200 Recent Changes in Lab Web retrieved at 13:05 (GMT)

Main.TWikiGuest

Statistics for nop Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and ...
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.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.DanielDeatherage

Barrick Lab :: Computational Protocols Command line Unix Commands Quick Reference Collection of useful Unix commands. SSH Public Key Authentication How ...
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 ...
Golden Gate Assembly Background and Design Golden Gate cloning or Golden Gate assembly is a molecular cloning method that allows a researcher to simultaneously ...
Main.DennisMishler

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

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 ...
Main.JeffreyBarrick

Barrick Lab Members who what when more information Prof. Jeffrey Barrick Principal Investigator 01/2011–present @barricklab Dr. Simon ...
Golden Gate Assembly: Creating a New Part This protocol describes how to clone a new Golden Gate part amplified from a template DNA (like a plasmid or a genome) or ...
SeanLeonard 14 Sep 2017
SeanLeonard 14 Sep 2017
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 ...
SeanLeonard 14 Sep 2017
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.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.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 ...
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 ...
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 ...
Main.JeffreyBarrick

Barrick Lab :: Research /collage.png Active Projects #PreventingEvolutionaryFailure Preventing Evolutionary Failure in Synthetic Biology Evolutionary half lives ...
Main.JeffreyBarrick

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. ...
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.GabrielSuarez

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

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 ...
General Conjugation Protocol Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol for conjugation using ...
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 ...
Main.JeffreyBarrick

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

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.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 ...
Keio and ASKA collections Dear internet: our lab is unable to distribute the Keio/ASKA strains to other institutions. If you need to use these great E. coli resources ...
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. ...
Main.JeffreyBarrick

Sequencing/Genotyping Primer Design This protocol is specifically for designing primers to PCR amplify a target region of interest from a genome and re sequence it ...
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 ...
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 ...
Media Recipes Liquid Media Included topic: ProtocolsRecipesSaline Included topic: ProtocolsRecipesLysogenyBroth Included topic: ProtocolsRecipesDavisMingioli ...
Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Do not overfill your culture vessels When growing cultures in Erlenmeyer ...
Protocol Updates Needed (as of 2016 Dec 15) Protocols needed or flagged for updates Flow protocol updates (Dan and Dacia) P1 transduction; FLP/FRT recombination ...
Profiling Ribose Operon Deletions Day 1: Search strain databank for desired population. 1. Login to lab website, open lab databases. 1. Search under "strains ...
Non canonical Amino Acid Stock Solutions Amino Acid(Abbreviation) CAS Number Solvent MW(g/mol) Stock Stock (mg/mL) Culture Notes Y 60 18 4 ...
Nonstandard Amino Acids The Genomically Recoded Organism and Its Genotype E. coli C321. #8710;A.exp (Lajoie, et al. 2013) Genotype: MG1655 #8710;(ybhB bioAB)::zeoR ...
#TransformingElectroporation Transforming E. coli Cells by Electroporation This procedure uses the TOP10 Electrocomp E. coli cells (but is identical in any other ...
MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by "twitching". 1L Final Component ...
Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen ...
Main.GabrielSuarez

Barrick Lab :: Reference Information Templates and Spreadsheets Circular and Rectangular Tube Labels Templates for printing cryotube labels. Petri Dish ...
Co culture Competition Assays The instructions below include the basic protocol. Be sure to check whether there are variations needed for your specific samples! For ...
Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering ...
Main.SimonDAlton

Liquid Nitrogen, Dry Ice, CO2 The dry ice and liquid nitrogen are contained in room 1.122. Follow the instructions on the computer in 1.122 to log quantity of dry ...
NGS Data Retrieval Overview This is a series of commands to download NGS data from the GSAF and back it up. Make sure you make it all the way through the steps to ...
Main.DanielDeatherage

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 ...
Purifying 6xHis Tagged Proteins from E. Coli by Immobilized Metal Affinity Chromatograpy (IMAC) under Native Conditions SUPPLIES: Equipment: Nutator or Rocking ...
Golden Gate Assembly: Assembly of Cassette Plasmids The simplest way to assemble a cassette is to include one part of each Type in a BsaI assembly. The plasmid ...
Main.SeanLeonard

.lst kix j6e0b0djltj7 5 li{counter increment:lst ctn kix j6e0b0djltj7 5}ol.lst kix z85vgyq93hwo 7.start{counter reset:lst ctn kix z85vgyq93hwo 7 0}.lst kix wk0a504iaux6 ...
Main.SeanLeonard

16S rRNA Sequencing to Identify Unknown Microbes Ever wonder what that contaminant in your culture is? Need to accurately identify an environmental isolate? Overview ...
Running breseq on TACC Installing breseq on stampede for mac Open a new terminal window and use the following commands: 1 ssh into stampede and set up folder ...
Making Presentations The purpose of this page is to provide a resource for how to make a good presentation for a variety of audiences and circumstances. Considerations ...
Running an SDS PAGE Gel: Note that the following uses pre cast gels and pre made running buffer, see accessory protocols NotDoneYetDudez for casting gels and making ...
Large scale Protein Expression in E. Coli: Notes: This can be applied to either soluble proteins (for a downstream prep in native conditions) or insoluble proteins ...
Main.DanielDeatherage

This is start of a protocol to split pooled samples which have internal barcodes into individual fastq files. 1 copy pooled files from corral to scratch 1 gunzip ...
Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at 4 ...
Regular Expressions In Python and other languages, regular expressions (otherwise known as regex) are a powerful way to perform queries on strings. Below are tips ...
Acinetobacter baylyi ADP1 Genome Manipulations Overview Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase ...
Main.DanielDeatherage

Overview This is an example command for renaming multiple files at once. Ideally it is presented as a method for shortening file names by removing common elements ...
Main.DaciaLeon

Fortessa Flow Cytometry The Fortessa is a shared resource through the microscopy core. If you want to use it you need to get access to it you should flow the ...
Unix Commands Quick Reference Useful commands and flags that we get tired of looking up... Disk Space The du command is verbose and confusing if you run it without ...
Strain Database Table Description Barrick lab strains are stored in a database on UT Box, accessible after login via this link. column example description ...
Main.GabrielSuarez

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 ...
Setting up SSH Public Key Authentication These instructions will allow you to connect as user1 on machine FROM to user2 on machine TO without typing your password ...
Main.JeffreyBarrick

Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD46 ...
Colony Transformation This is a theoretical protocol that has not been tested! This protocol and be used for the rapid preparation of chemically competent E. coli ...
DNA Concentration Determination For many applications in cloning and genome editing, it is critical to accurately measure the concentration of DNA in a sample. This ...
Modular Cloning using CIDAR MoClo kit The lab recently acquired a CIDAR MoClo ( C ross disciplinary I ntegration of D esign A utomation R esearch lab Mo ...
Main.JeffreyBarrick

Former Front Page Images Genome dynamics in experimental evolution Read article at NRG Flying Spaghetti Monster meet syntheticbiology? Caffeine addicted E. coliSupport ...
M9 Minimal Media 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g Sodium ...
Saved Article Searches PubMed / myNCBI to tutorial on setting up an alert Google Scholar Method 1: Click on the "Create alert" button after ...
Find Chemicals Often you come across a chemical structure or name in a publication and then you need to find a place to order some from for your research. Maybe you ...
Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et ...
DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 1L 5L Component MW 5.3 g 26.7 g Potassium ...
LB: Lysogeny Broth / Luria Bertani (Miller) Agar Combine in a 2 L flask the following: 1.5L Component 15 g Tryptone 7.5 g Yeast Extract ...
LB: Lysogeny Broth / Luria Bertani Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. 1L 5L ...
Setting up the BEACON Teleconference in GDC 7.808 1 Plug the television into the wall. (!!!) 1 Press the power button on the touchpad. It will take about 3 minutes ...
Main.JeffreyBarrick

R2A R2A is a medium that can be used to grow a wide variety of soil microbes. 1L 5L Component 0.5 g 2.5 g Yeast Extract 0.5 g 2 ...
Label Templates Templates for printing labels...
Barrick Lab Journal Club Archive April 13, 2015 Dacia : Reijns, Martin A M, Harriet Kemp, James Ding, Sophie Marion de Procé, Andrew P Jackson, and Martin S ...
Main.JeffreyBarrick

Barrick Lab :: Computational Tools Breseq (Bacterial Genome Resequencing)Determine mutations in evolved bacteria from next generation sequencing data. Failure Mode ...
TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 2 L flask: 1.5L Component 15 g Tryptone 1.5 g Yeast Extract 7.5 g NaCl 24 ...
MG: Minimal Glucose agar, aka DM: Davis Mingioli agar Note: When making these plates it is necessary to prepare and autoclave the 3 main parts (salts, agar, and sugar ...
Gene replacement using pKOV vector Before beginning part 1: design primers 1 Insert should be ~1kb with approximately 500bp on either side of mutation, without ...
Main.JeffreyBarrick

Publicly Archiving Data These locations can give you accession numbers for data that may not be easily communicated as supplementary information for a research report ...
Main.DanielDeatherage

Problem to be addressed: You wish to run a command which will take a long time to finish on a computer that you have to securely log into (ssh command). Steps This ...
Main.JeffreyBarrick

UV mutagenesis of Bacteria Determination of Optimal UV treatment This procedure is used to determine optimal treatment which will be used for library generation. ...
Main.JeffreyBarrick

Links to Product Manuals Molecular biology NEB DNA Polymerase HF DNA polymerase solution mix DNA Ligase DNA Ligase I, RNase free PNK Assembly Master Mix ...
Main.GabrielSuarez

S2 Used for Acinetobacter Recipe for 900mL (Autoclave in three separate bottles 300mL each) Bottle 1 (Erlenmeyer flask: 300mL) 300mL Component ...
Main.CraigBarnhart

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570007/
1416: 4 hydroxybenzoic acid medium (for JJ 1b, Bacillus sp.) 1L 4L Component 4.25 g 17.0 g Potassium Phosphate (dibasic) K2HPO4 trihydrate ...
Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels ...
Main.CraigBarnhart

List of NEBNext Index Primer Barcodes NEBNext Index Primer # Barcode Sequence Expected IP Sequence Read 1 CGTGAT ATCACG 2 ACATCG CGATGT ...
red mediated ssDNA gene modification Background Protocol designed based on 3/16/11 Court Lab Protocol (which is available here) with Barrick lab specific modifications ...
Gene Gorging Marker Mutations For competitive fitness assays, one must be able to distinguish two E. coli subpopulations in a mixed culture. One way this can be ...
Main.CraigBarnhart

Overview: 1. Harvest DNA and determine concentration. 1. Fragment DNA. 1. End Repair DNA. 1. dA tail 3' end of DNA fragments 1. Ligate barcoded adapters ...
Main.DanielDeatherage

Use of degenerate bases Spoke with IDT about some of their recommendations related to incorporation of degenerate bases in oligos. Machine Mix vs Hand Mix option ...
Main.JeffreyBarrick

Images for use on other pages...
RCV Medium RCV is a complex media consisting of 3 different sub componets that must be prepared ahead of time if they are not already made. Main recipe 1L ...
YPS Medium 1L 1.5L Component 3.0 g 4.5 g Yeast Extract 3.0 g 4.5 g Peptone 2.0 mL 3.0 mL 1 M Magnesium sulfate 2.0 ...
Main.AurkoDasgupta

TGY Medium 1.5L Component 7.5 g Pancreatic digest of casein 7.5 g Yeast Extract 1.5g Glucose 1.5 g K2HPO4 24g Agar ...
ELUTION of OLIGOS FROM PAGE GEL Crush Soak Eluting DNA/RNA from PAGE or denaturing PAGE Materials Crush Soak Buffer (CSB) 200mM NaCl , 10 mM tris HCl (pH 7.5 ...
Main.CraigBarnhart

M9 Minimal Media Plates 1L Component 6 g Sodium phosphate, Na2HPO4•H2O 3 g Potassium phosphate, KH2PO4 0.5 g Sodium chloride, NaCl ...
Primer Extension or Oligo Overlap Extension To stitch together large DNA templates from oligonucleotide fragments. Using Klenow Fragment (3 5 exo–) This reaction ...
Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution ...
Main.MichaelHammerling

Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011
Main.CraigBarnhart

SOC: Super Optimal Broth with Glucose Used for recovery of cells after electroporation or heat shock transformation. 1L Final Component ...
Day 1: Plating the Mixed Population 1. Find microsatellite containing strains in the 80°C freezer. They will be labeled with the appropriate microsatellite sequence ...
Main.CraigBarnhart

DR: Defined minimal media for D. radiodurans 250 ml 500 ml Component 50 ml 100 ml 5x M9 salts 250 ul 500 ul 5mM MnCl2 250 ul ...
Main.AurkoDasgupta

Using APE If APE is not currently installed on this computer, search APE plasmid on google, and download the software for the appropriate system. APE can open the ...
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 ...
Main.JeffreyBarrick

Be who you are and say what you want, because those who mind don't matter and those who matter don't mind. Dr. Seuss
Move Kishony cfp/yfp into REL606 background P1 transduction fails, probably due to the restriction modification system of the E. coli B derived REL606 differing ...
manB cpsG deletion 1 Amplify negative and positive selection cassette encoding sacB and cat from pKO3 adding genome specific regions to each end. Try two different ...
Tetrazolium marker for follow up competitions ASKA(AG1) is Ara–, Mal– Still need a marker... gene gorge deletion in ribose gene from Keio? Keio(BW25113 ...
Main.JeffreyBarrick

nop infB strain construction 1 REL606 with infB1 allele from JEB154. 1 JEB154 with ancestral REL606 allele. primer name sequence RL1041 ...
Breseq Results Reading the results files Look at the manual for information on output formats. Click around until you're familiar with what everything means. First ...
Petri Dish Patch Templates The Full Template is for patching as many colonies as possible per petri plate. The 96 Well Format is for patching 48 colonies per plate ...
Ordering Primers 1 Go to ICMB's IDT webpage ICMB's IDT page 1 Click Set up new Account tab on bottom left. 1 Fill out all of your information, including ...
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.CraigBarnhart

Chemical List Fisher supplied item name item # size/qty CAS Chemalert storage code Agar BP1423 2 2 kg 9002 18 0 gray ...
Veracode Golden Gate Genotyping How to process data from RTSF 1 Open nop GenomeStudio. 1 Create a new genotyping project. 1 Choose the option to "Load sample ...
ASKA Collection Evolution Experiment Starting Lines 1 Revive each strain by inoculating a scrape of frozen culture from a well of a microplate into 3 ml of 0.1x ...
Genomic DNA Preparation for Whole Genome Re sequencing of E. coli Current RTSF Instrument Information 454 Pyrosequencing (GSFlex machine) Read length is 100 ...
Main.JeffreyBarrick

asdasdf JeffreyBarrick 20 Jun 2009
Protocol for Determining Mutation Rate to Phage (T5) resistance Day 2: Prepare Media/Revive/Titer Phage 1. If necessary, revive the frozen stock of each strain ...
Space for temporary attachments...
Strains Deleterious Mutations (UV Mutation Accumulation) Strain Fitness Ara relative to REL607 Marker Fitness Ara relative to Ara #8211; Designation ...
The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines ...
Genome Minimization Growth / Death Assays In order to be able to compare parameters uniformly between evolved and ancestor strains, all growth in these tests is done ...
Main.JeffreyBarrick

JeffreyBarrick .WebChangesAlert, ., .TWikiRegistration
Main.JeffreyBarrick

Local TWiki Preferences favicon: Attach a favicon.ico to a web's WebPreferences or add a FAVICON setting to WebPreferences Set FAVICON ///favicon ...
Main.JeffreyBarrick

Attach graphics to be used throughout the site here.
Main.JeffreyBarrick

Blue Oyster Mushrooms Total Elapsed Time: ~10 days
Main.TWikiContributor

" else " nop TWiki's nop Lab web"}% /Lab
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Main.TWikiContributor

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