Untangling Whole Genomes of Individual Species From a Microbial Mix

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Newswise BETHESDA, MD May 23, 2014 A new approach to studying microbes in the wild will allow scientists to sequence the genomes of individual species from complex mixtures. It marks a big advance for understanding the enormous diversity of microbial communities including the human microbiome. The work is described in an article published May 22 in Early Online form in the journal G3: Genes|Genomes|Genetics, published by the Genetics Society of America.

This new method will allow us to discover many currently unknown microbial species that cant be grown in the lab, while simultaneously assembling their genome sequences, says co-author Maitreya Dunham, a biologist at the University of Washingtons Department of Genome Sciences.

Microbial communities, whether sampled from the ocean floor or a human mouth, are made up of many different species living together. Standard methods for sequencing these communities combine the information from all the different types of microbes in the sample. The result is a hodgepodge of genes that is challenging to analyze, and unknown species in the sample are difficult to discover.

Our approach tells us which sequence fragments in a mixed sample came from the same genome, allowing us to construct whole genome sequences for individual species in the mix, says co-author Jay Shendure, also of the University of Washingtons Department of Genome Sciences.

The key advance was to combine standard approaches with a method that maps out which fragments of sequence were once near each other inside a cell. The cells in the sample are first treated with a chemical that links together DNA strands that are in close proximity. Only strands that are inside the same cell will be close enough to link. The DNA is then chopped into bits, and the linked portions are isolated and sequenced.

This elegant method enables the study of microbes in the environment, says Brenda Andrews, editor-in-chief of the journal G3: Genes|Genomes|Genetics. Andrews is also Director of the Donnelly Centre and the Charles H. Best Chair of Medical Research at the University of Toronto. It will open many windows into an otherwise invisible world.

At a time when personal microbiome sequencing is becoming extremely popular, this method breaks important ground in helping researchers to build a complete picture of the genomic content of complex mixtures of microorganisms. This complete picture will be crucial for understanding the impact of varying microbiome populations and the relevance of particular microorganisms for individual health.

CITATION: Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps Joshua N. Burton, Ivan Liachko, Maitreya J. Dunham, and Jay Shendure. G3: Genes|Genomes|Genetics g3.114.011825; Early Online May 22, 2014, doi:10.1534/g3.114.011825; PMID 24855317.

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Untangling Whole Genomes of Individual Species From a Microbial Mix

Fish study could advance medicine

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A small fish that East Carolina University biologist Jeff McKinnon collected as a boy growing up in British Columbia will be the centerpiece of a study that could give insight to human genetics.

McKinnon, professor and chair of biology at ECU, is studying the threespine stickleback to find out why the bright colors of the male, which help it attract mates, sometimes show up in females. The findings could give scientists insight into the genes behind sex differences and help tailor medicine to better suit patients sex and race.

McKinnon and co-investigators Chris Balakrishnan of ECU and Catherine Peichel of the Fred Hutchinson Cancer Research Center in Seattle, have received a $316,241 grant from the National Institute of General Medical Sciences to fund the three-year study.

The fish lives on the northern Pacific and Atlantic coasts of Europe and Asia as well as North America. Fish from many populations spend most of their lives in the ocean but breed in brackish and fresh water. Purely freshwater forms also have evolved, independently on different continents and islands.

We are trying in general to understand how the sexes diverge despite sharing many genes, McKinnon said. This is a critical issue for medicine as well as evolution. We are looking at the genes involved and at patterns of gene expression.

McKinnon has studied the threespine stickleback for much of his career. His early work helped develop the stickleback as a model organism for genetic and evolutionary studies since it shows great morphological variation.

We hope to ... better understand the genetic mechanisms responsible for causing seemingly male traits to appear in female animals in some populations, McKinnon said. We also want to know if females who possess one male-like trait are only masculinized for that trait or more generally.

The research will shed light on whether some male-like traits are present in females because they benefit females or as a by-product of the benefits they provide to males and vice-versa, McKinnon said. Given the interest in better tailoring medicine by gender and ethnicity, we may provide useful insights on matters important to health.

ECU doctoral student Lenny Yong is playing a key role in this research program and helped write the grant application. The grant also will support the research of two masters students and a number of undergraduates who will be trained in behavioral studies, genetics and genomics.

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Anxiety Control ~ Relaxing Music + Relax Ambient Binaural Meditation – Video

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CCMR-IHPI Research Seminar: Are performance measures doing more harm than good? – Video

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CCMR-IHPI Research Seminar: Are performance measures doing more harm than good?
In this point-counterpoint debate organized by the VA Center for Clinical Management Research (CCMR), Rodney Hayward, M.D., and Sheldon Greenfield, M.D., discuss the merits and pitfalls of...

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How To Find a Health Care Provider In Redmond WA | Connected Wellness Center – Video

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http://ConnectedWellnessCenter.com Health Care Provider In Redmond WA Dr. Michelle Turcotte with Connected Wellness Center talks with You Be All You Are TV about "How To Find a Health Care...

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Global Gene Therapy Market: Analysis, Size, Share, Growth, Trends and Forecast 2013 – 2019

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Albany, New York (PRWEB) May 22, 2014

Gene therapy involves use of DNA as a pharmaceutical agent to treat diseases. It is one of the most important developments in the field of medicine that has potential to treat various lethal diseases such as HIV, cancer and cystic fibrosis. In the long run, biotechnology and clinical trial industries will benefit from developments in gene therapy and provide potential treatment solutions for various incurable diseases.

Browse the full report - http://www.transparencymarketresearch.com/gene-therapy-market.html.

In the present scenario, various pharmaceutical companies are using clinical data to validate the concept of gene therapy. Moreover, many venture capital investors are also showing their interest in gene therapy, and are investing heavily in its development. However, gene therapy is highly dependent on the regulatory approvals and most of the products are currently in clinical trial phase. Most of these gene therapy products are for cancer and cardiovascular diseases, and are in Phase III/ Phase II of clinical trials.

In addition, growing popularity of DNA vaccines boost advances in gene therapy and is likely to be practiced in clinics in the near future, with a number of therapy programs now in phase II/III trials, showing promising results.

Get report sample - http://www.transparencymarketresearch.com/sample/sample.php?flag=B&rep_id=1838.

Some of the major players operating in the market are AnGes MG, BioSante Pharmaceuticals, GenVec, Genzyme Corporation, Oxford BioMedica, Transgene, Urigen Pharmaceuticals and Vical.

This research report analyzes this market depending on its market segments, major geographies, and current market trends. Geographies analyzed under this research report include:

This report provides comprehensive analysis of:

This report is a complete study of current trends in the market, industry growth drivers, and restraints. It provides market projections for the coming years. It includes analysis of recent developments in technology, Porters five force model analysis and detailed profiles of top industry players. The report also includes a review of micro and macro factors essential for the existing market players and new entrants along with detailed value chain analysis.

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Global Gene Therapy Market: Analysis, Size, Share, Growth, Trends and Forecast 2013 - 2019

Suspended animation is about to make death political

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Can death be useful? Thats the central question of the quickly expanding field of suspended animation, the process of slowing the bodys major processes as much as possible to induce a state thats very muchlike death without actually causingthe patient to die.

What precisely wemean when wesay actually die is a bit of an open question these days; in aworld where we can often be resuscitated after long periods of brain death, the noun Deathis probably best definedas, Any state ofzerobrain activityfrom whicha person will never berevived. Thats not particularly helpful, though; if a person is brain-dead next to a machine that could revive them, are they truly dead if the machine is broken and truly alive if it is not? Is death an absence of life, or an absence of any future potentialfor life?

Such questions used to be nothing but navel-gazing, but today represent concrete issues that could affect our lives in the every-day. With the recent onset of a trial for suspended animation technology, we have taken our first steps downa path with no end in sight. The trial will catch otherwise hopeless patients at the point of death (or potentiallyafter), and swap out a large portion of their blood for a chilled, oxygenated saline solution. This quickly lowers the body to a chilly 10 degrees Celsius, which almost immediately induces a hypothermic state and lowers the metabolic rate to near zero. If cells arent doing anything then they also arent producing any of themetabolic products that normally build up to toxic levels without breathing and circulation. At this point, the question is not whether suspended animation is real but whether its medically useful.

Medical evacuation helicopters see a lot of death en-route to hospitals, but that could be about to change.

The field of suspended animation facedwidespread skepticism for manyyears, but recent studies in pigs and a generally pro-futurism trend within science have led toa rather abrupt wave of professionalacceptance. It mostly comes down to drastically reduced claims for the technology; rather than alienating everyday physicians and scientists with speculation abouteternal life, suspended animation is now mostly about keeping terminal patients in a revivable statelong enough to getthem to machinery that can do the reviving. Many, many people die in ambulances, or military medevac helicopters, and these new attempts at induced hibernation could help those patients to get them the help they need.

Yet, there is simply no way well stop there. The trend will begin at NASA, DARPA, Calico, and other moonshot research organizations: how do we put healthy people into a hibernative state? Getting astronauts to Mars is probably possible without suspended animation, but a trip toEuropa or Enceladus will be much harder; theres a reason that space-ships full of stasis pods aresuch a trope of science fiction, and not least of them is a crews demands on power and consumables. Butspace isnt the only out-there application for suspended animation; not every prisoner at Guantanamo is an intelligence asset, so why keep useless prisoners conscious and complaining? And if you take the time to have an enemy combatant declared dead after combat, does that corpse still have rights if you revive it later?

Waking from suspended animation could be automated for long-term space missions with no conscious crew members.

Right now the research only really implies that suspended animation can be safe on the order of hours, but theres every reason to believe that a stasis nap could safely last weeks or months, and years arent such a crazy idea either. We are about to start allowing people topay to feel out the borders of death. Peoplewill freeze themselves even in absence of any plausible future cure for their fatal problem; if you can affordto do so, why wouldnt you?

This technologywill force us to ask tough questions about society: Does the word death mean something different forrich people than forthe poor? Do we declare a patient as dead depending on whether they can afford to stay in stasis until some projected cure date? In this dystopia, a market crash could wipe out savings accounts andswitch thousands of suspended patients from Long Term Pre-Mortal Stasis to Med School Cadaver In Waiting.

Minority Report had stasis prisons, albeit based on a different technology.

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Suspended animation is about to make death political