From 2010.igem.org

Revision as of 11:54, 5 August 2010

Please add every important literature here. This don't necessarily only have to be papers... When you add something, please put a red big "NEW:" in front of it. I will delete once in a while the "News" from everything which is not new anymore. Please add a short sentence why it is interesting for us.

Tagging of PhyB

• Tagging PhyB to trigger factor (which binds to the ribosome) http://www.pnas.org/content/102/12/4246.short In the paper they fused TEV protease to trigger factor

• Tagging PhyB to the membrane: http://www.nature.com/nature/journal/v461/n7266/full/nature08446.html Levskaya 2009. "Spatiotemporal control of cell signalling using a light-switchable protein interaction", Nature 461.

Chemotaxis

• Time lines when E-Coli is in tumbling and when in straight forward movement: “Pausing of Flagellar Rotation Is a Component of Bacterial Motility and Chemotaxis” (LAPIDUS 1988, JOURNAL OF BACTERIOLOGY) http://jb.asm.org/cgi/content/abstract/170/8/3627

• Sensitivity and Receptor clustering: Victor Sourjik (2004), "Receptor clustering and signal processing in E. coli chemotaxis." Trends in Microbiology, Volume 12, Issue 12 http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TD0-4DS3M3V-7&_user=791130&_coverDate=12%2F01%2F2004&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1391336340&_rerunOrigin=scholar.google&_acct=C000043379&_version=1&_urlVersion=0&_userid=791130&md5=3156ae3c215bd8209d2ef743bc3b6305

Modeling Chemotaxis

• An overview over the current state in modeling Chemotaxis. Sounds extremly cool: "Overview of Mathematical Approaches Used to Model Bacterial Chemotaxis I: The Single Cell ", Tindall, 2008, Bulletin of Mathematical Biology ; http://www.springerlink.com/content/f602r72767124602/

• One of the models often cited: "A model of excitation and adaptation in bacterial chemotaxis", PNAS, Peter A. Spiro, 1997. http://www.pnas.org/content/94/14/7263.full

• Some rate constants and protein concentrations in E-Coli: http://www.pdn.cam.ac.uk/groups/comp-cell/Rates.html

• Some nice parameters with their citations: http://bionumbers.hms.harvard.edu/search.aspx?log=y&task=searchbytrmorg&trm=chemotaxis&org=Bacteria+Escherichia+coli Chemotaxis related models at the BioModels Database (not yet checked what they exactly model, please also look at the respective literature links): http://www.ebi.ac.uk/biomodels-main/MODEL6929313478 http://www.ebi.ac.uk/biomodels-main/BIOMD0000000200 http://www.ebi.ac.uk/biomodels-main/BIOMD0000000229

• Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174977/

• Modelling the CheY(D10K,Yl00W) Halobacterium salinarum mutant: sensitivity analysis allows choice of parameter to be modified in the phototaxis model http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=ISBEAT000001000004000207000001&idtype=cvips&gifs=yes&ref=no

• Chemotactic response and adaptation dynamics in Escherichia coli http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2873904/

• A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control http://linkinghub.elsevier.com/retrieve/pii/S0006349505728745

• Quantitative modeling of sensitivity in bacterial chemotaxis: The role of coupling among different chemoreceptor species. Mello & Yuhai.http://www.pnas.org/content/100/14/8223.abstract?cited-by=yes&legid=pnas;100/14/8223

• Stochastic modeling of chemotaxis pathway (modified version of Gillespie's Algo). "Predicting Temporal Fluctuations in an Intracellular Signalling Pathway". Firth & Bray (1998).http://www.ncbi.nlm.nih.gov/pubmed/9628844

• Origins of Individual Swimming Behavior in Bacteria, Matthew D. Levin 1998

• http://www.pdn.cam.ac.uk/groups/comp-cell/Publications.html

• Hauri, D.C. and Ross, J., 1995. A model of excitation and adaptation in bacterial chemotaxis. Biophys. J. 68, pp. 708–722 http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WMD-4C56NHR-1&_user=791130&_coverDate=07%2F07%2F2004&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000043379&_version=1&_urlVersion=0&_userid=791130&md5=5633f71fb83d94785831dde7600ba378#bbib17

PhyB/PIF Light Input

• People who have developed the PhyB/PIF3/Gal network: "A light-switchable gene promoter system", Shimizu-Sato (2002), nature biotech, http://www.nature.com/nbt/journal/v20/n10/abs/nbt734.html

• Same idea, a little bit differently constructed. “A switchable light-input, light-output system modelled and constructed in yeast”, Sorokina (2009), Journal of Biological Engineering

• Same genes, but a little bit more what we do. In vitro and maybe (didn't get it), in E-Coli: Leung (2008): “Genetically encoded photoswitching of actin assembly through the Cdc42-WASP-Arp2/3 complex pathway”. PNAS.

• Possibility of PCB production in E. coli (additional biobrick). http://www.pnas.org/content/98/19/10566.full.pdf+html

• Again PCB synthesis: We can use already existing parts: http://partsregistry.org/Part:BBa_I15008 and http://partsregistry.org/Part:BBa_I15009 . They have both "one star". Maybe a biologist takes a short look and finds out if we just have to throw them in or if we have to modify something.

• They produced a working light input system in E-Coli. Although I think we cannot use their idea, this paper is very interesting since they also used PCB as chromophore. Thus, this chromophore seems to work in E-Coli. When I understand it right these are the same guys who put the parts for PCB synthesis (see above) into the registry: • Levskaya."Synthetic biology: Engineering Escherichia coli to see light", Nature 438, 441-442 (24 November 2005). http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html

• More or less the same principal, but with a little bit more description of the experimental setup: http://polaris.icmb.utexas.edu/paper-pdfs/Cell_EdgeDetector_2009.pdf

Other Light sources

• Proteorodopsin pumps protons through the cell membrane upon light activation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892948/

Movies

• Chemotaxis E-Coli with cell tracking: http://www.youtube.com/watch?v=EZ5ATNJfuCs&NR=1

• Additional Movies of Chemotaxis: http://www.youtube.com/watch?v=AKHbqOD_OQU&NR=1 http://www.youtube.com/watch?v=2P9hvlsF9_c&NR=1 http://www.youtube.com/watch?v=tZE11gg4c1s

CheR

• The guys who found CheR: It's not membrane bound and \Delta CheR strains swimm smooth without tumbling in a constant environment (exactly what we want). However they can still react to step inputs: "Identification of a protein methyltransferase as the cheR gene product in the bacterial sensing system", PNAS February 1, 1977 vol. 74 no. 2 533-537, http://www.pnas.org/content/74/2/533.short

• The structure of CheR is already identified. Images and the .pdb files: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1AF7 and http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1BC5

Microscope Control, Cell Detection and Tracking

• The software our microscope control will be based on (only for those who are interested): http://www.micro-manager.org/

• Some cell detection and cell tracking, only for yeast and relatively slow, but relatively nice: http://www.nature.com/nmeth/journal/v4/n2/full/nmeth1008.html

• Matlab build in image processing/object detection capacities (fast): http://www.mathworks.com/access/helpdesk/help/toolbox/images/f0-8778.html

Che proteins

• This paper fused different Che proteins (CheY, CheZ, CheA) to fluorescent proteins for localization purposes. The CheA fusion was not functional, but the CheY and CheZ fusion was (3x or 5x glycine linker, C- and N-terminal fusion). http://www3.interscience.wiley.com/journal/119046035/abstract?CRETRY=1&SRETRY=0

• Here you see a nice summary of the effect of different Che Mutations and even double mutations on chemotactic behavior. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC220204/

Softwares

• NEW: BCT - deterministic software for simulating chemotaxis movement: http://www.pdn.cam.ac.uk/groups/comp-cell/BCT.html

• NEW: StochSim - extremely popular soft for stochastically simulating large number of biochemical networks: http://www.pdn.cam.ac.uk/groups/comp-cell/StochSim.html

Movement statistics

http://www.nature.com/nature/journal/v239/n5374/abs/239500a0.html

http://www.pnas.org/content/83/23/8987.abstract

http://www.pnas.org/content/72/8/3235.abstract

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC300951/pdf/mbc00099-0029.pdf