100 Recent Changes in Lab Web retrieved at 00:50 (GMT)

Main.JeffreyBarrick

Barrick Lab Style Guide Writing a Scientific Paper Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176) General Formatting ...
Denaturing Formaldehyde Gels for Verifying RNA size RNA can be sized correctly on an agarose gel. However, it needs to be denatured and then remain denatured during ...
Main.SimonDAlton

Isolation of Total RNA from Plant Material Plant tissues can be tough (roots), impenetrably waxy, or contain large amounts of RNase activity (leaves). Flash freezing ...
Back to Golden Gate Protocols First Stage Plasmid (Transcriptional Unit) Assembly Once you have all your desired part plasmids built you can assemble them into Transcriptional ...
Main.JeffreyBarrick

Barrick Lab Members Prof. Jeffrey E. BarrickPrincipal Investigator (01/2011–present)@barricklab Dr. Simon D'AltonResearch Associate (09/2015 present ...
Main.TWikiGuest

Statistics for nop Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and ...
Keio and ASKA collections Dear internet, Our lab is unable to distribute the Keio/ASKA strains to other institutions. If you want to use these fantastic E. coli ...
Main.SimonDAlton

Barrick Lab :: Laboratory Protocols Creating Protocols How to Create a Protocol Best practices for designing a protocol and for putting it on the lab Wiki. ...
JaredEller 14 Dec 2017 Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines and increase bioproduction ...
Golden Gate Assembly This page serves as the main repository for everything Golden Gate Assembly related. This page links to a number of protocol pages that will ...
Back to Golden Gate Protocols Troubleshooting your Golden Gate Assemblies Tips Inserts should be screened for the presence of internal BsaI/BsmBI sites before ...
Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here ...
Back to Golden Gate Protocols Part Plasmid Assembly Once you have designed your part and either amplified with PCR or ordered the desired gBlock (as described here ...
iGEM Part Plasmid Assembly Below is the "Dr. Mishler recommends" Golden Gate Assembly reaction for FRI/iGEM students. Alternative Golden Gate Assembly Reaction ...
Back to Golden Gate Protocols Designing a new part Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA ...
Golden Gate Assembly Background and Design Golden Gate cloning or Golden Gate assembly is a molecular cloning method that allows a researcher to simultaneously ...
Broad Host Range Toolkit The Broad host range toolkit (BTK) is a Golden Gate compatible toolkit of genetic parts designed for working with newly isolated, non model ...
Main.SimonDAlton

RNAseq Library Preparation Use RNA from RNASnap and Zymo coumn purification as outlined on wiki. rRNA Depletion Use the Ribozero (RZ) rRNA Removal Kit (Gram negative ...
Main.JeffreyBarrick

The University of Texas at Austin :: iGEM Team Donate to the UT Austin iGEM team to support travel, supplies, and research stipends for our excellent students! ...
Microplate Reader Quick Start 1 It's always best to start from single colony picks that had been grown overnight in liquid culture to saturation. 1 A typical ...
Main.JeffreyBarrick

The Lenski Long Term Evolution Experiment Arabinose Marker REL606 and REL607 (the ancestral strains of the E. coli long term evolution experiment) differ by a single ...
Main.JeffreyBarrick

Past Barrick Lab Members Xue Zhang Michael Hammerling Brian Renda Jordan Monk Craig Barnhart Aurko Dasgupta Lindsey Wolf Alvaro Rodriguez Neil Gottel Vinicio Reynoso ...
Media Amendment Stock Solutions Reagent Abb Stock Conc. Working Conc. Dilution Solvent MSDS Notes Ampicillin Amp 100 mg/mL ...
Main.DanielDeatherage

Instructions for how to analyze fluctuation test data using the command line. Please see this page for information regarding how to conduct a fluctuation analysis ...
Main.CamiloGomez

Commonly Used E. coli Strains OpenWetWare offers a comprehensive repository of the genotypes of the most commonly used E. coli strains. The following table points ...
Working with Serratia marcescens Serratia marcescens is a gram negative pathogenic bacteria known for its distinctive red pigmentation. While it is not found in ...
Determining Phage Titer 1 Microwave flask of Top Agar (LB 0.8% agar) to melt. Allow to cool until handleable, then prepare 4 ml aliquots in small test tubes for ...
Phage Lysate Preparation Definitely works with T4 and T7, should work with most E. coli phages (although lysis times and final titers may differ) Reagents / ...
Absolute QPCR for quantification of plasmid copy number in E. coli This protocol is based on methods described in Lee et al (2006), to paper. Designing primers ...
Main.JuliePerreau

Barrick Lab :: Computational Protocols Command line Unix Commands Quick Reference Collection of useful Unix commands. SSH Public Key Authentication How ...
Gibson Assembly Background and Design Gibson Cloning is a technique of DNA construct assembly that allows one to join multiple linear segments into either one large ...
#TransformingElectroporation Transforming E. coli Cells by Electroporation This procedure uses the TOP10 Electrocomp E. coli cells (but is identical in any ...
General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol ...
Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided ...
Autoclave Sterilization Overview Autoclaves heat their contents to 121°C, which is 21°C over the boiling point of water. To prevent the solutions from boiling over ...
Main.JeffreyBarrick

How to Create a Protocol Tips for Design You should generally organize a protocol to have sections that are relevant from this list: Supplies (materials, strains ...
Main.SimonDAlton

Quantitative real time PCR for differential gene expression The following is a comprehensive strategy for qPCR that works and is practically, mathematically and statistically ...
Main.PengGeng

Megaprimer whole plasmid cloning aka nop MEGAWHOP cloning aka Overlap Extension PCR cloning Adapted from Bryksin AV, Matsumura I. 2010. Overlap extension PCR Cloning ...
Main.DanielDeatherage

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. This ...
Main.JeffreyBarrick

Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab members Equal contributions ^corresponding author(s) 2017 72. Good ...
Main.DaciaLeon

Measuring Intracellular Reactive Oxygen Species (ROS) This procedure is commonly utilized to quantify ROS. For more information about limitations associated with this ...
Main.GabrielSuarez

ABMS: Acinetobacter Minimal Succinate Courtesy of the Averhoff lab, with modifications for available reagents. To make standard ABMS, combine the following pre sterilized ...
Main.GabrielSuarez

Growth Rates using "R studio" Overview Determining growth rates for many cultures or from plate reader data can be a daunting task. To automate this process, we ...
Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1µL of DpnI to ...
Main.JeffreyBarrick

Interested in working in the Barrick lab? We are always looking for outstanding undergraduate students, graduate students, and postdocs who are interested in experimental ...
"In plate" / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony "in situ" (in plate) transformation with minimal ...
Main.SimonDAlton

Contacts Campus Resources The following services may be able to help fix anything from a Faulty Freezer to a Questionable Qubit. Facilities. Have refrigerator and ...
SeanLeonard 14 Sep 2017
SeanLeonard 14 Sep 2017
SeanLeonard 14 Sep 2017
Upon publication, this page will be updated with a full description of the BTK, parts list, and overhang types. SeanLeonard 14 Sep 2017
Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial ...
Main.JeffreyBarrick

Barrick Lab :: Research /collage.png Active Projects #PreventingEvolutionaryFailure Preventing Evolutionary Failure in Synthetic Biology Evolutionary half lives ...
Protocol for harvesting Pfu Sso7d polymerase This protocol is for expressing and purifying the Pfu Sso7d polymerase from E. coli 1 . A variant of this protein with ...
Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded ...
Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator 50x TAE 242 g Tris base 57.1 ml ...
Main.SimonDAlton

Preparing a DNA fragment library for Illumina sequencing WARNING THIS PROTOCOL IS DEPRECATING RAPIDLY, KAPA BIOSYSTEM KITS ARE NOW BEING USED RATHER THAN ...
Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol ...
Measuring Burst Size of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates Overnight stock of permissive bacterial host ...
Main.DanielDeatherage

This page is meant to include instructions on how to clone dcamp, and push back to the repository. It is not well tested. Standardized TACC DCAMP instructions. This ...
Main.JeffreyBarrick

Barrick Lab :: Contact Information Jeffrey E. Barrick, Ph.D. Assistant Professor Department of Molecular Biosciences The University of Texas at Austin Office: ...
Main.DanielDeatherage

Genome Diff file Generation Overview This is a series of commands to automatically generate .gd files based on naming system present in .fastq files. This will typically ...
Main.JeffreyBarrick

Barrick Lab ' '' " then "" else ""}% Contact Members Join Us Research Publications Protocols Reference ...
Main.JeffreyBarrick

Overview Lab protocol for using the pSLTS plasmid method of scarless genome editing developed by the Copley lab. If you use this protocol, you should cite: Kim, J ...
Transforming Electrocompetent Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES: Equipment: ...
Main.GabrielSuarez

Standard Polymerase Chain Reaction (PCR) Basic Conditions using standard Taq polymerase PCR reactions involve template, forward and reverse primers, buffer, dNTPs ...
Measuring transcription in vitro : Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer tag that fluoresces with similar spectral properties ...
Working with Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation ...
Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated ...
Main.JeffreyBarrick

Barrick Lab :: Links Advice for graduate students (Saw this linked by Cooper) for Young Scientists (Andrew Hendry) Serial Mentor (Claus Wilke's Blog ...
Blood Heart Infusion Agar Heart Infusion Agar supplemented with sterile Sheep's Blood. Used for the cultivation of fastidious organisms (Bee gut microbiome species ...
Efficiently accessing journal articles while off campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related ...
Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated ...
Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow ...
Using Emulsions to Select by Yield Background Evolution in suspension culture proceeds by selecting for those strains that grow most rapidly, quickly depleting the ...
Does it behoove better lingo? Just like the good sommelier delights us with their expansive full bodied descriptions of wines, connoisseur molecular and evolutionary ...
Acinetobacter baylyi ADP1 quick reference Antibiotic/toxin resistance Antibiotic MIC Standard Conc. Status Notes Ampicillin (or carbenicillin ...
Main.StellaWang

Animations Saves a series of generated images to GIF, Flash, video, HTML, or PDF (LaTeX) formats. Installation install.packages("animation") library(animation) ...
Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES ...
Transforming Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES: Equipment: Shaking ...
Preparing Chemically Competent Cells using the Inoue Method Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES: ...
Targeted PCR and Sanger Resequencing of Mutations Page in need of additional improvements. Primer Design Sequence immediately 5' of the sequencing primer will always ...
Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae ...
FLP Recombination in E. coli Commonly used to eliminate the Kanamycin resistance cassette from E. coli strains from the Keio collection or produced by P1 transduction ...
Main.DanielDeatherage

P1 Transduction in Eschericha coli This protocol is adapted from Thomason, L. C., Costantino, N. and Court, D. L. 2007. E. coli Genome Manipulation by P1 Transduction ...
Working with Bartonella apis Bartonella apis is a gram negative bacterial member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated ...
Working with Lactobacillus "Firm 5" The Lactobacillus "Firm 5" clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota ...
Main.GabrielSuarez

1 DPLYR 1 READR 1 GGPLOT, incl: 1 COWPLOT 1 GGREPEL 1 COLOR SCHEMES 1 (calculate growth rates) SimonDAlton 02 Jun 2016
Working with Snodgrassella alvi Snodgrassella alvi is a member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated in vitro . Its ...
Working with Gilliamella apicola Gilliamella apicola is a gram negative bacterial member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated ...
Find Strains, Plasmids, and Genes Reminder: Always revive new organisms according to an established protocol and archive a lab stock of the original freeze dried culture ...
Main.JeffreyBarrick

Barrick Lab :: Home We are broadly interested in understanding evolution as a creative force. Our lab primarily uses experiments with microorganisms and molecules ...
Main.JeffreyBarrick

Attach images that can be used on the front page here.
Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from ...
breseq breseq is a computational pipeline for finding mutations relative to a reference sequence in short read DNA re sequencing data for haploid microbial sized ...
Main.DanielDeatherage

How to clean glassware Small flasks (50 ml) The 50 ml flasks are used in quantity in many experiments and need to be cleaned and sterilized on a regular basis. Summary ...
Main.SimonDAlton

Isolation of Total RNA Materials and Reagents Use filter tips. Keep all solutions, reagents and plastics to be used for RNA work separate from general supplies. Solutions ...
Main.SimonDAlton

Isolation of total RNA Reagents Materials Use filter tips, and designate all solutions, reagents and plastics as RNA only. Keep separate from other general stocks ...
Resuspending Primers 1 Your primers will arrive as a lyophilized film at the bottom of a cryo tube. To use them, you must resuspend them in autoclaved dH2O. ...
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Topic revision: r2 - 28 Mar 2005 - 09:40:13 - Main.TWikiContributor
 
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