Team:ETH Zurich/Modeling/References

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|style="font-size:2em; height: 30px" class="modeling"|Modeling References
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= Modeling - References =
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'''All of the previous work we included into our model is referenced here.'''
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{{:Team:ETH Zurich/Templates/SectionEnd}}
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{{:Team:ETH Zurich/Templates/SectionStart}}
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= Single-Cell Model =
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{|style="margin: 1em auto 1em auto;" class="wikitable sortable" width="90%"
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!style="white-space: nowrap; width: 1px;"|
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!class="unsortable"|Source
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|style="border-left: none;"|[[#Single-Cell Model|Single-Cell Model]]
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|style="text-align: center"|<span id="Ref1">[1]</span>
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|[[#Microfluidics Model|Microfluidics Model]]
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|[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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|[[#Combined Model|Combined Model]]
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|-
|-
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|colspan="2"|'''Of course, our models do not work without parameters, and in our case, there are quite a lot of them. In order to keep track of all of their respective values and units, we gathered them in a series of tables on this page.'''
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|style="text-align: center"|<span id="Ref2">[2]</span>
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|[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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|-
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|style="text-align: center"|<span id="Ref3">[3]</span>
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|[https://2010.igem.org/Team:MIT_tmodel MIT igem 2010]
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|-
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|style="text-align: center"|<span id="Ref4">[4]</span>
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|[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]
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|-
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|style="text-align: center"|<span id="Ref5">[5]</span>
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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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|-
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|style="text-align: center"|<span id="Ref6">[6]</span>
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|[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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{{:Team:ETH Zurich/Templates/SectionEnd}}
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{{:Team:ETH Zurich/Templates/SectionStart}}
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= Diffusion Model =
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{|style="margin: 1em auto 1em auto;" class="wikitable sortable" width="90%"
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!style="white-space: nowrap; width: 1px"|
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!class="unsortable"|Source
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|-
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|<span id="Ref8">[8]</span>
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|[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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|-
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|<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  '''EC 1.2.1.10 - acetaldehyde dehydrogenase (acetylating) BRENDA entry'''<br>BRENDA Enyzme Database]
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{|class="roundContainer"
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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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|-
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|<span id="Ref11">[11]</span>
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|[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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|-
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|<span id="Ref16">[16]</span>
|
|
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== Single-Cell Model ==
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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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Irena: Tidy up the references!
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<span id="Ref1">[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 ( http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html ) </span>
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[2] Jordi 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  ( http://www.pnas.org/content/101/30/10955.full )
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[3] MIT igem 2010 ( https://2010.igem.org/Team:MIT_tmodel )
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[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 (http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.20461/abstract;jsessionid=00173AFD03BE779CB9031A77277F1458.d01t01 )
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[5] Weber W. et al, '''Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology''', volume 22, number 11, November 2004 ( http://www.nature.com/nbt/journal/v22/n11/full/nbt1021.html )
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[6] Michalis Koutinas et al, 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 plasmidemi_2245 1705 ( http://onlinelibrary.wiley.com/doi/10.111/j.1462-2920.2010.02245.x/pdf )
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[7] Development and Testing of a Bacterial Biosensor for Toluene-Based Environmental Contaminants ( http://aem.asm.org/cgi/reprint/64/3/1006 )
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{|class="roundContainer"
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{{:Team:ETH Zurich/Templates/SectionEnd}}
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{{:Team:ETH Zurich/Templates/SectionStart}}
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= Combined Model =
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{|style="margin: 1em auto 1em auto;" class="wikitable sortable" width="90%"
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!style="white-space: nowrap; width: 1px"|
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!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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== Microfluidics Model ==
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|-
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|<span id="Ref9">[9]</span>
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{|class="roundContainer"
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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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|-
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|<span id="Ref15">[15]</span>
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== Combined Model ==
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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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{{:Team:ETH Zurich/Templates/SectionEnd}}
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{{:Team:ETH Zurich/Templates/HeaderNewEnd}}

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] [http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html 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] [http://www.pnas.org/content/101/30/10955.fullJordi 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] [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,
Automated Live Cell Imaging of Green Fluorescent Protein Degradation in Individual Fibroblasts,
Cytometry Part A, Volume 71A Issue 10, 2007]
[5] [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,
Gas-inducible transgene expression in mammalian cells and mice, Nature Biotechnology,
volume 22, number 11, November 2004]
[6] [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,
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] [http://www.gsi-net.com/en/publications/gsi-chemical-database/single/3.html GSI Environmental Inc,
Acetaldehyde,
GSI Chemical Database]
[10] [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
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.
BRENDA, the enzyme information system in 2011,
Nucleic Acids Res. 2011 Jan;39(Database issue):D670-6. Epub 2010 Nov 9.]

[11] [http://pubs.acs.org/doi/abs/10.1021/bi00529a026 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] [http://www.uniprot.org/uniprot/P77580 UniProt Knowledgebase (UniProtKB),
Acetaldehyde dehydrogenase]
[13] [http://www.bionumbers.org Milo et al.
Bionumbers.org,
Nucl. Acids Res. (2010) 38 (suppl 1): D750-D753]
[14] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC213663/?tool=pubmed Kubitschek HE, Friske JA.,
Determination of bacterial cell volume with the Coulter Counter,
J Bacteriol. 1986 Dec168(3):1466-7]
[16]

[http://jb.asm.org/cgi/content/full/189/23/8746 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]

[http://www.springerlink.com/content/v36128k24t558820/ 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] [http://jb.asm.org/cgi/content/full/185/5/1485 Philip S. Stewart,
Diffusion in Biofilms
Journal of Bacteriology, March 2003, p. 1485-1491, Vol. 185, No. 5]
[15]

[http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:56080 N-(3-oxododecanoyl)-L-homoserine lactone (CHEBI:56080) ChEBI Entry,
Chemical Entities of Biological Interest (ChEBI) Database]

[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.
(2009). Chemical entities of biological interest: an update.
Nucleic Acids Res. in the press.]


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