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

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

Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator 50x TAE Tris Acetate EDTA Used as a buffer...

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...

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://uisapp...

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

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...

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

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....

Golden Gate Assembly Under Construction Refer to Bee Toolkit pages for design and assembly of parts and plasmids for use with Bee Toolkit Generating Overhangs Assembly...

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...

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...

Past Barrick Lab Members Emmanuel Chavarria Kate Elston Dean Parenteau Elizabeth Robinson Jacob Risch Sarah Bialik Julie Perreau Shireen Shah Eleanor Young Peng Geng...

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

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...

Protocol Updates Needed Computation tool list Plannotate Standard PCR Anaconda should not be recommended Team R package/intro page

(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...

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...

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...

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...

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...

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...

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...

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...

DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 5L Component MW 2.67 g 5.34 g...

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...

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

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...

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

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...

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

(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....

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...

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

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

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

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

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

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

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...

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...

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

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...

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...

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...

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...

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...