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Keio and ASKA collections Dear internet, Our lab is unable to distribute the Keio/ASKA strains to other institutions. We did not create them! If you want to use ...

Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick #128011 ...

Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded ...

Isolating Phage Genomic DNA This protocol has been tested with phage T7. It has a double stranded genome that has a length of 40 kb. Materials 5× phage precipitation ...

Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate ...

The University of Texas at Austin :: iGEM Team Interested in joining the UT Austin iGEM Team? Participating in the iGEM competition is a unique opportunity for undergraduate ...

General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol ...

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 ...

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. ...

Determining Phage Titer Materials Phage lysate or freezer stock (Procedure: Phage Lysate Preparation) Top Agar (LB Miller 0.8% agar) LB MIller (for ...

Phage Lysate Preparation We have used this protocol with phages T4, T5, T6 and T7. The general procedure should work with most E. coli phages (although lysis times ...

Past Barrick Lab Members Gabriel Suarez Grace Stark Stratton Georgoulis Jenna McGuffey Dr. Simon D'Alton Dacia Leon Colin Brown Xue Zhang Michael Hammerling Brian ...

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

C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR What you are looking ...

Competence Assays Day 0: Inoculation • Prepare n 1 tubes with 5ml LB (n samples and 1 uninoculated control) • Inoculate tubes with either 2uL of liquid culture or ...

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 ...

(Numbers are PCR product dilution with "10" representing a 1:10 dilution of your 0.01ng/ul PCR product prepped as described above) Template Material Use PCR ...

(Numbers are cDNA dilution with "5" representing a 1:5 dilution and so on) Template Material The cDNA used for this is a pool of all your cDNA samples i.e. ...

Barrick Lab ' '' " then "" else ""}% Contact Research Publications Team Protocols Reference Computation ...

Media amendments Antibiotic concentrations and stock solutions This table lists “standard” concentrations of antibiotics commonly used in microbiology laboratories ...

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 ...

Media Recipes Liquid Media Included topic: ProtocolsRecipesSaline Included topic: ProtocolsRecipesLysogenyBroth Included topic: ProtocolsRecipesDavisMingioli ...

Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering ...

Major version notes Runs prior to February 2020 had a variety of formats and sample submission requirements. Suggested that individual runs be consulted on utbox for ...

...in progress...

Barrick Lab :: Code Also check out our code repository: Github/BarrickLab Breseq (Bacterial Genome Resequencing)Determine mutations in evolved bacteria from next ...

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 ...

Copying files to/from UT Box at the command line Follow the directions here to set up an additional Box password that you will use for connecting: https://uisapp2 ...

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 ...

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

Working with Git Setup GitHub Ask to be granted access to see private repositories Learning Git it – App for teaching you to use command line Git on ...

Interested in research in the Barrick lab? We are always looking for outstanding undergraduate students, graduate students, and postdocs who are interested in experimental ...

Working with Vibrio natriegens (Vmax) Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines ...

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

Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites ...

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 ...

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 ...

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 ...

Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen ...

Quantitative real time PCR for differential gene expression THIS PAGE IS CURRENTLY UNDER CONSTRUCTION APOLOGIES FOR ANYTHING THAT'S STILL A BIT MESSY! Quantitative ...

RCV Medium RCV is a complex media consisting of 3 different sub components that must be prepared ahead of time if they are not already made. Main recipe 1L ...

1 2 3 4 5 6 7 8 9 A C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 B C1BR2 C1BR2 ...

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 ...

Major version notes This is a protocol based on Kapa LTP Preparation Kit manual KR0453 v3.13 The main difference centers around the use of 1/2 volume in each reaction ...

Fluctuation Tests Introduction This protocol is for doing a Luria Delbrück fluctuation test to measure the rate at which mutations occur that enable growth on selective ...

SOB/SOC: Super Optimal Broth For SOB: 1L Final Component 5 g 0.5% yeast extract 20 g 2.0% tryptone 0.5 g 10 ...

MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by "twitching". 1L Final Component ...

Transforming Electrocompetent Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES: Equipment: ...

Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice ...

Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow ...

Barrick Lab :: Links Advice for graduate students (Saw this linked by Cooper) for Young Scientists (Andrew Hendry) Serial Mentor (Claus Wilke's Blog ...

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 ...

Barrick Lab :: Reference Information Templates and Spreadsheets Circular and Rectangular Tube Labels Templates for printing cryotube labels. Petri Dish ...

Lambda Red Protocol Lambda Red Plasmids These plasmids are available as part of the Lambda Red disruption kit from the E. coli Genetic Stock Center. pKD46 ...

M9 Minimal Medium 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g ...

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 ...

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 ...

Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES ...

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

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 ...

Introduction to Experimental Design Motivation Whether for just a summer or for the duration of an entire Ph.D project, working on a scientific problem is a process ...

Making Presentations The purpose of this page is to provide a resource for how to make an effective presentation to a variety of different audiences. Considerations ...

Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological ...

Targeted PCR and Sanger Resequencing of Mutations Page in need of additional improvements. Descriptions here are particularly tailored for resequencing of evolved ...

Site directed mutagenesis protocol (adapted from QuickChange) A protocol for changing one (or a few) bases on a plasmid SUPPLIES: Primer Design: Use the following ...

Sanger DNA Sequencing Go to the UT DNA Sequencing Facility website. This page explains the pricing for various orders and the methods by which samples should be prepared ...

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 ...

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 isolation ...

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 ...

Introduction This protocol was inspired (after failed site directed mutagenesis attempts using Quikchange) by the protocol listed here at the Colgate website here ...

Megaprimer whole plasmid cloning aka nop MEGAWHOP cloning aka Overlap Extension PCR cloning We describe two approaches to MEGAWHOP in this protocol page. Approach ...

Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Adapted from: Re engineering the ribosome for efficient selenoprotein synthesis Ross Thyer, 2012 ...

Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD46 ...

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

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 ...

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 ...

Working with Pseuodmonas syringae (PSY) Pseudomonas syringae (PSY) comprises many species of bacteria that live on or within different plant species, as noted ...

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 ...

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 ...

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 ...

Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated ...

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 ...

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 ...

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 ...

Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate ...

Barrick Lab Style Guide Writing a Scientific Paper Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176) General Formatting ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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

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 ...

"In plate" / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony "in situ" (in plate) transformation with minimal ...

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

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Animations Saves a series of generated images to GIF, Flash, video, HTML, or PDF (LaTeX) formats. Installation install.packages("animation") library(animation) ...

Preparing Chemically Competent Cells using the Inoue Method Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES: ...

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 ...

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 ...

1 DPLYR 1 READR 1 GGPLOT, incl: 1 COWPLOT 1 GGREPEL 1 COLOR SCHEMES 1 (calculate growth rates) SimonDAlton 02 Jun 2016

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 ...

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 ...

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 ...

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. ...

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 ...

Profiling Ribose Operon Deletions Day 1: Search strain databank for desired population. 1. Login to lab website, open lab databases. 1. Search under "strains ...

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 ...

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 ...

Purifying 6xHis Tagged Proteins from E. Coli by Immobilized Metal Affinity Chromatograpy (IMAC) under Native Conditions SUPPLIES: Equipment: Nutator or Rocking ...

.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 ...

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 ...

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 ...

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 ...

Acinetobacter baylyi ADP1 Genome Manipulations Overview Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase ...

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 ...

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 ...

Strain Database Table Description Barrick lab strains are stored in a database on UT Box, accessible after login via this link. column example description ...

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 ...

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 ...

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 ...

Former Front Page Images Genome dynamics in experimental evolution Read article at NRG Flying Spaghetti Monster meet syntheticbiology? Caffeine addicted E. coliSupport ...

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 Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. 1L 5L ...

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 ...

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 ...

Subtle Grammatical Usage Notes aka Common mistakes when writing scientific papers and grants. Usage Alternate / Alternative Alternate means "every other ...

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 ...

WarningThese instructions and the associated scripts have not been tested with more modern versions of R / Perl / Matlab / etc. The procedure may require updates to ...

Barrick Lab :: News Archive August 2014: Graduate student Michael Hammerling is awarded a UT Graduate School Named Continuing Fellowship. April 2014: Graduate ...

Problem to be addressed: You have a set of compressed files that all need to be extracted, and you don't want to manually extract each one. Steps 1 create a new ...

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 ...

Using Flexbar program to remove adapter sequences from NGS reads Installing the Flexbar Executable on Mac 1 Go to home page select the newest version (2.5 as of ...

Large Scale Metagenomic Soil Prep This is a protocol developed to extract large quantities of metagenomic DNA from large soil samples. Note that this preparation technique ...

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

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 ...

Gene Gorging Evolved Alleles This procedure can be used to directly create unmarked mutations in the E. coli genome. Transform Gene Gorging and Donor Plasmid ...

What to do in case of workplace injury Notify senior lab personnel asap. If major medical treatment is necessary UT personnel are instructed to go to the ...

To be filled out later....

Science Quotations The price of a metaphor is eternal vigilance. –Alexander Rosenbluth and Norbert Wiener I t is a rule of evolution that characters at first merely ...

Barrick Lab Style Guide for Figures General Workflow Use a program (Excel, R, CIRCOS, matplotlib, etc.) to graph your data. Output a file in a vector graphics ...

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

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570007/

Liquid Media LB 6 x 500ml DM 6 x 1000ml, 6 x 500ml Saline 4 x 1000ml Sterile H2O 6 x 500ml 80% glycerol 6 x 250ml Solid Media LB ...

Sterile Saline Purpose: Used make dilutions of viable cells for plating or transfer to new media. This saline concentration of 0.85% w/v (145 mM) is suitable for ...

Total Alkaline Digest of Embedded RNA Linkages Materials 0.2 N Sodium Hydroxide (NaOH) Molarity and Normality are related by N nM For example ...

Special Media

Which polymerase is right for me? Types of polymerase Our lab stocks two main types of polymerase: Type Vender Cost per unit Product Information ...

The Arabinose (Ara) Genetic Marker Background The Escherichia coli B strain REL606 has a mutation in the araA gene that renders it unable to utilize the sugar ...

1416: 4 hydroxybenzoic acid medium (for JJ 1b, Bacillus sp.) 1L 4L Component 4.25 g 17.0 g Potassium Phosphate (dibasic) K2HPO4 trihydrate ...

Bacterial Genetic Code (NCBI Translation Table 11) AAs FFLLSSSSYY CC WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts M M MMMM M Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG ...

Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels ...

Process for ordering Bacteria strains from NCIMB (UK company) Company website is http://www.ncimb.com/

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 ...

PA: Lac Papillation Agar Make 10 Minimal A Salts. 10 Minimal A Salts 1L Component MW 80 g Potassium Phosphate (dibasic) K2HPO4 ...

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 ...

Images for use on other pages...

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 ...

Mutation Rates from Genome Resequencing Motivation: You have re sequenced several genomes after a mutation accumulation or adaptive evolution experiment. How do ...

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 ...

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 ...

Measuring the Rate of Attrition in Frozen or Cooled Samples Plates stored at 4C 1. Day 1: Inoculate strain in approximately 5mL of LB in shaking incubator at 30C ...

Characteristics of the E. coli Genome The Origin of DNA Replication ( oriC ) is not at position zero (0°)! In E. coli B REL606: approximately 3,885 ...

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 ...

Stab Agar Making agar stabs for storage and transport of bacterial strains. 1L Component 10 g Tryptone 5 g Yeast extract 10 g Sodium ...

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 ...

Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011

Erratum for Woods et al. Science 2011 R. J. Woods, J. E. Barrick, T. F. Cooper, U. Shrestha, M. R. Kauth, and R. E. Lenski, Science 331 :1433 (2011). The main ...

Analyzing RNA Seq data for differential gene expression Materials and Software Data files RNA Seq data in FASTQ format (Ex: dataset1.fastq, dataset2 ...

Naturally Transformable Bactera Acinetobacter baylyi ADP1 Overview History Physiology Molecular Biology Natural Competence Deinococcus radiodurans R1 Overview ...

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 ...

TGY Medium 1L 5L Component 5 g 25 g Pancreatic digest of casein 5 g 25 g Yeast Extract 1g 5 g Glucose 1 g 5 g ...

MC: Minimal Citrate Prepared the same as MG: Minimal Glucose with the following changes: No glucose 4.5 g/L Sodium Citrate (trisodium, dihydrate)

Overlap PCR Background Before attempting this somewhat advanced PCR technique, be sure to read the PCR protocol and check out a reference describing PCR theory ...

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 ...

NZY Broth 1L Component 10 g NZ Amine (casein hydrolysate) 5 g Yeast Extract 5 g NaCl Add dH2O to final volume. Adjust pH to 7.5 ...

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 ...

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

Installing breseq on TACC Ranger Set up modules There seem to be compiler bugs with later versions of GCC and mixing Boost compiled with those later versions of ...

General Lab Rules UNDER CONSTRUCTION

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 ...

Setting up Autotools http://sourceware.org/autobook/autobook/autobook toc.html http://www.gnu.org/software/autoconf/ http://www.gnu.org/software/automake/ http://www ...

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 ...

Postdoctoral Fellow Position in the Barrick Lab Earliest Start Date: June 2011 Status: OPEN Posted March, 16, 2011 A position is open for a postdoctoral ...

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 ...

Chemical List Fisher supplied item name item # size/qty CAS Chemalert storage code Agar BP1423 2 2 kg 9002 18 0 gray ...

To Do Receive equipment and find locations to store items EHS inspection Find out about material sample transfer process CraigBarnhart 09 Feb 2011

References for Whole Genome Sequencing NCBI Short Read Archive (SRA) Documentation http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd show f doc m doc s doc ...

Breseq Developer Notes In addition to the normal prerequisites for breseq , you will also need updated versions of these tools to work on breseq development. On ...

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 ...

Presentation List 2010 03 17 MSU GEDD Next Gen.pdf: 2010 03 17 MSU GEDD Next Gen.pdf

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 ...

Pulsed Field Gel Electrophoresis Mapping Purpose: To validate mutations predicted from whole genome re sequencing and possibly discover rearrangements through repetitive ...

Predicting Riboswitch Regulation on a Genomic Scale This page describes how to install a set of Perl scripts designed to identify members of known classes in genomic ...

Genomic DNA Preparation for Whole Genome Re sequencing of E. coli Current RTSF Instrument Information 454 Pyrosequencing (GSFlex machine) Read length is 100 ...

topA Gene Sequencing The topA gene coordinates are 1329420 1332017. The topA mutation in the Ara 1 long term line is 1329516:C T. primer who coords ...

Materials Description Cat # Price Qiagen RNeasy Protect Bacteria Mini Kit (50) 74524 $386.00 Invitrogen Superscript Plus Indirect cDNA Labeling ...

Predicting Riboswitch Regulation on a Genomic Scale This page describes how to install a set of Perl scripts designed to identify members of known classes in genomic ...

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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 ...

Packaging a Tool for Release You need these environmental variables set to work with the current CVS setup: export CVSROOT ":ext:local@barricklab.org:/bliss/cvs" export ...

RNA Structure Mutual Information Overview: What do these programs do? information between columns in a sequence alignment of structured RNAs can provide evidence ...

Space for temporary attachments...

Changing Environment Long Term General Procedures Inoculating Tubes To start an experiment, obtain 98 test tubes. Split the test tubes into two racks, 49 in each ...

Population Genetics Long Term Daily Procedure Supplies 1 13 x 50 ml flasks filled with 9.9 ml of DM500 (DM0 supplemented with 0.05% glucose). 1 12 x tetrazolium ...

Competition Assays for Evolvability Lines Serial transfer of 3.5 µl of culture to 900 µl of fresh medium achieves 8.0120 generations per day (assuming the 3.5 µl is ...

The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines ...

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 ...

Using the Deep 96 Well Pin Tool The 96 well pin tool can be used to transfer long term evolution experiments and to make dilutions when plating many samples. Although ...

Plate 1: Single Carbon Sources, Glucose and Glycerol Timescale 1 1 D Glucose 2 2 Glycerol 3 3 D Ribose 4 4 Pyruvate 5 5 L ...

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 ...

JeffreyBarrick .WebChangesAlert, ., .TWikiRegistration

These groups can be used to define fine grained .TWikiAccessControl in TWiki: TWikiAdminGroup Add your groups to this list and define new group topics similar ...

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

Attach graphics to be used throughout the site here.

Education 2006 Ph.D, Molecular Biophysics and Biochemistry (MB B), Yale University 2001 B.S., Chemistry, California Institute of Technology.

Blue Oyster Mushrooms Total Elapsed Time: ~10 days

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TWiki Administrator Group Set GROUP JeffreyBarrick Set ALLOWTOPICCHANGE TWikiAdminGroup (Note: Set the members of TWiki Administrator Group in GROUP ...