Category Archives: Genomics

Scientists Create World’s Largest Coral Gene Database

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Promising findings from genomic analysis of corals:

Corals face four major threats from humans: Destruction of reefs by grenades and poison used to kill fish for food; nutrient pollution, usually from sewage or agricultural runoff, that overstimulates harmful algae; increased heat in the upper ocean, which causes most coral bleaching that can kill reefs; and acidification of the ocean, according to Falkowski.”Corals are the most diverse marine ecosystems on the planet,” he said. “But their value to marine ecosystems — and to our own use of marine resources — is very underappreciated.”

Perhaps the extreme diversity of coral systems help along an adaptive response to climate change:

Bhattacharya and coauthors found dozens of genes that allow corals to coordinate their response to changes in temperature, light and pH (acidity vs. alkalinity) and deal with stress triggered by the algae that live with them and exposure to high levels of light.
Surprisingly, some of these stress-related genes are of bacterial origin and were acquired to help corals survive. An intriguing theory that arose from the study is that the vast genetic repertoire of corals may help them adapt to changing ocean conditions.

Source: Scientists Create World’s Largest Coral Gene Database

a new salmon genomics project

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Genome British Columbia :: Salmon health: past, present and future.

Genome British Columbia, the Pacific Salmon Foundation and Fisheries and Oceans Canada are embarking on a remarkable partnership to discover the microbes present in salmon in BC that may be undermining the productivity of BC’s Pacific salmon. The project will conduct epidemiological assessments to explore the transmission dynamics and historical presence of detected microbes, with key focus on microbes that are suspected globally to be causing disease in salmon. Researchers will apply genomic technology to identify and verify which microbes are presently carried by BC’s wild and cultured fish.

The project is being managed in four sequential Phases with Phase 1 valued at $930,000. The first phase is taking place over 12 months, concluding mid-2013, and comprises the collection phase of both cultured and wild salmon. While later phases are subject to final funding, Phase 2 involves rigorous analysis of the tissue samples collected in Phase 1 and in previous research. Using molecular and genomic tools, the research team will attempt to determine when and where microbes may have been transmitted.  The research results will begin to rank microbes by their potential to cause disease in BC salmon based on relationships with microbes associated with disease in other parts of the world and histological evidence from salmon in BC.  Phase 3 will focus in on the microbes identified in Phase 2, with an emphasis on microbes that have not been extensively researched and that are thought to be of pathological significance in salmon. Phase 4 will include reporting of research and presentations to management agencies on the potential utility of methods developed and the application of outcomes to future monitoring.

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BioImplement: New Series on Complexity and Evolution

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So into the breach, I add my voice with some new arguments, after this small bit of throat-clearing. I will try to avoid being derivative as I come armed with my own capacity for inquiry, insight, and argument. My examples will show how ID concepts force the gerrymandering of human design history, and surround it with mystical borders to make their claims. The individual steps in human design are small, slow and absolutely require the intellectual imprinting of lessons by trial and error. Students who are led to think falsely about human design, or any complexity as having mystical origins are harmed by the diminishment of their own aspirations of creativity. We all need to understand how small steps and tools lead to human creativity and any object of complexity. I will reveal these small steps and show, where I can, the failures that led to success.

via bioimplement.blogspot.com

Chris Hogue has re-entered the blogosphere with a riff on how we can be informed by incrementalism in human design and evolutionary process, and understand the path to complexity. I'm looking forward to the next post. Hopefully soon.

Salmon Genome in Final Phases of Completion

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The International Cooperation to Sequence the Atlantic Salmon Genome (ICSASG, the "Cooperation") has awarded the Phase II contract for next-generation sequencing and analysis of the Atlantic salmon genome to the J. Craig Venter Institute (JCVI) in Rockville, Maryland. The JCVI will be sequencing the salmon genome using next-generation technologies, including assembly to integrate Sanger and next-generation sequence, and comparative genomics. This effort is expected to generate a high-quality resource for those responsible for the management of wild salmon stocks and the salmon aquaculture industry, as well as providing a reference genome for work with other salmonids.

via www.bioportfolio.com

CGRASP_fish_2Great to see the Venter Institute involved in this next stage of genomic resource development for salmon. This will work feed environmental genomics, aquaculture, and our understanding of the role of gene duplication in evolution. Exciting!

SPIEGEL Interview with Craig Venter: ‘We Have Learned Nothing from the Genome’

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Via Pharyngula, a great interview with Craig Venter in Der Spiegel. I love his point about the limited value so far of the human genome to medicine. So far. It's yielded an immense amount for science and our understanding of evolution and human origins, biological diversity, etc. but still not a lot of clinical application.Also, I can highly recommend Venter's biography.  The guy's a visionary.

SPIEGEL: So the Human Genome Project has had very little medical benefits so far?

Venter: Close to zero to put it precisely.

SPIEGEL: Did it at least provide us with some new knowledge?

Venter: It certainly has. Eleven years ago, we didn't even know how many genes humans have. Many estimated that number at 100,000, and some went as high as 300,000. We made a lot of enemies when we claimed that there appeared to be considerably fewer — probably closer to the neighborhood of 40,000! And then we found out that there are only half as many. I was just in Stockholm for the 200th anniversary of the Karolinska Institute. The first presentation was about the many achievements the decoding of the genome has brought. Then I spoke and said that this century will be remembered for how little, and not how much, happened in this field.

SPIEGEL: Why is it taking so long for the results of genome research to be applied in medicine?

Venter: Because we have, in truth, learned nothing from the genome other than probabilities. How does a 1 or 3 percent increased risk for something translate into the clinic? It is useless information.

via www.spiegel.de

Update: Larry Moran left a comment pointing out that most informed scientists expected the human genome to contain 30,000 or fewer genes, and points to this post on his site: Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome.  I also like this passage about the perceptions of our own complexity:

The second point will have to be put off for another time but it’s important enough to mention here. Ast thinks that humans need to make many times more proteins than worms and corn because we are so much more complex. There are two problems with such a point of view—are we, in fact, 2-3 times more complex than corn? And, does it take thousands of new proteins to generate the structures that make us unique?

I think some people exaggerate our complexity and the place of humans relative to other species. This incorrect perspective can cause some scientists to put their faith in weakly supported hypotheses that claim to explain why humans really are complex and important in spite of the fact that we don’t have a lot of genes.

Researchers estimate 9 million bacterial genes in the human gut

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Another reminder that the world,us included, belongs to bacteria.  A human is a bacterial/mammal hybrid.  This is relevant at even a behavioural level. How often does our digestion affect our actions?

From MicrobeWorld –

A new concept is to consider human as a super-organism containing those microbes in or on human body as well [7]. There are more than 100 trillion bacterial cells in human gut, which are about 10 times more than cells in human itself [8]. Those bacteria can help digest food and harvest nutrition and energy that otherwise cannot be collected by the human body directly [9]–[11], i.e., human has obtained many genes needed for itself though these genes did not evolve in human genome.”

nerd girl blogs swine

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Jennifer Gardy  notes the seeming disparity between the apparent mortality rates in Mexico and the U.S. / Canada. Since she posted this, a comparative analysis of the genomes indicates that the strains in Mexico and Canada are identical.  So why the Mexican deaths?

Some researchers suspect that pre-existing health factors in the
Mexican population might have influenced the disease's outcome, while one leading theory suggests that the increased mortality has to do with the Mexican patients' delays in seeing a physician.

I would also speculate that the number of deaths in Mexico could be the numerator over a very large denominator.  That is, the number of low level swine flu infections could be quite large among the Mexican population, but underreported due to poor access to health care and other confounding issues like the prevalence of other infectious diseases, with similar symptoms, among the poor.  In populations wracked with chronic respiratory and gastrointestinal infection, would low to moderate swine flu infections be distinguishable?  In that context, the actual mortality rate might be much lower than media reports.Child-licking-pig

Other good stuff in her post about tracking the outbreak by following money, and the sequencing efforts.

New Money for Genomics in Ontario

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Ontario to award $100M for genomics research.

Minister of Research and Innovation John Wilkinson announced the new $100 million Global Leadership Round in Genomics and Life Sciences will support "globally significant, collaborative research projects" headquartered in Ontario.
Scientists who work in either genomics, gene-related research, or research into stem cells or proteins will be eligible to compete for the new funds.

Great news for genomics research in Ontario.  I assume this will go through OGI. This will hopefully lessen the temptation for Canadian based scientists to head south to a US that is once again science friendly. I think Canada and other countries have benefited scientifically from the Bush years, and we need to work to keep our best and brightest, as well as the 'exiles', in place.

Budget 2009 Reaction | Genome Alberta Education

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Some further insight from Genome Alberta.  They've set up a few blogs to communicate genomics in general and the work they have been funding in specifics.  Here is the communications lead, Mike Spear, on his real time reaction to the budget.

Budget 2009 Reaction | Genome Alberta Education.

The facts of the matter proved to be quite easy to get out. I was truthful about the fact that Genome Canada got no money in the budget. No sense trying to cover it with corporate-speak. That being said we have had some good years of funding from Industry Canada so it was equally easy and truthful to talk about that as well. Money for projects underway is safe and nothing needs to be canceled. There are other sources of funds out there even in tough times and I was able to honestly say we would be looking at those. Reporters aren't dumb and there is no sense treating them as such, so when the interviewer points out that it is tough to get funding back once it is cut, why not agree and say we'll be lobbying to make sure we're on the federal Christmas list next year. Transparency will rule the day.