100 Recent Changes in Lab Web retrieved at 16:23 (GMT)

Main.JeffreyBarrick

Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab members Equal contributions ^corresponding author(s) Preprints 77 ...
Major version notes This is a protocol based on Kappa LTP Preparation Kit manual KR0453 v3.13 The main difference centers around the use of 1/2 volume in each reaction ...
Does it behoove better lingo? Just like the good sommelier delights us with their expansive full bodied descriptions of wines, connoisseur molecular and evolutionary ...
Main.DanielDeatherage

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. ...
Main.TWikiGuest

Statistics for nop Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and ...
Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded ...
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 ...
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 ...
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 ...
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 ...
Retired Protocols Designing a new part Designing a new part for use in the BTK Retired on May 23, 2014 Crush Soak ElutionRecover DNA or RNA samples from ...
Main.JeffreyBarrick

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

Past Barrick Lab Members Colin Brown Xue Zhang Michael Hammerling Brian Renda Jordan Monk Craig Barnhart Aurko Dasgupta Lindsey Wolf Alvaro Rodriguez Neil Gottel ...
Main.JeffreyBarrick

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

Bee Microbiome Toolkit The Bee Microbiome Toolkit (BTK) is a Golden Gate compatible toolkit of genetic parts designed for working with newly isolated, non model bacteria ...
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 ...
Main.SimonDAlton

Quantitative real time PCR for differential gene expression Quantitative real time PCR (qPCR) can seem like a real pain in the ass. Once you start reading up on it ...
Read trimming with trimmomatic Download and Install Download the "binary" version of trimmomatic from the lab. It's helpful to a create a shortcut so that you ...
Main.JeffreyBarrick

Barrick Lab :: Computational Protocols Command line Unix Commands Quick Reference Collection of useful Unix commands. SSH Public Key Authentication How ...
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 ...
Main.GabrielSuarez

How we handle strain requests and prepare them for mail delivery Intro Requests for any of Barrick Lab’s strains to be sent to other labs or overseas must be performed ...
Working with Pseuodmonas syringae (PSY) Pseudomonas syringae (PSY) comprises many species of bacteria that live on or within different plant species, as noted ...
Main.DanielDeatherage

This information is a stub to be added into a reworked NGS protocol as an alternative. Follows the duplex seq method developed by the Loeb lab This protocol is for ...
Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Adapted from: Re engineering the ribosome for efficient selenoprotein synthesis Ross Thyer, 2012 ...
Gel Electrophoresis In order to analyze PCR results, the products are run on an agarose gel, which is then analyzed in UV light to ascertain the length of DNA fragments ...
Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial ...
Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol ...
Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites ...
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 ...
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 ...
Main.SimonDAlton

Sensaphone Protocol The sensaphone is the alarm monitor connected to both of the 80C freezers in MBB. Below is an overview of the current settings and the expected ...
General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol ...
Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated ...
Shipping by FedEx/UPS/USPS The Easy Way to Ship is to CC Simon on correspondence with the collaborator. The Harder Way is as follows. USPS Fill out 'USPS Mail form ...
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 ...
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 ...
Main.JeffreyBarrick

Barrick Lab :: Contact Information Jeffrey E. Barrick, Ph.D. Assistant Professor Department of Molecular Biosciences The University of Texas at Austin Office ...
Media Amendment Stock Solutions Reagent Abb Stock Conc. Working Conc. Dilution Solvent MSDS Notes Ampicillin Amp 100 mg/mL ...
Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/"rescue" from counter selection ...
Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer ...
M9 Minimal Media Plates As with DM and MG media, make sure to autoclave the agar and phosphate separately. For 1 liter of media: 1L Component 6 g ...
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 ...
Media Recipes Liquid Media Included topic: ProtocolsRecipesSaline Included topic: ProtocolsRecipesLysogenyBroth Included topic: ProtocolsRecipesDavisMingioli ...
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 ...
How to Access Journal Articles when Electronic Copies are not Available This problem usually arises in two types of situations: i. The university does not have ...
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 ...
iGEM Part Plasmid Assembly NOTE: The following page is under revision. The GGA procedures and protocols below may not be optimal for your experiments. If you are ...
Main.JeffreyBarrick

Barrick Lab :: Computational Tools check out the BarrickLab on Github Breseq (Bacterial Genome Resequencing)Determine mutations in evolved bacteria from next generation ...
Evolutionary Stability of Fluorescent Protein or Chromoprotein Expression This protocol is a work in progress This procedure is to monitor the decay of a genetic ...
Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here ...
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 ...
Main.JeffreyBarrick

Barrick Lab :: Reference Information Templates and Spreadsheets Circular and Rectangular Tube Labels Templates for printing cryotube labels. Petri Dish ...
Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate ...
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 ...
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 ...
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 ...
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

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 ...
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.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 ...
#TransformingElectroporation Transforming E. coli Cells by Electroporation This procedure uses the TOP10 Electrocomp E. coli cells (but is identical in any ...
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.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.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
Main.JeffreyBarrick

Barrick Lab :: Research /collage.png Active Projects #PreventingEvolutionaryFailure Preventing Evolutionary Failure in Synthetic Biology Evolutionary half lives ...
Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator 50x TAE 242 g Tris base 57.1 ml ...
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.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

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 ...
Working with Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation ...
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 ...
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 ...
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 ...
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Topic revision: r2 - 28 Mar 2005 - 09:40:13 - Main.TWikiContributor
 
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