factors). Bennett presents a history of these ideas, then summarizes:
"As we saw, the idea that the natural world emerged through a process of 'self-development,' or 'self-organization,' had been gestating in Western thought for over 2,000 years, stretching from Owen and the 'structuralists' to Aquinas, Augustine and on back to Aristotle and the ancient Greeks."
The Lamarckian component of Bennett's integration keeps this "self-organizing" process from being wholly deterministic. Environmental contingencies impinge on organisms, influencing their bodies and/or behavior, with some of these changes being heritable. This is Lamarckism. During much of the history of evolution theory, biologists dismissed the Lamarckian model, a standard argument against it referencing the blacksmith's arm: Are the blacksmith's children born with one conspicuously developed arm? But Lamarckian effects can in some cases be observed, and new findings in the field of epigenetics provide an ostensible mechanism whereby acquired traits might be passed on to offspring. So, the door has opened to re-introduce Lamarckian thought to evolutionary theory.

In Bennett's model, evolution is an unfolding of inherent potential that absorbs or reacts to the environment's influences. And so evolution, or phylogeny, in his formulation takes on the character of development, or ontogeny. This parallelism is touched upon in the book but not developed thoroughly. We will return to it after examining Bennett's case from a broad perspective, that of complexity theory.

Bennett recruits complexity theory to serve as a general, overarching framework within which to understand evolutionary change. By situating evolution in the context of complexity theory, Bennett minimizes distinctions between biology and other sciences, which maybe is as it should be. Here is language typical of that which he uses to characterize his view of how nature works:
"In an unfolding sequence, quarks, guided by nothing more than the relationships between themselves, form atoms, which in time organize themselves into stars, solar systems and entire galaxies. These naturally developing relationships formed increasingly complex patterns which held the information for making stars, planets and eventually entire galaxies. These patterns contained the information for making the universe complex."
I share the author's conclusion that something is missing from evolution theory, that natural selection cannot do what it is supposed to do, and that some other mechanism is needed to pull up the slack. But I do not share Bennett's faith that the building blocks of complexity theory —emergence, patterns, relationships, self-assembly and other abstractions, as he constellates them—will do the job satisfactorily. Explanations in terms of patterns, self-organization, etc., smell like disguised appeals to vitalism, which is the notion that an undetectable, animating "life force" or similar construct accounts for biological processes. Vitalism long has been discredited as a scientific idea, but now it's back, camouflaged by the quasi-technical argot of complexity theory. Bennett writes, "Emergence is one manifestation of an even more transforming concept about nature: immaterial things can bring material things into existence. [. . . .] This is the third key to the new understanding of evolution: much of nature and evolution emerges from immaterial things, like relationships, and patterns."
 
It's not clear what such contentions bring to the table. Explanations of the particulars of the physical world in terms of gravity, thermodynamics, fluid flow, radiation, kinetics, and so on—normal scientific concepts—lend themselves to units of measure, to being quantified. Complexity theory offers no units of measure. And its reliance on "immaterial" causes makes it akin to a theology.

Nor does complexity theory articulate the necessary and sufficient conditions under which an assembly of parts will organize itself spontaneously into a self-regulating complex system. Sometimes it happens and sometimes it doesn't? And how can patterns, or relationships, be causal agents? I would argue that patterns and relationships are what we observe after causal agents have acted.

In short, complexity theory begs the question as to whether it explains what it purports to explain in terms of causality or just describes what is observed.

Nonetheless, complexity theorists claim vast explanatory powers that transcend biology to include everything from the particulars of chemistry and cosmology to sociocultural organization. The borders among the disciplines get fuzzy. A kind of conceptual freefall accompanies the adoption of complexity theory, and this is particularly highlighted when we pry natural selection theory from evolution.

Natural selection theory attached itself specifically to the biological world, not to other areas of science. The other disciplines don’t get jostled when it gets abandoned, nor when it gets replaced by complexity theory. But, once the peculiar mechanism of natural selection is set aside, what is left to distinguish biological evolution from other kinds of successive change? Without natural selection, is "evolution" just a multisyllabic synonym for "change"? Does biology become just another process that expresses the principles inherent in complexity theory?

Maybe so. And I am glad to join Bennett in discarding biology's specialness as a natural kind. But Bennett is not as vigilant as he ought to be in retaining distinctions among certain processes internal to biology's vast, ongoing complexification. He is out to proffer a totalizing metanarrative that accounts for change. But in doing so, he tends to gloss over distinctions among evolution, development, and plain old change. He would seem not to think that there was much difference in meaning among statements such as, "Look, that complex system is organizing itself" and "Look, that thing over there is developing" and "Look, that thing over there is evolving."

The difference between the latter two characterizations is critical. It must not be swept aside. To use evolution and development more or less interchangeably, as Bennett tends to do, muddies the waters precisely where clarity is needed, if we are trying to sort out the causal mechanisms that produce the particular outcomes that we observe. Consider this passage:
"The daunting challenge for Darwinists is this: if evolutionary change in every science - physics, chemistry, cosmology, geology and all the others - is predictable, why would evolution in biology be unpredictable? If the evolution of atoms, molecules, minerals, stars, planets, continents, mountains and oceans are [sic] predictable, why would the evolution of plants and animals suddenly be unpredictable?"
The processes inherent in the other disciplines don't qualify as instances of evolution, at least not in the usual sense of multigenerational descent with modification. But they might, so long as we're stretching definitions, qualify as instances or processes of development. Let's back up.

The word development attaches itself, for example, to the sequence that runs, egg >> hatchling >> hen. The egg-to-hen sequence is influenced genetically in a way that predisposes it to unfold in a predictable sequence: the process has a preferred direction. Given an accommodating environment, the internal energetics of a chicken proceeds along a predictable path. That's how development works.

The sciences have to deal with change, per se, of various kinds. But the term “evolution,” as specific to Bennett’s chosen target, biology, typically isn't used to designate change per se, but change of the type specifically that occurs during a sequence of generational turnovers. It's not clear how the normal usage of "evolution" would apply to the quarks of physics, the molecules of chemistry, or the mineral formations of geology.

That said, most readers, I suspect, will want to maintain distinctions among the related notions of evolution, development, growth, assembly, and just plain change. It's not clear that Bennett sees value in maintaining these distinctions.

In this light, consider that, as it has come to be used, "evolution," as distinct from "development," designates a nonteleological process. That is, the evolutionary process is taken by scientific officialdom to proceed without a preferred direction. It is extemporaneous and not developmental. Development, on the other hand, is predictable. It proceeds, so long as the environment accommodates it, along a preferred direction, toward the adult form of the species. It has a teleological character as it unfolds in its predictable sequence.

Bennett's other point in the passage cited earlier has to do with natural selection theory’s lack of forecasting prowess. And Bennett rightly points out that if natural selection theory were properly scientific, then it would lend itself to making predictions that were more than trivial. Because it doesn't do much by way of making predictions, it doesn't lend itself to falsification, weakening its status as a scientific theory.

Darwinian Theory, through all of its variously evolved forms, certainly failed to predict the intriguing findings that have come out of genomic sequencing and subsequent cross-species genomic statistical comparisons. The conservation of DNA across species? That was a stunning finding, at which a scientific theory of evolution might at least have hinted. But no. Did textbook evolution theory get ANYTHING right in this regard? If the theory is supposed to account for gene distributions, then why did it fail so miserably when given the chance to prove itself? Did natural selection theory belly up to the bar and say, "Well, now that you have the technology to sequence genomes and conduct detailed cross-species statistical analyses on the resulting databases, let me tell you beforehand what observations you shall make." No. It did not belly up. It sat on the sidelines, mute, unable to articulate anything that would vouchsafe itself as a usefully predictive tool of science. Natural selection theory? Bah-humbug.

If we take the ball from Bennett and run with it, emphasizing the developmental character of evolution--as an endogenously driven process, being variously facilitated and constrained by its environment--and re-categorize it explicitly as an instance of development, then we introduce implications that Bennett might not want to see commingling with his ideas. Namely, we imply that the evolution of life on Earth constitutes a succession of stages in the life cycle of an organism, with the ensuing teleological implications.

Framing evolution as a developmental process preserves the elements that Bennett wants to include in his revised theory and gathers those elements under a familiar heading: Development. Insofar as it simplifies the conceptual scheme and claims bragging rights to parsimony, re-classifying evolution as an instance of development is a move that leapfrogs natural selection theory to propose a more scientifically credible hypothesis.

But this move raises more questions. What is the adult form of a developing planetary biosphere? And, once we show up--we high-tech primates--do we have any obligations to the historical/developmental process? Are we obliged to play any kind of predetermined role in the unfolding of the historical program? As the zygote harbors the adult, does the caveman, or the amoeba for that matter, harbor the space colonist? And, if so, can creatures refuse their callings, and what happens if they do? The developmental model of evolution forces into the open issues of historical meaning, purpose, and obligation.

The foregoing remarks might seem to arrive from far out in left field, but they are of the moment. As endogenous factors continue to infiltrate evolutionary theorizing, evolution increasingly looks like an instance of development. If the theory continues in this direction, then at some point the notion of "life cycle" will need to be scaled up and applied to planetary biospheres. And then humankind's cosmic calling will assert itself as the elephant in the room, we must hope.

Admittedly, this review presents only an overview of an ambitious book. My copy is dog-eared from much note-taking, as I found the ideas and references presented required mindful consideration, page after page. The book delivers a wealth of insight into the history of evolution theory, (the retelling of the story of Ota Benga, the pygmy displayed in New York's Bronx Zoo in 1906, with a chimpanzee for a companion, reminds us of Darwinian theory's racist utility), documenting the gyrations that the theorists put the theory through with each new problem that scientific discovery threw at it. The anomalies continue to pile up, however, and if Thomas Kuhn got it right in The Structure of Scientific Revolutions, then natural selection theory's elasticity at some point will give way, with a conceptual SNAP, and scientists will be left to assemble a new evolutionary paradigm, one that we must hope will be devoid of utility to racists.
          Natural Selection is Dead. Long Live Evolution.   

Lecture: Evolution in Four Dimensions

Click the image for an excellent talk by Eva Jablonka, in which she describes provocative new findings in epigenetics and animal behavior. The findings move natural selection farther toward the periphery of evolutionary theory. Phenotypes, as they differetiate during evolution, seem to self-organize, as do the differentiating cells in a developing organism. My contention is that evolution and development resemble one another because they are two appearances of the same process, which is development.

If one could lay Darwin's concept of natural selection next to the current model of evolution, one would have a hard time finding much in common between them. Outside of the vaguest generalization of the evolutionary process, captured in Darwin's phrase, "Descent with modification," nothing much of the original formulation survives to contribute to the current model, the so-called Extended Synthesis.

Epigenetics, niche construction, phenotypic plasticity and other intriguing new developments in bioscience sit at the center of that synthesis and throw into question the foundations of the Darwinian model. Despite evolution theory's provisional character, however, the fossils record descent’s modifications, and they taunt us: What during descent accounts for these modifications?


The conventional answer is natural selection, which is the assertion that random phenotypic variation, which bestows "fitness advantages" disproportionately to particular individuals of a given species in a local population relative to their cohorts, accounts for differential reproductive success among those individuals. Because they enjoy greater reproductive success, the favored individuals disproportionately influence the gene distributions of subsequent generations. The shifting gene distributions account for macroevolutionary change. That's the general idea.

If we were satisfied to say that differences in reproductive success among individuals are taken to be the cause of gene distributions observed in subsequent generations, then we would have a noncontroversial theory of evolution. But that would be not so much a theory as just a description of what is observed.

If we want to explain what is observed and take differential reproductive success among individuals of a species in a local population to be in itself an effect, then we need to look for that effect's cause. Natural selection in fact can't be that cause, because it is merely a restatement of the effect that it is supposed to explain.

A longstanding criticism of natural selection theory is that it is tautological, an exercise in circular reasoning, because what constitutes a fitness advantage can be supposed only after reproductive success is evaluated. Moreover, even after differences in reproductive success (the effect) are sorted out, and genetic causes supposed, those supposed causes cannot be teased apart from mere environmental contingencies, at least not in the wild, where evolution actually occurs. And this is despite the formulations of the discipline of population genetics, which claims to distinguish between causal mechanisms (natural selection vs. genetic drift) based on ranges and thresholds within statistical distributions of genes and traits. Labeling distribution ranges doesn't explain anything.

The role of contingency takes center stage in the critique of natural selection theory that Jerry Fodor and Massimo Piatelli-Palmarini offer. In "What Darwin Got Wrong," they argue against natural selection playing a significant role in the modifications that occur during descent and offer instead the mechanism of natural history, which is just whatever happens, the contingent interplay of endogenous and exogenous factors. Directionless and extemporaneous, evolution lurches, plods, this way and that, a concatenation of occurances and nothing more that can be approached systematically. Natural history, they remind us, "is just one damned thing after another. This should seem, on reflection, unsurprising, since, to repeat, natural history is a species of history, and history is itself just one damned thing after another." Shit happens, and that's how phenotypes get to be how they get to be, say these guys.

 Theirs is not a theory, they explain, because there are no theories of history, natural or otherwise. There are descriptive narratives. Theories describe what had to happen, but nothing in history or evolution had to happen, or at least not as it did, as seen through natural history. Fodor and Piatelli-Palmarini seem to conclude that the new developments in the bioscience that marginalize natural selection as a cause of evolution fail to constellate into any recognizable pattern. They conclude that evolution just isn't the kind of thing that lets itself be explained by scientific laws. Contingencies rule.

But, new developments in biological science do fall into a recognizable pattern. Evolution looks like a process of development more than it does anything else. Below are described four recent discoveries that reveal the mechanisms of development to be also the mechanisms of evolution. Evolution is regulated by developmental mechanisms, because it is a developmental process.

1. Conservation of DNA 
The cells that make up a body share a common genotype, the one that they inherit from the zygote from which they all descend, even though the descendant cells are of distinct types, each functioning in its distinct way: skin cells, muscle cells, nerve cells, liver cells, and so on--very different phenotypically but sharing the same genotype. They don't evolve from the zygote by natural selection. They develop from it, retaining its genotype despite themselves displaying vast phenotypic variation. We now know that this same relationship between conserved DNA and phenotypic diversity also characterizes evolution. Some researchers propose that science adopt the concept of a universal genome, the genotype of biology per se. This proposal grows from the discovery that genomes vary only slightly among species comapared to the vast variation among phenotypes. DNA, it turns out, is highly conserved across generations of organisms, from ancestral to descendant species. There is nothing in the dramatic diversity of species phenotypes that would have indicated the paucity of variation among the various species' genomes. READ MORE
In Development and in Evolution,
DNA is Highly Conserved.
***
2. Epigenetic regulatory networks 
How is it that highly conserved DNA can produce so many variant phenotypes, in development and in evolution? It is because genes are not the whole story. DNA sports an entourage of attendants whose job it is to regulate genetic expression, essentially to turn genes on and off as needed. The mechanisms of DNA regulation are called epigenetic mechanisms, and they take various forms, the simplest of which is methylation, the attachment of a methyl group to DNA to regulate local genetic expression. Epigenetic regulatory mechanisms control which genes get expressed and which repressed during the various stages of an organism's life cycle. In this way, a single genotype can produce a variety of cellular phenotypes and stabilize them so that they breed true, so that, for exmaple, a liver cell gives rise to more liver cells and not to undifferentiated cells that resemble the original zygote. Now, it turns out that epigenetic mechanisms also regulate the expression of species phenotypes from the universal genome and stabilize the phenotypes so that they breed true, so that, for example, frogs give rise to more frogs and not to ancestral forms. READ MORE
In development and in evolution,
epigenetic mechanisms originate and stabilize phenotypes.
***
3. Niche construction 
 Traditionally, evolution theory saw the natural world as a bunch of of ecological keyholes, called niches, into which the various organisms fit, more or less, according to their adaptedness. It's remarkable that this view held on for so long, given that one can observe how handily all kinds of organisms modify their surroundings to suit their needs. These days researchers recognize niche construction as foundational to evolution. But what happens to natural selection theory when environments are the effect of phenotypic causes? The whole thing blows up, and something like Ptolemaic epicycles are invoked to preserve the paradigm. In the context of development, phenotypes also construct their niches. Differentiating cells release chemicals called morphogens which spread through the developing body and regulate cellular differentiation according to concentration gradients. In this way the cells construct their niches in the developing body, chemically. Phenotypes and environments shape each other. READ MORE.
In development and in evolution,
differentiating phenotypes condition their environments to make them more hospitable. Living entities construct their niches.
***
4. Genetic pre-adaptation
The zygote contains the full complement of genes needed for all of the cell types into which its descendants will differentiate. Early generations of cells in a developing organism carry genes that are "pre-adapted" to the needs of future generations. That is, in its genotype the zygote carries genes pre-adapted to the needs of skin, muscle, liver, etc. cells. It turns out that the story of evolution is chock full of instances of ancestral species harboring genes that are pre-adapted to the needs of descendant species. As ongoing genomic studies unearth more and more examples of such pre-adaptations handed down from ancestral to descendant species, the orthodox view becomes less and less aligned with the empirical data. READ MORE.
In development and in evolution,
ancestors carry genes for features and functions that their descendants will need.
Evolution and development are distinguishable only by their spatial and temporal scales. Evolution just is an instance of development. This interpretation poses a question: "What kind of creature is developing?"

The star larvae hypothesis answers: "On a clear day, you can see an instance of the type overhead. On a clear night, you can see many instances."

I invite Eva Jablonka and the other contributors to "Evolution, The Extended Synthesis" to evaluate the case that evolution operates by mechanisms already known to regulate development and to acknowledge that evolution looks more like an instance of development than it looks like anything else.
          Genome Alberta Starts New $20M Livestock Genomics Projects   
none
          Genome Prairie Lands $2.3M for Flax, Commercial Genomics   
none
           Understanding consumer evaluations of personalised nutrition services in terms of the privacy calculus: a qualitative study    
Berezowska, A., Fischer, A. R. .H., Ronteltap, A., Kuznesof, S., Macready, A. , Fallaize, R. and van Trijp, H. C. M. (2014) Understanding consumer evaluations of personalised nutrition services in terms of the privacy calculus: a qualitative study. Public Health Genomics, 17 (3). pp. 127-140. ISSN 1662-8063 doi: 10.1159/000358851
          23 December, 2010 – This Week in Science   
Genomic Fossils, Ecstasy Therapy, Brainy Photons, Smart Feels Good, Matter Matters, Anti-Microbial Colding, Correlation Station, BPA Eggs, ... tags: Amos_Nuranimalsastronomybioethicsbiologybiotechnologycell_biology23 December, 2010 – This Week in Science
This Week in Science - The Kickass Science Podcast
          Comment on How bacteria are like smartphones by How bacteria are like smartphones | bradyrhizob...   
[…] Here is one final post about our recent paper on rhizobium population genomics (1).  […]
          General Motors Cancer Research Foundation 2000 Annual Scientific Conference - Genomics and Cancer
(Day 1)    
General Motors Cancer Research Foundation 2000 Annual Scientific Conference - Genomics and Cancer
(Day 1)
Presented by: Sponsored by: General Motors Cancer Research Foundation
Category: Conferences
Aired date: 06/06/2000
          General Motors Cancer Research Foundation 2000 Annual Scientific Conference - Genomics and Cancer
(Day 2)    
General Motors Cancer Research Foundation 2000 Annual Scientific Conference - Genomics and Cancer
(Day 2)
Presented by: Sponsored by: General Motors Cancer Research Foundation
Category: Conferences
Aired date: 06/07/2000
          Comparative Genomics   
Comparative Genomics
Presented by: Roger Reeves, Johns Hopkins University
Category: Current Topics in Genome Analysis
Aired date: 10/24/2000
          Summer Lecture Series II - Individualizing Transplant Care with Genomic Tools   
Audio Podcast
Presented by: Hannah A. Valantine, MD, Chief Officer for Scientific Workforce Diversity, NIH
Aired date: 7/29/2015 12:00:00 PM
          #126 Dr. Ritchie Shoemaker on Surviving Mold   
On this episode of Bulletproof Radio, Dr. Ritchie Shoemaker, a practicing physician recovered from his own mold-related illness, talks the science behind the silent epidemic of mold. You will hear how genomics and testing is opening the door to understanding mold illness, and why microbes growing in water-damaged buildings make people sick. Have you ever wondered why some people can’t walk into a moldy building and others don’t seem to notice? Dr. Shoemaker has the answers and gives you the facts. Intimidated by the topic? Look for the Quick Reference Guide to this podcast on the Bulletproof Executive blog for terms and definitions, so you can easily be an expert too.     Dr. Ritchie Shoemaker is a practicing physician in Maryland and the author of eight books and multiple published academic papers. His latest book Surviving Mold: Life in the Era of Dangerous Buildings is a guide through diagnosis and treatment, remediation and a return to health. He is an expert on mold, having “looked death in the face” from his own mold-related illness. He lectures throughout the US on chronic inflammatory illnesses that are caused by exposure to moldy buildings and mycotoxins.
          Fred Blattner: genetics pioneer, entrepreneurial success, and all that jazz   
Fred Blattner has been doing DNA research for more than 50 years, and he founded or co-founded three successful companies all focused on DNA: DNASTAR, Nimblegen and Scarab Genomics.
          Talk of Iowa - Priscilla Wald   
Priscilla Wald, Professor of English at Duke University discusses the portrayals of genomic science and genetic research in popular culture, and how those portrayls impact public perceptions.
          Talk of Iowa - 9/13/07   
Kathy Hickok and Barb Blakely from the ISU Department of English discuss Mary Shelley's Frankenstein. Part of the Center for Excellence in the Arts and Humanities series "Book of Life in a Genomic Age"
          Story on Haircoats on Cattle Gains International Question   
Dear David,
I was very interested in an article I found posted on Facebook about haircoats on cattle (see original article here). So much so that I would like to use your scoring system for coat shedding to at least find  out whether it would work for us. We have an Angus stud herd in Tasmania (Australia's Island State) and obviously the months for observing will be different. I have a couple of questions, firstly when do you recommend that the score be given. I think from the article June would be a good month which would equate with December here. The other question is would this scoring system work for selecting young stock to keep as breeders or is it meant for adult cows. We calve in late winter early spring (mid July to mid September at the very latest) and make our selections for keepers bout now (late autumn early winter). It would be hard to judge these animals as calves but possibly the system could be used when they are yearlings. What it would mean is delaying a final selection until later on. Anyway to start with I would probably just make note a score and then see if there was a difference later on.

Regards,
Brian Stewart
Dunlop Park Angus Stud
4938 Frankford Main Road, Thirlstane, Tasmania 7307
Australia



Dear Brian,

The leader on this hair shedding project is Jared Decker, extension genomics specialist at the University of Missouri, Columbia.  His email is deckerje@missouri.edu  He may give you more details than I could.

From my perspective in the southwest part of Missouri where fescue is the dominant forage and we run lots of cattle the failure to shed hair is a problem.  The various ergot alkaloids contribute to the genetic problem of shedding and it all culminates in cattle that gain poorly and reproduction is compromised.

We’ve done some form of hair evaluation since the early 90’s and feel it’s valuable to try and select early shedders.  Late shedders obviously appear stressed when the temperatures exceed 80 degrees.

Dr. Decker will be doing a 3-year study to determine more about the gene makeup of cattle across the U.S. and their adaptability to the environment in which they’re raised.  Why he might even be interested in observations.  I’m sure your Angus cattle have some of the same breeding in them that we have in ours.  The folks who show their cattle like those that have lots of hair as it allows them to hid some little imperfections with good grooming.

I would argue though that long hair and slow shedding is not desirable under our warm, fescue-based conditions.

Let me know if you have other thoughts or questions and please try to contact Dr. Decker.

Eldon Cole
Livestock specialist
University of Missouri Extension

          May and June Good Months to Study Haircoats on Cattle   
Contact: Eldon Cole, livestock specialist
Headquartered in Lawrence County
Tel: (417) 466-3102
E-mail: colee@missouri.edu

MT. VERNON, Mo. -- May and June are good months to evaluate the hair shedding nature of cattle according to Eldon Cole, livestock specialist, University of Missouri Extension.

“Research at several institutions reveal that early shedding cows tend to be more productive regarding weaning weight of their calves.  Weight differences of 20 or more pounds favored the early shedders,” said Cole.

EARLY MU RESEARCH

University of Missouri researchers began scoring cows and yearlings for shedding ability and hair growth in 1992 at the Southwest Research Center.  The cattle in the studies were grazing fescue that contained the toxin producing endophyte. 

Studies dealt with shade, mineral supplementation and clean well water versus dirty pond water that had cattle traffic in it.

“In those early years, we suspected there could be genetic implications that caused some wooly cattle to perform poorly but no serious selection pressure was applied toward the early shedders,” said Cole.

In fact, most of the early effort was directed toward selecting novel or friendly endophytes in the development of non-toxic fescue instead of selecting adaptable cattle.

GENETICS MATTER NOW

We now are at the point where both cow-calf producers and seedstock raisers observe hair shedding more seriously. 

“Genomic studies are being used to evaluate the heritability of haircoat retention.  An important feature is to score haircoats of cattle about this time of the year,” said Cole.

Getting rid of the winter haircoatbegins in southwest Missouri around early April.  However, some animals still appear to have all their hair in June.

“These late, or never shedders, are the ones that suffer and are more likely to wean lightweight calves and have lower calving rates,” said Cole.

SHEDDING SCORES

Many factors influence shedding such as breed, individual genetic makeup, nutrition, forage, day length, temperature,and humidity.

“In the early 1990’s at the Southwest Research Center, we scored the cattle on a one to four scale for shedding and evidence of fescue sensitivity.  The scoring system has now been adjustedto a one to five range.  The one score is an animal that is completely shed off from front to rear and top to bottom.  I usually refer to them as ‘slick as a mole’,” said Cole.

The 2’s are mostly shedoff, 75 percent or so, and most of the long hair will be on the lower part of the body.  A three score is about 50 percent shed; a four is only 25 percent shed most of which is in the neck, shoulder region and down the back.  The 5’s still has its winter coat with no evidence of shedding.

“If you have the 5’s in the chute, you can try to pull hair out, and it is firmly attached,” said Cole.

The scoring system is subjective. However, if the same person does the scoring in their herd, it gives a producer a good idea of cattle that could give more problems from “hot” fescue and heat stress as we move into the summer. 

According to Cole, some of the 4’s and 5’s that are stressed will benefit from clipping.

“The individual scoring of cattle may even result in farmers realizing that late shedding is more of a problem than first thought,” said Cole.

MORE INFORMATION

For more information, contact any of the MU Extension livestock specialists in southwest Missouri: Eldon Cole in Lawrence County, (417) 466-3102; Andy McCorkill in Dallas County at (417) 345-7551; Dr. Randy Wiedmeier, in Howell County at (417) 256-2391; or Dr. Patrick Davis in Cedar County at (417) 276-3313.

###





          Cancer Moonshot Initiatives Unlock Technology Innovations Surrounding Algorithms for Predictive Diagnosis   
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                padding-bottom: 20px;
                padding-left: 20px;
                text-align: left;
            }

            /**
            * @tip Set the styling for your email's center column content links. Choose a color that helps them stand out from your text.
            */
            .centerColumnContent a:link, .centerColumnContent a:visited, /* Yahoo! Mail Override */ .centerColumnContent a .yshortcuts /* Yahoo! Mail Override */{
                color: #3d98c6;
                font-weight: normal;
                text-decoration: underline;
            }

            /**
            * @tip Set the styling for your email's right column content text. Choose a size and color that is easy to read.
            */
            .rightColumnContent{
                color: #505050;
                font-family: Helvetica;
                font-size: 14px;
                line-height: 150%;
                padding-top: 0;
                padding-right: 20px;
                padding-bottom: 20px;
                padding-left: 20px;
                text-align: left;
            }

            /**
            * @tip Set the styling for your email's right column content links. Choose a color that helps them stand out from your text.
            */
            .rightColumnContent a:link, .rightColumnContent a:visited, /* Yahoo! Mail Override */ .rightColumnContent a .yshortcuts /* Yahoo! Mail Override */{
                color: #3d98c6;
                font-weight: normal;
                text-decoration: underline;
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                height: auto;
                max-width: 260px;
            }

            /* ========== Footer Styles ========== */

            /**
            * @tip Set the background color and borders for your email's footer area.
            * @theme footer
            */
            #templateFooter{
                background-color: #F4F4F4;
                border-top: 1px solid #FFFFFF;
            }

            /**
            * @tip Set the styling for your email's footer text. Choose a size and color that is easy to read.
            * @theme footer
            */
            .footerContent{
                color: #808080;
                font-family: Helvetica;
                font-size: 10px;
                line-height: 150%;
                padding-top: 20px;
                padding-right: 20px;
                padding-bottom: 20px;
                padding-left: 20px;
                text-align: left;
            }

            .footerContent.social, .footerContent.social h4 {
                text-align: center;
            }

            .footerContent.social a {
                margin: 0 10px;
            }

            /**
            * @tip Set the styling for your email's footer links. Choose a color that helps them stand out from your text.
            */
            .footerContent a:link, .footerContent a:visited, /* Yahoo! Mail Override */ .footerContent a .yshortcuts, .footerContent a span /* Yahoo! Mail Override */{
                color: #606060;
                font-weight: normal;
                text-decoration: underline;
            }

            /* /\/\/\/\/\/\/\/\/ MOBILE STYLES /\/\/\/\/\/\/\/\/ */

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                /* /\/\/\/\/\/\/ CLIENT-SPECIFIC MOBILE STYLES /\/\/\/\/\/\/ */
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                body{width: 100% !important; min-width: 100% !important;} /* Prevent iOS Mail from adding padding to the body */

                /* /\/\/\/\/\/\/ MOBILE RESET STYLES /\/\/\/\/\/\/ */
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                /* /\/\/\/\/\/\/ MOBILE TEMPLATE STYLES /\/\/\/\/\/\/ */

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                /**
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                */
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                    line-height: 100% !important;
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                */
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                    line-height: 100% !important;
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                */
                #headerImage{
                    height: auto !important;
                    max-width: 600px !important;
                    width: 100% !important;
                }

                /**
                * @tip Make the header content text larger in size for better readability on small screens. We recommend a font size of at least 16px.
                */
                .headerContent{
                    font-size: 20px !important;
                    line-height: 125% !important;
                }

                /* ======== Body Styles ======== */

                /**
                * @tip Make the body content text larger in size for better readability on small screens. We recommend a font size of at least 16px.
                */
                .bodyContent{
                    font-size: 18px !important;
                    line-height: 125% !important;
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                .templateDataTableContainer {
                    background-color: #ffffff;
                }

                /**
                * @tip Set the background color and border for your email's data table.
                */
                .templateDataTable{
                    background-color: #FFFFFF;
                    border: 1px solid #DDDDDD;
                }

                /**
                * @tip Set the styling for your email's data table text. Choose a size and color that is easy to read.
                */
                .dataTableHeading{
                    background-color: #D8E2EA;
                    color: #336699;
                    font-family: Helvetica;
                    font-size: 14px;
                    font-weight: bold;
                    line-height: 150%;
                    text-align: left;
                }

                /**
                * @tip Set the styling for your email's data table links. Choose a color that helps them stand out from your text.
                */
                .dataTableHeading a:link, .dataTableHeading a:visited, /* Yahoo! Mail Override */ .dataTableHeading a .yshortcuts /* Yahoo! Mail Override */{
                    color: #3d98c6;
                    font-weight: bold;
                }

                /**
                * @tip Set the styling for your email's data table text. Choose a size and color that is easy to read.
                */
                .dataTableContent{
                    border-top: 1px solid #DDDDDD;
                    border-bottom: 0;
                    color: #202020;
                    font-family: Helvetica;
                    font-size: 12px;
                    font-weight: bold;
                    line-height: 150%;
                    text-align: left;
                }

                /**
                * @tip Set the styling for your email's data table links. Choose a color that helps them stand out from your text.
                */
                .dataTableContent a:link, .dataTableContent a:visited, /* Yahoo! Mail Override */ .dataTableContent a .yshortcuts /* Yahoo! Mail Override */{
                    color: #3d98c6;
                    font-weight: bold;
                }

                /* ======== Column Styles ======== */

                .templateColumnContainer{display: block !important; width: 100% !important;}

                /**
                * @tip Make the column image fluid for portrait or landscape view adaptability, and set the image's original width as the max-width. If a fluid setting doesn't work, set the image width to half its original size instead.
                */
                .columnImage{
                    height: auto !important;
                    max-width: 480px !important;
                    width: 100% !important;
                }

                /**
                * @tip Make the left column content text larger in size for better readability on small screens. We recommend a font size of at least 16px.
                */
                .leftColumnContent{
                    font-size: 16px !important;
                    line-height: 125% !important;
                }

                /**
                * @tip Make the center column content text larger in size for better readability on small screens. We recommend a font size of at least 16px.
                */
                .centerColumnContent{
                    font-size: 16px !important;
                    line-height: 125% !important;
                }

                /**
                * @tip Make the right column content text larger in size for better readability on small screens. We recommend a font size of at least 16px.
                */
                .rightColumnContent{
                    font-size: 16px !important;
                    line-height: 125% !important;
                }

                /* ======== Footer Styles ======== */

                /**
                * @tip Make the body content text larger in size for better readability on small screens.
                */
                .footerContent{
                    font-size: 14px !important;
                    line-height: 115% !important;
                }

                .footerContent a {
                    display:block !important;
                } /* Place footer social and utility links on their own lines, for easier access */

                .footerContent.social a {
                    display: inline-block !important;
                }
            }
      </style>
</HEAD>
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<div xmlns="http://www.w3.org/1999/xhtml" xmlns:xn="http://www.xmlnews.org/ns/" class="xn-newslines">

<h1 class="xn-hedline">Cancer Moonshot Initiatives Unlock Technology Innovations Surrounding Algorithms for Predictive Diagnosis</h1>

<h2 class="xn-hedline">Manufacturers increase assay development focus towards screening, preventive and therapy selection, finds Frost &amp; Sullivan's Transformational Health team</h2>

<p class="xn-distributor">PR Newswire</p>

<p class="xn-dateline">SANTA CLARA, Calif., June 28, 2017</p>
</div>

<div class="xn-content" xmlns="http://www.w3.org/1999/xhtml" xmlns:xn="http://www.xmlnews.org/ns/">

<p>
<span class="xn-location">SANTA CLARA, Calif.</span>, <span class="xn-chron">June 28, 2017</span> /PRNewswire/ --&nbsp;Non-invasive liquid biopsy assay testing is poised to transform the oncology diagnostics market in <span class="xn-location">the United States</span> (U.S.) by steadily replacing traditional invasive biopsies. While the technology for targeting and identifying different cancer biomarkers is available, understanding the downstream ramifications and the methodology to measure them will be the proprietary technology for new assays. Growth in cancer testing is augmented by advancements in next-generation sequencing (NGS), proteomics, and the rise of personalized medicine. Opportunities lie in screening, preventive and therapy selection areas as these are the most promising applications for liquid biopsies and companion diagnostics that increase positive outcomes. The clinical protocols for diagnosis of breast cancer and colon cancer now involve the use of imaging techniques as well as in vitro diagnostic tests. The augmentation of protocols to supplement clinical decisions drives a more definitive diagnosis. Other technologies that are poised to boost due to the growth in oncology diagnostics is digital pathology which will lead to digitization of workflows for pathologists.</p>

<p>"New developments in NGS and proteomics are allowing measurement of multiple biomarkers in blood and other body fluids with increased sensitivity and specificity for use in screening and management for each cancer type," said Transformational Health Industry Analyst <b>Divyaa Ravishankar</b>. "Another prominent trend is the heavy investment of pharmaceutical companies into liquid biopsy startup companies to develop companion diagnostics products. Insurance companies are motivating preventive medicine with cancer screening included in wellness programs offered through employer insurance to prevent more expensive chronic disease."</p>

<p>
<b>US Oncology Diagnostics Market, Forecast to 2021</b>, recent research from Frost &amp; Sullivan's <b><a href="http://ww2.frost.com/research/industry/transformational-health/life-sciences" rel="nofollow" target="_blank">Life Sciences</a></b> Growth Partnership Service program, examines the U.S. oncology diagnostics market and identifies growth segments, trends driving adoption, and strategic measures taken by market majors such as <a href="http://www.abbott.com/" rel="nofollow" target="_blank">Abbott</a>, <a href="http://www.roche.com/" rel="nofollow" target="_blank">Roche</a>, <a href="https://www.healthcare.siemens.com/" rel="nofollow" target="_blank">Siemens Healthineers</a>, <a href="https://www.qiagen.com/us/" rel="nofollow" target="_blank">Qiagen</a>, <a href="https://www.beckmancoulter.com/" rel="nofollow" target="_blank">Beckman Coulter</a>, <a href="http://www.orthoclinical.com/en-us" rel="nofollow" target="_blank">Ortho Clinical Diagnostics</a>, <a href="http://www.genomichealth.com/" rel="nofollow" target="_blank">Genomic Health</a> and <a href="https://myriad.com/" rel="nofollow" target="_blank">Myriad</a>. Cancer types covered include breast cancer, ovarian cancer, cervical cancer, colorectal cancer, prostate cancer, and lung cancer.</p>

<p class="prnml40" id="indentid">To know more about Frost &amp; Sullivan's research and to sign up for our Growth Strategy Dialogue, a complimentary one-hour interactive session with Frost &amp; Sullivan's thought leaders, please <a href="https://go.frost.com/forms/PR_ContactUs?PR=MF&RS=K165" rel="nofollow" target="_blank">click here</a>.</p>

<p>Developments and trends driving growth in the U.S. oncology diagnostics market include:</p>

<ul type="disc">

<li>Use of liquid biopsy as a therapy monitoring tool; </li>

<li>Automation and simplification of next-generation sequencing; </li>

<li>Mergers, acquisitions, investments and partnerships of liquid biopsy companies with NGS, and proteomics with commercial biomarkers; </li>

<li>Reimbursement by insurance companies in cancer prevention and screening; </li>

<li>Shift in care from treatment to screening as population health data is analyzed and interpreted by artificial intelligence algorithms; </li>

<li>Regulatory developments and remake of LDT landscape is anticipated in 2018 and beyond; and </li>

<li>Adoption of digital pathology.</li>
</ul>

<p>"In the future, cancer biomarker tests will be multiplexed and consist of multiple biomarker types and hereditary testing will be used to identify high-risk population for early signs of cancer," noted Ravishankar. "Micro ribonucleic acid (miRNA), small, single-stranded, non-coding RNA molecules that bind target Messenger RNA (mRNA) to prevent protein production will be used to regulate key cancer related pathways involved in cancer drug therapy resistance."</p>

<p>
<b>About Frost &amp; Sullivan</b>
</p>

<p>Frost &amp; Sullivan, the Growth Partnership Company, works in collaboration with clients to leverage visionary innovation that addresses the global challenges and related growth opportunities that will make or break today's market participants. For more than 50 years, we have been developing growth strategies for the global 1000, emerging businesses, the public sector and the investment community. </p>

<p class="prntac">
<b>US Oncology Diagnostics Market, Forecast to 2021<br>
</b>K165-55</p>

<p>Contact:<br>
<span class="xn-person">Mariana Fernandez</span>
<br>Corporate Communications &ndash; <span class="xn-location">North America</span>
<br>P: +54 11 4778 3540<br>F: +54 11 4777 0071<br>E: <a href="mailto:Mariana.Fernandez@frost.com" rel="nofollow" target="_blank">Mariana.Fernandez@frost.com</a>
</p>

<p>
<u><a href="http://ww2.frost.com/" rel="nofollow" target="_blank">http://ww2.frost.com</a></u>
</p>

<p>
<a href="https://twitter.com/FS_Healthcare" rel="nofollow" target="_blank">twitter: @FS_Healthcare</a>
<br>
<a href="https://www.linkedin.com/groups/4823253/profile" rel="nofollow" target="_blank">LinkedIn: Transform Health</a>
</p>

<p>&nbsp;</p>

<p>SOURCE  Frost &amp; Sullivan</p>

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<p>Web Site: <a class="release-link" href="http://www.frost.com" target="_newbrowser">http://www.frost.com</a>
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          Speeding Up Genomics Applications with Faster Compression   

After several years of work on genomics with industry and academia, Intel has introduced the Genomics Kernel Library (GKL). This open-source code gives developers access to performance optimizations that accelerate genomics applications on Intel® architecture. It targets hardware based on Intel® Xeon® processors, FPGAs, and Intel® Xeon Phi™ coprocessors. Intel is working with the Broad ...continue reading Speeding Up Genomics Applications with Faster Compression

The post Speeding Up Genomics Applications with Faster Compression appeared first on IT Peer Network.


          Annual Meeting of the Society for Molecular Biology and Evolution 2017   
SMBE 2017 will explore a diversity of topics within interdisciplinary genomics, proteomics, molecular biology and evolution. The meeting will see 1,500 attendees from around the world....
          Developing a Prototype System for Integrating Pharmacogenomics Findings into Clinical Practice   
Findings from pharmacogenomics (PGx) studies have the potential to be applied to individualize drug therapy to improve efficacy and reduce adverse drug events. Researchers have identified factors influencing uptake of genomics in medicine, but little is known about the specific technical barriers to incorporating PGx into existing clinical frameworks. We present the design and development of a prototype PGx clinical decision support (CDS) system that builds on existing clinical infrastructure and incorporates semi-active and active CDS. Informing this work, we updated previous evaluations of PGx knowledge characteristics, and of how the CDS capabilities of three local clinical systems align with data and functional requirements for PGx CDS. We summarize characteristics of PGx knowledge and technical needs for implementing PGx CDS within existing clinical frameworks. PGx decision support rules derived from FDA drug labels primarily involve drug metabolizing genes, vary in maturity, and the majority support the post-analytic phase of genetic testing. Computerized provider order entry capabilities are key functional requirements for PGx CDS and were best supported by one of the three systems we evaluated. We identified two technical needs when building on this system, the need for (1) new or existing standards for data exchange to connect clinical data to PGx knowledge, and (2) a method for implementing semi-active CDS. Our analyses enhance our understanding of principles for designing and implementing CDS for drug therapy individualization and our current understanding of PGx characteristics in a clinical context. Characteristics of PGx knowledge and capabilities of current clinical systems can help govern decisions about CDS implementation, and can help guide decisions made by groups that develop and maintain knowledge resources such that delivery of content for clinical care is supported.
          Asynchronous Transcriptional Silencing of Individual Retroviral Genomes in Embryonic Cells   
Background Retroviral DNAs are profoundly silenced at the transcriptional level in embryonic cell types. The transcriptional profile of pluripotent stem cells has been demonstrated to be extremely heterogeneous from cell to cell, and how the silencing of retroviral DNAs is achieved is not yet well characterized. Results In the current study, we investigated the transcriptional silencing dynamics in stem cells by independently monitoring the expression of two Moloney murine leukemia virus (MMLV) retroviral vectors newly introduced into embryonic carcinoma (EC) cells. Although MMLV is efficiently silenced by epigenetic mechanisms in most such cells, a small number of the doubly-transduced EC cells transiently show double-positive proviral expression. These cells were sorted and their expression patterns were studied over time as silencing is established. Conclusions Our data suggest that retroviral silencing occurs stochastically, in an individual locus-specific fashion, and often without synchronous silencing of both viruses in the same cells. Surprisingly, the chromatin modifications that mark the silenced proviruses are unchanged even in cells that temporarily escape silencing. This local silencing effect is a feature of stem cell epigenomic regulation that has not previously been revealed.
          Bioinformatics Specialist-Metagenomics/Proteomics - Signature Science, LLC - Austin, TX   
Travel to project and business development meetings as needed. Familiarity with machine learning, Git, and agile software development is a plus;... $90,000 a year
From Signature Science, LLC - Tue, 06 Jun 2017 09:05:50 GMT - View all Austin, TX jobs
          GA4GH Federated Analysis Proof of Concept   
A recent proof of concept aimed at providing insight into the potential power of federated analysis of genomics data saw Aridhia team up with several ...
          FHIR genomics pilots taking off for precision medicine   
HL7 News, September 2016
          Partners HealthCare and GE Healthcare Launch 10-year Collaboration on Artificial Intelligence   
Partners HealthCare and GE Healthcare Launch 10-year Collaboration on Artificial Intelligence

May 17, 2017 — Partners HealthCare and GE Healthcare announced a 10-year collaboration to rapidly develop, validate and strategically integrate deep learning technology across the entire continuum of care. The collaboration will be executed through the newly formed Massachusetts General Hospital and Brigham and Women’s Hospital Center for Clinical Data Science and will feature co-located, multidisciplinary teams with broad access to data, computational infrastructure and clinical expertise.

The initial focus of the relationship will be on the development of applications aimed to improve clinician productivity and patient outcomes in diagnostic imaging. Over time, the groups will create new business models for applying artificial intelligence (AI) to healthcare and develop products for additional medical specialties like molecular pathology, genomics and population health.

“This is an important moment for medicine,” said David Torchiana, M.D., CEO of Partners HealthCare. “Clinicians are inundated with data, and the patient experience suffers from inefficiencies in the healthcare industry. This partnership has the resources and vision to accelerate the development and adoption of deep learning technology and empower clinicians with the tools needed to store, analyze and leverage the flood of information to more rapidly and effectively deliver care.”

The vision for the collaboration is to implement AI into every aspect of a patient journey – from admittance through discharge. Once the deep learning applications are developed and deployed, clinicians and patients will benefit from a variety of tools that span disease areas, diagnostic modalities and treatment strategies and have the potential to do everything from decrease unnecessary biopsies to streamline clinical workflows to increase the amount of time clinicians spend with patients versus performing administrative tasks. Additionally, the teams will co-develop an open platform on which Partners HealthCare, GE Healthcare and third-party developers can rapidly prototype, validate and share the applications with hospitals and clinics around the world.

With the initial diagnostic imaging focus, early applications will address cases like:

  • Determining the prognostic impact of stroke,
  • Identifying fractures in the emergency room;
  • Tracking how tumors grow or shrink after the administration of novel therapies; and
  • Indicating the likelihood of cancer on ultrasound.

The applications are being developed based on three criteria:

  1. Patient impact;
  2. Technical capability; and
  3. Market appetite.

This is to ensure that the solutions being developed are not solely dependent on the data that’s available but specifically target the top clinician pain points and the most critically ill patients. The goal is to bring the most promising solutions to market faster, so they can start making an impact for hospitals, health systems and patients globally sooner.

Spinal injury patients represent the types of cases where deep learning applications can help clinicians deliver faster, more efficient care, as the patients need to be treated immediately or run the risk of significant and permanent damage. For a single patient, a lumbar spine magnetic resonance imaging (MRI) exam may generate up to 300 images. In addition, a doctor may need to review prior scans and notes in a patient’s electronic medical record before making a diagnosis. A deep learning application could be leveraged to quickly analyze the data and determine the most critical images for the radiologist to read, shortening the time to treatment for trauma patients, and enabling the clinician to deliver more personalized and comprehensive care for all patients – critically injured or not.

“We’re evolving the healthcare system to be able to take advantage of the benefits of deep learning, bringing together hospitals, data sets and clinical and technical minds unlike ever before,” said Keith Dreyer, DO, Ph.D., chief data science officer, Departments of Radiology at MGH and BWH. “The scope reflects the reality that advancements in clinical data science require substantial commitments of capital, expertise, personnel and cooperation between the system and industry.”

Watch a VIDEO interview with MGH Center for Clinical Data Science director Mark Michalski on the development of artificial intelligence to aid radiology.

Read the article "How Artificial Intelligence Will Change Medical Imaging."

For more information: www.gehealthcare.com, www.partners.org


          How Artificial Intelligence Will Change Medical Imaging   
AI, deep learning, artificial intelligence, medical imaging, cardiology, echo AI, clinical decision support, echocardiography

An example of artificial intelligence from the start-up company Viz. The image shows how the AI software automatically reviews an echocardiogram, completes an automated left ventricular ejection fraction quantification and then presents the data side by side with the original cardiology report. The goal of the software is to augment clinicians and cardiologists by helping them speed workflow, act as a second set of eyes and aid clinical decision support.

An example of how Agfa is integrating IBM Watson into its radiology workflow. Watson reviewed the X-ray images and the image order and determined the patient had lung cancer and a cardiac history and pulled in the relevant prior exams, sections of the patient history, cardiology and oncology department information. It also pulled in recent lab values, current drugs being taken. This allows for a more complete view of the patient's condition and may aid in diagnosis or determining the next step in care.  

Artificial intelligence (AI) has captured the imagination and attention of doctors over the past couple years as several companies and large research hospitals work to perfect these systems for clinical use. The first concrete examples of how AI (also called deep learning, machine learning or artificial neural networks) will help clinicians are now being commercialized. These systems may offer a paradigm shift in how clinicians work in an effort to significantly boost workflow efficiency, while at the same time improving care and patient throughput. 

Today, one of the biggest problems facing physicians and clinicians in general is the overload of too much patient information to sift through. This rapid accumulation of electronic data is thanks to the advent of electronic medical records (EMRs) and the capture of all sorts of data about a patient that was not previously recorded, or at least not easily data mined. This includes imaging data, exam and procedure reports, lab values, pathology reports, waveforms, data automatically downloaded from implantable electrophysiology devices, data transferred from the imaging and diagnostics systems themselves, as well as the information entered in the EMR, admission, discharge and transfer (ADT), hospital information system (HIS) and billing software. In the next couple years there will be a further data explosion with the use of bidirectional patient portals, where patients can upload their own data and images to their EMRs. This will include images shot with their phones of things like wound site healing to reduce the need for in-person follow-up office visits. It also will include medication compliance tracking, blood pressure and weight logs, blood sugar, anticoagulant INR and other home monitoring test results, and activity tracking from apps, wearables and the evolving Internet of things (IoT) to aid in keeping patients healthy.

Physicians liken all this data to drinking from a firehose because it is overwhelming. Many say it is very difficult or impossible to go through the large volumes of data to pick out what is clinically relevant or actionable. It is easy for things to fall through the cracks or for things to be lost to patient follow-up. This issue is further compounded when you add factors like increasing patient volumes, lower reimbursements, bundled payments and the conversion from fee-for-service to a fee-for-value reimbursement system. 

This is where artificial intelligence will play a key role in the next couple years. AI will not be diagnosing patients and replacing doctors — it will be augmenting their ability to find the key, relevant data they need to care for a patient and present it in a concise, easily digestible format. When a radiologist calls up a chest computed tomography (CT) scan to read, the AI will review the image and identify potential findings immediately — from the image and also by combing through the patient history  related to the particular anatomy scanned. If the exam order is for chest pain, the AI system will call up:

  • All the relevant data and prior exams specific to prior cardiac history;
  • Pharmacy information regarding drugs specific to COPD, heart failure, coronary disease and anticoagulants;
  • Prior imaging exams from any modality of the chest that may aid in diagnosis;
  • Prior reports for that imaging;
  • Prior thoracic or cardiac procedures;
  • Recent lab results; and
  • Any pathology reports that relate to specimens collected from the thorax.

Patient history from prior reports or the EMR that may be relevant to potential causes of chest pain will also be collected by the AI and displayed in brief with links to the full information (such as history of aortic aneurism, high blood pressure, coronary blockages, history of smoking, prior pulmonary embolism, cancer, implantable devices or deep vein thrombosis). This information would otherwise would take too long to collect, or its existence might not be known, by the physician so they would not have spent time looking for it.   

Watch the VIDEO “Examples of Artificial Intelligence in Medical Imaging Diagnostics.” This shows an example of how AI can assess aortic dissection CT images.
 

Watch the VIDEO “Development of Artificial Intelligence to Aid Radiology,” an interview with Mark Michalski, M.D., director of the Center for Clinical Data Science at Massachusetts General Hospital, explaining the basis of artificial intelligence in radiology.

At the 2017 Health Information and Management Systems Society (HIMSS) annual conference in February, several vendors showed some of the first concrete examples of how this type of AI works. IBM/Merge, Philips, Agfa and Siemens have already started integrating AI into their medical imaging software systems. GE showed predictive analytics software using elements of AI for the impact on imaging departments when someone calls in sick, or if patient volumes increase. Vital showed a similar work-in-progress predictive analytics software for imaging equipment utilization. Others, including several analytics companies and startups, showed software that uses AI to quickly sift through massive amounts of big data or offer immediate clinical decision support for appropriate use criteria, the best test or imaging to make a diagnosis or even offer differential diagnoses.  

Philips uses AI as a component of its new Illumeo software with adaptive intelligence, which automatically pulls in related prior exams for radiology. The user can click on an area of the anatomy in a specific MPI view, and AI will find and open prior imaging studies to show the same anatomy, slice and orientation. For oncology imaging, with a couple clicks on the tumor in the image, the AI will perform an automated quantification and then perform the same measures on the priors, presenting a side-by-side comparison of the tumor assessment. This can significantly reduce the time involved with tumor tracking assessment and speed workflow.  

Read the blog about AI at HIMSS 2017 "Two Technologies That Offer a Paradigm Shift in Medicine at HIMSS 2017."

 

AI is Elementary to Watson

IBM Watson has been cited for the past few years as being in the forefront of medical AI, but has yet to commercialize the technology. Some of the first versions of work-in-progress software were shown at HIMSS by partner vendors Agfa and Siemens. Agfa showed an impressive example of how the technology works. A digital radiography (DR) chest X-ray exam was called up and Watson reviewed the image and determined the patient had small-cell lung cancer and evidence of both lung and heart surgery. Watson then searched the picture archiving and communication system (PACS), EMR and departmental reporting systems to bring in:

  • Prior chest imaging studies;
  • Cardiology report information;
  • Medications the patient is currently taking;
  • Patient history relevant to them having COPD and a history of smoking that might relate to their current exam;
  • Recent lab reports;
  • Oncology patient encounters including chemotherapy; and
  • Radiation therapy treatments.

When the radiologist opens the study, all this information is presented in a concise format and greatly enhances the picture of this patient’s health. Agfa said the goal is to improve the radiologist’s understanding of the patient to improve the diagnosis, therapies and resulting patient outcomes without adding more burden on the clinician. 

IBM purchased Merge Healthcare in 2015 for $1 billion, partly to get an established foothold in the medical IT market. However, the purchase also gave Watson millions of radiology studies and a vast amount of existing medical record data to help train the AI in evaluating patient data and get better at reading imaging exams. IBM Watson is now licensing its software through third-party agreements with other health IT vendors. The contracts stipulate that each vendor needs to add additional value to Watson with their own programming, not just become a reseller. Probably the most important stipulation of these new contracts is that vendors also are required to share access to all the patient data and imaging studies they have access to. This allows Watson to continue to hone its clinical intelligence with millions of new patient records.  
 

The Basics of Machine Learning

Access to vast quantities of patient data and images is needed to feed the AI software algorithms educational materials to learn from. Sorting through massive amounts of big data is a major component of how AI learns what is important for clinicians, what data elements are related to various disease states and gains clinical understanding. It is a similar process to medical students learning the ropes, but uses much more educational input than what is comprehensible by humans. The first step in machine learning software is for it to ingest medical textbooks and care guidelines and then review examples of clinical cases. Unlike human students, the number of cases AI uses to learn numbers in the millions. 

For cases where the AI did not accurately determine the disease state or found incorrect or irrelevant data, software programers go back and refine the AI algorithm iteration after iteration until the AI software gets it right in the majority of cases. In medicine, there are so many variables it is difficult to always arrive at the correct diagnosis for people or machines. However, percentage wise, experts now say AI software reading medical imaging studies can often match, or in some cases, outperform human radiologists. This is especially true for rare diseases or presentations, where a radiologist might only see a handful of such cases during their entire career. AI has the advantage of reviewing hundreds or even thousands of these rare studies from archives to become proficient at reading them and identify a proper diagnosis. Also, unlike the human mind, it always remains fresh in the computer’s mind. 

AI algorithms read medical images similar to radiologists, by identifying patterns. AI systems are trained using vast numbers of exams to determine what normal anatomy looks like on scans from CT, magnetic resonance imaging (MRI), ultrasound or nuclear imaging. Then abnormal cases are used to train the eye of the AI system to identify anomalies, similar to computer-aided detection software (CAD). However, unlike CAD, which just highlights areas a radiologist may want to take a closer look at, AI software has a more analytical cognitive ability based on much more clinical data and reading experience that previous generations of CAD software. For this reason, experts who are helping develop AI for medicine often refer to the cognitive ability as “CAD that works.”

   

AI All Around Us and the Next Step in Radiology

Deep learning computers are already driving cars, monitoring financial data for theft, able to translate languages and recognize people’s moods based on facial recognition, said Keith Dreyer, DO, Ph.D., vice chairman of radiology computing and information sciences at Massachusetts General Hospital, Boston. He was among the key speakers at the opening session of the 2016 Radiological Society of North America (RSNA) meeting in November, where he discussed AI’s entry into medical imaging. He is also in charge of his institution’s development of its own AI system to assist physicians at Mass General. 

“The data science revolution started about five years ago with the advent of IBM Watson and Google Brain,” Dreyer explained. He said the 2012 introduction of deep learning algorithms really pushed AI forward and by 2014 the scales began to tip in terms of machines reading radiology studies correctly, reaching around 95 percent accuracy.

Dreyer said AI software for imaging is not new, as most people already use it on Facebook to automatically tag friends the platform identities using facial recognition algorithms. He said training AI is a similar concept, where you can start with showing a computer photos of cats and dogs and it can be trained to determine the difference after enough images are used. 

AI requires big data, massive computing power, powerful algorithms, broad investments and then a lot of translation and integration from a programming standpoint before it can be commercialized, Dreyer said. 

From a radiology standpoint, he said there are two types of AI. The first type that is already starting to see U.S. Food and Drug Administration approval is for quantification AI, which only requires a 510(k) approval. AI developed for clinical interpretation will require FDA pre-market approval (PMA), which involves clinical trials.

Before machines start conducting primary or peer review reads, Dreyer said it is much more likely AI will be used to read old exams retrospectively to help hospitals find new patients for conditions the patient may not realize they have. He said about 9 million Americans qualify for low-dose CT scans to screen them for lung cancer. He said AI can be trained to search through all the prior chest CT exams on record in the health system to help identify patients that may have lung cancer. This type of retrospective screening may apply to other disease states as well, especially if the AI can pull in genomic testing results to narrow the review to patients who are predisposed to some diseases. 

He said overall, AI offers a major opportunity to enhance and augment radiology reading, not to replace radiologists. 

“We are focused on talking into a microphone and we are ignoring all this other data that is out there in the patient record,” Dreyer said. “We need to look at the imaging as just another source of data for the patient.” He said AI can help automate qualification and quickly pull out related patient data from the EMR that will aid diagnosis or the understanding of a patient’s condition.  

Watch a VIDEO interview with Eliot L. Siegel, M.D., Dwyer Lecturer; Closing Keynote Speaker, Vice Chair of Radiology at the University of Maryland and the Chief of Radiology for VA Maryland Healthcare System, talks about the current state of the industry in computer-aided detection and diagnosis at SIIM 2016. 

Read the blog “How Intelligent Machines Could Make a Difference in Radiology.”


          The LASSO Estimator   

As far as I can tell, the LASSO estimator is the closest thing we have to a miracle in modern statistics.

The LASSO estimator is defined as a solution to the minimization problem $\frac{1}{n} \| Y - X \theta \|_2^2 + \lambda \| \theta \|_1$ over $\mathbb{R}^p$. The key insight here is that this is a convex problem in $\theta$ - this follows from both norms being convex and the sum of convex functions being convex. This allows us to design efficient solvers for this problem and thus handle large-scale problems - see, for example, ADMM, iterative shrinkage, gradient projection, etc.

The LASSO can be viewed as convex relaxation of a very natural problem in statistical estimation - finding the best $k$-sparse vector to minimize $\| Y - X \theta \| + \lambda \| \theta \|_0$, where the $L_0$ norm (indeed, not actually a norm) is to be interpreted as the number of non-zero coefficients in $\theta$. This comes from problems such as in signal processing and genomics array data where we have $p$ (the number of covariates) significantly larger than $n$, the number of observations. In this case, the usual least-squares estimation theory dating back to Gauss does not apply ($X$ cannot have full rank), and we must find other alternatives. The brute-force approach is combinatorially hard (we must check each $p \choose k$ sets of supports, which takes time exponential in $p$).

Thus, the LASSO objective can be seen as a natural convex relation of the original problem (e.g. taking $p$ from $0$ upwards and stopping as soon as $\| \theta \|_p$ is convex).

The "miracle" I refer to is the amazing result of Candes & Tao in a series of papers starting in 2005 that established that for a large class of observation matrices $X$, we have the amazing result that with very high probability, solving the LASSO problem is equivalent to solving the original combinatorially hard problem. Formally, we have the following theorem, which contains a germ of the restricted isometry property.

The Optimality of the LASSO estimator

Let $\theta_0$ be $k$-sparse with support $S_0$, and let $Y = X \theta + \epsilon$, with $\epsilon \sim N(0, \sigma^2 I_n)$. Let $\tilde \theta$ be the LASSO estimator of $(Y, X)$ with parameter $\lambda = 4 \overline \sigma \sqrt{\frac{t^2 + 2 \log p}{n}}$. Assume that $\| \tilde \theta_{S_0} - \theta_0 \|_1^2 \leq k r_0 (\tilde \theta - \theta_0)^T \hat \Sigma (\tilde \theta - \theta_0)$ with probability at least $1 - \beta$ for some $r_0$. Then with probability at least $1 - \beta - e^{-\frac{t^2}{2}}$, we have that \begin{equation} \frac{1}{n} \| X(\tilde \theta - \theta_0) \|_2^2 + \lambda \| \tilde \theta - \theta_0 \| \leq 4 k r_0 \lambda^2 \end{equation}

Proof

The proof is fairly elementary, requiring only a basic concentration of measure inequality for subgaussian random variables. The key step is recognizing that we can bound the event $\max_{j} \frac{2}{n} \| (\epsilon^T X)_j \| \geq \frac{\lambda}{2}$ on a set of measure less than $e^-\frac{t^2}{2}$. Once we have this result, we can apply the triangle inequality and the restricted isometry condition in the theorem to obtain the desired result.


          Breast Cancer Tests Betray 'Precision Medicine' Branding   
The biotech industry cheered President Obama's proposed $215 million Precision Medicine Initiative, but the varying results and genetic basis of three DNA-based tests to predict breast cancer recurrence show the gap remaining between branding and real precision in clinical genomics.
          Challenges For Genomics In The Age Of Big Data   
Last week, a group of respected researchers published a commentary about the coming data challenges in genomics. Comparing the projected growth of genomic data to three other sources considered among the most prolific data producers in the world—astronomy, Twitter, and YouTube—these scientists predict that by 2025, genomics could well represent the biggest of big data fields. With the raw data for each human genome taking up about 100 GB, we’re well on our way. Genomics only recently entered the big data realm, and we have major issues to address before it leapfrogs every other data-generating group.
          Copy number variation of functional RBMY1 is associated with sperm motility: an azoospermia factor-linked candidate for asthenozoospermia   
Abstract
STUDY QUESTION
What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes?
SUMMARY ANSWER
The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia.
WHAT IS KNOWN ALREADY
RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome. RBMY1 encodes an RNA-binding protein that serves as a pre-mRNA splicing regulator during spermatogenesis, and male mice deficient in Rbmy are sterile.
STUDY DESIGN, SIZE, DURATION
A total of 3127 adult males were recruited from 2009 to 2016; of this group, the dosage of RBMY1 functional copy were investigated in 486 fertile males. In the remaining 2641 males with known spermatogenesis status, 1070 Y-chromosome haplogroup (Y-hg) O3* or O3e carriers without chromosomal aberration or known AZF structure mutations responsible for spermatogenic impairment, including 506 men with normozoospermia and 564 men with oligozoospermia or/and asthenozoospermia, were screened, and the RBMY1 functional copy dosage and copy conversion were determined to explore their associations with sperm phenotypes. The correlation between RBMY1 dosage and its mRNA level or RBMY1 protein level and the correlation between sperm RBMY1 level and motility were analysed in 15 testis tissue samples and eight semen samples. Ten additional semen samples were used to confirm the subcellular localization of RBMY1 in individual sperm.
PARTICIPANTS/MATERIALS, SETTING, METHODS
All the Han volunteers donating whole blood, semen and testis tissue were from southwest China. RBMY1 copy number, copy conversion, mRNA/protein amount and protein location in sperm were detected using the AccuCopy® assay method, paralog ratio test, quantitative PCR, western blotting and immunofluorescence staining methods, respectively.
MAIN RESULTS AND THE ROLE OF CHANCE
This study identified Y-hg-independent CNV of functional RBMY1 in the enrolled population. A difference in the distribution of RBMY1 copy number was observed between the group with normal sperm motility and the group with asthenozoospermia. A positive correlation between the RBMY1 copy dosage and sperm motility was identified, and the males with fewer than six copies of RBMY1 showed an elevated risk for asthenozoospermia relative to those with six RBMY1 copies, the most common dosage in the population. The RBMY1 copy dosage was positively correlated with its mRNA and protein level in the testis. Sperm with high motility were found to carry more RBMY1 protein than those with relatively low motility. The RBMY1 protein was confirmed to predominantly localize in the neck and mid-piece region of sperm as well as the principal piece of the sperm tail. Our population study completes a chain of evidence suggesting that RBMY1 influences the susceptibility of males to asthenozoospermia by modulating sperm motility.
LIMITATIONS REASONS FOR CAUTION
High sequence similarity between the RBMY1 functional copies and a large number of pseudogenes potentially reduces the accuracy of the copy number detection. The mechanism underlying the CNV in RBMY1 is still unclear, and the effect of the structural variations in the RBMY1 copy cluster on the copy dosage of other protein-coding genes located in the region cannot be excluded, which may potentially bias our observations.
WIDER IMPLICATIONS OF THE FINDINGS
Asthenozoospermia is a multi-factor complex disease with a limited number of proven susceptibility genes. This study identified a novel genomic candidate independently contributing to the condition, enriching our understanding of the role of AZF-linked genes in male reproduction. Our finding provides insight into the physiological and pathological characteristics of RBMY1 in terms of sperm motility, supplies persuasive evidence of the significance of RBMY1 copy number analysis in the clinical counselling of male infertility resulting from asthenozoospermia
STUDY FUNDING/COMPETING INTEREST(S)
This work was funded by the National Natural Science Foundation of China (Nos. 81370748 and 30971598). The authors have no conflicts of interest.

          A Guide to Invertebrate Zoology on Twitter!!   
Marine invertebrates potpourri
image by the indubitable Arthur Anker
This week. Something a little different. I was doing a short presentation for some colleagues about using social media next week and I began accumulating Invertebrate Zoology accounts on Twitter... which at one time were quite rare and realized that it would be a good thing to share all of them.

It surprised me that SO MANY have since become established. I remember many years ago when it was less than 6 people and most of it was secondary to blogging!
Now, not ONLY are there many, MANY IZ Twitter themed accounts specializing on specific taxa, there are actually REGULAR twitter events...

Invertebrate Themed Twitter Events

Weekly..

#TrilobiteTuesdays. Held every Tuesday.  If you are into Paleozoic arthropods then Tuesdays are YOUR thing!

#WormWednesday: Held every Wednesday. These bring forth all manner of worm-like phyla: Polychaeta, Annelida, Nematoda, Platyhelminthes, Acoela, and so on and so forth..

#SpongeThursday: Held every Thursday. Love the Porifera? the Hexactinellida? Go forth and
enjoy/post about them!

Honorable mention goes to #FossilFriday which is mostly about Dinosaurs and vertebrates..but you get some ammonites and other invertebrates in there pretty regularly...

Yearly..
#CephalopodAwarenessWeek. aka #CephalopodAwarenessDays Every year from October 8 to 12.  You can keep on updates at @cephalopodday. Basically 5 days celebrating EACH class of cephalopods and then some...
  • October 8 – Octopus Day, for all the eight-armed species
  • October 9 – Nautilus Night, a time for all the lesser-known extant cephalopods
  • October 10 – Squid Day/Cuttlefish Day, or Squidturday, covering the tentacular species
  • October 11 – Myths and Legends Day, for all the fantastical cephalopods of movies, literature and legend. 
  • October 12 – Fossil Day
#Polychaete Day. Held yearly on July 1 ever year. (Older hashtag was #InternationalpolychaeteDay).  In conjunction with polychaete related events at the NMNH and other museums.   This day honors international polychaete worm expert Dr. Kristian Fauchald on his birthday July 1st. Celebrates all manner of polychaete (and related) topics!  Here were my posts from 2015 and 2016. 

#SeaSlugDay. Held every year on October 29th in honor of Dr. Terry Gosliner's birthday! Celebrate by posting images, videos and links to all manner of shell-less marine gastropods! Nudibranchs and their kin! My post from last year. 

And of course #Okeanos when the NOAA vessel Okeanos Explorer goes into research/streaming mode!  in which case, there are new deep-sea invertebrate posts for several hours every day for about 2 to 3 weeks!!

Various Twitter accounts/Persons with Invertebrate themed content
from the USNM Invertebrate Zoology FB page @InvertebratesDC
So, here we go. All said and done a list of about 65 IZ twitter accoutns! A list of all the accounts I could locate which focused primarily on Invertebrates, exclusive of insects and arachnids.  Yes, sorry land-based arthropods but you are a whole thing all on your own.

This will be a fairly subjective list-I focused mainly on marine groups and those with academic or otherwise focused content that I thought was appropriate. Activity was also a consideration. Some accounts looked essentially inactive and were not included.

Let me clear that there are a LOT of accounts which have a broader focus that regularly include Invertebrate Zoology themed tweets, including aquariums, natural history museums, etc. and frankly those have so many followers its unnecessary to give them much more publicity anyway..

There were MANY, many individual accounts of photographers, naturalists, educators, scientists, etc. who for one reason or another I just couldn't include for the sake of space, focus, etc.

And there are some topics, for example about coral reefs, there's a TON of coral-related accounts and I simply could not list them all... A search on Twitter's search engine will get you all of those names pretty quickly though.

So, please don't take an omission as an offense. In fact, if you've got an IZ twitter account that you'd like me to know about, please let me know and if I think its appropriate, I'd be happy to include it.

As a side note: my search for these Twitter accounts took me to some interesting places and its curious to see how many of of the phylum or other taxonomic names have made it into popular use: band names, student groups, social clubs, business organizations, video games, so on and so forth...

General Accounts:
Invertebrate Zoology department of the NMNH at the Smithsonian @InvertebratesDC The official account for one of the most active Invertebrate Zoology departments in the world.

Heidi Gartner. @RBCMInverts. Collection Manager at the Royal British Columbia Museum Invertebrate Zoology dept.

Annelida & Segemented Worms

Dr. Christoph Bleidorn @C_Blei. Evolutionary biologist at the MNCN in Madrid

Dr. Conrad Helm. @conrad_helm. Sars International Center at the University of Bergen. Works on the systematics of segmented worms.

Brachiopoda
Brachiopod research at the Natural History Museum in London @NHM_Brachiopoda.

Bryozoa
Bryozoan research at the Natural History Museum in London @BryozoanNHM This is, I daresay, the finest Twitter account about bryozoans I have seen to date!!  Both fossil and living!

Cnidaria
Dr. Allen Collins, NMFS/Invertebrate Zoology NMNH. @tesserazoa. Specialist in jellyfish systematics, sponges and metazoans relationships.

Australian Coral Reef Society. @AustCoralReefs. Official twitter account of the Australian Coral Reef Society.

Dr. Casey Dunn, Brown University. @caseywdunn. Evolutionary biologist at Brown with a special eye towards siphonophores! He also produces Creature Cast videos.

Dr. Cheryl Lewis Ames,  @boxjellytalkNMNH/University of Maryland, box jelly expert.

Coral Morphologic. @CoralMorph. Strong visuals, images, videos of cnidarians and many other invertebrates.

Gates Lab @GatesCoralLab. Coral Research at the Hawaii Institute of Marine Biology.

Dr. David Plachetzki. University of New Hampshire. @plachetzki.  Cnidarian genomics.

Dr. Mercer R. Brugler @ProfBrugler. Professor at City Tech, SUNY, Taxonomy & Systematics of Black Corals & Anemones.

Medusozoa Columbia. @Medusozoacol.  Jellyfishes of Columbia!

NOAA Coral Program @NOAACoral.  Official Twitter account for the NOAA Coral Reef Conservation Program.

Dr. Rebecca Helm. @RebeccaRHelm. Woods Hole Oceanographic Instition.  Jellyfishes and all manner of swimming cnidarian.

Dr. Paulyn Cartwright @pcart. Professor at the University of Kansas specializing in Cnidarian Evolution.

Dr. Andrea Quattrini. @quattrinia.  Harvey Mudd College. Studies deep-sea corals.

Crustacea
Miranda Lowe, @NatHistGirl. Principal curator of Marine Invertebrates at the Natural History Museum in London.

Dr. Tammy Horton, Amphipod taxonomist at the Discovery Collections in Southampton @tammy_horton. 

Adam Hadsall. @_Nezumiiro_  Tweets #craboftheday and many other items of carcinological interest!

Echinodermata
Chris Mah, Research Associate at the NMNH. @echinoblog. I work on sea stars but know stuff about things.

David Clark. @Clarkeocrinus. A great account for enjoying Paleozoic and fossil stalked crinoids!

Fossil Worms (Miscellaneous)
Luke Perry. At the University of Bristol in the UK/Natural History Museum. @Cambriannelids. Works on Cambrian worms, primarily annelids.

Hemichordates, deuterostomes, etc.

Dr. Chris Cameron. @InvertEvo at the University of Montreal. One of my colleagues who studies the evolution and development of deuterostomes, especially hemichordates.

Invertebrate Paleontology

Dr. Dave Rudkin, @RudkinDave. Royal Ontario Museum. Studies Paleozoic arthropods and other fossil invertebrates.

Invertebrate Vision
Dr. Michael Bok at the University of Hawaii @mikebok. Studies Vision in invertebrates.

Leeches (Hirudinea)
Dr. Anna Phillips, Curator of leeches and parasitic worms at the NMNH, Smithsonian. @Annalida500.

Dr. Mark Siddall Curator at the American Museum of Natural History. @theleechguy. 

Dr. Sebastian Kvist, Curator at the Royal Ontario Museum. @sebastian_kvist. Annelid & leech systematics.

Mollusks-Bivalves
Dr. David Hayes. @Gnarly_Larvae at Eastern Kentucky University. Works primarily on molecular ecology and freshwater mussels.

Freshwater Mussels. @WeNeedMussels. What more can you ask for? A Twitter account entirely devoted to Freshwater mussels!

Mollusks-Cephalopods
ALCES: The AUT Lab for Cephalopod Ecology and Systematics. @ALESonline.  Devoted to studying cephalopod biology, especially deep-sea squids

Research account for fossil cephalopods at the Natural History Museum in London. @NHM_cephalopoda

CIAC-The Cephalopod International Advisory Council. @cephCIAC. The Cephalopod International Advisory Council is a scientific group for cephalopod researchers worldwide

Dr. Louise Allock. @DrShmoo at the National University of Ireland, Galway. Deep-sea octopuses!

The Octopus Newsletter Online (TONMO) @cephs  A hub for cephalopod research and interest.

Dr. Stephanie Bush, Monterey Bay Aquarium. @podlett. Deep-sea Octopus biologist/systematist at MBA.

Mollusks-Gastropoda (shelled snails & slugs)
Dr. Chong Chen, Biologist at JAMSTEC who works on deep-sea snails @squamiferum.  

Jessica Goodheart. @sluglife28. PhD student at the University of Maryland/NMNH. Studies sea slug systematics and behavior.

Dr. Kevin Kokot, @kmkocot. University of Alabama. Mollusk & metazoan phylogeny.

Nematode Worms
The Blaxter Lab (Dr. Mark Blaxter, University of Edinburgh),@blaxterlab.  Nematode, tardigrade and other invertebrate genomics/genetics.

Nemerteans (Ribbon Worms)
Dr. Jon Norenburg, dept. chair of the Invertebrate Zoology dept. at the NMNH. @Jnorenburg and @nemertinator (personal account)  Specializes in ribbon worms and meiofauna.

Iberian Nemerteans. @nemertan. Truth in advertising. A Twitter account about ribbon worms based in Spain.

Parasites (broadly)
Twitter account for the American Society of Parasitologists @AmSocParasit All parasites. All the time.

Tommy Leung, Parasitologist who authors the "Parasite of the Day" blog. @The_Episiarch

Pelagic Invertebrates
Leann Biancani, @LeannMBiancani PhD student at the University of Maryland and the NMNH. Studies the biology and relationships among pelagic invertebrates, including amphipods and polychaetes.

Dr. Steve Haddock, MBARI. @beroe Dr. Haddock is an expert in ALL manner of pelagic deep-sea invertebrates.

Plankton
Dr. Richard Kirby, based in Plymouth, United Kingdom. @planktonpundit. A wonderful account with regular images and videos of planktonic/nektonic and other related organisms.

Platyhelminthes & Flatworms
Dr. Ulf Jondelius @ulfjo, specializes in aceolomorph "flatworms" at the Swedish Museum of Natural History.

Dr. Jean-Lou Justine, specialist on free-living land flatworms at the MNHN in Paris. @Plathelminthe4 If you are REALLY into Bipalium and other terrestrial, free living flatworms this feed is for you!

Polychaete Worms
UPDATE: Christoph Bliedorn has produced a magnificent list of Tweeting Polychaetologists here: https://bembecinus.wordpress.com/2016/10/05/a-list-of-tweeting-polychaetologists/

The Polychaeta Database @WpolyDB Twitter account of the World Polychaete Database (WoRMS)

ケムシ屋 @alciopidae. I don't have a full name unfortunately.  A Japanese polychaete taxonomist (Cirratuliformia/Alvinellidae/ Myzostomida/Opheliidae/Polynoidae etc...)

Dr. Helena Wiklund. @helena_wiklund, University of Gothenberg, Germany. Polychaetes and annelid diversity.

Maddie Brasier. @Madsbrasier.  Studying Antarctic polychaetes.

Dr. Shinri Tomioka. @Capitellico PhD student at Hokkaido University in Japan studying polychaetes.

Dr. Torkild Bakken. @TorkildBakken. Marine biologist at NTNU University Museum, polychaetes and other deep-sea diversity.

Porifera (the sponges)
Twitter account for deep-seasponges.org @Deepsea_sponges You don't get much more specific than this, where deep-sea Porifera are concerned!

Dr. Jackson Chu @jwfchu. Glass sponges and benthic ecology.

The Pawlik Lab @PawlikLab at the University of North Carolina, Wilmington. Sponge chemical ecology and biology.

Dr. Ana Riesgo at the Natural History Museum in London. @anariesgogil  Sponge researcher at the British Museum.

Dr. Bob Thacker at Stony Brook University. @thackerbob 
Ecology and systematics of sponges,  Involved with the Porifera Tree of Life Project.

Protists!
The International Society of Protistologists! @protistologists . Pretty much all in the title.

Psi Wavefunction.@PsiWavefunction. Protist blogger and scientist.

Tardigrades
Dr. Daiki Horikawa. University of Tokyo. @daikidhori  Tardigrade biology & genomics!


          Echinoderm Research at Museum Victoria! So long and thanks for all the Starfish!    
Tropical brittle stars (2)
In the same way that a particular class of echinoderms is made up of diverse members, so are the research labs which study them!  So, in my last installment of #EchinoblogInAustralia I thought I would do a brief profile of researchers doing various kinds of echinoderm research at Museum Victoria in the Marine Zoology Department!

I've done similar profiles for the researchers in Paris at the Museum natioinal d'Histoire naturelle (here)! I think this gives everyone a bit of insight into the many different crew members which staff the various roles in the big research seen in scientific papers. And Dr. Tim O'Hara's lab has had a good week for "big research paper drops" with more to come!!

Just as a refresher though.. Here's a pic with the BIG project that Tim O'Hara's lab has been working on for the last several years: the BIG ophiuroid (aka the brittle and basket star) phylogeny! aka the "family tree" of the ophiuroids!

As I've mentioned previously, the new phylogeny is a BIG deal. It involves a group with over 2000 species which has been a taxonomic headache to scientists for over 100 years. Their research has literally turned this whole field on its head! (if brittle stars had a head!)

The tree clarifies which groups show support for being "real" and elaborates on how different brittle star and basket groups are related to one another.  It will almost DOUBLE the number families!!!
The tree itself is HUGE. Here it is below printed out and mounted on the wall for easy reference. You can see that it extends from that lower bookshelf to the that top shelf-so the printout is easily 6 feet tall (or two meters)!!

The tree was made using a phylogenomic data set. This is different from a lot of the molecular trees made in the last 20 years because it includes a whopping 425 genes and over 60 taxa! (other trees generally use only 3 to 10)  You can see the big paper as published in Current Biology here.

The Echinoderm researchers at Museum Victoria includes a diversity of workers!

1. Dr. Andrew Hugall
Where Tim O'Hara provides the "Ophiuroid Taxonomy and context", Dr. Hugall is the phylogenetics and analytical guru part of the "Big Ophiuroid" team. Although he is currently working on marine invertebrates, he worked previously on birds, discovering "Accelerated speciation" in highly colorful birds, a paper which was published in Nature in 2012. You can see that here. 
Dr. Hugall worked on the analytical aspects of the project and, in conjunction with Dr. O'Hara, cleaned up the genetic data in order to make it ready for analysis. He also provides a good complement to the "natural history" side of the lab with a powerful analytical background.

2. Lupita Bribiesca
Lupita is a PhD student at the University of Melbourne and got her undergraduate degree from the Universidad Nacional Autónoma de México. She's not only very proficient in computer coding and analysis but she's already a prolific author in echinoderm systematics! Especially in anchialine cave echinoderms!
In Mexico, Lupita worked on echinoderms which lived in submarine caves fed by the ocean. Some of her work can be found




3. Skipton "Skip" Woolley

Skip is a relatively new name on the echinoderm scene! But started out in grand fashion! His name of course headlines last week's BIG NATURE paper on ophiuroid deep-sea diversity! (here)

He's been doing analytical work looking at "big picture" diversity patterns in ophiuroids. His prior paper looked at biogeographical subdivisions in Western Australia in the journal Diverstiy & Distributions

4. Dr. Kate Naughton
I featured Kate Naughton's work on the blog back in 2009 when she and Tim O'Hara discovered a brooding "cryptic" species of the Australian Biscuit Star Tosia using molecular tools to understand the relationships of Tosia australis along the Australian coast. (see this story here)

Since then Kate has received her PhD and continued to do her awesome work combining ecology, taxonomy and molecular phylogenetics at Museum Victoria.
These days she's been working a LOT on feather star (i.e., crinoid) taxonomy and diversity in Australia. It turns out that there's a LOT of these in Australia that remain to be discovered and what's known requires a lot of work. 

As with many of us, she seeks a good job, funding for her research and all of life's finer things!

She HAS however also been working on new species of brittle stars in the genus Ophionereis
photo by John Keesing

















5. P. Mark O'Loughlin and Deep Sea Sea Cucumbers
One of the most established echinoderm researchers at Museum Victoria was actually Tim O'Hara's original mentor!  

Mark O'Loughlin has been a fixture of the "marine invertebrates" scene in the Melbourne/Victoria area of Australia for decades. He's published a huge volume of work on echinoderms,  including sea stars and sea cucumbers. Here's his profile at ResearchGate! 

here's a sclerite from a new species of "sea pig" (Family Elpidiidae) that Mark is currently working on from the the Great Australian Bight (979 m)
Mark has been working steadfastly into his 80s but has assisted by many student workers (one of which is seen here)

My thanks to the Museum Victoria for my visit! About 1000 specimen lots identified! 
Until NEXT TIME, Melbourne!! 

          9,354,922   
以前带教会儿童班时鼓励孩子们带着自己的兴趣和热情去创造新的东西,因为这是伟大造物主赋予我们的能力。于是就有几个勇敢的女孩在白板上作画,也有一个内向的男孩写了一整页的诗感怀。



我很惭愧那时没有交上一份自己的作业做榜样,今天在2016年儿童节也算补上了。

经过两年的申请,我在IBM的第一项发明终于在昨天获得了美国专利(编号9354922)。专利发明是有关于在基因信息处理过程中的数据流程和管理。四年前,这项发明的主意就是在白板(white board)上涂鸦时蹦出来的。

以后我会对每一个勇敢的或内向的孩子说:把你的主意画出来或是写下来,也许有一天你也可以和老师一样去申请你自己的专利,而且越多越好,远远超过老师的!

Patent title: Metadata-driven workflows and integration with genomic data processing systems and techniques

Patent abstract: Systems, methods and computer program products configured to provide and perform metadata-based workflow management are disclosed. The inventive subject matter includes a computer readable storage medium having computer readable program instructions embodied therewith. The computer readable program instructions are configured to: initiate a workflow configured to process data; associate the data with metadata; and drive at least a portion of the workflow based on at least some of the metadata. The metadata include anchoring metadata; common metadata; and custom metadata. Inventive subject matter also encompasses a method for managing genomic data processing workflows using metadata includes: initiating a workflow; receiving a request to manage the workflow using metadata comprising: anchoring metadata, common metadata, and custom metadata, associating the metadata with the data; and driving at least a portion of the workflow based on the metadata. The workflow involves genomic analyzes.

USPTO Record: http://tinyurl.com/zfj4r6a

          新奥尔良四月天   
四月的第一天,新奥尔良的雨从早落到晚,喧嚣的旅馆和不息的车流点亮了清静的马路,就如呼朋唤友的游轮客反衬着我们这堆在学楼里闭门造车的科疯疯和学狂狂。

雨中的密西西比河缓缓流过游轮码头然后折转向南, 晨光中逆流而上的行船一如往昔地折射着新奥尔良和圣路易斯这两座前法属城市一衣带水的纽带。

对我这短短两天学霸式的出差,除了走马重温不少熟悉的老街熟景外,又领悟了两条与新奥尔良的新纽带:超级电脑和有轨电车。

靠近游轮码头的大使酒店(Embassy Suites)外街上行人稀少,但酒店里人声鼎沸大呼小叫,大概就等上中午起航的游轮了。

晨曦中的游轮码头。去年感恩节我们全家就是从这儿出发去的加勒比海度假。

晨光中的密西西比河

在Poydras St 和 Tchoupitoulas St 街角,有一家叫Mother's的是N年前我和玉玲带全家第一次来新奥尔良时领略特色三明治Po-Boy的Cajun餐馆。外面看上去还是老样子。

一辆当街而过的有轨电车. 车后的长辫连着电线,也画出一道老都市de风情。


希尔顿酒店里法式情调的装饰

酒店里有关新奥尔良的旅游指南

新奥尔良雨中夜景


生命科技纽带-超级电脑

我出差参加的是第四届路易斯安纳生科计算年会. 做的专题报告题为"生命科技时代的新一代信息技术构架"。
第四届路易斯安纳生科计算年会海报。

与年会主办者之一、路易斯安纳州立大学(LSU)朴教授合影。

朴教授领导的Center for Computation & Technology (计算科技中心)是IBM的科技合作伙伴,主导有关超算和大数据整合的尖端研发,我们合作开发的Delta超级电脑上月投入使用,加入基因医疗(Genomic Medicine)的科研和应用。


Delta的一项应用场景是研究在新奥尔良地区非洲裔居民高发性糖尿病和高血压的遗传因子和环境影(图表上部)。这也算是增加了一条我和新奥尔良的合作沟通纽带吧!


记忆纽带-无轨电车

开完第一天的会从Xavier大学回到希尔顿酒店时已近9点,大堂内人潮涌涌,猜想是今天游轮上下来的游客吧。在大堂一角的一处工艺展幽幽地吸引了我。这是一辆模型电车,就如早晨在街上看到的街车一般,只是装饰得绚丽斑斓。作品名为"Streetcart - Reflection of the City"(街车-都市反思),创作者是本地的艺术家Reggie Ford (www.reggieart.com) 。

我想Reggie在手创这华彩街车折射新奥尔良城市之光时,大概没想到会勾起一位观众的对另一个城市的回忆。在这回忆里,上海的带辫子电车里充满了少年的真挚快乐和青年的激情梦想:卖3分钱的票可以从爷爷家(地丰里)门口的乌鲁木齐路站乘到上海儿童书店的石门二路,再3分钱可以坐到河南中路集邮总公司,然后把压岁钱全花在三国演义连环画和TJ特种纪念邮票上;在9号电车上我带着一位乌鲁木齐来的年轻女孩从复旦出发去黄埔江口的复兴岛看潮,记得车窗半开风吹玲的俏发如飞是无法言喻的美..1990年离开复旦赴美留学时,坐的最后的一班电车也是9号从校门到五角场-记得那儿热闹的五角街市也算是一个杨浦版法国角(French Quarter)吧,我和玲在那儿看过通宵电影吃过地摊上的大腕面。

逝水流年,地丰里已经不再,五角场也已迥然,上海淡为一座遥远的梦中故乡,圣路易斯替而为之称了我们的家园,新奥尔良也成了我和玲共同喜欢的风情都市外加带孩子们出海的港口。但这眼前的街车,好像用它那充满快乐和激情的色彩,和那无形的长辫子连着无尽的电网,从梧桐成荫丁香馥郁的上海复兴西路,到春雨绵绵四月天的新奥尔良Poydras Street, 丁丁作响地行走,宛如穿越时空的纽带飘荡在心中。

我想真正的爱,可以耐住时间和空间的尺度考验。它埋藏心底,只要一有机会比如纽带传音,就又真又活地出来了。

初稿于2016年4月2日

“定格的方位”系列

          Cervical cancer subtypes identified   
An in-depth genomic and molecular analysis of cervical cancer, reported in Nature, reveals potential new therapeutic targets for the disease, which remains one of the leading causes of...
          New advances in pediatric neurologic and developmental disorders in the era of genomics / Gyula Acsadi, editor ; Bonita F. Stanton, consulting editor   
cover imagePeriodical
          New Open Access Journal from Nature Publishing Group   

This summer, Nature Publishing Group will launch Scientific Reports, an entirely open access journal covering all areas of the natural sciences:

Scientific Reports graphic depicting intermeshing cogs
  • Astrophysics
  • Cancer
  • Cell Biology
  • Chemical Biology
  • Chemistry
  • Earth and Environmental Sciences
  • Ecology and Evolutionary Biology
  • Genetics and Genomics
  • Immunology
  • Microbiology
  • Molecular Biology
  • Neuroscience
  • Plant Biology
  • Physics

The journal will feature a quick peer-review process and metrics measuring the frequency of paper downloads.   

Scientific Reports is now accepting submissions. To publish in Scientific Reports, all authors are required to pay an article-processing charge. The 2011 fee will be $1,350 per article. More information about submission is available from the guide for authors.


          Amazon, Google Race to Get Your DNA Into the Cloud   

 

Amazon is in a race against Google to store data on human DNA, seeking both bragging rights in helping scientists make new medical discoveries and market share in a business that may be worth $1 billion a year by 2018.

Academic institutions and healthcare companies are picking sides between their cloud computing offerings - Google Genomics or Amazon Web Services - spurring the two to one-up each other as they win high-profile genomics business, according to interviews with researchers, industry consultants and analysts.

That growth is being propelled by, among other forces, the push for personalized medicine, which aims to base treatments on a patient's DNA profile. Making that a reality will require enormous quantities of data to reveal how particular genetic profiles respond to different treatments.

Already, universities and drug manufacturers are embarking on projects to sequence the genomes of hundreds of thousands of people. The human genome is the full complement of DNA, or genetic material, a copy of which is found in nearly every cell of the body.

Clients view Google and Amazon as doing a better job storing genomics data than they can do using their own computers, keeping it secure, controlling costs and allowing it to be easily shared.

 The cloud companies are going beyond storage to offer analytical functions that let scientists make sense of DNA data. Microsoft and IBM are also competing for a slice of the market.

The "cloud" refers to data or software that physically resides in a server and is accessible via the internet, which allows users to access it without downloading it to their own computer.

Now an estimated $100 million to $300 million business globally, the cloud genomics market is expected to grow to $1 billion by 2018, said research analyst Daniel Ives of investment bank FBR Capital. By that time, the entire cloud market should have $50 billion to $75 billion in annual revenue, up from about $30 billion now.

"The cloud is the entire future of this field," Craig Venter, who led a private effort to sequence the human genome in the 1990s, said in an interview. His new company, San Diego-based Human Longevity Inc, recently tried to import genomic data from servers at the J. Craig Venter Institute in Rockville, Maryland.

The transmission was so slow, scientists had to resort to sending disks and thumb drives by FedEx and human messengers, or "sneakernet," he said. The company now uses Amazon Web Services.

So does a collaboration between Regeneron Pharmaceuticals Inc. and Pennsylvania-based Geisinger Health Systems to sequence 250,000 genomes. Raw DNA data is uploaded to Amazon's cloud, where software from privately-held DNAnexus assembles the millions of chunks into the full, 3-billion-letter long genome.

DNAnexus's algorithms then determine where an individual genome differs from the "reference" human genome, the company’s chief scientist Dr. David Shaywitz said, in hopes of identifying new drug targets.

HOSTING FOR FREE

Showing how important Google and Amazon view this business, and how they hope to use existing customers to lure future ones, each is hosting well-known genomics datasets for free.

Neither company discloses the amount of genomics data it holds, but based on interviews with analysts and genomic scientists, as well as the companies' own announcements of what customers they’ve won, Amazon Web Services may be bigger.

 Data from the "1000 Genomes Project," an international public-private effort that identified genetic variations found in at least 1 percent of humans, reside at both Amazon and Google "without charge," said Kathy Cravedi of the U.S. National Institutes of Health (NIH), one of the project's sponsors.


Other paying clients with a more specific focus are picking sides.

Google, for instance, won a project from the Autism Speaks foundation to collect and analyze the genomes of 10,000 affected children and their parents for clues to the genetic basis of autism.

Another customer is Tute Genomics, whose database of 8.5 billion human DNA variants can be searched for how frequently any given variant appears, what traits it's associated with and how people with a certain variant respond to particular drugs.

Amazon is hosting the Multiple Myeloma Foundation’s project to collect complete-genome sequences and other data from 1,000 patients to identify new drug targets. It also won the Alzheimer's Disease Sequencing Project, which has similar aims.

Amazon charges about $4 to $5 a month to store one full human genome, and Google about $3 to $5 a month. The companies also charge for data transfers or computing time, as when scientists run analytical software on stored data.

Amazon's database-analysis tool, Redshift, costs 25 cents an hour or $1,000 per terabyte per year, the company said. A terabyte is 1 trillion bytes, or 1,000 gigabytes, about enough to hold 300 hours of high-quality video.

GENETIC GOLD

Another part of the cloud services' pitch to would-be customers is that their analytic tools can fish out genetic gold - a drug target, say, or a DNA variant that strongly predicts disease risk - from a sea of data. Any discoveries made through such searches belong to the owners of the data.

"On the local university server it might take months to run a computationally-intense" analysis, said Alzheimer’s project leader Dr. Gerard Schellenberg of the University of Pennsylvania. "On Amazon, it's, 'how fast do you need it done?', and they do it."

Another selling point is security. Universities are "generally pretty porous," said Ryan Permeh, chief scientist at cybersecurity company Cylance Inc., of Irvine, California, and the security of federal government computers is "not at the top of the class."

While academic and pharmaceutical research projects are the biggest customers for genomics cloud services, they will be overtaken by clinical applications in the next 10 years, said Google Genomics director of engineering David Glazer.


Individual doctors will regularly access a cloud service to understand how a patient's genetic profile affects his risk of various diseases or his likely response to medication.

"We are at that transition point now," Glazer said.

Matt Wood, general manager for Data Science at Amazon Web Services, sees cloud demand in genomics now as "a perfect storm," as the amount of data being created, the need for collaboration and the move of genomics into clinical care accelerate.

Experts on DNA and data say without access to the cloud, modern genomics would grind to a halt.

Bioinformatics expert Dr. Atul Butte of the University of California, San Francisco, said that now, when researchers at different universities are jointly working on NIH and other genomic data, they don't have to figure out how to make their computers talk to each other. In March, NIH cleared the way for major research on the cloud when it began allowing scientists to upload important genomic data.

"My response was, it's about time," Butte said.
 
 Reuters

 


          Weighing The Promises Of Big Genomics   

 

“Success in sight: The eyes have it!” Thus the scientific journal Gene Therapy greeted the news, in 2008, that an experimental treatment was restoring vision to 12 people born with a congenital disorder that slowly left them blind. Healthy genes were injected to replace the faulty mutations in the patients’ retinas, allowing an 8-year-old to ride a bike for the first time. A mother finally saw her child play softball. Every patient, the researchers reported, showed “sustained improvement.” Five years in, a book declared this “breakthrough” — a good-gene-for-bad-gene swap long pursued as a silver bullet for genetic conditions — as The Forever Fix.

Earlier this month, two of the three research teams running these trials quietly reported that the therapy’s benefit had peaked after three years and then begun to fade. The third trial says its patients continue to improve. But in the other two, all the patients tracked for five years or more were again losing their sight.

Not all gene therapy ends in Greek-caliber tragedy. But these trials serve as a sadly apt parable for the current state of human genetics. This goes especially for the big-data branch of human genetics called Big Genomics. In five years of talking to geneticists, biologists, and historians, I’ve found that the field is too often distinguished by the arc shown here: alluring hope, celebratory hype, dark disappointment.

We live in an age of hype. But the overselling of the Age of Genomics — the hype about the hope, the silence about the disappointments — gobbles up funding that we might spend better elsewhere, warps the expectations of patients and the incentives of scientists, and has implications even for people who pay genetics scant attention. Many hospitals, for instance, are now collecting genetic information from patients that they may market to “research partners” such as drug companies. Some take more care than others do to secure informed consent. (Had blood drawn lately? Read everything you signed that day?) It’s not just that they’re selling you this stuff. They may well be selling you. And the sale depends on an exaggerated picture of genetic power and destiny.

To be sure, medical genetics has chalked up some sweet victories. Our growing ability to spot rare mutations, for instance, is helping doctors diagnose and sometimes treat nasty rare diseases. Last fall, for instance, doctors in St. Louis sequenced an infant dying of liver failure, saw that he had inherited a rare mutation that both his parents happened to pass to him, devised a way to counter the mutation’s disruption of his immune system, and saved his life.

But when it comes to how genes shape the traits and diseases that matter most to us — from intelligence and temperament to cancer and depression — genetic research overpromises and underdelivers on actionable knowledge. After 110 years of genetics, and 15 years after the $3.8 billion Human Genome Project promised fast cures, after more billions spent and endless hype about results just around the corner, we have few cures. And we basically know diddly-squat.

I know — diddly-squat is rough talk. Yet this is hardly a radical claim. Geneticists and doctors outside of Big Genomics — people studying genetics in songbirds, sea urchins, monkeys, microbes, fruit flies, and roundworms, for instance — often voice it privately. Others are eager to tell us what genes can’t do or warn that “precision medicine” will let us down. One of the world’s most respected geneticists, Britain’s Steve Jones, gives quite an entertaining lecture on our humble state of knowledge.“The more we learn, the less we understand,” he says. “We know almost nothing of genetics.”

The press, of course, too often falls hard for ludicrous memes such as “the slut gene.” But much of the time, the media is simply amplifying the signal sent by Big Genomics. Big Genomics outfits like the National Institutes of Health and the Broad Institute regularly assure us that their careful reading of the genome’s text will find crucial misspellings that generate disease — and let us revise, delete, or write around those errors.

In doing so, they continue a tradition as old as genetics itself. Historian Nathaniel Comfort, in The Science of Human Perfection, calls the history of genetics “a history of promises.” Cambridge geneticist William Bateson coined the term genetics in 1905; by 1927, biologists made the first of many assertions that genetics would cure cancer. In 1940, Canadian physician and embryologist Madge Macklin promised “a world in which doctors come to their patients and tell them what diseases they are about to have, and then begin treatments before the patient feels even the first symptoms.” In 1967, Stanford geneticist Joshua Lederberg predicted gene replacement therapy — the kind that is now failing in the blindness trial — “within a few years.”

In 2000 the leaders of the Human Genome Project doubled down. Standing next to President Bill Clinton, they announced that the project had sequenced the human genome, exposing the full genetic code to view. “Personalized genetic medicine,” an accompanying White House Statement said, would soon “cure diseases like Alzheimer’s, Parkinson’s, diabetes and cancer by attacking their genetic roots.” Francis Collins, the project’s director (now head of the National Institutes of Health), said the genomic revolution could reduce cancer to zero and would make gene-tailored personalized medicine common by 2010.

A century of hype is a lot, but this is particularly inspirational ground. The gene, especially after Franklin, Watson, and Crick gave us a peek at DNA in 1953, looked promising as hell. For decades, the gene was seen as the key to all of biology — or as President Clinton would eventually put it, “the language in which God created life.” In its code we would read the story of life, evolution, disease, and death.

But when the Genome Project finally revealed the links in Franklin, Watson, and Crick’s deceptively simple structure, it found few of the strong gene-to-trait connections one might have hoped for. Instead, it found a mess. Our DNA held far fewer genes than expected, almost 20,000, which was confusing. Few held obvious function. Some seemed to do nothing. Some seemed to work fine one day but not the next, or to do one thing in one situation and another in another. And these genes were surrounded by vast stretches of DNA material that aren’t really genes, and which some geneticists called junk, starting a big fight.

To clarify this mess — to figure out what did what, and to identify medically relevant genes — researchers started using sequencing machines to scan the genomes of tens or even hundreds of thousands of people for gene variants that appear more often in people with some condition, disease, or trait. These overrepresented genes are then presumed to contribute to the condition or trait in question.

Unfortunately, GWAs seldom revealed the sort of the neat or consistent gene-to-trait relationships that allow decisive treatment. Instead, they usually found “many genes of small effect”: handfuls and sometimes hundreds of gene variants carried by most (but not all) people with the condition in question, whose effects were seldom clear, and whose presence in a given person did little to predict risk.

“Many genes of small effect” became a sort of tepid curse. I myself prefer the stronger, more memorable phrase “Many Assorted Genes of Tiny Significance,” or MAGOTS — a mass of barely significant genes explaining little.

MAGOTS infest most GWA studies for a simple, brutal reason: If a gene variant reliably plays a large role in causing disease, both the variant and the disease it causes tend to be rare, because its carriers tend to die without leaving offspring. This is why the genetic contributions for common diseases and conditions usually come from MAGOTS — the effects of which, it bears repeating, are usually maddeningly obscure and unpredictable. This applies even to diseases and traits that run in families. Take height: Hundreds of genes of small effect, few clues to how they contribute, and no real target to tweak if, say, you want to make someone tall. The best way to engineer a tall person? Tell two tall people to tango.

Similarly, deep digs at cancer, schizophrenia, heart disease, hypertension, diabetes, intelligence, bipolar disorder, and height have found mostly MAGOTS. The biggest schizophrenia study so far, for instance, published last July to great fanfare, found 128 gene variants that appeared to account for perhaps 7% of a given person’s actual risk.

The genomic age’s signature finding is not any great discovery. It is the yawning gap between the genetic contributions that geneticists assume exist and the genetic contributions they can spot. It is as if they cracked a safe they knew was packed with cash and found almost nothing. The money’s got to be somewhere. But where?

Researchers in the field are quick to point to one of the handful of effective drugs to come from genomic insight, such as Gleevec, a leukemia drug developed in 2001. But Gleevec, however potent, falls far short of the medical miracles forecast 15 years ago. As science writer Ed Yong pointed out in a recent Twitter conversation about this, “Treasure was promised. Gleevec’s a coin.”

At this point, the problem is not so much that genetics fell short of its early promises. The problem is that big genomics players keep making similar promises.

Take, for instance, that schizophrenia study rife with MAGOTS. When the study came out last July, John Williams, head of neuroscience and mental health at the Wellcome Trust, Britain’s biggest biomedical funder, saw it as cause for humility. “What this research screams to me,” he wrote, “is how little we know about schizophrenia, and how far we are from biological tests and treatments for mental health disorders compared to other major diseases.”

Yet last July, the Broad Institute, a genomics powerhouse that played a big role in that schizophrenia study, triumphantly unveiled it as part of an announcement that a donor had given Broad $650 million to expand research at its Stanley Center for Psychiatric Genomics. Broad’s director called the study part of “a revolution in psychiatric disease.” Francis Collins, apparently deaf to how closely his promises echoed those he’d made 15 years before, when the Human Genome Project was unveiled, said psychiatric genomics now stood “poised for rapid advances.” The promises were a decade old, the rhetoric a century. The only things new were the event’s over-the-top staging and production — it views like an awards ceremony — and how boldly, even after 15 years of the “genomic age” with little to show, the Broad conjured big money from thin results.

Big Genomics is converting hype to cash at unsettling speed. After the FDA told consumer genomics company 23andMe it could no longer sell people health data, the company began selling that data to drug and biotech companies. An entire industry, potentially fed by almost anyone who draws blood, spit, or biopsies from you, is emerging to do likewise. Its growth, along with the increasingly routine collection of genetic data by hospitals, will feed the genomics bubble while putting private genetic and health information at increased risk.

Meanwhile, it’s becoming routine for researchers and research centers to leverage genomic findings into industry jobs or startups. This happened, for instance, with the research team that ran one of the sight restoration gene therapy trials whose effects faded after three years.

At the peak of the trials’ promise and publicity, the Children’s Hospital of Philadelphia (CHOP), which ran one of the studies, provided seed money and office space to Spark Therapeutics, a new startup that aims to develop genetic therapies. Spark’s ticker symbol, $ONCE, reportedly referred to the company’s intention to make treatments that would correct genetic faults with a single application.

Bolstered by a partnership with pharma giant Pfizer, Spark went public this January. It promptly became the first quarter’s hottest IPO, returning 256% on first-day investments and reaching a value over $1.5 billion by March. The vision trial had gotten great press — and its president, co-founder, and chief scientific officer, Katherine High, was one of the scientists leading the CHOP trial. High’s integrity may be bombproof. But this sort of bench-to-boardroom practice hardly encourages the critical interrogation of one’s own work that good science depends on.

None of this is to say we should pull the plug on Big Genomics. Some suggest — and I agree — that we’d do well to take some of the billions spent chasing genes for conditions like Type II diabetes, heart disease, or stroke and spend it instead on finding ways to change risk-elevating behaviors like smoking, overeating, overdrinking, and avoiding exercise.

It would be responsible, however, for researchers to temper their hype — though this seems unlikely, because hype pays.

So let me offer a hype filter. This one comes courtesy of the oceanographer Henry Bryant Bigelow, who helped found Woods Hole Oceanographic Institute. A century ago, Bigelow opened a letter his brother had written him from Cuba. His brother reported that while weathering a hurricane there, he had seen, flying by, what he was almost sure was a donkey.

With three words, Bigelow gently told his brother he didn’t quite believe him — and stated a maxim for maintaining the ever-curious but ever-skeptical stance that marks the good scientist.

“Interesting if true,” he wrote.

David Dobbs, Buzzfeed

 


          Jennifer S. Singh, Multiple Autisms: Spectrums of Advocacy and Genomic Science    
<span class="paragraphSection">SinghJennifer S., <span style="font-style:italic;">Multiple Autisms: Spectrums of Advocacy and Genomic Science</span>, Minneapolis: University of Minnesota Press, 2016, Pp. 296. $27. ISBN 978 0 8166 9831 8.</span>
          Sarah S. Richardson and Hallam Stevens (eds), Postgenomics: Perspectives on Biology after the Genome    
<span class="paragraphSection">RichardsonSarah S. and StevensHallam (eds), <span style="font-style:italic;">Postgenomics: Perspectives on Biology after the Genome</span>, Durham, Duke University Press, 2015. Pp. 304. £18.99. ISBN 978 0 8223 5922 7.</span>
          Bioinformatics Specialist-Metagenomics/Proteomics - Signature Science, LLC - Austin, TX   
Travel to project and business development meetings as needed. Familiarity with machine learning, Git, and agile software development is a plus;... $90,000 a year
From Signature Science, LLC - Tue, 06 Jun 2017 09:05:50 GMT - View all Austin, TX jobs
          New strong QTL for SRS resistance in salmon coho will contribute to decrease the use of antibiotics   
Thursday, June 29, 2017, 07:00 (GMT + 9) Puerto Varas - A collaboration between researchers in Chile and Norway, directed by the AquaGen company Blue Genomics Chile, has resulted in a breakthrough in breeding for SRS resistance in coho salmon. The discovery of a major QTL for SRS resistance has....
          Professional Python & Linux Administration Bundle for $49   
Discover the Many Uses of Python & Strive Towards a Successful IT System Administration Career with 60 Hours of Training
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The Ultimate Python Programming: From Beginner to Expert


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Python is widely considered one of the best first languages to learn for aspiring programmers because of its relative simplicity and usefulness. Python is commonly used in web, game, and software development, and is also the most used language for creating system security programs. Its applications are virtually endless. If you have an interest in coding, this massive course will be the one to get you hooked!
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An initiative by IIT IIM Graduates, eduCBA is a leading global provider of skill based education addressing the needs 500,000+ members across 40+ Countries. Our unique step-by-step, online learning model along with amazing 1700+ courses prepared by top notch professionals from the Industry help participants achieve their goals successfully. All our training programs are Job oriented skill based programs demanded by the Industry. At eduCBA, it is a matter of pride to us to make job oriented hands on courses available to anyone, any time and anywhere. Therefore we ensure that you can enroll 24 hours a day, seven days a week, 365 days a year. Learn at a time and place, and pace that is of your choice. Plan your study to suit your convenience and schedule. For more details on this course and instructor, click here.

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THE EXPERT

An initiative by IIT IIM Graduates, eduCBA is a leading global provider of skill based education addressing the needs 500,000+ members across 40+ Countries. Our unique step-by-step, online learning model along with amazing 1700+ courses prepared by top notch professionals from the Industry help participants achieve their goals successfully. All our training programs are Job oriented skill based programs demanded by the Industry. At eduCBA, it is a matter of pride to us to make job oriented hands on courses available to anyone, any time and anywhere. Therefore we ensure that you can enroll 24 hours a day, seven days a week, 365 days a year. Learn at a time and place, and pace that is of your choice. Plan your study to suit your convenience and schedule. For more details on this course and instructor, click here.

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Python is an extremely efficient language that can accomplish complicated tasks with minimal amounts of code. This makes it particularly well suited to system administration and performing security testing tasks. In this course you'll learn how to administer a Linux system with Python, giving you valuable background in the lucrative and growing system administration industry.
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THE EXPERT

An initiative by IIT IIM Graduates, eduCBA is a leading global provider of skill based education addressing the needs 500,000+ members across 40+ Countries. Our unique step-by-step, online learning model along with amazing 1700+ courses prepared by top notch professionals from the Industry help participants achieve their goals successfully. All our training programs are Job oriented skill based programs demanded by the Industry. At eduCBA, it is a matter of pride to us to make job oriented hands on courses available to anyone, any time and anywhere. Therefore we ensure that you can enroll 24 hours a day, seven days a week, 365 days a year. Learn at a time and place, and pace that is of your choice. Plan your study to suit your convenience and schedule. For more details on this course and instructor, click here.

Python with Django: Build Web Projects using Django & Python


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Django is an open-source web software written in Python that enables faster creation and deployment of web applications. This extensive course will give you a full immersion in all things Django so you can build projects and websites quickly and productively. Efficiency is a top priority in the programming market and that's exactly what you'll gain through this course.
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THE EXPERT

An initiative by IIT IIM Graduates, eduCBA is a leading global provider of skill based education addressing the needs 500,000+ members across 40+ Countries. Our unique step-by-step, online learning model along with amazing 1700+ courses prepared by top notch professionals from the Industry help participants achieve their goals successfully. All our training programs are Job oriented skill based programs demanded by the Industry. At eduCBA, it is a matter of pride to us to make job oriented hands on courses available to anyone, any time and anywhere. Therefore we ensure that you can enroll 24 hours a day, seven days a week, 365 days a year. Learn at a time and place, and pace that is of your choice. Plan your study to suit your convenience and schedule. For more details on this course and instructor, click here.

          New Website Explores National Effort to Better Understand Marine Life, Ecosystem Change   

U.S. MBON researchers prepare to deploy a beam trawl to collect ocean life samples. Image courtesy of Katrin Iken, AMBON principal investigator, University of Alaska Fairbanks

The U.S. Marine Biodiversity Observing Network (U.S. MBON), an effort to improve our understanding of changes and connections between marine biodiversity and ecosystems, recently launched a new website. In addition to exploring the vision and themes of the network's demonstration projects, the site offers profiles of projects in progress and outlines future goals for data integration, animated seascape mapping, and technology applications such as new methods for genomic sampling and analysis.

Continue reading →


          Next-generation metagenomics sequencing may sleuth out hard-to-find viruses in the blood   
1. Next-generation metagenomics detected Human Hepegivirus-1 (HhpgV-1) in a cohort of patients who inject drugs. 2. The clinical significance of detecting HHpgB-1 infection is currently unclear. Evidence Rating Level: 2 (Good) Study Rundown: Next-generation metagenomic sequencing (NGMS) is a technique that involves the sequencing of all the DNA or RNA in a tissue, following by interpretation […]
          The Emerging Field of Human Social Genomics   
Although we generally experience our bodies as being biologically stable across time and situations, an emerging field of research is demonstrating that external social conditions, especially our subjective perceptions of those conditions, can influence our most basic internal biological processes—namely, … Continue reading
          Inside the Human Genome: Darwin or Intelligent Design?   

Tuesday, October 21, 2014 - 7:00pm to 10:00pm

Location:
Whitsett Room, Sierra Hall 451, 4th Floor
Cost:
Free

Seating is limited. Reservations are requested. For more information and reservations, call 818.677.3330.

The CSU Northridge College of Social and Behavioral Sciences Presents a Richard W. Smith Lecture in Cultural Studies: "Inside the Human Genome: Darwin or Intelligent Design?"

Please join us as acclaimed evolutionary geneticist Dr. John C. Avise addresses the philosophical question of “why” with regards to the myriad of imperfections that exist in our biological world.

Approaching the subject from a biochemistry and molecular genetics perspective, Dr. Avise points out the scientific evidence for genomic flaws, providing a compelling argument to counter the notion of intelligent design.

Reception and book signing immediately following.

If you would like to learn more about the Richard W. Smith Lecture in Cultural Studies Series or about Dr. Avise please download the event brochure. (.pdf)

Communication services (sign language interpreters, note takers, real-time captionists, or assistive listening devices) are available for this event. Requests for services must be submitted at least five (5) working days in advance.

Parking is $6 per car at the Information Booth at Prairie Street and Darby Avenue.


          Orion Integrated Biosciences To Present At CHI’s Targeting the Microbiome/ Discovery on Target Conference   
On September 21-23 2015 Orion Integrated Biosciences will be presenting several research projects in the CHI’s conference Targeting the Microbiome. During this event Orion Integrated Biosciences will show the performance assessment of RIGEL-MTP (Molecular Taxonomic Profiling) using metegenomic samples of Ebola-infected patients and the assessment of the microbiome to determine survival to infection.
          Biosurveillance enterprise for operational awareness, a genomic-based approach for tracking pathogen virulence   
Willy A Valdivia-GrandaVirulence. 2013 November 15; 4(8): 745–751. Published online 2013 October 23. doi: 10.4161/viru.26893PMCID: PMC3925708 Article PubReader
          Biodefense Oriented Genomic-Based Pathogen Classification Systems: Challenges and Opportunities   
Willy A Valdivia-GrandaJ Bioterror Biodef. Author manuscript; available in PMC 2015 January 11.Published in final edited form as: J Bioterror Biodef. 2012 March 16; 3(1): 1000113. Published online 2012 March 16. doi: 10.4172/2157-2526.1000113PMCID: PMC4289626 Article PubReader
          Transcriptome sequencing and development of an expression microarray platform for the domestic ferret   
Carl E Bruder, Suxia Yao, Francis Larson, Jeremy V Camp, Ronald Tapp, Alexis McBrayer, Nicholas Powers, Willy Valdivia Granda, Colleen B JonssonBMC Genomics. 2010; 11: 251. Published online 2010 April 19. doi: 10.1186/1471-2164-11-251PMCID: PMC2873475 Article PubReader
          Horizontes cada vez más lejanos   
El anunciado recorte de 600 millones de euros para el I+D español ha sembrado el pesimismo entre buena parte de una comunidad científica que ve como las aportaciones públicas van reduciéndose de año en año. Proyectos, contrataciones y competitividad internacional empiezan a resentirse, pero lo que más preocupa son el futuro y el modelo. XAVIER PUJOL GEBELLÍ
          Temporary Research Associate - Synthetic Genomics   
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          Temporary Research Associate/Senior Research Associate - Synthetic Genomics   
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          Temporary LIMS Analyst, R&D Analytics - Synthetic Genomics   
La Jolla, CA - 17-0046 Temporary LIMS Analyst, R&D Analytics
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La Jolla, CA, USA
At Synthetic Genomics, Inc., we are dedicated to developing and commercializing genomic-driven solutions to address global
          Temporary Research Associate, Vaccines - Synthetic Genomics   
La Jolla, CA - 17-0017 Temporary Research Associate, Vaccines
Research and Development RESEA01398
Apply now

Full-time
La Jolla, CA, USA
Synthetic Genomics Vaccines Inc, (SGVI) is seeking a Research Associate I/II to work with the SGVI R&D team. The candidate will support the overall
          Sr Program Manager/Associate Director, R&D - Synthetic Genomics   
La Jolla, CA -

17-0043 Sr Program Manager/Associate Director, R&D
Research and Development 1700401434
Apply now

Posted: 9 June 2017
Full-time
La Jolla, CA, USA
SGI is seeking a Senior Program Manager/Associate Director, Program Management and Research Administration to work with the
          Proteogenomics - From Genome Annotation to Signaling Pathways   
Proteogenomics - From Genome Annotation to Signaling Pathways
Presented by: Akhilesh Pandey, M.D.,Ph.D., Johns Hopkins University
Category: Proteomics
Aired date: 11/04/2010
          Post-doctoral Fellow - Functional & Chemical Genomics - Oklahoma Medical Research Foundation - Oklahoma City, OK   
A postdoctoral fellow position is available immediately in the laboratory of Dr. Functional &amp; Chemical Genomics - Yoon....
From Indeed - Tue, 27 Jun 2017 19:39:34 GMT - View all Oklahoma City, OK jobs
          Bioinformatics Analyst - UES - Dayton, OH   
With 1-2 years&quot; postdoctoral experience in bioinformatics with a background in genomics, genetics, molecular biology, and biological pathways....
From UES - Thu, 25 May 2017 22:30:29 GMT - View all Dayton, OH jobs
          Research Scientist (Environmental Genomics and Systems Biology) - Lawrence Berkeley National Laboratory - Berkeley, CA   
Mentor graduate students and postdoctoral fellows, by devising projects based on original analysis, maximizing their skills and abilities addressing these...
From Lawrence Berkeley National Laboratory - Thu, 20 Apr 2017 02:51:08 GMT - View all Berkeley, CA jobs
          Graduate Programs   

Over the past 15 years, the IPHG faculty has established a vital and highly regarded graduate training program that remains the only one of its kind. We offer four unique interdisciplinary graduate degrees: Ph.D. and MPH in Public Health Genetics (PHG), an MS in Genetic Epidemiology, and a concurrent JD/MPH in PHG. Students enrolled in other UW graduate programs can earn a Graduate Certificate in PHG. Each of these programs has served as the standard in integrating scientific advancements with a broader interdisciplinary dialogue.

All IPHG degree programs emphasize an interdisciplinary approach to using genomic advances to improve population health. Graduates of the program will have a unique set of skills that qualifies them for a range of career options, including employment in academia, government, industry, and not-for-profit organizations. To find out more or apply to our programs please browse our website or contact us for more information phginfo@uw.edu.


          Public Health Genetics   

Over the past decade, dramatic advances in genomics have paved the way for a fuller understanding of the impact of genetic and environmental factors on human and population health. Such capabilities must however, be put into scientific, ethical, cultural, legal and policy context in order to realize the goal of improving population health. Through its research and training programs the Institute for Public Health Genetics (IPHG) provides the context for these discoveries and also equips graduates to tackle the complex ethical, legal, policy and social issues that are required to fully realize the benefits of these advances on population health. Our faculty and graduates are working locally, nationally and globally to ensure that health benefits from genomic knowledge are maximized and harms are minimized.


          Postdoctoral Position in Theoretical Neuroscience   
Postdoctoral Position in Theoretical Neuroscience at CNCR, Amsterdam Applications are invited for a 3-year postdoctoral research position in the Neuroinformatics Group of the Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam. The position is funded by a grant from the Netherlands Organisation for Scientific Research (NWO), Exact Sciences (EW). The project, which is [...]
          Bioinformatician   
Job Description   Open Targets is a recently established public-private initiative between the EBI, GlaxoSmithKline, Biogen and the Sanger Institute to combine large-scale genomic experiments with objective statistical and computational techniques to identify and validate the causal links between targets, pathways and diseases.  We are looking for an experienced Bioinformatician to be involved in large-scale biological data analysis and integration for target identification and prioritisatio...
          Searchlight Scientific Announces Plans to Target Additional Industries Such as the Aerospace, Pharmaceutical and Genomics With Its HPC2(TM)("High Performance Cloud Computing") Service   

ATLANTA, GA--(Marketwire - Jun 9, 2011) - Searchlight Scientific, a wholly owned subsidiary of Searchlight Solutions Ltd. (PINKSHEETS: SLLN), a technology venture holding company, today announces plans to target additional industries with its High Performance Cloud Computing HPC2TService. The Company's initial focus will be on serving the fire simulation, video rendering, bio-tech, military and university research. The Company believes high performance computing ("HPC") is very applicable to the computing needs for many industries. The sales plan will be extended in phases to target additional industries such as Aerospace, Pharmaceutical and Financial. More industries and business segments are planned to be added as the Company's business matures.

          Revealing cell fate decisions with organism-scale single-cell genomics   
Revealing cell fate decisions with organism-scale single-cell genomics
Presented by: Cole Trapnell, Ph.D., Department of Genome Sciences, University of Washington
Category: NIH Only
Aired date: 05/25/2017
          Comment on Do We Need More Money for Cancer Research? You Bet We Do! by Dr. Michael Wosnick   
Jim, Thank you so much. I should just commission you to write my posts for me :) You may be surprised, but I don't find your answer dismaying at all. I think we agree on far more than we disagree. In fact, I'm having a hard time seeing where we even *do* disagree :) Nowhere in my thinking (I hope not implied above either) was I assuming that the "more money" would just be same old, same old. I agree we have to spend more smartly, we have to be more accountable etc. In other words, all the stuff you said. But even then I still maintain there are not enough dollars to fuel the amount of creative, innovative and risk-taking (and therefore much more highly prone to fail) research, especially now in the genomics era. I would dearly love to see a LOT more highly qualified researchers get far more adequately funded than we seem to be able to do now. Unless of course you are implying that we have a dearth of younger i.e. not as well established researchers to spend the money wisely. I know you don't believe that. We both know way too many of them! Now as for your point on the "fund-raising machinery" I think we have to be very careful not to confuse the raising of funds with the investment of funds. I agree that there are many foundations and charities that are now into raising money it seems just to raise money. Let's look at some of the larger hospital foundations (not necessarily yours) and we see for example in PMHF one of the most successful fundraising operations in Canada. But how much of that money actually goes into the direct costs of research? I don't think it is fair to imply that if they spent more of the stockpile money on research that somehow it would not be well spent. On the contrary I think they need to put a lot MORE of the money they raise into a legitimate peer-reviewed system to more adequately fund real research. And at the risk of biting the hand that used to feed me (well, still does) I think that even cancer charities like the Canadian Cancer Society need to really assess where their priorities are. I stand by the CCS in knowing that the money is not wasted in the slightest, but I do not necessary agree with the priority of the allocation. I think that more of the pie should go to research and always have said that. So, I think you and I are pretty much on the same page. I am all for competition, I am a die hard when it comes to peer review, I want to see a broader funding base and not just "those that hath" as you put it. But I want to see "success" rates at a much more reasonable level than we are choosing to afford right now. Notice I said "choosing to afford" as opposed to "able to afford". As you know when I started at the NCIC in the early 90's, peer review was able to distinguish excellent applications from good applications, and we funded all the excellent ones. Today the discriminator is not on excellence or quality; it is strictly on dollars available. We draw our cut lines in any established competition where the money runs out, not where the science does. We make our distinctions now between excellent research and OTHER excellent research. I always believed, and still do, that the grants that get funded in our increasingly difficult competitions all deserve to be funded. These are not wasted dollars. But I cannot and do not believe the reverse, namely that all those that are not funded didn't also deserve, even equally deserve, or even better deserve to be funded. I just wish that were not so.
          Device Week Podcast - Episode 57   
On this week's podcast, we discuss the Verily-GSK joint venture in bioelectronics medicine, the US FDA patient-preference initiative, regulatory guidance for wellness devices and big milestone for Foundation Medicine toward FDA approval and expanded Medicare coverage of a novel genomic profiling platform.
          Podcast: FDA's Tezak Outlines Issues For Upcoming Genomic Workshops   
FDA's Zivana Tezak says she is pleasantly surprised at the high level of complexity that stakeholders brought to a recent meeting on using curated databases to support next generation sequencing (NGS). She says the conversations are a jumping point for the agency as it plans to hold back-to-back workshops on genomic testing in November.
          Genomics Day showcases NIEHS resources   

The showcase of in-house resources for the vital study of genomes and epigenomes was anchored by a keynote presentation from Paul Wade. (read more)
          Andrei Macsin added a discussion to the group Analytic, Data Science and Big Data Jobs   
Andrei Macsin added a discussion to the group Analytic, Data Science and Big Data Jobs
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Career Alert, June 23

Job SpotlightSoftware Developer - One Acre FundGenomic Systems Engineer - Kaiser PermanenteData Scientist - Consumer Insights - Fossil GroupSenior Director for Institutional Analytics - Rollins CollegeFeatured JobsKenya Product Innovations Analyst - One Acre FundSenior Data Scientist - Spreemo HealthEngineer, Data Science, Audience Studio - NBCUniversal MediaDeep Learning Content Creator - NVIDIAAnalytics and Insights Specialist - Ramsey Solutions, A Dave Ramsey CompanyDirector, Marketing Analytics & Strategy - The Ad CouncilData Science Manager, Analytics - FacebookResearch Scientist - SpotifyData Scientist – Analytics - Booking .comData Scientist, Risk Analytics - John DeereData Scientist - Reynolds Consumer ProductsProgram Manager, Data Analysis & Reporting - MasterCardDecision Science Analyst II - USAAData Scientist - TapjoyResearch Scientist, Sr - YahooHealthcare Data Scientist - PhilipsSenior Data Scientist - Warner Bros. EntertainmentData Scientist - ShareThisProduction Cytometry Lead, Verily Life Sciences - GoogleData Science Manager, Analytics - TumblrData scientist, Business Strategy - StarbucksCheck out the most recent jobs on AnalyticTalent.comFeatured BlogSix Great Articles About Quantum Computing and HPC This resource is part of a series on specific topics related to data science: regression, clustering, neural networks, deep learning, Hadoop, decision trees, ensembles, correlation, outliers, regression, Python, R, Tensorflow, SVM, data reduction, feature selection, experimental design, time series, cross-validation, model fitting, dataviz, AI and many more. Read full article.Upcoming DSC Webinars and ResourcesA Language for Visual Analytics - DSC Webinar, July 25Self-Service Machine Learning - DSC Webinar, July 18Maximize value of your IoT Data - DSC Webinar, June 29SPSS Statistics to Predict Customer Behavior - DSC Webinar, June 27The Data Incubator Presents: Data Science FoundationsDatabricks & The Data Incubator: Apache Spark Programming for DSArtificial Intelligence Blockchain Bootcamp with Job placement NYCGuarantee yourself a data science career - SpringboardData Science Boot Camp: Pharma and Healthcare - RxDataSciencePython Data Science Training - AccelebrateOnline Executive PGP in Data Science, Business Analytics & Big DataSee More

          EACR Cancer Genomics Day 2   
Churchill College, Cambridge:  Yesterday, the main focus at the EACR Cancer Genomics conference was on immunology-related topics as they pertain…
          Life Update and Research Update   



Life Update
A little over a month ago I made a very "grown up" decision. I stood up for myself, my future, and my happiness. I learned how hard those decisions can be.

To put it nicely, I severed an engagement and ended a relationship with the person I had become comfortable with the idea of accompanying for the rest of my life. I did this because of a long series of events that have spanned our entire relationship.

I would like to say to masqueradestar, bubblingbeebles, jboing, knightofstarz (and more) that I should have listened to you almost a year ago. I should have listened to you when you said not to forgive an ultimate betrayal of trust. What's done has been done, and I have learned so much about myself and my boundaries of tolerance.

On the bright side, I got to have one of those scenes in your life you don't think actually happen because they seem too much like cinema. I threw the temporary ring into the Ohio river, where if it is found by someone in all of its silver and glass glory, they can have the joy of saying "I HAVE THE RING" and I will never know about it, happily.





Research Update
Due to a series of unfortunate events, my thesis proposal has been post poned until the beginning of fall semester. These unfortunate events mainly surround the fact that my committee and PI were both extremely difficult when it came to scheduling an exact time. This is okay - I am allowed to begin data collection and proceed with my first aim during the summer.

After the completion of my metagenomic analysis research in Dr. Edenborn's lab, we discussed the current microbial research in her lab, what has currently been completed/discovered, and I was given a long list of topics for reading of current literature.

I will be conducting a geostatistical/geospatial analysis of microbial selection of propolis on three probiotic firmicute genera in their relation to honey bee disease/CCD events across the contiguous United States in order to determine variations due to flora, climate, age of hive, and the type of agriculture related to the hives in order to access the risk of pesticide use. This is fun data because I get to play the fun games that consist of "mwahahahahaha I will be applying graph theory!", "I have this pickaxe and I will mine the shit out of your data!" and "It's [not] growing!".

Aim 1 (ish) involves the collection of a minimum of 10 propolis samples from each northern and southern USDA region for the contiguous United States from stationary commercial apiaries (this is a total of 60-80 samples as a minimum). I will also be collecting voluntary survey data from these apiaries on the hives of origin. This aim will be started this summer, and continued through the fall. These surveys upon return will be analyzed and compiled with data mined from USDA and EPA databases. The propolis samples returned will be profiled and tested to determine the zone of inhibition on each firmicute when supplied at "equal" concentrations (crude extractions always get tricky). At this point, a few basic statistical tests will be used in order to filter variables. (Aim 1 was originally split into 2)

Aim 2 is the fun part where I get to use topology. This will mostly involve examining relationships between variables determined to possibly have influence on clustering and more. Both luckily and sadly I will be primarily using software already in existence for the majority of the analysis.

Sorry to be rushed - have spent too much time on this post.

Best to everyone and have an amazing summer!




           A low frequency persistent reservoir of a genomic island in a pathogen population ensures island survival and improves pathogen fitness in a susceptible host    
Neale, H. C., Laister, R., Payne, J., Preston, G., Jackson, R. W. and Arnold, D. L. (2016) A low frequency persistent reservoir of a genomic island in a pathogen population ensures island survival and improves pathogen fitness in a susceptible host. Environmental Microbiology, 18 (11). pp. 4144-4152. ISSN 1462-2912 doi: 10.1111/1462-2920.13482
           The stealth episome: suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola    
Godfrey, S. A. C., Lovell, H. C., Mansfield, J. W., Corry, D. S., Jackson, R. W. and Arnold, D. L. (2011) The stealth episome: suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola. PLoS Pathogens, 7 (3). e1002010. ISSN 1553-7374 doi: 10.1371/journal.ppat.1002010
           Confocal imaging of pseudomonas syringae pv. phaseolicola colony development in bean reveals reduced multiplication of strains containing the genomic island PPHGI-1.    
Godfrey, S.A.C., Mansfield, J.W., Corry, D.S., Lovell, H.C., Jackson, R.W. and Arnold, D.L. (2010) Confocal imaging of pseudomonas syringae pv. phaseolicola colony development in bean reveals reduced multiplication of strains containing the genomic island PPHGI-1. Molecular Plant-Microbe Interactions, 23 (10). pp. 1294-1302. ISSN 0894-0282 doi: 10.1094 /MPMI -05-10-0114
           In planta conditions induce genomic changes in Pseudomonas syringae pv. phaseolicola    
Lovell, H. C., Jackson, R. W. , Mansfield, J. W., Godfrey, S. A. C., Hancock, J. T., Desikan, R. and Arnold, D. L. (2010) In planta conditions induce genomic changes in Pseudomonas syringae pv. phaseolicola. Molecular Plant Pathology, 12 (2). pp. 167-176. ISSN 1464-6722 doi: 10.1111/j.1364-3703.2010.00658.x
           Bacterial evolution by genomic island transfer occurs via DNA transformation in planta    
Lovell, H. C., Mansfield, J. W., Godfrey, S. A. C., Jackson, R. W. , Hancock, J. T. and Arnold, D. L. (2009) Bacterial evolution by genomic island transfer occurs via DNA transformation in planta. Current Biology, 19 (18). pp. 1586-1590. ISSN 0960-9822 doi: 10.1016/j.cub.2009.08.018
           Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens    
Silby, M. W., Cerdeno-Tarraga, A. M., Vernikos, G. S., Giddens, S. R., Jackson, R. W. , Preston, G. M., Zhang, X. X., Moon, C. D., Gehrig, S. M., Godfrey, S. A. C., Knight, C. G., Malone, J. G., Robinson, Z., Spiers, A. J., Harris, S., Challis, G. L., Yaxley, A. M., Harris, D., Seeger, K., Murphy, L., Rutter, S., Squares, R., Quail, M. A., Saunders, E., Mavromatis, K., Brettin, T. S., Bentley, S. D., Hothersall, J., Stephens, E., Thomas, C. M., Parkhill, J., Levy, S. B., Rainey, P. B. and Thomson, N. R. (2009) Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology, 10 (5). p. 16. ISSN 1474-760X doi: 10.1186/gb-2009-10-5-r51
           Pseudomonas syringae genomics provides important insights to secretion systems, effector genes and the evolution of virulence    
Arnold, D.L., Godfrey, S.A.C. and Jackson, R.W. (2009) Pseudomonas syringae genomics provides important insights to secretion systems, effector genes and the evolution of virulence. In: Jackson, R.W. (ed.) Plant Pathogenic Bacteria: Genomics and Molecular Biology. Caister Academic Press, UK. ISBN 9781904455370
           Genomic islands in plant-pathogenic bacteria    
Arnold, D.L. and Jackson, R.W. (2008) Genomic islands in plant-pathogenic bacteria. In: Schmidt, H. and Hensel, M. (eds.) Horizontal Gene Transfer in the Evolution of Pathogenesis. Advances in Molecular and Cellular Microbiology. Cambridge University Press, Cambridge, UK, pp. 137-158. ISBN 9780521862974
           Pathogenicity and other genomic islands in plant pathogenic bacteria    
Arnold, D. L., Pitman, A. and Jackson, R. W. (2003) Pathogenicity and other genomic islands in plant pathogenic bacteria. Molecular Plant Pathology, 4 (5). pp. 407-420. ISSN 1464-6722 doi: 10.1046/j.1364-3703.2003.00187.x
          Association of Plasmodium falciparum with Human Endothelial Cells in vitro.   
Related Articles

Association of Plasmodium falciparum with Human Endothelial Cells in vitro.

Yale J Biol Med. 2017 Jun;90(2):183-193

Authors: Utter C, Serrano AE, Glod JW, Leibowitz MJ

Abstract
Endothelial abnormalities play a critical role in the pathogenesis of malaria caused by the human pathogen, Plasmodium falciparum. In serious infections and especially in cerebral malaria, red blood cells infected with the parasite are sequestered in small venules in various organs, resulting in endothelial activation and vascular occlusion, which are believed to be largely responsible for the morbidity and mortality caused by this infection, especially in children. We demonstrate that after incubation with infected red blood cells (iRBCs), cultured human umbilical vein endothelial cells (HUVECs) contain parasite protein, genomic DNA, and RNA, as well as intracellular vacuoles with apparent parasite-derived material, but not engulfed or adherent iRBCs. The association of this material with the HUVECs is observed over 96 hours after removal of iRBCs. This phenomenon may occur in endothelial cells in vivo by the process of trogocytosis, in which transfer of material between cells depends on direct cell contact. This process may contribute to the endothelial activation and disruption involved in the pathogenesis of cerebral malaria.

PMID: 28656007 [PubMed - in process]


          A Plastid Protein That Evolved from Ubiquitin and Is Required for Apicoplast Protein Import in Toxoplasma gondii.   
Related Articles

A Plastid Protein That Evolved from Ubiquitin and Is Required for Apicoplast Protein Import in Toxoplasma gondii.

MBio. 2017 Jun 27;8(3):

Authors: Fellows JD, Cipriano MJ, Agrawal S, Striepen B

Abstract
Apicomplexan parasites cause a variety of important infectious diseases, including malaria, toxoplasma encephalitis, and severe diarrhea due to Cryptosporidium Most apicomplexans depend on an organelle called the apicoplast which is derived from a red algal endosymbiont. The apicoplast is essential for the parasite as the compartment of fatty acid, heme, and isoprenoid biosynthesis. The majority of the approximate 500 apicoplast proteins are nucleus encoded and have to be imported across the four membranes that surround the apicoplast. Import across the second outermost membrane of the apicoplast, the periplastid membrane, depends on an apicoplast-specific endoplasmic reticulum-associated protein degradation (ERAD) complex and on enzymes of the associated ubiquitination cascade. However, identification of an apicoplast ubiquitin associated with this machinery has long been elusive. Here we identify a plastid ubiquitin-like protein (PUBL), an apicoplast protein that is derived from a ubiquitin ancestor but that has significantly changed in its primary sequence. PUBL is distinct from known ubiquitin-like proteins, and phylogenomic analyses suggest a clade specific to apicomplexans. We demonstrate that PUBL and the AAA ATPase CDC48AP both act to translocate apicoplast proteins across the periplastid membrane during protein import. Conditional null mutants and genetic complementation show that both proteins are critical for this process and for parasite survival. PUBL residues homologous to those that are required for ubiquitin conjugation onto target proteins are essential for this function, while those required for polyubiquitination and preprotein processing are dispensable. Our experiments provide a mechanistic understanding of the molecular machinery that drives protein import across the membranes of the apicoplast.IMPORTANCE Apicomplexan parasites are responsible for important human diseases. There are no effective vaccines for use in humans, and drug treatment faces multiple challenges, including emerging resistance, lack of efficacy across the lifecycle, and adverse drug effects. The apicoplast is a promising target for novel treatments: this chloroplast-like organelle is derived from an algal symbiont, is absent from the host, and is essential for parasite growth and pathogenesis. We use Toxoplasma gondii as a model to study the apicoplast due to its strong genetic tools and established functional assays. We identify a plastid ubiquitin-like protein (PUBL) which is a novel ubiquitin-like protein and demonstrate its importance and that of the motor protein CDC48AP for apicoplast protein import. These findings broaden our understanding of the evolution and mechanistic workings of a unique parasite organelle and may lead to new opportunities for treatments against important human pathogens.

PMID: 28655825 [PubMed - in process]


          Il Rosa è per Tutti   

Un percorso chiaro leggero e delicato che ti permette di accedere senza sforzo al tuo benessere nella sua essenza più profonda, creando il terreno fertile adatto a formulare con successo i tuoi desideri del Cuore.

Un percorso verso la tua realizzazione.

Moltissimi i libri in questo periodo che parlano della “legge di attrazione” poche purtroppo le persone che leggendoli riescono praticamente a “formulare” il loro desiderio del Cuore e ad accedere alla realizzazione del proprio progetto.

Qual è il motivo di tali fallimenti se la “formula” è esatta e credetemi lo è.

Ognuno nelle proprie potenzialità di attivazione del proprio benessere è integro, cosa allora non fa scattare l’interruttore.

Uno dei primi passi da fare è,

allineare dentro se stessi le proprie capacità

e potenzialità mettendo ordine nelle parti

fondamentali ed essenziali del proprio essere.

Senza ordine non c’è Consapevolezza, e senza consapevolezza non c’è leggerezza, e senza questa non si può formulare nulla.

Noi siamo magneti, siamo antenne e risuoniamo con l’universo

In questo manuale non si è soli nei passi, si viene guidati dalla voce dell’autore attraverso un prezioso cd di circa due ore che indica i passi, sgombrando la via dagli irretimenti e interferenze personali.

Attraverso tecniche e metodologie antiche, elaborate per il presente, accessibili a tutti, sarai orientato nell’attivazione del tuo proprio potenziale creativo, ed in quello spazio sospeso tra l’antico e l’eterno, dove i germogli del futuro diventano reali.

I racconti della serie "Soluzioni Incantate"

Il primo racconto contenuto nel cd "Rilassati" consiste in un esercizio per imparare il rilassamento, di tipo training autogeno. Questo CD Relax, svolto ogni giorno per circa tre mesi consente di acquisire un rilassamento fisico mentale ed emotivo che faciliterà varie situazioni.

Ad esempio può migliorare la qualità del sonno, rinforzare l'autostima, aiutare la concentrazione nello studio, migliorare varie prestazioni da quelle sportive, lavorative ed altre, è stato sperimentato per anni con ottimi risultati.

Il secondo racconto contenuto nel cd "La stella Gemella" si divide in due brani, il primo è di preparazione a livello (psico-fisico) per il secondo racconto. Questo secondo CD è utile per la riarmonizzazione e la centratura della persona.

E' un racconto che aiuta a riconnettersi con la nostra parte armoniosa e gioiosa.

Il terzo "Lo Scivolo d'Argento" e quarto "L'Aquila e la Montagna".

Il terzo ti aiuta a rimetterti in paro con ciò che moltissime persone stanno ancora aspettando per andare avanti nella vita, cioè "l'Autorizzazione ad essere felici" Il quarto invece si può utilizzare per cercare di superare piccoli e grandi ostacoli "problemi"

Il quinto racconto "La Foresta Incantata" è una storia che ogni volta mi commuove, ti guida nei luoghi antichi dove hanno avuto origine gli "incastri" che ti legano ad un "destino difficile" e dove puoi riordinare il presente attraverso un "pellegrinaggio rispettoso verso il Tuo Tutto"

Il sesto racconto "La Stanza del Tesoro" ti accompagna nel tuo posto privato e segreto dove risiedono tutti i tuoi Beni e dove possono essere da te recuperati ed utilizzati per la tua vita presente.

DNA dell’Anima

Le leggende le storie i racconti, non affascinano soltanto i bambini, le emozioni che esse suscitano, toccano l’Anima di chi le ascolta, o le legge immaginando.

E’ così che le parole attraverso il suono e la creazione delle immagini, raggiungono la profondità dell’inconscio.

Questo nutrimento accresce il senso di meraviglia e di stupore che è l’accesso a quello “spazio” dove è possibile ripristinare nella sua forma originaria il bene-essere che in ognuno dimora.

Al cuore della “Soluzione” si trova l’Intuizione dell’inconscio che opera di continuo per aiutare la parte cosciente ad integrare tutti gli aspetti dell’esistenza.

Simboli ed analogie sono una chiave per instaurare un dialogo con la parte più profonda, quella parte che contiene ed è in grado di guarire e di realizzare i nostri desideri, quando l’Anima dell’uomo è pienamente espressa,  la salute prospera.

Un primo buon sostegno per la realizzazione è dato dalla sensazione di avere le proprie radici nella terra degli antenati.

Da tempo molti studiosi dei vari campi e discipline, dalla medicina alla psicologia alla fisica all’ingegneria, all’architettura, sono impegnati nella comprensione della radice del benessere e di cosa ne impedisce la realizzazione.

Un allergia può essere indotta da fiore finto quanto da uno vero, ed un operazione chirurgica può essere svolta senza l’anestesia farmacologia ma in stato di trans ipnotica.

Sappiamo che i geni controllano la funzione biologica e che l’attività dei geni “genomica” può essere attivata e riprogrammata utilizzando lo stato di coscienza in cui si attivano le frequenze che la governano. Alfa beta delta theta.

 

Segui bene le indicazioni, da subito sentirai che qualcosa in te si alleggerisce, dopo qualche tempo il tuo Cuore dirà così:

"Dovunque Io Vada Mi Guida la Strada A gioia e Successo C’è Accesso da Adesso Nell’Agio mi Adagio Svanisce il Retaggio"

Ma se glielo suggerisci, spesso lo farà prima.........


          10 Penemuan Paling Menarik    
1. Penemuan Higgs Boson
Para ilmuwan di Large Hadron Collider telah melalui lima dekade untuk menemukan Higgs Boson pada bulan Juli. Partikel yang telah lama dicari ini melengkapi  elemen-elemen lain, seperti proton dan elektron, dan merupakan bagian terakhir dari Standard Model, yang mendeskripsikan interaksi dari semua partikel dan kekuatannya. Penemuan ini menjadi amat penting bagi bidang fisika dasar.
2. Penasaran akan Mars?
Jutaan orang berusaha menjadi saksi pendaratan  NASA’s rover (pengelana) untuk menjelajah Mars pada bulan Agustus. Mereka penasaran dengan informasi tentang batuan, regolith dan atmosfer di Mars. Namun yang terpenting, pesawat ini mengirimkan foto yang sangat banyak, yang memberikan pengetahuan baru. Rover akan melanjutkan misinya selama 2,5 tahun menjelajahi  Mount Sharp, mencari senyawa organik, dan memperhatikan bila ada  tanda-tanda adanya habitat di Mars, baik pada  masa lalu ataupun masa kini.
20121231-005321.jpg
3. Perkembangan Jenis Genetik yang Unik
Studi genomics tentang penyakit, menghasilkan kenyataan yang tidak mengenakkan, dari semua penyakit yang umum dan ancamannya yang nyata, peneliti hanya dapat menghubungkan sebagian kecil di antaranya dengan gen, sehingga mereka menamakannya teka-teki warisan yang hilang (conundrum the missing heritability). Penemuan lain yang didapatkan adalah variasi genetik yang berbahaya merupakan hal yang benar-benar baru, sehingga belum jelas seperti apa, dan dapat menyebabkan masalah bagi kesehatan manusia.
4. Urutan Genome untuk Janin
Pada bulan Juni,  ilmuwan dari Universitas Washington di Seattle mengumumkan kesuksesan mereka mengurutkan gen janin yang lengkap dengan menggunakan sedikit DNA dari darah  ibu. Sebelumnya, DNA/RNA bentuknya non-coding. Tidak seperti teknik sebelumnya, cara ini tidak memiliki resiko pada bakal calon bayi. Penemuan ini bisa digunakan untuk keperluan medis, seperti penyakit bawaan, informasi mengenai ciri-ciri kepribadian dan fisik anak.
5. Rekor Teleportasi Quantum Telah Dipecahkan
Dua peneliti  dari China dan Austria, memecahkan rekor dunia dengan melakukan teleportasi partikel quantum lebih dari 50 miles melalui udara terbuka. Trik yang digunakan adalah melibatkan dua partikel, seperti photons, sehingga mereka memiliki sifat yang sama.  Yang dikembangkan sekarang adalah melakukan teleport partikel ke satelit dan memindahkan mereka ke lokasi manapun di bumi.
20121231-005047.jpg
6. Kode Baru Kimia
Selama tiga milyar tahun, informasi tentang kehidupan dinyatakan disimpan pada DNA dan RNA. Saat ini muncul yang ketiga,  yaitu  XNA, sebuah polimer yang disintesiskan oleh ahli biologis Vitor Pinheiro dan Philipp Holliger dari The Medical Research Council di Inggris. Seperti DNA, XNA mampu menyimpan informasi genetika dan kemudian dikembangkan  melalui seleksi alam. Tidak seperti DNA, XNA dapat dimanipulasi dengan hati-hati. Rencananya kode ini akan digunakan untuk pengobatan dan keperluan industri.
7. SpaceX Meluncurkan Pesawat ke International Space Station (ISS)
Setelah sukses meluncurkan pesawat luar angkasa Dragon mengelilingi bumi di tahun 2010, SpaceX  mengirimkan Dragon ke ISS pada bulan Mei. SpaceX merupakan perusahaan swasta pertama yang melakukan hal itu. CEO SpaceX, Elon Musk, menyatakan berulang kali bahwa dia mengharapkan suatu saat ada koloni manusia di Mars.
8. Kembaran Planet Bumi
Sebuah batu, dengan ukuran seperti  bumi, mengorbit pada Alpha Centauri B, bintang yang paling dekat dengan sistem gugus bintang kita. Dilaporkan pada bulan Oktober, planet itu hanya berjarak 4,4 tahun cahaya dari bumi. Para ilmuwan menduga masih ada planet lain yang menyerupai bumi dari tiga bintang Alpha Centauri.
9. Ilmuwan Mencapai Danau  Vostok
Setelah satu dekade menggali, ilmuwan Rusia akhirnya berhasil mencapai danau Vostok yang telah  14 juta tahun terkubur di bawah es, pada bulan Februari. Vostok adalah danau yang terbesar di dunia. Ilmuwan Rusia melakukannya dengan memecah permukaan dan menggali es sedalam  2,2 miles.
20121231-005232.jpg
10. Mengakhiri Penelitian dengan Menggunakan Simpanse yang Merugikan
Selama beberapa dekade, penyelidikan dengan menggunakan simpanse memunculkan pertentangan dalam hati nurani ilmu medis di Amerika Serikat. Saudara terdekat manusia itu memiliki kemampuan berpikir dan berperasaan yang sama seperti manusia, sehingga ribuan simpanse telah ditangkap untuk kepentingan penelitian.  Namun tahun 2012 memunculkan tren, lembaga-lembaga penelitian akan berhenti menggunakan simpanse sebagai kelinci percobaan.

          Comment on The Spirit Of The World by Patrick Coyle   
Seeing an unread Genomicon post pop up has made my whole month! Glad you've returned!
          Comment on A Machine to Steal Souls by Alex Funke, ASC   
Great showdown, but i would say that for 'directing the eye' the showdown between Bronson and Fonda at the end of Once Upon a Time in the West beats it. Hooray foe Genomicon!!! Alex
          Concierge Medicine Today and Sequencing.com Announce Partnership to Help Physicians Bring Whole Genome Sequencing andamp; Genetic Data to Life via Innovative Apps andamp; Tools   
New Partnership Provides First-of-its-Kind Solutions for Transforming Genetic Data into Meaningful Information with Concierge Physicians andamp; Sequencing.com at the Forefront of the Personal Genomics Revolution.
           Systematic cloning of human minisatellites from ordered array charomid libraries.    
Armour, JA; Povey, S; Jeremiah, S; Jeffreys, AJ; (1990) Systematic cloning of human minisatellites from ordered array charomid libraries. Genomics , 8 (3) pp. 501-512.
           The α subunit of cytochrome b-245 mapped to chromosome 16    
Bu-Ghanim, HN; Casimir, CM; Povey, S; Segal, AW; (1990) The α subunit of cytochrome b-245 mapped to chromosome 16. Genomics , 8 (3) pp. 568-570. 10.1016/0888-7543(90)90045-V .
           Cloning of genomic and cDNA sequences encoding an invertebrate gamma-aminobutyric acidA receptor subunit.    
Harvey, RJ; Vreugdenhil, E; Barnard, EA; Darlison, MG; (1990) Cloning of genomic and cDNA sequences encoding an invertebrate gamma-aminobutyric acidA receptor subunit. Biochem Soc Trans , 18 (3) pp. 438-439.
           The alpha subunit of cytochrome b-245 mapped to chromosome 16.    
Bu-Ghanim, HN; Casimir, CM; Povey, S; Segal, AW; (1990) The alpha subunit of cytochrome b-245 mapped to chromosome 16. Genomics , 8 (3) pp. 568-570.
          JIPMER Genomic Biomarkers JRF Vacancy | JIPMER Recruits @ helpBIOTECH   

          Angelicus, ángeles creados con ingeniería genética   

Imagina que luego de un tratamiento genético donde son activados y desactivados miles de distintos genes propios y otros importados de distintas especies animales, despiertas, para encontrar que ahora posees seis extremidades, dos de ellas alas de una envergadura de 7 metros. Estas se extienden y contraen articuladamente como las de un ave, se unen perfectamente a omóplatos, clavículas y otros huesos que han reducido tamaño y peso; y al mismo tiempo músculos, tendones, arterias, vasos y nervios se extienden adecuadamente a las alas. Imagina que tu corazón bombea más fuerte y tus pulmones procesan más aire, mientras que otros órganos se adaptan a la nueva fisiología; una nueva área del cerebro se ha desarrollado para procesar nuevas entradas de información y coordinar el movimiento de las alas; mientras que los nervios han evolucionado para percibir mejor las condiciones ambientales de humedad, calor, dirección y sentido del viento. Imagina que a medida que pones en práctica tus alas tu alimentación cambia, tus costumbres cambian y tus preferencias sobre pareja también: otros humanos alados, tu vida entera cambia, te has convertido en una nueva especie humanoide: en una que puede volar.

Aunque los avances en ingeniería genética siempre me interesaron por el hecho de ser beneficiario de uno, juzgué que crear humanoides con características de seres mitológicos era sólo una curiosidad científica sin mercado posible. Me equivoqué, y en gran medida.

Sorprendentemente, el anuncio de haber desarrollado seres humanos con alas viables, no solo era un avance digno del Premio Atenea Nobel (El comité del Nobel se mudó a Atenea en el 2223) sino que además produjo una avalancha de órdenes de tratamientos genéticos para obtener alas y una fuerte subida de las acciones de ACS Metagenomics la empresa que logró el avance, pareciera que todos en el planeta quisieran autopropulsarse en lugar de usar aeronaves. ¿Cuál la finalidad? ¿Cuál el sentido?

Indagué en mi experiencia personal y recordé que yo mismo cuando niño fantaseaba con volar sobre las campiñas y los mares interiores de Capitolia, los enormes montes de Vulcania y los valles de Arborea, poblados por kilométricos árboles también genéticamente modificados. Me atraía esa sensación de plena libertad, de ausencia de ataduras, de infinita capacidad para recorrer distancias con el pensamiento. Es esa sensación la que habría motivado a miles a conseguir sus alas, aún cuando el tratamiento no está disponible todavía y sus riesgos y consecuencias están por determinarse.

No se puede ser duro juzgando a la avalancha de aspirantes a ángeles y demonios alados. Esta búsqueda de libertad plena que todo ser humano tiene desde niño es natural, comprensible, es lo que nos hace seres conscientes, capaces, talentosos, villanos o virtuosos. No siempre nuestros deseos de libertad caminan con inteligencia, no, en busca de nuestros objetivos erramos y a veces herimos a otros o nos causamos daño a nosotros mismos, y allí es cuando aprendemos que nuestras acciones tienen consecuencias, de estas consecuencias aprendemos, nos permiten corregir el rumbo, pero ello solamente es posible con libertad, no existe otro modo.

En cierto modo, todos en Atenea de una u otra forma venimos a buscar nuestras alas, desde el primer colono ambicioso hasta el recién llegado inmigrante que arriesgó su vida para salir de la maldita Tierra. Todos buscamos nuestra libertad, todos elegimos un sendero para alcanzar nuestros sueños que en este planeta parecen posibles, todos buscamos extender nuestras alas y elevarnos buscando libertad.

Por mi parte, he decidido no ordenar ningún tratamiento genético, me es suficiente aquel que me permite reparar el ADN para hacerle frente a la radiación del manto planetario y para lidiar con las emisiones de masa coronaria del Sol y de Zeus. Pero como es de esperar en la Tierra, la Comisión Planetaria de Salud y Buen Vivir ha prohibido cualquier tratamiento de esta índole y ha iniciado toda una gama de normas regulatorias para impedir y castigar a los beneficiarios de este u otro tratamiento similar; la Comisión ha determinado también que cualquier mutante será detenido indefinidamente en campos de reeducación y sociabilización.

El gobierno de la Tierra abre un nuevo frente ahora contra los mutantes y continúa su guerra contra los robots autoconscientes, guerra en la que por cierto la Tierra va perdiendo. La Resistencia compuesta ahora por humanos y robots (¿pronto se integrarán los mutantes?) da golpes cada vez más fuertes al ejército de la Unión de Estados Sociales de la Tierra. El último fue la destrucción de dos fábricas de armamento en la Provincia Belga que retrasará por un año la construcción del Anillo Orbital de Vigilancia. El golpe no salió en los medios regulados o estatales pero todo el mundo se enteró por las emisiones de La Resistencia, que muchos contrabandistas retransmitimos automáticamente desde nuestras naves, incluido su servidor. Para que vean de lo que somos capaces con o sin alas.


          Agena Bioscience Launches CE-IVD System For Hospitals And Diagnostic Laboratories In Europe   

Agena Bioscience develops, manufactures, and supplies genetic analysis systems and reagents, including the MassARRAYÂ(R) System. The system is a highly sensitive, cost-effective, mass spectrometry-based platform for high-throughput genetic analysis, and is used globally in diverse research fields such as cancer profiling for solid tumors and liquid biopsies, inherited genetic disease testing, pharmacogenetics, agricultural genomics, and clinical research. (PRNewsFoto/Agena Bioscience) (PRNewsFoto/)SAN DIEGO, June 29, 2017 /PRNewswire/ -- Agena Bioscience today announced the European launch of the MassARRAY® System with CHIP Prep Module (CPM), marketed as a CE-IVD product under the Directive 98/79/EC for in vitro diagnostic medical devices.   The MassARRAY Dx product offers clin...



          Offer - World Congress on Embryology and In vitro Fertilization - USA   
World Congress on Embryology and In vitro Fertilization focuses on human embryology and aims to provide an up-to-date source of information on a variety of selected topics. .The conference will be organized on the theme of Exploring the Novel Research & Techniques in Reproductive Health, this conference is going to be held during November 2-3, 2017 at Chicago, USA. Embryology is a branch of science deals with the morphological aspects of organismal development. The genomic and molecular revolution of the second half of the 20th century, together with the classic descriptive aspects of science that allowed greater integration in our understanding in many developmental events. Through such integration, modern embryology helps to provide practical knowledge that is applied to assisted reproduction, stem cell therapy, birth defects, fetal surgery and other fields. The conference organized into three sections, namely: 1) Gametes and infertility, 2) Implantation, placentation and early birth, and 3) Prospects of embryology. International conference on Embryology will offer an exciting, & wide range of scientific programme designed to engage high profile scientific international on topics of importance related to the Embryology. This conference will be the perfect occasion for the international and Indian experts to share their leading edge knowledge on innovation and technology balanced by critically important insight into their practical application. The conference will also feature over scientific poster presentations, a large trade exhibition and a packed social programme providing an excellent opportunity to learn, network and exchange ideas. This conference focus interest to all fertility and reproductive experts including Andrologists, embryologists ,Consultants in reproductive medicine Counselors , Gynecologists , Reproductive biologists ,Reproductive nurses ,biology and medical students, clinical embryologists, laboratory researchers and anyone who wishes to know more about recent advances embryology. For more details PS: http://embryology.alliedacademies.com Scientific Session: · Fertility and conception · Placentation · Implantation · Early Birth · Embryo-Lab Quality · Cleavage Stage Embryo · Epididymis and Infertility · Artificial Insemination · IVF Treatment · Fertility Surgery · In vitro Maturation Techniques and many more….. · Regards Alicia Williams Program Director / Embryology 2017 Allied Academies 40 Bloomsbury Way Lower Ground Floor London, United Kingdom WC1A 2SE Phone: (828) 214-3944 Emails: embryology@alliedconferences.org
          ACPFG Genomics Symposium: The Genomics of Drought    

2007 ACPFG Genomics Symposium: The Genomics of Drought, to be held from the 22nd to the 24th October 2007 at the Holiday Inn Adelaide.

The preliminary program includes:
DAY 1 - FOR GRAIN GROWERS, INDUSTRY AND RESEARCHERS
* The low rainfall environment
* Predictions of the future cropping environment
* Biotechnology and the low yielding environment

DAY 2: FOR RESEARCHERS
* Techniques of drought tolerance assessment
* Drought tolerance studies in model species

DAY 3: FOR RESEARCHERS
* Genetics of drought tolerance in wheat and barley
* New genomics tools for studying drought tolerance
* Relationship between drought and other stresses


          Plant Genomics European Meeting, Plant GEM5   

the latest version of the scientific program for the Plant Genomics European Meeting, Plant GEM5, to be held in Venice, 11-14 October 2006, has now been uploaded on the Congress website at http://www.plant-gems.org

Discounted early registration rate ends June 30.

The deadline for sending the abstract is July 15.


          2006 ITMI Summer Workshop   

ITMI Workshop and Genomics Symposium
August 27 - 31
McCracken Country Club
Victor Harbor, South Australia
(Just south of Adelaide)

Registration and information can be found here http://www.acpfg.com.au

Draft programe is available at:
http://wheat.pw.usda.gov/ITMI/2006/ITMI-ACPFG_Meeting_Program_CURRENT.doc


          International Mycoglobe Conference   

"Advances on genomics, biodiversity and rapid systems for detection of toxigenic fungi and Mycotoxins"

A three-day conference will be organized in Bari (Italy) by the Institute of Sciences of Food Production ISPA-CNR, fully supported by the Mycoglobe Specific Support Action within the EU 6 Frameworks Programme.


          Unchained Labs racks up another one, acquires Trinean!   

PLEASANTON, Calif., June 29, 2017 /PRNewswire/ -- Unchained Labs, the life sciences company that's all about getting biologics researchers the right tool for the job, acquired Trinean today. Trinean's DropSense systems measure protein, DNA and RNA concentration in biologics and genomics...



          Trovagene Announces Manufacturing Agreement with NerPharMa for Supply of PCM-075 for AML Trial   

SAN DIEGO, June 29, 2017 /PRNewswire/ -- Trovagene, Inc. (NASDAQ: TROV), a precision medicine biotechnology company, today announced it has executed a supplier agreement with NerPharMa, S.r.l., a pharmaceutical manufacturing company and a subsidiary of Nerviano Medical Sciences S.r.l., in Milan, Italy, to manufacture drug product for PCM-075. The agreement covers the clinical and commercial supply of PCM-075 for Trovagene, and includes both Active Pharmaceutical Ingredients (API) and GMP (Good Manufacturing Process) production of capsules.

NerPharMa has previously supplied drug product for PCM-075 in a completed phase 1 study conducted by Nerviano Medical Sciences.  NerPharMa has an established manufacturing process scaled for producing PCM-075 for future clinical studies and commercial use.  Under the terms of the agreement, Trovagene directs NerPharMa to produce GMP-grade PCM-075 drug substance for use in Trovagene's Phase 1b/2 clinical program and for other related clinical and commercial activities. Trovagene is developing PCM-075, a polo-like kinase 1 (PLK1) inhibitor, and plans to initiate a Phase 1b/2 clinical trial in patients with acute myeloid leukemia (AML).

"This contract represents a significant step forward for the development of PCM-075," said Bill Welch, Chief Executive Officer of Trovagene. "We are excited to have a manufacturer of NerPharMa's caliber and experience producing GMP supply of PCM-075 bulk product and finished capsules. The availability of validated API and the ability to immediately initiate capsule production enables a cost-effective and accelerated start-up of our Phase 1b/2 clinical program."

NerPharMa's GMP manufacturing facility is approved by both the Italian Medicines Agency (AIFA), the national authority responsible for drug regulation in Italy, and the U.S. Food and Drug Administration (FDA) for the production of PCM-075.

"We are pleased to be working with Trovagene to manufacture and provide finished product for their investigational and commercial needs," said Angelo Colombo, CEO of NerPharMa.

About PCM-075

PCM-075 is a highly-selective adenosine triphosphate (ATP) competitive inhibitor of the serine/threonine polo-like-kinase 1 (PLK 1) enzyme, which is over-expressed in several different hematologic malignancies, as well as solid tumors such as breast, prostate, ovarian, lung, gastric and colon cancers. PCM-075 is orally bioavailable and has been explored in an initial Phase 1, open-label, dose-escalation safety study in patients with advanced metastatic solid tumor cancers. In this study, PCM-075 demonstrated an acceptable safety profile, as well as anti-tumor activity. Trovagene plans to initiate clinical trials of PCM-075 in AML, since it has significant advantages over prior PLK1 inhibitors evaluated in this indication, including a higher selectivity, greater potency, oral bioavailability and shorter half-life.

About Nerviano Medical Sciences (NMS)

Nerviano Medical Sciences, part of the NMS Group, is the largest pharmaceutical research and development facility in Italy and one of the largest oncology-focused, integrated discovery and development companies in Europe.

About Trovagene, Inc.

Trovagene is a precision medicine biotechnology company developing oncology therapeutics for improved cancer care by leveraging its proprietary Precision Cancer Monitoring® (PCM) technology in tumor genomics.  Trovagene has broad intellectual property and proprietary technology to measure circulating tumor DNA (ctDNA) in urine and blood to identify and quantify clinically actionable markers for predicting response to cancer therapies.  Trovagene offers its PCM technology at its CLIA/CAP – accredited laboratory and plans to continue to vertically integrate its PCM technology with precision cancer therapeutics.  For more information, please visit https://www.trovagene.com.

Forward-Looking Statements

Certain statements in this press release are forward-looking within the meaning of the Private Securities Litigation Reform Act of 1995. These statements may be identified by the use of words such as "anticipate," "believe," "forecast," "estimated" and "intend" or other similar terms or expressions that concern Trovagene's expectations, strategy, plans or intentions. These forward-looking statements are based on Trovagene's current expectations and actual results could differ materially.  There are a number of factors that could cause actual events to differ materially from those indicated by such forward-looking statements.  These factors include, but are not limited to, our need for additional financing; our ability to continue as a going concern; clinical trials involve a lengthy and expensive process with an uncertain outcome, and results of earlier studies and trials may not be predictive of future trial results; our clinical trials may be suspended or discontinued due to unexpected side effects or other safety risks that could preclude approval of our product candidates; uncertainties of government or third party payer reimbursement; dependence on key personnel; limited experience in marketing and sales; substantial competition; uncertainties of patent protection and litigation; dependence upon third parties; our ability to develop tests, kits and systems and the success of those products; regulatory, financial and business risks related to our international expansion and risks related to failure to obtain FDA clearances or approvals and noncompliance with FDA regulations.  There are no guarantees that any of our technology or products will be utilized or prove to be commercially successful, or that Trovagene's strategy to design its liquid biopsy tests to report on clinically actionable cancer genes will ultimately be successful or result in better reimbursement outcomes.  Additionally, there are no guarantees that future clinical trials will be completed or successful or that any precision medicine therapeutics will receive regulatory approval for any indication or prove to be commercially successful.  Investors should read the risk factors set forth in Trovagene's Form 10-K for the year ended December 31, 2016, and other periodic reports filed with the Securities and Exchange Commission.  While the list of factors presented here is considered representative, no such list should be considered to be a complete statement of all potential risks and uncertainties.  Unlisted factors may present significant additional obstacles to the realization of forward-looking statements.  Forward-looking statements included herein are made as of the date hereof, and Trovagene does not undertake any obligation to update publicly such statements to reflect subsequent events or circumstances.

Trovagene Contact:

Vicki Kelemen
VP, Corporate Communications
858-952-7652
vkelemen@trovagene.com

 

SOURCE Trovagene, Inc.

The post Trovagene Announces Manufacturing Agreement with NerPharMa for Supply of PCM-075 for AML Trial appeared first on San Diego Biotechnology Network.


          GenomeDx Announces New York State CLEP Approval of Decipher Prostate Cancer Tests   

Decipher Biopsy and Post-Op Now Widely Available to New York State Physicians and Patients

SAN DIEGO, June 29, 2017 /PRNewswire/ -- GenomeDx Biosciences, a leader in the field of urologic cancer genomics, today announced approval by the New York State Clinical Laboratory Evaluation Program (CLEP) of GenomeDx's prostate cancer classifier tests, Decipher® Biopsy and Decipher Post-Op, which are genomic tests intended to improve clinical decision-making following biopsy or radical prostatectomy, respectively, in men with prostate cancer. With this approval, Decipher Biopsy and Post-Op are now widely available to physicians and patients in New York state.

The New York State Department of Health (NYSDOH) regulates and oversees clinical diagnostic laboratories that test specimens from New York state residents. The CLEP seeks to ensure the accuracy and reliability of test results in clinical laboratories located in New York state or accepting specimens from its residents. Prior to CLEP approval, Decipher Biopsy and Post-Op were available to New York state residents on a patient-by-patient basis through the non-permitted laboratory testing program administered by the NYSDOH. In addition to the CLEP approval, the GenomeDx laboratory has been accredited by the College of American Pathologists (CAP) and has Clinical Laboratory Improvement Amendments (CLIA) certification.

"Obtaining CLEP approval is a rigorous process, further demonstrating the robust performance of Decipher Biopsy and Decipher Post-Op," said Doug Dolginow, M.D., chief executive officer of GenomeDx. "Now physicians and patients of New York state have the same unrestricted access to our genomic prostate tests as physicians and patients have in the rest of the United States, allowing them the ability to facilitate better decision-making at multiple stages of prostate cancer."

About Decipher Cancer Classifier Tests and GRID®

GenomeDx's Decipher prostate and bladder cancer classifier tests are commercially available genomic tests that provide a genomic assessment of tumor aggressiveness for individual patients. Decipher Biopsy is indicated for men with localized prostate cancer at diagnosis, Decipher Post-Op is indicated for men after prostate removal surgery, and Decipher Bladder is indicated for patients being considered for neoadjuvant chemotherapy prior to bladder removal surgery. The Decipher tests are used by physicians to stratify patients into more accurate risk groups than determined by traditional diagnostic tools and to help determine which patients may be more likely to benefit from additional treatment.

The Decipher tests are derived from GenomeDx's Decipher Genomics Resource Information Database (GRID). GRID contains the genomic profiles of thousands of tumors from patients with urological cancers, and is believed by GenomeDx to be the largest shared genomic expression database in urologic cancer as well as one of the world's largest global RNA expression databases using cloud-based analytics. Each tumor analyzed with a Decipher test adds new data to the GRID database, which is compiled into a Decipher GRID Profile that may reveal additional biological characteristics of the tumor for ongoing research purposes. Going beyond risk stratification, Decipher and GRID make genetic information accessible for researchers to predict responses to therapy better and to guide treatment more precisely. In addition, GRID is a platform for interactive research collaboration, and may enable more rapid discovery, development, commercialization and adoption of new genomic solutions for key clinical questions in cancer treatment.

Learn more at www.deciphertest.com and www.deciphergrid.com

About GenomeDx Biosciences

GenomeDx is reimagining the use of genomics as a platform for mass collaboration to improve patient treatment and outcomes through its currently available genomic tests for prostate and bladder cancer as well as potential future tests. GenomeDx is headquartered in Vancouver, British Columbia, and operates a clinical laboratory in San Diego, California.

Learn more at www.GenomeDx.com

 

SOURCE GenomeDx Biosciences

The post GenomeDx Announces New York State CLEP Approval of Decipher Prostate Cancer Tests appeared first on San Diego Biotechnology Network.


          Group Leader   
PA-Lancaster, Eurofins is the world leader in the food, bio/pharmaceutical product testing. It is also number one in the field of environmental laboratory services and one of the global market leaders in agroscience, genomics, discovery pharmacology, and central laboratory services. With over $2 billion in annual revenues and 25,000 employees across 250 sites in 39 countries, Eurofins is a leading international
          Microbiology blogs: a list of 20 great blogs for microbe lovers   


Bertalan Meskó (@Berci) has compiled a list of microbiology blogs that you may find useful: Microbiology in the Blogosphere.

Envious, I decided to make my own list of microbiology blogs. After checking my Google Reader, I came up with a collection of 20 great blogs. I know there are many more out there, so please feel free to add a comment and suggest any microbiology blogs that may be missing from my list.

So, here they come, in strict alphabetical order:

1 - Aetiology by Tara C. Smith (@aetiology): "Discussing causes, origins, evolution, and implications of disease and other phenomena."



2 - Bactérioblog [in French] by Benjamin (@bacterioblog):"Le blog des bactéries et de l'évolution".



3 - BacterioFiles by Jesse Noar (@BacterioFiles): "The podcast for microbe lovers: reporting on exciting news about bacteria, archaea, and sometimes even eukaryotic microbes and viruses".



4 - Cornell Mushroom Blog by a collective of faculty, staff and students from Cornell University: "Even in the fullness of their horrific evilness, fungi are cool. That’s what we’re all about here."



5 - Curiosidades de la Microbiología [in Spanish] by Manuel Sánchez (@Manuel_SanchezA) (no relation!): "Este blog está dedicado a la Microbiología pero en general cualquier tema científico de interés tambien puede aparecer".



6 - Life of a Lab Rat ("occasional insights into the life of a lab rat") and Lab Rat ("Exploring the life and times of bacteria") by S. E. Gould (@labratting).



7 - Memoirs of a Defective Brain by The Defective Brain: "Science as told by malfunctioning neurones. A blog of Life, labs and bacteria."



8 - Microbichitos [in Spanish] by Miguel Vicente: "Los microbios no los vemos, pero sus efectos, para bien o para mal nos afectan a diario." Previously, Miguel used to blog at Esos pequeños bichitos.



9 - MicrobiologyBytes by Alan Cann (@MicroBytes): "The latest news about microbiology".



10 - MIKROB(io)LOG [in Slovenian] by Franc Nekrep (@fvnek): "srečevali se bomo mikrobiologi: študenti, učitelji, kolegi iz stroke pa seveda VSI LJUDJE DOBRE VOLJE..."



11 - MycoRant by Philip McIntosh (@MycoRant): "Philip has been writing, researching, publishing and doing other things in the realm of fungi since 1993".



12 - Mystery Rays from Outer Space by Ian York (@iayork): "This blog is intended to be a place for commentary on immunology, virology, and random other stuff that catches my eye."



13 - Skeptic Wonder ("protists, memes and random musings") and The Ocelloid ("Through the eye of a microbe") by Psi Wavefunction (@PsiWavefunction).



14 - Small Things Considered by Elio Schaechter, Merry Youle and collaborators: "The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet".



15 - The Artful Amoeba by Jennifer Frazer (@JenniferFrazer): "a blog about the weird wonderfulness of life on Earth". Older posts can be found here.



16 - The Febrile Muse by CMDoran (@TheFebrileMuse): "Portrayal of Infectious Diseases in Literature and the Arts".



17 - The Gene Gym by Jim Caryl (@mentalindigest): "Bad bugs, drugs and antibiotic resistance, all in a day's work at The Gene Gym, brought to you from the gym floor by a researcher (fitness instructor) in bacterial evolution".



18 - The Tree of Life by Jonathan Eisen (@phylogenomics), "evolutionary biologist, microbiologist and genomics researcher, Open Access and Open Science advocate".



19 - ViroBlogy by Ed Rybicki (@edrybicki): "Up-to-date Virology-related posts, mainly for students at the University of Cape Town".



20 - Virology blog by Vincent Racaniello (@profvrr): "about viruses and viral disease".




Note: I don't speak French or Slovenian, but that's what Google Translate is for, isn't it?



          Cornering multiple sclerosis -- still a long way to go   

Multiple sclerosis is an autoimmune disease of the central nervous system that causes neurological disability in young adults. Several environmental and genetic factors have been linked to the disease, but the precise mechanisms involved, and whether neurological damage precedes inflammation or vice versa, remain unclear.

In a recent article published in Nature, an international consortium of researchers report the identification of 29 new susceptibility loci, most of which are related to immune system function and, in particular, to T-helper-cell differentiation.

Previous genome-wide association studies (GWAS) that analysed relatively modest numbers of multiple sclerosis patients identified more than 20 risk loci, especially some that encode components of the major histocompatibility complex (MHC). To identify a more complete set of susceptibility loci and obtain new insights into disease mechanisms, an international team of researchers carried out a large GWAS in which they analyzed over 465,000 autosomal single nucleotide polymorphisms (SNPs) from about 9,800 patients and 17,400 controls (that is, people not affected by multiple sclerosis) from 15 countries.

This analysis confirmed 23 loci that had previously been linked to the disease, and revealed another 29 new loci. Most of the risk attributable to the MHC could be accounted by four mutations, one in class-I locus HLA-A and three in class-II locus HLA-DRB1.

A statistical analysis of the functions of the 52 loci (as annotated in the Gene Ontology database) showed that they are enriched for lymphocyte functions. In particular, many genes encoding cell surface receptors (such as CXCR5 and IL7R) with roles in T-helper-cell differentiation showed strong association with multiple sclerosis. In addition, the researchers identified two susceptibility loci with a role in vitamin D synthesis (CYP27B1 and CYP24A1) and others that encode known targets of therapies for multiple sclerosis such as natalizumab (VCAM1) and daclizumab (IL2RA). By contrast, very few genes with known roles in inflammation-independent neurodegeneration were identified.

The overrepresentation of susceptibility genes with roles in T-cell maturation suggests that multiple sclerosis is primarily caused by immune dysfunction, which is followed by neurological damage. However, the 52 variants can explain only ~20% of the heritability of the disease, and therefore a myriad of other susceptibility loci, each adding a tiny percentage to the overall risk of developing multiple sclerosis, remain to be identified.


Original article:
The International Multiple Sclerosis Genetics Consortium & The Wellcome Trust Case Control Consortium 2 (2011). Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis Nature, 476 (7359), 214-219 DOI: 10.1038/nature10251


The same story in the news:
- Study identifies 57 genes linked with MS, Multiple Sclerosis Society, UK (10 Aug 2011).
- Multiple sclerosis genes identified in largest-ever study of the disease by Alok Jha, The Guardian (10 Aug 2011).
- Scientists unravel genetic clues to multiple sclerosis by Kate Kelland, Reuters (10 Aug 2011).


Note:
During the last 10 months, I have written 18 Research Highlights (short pieces of 300-400 words that summarize recent scientific articles) for Nature Reviews Microbiology. This blog post is based on my first attempt to write a similar piece about a non-microbiological article. However, to make the post more 'blog-friendly', I have embedded some links to definitions of key terms. You can read the definitions by rolling your mouse over the highlighted terms, or you can click on the term to visit a website with more information. Also, I have added a couple of links to news articles that covered the same story.




          A voyage from molecular genetics to microbial ecology -- includes a fish tank and some cartoons   
The March issue of International Microbiology included a very nice article by Roberto Kolter, professor of Microbiology and Molecular Genetics at Harvard Medical School. The title is Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology (freely available as PDF).

In the article, the author gives an entertaining account of the path that lead him to the study of biofilms -- that is, aggregations of microbes growing on solid substrates. He also highlights some of his recent research on the ecology of microbial islands.

There is also a fish tank anecdote. And I added a couple of microbial cartoons, just for fun!

Do microorganisms have microorgasms? (cartoon)
Microbes are excellent model organisms... at least for studies on basic cellular processes. As Jacques Monod put it: Ce qui est vrai pour le colibacille est vrai pour l’éléphant ("what is true for the colibacillus is true for the elephant"). That is why Roberto Kolter (and many other researchers) soon fell under the spell of bacteria and, in particular, the colibacillus Escherichia coli.

For some time, Kolter studied the regulation of cell growth in E. coli. Under the right conditions, cells divide to yield daughter cells, which grow and divide quickly again, and so on -- and the bacterial population undergoes exponential growth. This exponential phase of growth (a.k.a. log phase) is typically followed by a stationary phase, when the growth rate slows down due to a scarcity of nutrients and accumulation of toxic products. Eventually, the bacterial population shrinks, in what is known as death phase (you can visit Cells alive! or Wikipedia for basic information on bacterial growth).

These processes are typically studied in the laboratory using shaken cultures. The shaking of flasks and test tubes keeps the broth composition uniform throughout the flask, and provides a continuous supply of fresh air that helps microbes grow fast. As a result, the cells are in a planktonic state; that is, they grow in suspension in the broth.

Shaker sick microbes (cartoon)From these shaker-sick cultures, Kolter and coworkers learnt a few interesting things about what happens during the stationary and death phases. In the International Microbiology article, he summarizes their findings as follows:
"And what we found through genetic analyses was rather extraordinary. Death allowed new life; we were witnessing evolution in real time [...]. Underlying the usually observed death phase was a dynamic world of dying and growing bacteria. There were constant population takeovers such that pre-existing fitter bacterial mutants grew as the original population met its demise. Evolutionary cheating we would call it later on [...]"
In other words, the adverse conditions occurring in the E. coli cultures during the death phase (toxic products, little food) appeared to have two contrasting effects. It was obvious that many cells were dying -- but, at the same time, successive waves of different spontaneous mutants were able to thrive and outgrow their dying siblings in this less-than-optimal environment. These findings were reviewed in two papers with memorable titles: Life after log and GASPing for life in stationary phase.

Isn't that a fascinating microcosms? The little creatures in the test tube were not just dying; they were evolving!

Pathogenic microbes (cartoon)

And now, the fish tank anecdote. Or, in Kolter's own words, the epiphany of the fish tank:
"The years that followed represented for me a dramatic turn of direction in my research. One might ascribe the change to some sort of “post-tenure depression”; I refer to it as the “epiphany of the fish tank” now. [...]
Microbial life on surfaces, for decades studied by Bill Costerton and other intrepid pioneers of the biofilm field, had been long ignored by most microbial physiologists and molecular geneticists, myself included. However, things changed for me in 1994 when, noticing my depressed state, members of my laboratory gave me a fish tank in a effort to draw me out of the blues. As I sat locked-up in the office staring at the tank, I realized that by studying shaken cultures of E. coli I had been barking up the wrong tree. The water in the fish tank remained crystal clear, it was on the surfaces where most microbial activity was occurring."


Biofilm of Desulfovibrio desulfuricans.That observation applies well beyond fish tanks. It is possible that the majority of microbes on Earth spend most of their lives in aggregates attached to surfaces, and therefore not in a free-floating or swimming, planktonic state. Obviously, they are not solitary guys: we could view biofilms in nature as quite complex 'societies' or 'cities' where different types of microorganisms inhabit buildings made out of sticky macromolecules (polysaccharides, proteins, DNA). Importantly, microbes in biofilms are sometimes resistant to the action of antibiotics, to which the same organisms are sensitive when in planktonic state.

So, have microbiologists been "barking up the wrong tree" all this time? Well, not exactly. Experiments using shaken cultures have been, and will continue to be, extremely useful. They are, without doubt, highly valuable to learn about the biochemistry, genetics and many other aspects of the biology of microbes. And they have been instrumental in providing us with antibiotics and vaccines to fight infectious disease.

But it is true that shaken cultures are sometimes not the best research models, especially if we try to understand 'the real life' of a microbe in its natural environment.



Biofilms formed by Bacillus subtilis.The 'fish tank epiphany' lead Kolter into biofilm research. A first approach he and his collaborators took was to study the biofilms formed by certain Bacillus subtilis strain. The accompanying image shows --on the left-- a beaker with a floating film that the microbe forms when grown in a standing (not shaken!) liquid culture, and --on the right-- a magnified view of a colony grown on an agar plate. Although these biofilms consist only of a single organism, they are actually highly structured, with several layers composed of different cell types engaged in various activities: some cells are actively producing the matrix (not the Wachowskis' movie but the glue that keeps the biofilm together), others are swimming around, and there are also some cells in the process of becoming spores. How close is that to a multicellular organism?

The B. subtilis biofilm is a very useful model -- but you may well think that a beaker containing a single microbial species is a very artificial setting.

Then, how can scientists study biofilms in natural environments? For Kolter, the inspiration came -- no fish tank involved -- from the writings of biologist E. O. Wilson. In collaboration with Robert MacArthur, Wilson developed in the 1960s the theory of island biogeography, which has become fundamental in ecology and evolutionary biology. The theory tries to explain the factors that control the number of species in a natural community (it was originally developed for islands but now it is applied to any ecosystem that is surrounded by other ecosystems). Kolter was fascinated by the ways Wilson studied newly formed islands to put the theory to the test (what Wilson actually did was to fumigate some small islands to kill all arthropods, and then observe how the islands were recolonized). However, Kolter was wise enough and did not try to make free from microbes any islands (that would be tough!). His approach, much less destructive, consisted of studying two natural microbial islands: the pitchers of a carnivorous plant, and the human lungs.

Sarracenia purpureaThe first island is Sarracenia purpurea, a carnivorous plant feeding on the insects and spiders that fall into its water-filled pitchers. Kolter and collaborators found that the inside of unopened, newly formed pitchers was sterile -- there you go, a microbial island is born! This allowed them to analyse the composition of the nascent bacterial population in the pitchers during the season, as microbes colonized the island. Among other results, the researchers found that pitchers containing certain mosquito larvae (keystone predators) had a greater bacterial diversity.

The second microbial island studied by Kolter and coworkers is the respiratory tract of humans suffering from cystic fibrosis (CF). As long as you are healthy, your lungs are supposed to be mostly sterile. However, respiratory diseases such as CF or asthma open the gates to outside microbial colonizers, which can make a lot of harm. In CF, the major microbial pathogen is the bacterium Pseudomonas aeruginosa, which forms biofilms inside the lungs and can easily become resistant to antibiotics. Using culture-independent methods, Kolter's laboratory compared the microbial communities in the lungs of different CF patients. The researchers showed that the presence of P. aeruginosa was correlated with lower microbial diversity, worse lung function, and patient age. In other words, it appears that the arrival of P. aeruginosa (an 'invasive species') greatly affects the microbial community in CF lungs, resulting in a decrease in diversity. The researchers suggest that the composition of the microbial community could be a better predictor of disease progression than the presence of P. aeruginosa alone.


Well, that was a long post. Please read Roberto Kolter's article (it is free), which includes a few more interesting thoughts and quotes. The concept of microbial islands is fascinating. And the growing interaction between the long-time isolated fields of ecology and microbiology is, I think, changing the way microbiologists view their study subjects. Hopefully, ecologists will also become more aware of the organisms that rule the planet -- which are not humans, you know.


Reference for Roberto Kolter's article:
Roberto Kolter (2010). Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology. Int. Microbiol., 13, 1-7. DOI: 10.2436/20.1501.01.105 (pdf)



Related links:

- Biology of microbial communities - Interview to Roberto Kolter (video). JoVE, May 2007.

- Roberto Kolter - Bacillus subtilis and bacteria as multicellular organisms (podcast). Meet the Scientist, episode 20, March 2009. MicrobeWorld.

- The evolution of the biofilm concept: a long and winding road (free PDF), by J.W. Costerton. Sartoniana (2008) 21:59-67.

- About the existence of microbes (viruses) in healthy and diseased human lungs: Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals (2009). PLoS ONE 4(10): e7370. doi:10.1371/journal.pone.0007370 (free article).



Image credits:

- Cartoons by Sanja Saftic. Many thanks to her for allowing me to use the cartoons for this blog post. Source: Biotoon.com - Microbiological Edutainment.

- Color-enhanced scanning electron microscope (SEM) image of a biofilm formed by Desulfovibrio desulfuricans bacteria. Image by PNNL - Pacific Northwest National Laboratory. Source: Flickr.

- Beaker and colony: highly structured biofilms formed by Bacillus subtilis strain NCIB 3610. Source: International Microbiology.

- Sketch of carnivorous plant: Sarracenia purpurea. Source: Wikimedia Commons.



          Live webcast & Twitter: great combination for scientific conferences   



Sing-along tweet
As I mentioned in my previous post, thanks to the internet, I could peek into the meeting of the American Society for Microbiology (ASM), recently held in California, from the comfort of my home at London, UK. This was possible because some of the meeting attendees posted comments on Twitter, in real time, and also because the meeting organizers made a live video broadcast available to everyone through the internet (that is, a webcast).

ASM Live on UStream
The webcast, called ASM Live, consisted of nine interviews to researchers on their latest findings. The interviews were very aptly handled by Jeff Fox, Features Editor for Microbe Magazine (a freely available, monthly magazine published by the ASM). Moreover, viewers were allowed to submit questions to the researchers by either using the online chat (provided by UStream) or tweeting to @MicrobeWorld.

Two of the most popular interviews seemed to be The Gulf oil spill: microbes to the rescue? and The first synthetic genome: what does this mean for microbiology, and for everybody else?? [note that there were two question marks in the original title, and this is not necessarily a typo :) ]

Twitter - ASMnewsroom
All the interviews were really interesting -- and you can still watch them: they are archived at MicrobeWorld (an online community for sharing multimedia resources related to microbiology) and UStream.tv (the live interactive broadcast platform that was used for the ASM webcast).

Twitter - Cesar Sanchez
My sincere congratulations to everybody involved in the making and broadcasting of the interviews, that was a great piece of work!


And now, let's focus on Twitter.

Twitter - Michael Barton
About 1,200 messages containing the #asmgm hashtag were posted to Twitter in relation to the ASM meeting. There were all kinds of messages, and many of them were informative, insightful, or funny. Some of them included links to interesting articles or websites, while others redirected to photos captured during the meeting. I mentioned a couple of popular tweets in a previous blog post, and I'm including here a few more as illustrations.

Twitter - Morgan Langille
However, if you search for the #asmgm hashtag on Twitter, you will only get recent messages posted during the last 7-10 days -- which is really disappointing.

Luckily, Alan Wolf had the brilliant idea of creating an archive for #asmgm tweets on Twapper Keeper. The archive is freely available online, so anybody can read and download all the messages.

Twitter - Jonathan Eisen
In addition to archiving, there are other ways of reading 'old' Twitter messages: for instance, I find Topsy quite useful. However, archiving seems a very sensible idea to me -- especially for scientific conferences.

[Note: Twapper Keeper can only reach back as far as Twitter allows, so the archive needs to be started as soon as possible (ideally a few days before the conference, to include any pre-meeting tweets)]

Twitter - Jonathan EisenOnce the ASM meeting was over, I thought that a word cloud, as a visual representation of 'hot topics' (the most tweeted), could be a nice illustration for a blog post. So, I searched the internet looking for a suitable, user-friendly online tool that would generate -- automagically -- the perfect word cloud for me. But I did not find it.

After a trial-and-error process, I finally made a nice-looking cloud (which was featured image of the week at MicrobeWorld) using Wordle, but the result wasn't exactly what I had in mind:

Word cloud for tweets containing the ASMGM hashtag
Why wasn't I fully satisfied with my cloud? Firstly, because I had to do a lot of manual editing of the tweets: removing highly repetitive terms (such as "#asmgm", "RT"), fixing typos, stemming (a little), putting some words together to create meaningful tags (e.g. "San-Diego")... Also, the cloud was colourful and nice-looking, but the words were not individually hyperlinked (as in most tag clouds, see for instance the cloud located at the upper right side of my blog).

Twitter - Comprendia[Note: a tweetup is a meeting of two or more people who know each other through Twitter]

There are some online tools to generate tag clouds from Twitter messages. For instance, Tweetcloud seems to get quite close to what I have in mind. It indeed generates a tag cloud for a specific keyword (or user). But it seems to be limited by the Twitter search function (it only uses messages posted in the last 7-10 days). So, I guess I could have used this tool the day after the ASM meeting to create a cloud... but I didn't known about Tweetcloud at the time. Still, the cloud is not customizable at all.

Twitter - Mr. Gunn
So, I want to finish this post summarizing the characteristics of what I think would be an ideal tool to create word clouds from Twitter messages:

A) General
  • Freely available, online tool.

  • It could make a cloud for a hashtag, a word, a term composed of several words, or a Twitter user.

B) Searching Twitter
  • It wouldn't be limited by the 7-10 days boundary of the present search function of Twitter.

  • It would provide options to define specific limits for time (e.g. "only tweets posted between two given dates") and number of tweets ("only the last 100 tweets").

  • Options to exclude, or include, certain types of messages (replies, retweets, containing links, linking to images, linking to videos) or users ("exclude these users").

C) Creating the cloud
  • Options to use only hashtags (similar to My Tweet Cloud), exclude particular words (common words, numbers), use only particular types of words (e.g. nouns?).

  • Stemming.

  • It would detect possible typos, showing a list of candidates to be fixed. The user would decide if they should be corrected or not.

  • It would suggest possible tags composed of more than one word (e.g. "San" and "Diego" are always found together, do you want the tool to combine them into a single tag "San Diego"?). The user would decide.

  • The tags in the cloud should be hyperlinked. That is, clicking on a term such as "San Diego" would redirect to a list of tweets that included such a term.

D) Customizing the aspect of the cloud
  • Options to change the colour and relative orientation of tags, and the general aspect of the cloud (similar to Wordle).

  • Options to create an animated cloud showing changes in time (or location, user, etc). For instance, several clouds could be generated for a hashtag for different days (similar to this example) and could be combined into a single animated cloud. The user would define the period used to create each 'sub-cloud' (e.g. every day, every 6 hours) and the number of clouds needed for a smooth animation.




Please leave your comments, ideas or suggestions on creating Twitter tag clouds, or on the use of live webcast and Twitter for scientific conferences.




Twitter - Jennifer Gardy


Twitter - Cesar Sanchez



Note added on June 23rd:
I just read a great article on this topic: Twitterpated: Using Social Media at Academic Conferences. I found it via Hacking the Academy, a book that was crowdsourced on Twitter in one week. It deals with online education, scholarly communication and much more.


Related links:

- Added July 3rd: How to create a PDF archive of hashtagged tweets by Andrew Spong, STweM. It describes a simple workflow for archiving conference tweets. Found via FriendFeed.

- Added August 15th: SfN the Meh by DrugMonkey. Advice to the Society for Neuroscience (and other scientific societies): how to use social media for your next conference.

- Added August 22nd: Tagxedo - Tag Cloud with Styles. Tagxedo turns any word set (texts, blogs, tweets) into a visually appealing tag cloud. The cloud can fit a predetermined shape or silhouette. Link found via Andrew Spong's FriendFeed.

- Added September 4, 2010: Summarizr is a service that creates "a brief summary of a Twapper Keeper tweet archive. It works for #hashtag archives, keyword archives and @person archives. Just enter a hashtag, keyword, Twitter account name or archive URL in the form". See Twitter usage at the ASM meeting, based on TwapperKeeper archive of hashtag #asmgm.



          Year of Biodiversity: only for cute animals and plants?   
International Year of Biodiversity LogoThe United Nations declared 2010 to be the International Year of Biodiversity. This sounds great, let's celebrate and protect the variety of life on Earth! We must learn more about current (and past) biodiversity and the impact that human activities have on the distribution and abundance of organisms. Also, we should explore any effective ways to protect biodiversity, if only because it benefits us.

However, it strikes me as short-sighted that most biodiversity advocates seem to care only about "the cute organisms" (cute by most human standards, I guess); that is, a few particular animals and plants. But... for Pete's sake, life on Earth goes well beyond a few vertebrates, trees and corals! Surprisingly, the true diversity of life is not obvious at all in the writings of most biologists, conservationists or environmental scientists when discussing biodiversity and its protection.

I know, I know -- when a clear message is to be delivered to the general public, you cannot be comprehensive. If you can mention only a couple of examples for endangered species, you better go for the much-like-us mammal, or the colourful bird, or the pretty tree or flower. Most of us can easily sympathize with a chimpanzee (that is, really, almost one of us) or with many animals: they have faces, with two eyes and a mouth, and it's hard not to see part of our own reflection there. We often show emotional responses also to trees, flowers or grasses (even mushrooms). So, when explaining the importance of biodiversity to a general audience, sticking to the cute guys might be the wise choice.

But how is this topic treated inside the scientific community? Well, in general, I don't see much difference. When biodiversity is discussed -- in general terms -- in scientific articles, editorials or websites, the focus is again on certain plants and animals that can be seen by the unaided human eye (that is, macro-organisms). By contrast, microbes are hardly ever referenced, if at all.

Why are microbes not even mentioned most of the times? Why are some particular organisms (let's call them "the cuties" for short) the focus of research and protectionist efforts? I can think of a few possible answers:

1 - The cuties, among all the living beings, might suffer the highest risk of extinction.
2 - Although there are other organisms at higher risk, the cuties are perhaps more important (in some way) either for the preservation of particular ecosystems or for human well-being.
3 - Our current knowledge of life diversity might be very limited, and is focused on particular organisms because of historical and technical reasons.

I guess that most scientists and many learned people would agree with me that answer number 3 seems about right (but if you think otherwise, please leave a comment). Actually, it seems that we know very little on the matter. Scientists are starting to agree -- I think -- on a broad definition of biodiversity. But the field faces (at least) two huge challenges. First, there are many organisms living on (and inside) this planet that we haven't met yet, and our estimates of how many species are awaiting discovery are little more than educated guesses. Second, although biodiversity can be measured at various levels, it's often understood as referring to the number and relative abundance of different species. And deciding if two organisms belong to a single species, or to two different ones, can be really hard. Moreover, the difficulty in agreeing on species definition depends greatly on the type of organism it applies to: whereas this issue causes some serious troubles when studying cuties, it appears almost insurmountable when trying to define microbial species. Why is this so? Well, I'm not getting into this here, but let's say that the species concept was originally created and crafted for the cuties, and microorganisms just don't fit into such clothes.

However, even lacking a suitable species definition (to the embarrassment of microbiologists), we can confidently say that the microbes are much more diverse than the cuties. This diversity is shown at different levels: genetics, biochemistry, ecology... You can find microbes almost everywhere, and often in amazingly high numbers. No matter if you count individuals or you measure biomass: microbes are the (silent?) majority. Some microorganisms are essential not just for the preservation of particular ecosystems but for the continuity of life on Earth as we know it (and when I write "life" I mean "life", not just "cuties"). Under any non-human-centred point of view, life is microbial -- with a few exceptions, yes.

So, just to recapitulate... Some animals and plants appear to be on the brink of extinction because of human actions, and it doesn't seem a good idea to let them go. However, we don't know how many types of organisms are out there, or how many of them are endangered by our activities, and we don't understand the long-term effects of the extinction of any particular life form. Yes, more research is definitely needed.

But we do know that life is incredibly diverse and mostly invisible to the human eye, and that the cuties are not even the tip of the iceberg. So, any serious research or scientific communication on the diversity of life should include (in my opinion) some mention to microbes, the main actors on this movie -- at least we should acknowledge our ignorance! Microbes play key roles in nature: shouldn't we worry about the preservation of microbial diversity?

Don't get me wrong: I don't want any cuties to become extinct. But I think that scientists can do a much better job when discussing biodiversity.



Further reading:

If you find the topic of this post interesting, you must read the following excellent articles written by Sean Nee, University of Edinburgh, UK (articles can be downloaded from the author's website):

- The great chain of being. Nature (2005) 435: 429.
"Our persistence in placing ourselves at the top of the Great Chain of Being suggests we have some deep psychological need to see ourselves as the culmination of creation."

- Extinction, slime and bottoms. PLoS Biology (2005) 2(8): e272.
"There is an old Chinese curse: ‘May you live in interesting times.’ According to those who know about such things, we live in a momentous time, the time of the Sixth Mass Extinction! But most of us do not feel at all cursed. Because, in fact, the Sixth is quite different to the previous Big Five—no-one would notice this one if we were not repeatedly reminded of it by ecologists."

- More than meets the eye: Earth's real biodiversity is invisible. Nature (2004) 429: 804-805.
"We are still at the very beginning of a golden age of biodiversity discovery, driven largely by the advances in molecular biology and a new open-mindedness about where life might be found. But for this golden age to be as widely appreciated as it should, our view of the natural world must change — as radically as did our view of the cosmos when we began looking at it with technologies that allowed us to see more than can be seen with the naked eye."

- Beyond the tangled bank (pdf). This manuscript seems a slightly longer version of More than meets the eye: Earth's real biodiversity is invisible. Interestingly, it includes many references that were not incorporated into the published article.


I also recommend a thought-provoking article by Maureen A. O’Malley & John Dupré, University of Exeter, UK:

- Size doesn’t matter: towards a more inclusive philosophy of biology. Biology and Philosophy (2007) 22, 155-191.


NOTE added on April 17, 2010:
A Letter has just been published by Andrew Beattie and Paul Ehrlich in Science, highlighting what The Missing Link in Biodiversity Conservation is:
"the many millions of species within the numerous phyla of microbes and invertebrates, which represent perhaps 95% of total species and genetic biodiversity."
The authors propose to deliver a new message to the public:
"a new message, one we would like to label "production biodiversity": By protecting microbes and invertebrates, we also protect the primary industries upon which we all depend."

I agree!


Related links:
- (Added April 20, 2010) A commentary on the same subject has been published by Mercè Piqueras in her blog, La lectora corrent (in Catalan): La biodiversitat invisible.

- (Added June 23, 2010) See Dear New Scientist by Ed Rybicki, who reminds us that "the greatest part of the biodiversity on this (and probably any other) planet is viruses."

- (Added August 19, 2010) Preserving endangered species – of gut microbes, by Grant Jacobs. Or the need to preserve the human gut microbes found in ancient rural populations.

- (Added September 11, 2011) Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet, by Jonathan Eisen.

- (Added September 11, 2011) Don’t forget to count microbes, by David Hooper & Bonnie Bassler.



          The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.   
Related Articles

The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.

Nat Genet. 2016 Jun;48(6):648-56

Authors: Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, University of Washington Center for Mendelian Genomics, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB

Abstract
Cilia use microtubule-based intraflagellar transport (IFT) to organize intercellular signaling. Ciliopathies are a spectrum of human diseases resulting from defects in cilia structure or function. The mechanisms regulating the assembly of ciliary multiprotein complexes and the transport of these complexes to the base of cilia remain largely unknown. Combining proteomics, in vivo imaging and genetic analysis of proteins linked to planar cell polarity (Inturned, Fuzzy and Wdpcp), we identified and characterized a new genetic module, which we term CPLANE (ciliogenesis and planar polarity effector), and an extensive associated protein network. CPLANE proteins physically and functionally interact with the poorly understood ciliopathy-associated protein Jbts17 at basal bodies, where they act to recruit a specific subset of IFT-A proteins. In the absence of CPLANE, defective IFT-A particles enter the axoneme and IFT-B trafficking is severely perturbed. Accordingly, mutation of CPLANE genes elicits specific ciliopathy phenotypes in mouse models and is associated with ciliopathies in human patients.

PMID: 27158779 [PubMed - indexed for MEDLINE]


          Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.   
Related Articles

Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis.

Nat Genet. 2016 Jun;48(6):687-93

Authors: Li C, Gu L, Gao L, Chen C, Wei CQ, Qiu Q, Chien CW, Wang S, Jiang L, Ai LF, Chen CY, Yang S, Nguyen V, Qi Y, Snyder MP, Burlingame AL, Kohalmi SE, Huang S, Cao X, Wang ZY, Wu K, Chen X, Cui Y

Abstract
SWI/SNF-type chromatin remodelers, such as BRAHMA (BRM), and H3K27 demethylases both have active roles in regulating gene expression at the chromatin level, but how they are recruited to specific genomic sites remains largely unknown. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), a plant-unique H3K27 demethylase, targets genomic loci containing a CTCTGYTY motif via its zinc-finger (ZnF) domains and facilitates the recruitment of BRM. Genome-wide analyses showed that REF6 colocalizes with BRM at many genomic sites with the CTCTGYTY motif. Loss of REF6 results in decreased BRM occupancy at BRM-REF6 co-targets. Furthermore, REF6 directly binds to the CTCTGYTY motif in vitro, and deletion of the motif from a target gene renders it inaccessible to REF6 in vivo. Finally, we show that, when its ZnF domains are deleted, REF6 loses its genomic targeting ability. Thus, our work identifies a new genomic targeting mechanism for an H3K27 demethylase and demonstrates its key role in recruiting the BRM chromatin remodeler.

PMID: 27111034 [PubMed - indexed for MEDLINE]


          "Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements.   
Related Articles

"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements.

Mol Biol Evol. 2016 May;33(5):1358-69

Authors: Marcovitz A, Jia R, Bejerano G

Abstract
Evolutionary changes in cis-regulatory elements are thought to play a key role in morphological and physiological diversity across animals. Many conserved noncoding elements (CNEs) function as cis-regulatory elements, controlling gene expression levels in different biological contexts. However, determining specific associations between CNEs and related phenotypes is a challenging task. Here, we present a computational "reverse genomics" approach that predicts the phenotypic functions of human CNEs. We identify thousands of human CNEs that were lost in at least two independent mammalian lineages (IL-CNEs), and match their evolutionary profiles against a diverse set of phenotypes recently annotated across multiple mammalian species. We identify 2,759 compelling associations between human CNEs and a diverse set of mammalian phenotypes. We discuss multiple CNEs, including a predicted ear element near BMP7, a pelvic CNE in FBN1, a brain morphology element in UBE4B, and an aquatic adaptation forelimb CNE near EGR2, and provide a full list of our predictions. As more genomes are sequenced and more traits are annotated across species, we expect our method to facilitate the interpretation of noncoding mutations in human disease and expedite the discovery of individual CNEs that play key roles in human evolution and development.

PMID: 26744417 [PubMed - indexed for MEDLINE]


          9th International Conference on Genomics & Pharmacogenomics - $ 599 USD   
Genomics-2017Genomics is an area within genetics that concerns the sequencing and analysis of an organism?s genome. Genomics also involves the study of intrag...
          Duke Researchers Find a Shortcut to Predicting New Magnetic Materials   

High-performance magnets are ubiquitous in technology today, from hard drives to hybrid and electric vehicles to medical imaging equipment. The development of these magnets is a story itself. Only about 5 percent of inorganic materials are magnetic at all, and the development of high-performance magnets has proven to be a long and unpredictable process that largely relied on trial and error.
 
Magnetism is a highly sensitive phenomenon. From the perspective of the atomic structure, it requires the right confluence of properties and conditions, yielding a multitude of mechanisms for achieving magnetic ordering. It’s also not a very intuitive process, which makes it hard for humans to predict. Today, there are only about two dozen magnets suitable for technological applications.

Materials scientists from Duke University have demonstrated a shortcut to the traditional trial-and-error process. Using high throughput computational models that predict magnetism in new materials, the scientists have successfully developed, atom by atom, two new magnetic materials: cobalt, magnesium and titanium (Co2MnTi); and manganese, platinum and palladium (Mn2PtPd).

Using the computer model, the researchers focused on Heusler alloys, or materials made with atoms from three different elements arranged in one of three different structures. With 55 elements to choose from (and all possible potential arrangements), the manual process would have required testing 236,115 combinations. The model permitted the team to test hundreds of thousands of possibilities rapidly, resulting in two magnets that could be fabricated at thermodynamic equilibrium.

Corey Oses, a doctoral student in the Center for Materials Genomics at Duke and one of the co-authors of the research paper, told Design News that the goal was to speed up the process of developing new magnets.
“Not much progress had been made since about the 1980s, considering the current market for permanent magnets is still dominated by neodymium/samarium-based materials,” he said. “Unfortunately, the trial-and-error approach is not systematic: there is no known or direct path to the discovery of a new magnets. This research represents such a path, and has been validated by the discovery of two new magnets.”

 

Duke magnets

1Unit cells and phase stability of HAs. Possible HAs: (A) regular Heusler, (B) inverse Heusler, and (C) half Heusler. In (D), we show the unit cell used to construct the electronic structure database. (E) Ternary convex hull diagram for Al-Mn-Ni (note the presence of the stable HA, Ni2MnAl). (Image Source: Duke)

 

The team used the High-Throughput Framework AFLOW (Automatic FLOW for Materials Discovery), which leverages VASP (the Vienna Ab-Initio Simulation Package) for calculating the electronic structure and optimized atomic geometries. The AFLOW package populates the AFLOW.org repositories consisting of nearly 1.7 million compounds and their properties. One of these repositories is the Heusler database used by the team in their research. From the 236,115 possible combinations, the computational model identified 35,602 potentially stable compounds. Further testing for stability narrowed the list to 248, but only 22 materials showed a calculated magnetic moment. From here, the team narrowed the list to 14 by eliminating any materials with competing alternative structures “too close for comfort.”

“A thermodynamic analysis indicates the stability of candidate materials, determined by characterizing the energetic landscape,” Oses told Design News. “Stable structures define the minimum of this surface.  This can be seen as a ‘competition’ among structures of similar compositions for the minimum energy stable position. Depending on the particular system and the local environment of similar structures, the competition can be high (many similar structures near the minimum), or low (a clear ‘winner’ is present, with others far behind).  We defined a descriptor to quantify the intensity of this competition, and screened for the clear ‘winners.’”

When it came time to synthesize the materials, the lead researcher, Stefano Curtarolo, professor of mechanical engineering and materials science and director of Duke’s Center for Materials Genomics, and the team worked with Stefano Sanvito, professor of physics at Trinity College in Dublin, Ireland. Attempts to create four new materials predicted by the computer model resulted in success with the two final materials.

The materials developed are significant because they don’t involve the use of any rare-earth minerals, which are difficult to obtain. The high costs and limited availability of many existing high-performance magnets make them impractical for many applications. Additionally, one of the materials, Co2MnTi, also featured an unusually high "Curie temperature,” which is desirable in a high-performance magnet.

“Magnetization in ferromagnetic materials is the result of the alignment of electronic spins,” Oses told Design News. “Temperature can disrupt such alignment, as it can induce spin-flips. The Curie temperature is the (material-specific) temperature at which the alignment disappears (cancellation of spin up vs. spin down). In other words, the temperature at which the material loses its magnetization.  A high Curie temperature ensures that the material can function in a wide range of operating conditions.”

The research team notes that their work isn’t about the two specific magnetic materials they developed, but the process itself, which paves the way for large-scale design of novel magnetic materials at potentially high speed. These new materials will be significant to any device or apparatus that uses an electromagnet: motors, wind turbines, transformers, MRI machines, hard disks for computer memory and more, including (potentially) the long-anticipated promises of maglev transportation devices.

Going forward, the team plans to continue combing through the Heusler family for more magnets and leveraging the same approach in new families of materials. The researchers’ work was published in Science Advances.


          Incyte-Proprietary Microarrays   
Incyte-Proprietary Clones on Microarrays Incyte has combined its in-house bioinformatics expertise and unparalleled genomic databases to develop several new prefabricated microarrays. Each contains up to 10,000 sequence-verified, Incyte-proprietary clones represented in our LifeSeq, ZooSeq, and PathoSeq databases and in our GeneAlbum reagent set. Following is a list of Incyte-proprietary microarrays and their expected availability. Family […]
          Top Geneticist Rejects the "Junk DNA" viewpoint   



Oh look! I have in my hand the most up-to-date book available,
on Mobile DNA. Its by the world's leading expert on that topic.

Oh oh, he's not an ID guy. He's not a creationist.
OMG he's not even a Christian or Jew, or muslim.

The title is hilariously "Mobile DNA", by H.H. Kazazian, (2012, FT Press).


We'd better check his credentials:
We wouldn't want any 'unscientific' amateurs sneaking in,
misrepresenting themselves and taking credit for BAs in philosophy,
or PhDs in religion here:


Hmmm. lets see:

finished his M.D. degree at Johns Hopkins University School of Medicine.

Interned in Pediatrics at University of Minnesota Hospital.

Returned to Johns Hopkins for a Fellowship in Genetics,

Then Trained in molecular biology at the NIH.

Rejoined the Faculty at Johns Hopkins.

Rose to full professorship there in 1977.

Became Director of the Center for Medical Genetics (Johns Hopkins) 1988.

Spent 25 years on the John Hopkins Faculty.

Recruited to University of Pennsylvania School of Medicine, as
Chair of the Dept. of Genetics in 1994.

Remained as Seymour Grey Professor of Molecular Medicine in Genetics till 2010.

Returned to Johns Hopkins in July 2010.

Heavily involved in molecular genetic research for the past 20 years
specializing in mammalian and human transposable elements, "jumping genes".

Personally characterized much of the variation in the cluster of genes
involved in production of the beta chain of human hemoglobin.

His work led to the nearly complete characterization of the mutations
causing the Beta-thalassemias, common anemias in malaria regions.

Received many honours for his research, most notably the
2008 William Allan Award, the top honour of the
American Society of Human Genetics.


Well, what does he say about Junk DNA?


"...most genes are broken up by sections of DNA called introns
that need to be removed at the RNA stage in order for the genes
to function. ...the protein-coding regions of the genes make up
a very small fraction of mammalian genomes.
...In the late 1970s, introns were found...
Soon we knew that introns were much larger than protein-coding regions,
then called exons.
The DNA between the genes was thought to be functionless,
and was called "junk DNA" (Orgel and Crick, 1980).
However, now we know that introns make up about 30% of human
and mammalian genomes, and exons only encode between 1 and 2%
of the human genome (Lander et al., 2001).
What a comedown for the protein-encoding regions!
Thus over 98% of human DNA had been dismissed as "junk".

Transposable elements were then found, and this active mobile DNA
along with the remnants is now known to account for at least 50%
of human genomic DNA. Both the relatively few presently mobile
sequences, and the many remnants of old events are now
demonstrating function.

...evident in the many ways mobile DNA can modify the genome over evolutionary time.
It can also be co-opted for useful purposes...
Moreover, DNA encoding small RNAs of different types and functions
has been discovered amidst the "junk". Enhancer sequences at great
distances from the genes upon which they act are being found continually.
...
The bottom line is that "junk" DNA is gradually being eroded away as
function is found for a greater and greater fraction of the genomic DNA
."


- Mobile DNA, pp. 1-3

His comfortable use of "evolutionary" makes clear he is an evolutionist,
as well as one of the top experts in human DNA.

          Practicing qigong can change your genes response to stress   












Practicing qigong can change your genes response to stress

Below are some excerpts from "Researching the Benefits of Mind-Body Practice by Investigating Genetic Expression" by Roger Jahnke, OMD.

The full report on this exciting breakthrough in how practices like qigong can actually change gene expression is available on his website at www.instituteofintegralqigongandtaichi.org/pdfs/Qigong_GeneExpression.pdf

I have included a link to one of my earlier articles on telomeres, the protective caps on immune cells, and have made a few comments about holistic practices at the end of the quote.

First: Just what is "Gene Expression?" This, from wikipedia Gene expression is the process by which inheritable information from a gene, such as the DNA sequence, is made into a functional gene product, such as protein or RNA.

Regulation of gene expression is the cellular control of the amount and timing of appearance of the functional product of a gene. Any step of gene expression may be modulated, from the DNA-RNA transcription step to post-translational modification of a protein. Gene regulation gives the cell control over structure and function, and is the basis for cellular differentiation, morphogenesis and the versatility and adaptability of any organism.

Source: http://en.wikipedia.org/wiki/Gene_expression

So, with that in mind, here is the feature article:

*** Begin Quote ***

Page 4 – 5

In a number of press releases the authors of Genomic counter-stress changes induced by the relaxation response made a number of comments that are easily applicable to all three studies. They state that:

"This study provides the first compelling evidence that the RR [relaxation response] elicits specific gene expression changes in short-term and long- term practitioners."

Actually the other studies were earlier and they all suggest this.

The Genomic Counter-stress authors wrote that their findings suggest:

"Consistent and constitutive changes in gene expression resulting from RR may relate to long term physiological effects," and that "Our study may stimulate new investigations into applying transcriptional profiling for accurately measuring RR and stress related responses in multiple disease settings."

It is likely that these studies portend a “sea change” in research and will trigger an outpouring of similar research. Dr. Herbert Benson, professor emeritus of Harvard University and director emeritus of the Benson-Henry Institute and co-senior author of the study said:

"Now we've found how changing the activity of the mind can alter the way basic genetic instructions are implemented," said Benson.

Dr. Towia Libermann, director of the BIDMC Genomics Center and also co-senior

author of the study added:

"This is the first comprehensive study of how the mind can affect gene expression, linking what has been looked on as a 'soft' science with the 'hard' science of genomics.” "It is also important because of its focus on gene expression in healthy individuals, rather than in disease states," explained Libermann.

The authors said their study showed that the relaxation response changed the expression of genes involved with inflammation, programmed cell death and the handling of free radicals. Free radicals are normal byproducts of metabolism that the body neutralizes in order to stop damage to cells and tissues.

Page 5 – 6

Probably the most compelling statement from the article on the findings of the study was “It is becoming increasingly clear that psychosocial stress can manifest as system-wide perturbations of cellular processes, generally increasing oxidative stress and promoting a pro-inflammatory milieu. Stress associated changes in peripheral blood leukocyte expression of single genes have been identified. More recently, chronic psychosocial stress has been associated with accelerated aging at the cellular level. Specifically, shortened telomeres, low telomerase activity, decreased anti-oxidant capacity and increased oxidative stress are correlated with increased psychosocial stress and with increased vulnerability to a variety of disease states.”

These 3 studies strongly suggest that Mind-Body practices, especially those that trigger a sustained and accumulative RR effect – a counter stress effect – can prevent and ameliorate disease. This effect of Mind-Body practice on gene expression transforms the landscape of scientific exploration and launches an entirely new direction for the investigation for the emerging field of health maximization based integrative medicine.

Page 21 – 22

It is becoming increasingly clear that psychosocial stress can manifest as system-wide perturbations of cellular processes, generally increasing oxidative stress and promoting a pro-inflammatory milieu [23]–[25]. Stress associated changes in peripheral blood leukocyte expression of single genes have been identified [26]–[28]. More recently, chronic psychosocial stress has been associated with accelerated aging at the cellular level. Specifically, shortened telomeres, low telomerase activity, decreased anti-oxidant capacity and increased oxidative stress are correlated with increased psychosocial stress [29] and with increased vulnerability to a variety of disease states [30]. Stress-related changes in GEP have been demonstrated by microarray analysis in healthy subjects, including up-regulation of several cytokines/chemokines and their receptors [31], and in individuals suffering from post-traumatic stress disorder, including inflammation, apoptosis and stress response [32] as well as metabolism and RNA processing pathways [33]. The pro-inflammatory transcription factor NF-kappa B (NF-κB) which is activated by psychosocial stress has been identified as a potential link between stress and oxidative cellular activation [34].




Immune cells - blue



Telomere protective end-caps - yellow





[For a brief explanation of the connection between telomeres (the protective caps on the ends of immune cells) and stress, see my post "Scientists identify mechanism behind mind-body connection" http://successstressrelief.blogspot.com/2008/07/scientists-identify-mechanism-behind.html on my Stress Relief for Savvy Women blog.]


The RR is clinically effective for ameliorating symptoms in a variety of stress-related disorders including cardiovascular, autoimmune and other inflammatory conditions and pain [15]. We hypothesize that RR elicitation is associated with systemic gene expression changes in molecular and biochemical pathways involved in cellular metabolism, oxidative phosphorylation/generation of reactive oxygen species and response to oxidative stress and that these changes to some degree serve to ameliorate the negative impact of stress. Genome-wide evaluation of PBL GEP is a reasonable approach to survey the transcriptional changes that are involved in elicitation of the RR. The GEP of RR practitioners presented here reveals altered gene expression in specific functional groups which suggest a greater capacity to respond to oxidative stress and the associated cellular damage. Genes including COX7B, UQCRB and CASP2 change in opposite direction from that in the stress response [31], [32].

Our findings are relatively consistent with those found in a study of Qi Gong [17], a practice that elicits the RR. In their study of 6 Qi Gong practitioners and 6 aged matched controls, practitioners had down-regulation of ubiquitin, proteasome, ribosomal protein and stress response genes and mixed up- and down-regulation of genes involved in apoptosis and immune function. We find a similar pattern of GO categories that are significantly over-represented in GO or enriched in GSEA in our cross sectional comparison, M vs. N1. However, in our data-set ribosomal proteins were up-regulated.

Overall, similar genomic pattern changes occurred in practitioners of a specific mind body technique (Qi Gong) as well as in our long-term practitioners who utilized different RR practices including Vipassana, mantra, mindfulness or transcendental meditation, breath focus, Kripalu or Kundalini Yoga, and repetitive prayer. This indicates there is a common RR state regardless of the techniques used to elicit it.

Footnotes included in the above quoted materials:

15. Astin JA, Shapiro SL, Eisenberg DM, Forys KL (2003) Mind-body medicine: state of the science, implications for practice. J Am Board Fam Pract 16: 131–147.

17. Li QZ, Li P, Garcia GE, Johnson RJ, Feng L (2005) Genomic profiling of neutrophil transcripts in Asian Qigong practitioners: a pilot study in gene regulation by mind-body interaction. J Altern Complement Med 11: 29–39.

23. Irie M, Asami S, Nagata S, Miyata M, Kasai H (2002) Psychological mediation of a type of oxidative DNA damage, 8-hyDr.oxydeoxyguanosine, in peripheral blood leukocytes of non-smoking and non-Dr.inking workers. Psychother Psychosom 71: 90–96.

24. Yamaguchi T, Shioji I, Sugimoto A, Yamaoka M (2002) Psychological stress increases bilirubin metabolites in human urine. Biochem Biophys Res Commun 293: 517–520.

25. Zheng KC, Ariizumi M (2007) Modulations of immune functions and oxidative status induced by noise stress. J Occup Health 49: 32–38.

26. Glaser R, Kennedy S, Lafuse WP, Bonneau RH, Speicher C, et al. (1990) Psychological stress-induced modulation of interleukin 2 receptor gene expression and interleukin 2 production in peripheral blood leukocytes. Arch Gen Psychiatry 47: 707–712.

27. Glaser R, Lafuse WP, Bonneau RH, Atkinson C, Kiecolt-Glaser JK (1993) Stress-associated modulation of proto-oncogene expression in human peripheral blood leukocytes. Behav Neurosci 107: 525–529.

28. Platt JE, He X, Tang D, Slater J, Goldstein M (1995) C-fos expression in vivo in human lymphocytes in response to stress. Prog Neuropsychopharmacol Biol Psychiatry 19: 65–74.

29. Epel ES, Blackburn EH, Lin J, Dhabhar FS, Adler NE, et al. (2004) Accelerated telomere shortening in response to life stress. Proc Natl Acad Sci U S A 101: 17312–17315.

30. Epel ES, Lin J, Wilhelm FH, Wolkowitz OM, Cawthon R, et al. (2006) Cell aging in relation to stress arousal and cardiovascular disease risk factors. Psychoneuroendocrinology 31: 277–287.

31. Morita K, Saito T, Ohta M, Ohmori T, Kawai K, et al. (2005) Expression analysis of psychological stress-associated genes in peripheral blood leukocytes. Neurosci Lett 381: 57–62.

32. Zieker J, Zieker D, Jatzko A, Dietzsch J, Nieselt K, et al. (2007) Differential gene expression in peripheral blood of patients suffering from posttraumatic stress disorder. Mol Psychiatry 12: 116–118.

33. Segman RH, Shefi N, Goltser-Dubner T, Friedman N, Kaminski N, et al. (2005) Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors. Mol Psychiatry 10: 500–513, 425.

34. Bierhaus A, Wolf J, AnDr.assy M, Rohleder N, Humpert PM, et al. (2003) A mechanism converting psychosocial stress into mononuclear cell activation. Proc Natl Acad Sci U S A 100: 1920–1925.

*** EndQuote ***


Bottom Line: Qigong, mindfulness meditation, the use of mantras and other chants, and other mind-body practices can change how your genes respond to stress! If this occurs at the cellular level, it is an indication that qigong and other mind-body practices can actually change your cells or cellular activity.

As a stress-relief consultant and qigong instructor, I can help you to use these methods, enabling you to be healthier, avoid "a variety of stress-related disorders including cardiovascular, autoimmune and other inflammatory conditions and pain" (see above), age slower, look younger, live longer, and life a fuller and happier life!

Contact me through the form in the sidebar or through my email address in my profile. I am committed to helping you relieve stress in the natural and holistic ways that work best for your mind, body, and spirit.


          The Lancet Infectious Diseases: January 17, 2014   

Yonatan Grad discusses the genomic epidemiology of antibiotic resistant gonorrhoea in the USA.


          Trovagene Announces Manufacturing Agreement with NerPharMa for Supply of PCM-075 for AML Trial   

SAN DIEGO, June 29, 2017 /PRNewswire/ -- Trovagene, Inc. (NASDAQ: TROV), a precision medicine biotechnology company, today announced it has executed a supplier agreement with NerPharMa, S.r.l., a pharmaceutical manufacturing company and a subsidiary of Nerviano Medical Sciences S.r.l., in Milan, Italy, to manufacture drug product for PCM-075. The agreement covers the clinical and commercial supply of PCM-075 for Trovagene, and includes both Active Pharmaceutical Ingredients (API) and GMP (Good Manufacturing Process) production of capsules.

NerPharMa has previously supplied drug product for PCM-075 in a completed phase 1 study conducted by Nerviano Medical Sciences.  NerPharMa has an established manufacturing process scaled for producing PCM-075 for future clinical studies and commercial use.  Under the terms of the agreement, Trovagene directs NerPharMa to produce GMP-grade PCM-075 drug substance for use in Trovagene's Phase 1b/2 clinical program and for other related clinical and commercial activities. Trovagene is developing PCM-075, a polo-like kinase 1 (PLK1) inhibitor, and plans to initiate a Phase 1b/2 clinical trial in patients with acute myeloid leukemia (AML).

"This contract represents a significant step forward for the development of PCM-075," said Bill Welch, Chief Executive Officer of Trovagene. "We are excited to have a manufacturer of NerPharMa's caliber and experience producing GMP supply of PCM-075 bulk product and finished capsules. The availability of validated API and the ability to immediately initiate capsule production enables a cost-effective and accelerated start-up of our Phase 1b/2 clinical program."

NerPharMa's GMP manufacturing facility is approved by both the Italian Medicines Agency (AIFA), the national authority responsible for drug regulation in Italy, and the U.S. Food and Drug Administration (FDA) for the production of PCM-075.

"We are pleased to be working with Trovagene to manufacture and provide finished product for their investigational and commercial needs," said Angelo Colombo, CEO of NerPharMa.

About PCM-075

PCM-075 is a highly-selective adenosine triphosphate (ATP) competitive inhibitor of the serine/threonine polo-like-kinase 1 (PLK 1) enzyme, which is over-expressed in several different hematologic malignancies, as well as solid tumors such as breast, prostate, ovarian, lung, gastric and colon cancers. PCM-075 is orally bioavailable and has been explored in an initial Phase 1, open-label, dose-escalation safety study in patients with advanced metastatic solid tumor cancers. In this study, PCM-075 demonstrated an acceptable safety profile, as well as anti-tumor activity. Trovagene plans to initiate clinical trials of PCM-075 in AML, since it has significant advantages over prior PLK1 inhibitors evaluated in this indication, including a higher selectivity, greater potency, oral bioavailability and shorter half-life.

About Nerviano Medical Sciences (NMS)

Nerviano Medical Sciences, part of the NMS Group, is the largest pharmaceutical research and development facility in Italy and one of the largest oncology-focused, integrated discovery and development companies in Europe.

About Trovagene, Inc.

Trovagene is a precision medicine biotechnology company developing oncology therapeutics for improved cancer care by leveraging its proprietary Precision Cancer Monitoring® (PCM) technology in tumor genomics.  Trovagene has broad intellectual property and proprietary technology to measure circulating tumor DNA (ctDNA) in urine and blood to identify and quantify clinically actionable markers for predicting response to cancer therapies.  Trovagene offers its PCM technology at its CLIA/CAP – accredited laboratory and plans to continue to vertically integrate its PCM technology with precision cancer therapeutics.  For more information, please visit https://www.trovagene.com.

Forward-Looking Statements

Certain statements in this press release are forward-looking within the meaning of the Private Securities Litigation Reform Act of 1995. These statements may be identified by the use of words such as "anticipate," "believe," "forecast," "estimated" and "intend" or other similar terms or expressions that concern Trovagene's expectations, strategy, plans or intentions. These forward-looking statements are based on Trovagene's current expectations and actual results could differ materially.  There are a number of factors that could cause actual events to differ materially from those indicated by such forward-looking statements.  These factors include, but are not limited to, our need for additional financing; our ability to continue as a going concern; clinical trials involve a lengthy and expensive process with an uncertain outcome, and results of earlier studies and trials may not be predictive of future trial results; our clinical trials may be suspended or discontinued due to unexpected side effects or other safety risks that could preclude approval of our product candidates; uncertainties of government or third party payer reimbursement; dependence on key personnel; limited experience in marketing and sales; substantial competition; uncertainties of patent protection and litigation; dependence upon third parties; our ability to develop tests, kits and systems and the success of those products; regulatory, financial and business risks related to our international expansion and risks related to failure to obtain FDA clearances or approvals and noncompliance with FDA regulations.  There are no guarantees that any of our technology or products will be utilized or prove to be commercially successful, or that Trovagene's strategy to design its liquid biopsy tests to report on clinically actionable cancer genes will ultimately be successful or result in better reimbursement outcomes.  Additionally, there are no guarantees that future clinical trials will be completed or successful or that any precision medicine therapeutics will receive regulatory approval for any indication or prove to be commercially successful.  Investors should read the risk factors set forth in Trovagene's Form 10-K for the year ended December 31, 2016, and other periodic reports filed with the Securities and Exchange Commission.  While the list of factors presented here is considered representative, no such list should be considered to be a complete statement of all potential risks and uncertainties.  Unlisted factors may present significant additional obstacles to the realization of forward-looking statements.  Forward-looking statements included herein are made as of the date hereof, and Trovagene does not undertake any obligation to update publicly such statements to reflect subsequent events or circumstances.

Trovagene Contact:

Vicki Kelemen
VP, Corporate Communications
858-952-7652
vkelemen@trovagene.com

 

SOURCE Trovagene, Inc.

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          Celmatix Lands $4,799,999 New Round   
Feed Type Link http://www.venturedeal.com/Search/SearchResultTransactionDetail.aspx?TransactionId=c018e6ec-d305-45f7-b092-ebae9d2d3a8e Date 4/4/2016 Company Name Celmatix Mailing Address 54 West 40th Street New York, NY 10018 USA Company Description Celmatix uses big data analytics and genomics to improve fertility treatments and pave the way for proactive fertility management. Website http://www.celmatix.com Transaction Type Venture Equity Transaction Amount $4,799,999 Transaction Round Undisclosed Proceeds Purposes […]
          Breve aporte a la nutrigenomica experiencial. Evaluacion del perfil absortivo de lipidos y sacarosa en pacientes obesos sometidos a dieta VLCD de corta duracion y evaluacion de la accion antilipasa de las arvejas secas remojadas   
La nutrigenómica estudia la interacción de los alimentos con los genes y sus expresiones fenotípicas, las enzimas. Es conocido desde hace mucho tiempo que los nutrientes y otras moléculas del entorno celular están implicadas en la diferenciación celular a través de la expresión de genes que las mismas inducen.Los primeros tejidos capaces de recibir algún tipo de modulación por parte de los nutrientes son los del tracto digestivo que están en contacto directo con los alimentos, y aquellos encargados de producir las enzimas necesarias para la absorción de tales nutrientes.
          Ancestry's first work from Droga5 makes a bold statement about America's diversity   
The genomics brand brings together 29 descendants of the founding fathers for an atypical July Fourth campaign.
          CHOP launches data platform for White House pediatric cancer initiative   
The Children's Hospital of Philadelphia's newly launched Center for Data Driven Discovery in Biomedicine will continue its commitment to the White Precision Medicine Initiative after announcing the completion of a new cloud-based platform to store, share and analyze genomics data on pediatric cancer patients.