Team:ETH Zurich/References

From 2013.igem.org

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<b>Quorum sensing</b>
<b>Quorum sensing</b>
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<p>Hai-Bao Zhang, Lian-Hui Wang, Lian-Hui Zhang, 1 JUN 2007 ; DOI: 10.1002/9780471729259.mc01c03s05 UNIT 1C.3 <br><i>Detection and Analysis of Quorum-Quenching Enzymes Against Acyl Homoserine Lactone Quorum-Sensing Signals</i>[http://onlinelibrary.wiley.com/doi/10.1002/9780471729259.mc01c03s05/full  Wiley Online library]</p>
+
<html><a id="Antunes2007" class="frog"></a></html>
 +
<p> Antunes L.C., Ferreira R.B., Lostroh C.P., Greenberg E.P.; <i>Journal of bacteriology</i> 2008 July; 190(13): 4392–4397.<br>
 +
<i>A Mutational Analysis Defines Vibrio fischeri LuxR Binding Sites</i>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/18083819 PMC]</p>
-
<p>Ravn L, Christensen AB, Molin S, Givskov M, Gram L. J Microbiol Methods ; 2001 Apr;44(3):239-51<br>
+
<html><a id="Basu2005" class="frog"></a></html>
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<i>Methods for detecting acylated homoserine lactones produced by Gram-negative bacteria and their application in studies of AHL-production kinetics</i> [http://www.ncbi.nlm.nih.gov/pubmed/11240047  PubMed]</p>
+
<p>Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R.; <i>Nature</i>; 2005 Apr; 434: 1130-1134. <br>
 +
<i>A synthetic multicellular system for programmed pattern formation</i>.
 +
[http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html Nature]</p>
-
<p>Lingchong You, Robert Sidney Cox, Ron Weiss3 & Frances H. Arnold; Nature 428, 868-871<br><i>Programmed population control by cell–cell communication and regulated killing</i></p>
+
<html><a id="Garcia2004" class="frog"></a></html>
 +
<p> Garcia-Ojalvo J., Elowitz M.B., Strogatz S.H.; <i>PNAS</i>; 2004 Jul; 101(30): 10955–10960. <br>
 +
<i>Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing. </i>
 +
[http://www.pnas.org/content/101/30/10955.long PNAS]</p>
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<p>Ramiz Daniel1 Jacob R. Rubens Rahul Sarpeshkar & Timothy K. Lu;doi:10.1038/nature12148<br>
+
<p>Geske G.D., Mattmann  M.E., Blackwell H.E.; <i> Bioorganic & Medicinal Chemistry Letters</i>; 2008 Nov; 18(12): 5978–5981. <br>
-
<i>Synthetic analog computation in living cells</i> [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12148.html Nature]</p>
+
<i>Evaluation of a focused library of N-aryl L-homoserine lactones reveals a new set of potent quorum sensing modulators. </i>[http://www.ncbi.nlm.nih.gov/pubmed/18760602 PubMed]</p>
-
<p>Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold & Ron Weiss;Nature 434, 1130-1134 (28 April 2005)<br><i> A synthetic multicellular system for programmed pattern formation </i>[http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html Nature]</p>
+
<html><a id="Horswill2007" class="frog"></a></html>
 +
<p>Horswill A.R., Stoodley P., Stewart P.S., Parsek M.R.; <i> Anal Bioanal Chem</i>.; 2007 Jan; 387(2): 371–380.<br>
 +
<i>The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities. </i>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797063/ PMC] </p>
-
<p>Grant D. Geske, Margrith E. Mattmann, Helen E. Blackwell;Bioorganic & Medicinal Chemistry Letters
+
<p>Daniel R., Rubens J.R., Sarpeshkar R., Lu TK.; <i> Nature</i>; 2013 May; 497: 619–623.<br>
-
Volume 18, Issue 22, 15 November 2008, Pages 5978–5981<br>
+
<i>Synthetic analog computation in living cells. </i> [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12148.html Nature]</p>
-
<i>Evaluation of a focused library of N-aryl l-homoserine lactones reveals a new set of potent quorum sensing modulators</i>
+
-
[http://www.sciencedirect.com/science/article/pii/S0960894X08008652link Science direct]</p>
+
-
<p>Horswill AR, Stoodley P, Stewart PS, Parsek MR; Anal Bioanal Chem. 2007 Jan; 387(2): 371–380.<br>
+
<p>Ravn L, Christensen AB, Molin S, Givskov M, Gram L. J Microbiol Methods; 2001 Apr;44(3):239-51<br>
-
<i>The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities</i>
+
<i>Methods for detecting acylated homoserine lactones produced by Gram-negative bacteria and their application in studies of AHL-production kinetics. </i>[http://www.ncbi.nlm.nih.gov/pubmed/11240047  PubMed]</p>
-
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797063/ Pubmed] </p>
+
 +
<p>Schaefer A.L., Val D.L., Hanzelka B.L. , Cronan, Jr J.E., Greenberg  E.P.; <i> Proc Natl Acad Sci. </i>; 1996 Sept; 93(18): 9505–9509.<br>
 +
<i>Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein. </i>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC38458/ PMC] </p> 
 +
 +
<html><a id="Stewart2003" class="frog"></a></html>
 +
<p>Stewart P.S.;<i> Journal of Bacteriology</i>; 2003 Mar.; 185(5): 1485-1491. <br>
 +
<i>Diffusion in Biofilms.</i>
 +
[http://jb.asm.org/content/185/5/1485.full JB]</p>
 +
 +
<p>You L., Cox R.S., Weiss R., Arnold F.H.; <i>Nature</i> 428, 868-871<br>
 +
<i>Programmed population control by cell–cell communication and regulated killing</i>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/15064770 PubMed] </p>
 +
 +
<p>Zhang H.B., Wang L.H., Zhang L.H.;<i>Curr Protoc Microbiol.</i> 2007 Jun; <br>
 +
<i>Detection and Analysis of Quorum-Quenching Enzymes Against Acyl Homoserine Lactone Quorum-Sensing Signals.</i> [http://onlinelibrary.wiley.com/doi/10.1002/9780471729259.mc01c03s05/full  Wiley Online library]</p>
 +
<br>
<b>Hydrolases</b>
<b>Hydrolases</b>
-
<p>J. C. Jokerst,J. A. Adkins,B. Bisha,M. M. Mentele, L. D. Goodridge and C. S. Henry ;  Chem. 2012, 84, 2900−2907<br>
 
-
<i>Development of a Paper-Based Analytical Device for Colorimetric, Detection of Select Foodborne Pathogens</i>
 
-
[http://pubs.acs.org/doi/pdf/10.1021/ac203466y  pubs.acs]</p>
 
<p>Choi JH, Jeong KJ, Kim SC, Lee SY; Appl Microbiol Biotechnol. 2000 Jun; 53(6): 640-5.
<p>Choi JH, Jeong KJ, Kim SC, Lee SY; Appl Microbiol Biotechnol. 2000 Jun; 53(6): 640-5.
<i>Efficient secretory production of alkaline phosphatase by high cell density culture of recombinant Escherichia coli using the Bacillus sp. endoxylanase signal sequence.</i>[http://www.ncbi.nlm.nih.gov/pubmed/10919319 PubMed]</p>
<i>Efficient secretory production of alkaline phosphatase by high cell density culture of recombinant Escherichia coli using the Bacillus sp. endoxylanase signal sequence.</i>[http://www.ncbi.nlm.nih.gov/pubmed/10919319 PubMed]</p>
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<p> Kiernan JA; Biotech Histochem. 2007 Apr; 82(2):73-103. <span id="Kiernan2007"></span>
+
<html><a id="Farias2007" class="frog"></a></html>
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Indigogenic substrates for detection and localization of enzymes. [http://www.ncbi.nlm.nih.gov/pubmed/17577701 PubMed]</p>
+
<p> Farias T, Mandrich L, Rossi M, Manco G; Protein Pept Lett. 2007; 14(2):165-9.  
 +
<i>Biochemical and thermostability features of acetyl esterase Aes from Escherichia coli.</i>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/17305603 PubMed] </p>
-
<p> Jefferson RA; US 5432081 A. 1995 Jul. <span id="Jefferson1995"></span>
+
<html><a id="Jefferson1995" class="frog"></a></html>
 +
<p> Jefferson RA; US 5432081 A. 1995 Jul.  
<i>Host cells transformed with the ''E. coli'' glucoronide permease gene</i> </p>
<i>Host cells transformed with the ''E. coli'' glucoronide permease gene</i> </p>
-
<p> Farias T, Mandrich L, Rossi M, Manco G; Protein Pept Lett. 2007; 14(2):165-9. <span id="Farias2007"></span>
+
<p>Jokerst J.C., Adkins J.A., Bisha B., Mentele M.M., Goodridge L. D., Henry C. S.; Chem.; 2012, 84:2900−2907<br>
-
<i>Biochemical and thermostability features of acetyl esterase Aes from Escherichia coli.</i>
+
<i>Development of a Paper-Based Analytical Device for Colorimetric Detection of Select Foodborne Pathogens</i>
-
[http://www.ncbi.nlm.nih.gov/pubmed/17305603 PubMed] </p>
+
[http://pubs.acs.org/doi/pdf/10.1021/ac203466y  pubs.acs]</p>
 +
 
 +
<p> Joly N., Danot O., Schlegel A., Boos W., Richet E.; J Biol Chem. 2002 May; 277(19):16606-13. <span id="Joly2002"></span><br>
 +
<i>The Aes protein directly controls the activity of MalT, the central transcriptional activator of the ''Escherichia coli'' maltose regulon.</i>  
 +
[http://www.ncbi.nlm.nih.gov/pubmed/11867639 PubMed]</p>
-
<p> Kanaya S, Koyanagi T, Kanaya E; Biochem. J. 1998; 332:75-80. <span id="Kanaya1998"></span><br>
+
<p> Kanaya S., Koyanagi T., Kanaya E.; Biochem. J. 1998; 332:75-80. <span id="Kanaya1998"></span><br>
<i>An esterase from ''Escherichia coli'' with a sequence similarity to hormone-sensitive lipase.</i>  
<i>An esterase from ''Escherichia coli'' with a sequence similarity to hormone-sensitive lipase.</i>  
[http://www.ncbi.nlm.nih.gov/pubmed/9576853 PubMed] </p>
[http://www.ncbi.nlm.nih.gov/pubmed/9576853 PubMed] </p>
-
<p> Joly N, Danot O, Schlegel A, Boos W, Richet E; J Biol Chem. 2002 May; 277(19):16606-13. <span id="Joly2002"></span><br>
+
<p> Kiernan JA; Biotech Histochem. 2007 Apr; 82(2):73-103. <span id="Kiernan2007"></span>
-
<i>The Aes protein directly controls the activity of MalT, the central transcriptional activator of the ''Escherichia coli'' maltose regulon.</i>  
+
Indigogenic substrates for detection and localization of enzymes. [http://www.ncbi.nlm.nih.gov/pubmed/17577701 PubMed]</p>
-
[http://www.ncbi.nlm.nih.gov/pubmed/11867639 PubMed]</p>
+
<br>
 +
 
 +
<b> Others </b>
 +
<html><a id="Corish1999" class="frog"></a></html>
 +
<p>Corish P, Tyler-Smith C; <i>Protein Engineering</i>. 199; 12(12): 1053-1040. <br>
 +
<i>Attenuation of green fluorescent protein half-life in mammalian cells.</i>
 +
[http://peds.oxfordjournals.org/content/12/12/1035.full peds]</p>
 +
 
 +
<html><a id="Fatin2004" class="frog"></a></html>
 +
<p>Fatin-Rouge N., Starchev K., Buffle J.; <i>Biophysical Journal</i>. 2004 May; 86:2710–2719.<br>
 +
<i>Size Effects on Diffusion Processes within Agarose Gels</i>
 +
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304142/ PMC]</p>
 +
 
 +
<p>Gordon P.V., Muratov C.B., Shvartsman S.Y.;<i> J Chem Phys </i>. 2013 Mar; 138(10):104121</p>
 +
<i>Local accumulation times for source, diffusion, and degradation models in two and three dimensions. </i>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/23514479 PubMed]
 +
 
 +
<br clear="all"/>
 +
 
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Latest revision as of 01:03, 29 October 2013

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References

Quorum sensing

Antunes L.C., Ferreira R.B., Lostroh C.P., Greenberg E.P.; Journal of bacteriology 2008 July; 190(13): 4392–4397.
A Mutational Analysis Defines Vibrio fischeri LuxR Binding Sites [http://www.ncbi.nlm.nih.gov/pubmed/18083819 PMC]

Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R.; Nature; 2005 Apr; 434: 1130-1134.
A synthetic multicellular system for programmed pattern formation. [http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html Nature]

Garcia-Ojalvo J., Elowitz M.B., Strogatz S.H.; PNAS; 2004 Jul; 101(30): 10955–10960.
Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing. [http://www.pnas.org/content/101/30/10955.long PNAS]

Geske G.D., Mattmann M.E., Blackwell H.E.; Bioorganic & Medicinal Chemistry Letters; 2008 Nov; 18(12): 5978–5981.
Evaluation of a focused library of N-aryl L-homoserine lactones reveals a new set of potent quorum sensing modulators. [http://www.ncbi.nlm.nih.gov/pubmed/18760602 PubMed]

Horswill A.R., Stoodley P., Stewart P.S., Parsek M.R.; Anal Bioanal Chem.; 2007 Jan; 387(2): 371–380.
The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797063/ PMC]

Daniel R., Rubens J.R., Sarpeshkar R., Lu TK.; Nature; 2013 May; 497: 619–623.
Synthetic analog computation in living cells. [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12148.html Nature]

Ravn L, Christensen AB, Molin S, Givskov M, Gram L. J Microbiol Methods; 2001 Apr;44(3):239-51
Methods for detecting acylated homoserine lactones produced by Gram-negative bacteria and their application in studies of AHL-production kinetics. [http://www.ncbi.nlm.nih.gov/pubmed/11240047 PubMed]

Schaefer A.L., Val D.L., Hanzelka B.L. , Cronan, Jr J.E., Greenberg E.P.; Proc Natl Acad Sci. ; 1996 Sept; 93(18): 9505–9509.
Generation of cell-to-cell signals in quorum sensing: acyl homoserine lactone synthase activity of a purified Vibrio fischeri LuxI protein. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC38458/ PMC]

Stewart P.S.; Journal of Bacteriology; 2003 Mar.; 185(5): 1485-1491.
Diffusion in Biofilms. [http://jb.asm.org/content/185/5/1485.full JB]

You L., Cox R.S., Weiss R., Arnold F.H.; Nature 428, 868-871
Programmed population control by cell–cell communication and regulated killing [http://www.ncbi.nlm.nih.gov/pubmed/15064770 PubMed]

Zhang H.B., Wang L.H., Zhang L.H.;Curr Protoc Microbiol. 2007 Jun;
Detection and Analysis of Quorum-Quenching Enzymes Against Acyl Homoserine Lactone Quorum-Sensing Signals. [http://onlinelibrary.wiley.com/doi/10.1002/9780471729259.mc01c03s05/full Wiley Online library]


Hydrolases

Choi JH, Jeong KJ, Kim SC, Lee SY; Appl Microbiol Biotechnol. 2000 Jun; 53(6): 640-5. Efficient secretory production of alkaline phosphatase by high cell density culture of recombinant Escherichia coli using the Bacillus sp. endoxylanase signal sequence.[http://www.ncbi.nlm.nih.gov/pubmed/10919319 PubMed]

Farias T, Mandrich L, Rossi M, Manco G; Protein Pept Lett. 2007; 14(2):165-9. Biochemical and thermostability features of acetyl esterase Aes from Escherichia coli. [http://www.ncbi.nlm.nih.gov/pubmed/17305603 PubMed]

Jefferson RA; US 5432081 A. 1995 Jul. Host cells transformed with the E. coli glucoronide permease gene

Jokerst J.C., Adkins J.A., Bisha B., Mentele M.M., Goodridge L. D., Henry C. S.; Chem.; 2012, 84:2900−2907
Development of a Paper-Based Analytical Device for Colorimetric Detection of Select Foodborne Pathogens [http://pubs.acs.org/doi/pdf/10.1021/ac203466y pubs.acs]

Joly N., Danot O., Schlegel A., Boos W., Richet E.; J Biol Chem. 2002 May; 277(19):16606-13.
The Aes protein directly controls the activity of MalT, the central transcriptional activator of the Escherichia coli maltose regulon. [http://www.ncbi.nlm.nih.gov/pubmed/11867639 PubMed]

Kanaya S., Koyanagi T., Kanaya E.; Biochem. J. 1998; 332:75-80.
An esterase from Escherichia coli with a sequence similarity to hormone-sensitive lipase. [http://www.ncbi.nlm.nih.gov/pubmed/9576853 PubMed]

Kiernan JA; Biotech Histochem. 2007 Apr; 82(2):73-103. Indigogenic substrates for detection and localization of enzymes. [http://www.ncbi.nlm.nih.gov/pubmed/17577701 PubMed]


Others

Corish P, Tyler-Smith C; Protein Engineering. 199; 12(12): 1053-1040.
Attenuation of green fluorescent protein half-life in mammalian cells. [http://peds.oxfordjournals.org/content/12/12/1035.full peds]

Fatin-Rouge N., Starchev K., Buffle J.; Biophysical Journal. 2004 May; 86:2710–2719.
Size Effects on Diffusion Processes within Agarose Gels [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304142/ PMC]

Gordon P.V., Muratov C.B., Shvartsman S.Y.; J Chem Phys . 2013 Mar; 138(10):104121

Local accumulation times for source, diffusion, and degradation models in two and three dimensions. [http://www.ncbi.nlm.nih.gov/pubmed/23514479 PubMed]


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