Genome Alberta Newsletter GeneSnips - May 1, 2009
Genome Alberta News
ABC Results
The results are in and Genome Alberta is very pleased with Alberta’s showing in the Applied Bioproducts and Crops competition. The Honourable Gary Goodyear, Minister of State for Science and Technology, and Dr. Calvin Stiller, Chairman of the Board of Genome Canada, announced 12 new genomics and proteomics research projects while in Saskatoon on April 20th. Genome Alberta is the lead in 2 new projects totalling 25 million dollars. We are also playing a key role in the new Mountain Pine Beetle project led by Genome B.C.
For full details on the ABC results go to http://genomecanada.ca/
We’ll have more on the new Genome Alberta projects in coming issues of Gene Snips and on our web site.
- Genome Alberta
- Synthetic Biosystems for the Production of High Value Plant Metabolites
(Peter Facchini, University of Calgary; Vincent Martin, Concordia University)
- Metagenomics for Greener Production and Extraction of Hydrocarbon Energy: Creating Opportunities for Enhanced Recovery with Reduced Environmental Impact
(Gerrit Voordouw, University of Calgary )- Genome B.C.
- Genomics of Sunflowers
- Grape and Wine Genomics
- Genomics‐Enhanced Forecasting Tools to Secure Canada’s Near‐Term Lignocellulosic Feedstock Supply for Bioenergy using the Mountain Pine Beetle‐Pinus spp. System
(Genome Alberta is involved in this project as well through the work of Dr. Janice Cook at the University of Alberta )- Genome Prairie
- Value Generation through Genomics (GE3LS project)
- Microbial Genomics for Biofuels and Co‐products from Biorefining Processes
- Total Utilization Flax Genomics
- Genome Quebec
- Genozymes for Bioproducts and Bioprocesses Development
- Bridging Comparative, Population and Functional Genomics to Identify and Experimentally Validate Novel Regulatory Regions and Genes for Crop Improvement
- Ontario Genomics Institute
- BEEM: Bioproducts and Enzymes from Environmental Metagenomes
- Genomics in Agricultural Pest Management
Genome Alberta at the Alberta Legislature
The following statement was read in the Alberta Legislature last week and we would like to thank Alberta Advanced Education and the Honourable Doug Griffiths ( PC Battle River – Wainwright ) for making this possible.
From April 23, 2009 Alberta Hansard page 787
http://www.assembly.ab.ca/ISYS/LADDAR_files/docs/ hansards/han/legislature_27/ session_2/20090423_1330_01_ han.pdf Genome Alberta
Mr. Griffiths: Mr. Speaker, Saturday, April 25 marks the 56th anniversary of James Watson and Francis Crick announcing the discovery of the double helix as the basis for the structure of DNA.
In plants DNA controls the genetics and genetic selection which allows plants to thrive in different climates. Livestock farmers track the genetics of their herds to raise quality Alberta beef. In humans DNA is largely what makes us who we are. It determines the colour of our eyes and our hair. Unfortunately, it can also lead to a host of diseases.
DNA- and genome-based technologies and knowledge can provide the world with tools for better diagnostics, open the door to more informed choices in therapeutics, and offer lifestyle choices which promote health and lower the incidence of disease. In our province Genome Alberta is helping to put Alberta on the North American genetics map and ensuring that Albertans may be among the first to benefit from new discoveries. Established in 2006 through funding from the Alberta government and Genome Canada, this group is making good headway in the study of how genes interact with each other and the environment. Genome Alberta is working with research organizations across Canada in tackling mountain pine beetle problems by looking at the complex interaction between the tree, the beetle, and the deadly blue stain fungus which ultimately is killing sections of our province’s forest. Field crews are set to sequence the previously unknown genome of the fungus.
Genome Alberta is now launching a couple of new projects. In one project scientists will sequence the active genes of many important plant species, and in the second project they will look deep beneath Alberta’s surface into hydrocarbon deposits, where naturally occurring microbes may be able to play a role in sustainable ways of extracting oil and in managing tailings ponds.
In the 56 years since the double helix was discovered, the world has come a long way in understanding and finding the genetic basis for many human diseases and conditions. With the work that Genome Alberta is doing, Alberta will soon be at the forefront of international metagenomics research and innovation.
April 25 is an important day in the world of science, Mr. Speaker. I encourage all members to recognize the achievements of Alberta’s genetic science community.
Thank you.
BIO 2009
The annual BIO International Convention is taking place in Atlanta from May 18-21 and Genome Alberta will be ready to show off our work to the 20,000 plus in attendance. We are part of the Alberta Pavilion organized by BioAlberta which gives us a good location and presence on the trade show floor. The new Synthetic Biology and Hydrocarbon Metagenomics projects have helped prepare displays and this will be the first time the projects will be shown off to a general audience. Dr. Christoph Sensen’s 4D Project will also be highlighted at BIO. Jung Soh and Mei Xiao will be there with the portable CAVEman which will feature a loop showing the capabilities of the project. Genome Alberta’s Mike Spear will be a guest blogger for BIO and with the help of a ‘back stage pass’ hopes to bring some interesting stories to the blog pages of BIO and Genome Alberta.
Also attending BIO this year will be Alberta Advanced Education and Technology Minister Doug Horner, Industry Canada Minister Tony Clement, and we are optimistic that Premier Stelmach will be in attendance for part of the event as well.
We’re looking forward to being part of BIO once again and hope to make some good contacts for future partnerships and collaborations.
Editorial Board
Genome Alberta’s President and CEO Dr. David Bailey, Dr. Peter Faccini co-lead in the new Synthetic Biology project, and Dr. Karen Budwill, a co-investigator with the new Hydrocarbon Metagenomics initiative met with some members of the Edmonton Journal’s Editorial Board. The discussion lasted an hour and was a chance to talk about genomics, Genome Alberta, and our latest initiatives in an informal session. We’re looking forward to similar sessions with other Alberta media.
Manning Innovation Awards, Southern Alberta Chapter Reception
Dr. David Bailey, Chair of the Southern Alberta Chapter of the Ernest C. Manning Awards Foundation and of course President and CEO, Genome Alberta will be co-hosting a reception for the 2009 Manning Innovation Award Nominees. Joining him will be Dr. Lorne Tyrell from the University of Alberta and together they will introduce the individuals being put forward for the awards which have been running since 1982. This year’s total award money is $165,000 for the leading innovators and young Canadians chosen at the 2009 Canada Science Fair.
The reception is on May 6, 2009 from 5:00 – 7:00 in the lobby of Genome Alberta’s location , the Alastair Ross Technology Centre, 3553-31st St. N.W. in Calgary. Please RSVP using the form at http://tinyurl.com/cdk7pq or contact sansom@uti.ca
To learn more about the Manning Innovation Awards, please visit www.manningawards.ca
Hydrocarbon Metagenomics
Genome Alberta’s new Hydrocarbon Metagenomics project has hired Sean Caffrey as the Project Manager. Sean completed his Ph.D. in Microbial Functional Genomics at the University of Calgary with the Petroleum Microbiology Research Group. Sean's research activities at the University of Calgary were diverse and included both wet lab and bioinformatics work. His research focused on microbial influenced corrosion and involved the design and development of a Sulfate-Reducing Bacteria microarray platform. You can reach Sean at scaffrey@genomealberta.ca
In addition to his academic interests, Sean is an award winning travel photographer. His photos have appeared in several publications including National Geographic Traveler. Some of his photos can be seen at www.n-images.net.
Daggoo
University of Calgary’s Paul Gordon has been busy developing a new piece of software known as Daggoo. The software will allow biologists to automate their web-based analysis and bioinformatics work flows more easily. Biologists who don't have programming abilities will benefit greatly from the program, which will be made available free of charge. The software leverages the BioMoby technology developed by the Genome Canada Bioinformatics Platform. His work is funded by Genome Canada/Genome Alberta and the software is scheduled to be available over the coming months.
Moby and Moby 2: Creatures of the Deep Web
Dr. Wilkinson, a researcher and instructor for the Genome Canada funded Applied Computational Genomics Course has also been working on a unique piece of software. SHARE (Semantic Health and Research Environment) is a simple interface into the SADI (Semantic Automated Discovery and Integration) framework of bioinformatics Web Services. The program provides a straightforward simply query box where you can compose a wide range of queries about gene, protein, and pathway data. Instead of digging into an existing database, the data required to answer your query is dynamically discovered, downloaded, and integrated at the moment you ask the question. This effectively creates a database specifically for your question. The website teaches you how to compose your own queries, and gives you several sample queries to get you started. Dr. Wilkinson invites all providers of data and analytical tools on the Web to help them build global network of interoperable bioinformatics resources. You can read some background on the project at http://bib.oxfordjournals.org/
cgi/content/abstract/10/2/114 or get involved in the project at http://sadiframework.org
U.S. President Commits to Raise Federal R&D Spending to 3 Percent of GDP
President Obama announced earlier this week that the U.S. would increase its investment in basic and applied research and science and mathematics education to match the historic levels reached during the height of the space race. The president pledged to raise total government and industry spending on R&D to 3 percent of U.S. gross domestic product (GDP). In a speech to the U.S. National Academy of Science he said those “who say we cannot afford to invest in science, that support for research is somehow a luxury at a moment defined by necessities,” ....” I fundamentally disagree. Science is more essential for our prosperity, our security, our health, our environment, and our quality of life than it has ever been.”
You can find an audio version of that speech at http://www.nap.edu/obama/
audioplayer.html
Age of Personalized Genomics.
The final agenda and speakers are now available at the 5th International DNA Sampling Conference website. Head for www.genomealberta.ca/APG for all the details. Call for abstracts closes May 15, 2009
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GE3LS Digest
Stem Cell Fairy Tales and Stem Cell Fables: Critics of Research Ignore Use In Drug Discovery and Cell Development Studies – March 30, 2009
http://www.scienceprogress.org/2009/03/stem-cell-fairy- tales/
They’re supposedly for kids, but fairy tales can be haunting. So perhaps I should have known that a “fairy tale” quote I got from a stem cell scientist five years ago would come back to haunt me—over and over, like the undead. Now it’s time for a silver bullet of sorts, or a wooden stake, to put that tired quote to rest at last. The quote was from Ronald McKay, a stem cell researcher at the National Institutes of Health, and the topic was human embryonic stem cells. In an interview I did for The Washington Post in 2004, I asked McKay why so many people kept talking about the possibility that injections of stem cells into the brains of people with Alzheimer’s disease might someday cure these people when, in fact, the scientific consensus at the time (and still today) was that such injections were unlikely to benefit such patients.Hidden dangers of genetically modified food – April 6, 2009
Era of personalised medicine awaits – April 8, 2009
http://www.delawareonline.com/article/20090406/OPINION07/ 904060311/1004/OPINION
Genetically modified crops grown illegally in Prime Hook Refuge have called attention to genetic modification in our midst, but few understand its impact. GM crops entered the United States' food supply without notice or labeling in 1996. Unlike traditional breeding methods, genetic modification crosses the species barrier. A "gene gun" literally blasts altered foreign-species' genes (transgenes) at host cells, hoping the DNA in some cells is "hit" and the insertion "takes." Adjacent genes may be damaged or removed by the process, and up to 5 percent of the DNA spontaneously mutates in unpredictable ways. Results include bacterium genes in corn and cotton (internal pesticide production), human genes in corn (spermicidal corn), daffodil genes in rice (more vitamin A), spider genes in goats, virus genes in pharmaceuticals, etc
http://news.bbc.co.uk/2/hi/health/7954968.stm
A revolution in genome screening has been promised by a biotech company in the US.
Complete Genomics, says it will sequence one thousand complete genomes between June 2009 and the end of the year and one million over five years. I visited the company, based in Silicon Valley near San Francisco, and saw, first hand, the potential significance of mass gene mapping. Silicon Valley in California is a key centre for genetics, bio-tech research and computer technology - all of which are key for genome mapping.
To subscribe to the GE3LS Digest, visit http://www.genomealberta.ca/ge3ls/subscribe.aspx
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Genome Alberta in Pictures
Winners from the Calgary Youth Science Fair gathered
together in the Alastair Ross Technology Centre to get ready for their national
appearance. See more photos of up and coming scientists at http://picasaweb.google.com/
Thanks to Gerry Ward for the pictures.
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