Team:University of Chicago/Papers

From 2008.igem.org

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''[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TWB-4NYSH9P-2&_user=5745&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000001358&_version=1&_urlVersion=0&_userid=5745&md5=131ccdf044aaaa423459eada8b774168#secx3  Cell adhesion biomaterial based on mussel adhesive protein fused with RGD peptide].''--Nora
''[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TWB-4NYSH9P-2&_user=5745&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000001358&_version=1&_urlVersion=0&_userid=5745&md5=131ccdf044aaaa423459eada8b774168#secx3  Cell adhesion biomaterial based on mussel adhesive protein fused with RGD peptide].''--Nora
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====Peptides, Messersmith====
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"[http://biomaterials.bme.northwestern.edu/Papers/Polydopamine_Final_Science2007.pdf Mussel-Inspired Surface Chemistry for Multifunctional Coatings]." Use of dopamine for the coating of materials. --Rob
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"[http://www.nature.com/nature/journal/v448/n7151/full/nature05968.html A reversible wet/dry adhesive inspired by mussels and geckos]." Messersmith's combination of gecko-foot "pillars" and mussel-foot adhesive. Was on the cover of nature!!
====Yeast/Tyrosinase====
====Yeast/Tyrosinase====
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''[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T1V-3XX6VB3-2H&_user=5745&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000001358&_version=1&_urlVersion=0&_userid=5745&md5=cc4d2fbcbd990c68b62f4a042239f15c  Molecular cloning and nucleotide sequence of the protyrosinase gene, melO, from Aspergillus oryzae and expression of the gene in yeast cells].'' --Jata
''[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T1V-3XX6VB3-2H&_user=5745&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000001358&_version=1&_urlVersion=0&_userid=5745&md5=cc4d2fbcbd990c68b62f4a042239f15c  Molecular cloning and nucleotide sequence of the protyrosinase gene, melO, from Aspergillus oryzae and expression of the gene in yeast cells].'' --Jata
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"[http://www.pnas.org/content/92/7/2964.abstract Tyrosine Inhibitory Peptide found in Flies. Potential "off switch" for tyrosinase activity - perhaps to terminate the continued growth of a glue-glob, or perhaps to prevent the conversion of DOPA into a quinone. Also potential for a negative feedback loop, as the peptide contains a potentially important DOPA.]." --Rob
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[[Media:MushroomTyr Spectroscopy.pdf | "Direct spectrophotometric assay of monooxygenase and oxidase activities of mushroom tyrosinase in the presence of synthetic and natural substrates"]]--a good methods paper for tyrosinase spectroscopy. --Daniel.
====Computer Modeling====
====Computer Modeling====
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''[http://openwetware.org/wiki/IGEM:MIT/2007/Ideas3 2007 Ideas].'' Great big honking list of references. ---Thomas Graham
''[http://openwetware.org/wiki/IGEM:MIT/2007/Ideas3 2007 Ideas].'' Great big honking list of references. ---Thomas Graham
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"[http://weisswebserver.ee.princeton.edu/papers/brenner-2007.pdf Quorum Sensing in E.Coli]" Bioluminescence Activation via Q.S.  -Rob M
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"[http://weisswebserver.ee.princeton.edu/papers/brenner-2007.pdf Quorum Sensing in E.Coli]" Bioluminescence Activation via Q.S.  -Rob  
"[http://www.patentstorm.us/patents/005466592.pdf]." Patent for stable extracellular tyrosinase which may or may not be useful --Laura
"[http://www.patentstorm.us/patents/005466592.pdf]." Patent for stable extracellular tyrosinase which may or may not be useful --Laura
[[Media:Molecular_Biology_Primer.pdf|Molecular Biology Primer]] written by yours truly--Daniel
[[Media:Molecular_Biology_Primer.pdf|Molecular Biology Primer]] written by yours truly--Daniel
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[[Media:Fish_Shellfish_Immun_2008_24.pdf|"Isolation, purification and characterization of b-1,3-glucan binding protein from the plasma of marine mussel Perna viridis"]] Assays for another binding protein that may be useful for our methods section.--Daniel
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[[Media:Hydrox PhenAlan Tyr.pdf|"The Hydroxylation of Phenylalanine and Tyrosine: A Comparison with Salicylate and Tryptophan."]] How the Fenton Reaction can hydroxylize Tyr into DOPA.--Daniel

Latest revision as of 22:07, 26 August 2008

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Home Team Project Parts Modeling Notebook Meetings Papers


Please post links to relevant papers here with brief descriptions. Sign your name in case we have questions. I'll start us off with everything I've gotten by email so far.

Contents

Expression

Patent: [http://www.google.com/patents?id=pLIgAAAAEBAJ&dq=5202236 Method of producing bioadhesive protein]. Making mussel proteins since 1990! ---Steve Kron

Patent: [http://www.google.com/patents?id=U-kgAAAAEBAJ&dq=mussel+adhesive Bioadhesive precursor protein expression vectors]. I swear these people just photocopied their application and mailed it out again. ---Steve Kron

Patent: [http://www.google.com/patents?id=nrQcAAAAEBAJ&dq=mussel+adhesive Production of bioadhesive precursor protein analogs by genetically engineered organisms]. New pictures this time. ---Steve Kron

Secretion

[http://www.springerlink.com/content/w8gj1t1j6v540083/fulltext.pdf An E. coli Expression System for the Extracellular Secretion of Barley α-Amylase (pdf)]. Entry into the wide-word of secretion-system manipulation.

[http://mmbr.asm.org/cgi/reprint/62/2/379 Type III protein secretion systems in Bacterial Pathogens of Plants and Animals (pdf)]. A nice review of natural type III secretion systems we can take advantage of, preferably without getting bubonic plague.


Salmonella Secretion pathway

[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2074921&blobtype=pdf Cloning and Transfer of the Salmonella Pathogenicity Island 2 Type III Secretion System for Studies of a Range of Gram-Negative Genera (pdf)]. Wilson, et al.

[http://www.springerlink.com/content/1q94h5030m3hf507/fulltext.pdf Cellular microbiology of intracellular Salmonella enterica: functions of the type III secretion system (pdf)]. Kuhle, et al.

[http://www.pnas.org/cgi/reprint/97/13/7539 A conserved amino acid sequence directing intracellular type III secretion(pdf)]. Miao, et al.

[http://iai.asm.org/cgi/reprint/74/10/5826 Optimization of the Delivery of Heterologous Proteins by the Salmonella enterica Serovar Typhimurium Type III Secretion System for Vaccine Development(pdf)]. Chen, et al.

[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15231802 Delineation of Upstream Signaling Events in the Salmonella Pathogenicity Island 2 Transcriptional Activation Pathway]. Kim et al. What turns on SPI-2.

Mgfp-5

[http://www.sciencedirect.com/science/article/B6T3C-4KXDR0V-2/1/a80e68f3d0ada12719651719e1cc11ec Recombinant mussel adhesive protein Mgfp-5 as cell adhesion biomaterial]. Modified Mgfp-5 is better than Cell-Tak or poly-L-lysine; unmodified is about the same as Cell-Tak. It survives harsher washes on glass than BSA or Cell-Tak. ---Steve Kron

[http://www.sciencedirect.com/science/article/B6TWB-4NMWRCS-F/1/9587d2845309a42beb00a6663a1b5085 Practical recombinant hybrid mussel bioadhesive fp-151]. A recombinant fp-1/fp-5 fusion protein works in cell bioadhesion assays. 1g/L production and soluble. ---Steve Kron

[http://pubs.acs.org/cgi-bin/sample.cgi/bipret/2008/24/i03/pdf/bp0703477.pdf Enhancement of Mussel Adhesive Protein Production in Escherichia coli by Co-expression of Bacterial Hemoglobin]. --Jata

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TWB-4NYSH9P-2&_user=5745&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000001358&_version=1&_urlVersion=0&_userid=5745&md5=131ccdf044aaaa423459eada8b774168#secx3 Cell adhesion biomaterial based on mussel adhesive protein fused with RGD peptide].--Nora

Peptides, Messersmith

"[http://biomaterials.bme.northwestern.edu/Papers/Polydopamine_Final_Science2007.pdf Mussel-Inspired Surface Chemistry for Multifunctional Coatings]." Use of dopamine for the coating of materials. --Rob

"[http://www.nature.com/nature/journal/v448/n7151/full/nature05968.html A reversible wet/dry adhesive inspired by mussels and geckos]." Messersmith's combination of gecko-foot "pillars" and mussel-foot adhesive. Was on the cover of nature!!

Yeast/Tyrosinase

[http://www.jcb.org.proxy.uchicago.edu/cgi/reprint/131/4/895 The Golgi-localization of Yeast Emp47p Depends on Its Di-lysine Motif But Is Not Affected by the retl-1 Mutation in oL-COP]. --Jata

[http://web.ebscohost.com.proxy.uchicago.edu/ehost/pdf?vid=2&hid=13&sid=3f8e30a7-87ae-482e-8d71-5483a950a5e3%40sessionmgr9 Global analysis of protein localization in budding yeast ]. --Jata

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T20-4G4WYG2-1&_user=5745&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000001358&_version=1&_urlVersion=0&_userid=5745&md5=37ee3677ce5f8f5d095c73b898da414c Protein transport from the late Golgi to the vacuole in the yeast Saccharomyces cerevisiae]. --Jata

[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T1V-3XX6VB3-2H&_user=5745&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000001358&_version=1&_urlVersion=0&_userid=5745&md5=cc4d2fbcbd990c68b62f4a042239f15c Molecular cloning and nucleotide sequence of the protyrosinase gene, melO, from Aspergillus oryzae and expression of the gene in yeast cells]. --Jata

"[http://www.pnas.org/content/92/7/2964.abstract Tyrosine Inhibitory Peptide found in Flies. Potential "off switch" for tyrosinase activity - perhaps to terminate the continued growth of a glue-glob, or perhaps to prevent the conversion of DOPA into a quinone. Also potential for a negative feedback loop, as the peptide contains a potentially important DOPA.]." --Rob

"Direct spectrophotometric assay of monooxygenase and oxidase activities of mushroom tyrosinase in the presence of synthetic and natural substrates"--a good methods paper for tyrosinase spectroscopy. --Daniel.

Computer Modeling

"[http://weisswebserver.ee.princeton.edu/papers/batt-2007-c.pdf Robustness analysis and tuning of synthetic gene networks]." Modeling gene networks (Weiss). ---Nora

"[http://weisswebserver.ee.princeton.edu/papers/batt-2007-b.pdf Model checking genetic regulatory networks with parameter uncertainty]." Another Weiss paper. --Nora

Other

[http://openwetware.org/wiki/IGEM:MIT/2007/Ideas3 2007 Ideas]. Great big honking list of references. ---Thomas Graham

"[http://weisswebserver.ee.princeton.edu/papers/brenner-2007.pdf Quorum Sensing in E.Coli]" Bioluminescence Activation via Q.S. -Rob

"[http://www.patentstorm.us/patents/005466592.pdf]." Patent for stable extracellular tyrosinase which may or may not be useful --Laura

Molecular Biology Primer written by yours truly--Daniel

"Isolation, purification and characterization of b-1,3-glucan binding protein from the plasma of marine mussel Perna viridis" Assays for another binding protein that may be useful for our methods section.--Daniel

"The Hydroxylation of Phenylalanine and Tyrosine: A Comparison with Salicylate and Tryptophan." How the Fenton Reaction can hydroxylize Tyr into DOPA.--Daniel

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