Team:ETH Zurich/Modeling/References
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- | + | = Modeling - References = | |
- | + | '''All of the previous work we included into our model is referenced here.''' | |
+ | {{:Team:ETH Zurich/Templates/SectionEnd}} | ||
+ | {{:Team:ETH Zurich/Templates/SectionStart}} | ||
+ | = Single-Cell Model = | ||
+ | {|style="margin: 1em auto 1em auto;" class="wikitable sortable" width="90%" | ||
+ | !style="white-space: nowrap; width: 1px;"| | ||
+ | !class="unsortable"|Source | ||
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- | |style=" | + | |style="text-align: center"|<span id="Ref1">[1]</span> |
- | |[ | + | |[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss,<br> '''A synthetic multicellular system for programmed pattern formation''', <br>Nature Vol. 434, 2005] |
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- | | | + | |style="text-align: center"|<span id="Ref2">[2]</span> |
+ | |[http://www.pnas.org/content/101/30/10955.fullJordi Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz, <br>'''Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing''', <br>PNAS vol. 101 no. 30, 2004] | ||
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+ | |style="text-align: center"|<span id="Ref3">[3]</span> | ||
+ | |[https://2010.igem.org/Team:MIT_tmodel MIT igem 2010] | ||
+ | |- | ||
+ | |style="text-align: center"|<span id="Ref4">[4]</span> | ||
+ | |[http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.20461/abstract;jsessionid=00173AFD03BE779CB9031A77277F1458.d01t01 Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,<br>''' Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts''',<br>Cytometry Part A, Volume 71A Issue 10, 2007] | ||
+ | |- | ||
+ | |style="text-align: center"|<span id="Ref5">[5]</span> | ||
+ | |[http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html Wilfried Weber, Markus Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique Aubel, Cornelia C Weber & Martin Fussenegger, <br>'''Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology''',<br>volume 22, number 11, November 2004] | ||
+ | |- | ||
+ | |style="text-align: center"|<span id="Ref6">[6]</span> | ||
+ | |[http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02245.x/abstract Michalis Koutinas, Ming-Chi Lam, Alexandros Kiparissides, Rafael Silva-Rocha, Miguel Godinho, Andrew G. Livingston, Efstratios N. Pistikopoulos, Victor de Lorenzo, Vitor A. P. Martins dos Santos and Athanasios Mantalaris,<br>'''The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid''',<br>Environmental Microbiology vol. 12, Issue 6, 2010] | ||
|} | |} | ||
+ | {{:Team:ETH Zurich/Templates/SectionEnd}} | ||
+ | {{:Team:ETH Zurich/Templates/SectionStart}} | ||
+ | = Diffusion Model = | ||
+ | {|style="margin: 1em auto 1em auto;" class="wikitable sortable" width="90%" | ||
+ | !style="white-space: nowrap; width: 1px"| | ||
+ | !class="unsortable"|Source | ||
+ | |- | ||
+ | |<span id="Ref8">[8]</span> | ||
+ | |[http://www.gsi-net.com/en/publications/gsi-chemical-database/single/3.html GSI Environmental Inc,<br>'''Acetaldehyde''',<br>GSI Chemical Database] | ||
+ | |- | ||
+ | |<span id="Ref10">[10]</span> | ||
+ | |[http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.2.1.10&Suchword=&organism[]=Escherichia+coli&show_tm=0 '''EC 1.2.1.10 - acetaldehyde dehydrogenase (acetylating) BRENDA entry'''<br>BRENDA Enyzme Database] | ||
- | + | [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013686/?tool=pubmed Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D.<br>'''BRENDA, the enzyme information system in 2011''',<br>Nucleic Acids Res. 2011 Jan;39(Database issue):D670-6. Epub 2010 Nov 9.] | |
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+ | |<span id="Ref11">[11]</span> | ||
+ | |[http://pubs.acs.org/doi/abs/10.1021/bi00529a026 Clifford C. Shone, Herbert J. Fromm,<br>'''Steady-state and pre-steady-state kinetics of coenzyme A-linked aldehyde dehydrogenase from Escherichia coli''',<br>Biochemistry, 1981, 20 (26), pp 7494–7501] | ||
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+ | |<span id="Ref12">[12]</span> | ||
+ | |[http://www.uniprot.org/uniprot/P77580 UniProt Knowledgebase (UniProtKB),<br>'''Acetaldehyde dehydrogenase'''] | ||
+ | |- | ||
+ | |<span id="Ref13">[13]</span> | ||
+ | |[http://www.bionumbers.org Milo et al.<br>'''Bionumbers.org''',<br>Nucl. Acids Res. (2010) 38 (suppl 1): D750-D753] | ||
+ | |- | ||
+ | |<span id="Ref14">[14]</span> | ||
+ | |[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC213663/?tool=pubmed Kubitschek HE, Friske JA.,<br>'''Determination of bacterial cell volume with the Coulter Counter''',<br>J Bacteriol. 1986 Dec168(3):1466-7] | ||
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+ | |<span id="Ref16">[16]</span> | ||
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- | + | [http://jb.asm.org/cgi/content/full/189/23/8746 Sezonov G, Joseleau-Petit D, D'Ari R.<br>'''Escherichia coli physiology in Luria-Bertani broth.'''<br>J Bacteriol. 2007 Dec189(23):8746-9 Fig. 1a] | |
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|} | |} | ||
- | {|class=" | + | {{:Team:ETH Zurich/Templates/SectionEnd}} |
+ | {{:Team:ETH Zurich/Templates/SectionStart}} | ||
+ | = Combined Model = | ||
+ | {|style="margin: 1em auto 1em auto;" class="wikitable sortable" width="90%" | ||
+ | !style="white-space: nowrap; width: 1px"| | ||
+ | !class="unsortable"|Source | ||
+ | |- | ||
+ | |<span id="Ref7">[7]</span> | ||
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- | + | [http://www.springerlink.com/content/v36128k24t558820/ Alexander R. Horswill, Paul Stoodley, Philip S. Stewart and Matthew R. Parsek,<br>'''The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities''',<br>Analytical and Bioanalytical Chemistry, Volume 387, Number 2, 371-380] | |
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- | | | + | |<span id="Ref9">[9]</span> |
- | + | |[http://jb.asm.org/cgi/content/full/185/5/1485 Philip S. Stewart,<br>'''Diffusion in Biofilms'''<br>Journal of Bacteriology, March 2003, p. 1485-1491, Vol. 185, No. 5] | |
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+ | |<span id="Ref15">[15]</span> | ||
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- | = | + | [http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:56080 '''N-(3-oxododecanoyl)-L-homoserine lactone (CHEBI:56080) ChEBI Entry''',<br>Chemical Entities of Biological Interest (ChEBI) Database] |
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+ | [http://nar.oxfordjournals.org/content/early/2009/10/23/nar.gkp886.abstract de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., and Steinbeck, C.<br>'''(2009). Chemical entities of biological interest: an update.'''<br>Nucleic Acids Res. in the press.] | ||
|} | |} | ||
+ | {{:Team:ETH Zurich/Templates/SectionEnd}} | ||
+ | {{:Team:ETH Zurich/Templates/HeaderNewEnd}} |
Latest revision as of 15:14, 28 October 2011
Modeling - References
All of the previous work we included into our model is referenced here.
Single-Cell Model
Diffusion Model
Combined Model
Source | |
---|---|
[7] | |
[9] | Philip S. Stewart, Diffusion in Biofilms Journal of Bacteriology, March 2003, p. 1485-1491, Vol. 185, No. 5 |
[15] |