Thermal / Diagnostic Detection
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Diagnostic Detection
Interacting with metals
- Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires. Mao et al. Science 2004. pdf This was presented at the Designing Biology conference last month. Angela Belcher's lab at MIT has been able to synthesize every kind of inorganic nanomaterial you can think of by having a simple virus express proteins that bind metal compounds in solution. If we're interested in having our bacteria interact with inorganic materials, this is an excellent jumping-off point. See next reference as well.
- Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Whaley et al. Nature 2000. pdf This describes how the Belcher lab developed their semiconductor-binding proteins by mutation and selection.
Belcher mentioned at the conference a really, really cool application of this which is already in the works: microorganisms which can bind to tiny cracks in the surface of smooth metals, such as airplane wings, and then give some kind of ouput which makes detecting the crack much more easy.
General mechanisms of bacterial signaling
- Receptor signaling: Dimerization and beyond. Jeff Stock, Current Biology 1996. pdf The UT Austin team used a hybrid signaling protein based on an E. coli surface receptor of the sort mentioned here. This sort of protein is very useful from an engineering point of view as it is possible to mix and match input and output by combining various extra- and intracellular domains.
Carbon Monoxide
- Aono et al., 1999, Leduc et al., 2001, He et al., 1996, and He et al., 1999 on the CO dependent trascription factor CooA. The CooA protein comes from Rhodospirillum rubrum, but has been introduced to E. coli successfully with some modifications.
- Probably not useful, but Cameron and Hales, 1998 investigates the pathway in which CO inhibts MO-nitogenase action. A couple of sources of Mo-nitrogenase are Azotobacter vinelandii and Rhodobacter capsulatus.
--YvesWang 01:14, 6 Jun 2005 (EDT)
Heavy Metals
- CmtR: a repressor that detects cadmium and lead from Mycobacterium tuberculosis (Cavet et al., 2003)
- HydH/G: genes from E. coli that are stimulated by zinc and lead and stimulates the HycA promoter that triggers hydrogenase 3 (Leonhartsberger et al., 2001)
- pbr: a lead resistance operon from CH34, a strain of Ralstonia metallidurans (formerly Alcaligenes eutrophus (Boremans et al., 2001)
- mer: a mercury resistance gene in bacteria that is being investigated for bioremediation (Review: Nascimento and Chartone-Souza, 2003)
--YvesWang 01:14, 6 Jun 2005 (EDT)
- The role of host organism, transcriptional switches and reporter mechanisms in the performance of Hg-induced biosensors. Harkins et al. Journal of Applied Microbiology 2004. pdf
There are lots of mercury-induced promoters and biosensors have been constructed using most of them. So the simple "detect mercury and fluoresce" is no longer a novelty. In fact, such sensors have been constructed for lead, arsenic, copper and cadmium as well. Now the protein engineering approach Thomas and I came up with (based on the Belcher lab metal-binding peptides) represents a novel way of going about the detection, but first of all, this is probably more complicated than the task calls for, and second of all, it's still not accomplishing anything new. If we want to pursue the heavy metals project we should take the design further - come up with something more complex than simple detection and reporting. Chris 01:25, 7 Jun 2005 (EDT)
Thermal Sensing
- Review article: Patapoutian et al. Nature 2003 (pdf). Mostly discusses vertebrae, but maybe something can be done with the thermoTRPs. ThermoTRPs are channels that are involved in temperature sensation.
- Yea, TRPs were the channels that I was referring to during the group discussion on Friday. Pam and George thought that it would be too much work to import a mammalian (actually generally eukaryotic) system into E. coli. E. coli and other bacteria have their own temperature-sensitive promoters/enzymes. They mentioned heat-shock protein promoters. --dna1112 18:45, 4 Jun 2005 (EDT)
Photosensing
It seems that many photosynthetic bacteria have photoreceptors that respond to certain wavelengths of light, i.e. many archaebacteria are repelled by blue light but are attracted to red. Concerns and possible issues: exact pathways don't seem to be very well understood, and it seems uncertain whether it would be possible to transform E. coli with genes from these bacteria and still maintain functionality.
- Review: Light-induced behavioral responses ('phototaxis') in prokaryotes. link
- Review: Behavioral responses of bacteria to light and oxygen. link
- Review: Blue light perception in bacteria. link
- Color discrimination in halobacteria. link
-Cheng2 22:33, 5 Jun 2005 (EDT)
Might be useful
Sasha:
Overview of Benenson- First, it is worthwhile to note that this system is in vitro and seems to have a different style than what we have talked about. That being said, the author notes that much of this could be done in vivo, and a lot of the concepts seem relevant.
Benenson describes a system, that functions very much like a simple finite state machine as we talked about in dicsussion this afternoon. He describes this process as a 'diagnostic' engine. The 'computer' goes through each of its checks, determines if a certain chemical is there, and moves on to the next state. This process is done stochastically, so the likelihood of a yes or no transition is not guided by a threshold level, but is more likely with more of the item. (not sure if this is a sigmoid activation or a more linear transition). Any way these ideas of both a state machine system in vitro and a multi-part diagnostic system are relevant for both the Password acceptor and the poison detector.
Overview of Lipton This is a great article for CS people. Not sure if it has much relevance to what we're doing, but it presents DNA in the standard CS121 style.
- Breaking DES using a molecular computer. by D. Boneh, C. Dunworth, and R. Lipton. In Proceedings of DIMACS workshop on DNA computing, 1995. published by the AMS. link
- DNA solution of hard computational problems. Lipton RJ. Princeton University, NJ 08540, USA.
- Yaakov Benenson, Binyamin Gil ,Uri Ben-Dor, Rivka Adar & Ehud Shapiro, (2004), An autonomous molecular computer for logical control of gene expression, Nature, 429, 423-429 (published online on April 28, 2004) pdf
