Genome Alberta's Official Newsletter

Genome Alberta Newsletter GeneSnips - July 2, 2009

Genome Alberta News

Alberta and B.C. Join Forces to Deal with the Mountain Pine Beetle Problem

When the IUFRO met in Whistler, British Columbia this week, Genome B.C. announced the launch of a new project from the ABC Competition. This one is led by Genome B.C. with Genome Alberta as a major partner with co-leader Janice Cooke from the University of Alberta.

As Canada and the world begin to reduce their dependence on fossil fuels, the emerging bioenergy sector faces a key challenge: the sheer volume of biomass required to produce biofuels, and how to guarantee a steady supply. The new research project largely funded by Genome Canada, Genome BC and Genome Alberta will tackle this problem, by developing genomic tools that will allow a more strategic approach to resource planning.

The research project titled, Genomics-Enhanced Forecasting Tools to Secure Canada’s Near- Term Lignocellulosic Feedstock Supply for Bioenergy using the Mountain Pine Beetle System,  is expected to generate new genomics-based information and tools for improved prediction of renewable energy feedstock supply from conifer forests, using the current mountain pine beetle epidemic as an example of an important host-pest-pathogen system.

The new project is an excellent addition to the current Mountain Pine Beetle project (also known as the Tria project) which is also a joint initiative between B.C. and Alberta.  For more information on the Tria Project go to our Mountain Pine Beetle pages and for more on the new project visit Genome B.C. to see the original press release.

Plant Forensic Genomics – A Possible Future Research Area.

Odd and interesting things can happen when you are involved in a unique and ever changing field such as genetics. With television programs such as CSI putting the forensic side of the science at the top of mind for many people we can me sure it will get even more interesting. Genome Alberta Project Manager Jeff Parker got an unusual call from police in Ontario recently and offers this story for Gene Snips:

“I recently had the interesting experience of being contacted by the Ontario Provincial Police regarding the ability to use Genomics/ DNA/molecular markers as a way to link cannabis (marijuana) seizures to the GH or field where they were grown. There currently is very little information on the genetic diversity and variation in cannabis strains grown in Canada and how to identify these forensically through Genomics technologies. In this case, the OPP Constable had a seizure of 40,000 plants (a huge grow op by Canadian standards) that was seized in a tractor trailer and a field in Oration with plant residue where they believed the seizure was grown (the plants were grown interspaced in a corn field and trickle irrigated). To be able to conclusively link the seizure to the field and thus the grower/owner would have greatly strengthened the case for the prosecution.

Well, I took the request for help quite seriously having watched too many CSI shows over the years and after many phone calls, much reading and web searching I came to a number of conclusions.

1. We have very limited markers available, especially SNP markers, in the cannabis plant. Some in Hemp.
2. Other countries (particularly Australia)have used SSR (micro satellite)  markers and have created national cannabis data bases to assist their police forces with cannabis identification.
3. The regulatory system in Canada is difficult to work around so even moving samples of cannabis to various labs (such as NRC/PBI or ARC) is extremely difficult.
4. We have no commercial labs in Canada providing plant DNA analysis for forensic purposes.

The outcome of this was that I had to inform the OPP Constable that there was insufficiently developed genomics resources in Canada to assist him with his case. While this was disappointing I also see this as a tremendous future possibility. The development of forensic plant DNA capability, cannabis databases, metabolomic databases and other quick forensic test could be the basis for some future joint project between the RCMP and Genome Canada.  Anyone know a higher up in the RCMP?”

So as Jeff noted, any ideas for a whole new project ....?

ISMOS Conference

Genome Alberta’s Chief Scientific Officer Gijs van Rooijen, and Hydrocarbon Metagenomics Project Manager Sean Caffrey, attended the International Symposium on Applied Microbiology and Molecular Biology in Oil Systems  (ISMOS-2)  held June 16-18 in Aarhus, Denmark. The Symposium was the second in the series and it is held every two years. It links  the activity of chemists, geologists, engineers and molecular microbiologists that are interested in specific issues such as oil filed souring, microbiologically influenced corrosion (MIC), microbial enhanced oil recovery (MEOR), bio-remediation of oilsands tailing ponds etc.

Alberta researchers, Drs Gerrit Voordouw and Julia Foght, Project Leader and co-investigator on the Genome Alberta-led Hydrocarbon Metagenomics Project respectively presented the results of their ongoing research at this symposium. The research results that will come out of the Hydrocarbon Metagenomics Project in the next couple of years will significantly enhance the genomics knowledge base in this area.The next ISMOS will be hosted by Genome Alberta and the University of Calgary and be held in Calgary June 2011. This will provide Genome Alberta an excellent opportunity to showcase its research capacity in this area.

Bartha Knoppers

Bartha Knoppers has been named director of the new Centre of Genomics and Policy at the McGill University and Genome Quebec Innovation Centre. Knoppers previously was a senior researcher and law professor at the University of Montreal, was chair of the International Ethics Committee of the Human Genome Organization, and she was a member of the International Bioethics Committee of UNESCO.

The McGill University and Génome Québec Innovation Centre is located on the McGill campus and is a research facility for genomics and proteomics. The Centre has expertise in complex genetic disorders such as cardiac disease, asthma and Type 2 diabetes, and has become a networking site for various research initiatives. The Innovation Centre provides complete DNA analysis services, from a few samples to several tens of thousands per week.

Imagining Science

The Imagining Science art exhibition and book continues to draw attention. The June 23^rd issue of the Canadian Medical Association Journal features a review of the Imagining Science book. http://www.cmaj.ca/cgi/content/full/180/13/1332   The book is available from University of Alberta Press and is edited by Genome Alberta Principal GE3LS Researcher Timothy Caulfield and his brother and artist Sean Caulfield. Not only does the book contain some pictures of the stunning art from the exhibition but it also has an excellent collection of essays about the intersection of art and science.

The review is written by Stuart Kimmond who was the 3^rd place winner of our Digital Art contest held last year as part of the 2008 GE3LS International Symposium.  You can view Stuart’s entry at http://genomealberta.ca/vote.aspx

Latest Edition of Canadian Bioinformatics Help Desk Newsletter

http://gchelpdesk.ualberta.ca/news/24jun09/cbhd_news_24jun09.htm

How to use the Database of Genomic Variants (DGV) Webinar

The Centre for Applied Genomics (TCAG) and the Ontario Genomics Institute (OGI) are hosting a 1 hour web conference/webinar about the Database of Genomic Variants (DGV) – a curated database that catalogues structural variation in the human genome, including copy number variations, segmental duplications, inversions, insertions, deletions, etc.

The webinar will be appropriate for all levels from graduate student to principal investigator, and can benefit both new and experienced researchers in the areas of genetics and genomic biology. The presentation will be led by Dr. Richard Wintle, Assistant Director at TCAG, The Hospital for Sick Children.

The webinar will include:

• An overview of the DGV
• How to browse and search the database
• Examples of how the DGV can be used
• Related resources (e.g., available control DNA samples)
• Summary

We require all attendees to register so click the link below:

Register for webinar on Thursday, July 23, 1:30 pm EST

Make sure to provide your name, title (student, PI, etc.), institution and valid e-mail address so that we can send you an invite with webinar instructions.

Feel free to pass this invitation along to colleagues who may benefit from learning about these valuable resources.

Thanks and we look forward to hearing from you

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GE³LS Digest

Breeding vs. genetic engineering: Debating the best approach for livestock – May 25, 2009
http://www.cbc.ca/technology/story/2009/05/22/f-stephen-strauss-genomics-genetic-engineering-farm-animals.html
Last year Stuart Brand, principal author of the back-to-the-land, simplicity-is-god, do-it-yourself, hippie bible known as The Whole Earth Catalogue, opined about the irreversibility of technological progress. "Good old stuff sucks. Sticking with the fine old whatevers is like wearing 100 per cent cotton in the mountains; it's just stupid," he said. Brand — who was also one of the promoters of the mind-changing powers of LSD — then urged the truly smart modern citizen to buy the latest laptop, the newest drug and "genetically modified food [from a farmers' market, preferably]." I mention this remark both because it captures the absolutism that has characterized the debates over genetically modified food, and because of something quite surprising. Without most of the public being aware of it, geneticists have begun to believe that disdain for the "good old stuff" when it comes to traditional livestock food production is somewhere between chuckleheaded and — incredible as it sounds — a technological backward step.

Monsanto’s Terminator Making a Comeback? Enter the Zombie!—June 2, 2009
http://watchingthewatchers.org/article/15673/monsantos-terminator-making
Monsanto and its cohorts in crime promised us that they would not be using Terminator technology called GURT, or genetic use restricted technology. In fact, the United Nations actually issued a moratorium on the project. So we’re safe, right? Wrong. Monsanto and its cohorts in crime promised us that they would not be using Terminator technology called GURT, or genetic use restricted technology. In fact, the United Nations actually issued a moratorium on the project. So we’re safe, right? Wrong.
As usual, the boys in the little white lab coats have not been idle. In spite of the moratorium, not only are they working heatedly on Terminator technology, but are getting ready to introduce Zombie technology. Terminator, and Traitor or Zombie technologies are just variations of GURT. Whereas Terminator technology produces plants with sterile seeds, Zombie technology carries this a step further by creating plants that could require a chemical application to trigger seed fertility every year. Pay for the chemical or get sterile seed. This is called reversible transgenic sterility.

Risks of sharing personal genetic information online need more study, bioethicists say – June 5, 2009
http://www.physorg.com/news163394275.html
With just $399 and a bit of saliva in a cup, consumers can learn about their genetic risk for diseases from breast cancer to diabetes. Now, thanks to social networking sites set up by personal genomics companies, they can also share that information with family, friends and even strangers on the Internet.
Bonding over a similar genetic background sounds relatively harmless. But according to bioethicists from the Stanford University School of Medicine, sharing genetic information online raises a host of ethical questions. "Genetic information is unique in that it's not only relevant for the individuals who receive the information, but also for their family members, their children and even their children's children," said Sandra Soo-Jin Lee, PhD, senior research scholar at the school's Center for Biomedical Ethics.

To subscribe to the GE³LS Digest, visit http://www.genomealberta.ca/ge3ls/subscribe.aspx

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Found on Twitter

Synthetic biology. Advice to scientists: Brief on the benefits. Shout about the risks. Engage with the debate. @TheArtsCatalyst

@Phylogenomics Finalists for the Royal Society Science Book Prize: | The Loom http://ff.im/-4qniF

@mactonnies : Building organisms with a built-in expiration date. Sound familiar? http://tinyurl.com/lkfn5w  #syntheticbiology

@wyattsgirl Check out the whole series on science journalism at NPG http://bit.ly/Hm0QQ

doe_jgi  A list of projects DOE JGI will be working on can be found at  http://www.jgi.doe.gov/sequencing/cspseqplans2010.html

@Comprendia  RT @swoodruff : Today's Top Three in Pharma News - Impactiviti blog http://ow.ly/g4vj  A lot more than 3 today, actually!

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Genome Alberta in Pictures

Bill Cochrane has retired from Genome Alberta’s Board of Directors. Bill has been with the Genome Alberta Board from the beginning in 2005 and we have valued his experience and appreciated his input and the time he devoted to getting the organization off the ground.  Pictured here is Genome Alberta President and CEO David Bailey (on the right ) presenting Bill with a hand tooled leather portfolio.

For more pictures of Bill and the rest of the Genome Alberta Board go to our Picasa photo-sharing site at http://picasaweb.google.com/MikesGene/BoardMembers#

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