Team:ETH Zurich/Modeling/References

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|style="font-size:2em; height: 30px" class="modeling"|Modeling References
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|style="border-left: none;"|[[#Single-Cell Model|Single-Cell Model]]
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|colspan="2"|'''All of the previous work we included into our model is referenced here.'''
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= Modeling - References =
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== Single-Cell Model ==
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'''All of the previous work we included into our model is referenced here.'''
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= Single-Cell Model =
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|style="text-align: center"|<span id="Ref5">[5]</span>
|style="text-align: center"|<span id="Ref5">[5]</span>
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|[http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html Weber W. et al,<br>'''Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology''',<br>volume 22, number 11, November 2004]
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|[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]
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|style="text-align: center"|<span id="Ref6">[6]</span>
|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]
|[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]
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= Diffusion Model =
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== Microfluidics Model ==
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|<span id="Ref8">[8]</span>
|<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]
|[http://www.gsi-net.com/en/publications/gsi-chemical-database/single/3.html GSI Environmental Inc,<br>'''Acetaldehyde''',<br>GSI Chemical Database]
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|<span id="Ref9">[9]</span>
 
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|[http://jb.asm.org/cgi/reprint/185/5/1485 FIX ME Diffusion in Biofilms]
 
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|<span id="Ref10">[10]</span>
|<span id="Ref10">[10]</span>
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|[http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.2.1.10&Suchword=&organism&#91;&#93;=Escherichia+coli&show_tm=0 FIX ME BRENDA Acetaldehyde Dehydrogenase]
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|[http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.2.1.10&Suchword=&organism&#91;&#93;=Escherichia+coli&show_tm=0 '''EC 1.2.1.10 - acetaldehyde dehydrogenase (acetylating) BRENDA entry'''<br>BRENDA Enyzme Database]
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[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>
|<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]
|[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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|-
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|<span id="Ref12">[12]</span>
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|[http://www.uniprot.org/uniprot/P77580 UniProt Knowledgebase (UniProtKB),<br>'''Acetaldehyde dehydrogenase''']
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|-
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|<span id="Ref13">[13]</span>
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|[http://www.bionumbers.org Milo et al.<br>'''Bionumbers.org''',<br>Nucl. Acids Res. (2010) 38 (suppl 1): D750-D753]
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|-
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|<span id="Ref14">[14]</span>
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|[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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= Combined Model =
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== Combined Model ==
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!class="unsortable"|Source
!class="unsortable"|Source
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|<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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|-
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|<span id="Ref9">[9]</span>
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|[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.]
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Latest revision as of 15:14, 28 October 2011

Can you feel the smoke tonight?
 

Contents

Modeling - References

All of the previous work we included into our model is referenced here.

Single-Cell Model

Source
[1] Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss,
A synthetic multicellular system for programmed pattern formation,
Nature Vol. 434, 2005
[2] Garcia-Ojalvo, Michael B. Elowitz, and Steven H. Strogatz,
Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing,
PNAS vol. 101 no. 30, 2004
[3] MIT igem 2010
[4] Michael Halter, Alex Tona, Kiran Bhadriraju, Anne L. Plant, John T. Elliott,
Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,
Cytometry Part A, Volume 71A Issue 10, 2007
[5] Wilfried Weber, Markus Rimann, Manuela Spielmann, Bettina Keller, Marie Daoud-El Baba, Dominique Aubel, Cornelia C Weber & Martin Fussenegger,
Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology,
volume 22, number 11, November 2004
[6] 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,
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,
Environmental Microbiology vol. 12, Issue 6, 2010


Diffusion Model

Source
[8] GSI Environmental Inc,
Acetaldehyde,
GSI Chemical Database
[10] EC 1.2.1.10 - acetaldehyde dehydrogenase (acetylating) BRENDA entry
BRENDA Enyzme Database

Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Söhngen C, Stelzer M, Thiele J, Schomburg D.
BRENDA, the enzyme information system in 2011,
Nucleic Acids Res. 2011 Jan;39(Database issue):D670-6. Epub 2010 Nov 9.

[11] Clifford C. Shone, Herbert J. Fromm,
Steady-state and pre-steady-state kinetics of coenzyme A-linked aldehyde dehydrogenase from Escherichia coli,
Biochemistry, 1981, 20 (26), pp 7494–7501
[12] UniProt Knowledgebase (UniProtKB),
Acetaldehyde dehydrogenase
[13] Milo et al.
Bionumbers.org,
Nucl. Acids Res. (2010) 38 (suppl 1): D750-D753
[14] Kubitschek HE, Friske JA.,
Determination of bacterial cell volume with the Coulter Counter,
J Bacteriol. 1986 Dec168(3):1466-7
[16]

Sezonov G, Joseleau-Petit D, D'Ari R.
Escherichia coli physiology in Luria-Bertani broth.
J Bacteriol. 2007 Dec189(23):8746-9 Fig. 1a


Combined Model

Source
[7]

Alexander R. Horswill, Paul Stoodley, Philip S. Stewart and Matthew R. Parsek,
The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities,
Analytical and Bioanalytical Chemistry, Volume 387, Number 2, 371-380

[9] Philip S. Stewart,
Diffusion in Biofilms
Journal of Bacteriology, March 2003, p. 1485-1491, Vol. 185, No. 5
[15]

N-(3-oxododecanoyl)-L-homoserine lactone (CHEBI:56080) ChEBI Entry,
Chemical Entities of Biological Interest (ChEBI) Database

de Matos, P., Alcántara, R., Dekker, A., Ennis, M., Hastings, J., Haug, K., Spiteri, I., Turner, S., and Steinbeck, C.
(2009). Chemical entities of biological interest: an update.
Nucleic Acids Res. in the press.


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