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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...

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 ...

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...

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

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...

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

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

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

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...

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

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

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

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...

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...

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...

(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...

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...

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...

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....

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...

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 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...

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...

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...

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...

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...

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

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...

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...

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...

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

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...

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...