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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...

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...

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...

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...

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...

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...

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...

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...

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...

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

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...

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...

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 Lactobacillus `Firm 5` The Lactobacillus `Firm 5` clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota...

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

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...

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....

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

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...

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

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...

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...

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

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...

SeanLeonard 14 Sep 2017

SeanLeonard 14 Sep 2017

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...

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

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

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

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...

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...

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

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

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...

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

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

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...

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

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...

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...

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

Label Templates Templates for printing labels...

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...

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...

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...

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

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

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

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....

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...

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

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...

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

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...

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...

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...

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...

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...

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

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

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

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

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...

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

Space for temporary attachments...

Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011

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

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

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...

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

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

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

General Lab Rules UNDER CONSTRUCTION

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

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...

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

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...

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

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...

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...

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...

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...

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

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...

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

Attach graphics to be used throughout the site here.

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

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...

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...

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

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

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...

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

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...

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...