Team:Illinois/Research

From 2009.igem.org

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== '''Research''' ==
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This page lists various sources used in our research organized by topic.  Please note that most of the links to articles on this page will take you only to the abstract of the paper.
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== '''General''' ==
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== '''Research''' ==
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*[http://www.neb.com/nebecomm/default.asp New England Biolabs Web Page]
 +
Includes catalog for restriction endonucleases/other lab products, a resource called [http://tools.neb.com/NEBcutter2/index.php NEBcutter] that tells you what restriction endonucleases will cut your gene/DNA sequence of interest, and a tool called the [http://www.neb.com/nebecomm/DoubleDigestCalculator.asp? Double Digest Finder] that will tell you how compatible two restriction endonucleases are by comparing what conditions they work best in.
 +
 
 +
*[http://genolist.pasteur.fr/Colibri/ Colibri]
 +
Contains a complete list of genes in E. coli and their base pair sequences.
 +
 
 +
*[http://ecogene.org/ EcoGene]
 +
Useful for finding gene sequences and functions in E. coli.
 +
 
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]
 +
A very useful online database for finding research papers and gene sequences.
 +
 
 +
*[http://srnamap.mbc.nctu.edu.tw/ sRNAMap]
 +
"collect the annotations of the sRNAs and the regulatory relationship between transcriptional regulator and sRNA, and between sRNA and its target genes. Additionally, more valuable information of sRNAs, such as the secondary structure of sRNAs, the expressed conditions of sRNAs, the expression profiles of sRNAs, the transcriptional start sites of sRNAs and the cross-links to other biological databases, are provided for further investigation."
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== '''Small RNAs''' ==
 +
 
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/16951250?dopt=Abstract: Modulating the outer membrane with small RNAs.]: Guillier M, Gottesman S, Storz G Genes Dev. 2006 Sep 1; 20(17): 2338-48
 +
An overview of small RNAs that regulate membrane proteins.
 +
 
 +
*[http://www.ncbi.nlm.nih.gov/pubmed/15466019?dopt=Abstract: MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli]: Chen S, Zhang A, Blyn LB, Storz G J Bacteriol. 2004 Oct ; 186(20): 6689-97
 +
Concerns the method regulation of OmpC by the sRNA MicC
 +
 
 +
*[http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.micro.58.030603.123841?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov The Small RNA Regulators of E. coli: Roles and Mechanisms]: Susan Gottesman, 2004
 +
An overview on small RNAs and their functions, discussing the roles of Hfq and RNase E, and mentioning advantages to sRNA use.
 +
 
 +
*[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4VNHRSC-B&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=997a0feec59ee5290a51b6ffcde5b7bb Regulatory RNAs in Bacteria]: Lauren S. Waters and Gisela Storz, <html><u>Cell</u></html>, Vol. 136, Issue 4, pg. 615-628, 2009
 +
Discusses various RNA regulators in bacteria, including riboswitches and sRNAs.  Gives examples of well-characterized sRNAs and lists advantages of sRNAs over other types of gene regulation.
 +
 
 +
*[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1807950 Translational Control and Target Recognition by Escherichia coli Small RNAs in Vivo]: Johannes H. Urban and Jörg Vogel, 2007
 +
Documents successful fusions of sRNA target sequences to GFP in order to study regulatory activity of various sRNAs.
 +
 
 +
*[http://nar.oxfordjournals.org/cgi/content/abstract/33/3/1040 Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli]: Mitsuoki Kawano, April A. Reynolds, Juan Miranda-Rios, and Gisela Storz, 2005
 +
Describes sRNAs that act on the 3' untranslated region (UTR) of a target mRNA.
 +
 
 +
*[http://genesdev.cshlp.org/content/15/13/1637.long Identification of novel small RNAs using comparative genomics and microarrays]: Karen M. Wassarman, Francis Repoila, Carsten Rosenow, Gisela Storz, and Susan Gottesman, 2001
 +
Describes sRNAs that act on the 3' untranslated region (UTR) of a target mRNA.
 +
 
 +
*[http://jb.asm.org/cgi/content/abstract/186/20/6698 GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli] Jason A. Opdyke, Ju-Gyeong Kang, and Gisela Storz, 2004
 +
A paper on GadY, a small RNA in E. coli that acts on the 3' UTR of the acid response gene it regulates.
 +
<html>
 +
</div>
 +
</html>
 +
<html>
 +
<div id="uicontentbox">
 +
</html>
 +
== '''Modeling''' ==
 +
 
 +
*1. [http://www.nature.com/msb/journal/v3/n1/full/msb4100181.html Regulation of Gene Expression by Small Non-Coding RNAs: A Quantitative View]: Yishai Shimoni, Gilgi Friedlander, Guy Hetzroni, Gali Niv, Shoshy Altuvia, Ofer Biham, and Hanah Margalit, 2007
 +
Provides a basic model and differential equations for sRNA regulation of a gene, and quantitatively compares sRNA regulation with other types of regulation.
 +
*2. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4NB38NK-6&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7725715b97f86294f80fbc40ef60d3f3 Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress]: Carin Vanderpool, 2007
 +
Provides a model of small RNA SgrS and its role in the glucose-phosphate stress response in E. coli.
 +
*3. An Introduction to Systems Biology: Design Principles of Biological Circuits: Uri Alon, 2007
 +
A book that provides simple models for transcriptional regulation and analyzes natural gene networks to find network motifs. These network motifs are characterized based on advantages in use and robustness.  Recommended by Dr. Golding.
 +
*[http://www.nature.com/msb/journal/v4/n1/full/msb200858.html A quantitative comparison of sRNA-based and protein-based gene regulation]: Pankaj Mehta, Sidhartha Goyal, &  Ned S Wingreen, 2008
 +
A detailed comparison of sRNA regulation and transcription factor regulation, focusing on aspects such as intrinsic noise, gain, filtering, and small-input fidelity.
 +
*[http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050229 Quantitative Characteristics of Gene Regulation by Small RNA]: Erel Levine, Zhongge Zhang, Thomas Kuhlman, & Terence Hwa. PLoS Biol 5(9): e229. 2007
 +
Discusses and models the threshold-linear nature of ''trans''-encoded sRNA repression.
 +
<html>
 +
</div>
 +
</html>
 +
<html>
 +
<div id="uicontentbox">
 +
</html>
 +
 
 +
== '''Laboratory''' ==
 +
 
 +
*[http://www.protocol-online.org/ Protocol Online]
 +
Useful website for finding protocols online.
 +
 
 +
*[http://cda.currentprotocols.com/WileyCDA/CPTitle/isbn-047150338X,descCd-tableOfContents.html Current Protocols in Molecular Biology]
 +
A useful and free online resource explaining protocols and the biological relevance of each step.  Recommended by Dr. Golding.
 +
 
 +
*[http://www.5prime.com/media/29661/perfectprep%20spin%20mini%20kit%20manual_5prime_1048299_072007.pdf PerfectPrep Spin Mini Kit Manual]
 +
Protocol for plasmid purification using the PerfectPrep Spin Mini Kit.
-
This page lists various sources used in our research organized by topic.
+
*[http://www.promega.com/tbs/tb374/tb374.pdf PureYield Plasmid Miniprep System Protocol]
 +
Protocol for plasmid purification using the PureYield Plasmid Miniprep System.
 +
*Supplementary Material: Translational Control and Target Recognition by Escherichia coli Small RNAs in Vivo: Johannes H. Urban and Jörg Vogel, 2007
 +
Includes step-by-step protocols for fusion cloning into a standard plasmid (pXG-10), fusion cloning via 5' RACE (pXG-20), and operon fusion cloning into pXG-30.
-
Questions about our Wiki page?  Please email Dave Korenchan at [mailto:korench1@illinois.edu korench1@illinois.edu].
+
*[http://www.springerlink.com.proxy2.library.uiuc.edu/content/h752r3415261357p/ A Green Fluorescent Protein (GFP)-Based Plasmid System to Study Post-Transcriptional Control of Gene Expression In Vivo]: Johannes H. Urban and Jörg Vogel, 2009
 +
Details a modular two-plasmid system that uses GFP to study sRNA regulation in vivo.
 +
<html>
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</div>
 +
</html>
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{{IllinoisBottomNav}}

Latest revision as of 05:13, 16 October 2009

Click to go to the Illinois home page



Home
Team
Project
Experiments
Biobricks Notebook

Research

This page lists various sources used in our research organized by topic. Please note that most of the links to articles on this page will take you only to the abstract of the paper.

General

  • [http://www.neb.com/nebecomm/default.asp New England Biolabs Web Page]

Includes catalog for restriction endonucleases/other lab products, a resource called [http://tools.neb.com/NEBcutter2/index.php NEBcutter] that tells you what restriction endonucleases will cut your gene/DNA sequence of interest, and a tool called the [http://www.neb.com/nebecomm/DoubleDigestCalculator.asp? Double Digest Finder] that will tell you how compatible two restriction endonucleases are by comparing what conditions they work best in.

  • [http://genolist.pasteur.fr/Colibri/ Colibri]

Contains a complete list of genes in E. coli and their base pair sequences.

  • [http://ecogene.org/ EcoGene]

Useful for finding gene sequences and functions in E. coli.

  • [http://www.ncbi.nlm.nih.gov/pubmed/ Pubmed]

A very useful online database for finding research papers and gene sequences.

  • [http://srnamap.mbc.nctu.edu.tw/ sRNAMap]

"collect the annotations of the sRNAs and the regulatory relationship between transcriptional regulator and sRNA, and between sRNA and its target genes. Additionally, more valuable information of sRNAs, such as the secondary structure of sRNAs, the expressed conditions of sRNAs, the expression profiles of sRNAs, the transcriptional start sites of sRNAs and the cross-links to other biological databases, are provided for further investigation."

Small RNAs

  • [http://www.ncbi.nlm.nih.gov/pubmed/16951250?dopt=Abstract: Modulating the outer membrane with small RNAs.]: Guillier M, Gottesman S, Storz G Genes Dev. 2006 Sep 1; 20(17): 2338-48

An overview of small RNAs that regulate membrane proteins.

  • [http://www.ncbi.nlm.nih.gov/pubmed/15466019?dopt=Abstract: MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli]: Chen S, Zhang A, Blyn LB, Storz G J Bacteriol. 2004 Oct ; 186(20): 6689-97

Concerns the method regulation of OmpC by the sRNA MicC

  • [http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.micro.58.030603.123841?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dncbi.nlm.nih.gov The Small RNA Regulators of E. coli: Roles and Mechanisms]: Susan Gottesman, 2004

An overview on small RNAs and their functions, discussing the roles of Hfq and RNase E, and mentioning advantages to sRNA use.

  • [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4VNHRSC-B&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=997a0feec59ee5290a51b6ffcde5b7bb Regulatory RNAs in Bacteria]: Lauren S. Waters and Gisela Storz, Cell, Vol. 136, Issue 4, pg. 615-628, 2009

Discusses various RNA regulators in bacteria, including riboswitches and sRNAs. Gives examples of well-characterized sRNAs and lists advantages of sRNAs over other types of gene regulation.

  • [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1807950 Translational Control and Target Recognition by Escherichia coli Small RNAs in Vivo]: Johannes H. Urban and Jörg Vogel, 2007

Documents successful fusions of sRNA target sequences to GFP in order to study regulatory activity of various sRNAs.

  • [http://nar.oxfordjournals.org/cgi/content/abstract/33/3/1040 Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli]: Mitsuoki Kawano, April A. Reynolds, Juan Miranda-Rios, and Gisela Storz, 2005

Describes sRNAs that act on the 3' untranslated region (UTR) of a target mRNA.

  • [http://genesdev.cshlp.org/content/15/13/1637.long Identification of novel small RNAs using comparative genomics and microarrays]: Karen M. Wassarman, Francis Repoila, Carsten Rosenow, Gisela Storz, and Susan Gottesman, 2001

Describes sRNAs that act on the 3' untranslated region (UTR) of a target mRNA.

  • [http://jb.asm.org/cgi/content/abstract/186/20/6698 GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli] Jason A. Opdyke, Ju-Gyeong Kang, and Gisela Storz, 2004

A paper on GadY, a small RNA in E. coli that acts on the 3' UTR of the acid response gene it regulates.

Modeling

  • 1. [http://www.nature.com/msb/journal/v3/n1/full/msb4100181.html Regulation of Gene Expression by Small Non-Coding RNAs: A Quantitative View]: Yishai Shimoni, Gilgi Friedlander, Guy Hetzroni, Gali Niv, Shoshy Altuvia, Ofer Biham, and Hanah Margalit, 2007

Provides a basic model and differential equations for sRNA regulation of a gene, and quantitatively compares sRNA regulation with other types of regulation.

  • 2. [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4NB38NK-6&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7725715b97f86294f80fbc40ef60d3f3 Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress]: Carin Vanderpool, 2007

Provides a model of small RNA SgrS and its role in the glucose-phosphate stress response in E. coli.

  • 3. An Introduction to Systems Biology: Design Principles of Biological Circuits: Uri Alon, 2007

A book that provides simple models for transcriptional regulation and analyzes natural gene networks to find network motifs. These network motifs are characterized based on advantages in use and robustness. Recommended by Dr. Golding.

  • [http://www.nature.com/msb/journal/v4/n1/full/msb200858.html A quantitative comparison of sRNA-based and protein-based gene regulation]: Pankaj Mehta, Sidhartha Goyal, & Ned S Wingreen, 2008

A detailed comparison of sRNA regulation and transcription factor regulation, focusing on aspects such as intrinsic noise, gain, filtering, and small-input fidelity.

  • [http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0050229 Quantitative Characteristics of Gene Regulation by Small RNA]: Erel Levine, Zhongge Zhang, Thomas Kuhlman, & Terence Hwa. PLoS Biol 5(9): e229. 2007

Discusses and models the threshold-linear nature of trans-encoded sRNA repression.

Laboratory

  • [http://www.protocol-online.org/ Protocol Online]

Useful website for finding protocols online.

  • [http://cda.currentprotocols.com/WileyCDA/CPTitle/isbn-047150338X,descCd-tableOfContents.html Current Protocols in Molecular Biology]

A useful and free online resource explaining protocols and the biological relevance of each step. Recommended by Dr. Golding.

  • [http://www.5prime.com/media/29661/perfectprep%20spin%20mini%20kit%20manual_5prime_1048299_072007.pdf PerfectPrep Spin Mini Kit Manual]

Protocol for plasmid purification using the PerfectPrep Spin Mini Kit.

  • [http://www.promega.com/tbs/tb374/tb374.pdf PureYield Plasmid Miniprep System Protocol]

Protocol for plasmid purification using the PureYield Plasmid Miniprep System.

  • Supplementary Material: Translational Control and Target Recognition by Escherichia coli Small RNAs in Vivo: Johannes H. Urban and Jörg Vogel, 2007

Includes step-by-step protocols for fusion cloning into a standard plasmid (pXG-10), fusion cloning via 5' RACE (pXG-20), and operon fusion cloning into pXG-30.

  • [http://www.springerlink.com.proxy2.library.uiuc.edu/content/h752r3415261357p/ A Green Fluorescent Protein (GFP)-Based Plasmid System to Study Post-Transcriptional Control of Gene Expression In Vivo]: Johannes H. Urban and Jörg Vogel, 2009

Details a modular two-plasmid system that uses GFP to study sRNA regulation in vivo.

Questions about our Wiki page? Please email us at illinoisiGEM@gmail.com.

Retrieved from "http://2009.igem.org/Team:Illinois/Research"