Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from...

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...

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

Assembly Reactions Under Construction Protocols from NEB and https://www.neb.com/protocols/2020/01/15/golden gate assembly protocol for using neb golden gate assembly...

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...

Autoclave Sterilization Overview Autoclaves heat their contents to 121...

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

Bee Functional Genomics Using Engineered Symbionts Welcome to the temporary website for our new NSF EDGE project! Insects are among the most widespread and diverse...

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...

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...

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...

(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....

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

Coding 101: Best Practices for Writing Software Build Your Development Suite To code effectively, you need an appropriate development setup. We recommend at least...

Copying files to/from UT Box at the command line If you use SSO (through UT Box), you need to first up an external password. You will need LFTP installed on your system...

Attach graphics to be used throughout the site here.

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

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...

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...

Isolation of dsRNA from bacteria Materials and Reagents This protocol can be used to validate expression of dsRNA in E. coli (e.g. E.coli HT115(DE3)) or in other...

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

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...

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...

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...

C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Conditions If you want to be extra safe you should also include a negative control (usually...

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...

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

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...

Attach images that can be used throughout the Wiki here. Barrick Lab Overview is linked to on the UT CNS website, so don`t move it!

Generating Overhangs If generating overhangs for Golden Gate Assembly outside of YTK/BTK framework, NEB`s GETSET tool can be useful for generating a set of high fidelity...

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...

Golden Gate Assembly Golden Gate Assembly is a cloning method used to recombine multiple DNA components into a single linear piece or plasmid. It bears similarity...

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...

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

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...

Barrick Lab Journal Club Archive April 13, 2015 Dacia : Reijns, Martin A M, Harriet Kemp, James Ding, Sophie Marion de Proc...

General Lab Rules UNDER CONSTRUCTION

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

Lab Notebook Best Practices Notebook Setup Preferred Platform: Benchling Electronic Notebooks Have an administrator add you to the Barrick Lab organization on Benchling...

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

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

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

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...

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

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

Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011

Microplate Reader Quick Start Best Practices 1 Follow typical best practice for experimental design. Utilize technical replicates from the same biological sample...

Space for temporary attachments...

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

Back to Golden Gate Protocols Old Golden Gate Assembly Protocols This page contains a collection of old protocols for Golden Gate Assembly. All these protocols should...

Past Barrick Lab Members Jack Dwenger Elizabeth Manriquez Dan Deathrage Victor Li Matt McGuffie Laurel Miller Aneesa Bhakta Braydin McReynolds Joseph Reitman Emmanuel...

Phenol/chloroform extraction Extracting genomic bacterial DNA from pellet with phenol/chloroform with a combined EtOH precipitation step for salt/SDS/small nucleic...

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...

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

Barrick Lab :: Previous Research Identifying Mutations that Promote Bacterial Evolvability Epistasis Poker. Early draws of cards that are more beneficial to...

Custom Primer Design Overview While there are tools available for automatically designing primers (such as the Primer BLAST) often specialized PCR applications, such...

(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...

Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution...

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...

Day 1: Plating the Mixed Population 1. Find microsatellite containing strains in the 80...

FLP Recombination in E. coli This procedure is commonly used to eliminate the Kanamycin resistance cassette from E. coli strains from the Keio collection or produced...

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...

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. pKD...

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...

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

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...

Using Emulsions to Select by Yield Background Evolution in suspension culture proceeds by selecting for those strains that grow most rapidly, quickly depleting the...

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...

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

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...

Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using...

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....

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

Evolution Experiments Introduction An evolution experiment typically consists of evolving one or more ancestor strains in laboratory culture and assessing the types...

Competition Assays for Evolvability Lines Serial transfer of 3.5 ...

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

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...

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...

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...

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...

Label Templates Templates for printing labels...

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...

Strains Deleterious Mutations (UV Mutation Accumulation) Strain Fitness Ara relative to REL607 Marker Fitness Ara relative to Ara #8211; Designation...

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...

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...

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...

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

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...

Sequencing/Genotyping Primer Design This protocol is specifically for designing primers to PCR amplify a target region of interest from a genome and re sequencing...

Primer Extension or Oligo Overlap Extension To stitch together large DNA templates from oligonucleotide fragments. Using Klenow Fragment (3 5 exo...

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

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...

Gel Electrophoresis Overview Gel electrophoresis separates DNA fragments based on size. Electric current moves the negatively charged DNA through the gel, which slows...

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

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

Veracode Golden Gate Genotyping How to process data from RTSF 1 Open GenomeStudio. 1 Create a new genotyping project. 1 Choose the option to `Load sample...

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...

Calculating Growth Rates with Grofit The following are instructions for calculating growth rates using Grofit, an R package that is no longer supported by the current...

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...

Barrick Lab :: Laboratory Protocols Updating Protocols How to Create a Protocol Best practices for designing a protocol and for putting it on the lab Wiki....

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

Protocol Updates Needed Add a page with standard plate reader settings for different fluorophores (with citations) Also explain setting the gain!...

16S rRNA Sequencing to Identify Unknown Microbes Ever wonder what that contaminant in your culture is? Need to accurately identify an environmental isolate? Overview...

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

Acinetobacter baylyi ADP1 Overview ADP1 Resources Genome Sequences type strain (GenBank Format) In general, use this genome as a reference when referring...

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

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

Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing...

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

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

Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/`rescue` from counter selection...

Media amendments Antibiotic concentrations and stock solutions This table lists ...

Aphid Care and Protocols Rearing and Caring for Aphid Species Protocols and Primers

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...

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 First Stage Plasmid (Transcriptional Unit) Assembly Once you have all your desired part plasmids built you can assemble them into Transcriptional...

SeanLeonard 14 Sep 2017

SeanLeonard 14 Sep 2017

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...

Upon publication, this page will be updated with a full description of the BTK, parts list, and overhang types. SeanLeonard 14 Sep 2017

SeanLeonard 14 Sep 2017

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...

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...

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...

Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer...

CFU Counts This is an outline for a general protocol to assess the number of colony forming units in a sample using spot plating. This method cuts down on the number...

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...

CRISPR Associated Transposons (CASTs) The CRISPR Associated Transposon system allows for the targeted insertion of a large genetic cargo (up to 10 kb) into a bacterial...

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

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

Preparing Chemically Competent Cells using the Inoue Method 2 4H2O 10.88 g 55 mM CaCl2 2H2O 2.20 g 15 mM KCl 18.65g 250 mM PIPES (0....

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...

Computer Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for your science...

Computing Environment Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for...

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 Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation...

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...

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...

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...

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...

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...

Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1...

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

Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at...

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...

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...

Fluctuation Tests Introduction This protocol is for doing a Luria Delbr...

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...

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

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...

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...

Getting Started with Lab Techniques General molecular lab techniques Engineering: A Primer to Get You Started General microbiology lab techniques...

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...

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

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...

Measuring Microbial Growth Rates in a Plate Reader The following protocol can be used to determine the growth rate of a bacterial culture using a plate reader by measuring...

Tobacco hornworm (Manduca sexta) care The tobacco hornworm is the caterpillar stage of the five spotted hawk moth ( Manduca sexta ). They constitute a major pest of...

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

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

Labeling Glassware and Other Containers All bottles, flasks, tubes, graduated cylinders, and beakers that contain liquid or any substance must be labeled with a description...

Labeling Glassware and Other Containers All bottles, flasks, tubes, graduated cylinders, and beakers that contain liquid or any substance must be labeled with a description...

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...

Leafhopper Care and Protocols Rearing and Caring for Leafhopper Species Leafhopper species are kept in BugDorms (BugDorm 4F3030 and 4F2222). We have the following...

Learn Biocomputing General Resources / Courses Software Carpentry https://software carpentry.org/lessons/ Code Academy https://www.codecademy.com/ edX Computer...

Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae...

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...

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...

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

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

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

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...

P1 Transduction in Escherichia coli This protocol is adapted from Thomason, L. C., Costantino, N. and Court, D. L. 2007. E. coli Genome Manipulation by P1 Transduction...

PA: Lac Papillation Agar Make 10 Minimal A Salts. 10 Minimal A Salts 1L Component MW 80 g Potassium Phosphate (dibasic) K2HPO...

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...

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...

Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial...

Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture...

Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred...

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...

Python snippets for biology Requires BioPython to be installed Open common formats: .gbk / .gbf / .gb import SeqIO with open(`/my/path/file.gb`,`r`) as file handle...

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...

Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator Gel Electrophoresis 50 TAE (Tris Acetate...

Dear internet, We don`t distribute this plasmid. If you want to purify your own enzymes to save money, here are some options to investigate: Bioeconomy Lab ...

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

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

Blood Heart Infusion Agar Heart Infusion Agar supplemented with sterile Sheep`s Blood. Used for the cultivation of fastidious organisms (Bee gut microbiome species...

Czapek Broth (CB) Combine in a flask: 500 mL 1 L Component 1.5 g 3 g sodium nitrate 0.5 g 1 g potassium phosphate dibasic 0.25 g...

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...

DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.4L 5L Component MW 2.67 g...

LB: Lysogeny Broth / Luria Bertani Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. Add dH2O to desired...

LB: Lysogeny Broth / Luria Bertani (Miller) Agar Add dH2O to full volume in an appropriately sized flask. Combine the following, making sure each component fully dissolves...

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...

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

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...

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...

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...

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

SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract...

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...

Special Media

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

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...

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...

YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract...

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....

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...

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....

Retired Protocols Designing a new part Designing a new part for use in the BTK Bee Microbiome Toolkit (BTK) Golden Gate part kit for work in non model bacterial...

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...

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...

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...

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...

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...

Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified double stranded DNA product from template DNA. In addition to the template, the reactions...

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

Barrick Lab Style Guide Writing a Scientific Paper Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and...

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...

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

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

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...

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

Unix Commands Quick Reference Useful commands and flags that we get tired of looking up... Alphabetical Reference cat yourfile.txt Prints the contents of the given...

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...

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

Working with Serratia marcescens Serratia marcescens is a gram negative pathogenic bacteria known for its distinctive red pigmentation. While it is not found in...

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

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

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

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...

Comparative Quantitative PCR (qPCR) Quantitative PCR (qPCR) is a tool routinely used for the quantitation of target nucleic acid sequences. If it is your first time...

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...

Quantitative PCR (qPCR) Quantitative PCR (qPCR) is a tool routinely used for the quantitation of target nucleic acid sequences. If it is your first time performing...

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

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...

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...

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

in vitro RNA synthesis(T7 RNA Polymerase ) T7 RNA Polymerase is used for in vitro mRNA synthesis and is highly specific for the T7 phage promoter. T7 in vitro transcription...

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...

C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR Note: Once you...

Characteristics of the E. coli Genome The Origin of DNA Replication ( oriC ) is not at position zero (0...

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...

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 :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology...

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

Barrick Lab :: Research Listen to an introduction to our research: Evolution and Engineering Bee Guts (EBRC in Translation Podcast) https://barricklab.org/twiki/pub...

Creating animations for visualizing time resolved data. Rename files via command line How to use sed to rename multiple files in a single directory. Mass...

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...

Science Quotations The price of a metaphor is eternal vigilance. ...

Images for use on other pages...

Barrick Lab :: Software Also check out our GitHub code repositories: http://plannotate.barricklab.org pLannotate (Plasmid Annotation)Automated annotation of engineered...

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

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...

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

Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et...

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...

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...

Synthetic Biology 101 What is Synthetic Biology? Roughly, synthetic biology is the discipline that engineers cell and cell free systems to behave and produce products...

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...

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

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...

asdasdf JeffreyBarrick 20 Jun 2009

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Blue Oyster Mushrooms Total Elapsed Time: ~10 days

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...

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...

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

The University of Texas at Austin :: iGEM Team What is synthetic biology? What is iGEM? `Synthetic biology is the design and construction of biological devices...

To be filled out later....

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...

1 DPLYR 1 READR 1 GGPLOT, incl: 1 COWPLOT 1 GGREPEL 1 COLOR SCHEMES 1 (calculate growth rates) 1 SURVMINER (create survival curves) 1 SURVIVAL...

TWiki`s Lab web The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise.

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

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Barrick Lab Contact Research Publications Team Protocols Reference Software UT Austin Mol Biosciences...

This is a subscription service to be automatically notified by e mail when topics change in this 1 web. This is a convenient service, so you do not have to come...

/Lab The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise.

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

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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...