Team:Illinois/Research

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
Includes catalog for restriction endonucleases/other lab products, a resource called 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.
 * New England Biolabs Web Page

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

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

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

"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."
 * sRNAMap

Small RNAs
An overview of small RNAs that regulate membrane proteins.
 * Modulating the outer membrane with small RNAs.: Guillier M, Gottesman S, Storz G Genes Dev. 2006 Sep 1; 20(17): 2338-48

Concerns the method regulation of OmpC by the sRNA MicC
 * 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

An overview on small RNAs and their functions, discussing the roles of Hfq and RNase E, and mentioning advantages to sRNA use.
 * The Small RNA Regulators of E. coli: Roles and Mechanisms: Susan Gottesman, 2004

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.
 * Regulatory RNAs in Bacteria: Lauren S. Waters and Gisela Storz, Cell, Vol. 136, Issue 4, pg. 615-628, 2009

Documents successful fusions of sRNA target sequences to GFP in order to study regulatory activity of various sRNAs.
 * Translational Control and Target Recognition by Escherichia coli Small RNAs in Vivo: Johannes H. Urban and Jörg Vogel, 2007

Describes sRNAs that act on the 3' untranslated region (UTR) of a target mRNA.
 * 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.
 * Identification of novel small RNAs using comparative genomics and microarrays: Karen M. Wassarman, Francis Repoila, Carsten Rosenow, Gisela Storz, and Susan Gottesman, 2001

A paper on GadY, a small RNA in E. coli that acts on the 3' UTR of the acid response gene it regulates.
 * GadY, a Small-RNA Regulator of Acid Response Genes in Escherichia coli Jason A. Opdyke, Ju-Gyeong Kang, and Gisela Storz, 2004

Modeling
Provides a basic model and differential equations for sRNA regulation of a gene, and quantitatively compares sRNA regulation with other types of regulation. Provides a model of small RNA SgrS and its role in the glucose-phosphate stress response in E. coli. 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. A detailed comparison of sRNA regulation and transcription factor regulation, focusing on aspects such as intrinsic noise, gain, filtering, and small-input fidelity. Discusses and models the threshold-linear nature of trans-encoded sRNA repression.
 * 1. 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
 * 2. Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress: Carin Vanderpool, 2007
 * 3. An Introduction to Systems Biology: Design Principles of Biological Circuits: Uri Alon, 2007
 * A quantitative comparison of sRNA-based and protein-based gene regulation: Pankaj Mehta, Sidhartha Goyal, & Ned S Wingreen, 2008
 * Quantitative Characteristics of Gene Regulation by Small RNA: Erel Levine, Zhongge Zhang, Thomas Kuhlman, & Terence Hwa. PLoS Biol 5(9): e229. 2007

Laboratory
Useful website for finding protocols online.
 * Protocol Online

A useful and free online resource explaining protocols and the biological relevance of each step. Recommended by Dr. Golding.
 * Current Protocols in Molecular Biology

Protocol for plasmid purification using the PerfectPrep Spin Mini Kit.
 * PerfectPrep Spin Mini Kit Manual

Protocol for plasmid purification using the PureYield Plasmid Miniprep System.
 * PureYield Plasmid Miniprep System Protocol

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

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