IGEM:Idea exchange

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==Most-wanted parts==
==Most-wanted parts==
'''[[User:Jason R. Kelly|Jason R. Kelly]] 00:47, 9 May 2008 (EDT):''' The MIT Synthetic Biology Working Group had a brainstorming session a bit back about the [[SynBERC:MIT/Calendar/2007-8-8|most-wanted parts that aren't in the Registry.]]  Might be some cool things to build in there.
'''[[User:Jason R. Kelly|Jason R. Kelly]] 00:47, 9 May 2008 (EDT):''' The MIT Synthetic Biology Working Group had a brainstorming session a bit back about the [[SynBERC:MIT/Calendar/2007-8-8|most-wanted parts that aren't in the Registry.]]  Might be some cool things to build in there.
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==Miscelaneous ideas==
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'''[[User:Federico_Castro_M|Federico C]] 29 may 2008 (EDT)'''
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These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some of these ideas or are already working on them or something related, please contact me, I would be very glad to share information, collaborate and know about the outcome of the project.
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#Make a self destructive F plasmid, this would allow some information to be quickly delivered and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed.
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#We could use hormones as means of communication betwen bacteria. While there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team (very interesting). It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.
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#Use DAP as means to produce a cell communication system, all the parts seemed to work (check the Paris iGEM team of 2007). That also would offer an alternative to the LuxR/LuxL.
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#We could also measure POPs by other means than fluorescente such as the concentration of a diffusible insulin (insulin levels can be quantified very fast and fairly cheap) or antibiotic resistance (we could manually count the number of colonies). This could make the measurement available to laboratories with no funds or equipment and perhaps it would make it all easier.
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#The problem with antibiotic resistance and VIH drug resistance is an evolutive problem. We could deal with that with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak.[[User:Federico_Castro_M/Adaptive_Landscape | check this]]
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#The immune system uses a library of sequences to assemble a great variety of proteins. We could construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).
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#Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for that behavior and introduce it in ''Escherichia coli''?
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#A devise capable of certain function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks.
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#Also check [[User:Federico_Castro_M/Projects | my undeveloped projects]]
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==Square bacteria==
==Square bacteria==

Current revision

Contents

Most-wanted parts

Jason R. Kelly 00:47, 9 May 2008 (EDT): The MIT Synthetic Biology Working Group had a brainstorming session a bit back about the most-wanted parts that aren't in the Registry. Might be some cool things to build in there.

Miscelaneous ideas

Federico C 29 may 2008 (EDT)

These are ideas that are not completely developed; they might be very basic very crazy or form part of a project that is not currently developed. If you are interested in developing some of these ideas or are already working on them or something related, please contact me, I would be very glad to share information, collaborate and know about the outcome of the project.

  1. Make a self destructive F plasmid, this would allow some information to be quickly delivered and once it is expressed it would disappear. The plasmid should codify for a restriction endonuclease that would digest the plasmid to tiny bits of DNA, the endonuclease should be very specific and have a very long recognition sequence to ensure that the Bacteria will not be harmed.
  2. We could use hormones as means of communication betwen bacteria. While there are some mechanisms implemented for communication, they lack the fast response that is often needed in a multicellular organism to coordinate cells (the molecule used by the luxR/l system as a signal, HSL, takes up to 24 hours to degradate). The system used for producing insulin and detecting the levels of sugars have already been developed by the NYMU 2007 iGEM team (very interesting). It could be easily modified for communication between cells and the activity of the devise could be easily quantified with cheap medical equipments.
  3. Use DAP as means to produce a cell communication system, all the parts seemed to work (check the Paris iGEM team of 2007). That also would offer an alternative to the LuxR/LuxL.
  4. We could also measure POPs by other means than fluorescente such as the concentration of a diffusible insulin (insulin levels can be quantified very fast and fairly cheap) or antibiotic resistance (we could manually count the number of colonies). This could make the measurement available to laboratories with no funds or equipment and perhaps it would make it all easier.
  5. The problem with antibiotic resistance and VIH drug resistance is an evolutive problem. We could deal with that with an evolutionary approach; we should lead the bacteria or viruses to an isolated peak of adaptation and then submerge that peak. check this
  6. The immune system uses a library of sequences to assemble a great variety of proteins. We could construct and use a similar library of proteins for protein design (The Silver/Phillips method of assembly would be very useful for achieving this goal).
  7. Myxobacteria have the ability to generate complex structures. Could we isolate the genes responsible for that behavior and introduce it in Escherichia coli?
  8. A devise capable of certain function could be achieved, by randomly rewiring a genetic network with invertases and selecting the desired networks.
  9. Also check my undeveloped projects


Square bacteria

Apparently, there is a bacteria that grows into square colonies. I heard about it from an interview with Sydney Brenner, however after looking pretty hard I can't find any more information about it. he thought it was called tetramitus, but that's an amoebae as far as I can tell. I tried getting a hold of him to see if he remembers what it's actually called, but no luck (getting a hold of him). If you can find it there's probably lots of cool stuff to be done with it. His quote from the interview follows:

Brenner Quote about Square Bacterial Colonies

"As a model of polarity I, I played around in 1965, this is very early, with caulobacter. In fact, I made some mutants of caulobacter. Caulobacter is a bacterium that has a very interesting life cycle which involves a polar, polar growth. That is, one side of the bacterium is different from the other. One side carries a stalk, to which the bacterium attaches, when it divides one of the daughters makes a flagellum and the other one- and, and then when that divides, one of its daughters makes a stalk again. So one has to, one has to say- how does this bacterium know which is its left side and which is its right side? These caulobacters had been discovered by Roger Stanier, who I knew at Berkeley, and so I got some cultures from him and grew colonies and made some mutants, they were nutritional mutants. And the idea was what can we make mutants to control this cycle and use bacteria as a model of differentiation. I also played around with a wonderful bacteria which I think is called tetramitus. This little bacterium that grows in plates. I found it very difficult to grow. It grows as a square plate of bacte- of, of- a square colony, one layer thick. It's a very interesting bacterium, because it means that successive divisions are polarised at right angles to each other. And we did grow some in the lab, and wondered whether this wouldn't be something to work on in order to see how was it that a plane of division in something like a bacterium could in successive divisions be rotated through 90 degrees."

  • he got back to me eventually: "The organism is Lampropedia hyalina and a paper on the division was written by Kuhn and Starr in 1965. -Sydney Brenner"
  • Another square bacteria is Haloquadratum Walsbyi (pointed out by Josh Michener)
    • Another paper on it here: [1]
  • Contact: Jason Kelly (MIT iGEM team)

Helical Bacteria

  • Crescentin is believed to cause Caulobacter to form a helical shape. Disrupting the CreS gene causes the bacteria to revert to a rod shape (necessity). Could importing the gene into E. coli produce the reverse effect (sufficiency)? [2]

Random Number Generator

  • FimE inverts a specific stretch of DNA, defined by a pair of sequence elements (IRR and IRL), forming a DNA loop between the two elements[3]. If we add multiple copies of one of these elements (one IRR, two IRL), would FimE randomly choose one of the sites (one IRL out of the pair) to invert between? Either choose one of several promoters to attach to a given gene, or one of several genes to attach to a given promoter.
  • Then, can we tune the probability (from, say, 60:40 to 80:20 to 20:80)? Ideally do this dynamically (based on some small molecule) - use proteins that bend DNA to affect the probability of loop formation.

Population Variability

  • Slipped-strand mispairing [4] can produce a heritable variation in the expression from a promoter. Roughly one in 1000 divisions produces a change in expression. Couple this expression to a selectable/counterselectable marker. Under any given condition (selection, say), the population thrives, but with a small group of the opposite phenotype (non-expressing). Switch conditions (to counterselecting), and the population can use these revertants to recover.
  • Under constantly varying conditions, most circuits would die. These cells, though, can adapt and pass that adaptation on to their descendants.

Hack some moss

Jason R. Kelly: This moss seems pretty engineer-able. Do something cool with it. Let me know if you do, I'll help if I can :)

Protein sequences and music

References

  1. Bolhuis H, Poele EM, and Rodriguez-Valera F. . pmid:15560825. PubMed HubMed [walsby]
  2. Margolin W. . pmid:15043836. PubMed HubMed [shape]
  3. Ham TS, Lee SK, Keasling JD, and Arkin AP. . pmid:16534780. PubMed HubMed [fim]
  4. Torres-Cruz J and van der Woude MW. . pmid:14617664. PubMed HubMed [phase]
All Medline abstracts: PubMed HubMed
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