Team:Virginia Commonwealth/Internal/Papers

From 2009.igem.org

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Revision as of 03:25, 7 June 2009

Reflections/responses to the papers we've read together

Please share with the team what was meaningful about the reading, how it might be applied to the team's research and what questions you may have. Links to papers can be found in the literature compilation section.

Extreme genetic engineering: an introduction to synthetic biology by the ETC Group
- There seems to be so many different areas of research that are considered synthetic biology. Which areas apply to iGEM and which area(s) will the VCU team be involved in? - GMcArthurIV 16:44, 15 May 2009 (UTC)
  - The New Synthetic Energy Agenda section on page 27 reflected the type of work the VCU team will be doing. The cellulose to biofuel and bio remediation to biofuel projects would fall well under this area of syn bio. Obviously our projects will pertain to biofuel production but the section regarding synbiosafety cannot be ignored - Bussingkm 21:34, 3 June 2009 (UTC)
    - What you've mentioned certainly fits within the scope of the research currently going on in the Systems Biological Engineering Lab, but let's talk a bit more broadly. This paper lists five major research areas in synthetic biology: minimal cells, assembly-line DNA, artifical cells, pathway engineering and novel genetics. Which areas do you think we could or will be involved in? - GMcArthurIV 00:08, 4 June 2009 (UTC)
  - As you could guess from my comment below, I think the effects of the cellular "environment" on the functions of individual genetic parts is fascinating and of critical importance, in the same way that your boundaries must be defined for any engineered system. To this end, I think the minimal genome work is very interesting. In what situations is it better (or not) to pay attention to all the varied species nature provides us rather than engineering rational systems in the carefully designed, minimal environment provided by a minimal or artificial cell? My work with thermocellum and the lab's work in general with T. fusca and others tends to rely on existing systems. At what point do we scrap all that and build the pathways we want into a blank or nearly blank cell? - Chris 02:38, 4 June 2009 (UTC)
  - When we can actually pare down the models we have to a bare minimum. There's a whole lot of bugs and gray area still in our models and other work. I think the minimal cell projects are coming from the other end; starting blank and adding systems until it fulfills all definitions of a cell. Our work is very important, as the next step after minimal construction will be to direct modification towards a specific purpose. That will proceed much faster if the networks have already been deconstructed. - Jalvin 16:33, 4 June 2009 (UTC)
- Why is DNA synthesis technology so important to the development of synthetic biology? Or is it at all? - GMcArthurIV 00:12, 4 June 2009 (UTC)
  - I think improvements in DNA synthesis technology are very important to the development of synthetic biology. With these improvements comes the ability to generate DNA code faster and at a lower cost. Since the building blocks of synthetic biology are comprised of this DNA code, improvements in the synthesis technology go hand in hand with the development of synthetic biology. - Albergca 14:20, 5 June 2009 (UTC)

The iGEM competition: building with biology by James Brown
- Does this [the iGEM competition] sound exciting to you? - GMcArthurIV 00:12, 4 June 2009 (UTC)

Foundations for engineering biology by Drew Endy
- Drew Endy lists standardization as a key foundational element to enable biological systems. In what ways do you think we can standardize biological research? - GMcArthurIV 00:08, 4 June 2009 (UTC)
- I think this paper is hilarious. "...microprocessors and other electronic systems are not built directly from chunks of metal and silicon lying about the countryside." He alludes to the standardization of a cellular "chassis" when he talks about the different groups using different strains of ecoli to develop different devices (p450, right column). Do you think it makes more sense to use a standard strain or to more clearly define the differences between strains or even different organisms. For example, wouldn't it be nice if work on e. coli could be reliably translated for use in T. fusca? - chris 02:17, 4 June 2009 (UTC)
- Cellular devices developed for a standard strain seem to be advantageous for many reasons. For instance, if the devices are interchangeable with other strains and potentially other organisms, time and money can be saved by not having to redevelop the devices. A standardized stripped down device also lends itself to the idea of abstraction and decoupling. These minimal devices can be built up and combined into more complex devices or systems capable of achieving more complicated goals. - Albergca 14:54, 5 June 2009 (UTC)

The promise and perils of synthetic biology by J. Tucker and R. Zilinskas
- What are some of the major risks associated with synthetic biology research projects? - GMcArthurIV 00:08, 4 June 2009 (UTC)
  - The risks range from accidental to deliberate and include accidental release, testing in an open environment, and the deliberate misuse of the technology. Self-regulation seems to be the best avenue to address these risks early before any unforeseen mishaps. - Albergca 15:04, 5 June 2009 (UTC)
  - Anyone with a decent knowledge of genomic engineering and access to University equipment and literature could easily turn into a crazed bio-terrorist. It's not too difficult to isolate something like MRSA and just grow massive vats of it, putting it into spray bottles and hosing down public transport and other high-volume/distance transmission venues. Not that I've ever thought of that. - Jalvin 16:45, 5 June 2009 (UTC)

Refinement and standardization of synthetic biological parts and devices - discussion on Monday, June 8

Measuring the activity of BioBrick promoters using an in vivo reference standard - discussion on Monday, June 8

Engineering BioBrick vectors from BioBrick parts - discussion on Monday, June 8

Synthetic biology: lessons from the history of synthetic organic chemistry (discussion on Tuesday, June 9)

Systems biology as a foundation for genome-scale synthetic biology (discussion on Tuesday, June 9)

Biology by design: reduction and synthesis of cellular components and behaviour (discussion on Wednesday, June 10)

Genetic parts to program bacteria (discussion on Thursday, June 11)

Toward scalable parts families for predictable design of biological circuits (discussion on Friday, June 12)

@@ Line 20: / Line 20: @@
 **Drew Endy lists ''standardization'' as a key foundational element to enable biological systems.  In what ways do you think we can standardize biological research? - [[User:GMcArthurIV|GMcArthurIV]] 00:08, 4 June 2009 (UTC)
 ** I think this paper is hilarious. "...microprocessors and other electronic systems are not built directly from chunks of metal and silicon lying about the countryside."  He alludes to the standardization of a cellular "chassis" when he talks about the different groups using different strains of ecoli to develop different devices (p450, right column).  Do you think it makes more sense to use a standard strain or to more clearly define the differences between strains or even different organisms.  For example, wouldn't it be nice if work on e. coli could be reliably translated for use in ''T. fusca''? - [[User:Chris.m.gowen|chris]] 02:17, 4 June 2009 (UTC)
-***Cellular devices developed for a standard strain seem to be advantageous for many reasons.  For instance, if the devices are interchangeable with other strains and potentially other organisms, time and money can be saved by not having to redevelop the devices.  A standardized stripped down device also lends itself to the idea of abstraction and decoupling.  These minimal devices can be built up and combined into more complex devices or systems capable of achieving more complicated goals. - [[User:Albergca|Albergca]] 14:54, 5 June 2009 (UTC)
+**Cellular devices developed for a standard strain seem to be advantageous for many reasons.  For instance, if the devices are interchangeable with other strains and potentially other organisms, time and money can be saved by not having to redevelop the devices.  A standardized stripped down device also lends itself to the idea of abstraction and decoupling.  These minimal devices can be built up and combined into more complex devices or systems capable of achieving more complicated goals. - [[User:Albergca|Albergca]] 14:54, 5 June 2009 (UTC)
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 *'''''The promise and perils of synthetic biology''''' by J. Tucker and R. Zilinskas