iBiome

Researchers estimate 9 million bacterial genes in the human gut

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

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.

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

New Money for Genomics in Ontario

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

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.

Genome Canada cut good for science?

Chris Hogue weighs in and makes an excellent point about co-funding.  GC only provides 50 cent dollars, and the other 50 will be harder to find over the next few years.  Redirection of research funds to labs and other funding mechanisms may be a prudent way forward.

BioImplement: Market Driven Science in Crisis?. While it is certain that many Genome Canada funded scientists have become international leaders in their fields, one problem is that Genome Canada has no long-term strategy to fund these projects. Industry partnered three-year projects with no provision for renewal are the staple of Genome Canada's co-funding strategy.
 
Expectations of commercial spin-offs and an market-driven afterlife is the fairy-tale ending for Genome Canada's approach to science. Yet the horizon for success in life sciences research can be longer than a decade. So, sadly, when a researcher becomes an international leader, Genome Canada has no strategy to keep them in that position, economic downturn or not. Genome Canada is a market-driven organization.

Perhaps it is reasonable to expect that co-funding - the money contributed by industry to the Genome Canada funding scheme - will simply dry up during this recession. By its own design, Genome Canada cannot hand out its money without co-funders. If Genome Canada has no hope of attracting co-funding this year, then this budget may in fact (gasp) be a reasonable one.

And now, the walkback

Someone got a call from Industry Canada:

Researchers now pleased with budget.

The controversy continued to simmer yesterday, just as Genome Canada's board of directors issued a list of "key messages" that expressed overwhelming support for the budget. "Genome Canada is pleased with the federal government's 2009 budget in which millions will be invested in research infrastructure over the next two years," read the statement. "This is good news for the scientific community across the country."

While Genome Canada received no new funding in the 2009 budget, the board said it already has a pair of five-year funding arrangements in place with the federal government worth a total of $240-million and will be able to meet all its current funding obligations.

The organization has received $840-million in federal funding since its inception in 2000. Genome Canada received no mention in the Conservatives' first budget in 2006, but was given $100-million in new funding in 2007 and an additional $140-million last year.

No representative of Genome Canada was available yesterday to explain the group's apparent change in position on the budget, a spokeswoman said. Gary Goodyear, the Minister of State for Science and Technology, said the controversy stemmed from a "misunderstanding between a president and his board."

Genome Canada ignored in federal Budget

The budget was alarmingly silent on the future of Genome Canada, Canada's core funding source for "big science".  Genome Canada has established Canadian leadership in a range of genomics, proteomics, and bioinformatics global research initiatives. 

globeandmail.com: Budget erases funding for key science agency:
The only agency that regularly finances large-scale science in Canada was shut out of Tuesday's federal budget, putting at risk thousands of jobs and some of the most promising medical research, and forcing the country to pull out of key international projects. For the first time in nine years, Genome Canada, a non-profit non-governmental funding organization, was not mentioned in the federal budget and saw its annual cash injection from Ottawa - $140-million last year - disappear.

Without minimizing the importance of Genome Canada and the value it brings to Canada's scientific community and the broader economy, I would note that the article sensationalizes the situation a wee bit.  Genome Canada was established and funded out of government surplus, and it's hardly a surprise the first deficit in 9 years would mean a break in funding.  Further, we are in year 2 of a 5 year funding program, so no one is losing a job any time soon.  This time next year the economy should be in recovery, and I expect that some restoration of GC funding will occur.  More worrying perhaps are provincial plans for their contributions to regional genome centres.  BC and Quebec for example of have been strongly supporting the growth of life sciences through investments in Genome BC and Genome Quebec.  While continued investment in science might not seem 'shovel ready', it keeps global scientific talent tied to local jobs and the local economy, and as Genome BC and others have shown, fosters the spin off of lab based research into private sector ventures.

Blue Biotechnology

My cGRASP blurb in the European Life Sciences Journal:

Salmon,trout, and the other salmonids are species of great economic and social importance to
Canada and many other nations worldwide, particularly for coastal, rural and Aboriginal communities. The Consortium for Genomic Research on All Salmonids Project (cGRASP) integrates salmonid programmes in four nations – Canada, Norway, USA and the UK – into a unified research effort to develop critical genomics resources and tools that will further our understanding of salmonids, and support research in the areas of aquaculture, wild stock management and environmental protection.

Super Bugs from Outer Space

Salmonella exposed to space travel come back nastier.   National Geographic:

When the bacteria—which had been safely isolated from the space crew—returned to Earth, scientists injected them into mice.

They found the space-faring bacteria caused death quicker and more often than Earth-restricted organisms.

The findings are concerning for future astronauts who will embark on longer space missions farther away from Earth-based medical help, experts say.

Genetic Transformations

Cheryl Nickerson is an associate professor of microbiology at Arizona State University's Biodesign Institute and lead author of the study....

...When the bacteria returned to Earth, genetic sequencing showed that 167 genes and 73 proteins had been altered.

One protein, called Hfq, helped control more than a third of the altered genes. Hfq regulates RNA—the code of bacterial life—during stressful events. When activated, the protein previously had been shown to strengthen several types of pathogens.

An technique called scanning electron microscopy also showed some Salmonella were starting to form biofilms, a protective slime layer.

On Earth, biofilms can grow on ship hulls and clog pipes, costing industry billions of dollars. Biofilms also worsen some diseases and reduce the effectiveness of many antibiotics.

Could it be....the cosmic rays?!

new money for applied genomics

$40 million for new Genomics research in British Columbia.