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Archive for the ‘David Monje Jonston’ tag

OGem – Ontario iGem Mini-Conference

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Teams from the Southern Ontario University iGem teams came together on May 29th for a miniature conference at the University of Waterloo. We had members from Guelph, Toronto, Mississauga (U of T’s West Campus), Queen’s and Ottawa. The basic trend of the show was finding the fun and profit from synthetic biology. I could only stay for the morning and early afternoon segment– but I really would have loved to stay for dinner.

Dave Johnston — our very own team leader from last year at Guelph showed up with Brendan. It was kind of neat to see them again, and more so since they didn’t know I had betrayed them and joined the Waterloo team this year (amicably of course).

Meeting with like-minded individuals is a bit of a relief. It is good to need to argue, convince and learn from others in science– and out of science… but when it comes to something as difficult for outsiders to enjoy as synthetic biology, sometimes it’s a nice break to just discuss the facets within the discipline, rather than abstractly and vaguely defending it against misunderstandings. Actually, one of the standing objectives we discussed was improving public image.

Along with the theme of the fun and profit of the beast came the odd realization that what we’re studying now is likely to become obsolete within the decade– however, with that risk comes the potential for each of us attending to contribute something truly worthwhile in short notice.

One key idea that stuck with me was the development and deployment of nanometre-scale sensors to detect the changes of magnetic flux while molecules are moved within a single cell. I’d imagine that one would need to be well versed with trigonometry and calculus to write software to solve the diffraction patterns of the fields in real time. It might look something like a dynamic/real-time x-ray crystallographic analysis. Another key idea is the 1Mbp/1hr/$100 device. If DNA can be printed at the rate of one million base pairs for each hour at the price of a hundred bucks– it wouldn’t matter what currency that’s in, it would win.

Culture was something else I noticed about the group. There was the ever present odd scientist humour. We managed to have running jokes about the phrase “Killer App”, as soon as it was accidentally introduced to refer to engineered microbes.

All in all, it was a good conference.

Something that I’ll need to follow up on is the idea of doing a group / mass booking for a tour bus from Southern Ontario down to Boston come iGem conference time. This along with a group / mass hotel booking would solve a lot the travel and accomodation fragmentation everyone experienced last year.

Eddie Ma

June 1st, 2009 at 1:01 am

Meeting with Danielle

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Met with Danielle Nash, coordinator at iGEM Waterloo today. There are three branches of projects this year, first the completion of last year’s project and the introduction of one new project in two parts.

Last year’s project consists of a delivery system, wherein one introduces bacteria that have been modified so that all genomic DNA is lost. The bacteria thus function as subcellular-sized vehicles that are broken down, so that some arbitrary payload is released into a patient. The focus of the team working on this subproject is its completion; elucidation and final characterization of the system behaviour.

This year’s project consists first of a “foundational advance” submission which formally defines a consistent means to create cassettes for the exchange of genetic material between some vector and a target bacterial chromosome. This involves the definition of a new mutant strain with the homologous recombination sites, suitable for the integrase used; a well defined and consistent cassette, which one would use to enclose the biobricks or other genes of interest; and a short integrase plasmid, likely with just the gene and a promoter of some arbitrary strength. The second is an extension to this project, which defines a different chasis (target organism); this time a plant, likely arabidopsis.

David Monje Johnston immediately comes to mind; he oversaw iGem Guelph last year, in his plant agriculture lab. His advice could likely benefit the team.

What am I doing?

Well, I’ve contacted Andre Masella who currently lives and reigns at Laurier. He’s the head of modeling this year for Waterloo and has summarized the objectives as the creation of some software that will anticipate the best sequence of sites needed to ensure the highest probability of consistent exchange between the cassette and the chasis chromosome.

We’ve all settled on the idea that I would be assisting Andre, with the likelihood of coaching an undergraduate in bioinformatics software design, deployment and utility all the while.

I’m very interested in seeing the background work on this, since I have little idea of what the problem constraints are. What makes a given sequence a good sequence (high in stability, high in predictability), what makes a given sequence bad (high in variance, low likelihood of working)? I’ve written back to ask about related papers he’s worked with, seen or written.

This should be a BLAST.

Eddie Ma

May 15th, 2009 at 9:14 am