http://www.barricklab.org/twiki/bin/view/Lab The Lab web of TWiki. TWiki is a Web-Based Collaboration Platform for the Enterprise. en-us Copyright 2012 by contributing authors Jeffrey Barrick [webmaster@barricklab.org] The contributing authors of TWiki TWiki http://www.barricklab.org/twiki/bin/view/Lab http://www.barricklab.org/twiki/pub/TWiki/TWikiLogos/T-logo-140x40-t.gif http://www.barricklab.org/twiki/bin/view/Lab/ProceduresPolyacrylamideGelElectrophoresis Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels ... (last changed by JeffreyBarrick) 2012-02-19T22:50:52Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/PublicationList Publications 32. Meyer, J.R., Dobias, D.T., Weitz, J.S., Barrick, J.E. , Quick, R.T., Lenski, R.E. 2012. Repeatability and Contingency in the Evolution of a Key ... (last changed by JeffreyBarrick) 2012-02-19T20:14:57Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsFluctuationTests Fluctuation Tests This protocol is for doing a Luria Delbrück fluctuation test to measure the rate at which mutations occur that enable growth on selective agar. ... (last changed by JeffreyBarrick) 2012-02-19T00:38:20Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsRNASeqDifferentialExpression Analyzing RNA Seq data for differential gene expression Materials and Software Data files RNA Seq data in FASTQ format (Ex: dataset1.fastq, dataset2 ... (last changed by JeffreyBarrick) 2012-02-11T17:41:54Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/ContactInformation Contact Information Jeffrey E. Barrick, Ph.D. Assistant Professor Chemistry and Biochemistry Institute for Cellular and Molecular Biology The University of Texas ... (last changed by JeffreyBarrick) 2012-02-09T20:18:20Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/ProtocolList Protocols and Laboratory Reference Updates Needed Lab Stocks Media Recipes Solid and liquid media for bacterial growth. Antibiotics and Supplements ... (last changed by JeffreyBarrick) 2012-02-08T16:49:15Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsRestrictionEnzymeCloning Restriction Enzyme Cloning Restriction enzyme cloning is a bread and butter technique in molecular biology for modifying plasmids to contain genes or other DNA sequences ... (last changed by JeffreyBarrick) 2012-02-06T19:16:36Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsAntibioticStockSolutions Media Amendment Stock Solutions Reagent Abb Stock Conc. Working Conc. Dilution Solvent Notes Ampicillin Amp 100 mg/ml 100 µg ... (last changed by CraigBarnhart) 2012-02-06T14:37:01Z CraigBarnhart http://www.barricklab.org/twiki/bin/view/Lab/InternalBrianRendaKB Naturally Transformable Bactera Acinetobacter baylyi ADP1 Overview History Physiology Molecular Biology Natural Competence Deinococcus radiodurans R1 Overview ... (last changed by BrianRenda) 2012-02-03T17:12:42Z BrianRenda http://www.barricklab.org/twiki/bin/view/Lab/LabPersonnel Barrick Lab Members Dr. Jeffrey Barrick Craig Barnhart Lindsey Wolf Austin Meyer Michael Hammerling Brian Renda Eric Bryan Geoff Colburn Matt Strand Aaron Reba ... (last changed by JeffreyBarrick) 2012-02-01T20:37:32Z JeffreyBarrick http://www.barricklab.org/twiki/bin/view/Lab/ProcedureBacterialMutationAccumulation Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution ... (last changed by AurkoDasgupta) 2012-01-27T19:14:00Z AurkoDasgupta http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsStandardPCR Standard Polymerase Chain Reaction (PCR) Basic Conditions PCR reactions involve template, forward and reverse primers, buffer, dNTPs, DNA polymerase and water. A ... (last changed by BrianRenda) 2012-01-24T16:25:35Z BrianRenda http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsSoilGenomicDNAPrep Large Scale Metagenomic Soil Prep Combine 80g soil with 87mL 0.1M pH 6.6 monobasic sodium phosphate in a beaker on a stir plate with a stir bar. Allow this to mix ... (last changed by BrianRenda) 2012-01-20T21:21:02Z BrianRenda http://www.barricklab.org/twiki/bin/view/Lab/ReferencePlasmids Commonly Used Plasmids plasmid markers description pCA24N ??? ASKA collection vector pKD46 AmpR Wanner lambda red plasmid, TS origin – ... (last changed by BrianRenda) 2012-01-20T21:09:16Z BrianRenda http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsRecipesSOBplates SOB: Super Optimal Broth Plates 1L Final Component 5 g 0.5% yeast extract 20 g 2.0% tryptone 0.5 g 10 mM NaCl ... (last changed by CraigBarnhart) 2012-01-11T18:13:21Z CraigBarnhart http://www.barricklab.org/twiki/bin/view/Lab/ProtocolsRecipesSOB SOB: Super Optimal Broth 1L Final Component 5 g 0.5% yeast extract 20 g 2.0% tryptone 0.5 g 10 mM NaCl 0 ... (last changed by CraigBarnhart) 2012-01-11T18:12:27Z CraigBarnhart