Team:UNAM Genomics Mexico/Project/DeeperDescription

From 2012.igem.org

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<h1>Deep Description</h1><br />
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[1] Busenlehner LS, Pennella MA, Giedroc DP (2003). The SmtB/ArsR family of metalloregulatory transcriptional repressors: Structural insights into prokaryotic metal resistance. FEMS Microbiol Rev , 27:131-143. [http://dx.doi.org/10.1016/S0168-6445(03)00054-8]
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Our boolean constructions are two, the AND & OR, for it to form a system, but how we will connect this two operations? With the nanotubes that Bacillus subtilis form. <br />
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[2] Charles M Moore and John D Helmann(2005). Metal ion homeostasis in Bacillus subtilis. Current Opinion in Microbiology, 8:188–195. [http://dx.doi.org/10.1016/j.mib.2005.02.007]
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Why B. subtilis? <br />
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We found a paper in which Ben-Yehuda et. al. demostrated that Bacillus subtilis form nanotubes between them, Escherichia coli and Staphylococcus aureus. And they were able to get through a GFP and some other smaller molecules. So, we decided to use this connection to form the principles of a molecular computer. How? The output of the first operation will the input for the next one, and that was what we did. Also, there is not many work in the B. subtilis at the iGEM competition, so we decided to standardize the protocols of competent cells and transformation, and to send biobricks that B. subtilis could transform and integrate for them to work correctly (link al new standar protocol). <br /><br />
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[3] Moore CM, Gaballa A, Hui M, Ye RW, Helmann JD (2005). Genetic and physiological responses of Bacillus subtilis to metal ion stress. Mol Microbiol(1) , 27–40. [http://dx.doi.org/10.1111/j.1365-2958.2005.04642.x]
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[4] Camacho A & Salas M (2010) DNA bending and looping in the transcriptional control of bacteriophage ϕ29. FEMS Microbiol Rev. 34(5):828-841. [http://dx.doi.org/10.1111/j.1574-6976.2010.00219.x]
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<p class='captionInside'>2011 Gyanendra P. Dubey, Sigal Ben-Yehuda. Intercellular Nanotubes Mediate Bacterial Communication. Cell, 2011; 144 (4): 590 DOI:10.1016/j.cell.2011.01.015<br /></p>
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[5] Rojo F, Mencía M, Monsalve M & Salas M (1998) Transcription activation and repression by interaction of a regulator with the a subunit of RNA polymerase: the model of phage ϕ29 protein p4. Nucleic Acid Re 60: 29–46 [http://dx.doi.org/10.1016/S0079-6603(08)60888-0]
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[6] http://partsregistry.org/Part:BBa_E1010
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<p class='captionInside'>2011 Gyanendra P. Dubey, Sigal Ben-Yehuda. Intercellular Nanotubes Mediate Bacterial Communication. Cell, 2011; 144 (4): 590 DOI:10.1016/j.cell.2011.01.015<br /></p>
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[7] Pierre Prentki, Anna Bind and Andrée Epstein (1991). Plasmid vectors for selecting ISI-promoted deletions in cloned DNA: sequence analysis of the omega interposon. Gene, 103:17-23. [http://dx.doi.org/10.1016/0378-1119(91)90385-O]
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[8] Pierre Prentki and Henry M. Krisch (1984). In vitro insertional mutagenesis with a selectable DNA fragment. Gene, 29:303-313 [http://dx.doi.org/10.1016/0378-1119(84)90059-3]
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[9] Lee, N. (1980) Molecular Aspects of ara Regulation. In The Operon, J. H. Miller and W. S. Reznikoff, eds. (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory), pp. 389-410. [http://dx.doi.org/10.1101/087969133.7.389]
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[10] Lee, N., Francklyn, C., and Hamilton, E. P. (1987). Arabinose-Induced Binding of AraC Protein to araI2 Activates the araBAD Operon Promoter. Proc. Natl. Acad. Sci. USA 84, 8814-8818. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC299641/]
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[11] Shamanna, D. K., and K. E. Sanderson. 1979. Genetics and regulation of D-xylose utilization in Salmonella typhimurium LT2. J. Bacteriol. 139:71-79. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC216828/]
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[12] D Gartner, M Geissendorfer, & W Hillen(1988). Expression of the Bacillus subtilis xyl Operon Is Repressed at the Level of Transcription and Is Induced by Xylose J Bacteriol 170:7,3102-3109. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC211255/]
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[13] Moran CP, Lang N, LeGrice SF, Lee G, Stephens M, Sonenshein AL, Pero J, Losick R (1982). Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis. Mol Gen Genet; 186(3): 339-46
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[14] Kreuzer P, Gärtner D, Allmansberger R, Hillen W (1989). Identification and sequence analysis of the Bacillus subtilis W23 xylR gene and xyl operator. J Bacteriol. Jul;171(7):3840-5.
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[15] Schlief, R. (2000). Regulation of the L-arabinose operon of Escherichia coli. Trends in Genetics. 16(12):559-565.
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[16] Sogo JM, Inciarte MR, Corral J, Viñuela E & Salas M(1979) RNA polymerase binding sites and transcription map of the DNA of Bacillus subtilis phage ϕ29. J Mol Biol 127: 411–436.
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[17] Nuez B, Rojo F & SalasM(1992) Phage ϕ29 regulatory protein p4 stabilizes the binding of the RNA polymerase to the late promoter in a process involving direct protein–protein contact. P Natl Acad Sci USA 89: 11401–11405.
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[18]Cutting, S M.; Vander-Horn, P B. Genetic analysis. In: Harwood C R, Cutting S M. , editors. Molecular biological methods for Bacillus. Chichester, England: John Wiley & Sons, Ltd.; 1990. pp. 27–74.
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[19] http://partsregistry.org/Part:BBa_K143001
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[20]http://regtransbase.lbl.gov/cgi-bin/regtransbasepage=regulatorinfo&type=site&g
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[21]Analysis of the Pseudomonas aeruginosa elastase (lasB) regulatory region. L Rust, E C Pesci and B H Iglewski, J. Bacteriol. February 1996 vol. 178 no. 4 1134-1140
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[22] http://partsregistry.org/Part:BBa_K330002
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Revision as of 09:34, 26 September 2012


UNAM-Genomics_Mexico


Under Construction




Nanotubes!!

The logic

Random info

Deep Description



Our boolean constructions are two, the AND & OR, for it to form a system, but how we will connect this two operations? With the nanotubes that Bacillus subtilis form.

Why B. subtilis?
We found a paper in which Ben-Yehuda et. al. demostrated that Bacillus subtilis form nanotubes between them, Escherichia coli and Staphylococcus aureus. And they were able to get through a GFP and some other smaller molecules. So, we decided to use this connection to form the principles of a molecular computer. How? The output of the first operation will the input for the next one, and that was what we did. Also, there is not many work in the B. subtilis at the iGEM competition, so we decided to standardize the protocols of competent cells and transformation, and to send biobricks that B. subtilis could transform and integrate for them to work correctly (link al new standar protocol).

  • 2011 Gyanendra P. Dubey, Sigal Ben-Yehuda. Intercellular Nanotubes Mediate Bacterial Communication. Cell, 2011; 144 (4): 590 DOI:10.1016/j.cell.2011.01.015

  • 2011 Gyanendra P. Dubey, Sigal Ben-Yehuda. Intercellular Nanotubes Mediate Bacterial Communication. Cell, 2011; 144 (4): 590 DOI:10.1016/j.cell.2011.01.015

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