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| < < | Results from Lab web retrieved at 02:07 (GMT)<--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Autoclave Sterilization Overview Autoclaves heat their contents to 121... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Genetic Code (NCBI Translation Table 11) AAs FFLLSSSSYY CC WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts M M MMMM M Base1 TTTTTTTTTTTTTTTTCCCCCCCCC... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemical List Fisher supplied item name item # size/qty CAS Chemalert storage code Agar BP1423 2 2 kg 9002 18 0 gray... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Coding 101: Best Practices for Writing Software Build Your Development Suite To code effectively, you need an appropriate development setup. We recommend at least... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Attach graphics to be used throughout the site here. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Contact Information Jeffrey E. Barrick, PhD John A. Hannah Distinguished ProfessorDepartment of Microbiology, Genetics, Immunology Department... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Education 2006 Ph.D, Molecular Biophysics and Biochemistry (MB B), Yale University 2001 B.S., Chemistry, California Institute of Technology. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General guidelines for sorting bacteria with fluorescence activated cell sorting (FACS) FACS is a powerful tool for high throughput analysis and manipulation of complex... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Former Front Page Images Genome dynamics in experimental evolution Read article at NRG Flying Spaghetti Monster meet syntheticbiology? Caffeine addicted E. coliSupport... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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! <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> How to clean glassware LTEE flasks and lids LTEE glassware... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Handling High Molecular Weight DNA Introduction Long read sequencing, such as Oxford Nanopore or PacBio sequencing, is becoming increasingly important for genome... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Naturally Transformable Bactera Acinetobacter baylyi ADP1 Overview History Physiology Molecular Biology Natural Competence Deinococcus radiodurans R1 Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Journal Club Archive April 13, 2015 Dacia : Reijns, Martin A M, Harriet Kemp, James Ding, Sophie Marion de Proc... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Lab Rules UNDER CONSTRUCTION <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Interested in research in the Barrick lab? We are always looking for outstanding undergraduate students, graduate students, and postdocs who are interested in experimental... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lab Notebook Best Practices Notebook Setup Preferred Platform: Benchling Electronic Notebooks Have an administrator add you to the Barrick Lab organization on Benchling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To Do Receive equipment and find locations to store items EHS inspection Find out about material sample transfer process CraigBarnhart 09 Feb 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Links Advice for graduate students (Saw this linked by Cooper) for Young Scientists (Andrew Hendry) Serial Mentor (Claus Wilke`s Blog... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bioinformatics Master List This page is a master list of bioinformatics software frequently used in the lab, and their purposes. It also includes additional notes... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570007/ <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Megaprimer whole plasmid cloning aka MEGAWHOP cloning aka Overlap Extension PCR cloning We describe two approaches to MEGAWHOP in this protocol page. Approach... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Microplate Reader Quick Start Best Practices 1 Follow typical best practice for experimental design. Utilize technical replicates from the same biological sample... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Space for temporary attachments... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: News Archive August 2014: Graduate student Michael Hammerling is awarded a UT Graduate School Named Continuing Fellowship. April 2014: Graduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Past Barrick Lab Members Devin Lake Lucio Navarro Vibhav Iyengar Anna Grove Krisha Chaudhari Korin Jones Dr. Patrick Lariviere Dr. Dennis Mishler Alexa Morton Cameron... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Phenol/chloroform extraction Extracting genomic bacterial DNA from pellet with phenol/chloroform with a combined EtOH precipitation step for salt/SDS/small nucleic... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Presentation List 2010 03 17 MSU GEDD Next Gen.pdf: 2010 03 17 MSU GEDD Next Gen.pdf <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Previous Research Leafhoppers: Evolution and Biochemistry of Natural Nanoparticles Leafhopper and SEM image of brochosomes on its wing Leafhoppers... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Custom Primer Design Overview While there are tools available for automatically designing primers (such as the Primer BLAST) often specialized PCR applications, such... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Day 1: Plating the Mixed Population 1. Find microsatellite containing strains in the 80... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Allelic exchange using pKOV or pKOV style vectors Before beginning part 1: design primers 1 Insert should be ~1kb with approximately 500bp on either side of mutation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Using Emulsions to Select by Yield Background Evolution in suspension culture proceeds by selecting for those strains that grow most rapidly, quickly depleting the... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Mutation Rates from Genome Resequencing Motivation: You have re sequenced several genomes after a mutation accumulation or adaptive evolution experiment. How do... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Materials Description Cat # Price Qiagen RNeasy Protect Bacteria Mini Kit (50) 74524 $386.00 Invitrogen Superscript Plus Indirect cDNA Labeling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Evolution Experiments Introduction An evolution experiment typically consists of evolving one or more ancestor strains in laboratory culture and assessing the types... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competition Assays for Evolvability Lines Serial transfer of 3.5 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Label Templates Templates for printing labels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strains Deleterious Mutations (UV Mutation Accumulation) Strain Fitness Ara relative to REL607 Marker Fitness Ara relative to Ara #8211; Designation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Primer Extension or Oligo Overlap Extension To stitch together large DNA templates from oligonucleotide fragments. Using Klenow Fragment (3 5 exo... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Pulsed Field Gel Electrophoresis Mapping Purpose: To validate mutations predicted from whole genome re sequencing and possibly discover rearrangements through repetitive... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Gel Electrophoresis Overview Gel electrophoresis separates DNA fragments based on size. Electric current moves the negatively charged DNA through the gel, which slows... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Total Alkaline Digest of Embedded RNA Linkages Materials 0.2 N Sodium Hydroxide (NaOH) Molarity and Normality are related by N nM For example... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Protocol Updates Needed this page on DNA sequencing needs to be updated and be made more for the general public than to the lab General guide for sorting... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 16S rRNA Sequencing to Identify Unknown Microbes Ever wonder what that contaminant in your culture is? Need to accurately identify an environmental isolate? Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Purifying 6xHis Tagged Proteins from E. Coli by Immobilized Metal Affinity Chromatograpy (IMAC) under Native Conditions SUPPLIES: Equipment: Nutator or Rocking... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Overview ADP1 Resources Genome Sequences type strain (GenBank Format) In general, use this genome as a reference when referring... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase expression... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> `In plate` / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony `in situ` (in plate) transformation with minimal... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/`rescue` from counter selection... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media amendments Preparation: Generally, prepare 30 50 mL of solution in a 50 mL conical tube. Then, filter sterilize solutions by pushing them through a 50 mL syringe... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Aphid Care and Protocols Rearing and Caring for Aphid Species Protocols and Primers <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Re engineering the ribosome for efficient selenoprotein synthesis SUPPLIES: Equipment:... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computer Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for your science... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computing Environment Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Lactobacillus `Firm 5` The Lactobacillus `Firm 5` clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Fluctuation Tests Introduction This protocol is for doing a Luria Delbr... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Getting Started with Lab Techniques General molecular lab techniques Engineering: A Primer to Get You Started General microbiology lab techniques... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Intracellular Reactive Oxygen Species (ROS) This procedure is commonly utilized to quantify ROS. For more information about limitations associated with this... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Leafhopper Care and Protocols Rearing and Caring for Leafhopper Species Leafhopper species are kept in BugDorms (BugDorm 4F3030 and 4F2222). We have the following... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Learn Biocomputing General Resources / Courses Software Carpentry https://software carpentry.org/lessons/ Code Academy https://www.codecademy.com/ edX Computer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media Recipes When making media, make sure the autoclave bin you`re using contains water (DI or tap) at least half an inch deep to help prevent excess water loss... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Introduction This protocol was inspired (after failed site directed mutagenesis attempts using Quikchange) by the protocol listed here at the Colgate website here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by `twitching`. 1L Final Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> PA: Lac Papillation Agar Make 10 Minimal A Salts. 10 Minimal A Salts 1L Component MW 80 g Potassium Phosphate (dibasic) K2HPO... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Burst Size of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates Overnight stock of permissive bacterial host... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator Gel Electrophoresis 50 TAE (Tris Acetate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 1416: 4 hydroxybenzoic acid medium (for JJ 1b, Bacillus sp.) 1L 4L Component 4.25 g 17.0 g Potassium Phosphate (dibasic) K2HPO4 trihydrate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> ABMS: Acinetobacter Minimal Succinate Courtesy of the Averhoff lab, with modifications for available reagents. To make standard ABMS, combine the following pre sterilized... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blood Heart Infusion Agar Heart Infusion Agar supplemented with sterile Sheep`s Blood. Used for the cultivation of fastidious organisms (Bee gut microbiome species... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.5L 5L Component MW 2.67 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> M9 Minimal Medium 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MC: Minimal Citrate Prepared the same as MG: Minimal Glucose with the following changes: No glucose 4.5 g/L Sodium Citrate (trisodium, dihydrate) <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> S2 Used for Acinetobacter Recipe for 900mL (Autoclave in three separate bottles 300mL each) Bottle 1 (Erlenmeyer flask: 300mL) 300mL Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Special Media <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Stab Agar Making agar stabs for storage and transport of bacterial strains. 1L Component 10 g Tryptone 5 g Yeast extract 10 g Sodium... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 1 L flask: 500 mL Component 5 g Tryptone 500 mg Yeast Extract 2.5 g NaCl 8 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified double stranded DNA product from template DNA. In addition to the template, the reactions... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strain Database Table Description Barrick lab strains are stored in a database on UT Box, accessible after login via this link. column example description... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Which polymerase is right for me? Types of polymerase NEB polymerases may be purchased from the NEB freezer, which is located in the Biomedical Research Supply Core... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> _... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> UV mutagenesis of Bacteria Determination of Optimal UV treatment This procedure is used to determine optimal treatment which will be used for library generation.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Pseuodmonas syringae (PSY) Pseudomonas syringae (PSY) comprises many species of bacteria that live on or within different plant species, as noted... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia marcescens Serratia marcescens is a gram negative pathogenic bacteria known for its distinctive red pigmentation. While it is not found in... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Vibrio natriegens (Vmax) Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Legend: Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Animations Saves a series of generated images to GIF, Flash, video, HTML, or PDF (LaTeX) formats. Installation install.packages(`animation`) library(animation)... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR Note: Once you... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Characteristics of the E. coli Genome The Origin of DNA Replication ( oriC ) is not at position zero (0... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Research Listen to an introduction to our synthetic biology research:Evolution and Engineering Bee Guts (EBRC in Translation Podcast) Watch a public... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Science Quotations The price of a metaphor is eternal vigilance. ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Images for use on other pages... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Software Also check out our GitHub code repositories: http://plannotate.barricklab.org pLannotate (Plasmid Annotation)Automated annotation of engineered... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Subtle Grammatical Usage Notes aka Common mistakes when writing scientific papers and grants. Usage Alternate / Alternative Alternate means `every other... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki Administrator Group Set GROUP JeffreyBarrick Set ALLOWTOPICCHANGE TWikiAdminGroup (Note: Set the members of TWiki Administrator Group in GROUP... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Local TWiki Preferences favicon: Attach a favicon.ico to a web`s WebPreferences or add a FAVICON setting to WebPreferences Set FAVICON ///favicon... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> asdasdf JeffreyBarrick 20 Jun 2009 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .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 wk0a504iaux... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blue Oyster Mushrooms Total Elapsed Time: ~10 days <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> RNA Structure Mutual Information Overview: What do these programs do? information between columns in a sequence alignment of structured RNAs can provide evidence... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Bar of TopMenuSkin Top bar of TopMenuSkin, replacing WebTopBar. var twTopMenuBarCloseTimer null; var twTopMenuBarTimerMsec 1000; function twToggleTopMenuBar... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The University of Texas at Austin :: iGEM Team The Barrick lab sponsored and mentored the UT Austin iGEM team from 2012 2025 when we were located at The University... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To be filled out later.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki`s Lab web The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the faster 1 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Contact Research Publications Team Protocols Reference Software UT Austin Mol Biosciences... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> /Lab The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Statistics for Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Menu of Lab Web This topic defines the menu structure of the Lab web, used by the TopMenuSkin . Barrick Lab Homepage Contact Information... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the verbose 1 . <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> Number of topics: 305 <--/patternSearchResultCount-->See also the faster WebTopicList | |||||||
| > > | Results from Lab web retrieved at 02:07 (GMT)<--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Autoclave Sterilization Overview Autoclaves heat their contents to 121... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Genetic Code (NCBI Translation Table 11) AAs FFLLSSSSYY CC WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts M M MMMM M Base1 TTTTTTTTTTTTTTTTCCCCCCCCC... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemical List Fisher supplied item name item # size/qty CAS Chemalert storage code Agar BP1423 2 2 kg 9002 18 0 gray... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Coding 101: Best Practices for Writing Software Build Your Development Suite To code effectively, you need an appropriate development setup. We recommend at least... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Attach graphics to be used throughout the site here. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Contact Information Jeffrey E. Barrick, PhD John A. Hannah Distinguished ProfessorDepartment of Microbiology, Genetics, Immunology Department... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Education 2006 Ph.D, Molecular Biophysics and Biochemistry (MB B), Yale University 2001 B.S., Chemistry, California Institute of Technology. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General guidelines for sorting bacteria with fluorescence activated cell sorting (FACS) FACS is a powerful tool for high throughput analysis and manipulation of complex... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Former Front Page Images Genome dynamics in experimental evolution Read article at NRG Flying Spaghetti Monster meet syntheticbiology? Caffeine addicted E. coliSupport... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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! <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> How to clean glassware LTEE flasks and lids LTEE glassware... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Handling High Molecular Weight DNA Introduction Long read sequencing, such as Oxford Nanopore or PacBio sequencing, is becoming increasingly important for genome... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Naturally Transformable Bactera Acinetobacter baylyi ADP1 Overview History Physiology Molecular Biology Natural Competence Deinococcus radiodurans R1 Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Journal Club Archive April 13, 2015 Dacia : Reijns, Martin A M, Harriet Kemp, James Ding, Sophie Marion de Proc... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Lab Rules UNDER CONSTRUCTION <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Interested in research in the Barrick lab? We are always looking for outstanding undergraduate students, graduate students, and postdocs who are interested in experimental... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lab Notebook Best Practices Notebook Setup Preferred Platform: Benchling Electronic Notebooks Have an administrator add you to the Barrick Lab organization on Benchling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To Do Receive equipment and find locations to store items EHS inspection Find out about material sample transfer process CraigBarnhart 09 Feb 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Links Advice for graduate students (Saw this linked by Cooper) for Young Scientists (Andrew Hendry) Serial Mentor (Claus Wilke`s Blog... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bioinformatics Master List This page is a master list of bioinformatics software frequently used in the lab, and their purposes. It also includes additional notes... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570007/ <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Megaprimer whole plasmid cloning aka MEGAWHOP cloning aka Overlap Extension PCR cloning We describe two approaches to MEGAWHOP in this protocol page. Approach... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Microplate Reader Quick Start Best Practices 1 Follow typical best practice for experimental design. Utilize technical replicates from the same biological sample... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Space for temporary attachments... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: News Archive August 2014: Graduate student Michael Hammerling is awarded a UT Graduate School Named Continuing Fellowship. April 2014: Graduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Past Barrick Lab Members Devin Lake Lucio Navarro Vibhav Iyengar Anna Grove Krisha Chaudhari Korin Jones Dr. Patrick Lariviere Dr. Dennis Mishler Alexa Morton Cameron... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Phenol/chloroform extraction Extracting genomic bacterial DNA from pellet with phenol/chloroform with a combined EtOH precipitation step for salt/SDS/small nucleic... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Presentation List 2010 03 17 MSU GEDD Next Gen.pdf: 2010 03 17 MSU GEDD Next Gen.pdf <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Previous Research Leafhoppers: Evolution and Biochemistry of Natural Nanoparticles Leafhopper and SEM image of brochosomes on its wing Leafhoppers... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Custom Primer Design Overview While there are tools available for automatically designing primers (such as the Primer BLAST) often specialized PCR applications, such... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Day 1: Plating the Mixed Population 1. Find microsatellite containing strains in the 80... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Allelic exchange using pKOV or pKOV style vectors Before beginning part 1: design primers 1 Insert should be ~1kb with approximately 500bp on either side of mutation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Using Emulsions to Select by Yield Background Evolution in suspension culture proceeds by selecting for those strains that grow most rapidly, quickly depleting the... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Mutation Rates from Genome Resequencing Motivation: You have re sequenced several genomes after a mutation accumulation or adaptive evolution experiment. How do... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Materials Description Cat # Price Qiagen RNeasy Protect Bacteria Mini Kit (50) 74524 $386.00 Invitrogen Superscript Plus Indirect cDNA Labeling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Evolution Experiments Introduction An evolution experiment typically consists of evolving one or more ancestor strains in laboratory culture and assessing the types... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competition Assays for Evolvability Lines Serial transfer of 3.5 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Label Templates Templates for printing labels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strains Deleterious Mutations (UV Mutation Accumulation) Strain Fitness Ara relative to REL607 Marker Fitness Ara relative to Ara #8211; Designation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Primer Extension or Oligo Overlap Extension To stitch together large DNA templates from oligonucleotide fragments. Using Klenow Fragment (3 5 exo... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Pulsed Field Gel Electrophoresis Mapping Purpose: To validate mutations predicted from whole genome re sequencing and possibly discover rearrangements through repetitive... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Gel Electrophoresis Overview Gel electrophoresis separates DNA fragments based on size. Electric current moves the negatively charged DNA through the gel, which slows... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Total Alkaline Digest of Embedded RNA Linkages Materials 0.2 N Sodium Hydroxide (NaOH) Molarity and Normality are related by N nM For example... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Protocol Updates Needed this page on DNA sequencing needs to be updated and be made more for the general public than to the lab General guide for sorting... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 16S rRNA Sequencing to Identify Unknown Microbes Ever wonder what that contaminant in your culture is? Need to accurately identify an environmental isolate? Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Purifying 6xHis Tagged Proteins from E. Coli by Immobilized Metal Affinity Chromatograpy (IMAC) under Native Conditions SUPPLIES: Equipment: Nutator or Rocking... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Overview ADP1 Resources Genome Sequences type strain (GenBank Format) In general, use this genome as a reference when referring... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase expression... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> `In plate` / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony `in situ` (in plate) transformation with minimal... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/`rescue` from counter selection... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media amendments Preparation: Generally, prepare 30 50 mL of solution in a 50 mL conical tube. Then, filter sterilize solutions by pushing them through a 50 mL syringe... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Aphid Care and Protocols Rearing and Caring for Aphid Species Protocols and Primers <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Re engineering the ribosome for efficient selenoprotein synthesis SUPPLIES: Equipment:... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computer Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for your science... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computing Environment Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Lactobacillus `Firm 5` The Lactobacillus `Firm 5` clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Fluctuation Tests Introduction This protocol is for doing a Luria Delbr... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Getting Started with Lab Techniques General molecular lab techniques Engineering: A Primer to Get You Started General microbiology lab techniques... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Intracellular Reactive Oxygen Species (ROS) This procedure is commonly utilized to quantify ROS. For more information about limitations associated with this... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Leafhopper Care and Protocols Rearing and Caring for Leafhopper Species Leafhopper species are kept in BugDorms (BugDorm 4F3030 and 4F2222). We have the following... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Learn Biocomputing General Resources / Courses Software Carpentry https://software carpentry.org/lessons/ Code Academy https://www.codecademy.com/ edX Computer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media Recipes When making media, make sure the autoclave bin you`re using contains water (DI or tap) at least half an inch deep to help prevent excess water loss... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Introduction This protocol was inspired (after failed site directed mutagenesis attempts using Quikchange) by the protocol listed here at the Colgate website here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by `twitching`. 1L Final Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> PA: Lac Papillation Agar Make 10 Minimal A Salts. 10 Minimal A Salts 1L Component MW 80 g Potassium Phosphate (dibasic) K2HPO... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Burst Size of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates Overnight stock of permissive bacterial host... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator Gel Electrophoresis 50 TAE (Tris Acetate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 1416: 4 hydroxybenzoic acid medium (for JJ 1b, Bacillus sp.) 1L 4L Component 4.25 g 17.0 g Potassium Phosphate (dibasic) K2HPO4 trihydrate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> ABMS: Acinetobacter Minimal Succinate Courtesy of the Averhoff lab, with modifications for available reagents. To make standard ABMS, combine the following pre sterilized... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blood Heart Infusion Agar Heart Infusion Agar supplemented with sterile Sheep`s Blood. Used for the cultivation of fastidious organisms (Bee gut microbiome species... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.5L 5L Component MW 2.67 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> M9 Minimal Medium 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MC: Minimal Citrate Prepared the same as MG: Minimal Glucose with the following changes: No glucose 4.5 g/L Sodium Citrate (trisodium, dihydrate) <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> S2 Used for Acinetobacter Recipe for 900mL (Autoclave in three separate bottles 300mL each) Bottle 1 (Erlenmeyer flask: 300mL) 300mL Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Special Media <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Stab Agar Making agar stabs for storage and transport of bacterial strains. 1L Component 10 g Tryptone 5 g Yeast extract 10 g Sodium... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 1 L flask: 500 mL Component 5 g Tryptone 500 mg Yeast Extract 2.5 g NaCl 8 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified double stranded DNA product from template DNA. In addition to the template, the reactions... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strain Database Table Description Barrick lab strains are stored in a database on UT Box, accessible after login via this link. column example description... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Which polymerase is right for me? Types of polymerase NEB polymerases may be purchased from the NEB freezer, which is located in the Biomedical Research Supply Core... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> _... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> UV mutagenesis of Bacteria Determination of Optimal UV treatment This procedure is used to determine optimal treatment which will be used for library generation.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Pseuodmonas syringae (PSY) Pseudomonas syringae (PSY) comprises many species of bacteria that live on or within different plant species, as noted... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia marcescens Serratia marcescens is a gram negative pathogenic bacteria known for its distinctive red pigmentation. While it is not found in... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Vibrio natriegens (Vmax) Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Legend: Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Animations Saves a series of generated images to GIF, Flash, video, HTML, or PDF (LaTeX) formats. Installation install.packages(`animation`) library(animation)... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR Note: Once you... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Characteristics of the E. coli Genome The Origin of DNA Replication ( oriC ) is not at position zero (0... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Research Listen to an introduction to our synthetic biology research:Evolution and Engineering Bee Guts (EBRC in Translation Podcast) Watch a public... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Science Quotations The price of a metaphor is eternal vigilance. ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Images for use on other pages... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Software Also check out our GitHub code repositories: http://plannotate.barricklab.org pLannotate (Plasmid Annotation)Automated annotation of engineered... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Subtle Grammatical Usage Notes aka Common mistakes when writing scientific papers and grants. Usage Alternate / Alternative Alternate means `every other... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki Administrator Group Set GROUP JeffreyBarrick Set ALLOWTOPICCHANGE TWikiAdminGroup (Note: Set the members of TWiki Administrator Group in GROUP... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Local TWiki Preferences favicon: Attach a favicon.ico to a web`s WebPreferences or add a FAVICON setting to WebPreferences Set FAVICON ///favicon... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> asdasdf JeffreyBarrick 20 Jun 2009 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .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 wk0a504iaux... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blue Oyster Mushrooms Total Elapsed Time: ~10 days <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> RNA Structure Mutual Information Overview: What do these programs do? information between columns in a sequence alignment of structured RNAs can provide evidence... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Bar of TopMenuSkin Top bar of TopMenuSkin, replacing WebTopBar. var twTopMenuBarCloseTimer null; var twTopMenuBarTimerMsec 1000; function twToggleTopMenuBar... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The University of Texas at Austin :: iGEM Team The Barrick lab sponsored and mentored the UT Austin iGEM team from 2012 2025 when we were located at The University... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To be filled out later.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki`s Lab web The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the faster 1 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Contact Research Publications Team Protocols Reference Software UT Austin Mol Biosciences... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> /Lab The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Statistics for Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Menu of Lab Web This topic defines the menu structure of the Lab web, used by the TopMenuSkin . Barrick Lab Homepage Contact Information... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the verbose 1 . <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> Number of topics: 305 <--/patternSearchResultCount-->See also the faster WebTopicList | |||||||
Revision 22001-11-24 - PeterThoeny
Results from Lab web retrieved at 02:07 (GMT)<--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Autoclave Sterilization Overview Autoclaves heat their contents to 121... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Genetic Code (NCBI Translation Table 11) AAs FFLLSSSSYY CC WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts M M MMMM M Base1 TTTTTTTTTTTTTTTTCCCCCCCCC... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemical List Fisher supplied item name item # size/qty CAS Chemalert storage code Agar BP1423 2 2 kg 9002 18 0 gray... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Coding 101: Best Practices for Writing Software Build Your Development Suite To code effectively, you need an appropriate development setup. We recommend at least... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Attach graphics to be used throughout the site here. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Contact Information Jeffrey E. Barrick, PhD John A. Hannah Distinguished ProfessorDepartment of Microbiology, Genetics, Immunology Department... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Education 2006 Ph.D, Molecular Biophysics and Biochemistry (MB B), Yale University 2001 B.S., Chemistry, California Institute of Technology. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General guidelines for sorting bacteria with fluorescence activated cell sorting (FACS) FACS is a powerful tool for high throughput analysis and manipulation of complex... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Former Front Page Images Genome dynamics in experimental evolution Read article at NRG Flying Spaghetti Monster meet syntheticbiology? Caffeine addicted E. coliSupport... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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! <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> How to clean glassware LTEE flasks and lids LTEE glassware... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Handling High Molecular Weight DNA Introduction Long read sequencing, such as Oxford Nanopore or PacBio sequencing, is becoming increasingly important for genome... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Naturally Transformable Bactera Acinetobacter baylyi ADP1 Overview History Physiology Molecular Biology Natural Competence Deinococcus radiodurans R1 Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Journal Club Archive April 13, 2015 Dacia : Reijns, Martin A M, Harriet Kemp, James Ding, Sophie Marion de Proc... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Lab Rules UNDER CONSTRUCTION <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Interested in research in the Barrick lab? We are always looking for outstanding undergraduate students, graduate students, and postdocs who are interested in experimental... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lab Notebook Best Practices Notebook Setup Preferred Platform: Benchling Electronic Notebooks Have an administrator add you to the Barrick Lab organization on Benchling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To Do Receive equipment and find locations to store items EHS inspection Find out about material sample transfer process CraigBarnhart 09 Feb 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Links Advice for graduate students (Saw this linked by Cooper) for Young Scientists (Andrew Hendry) Serial Mentor (Claus Wilke`s Blog... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bioinformatics Master List This page is a master list of bioinformatics software frequently used in the lab, and their purposes. It also includes additional notes... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570007/ <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Megaprimer whole plasmid cloning aka MEGAWHOP cloning aka Overlap Extension PCR cloning We describe two approaches to MEGAWHOP in this protocol page. Approach... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Microplate Reader Quick Start Best Practices 1 Follow typical best practice for experimental design. Utilize technical replicates from the same biological sample... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Space for temporary attachments... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: News Archive August 2014: Graduate student Michael Hammerling is awarded a UT Graduate School Named Continuing Fellowship. April 2014: Graduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Past Barrick Lab Members Devin Lake Lucio Navarro Vibhav Iyengar Anna Grove Krisha Chaudhari Korin Jones Dr. Patrick Lariviere Dr. Dennis Mishler Alexa Morton Cameron... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Phenol/chloroform extraction Extracting genomic bacterial DNA from pellet with phenol/chloroform with a combined EtOH precipitation step for salt/SDS/small nucleic... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Presentation List 2010 03 17 MSU GEDD Next Gen.pdf: 2010 03 17 MSU GEDD Next Gen.pdf <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Previous Research Leafhoppers: Evolution and Biochemistry of Natural Nanoparticles Leafhopper and SEM image of brochosomes on its wing Leafhoppers... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Custom Primer Design Overview While there are tools available for automatically designing primers (such as the Primer BLAST) often specialized PCR applications, such... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Day 1: Plating the Mixed Population 1. Find microsatellite containing strains in the 80... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Allelic exchange using pKOV or pKOV style vectors Before beginning part 1: design primers 1 Insert should be ~1kb with approximately 500bp on either side of mutation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Using Emulsions to Select by Yield Background Evolution in suspension culture proceeds by selecting for those strains that grow most rapidly, quickly depleting the... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Mutation Rates from Genome Resequencing Motivation: You have re sequenced several genomes after a mutation accumulation or adaptive evolution experiment. How do... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Materials Description Cat # Price Qiagen RNeasy Protect Bacteria Mini Kit (50) 74524 $386.00 Invitrogen Superscript Plus Indirect cDNA Labeling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Evolution Experiments Introduction An evolution experiment typically consists of evolving one or more ancestor strains in laboratory culture and assessing the types... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competition Assays for Evolvability Lines Serial transfer of 3.5 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Label Templates Templates for printing labels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strains Deleterious Mutations (UV Mutation Accumulation) Strain Fitness Ara relative to REL607 Marker Fitness Ara relative to Ara #8211; Designation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Primer Extension or Oligo Overlap Extension To stitch together large DNA templates from oligonucleotide fragments. Using Klenow Fragment (3 5 exo... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Pulsed Field Gel Electrophoresis Mapping Purpose: To validate mutations predicted from whole genome re sequencing and possibly discover rearrangements through repetitive... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Gel Electrophoresis Overview Gel electrophoresis separates DNA fragments based on size. Electric current moves the negatively charged DNA through the gel, which slows... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Total Alkaline Digest of Embedded RNA Linkages Materials 0.2 N Sodium Hydroxide (NaOH) Molarity and Normality are related by N nM For example... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Protocol Updates Needed this page on DNA sequencing needs to be updated and be made more for the general public than to the lab General guide for sorting... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 16S rRNA Sequencing to Identify Unknown Microbes Ever wonder what that contaminant in your culture is? Need to accurately identify an environmental isolate? Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Purifying 6xHis Tagged Proteins from E. Coli by Immobilized Metal Affinity Chromatograpy (IMAC) under Native Conditions SUPPLIES: Equipment: Nutator or Rocking... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Overview ADP1 Resources Genome Sequences type strain (GenBank Format) In general, use this genome as a reference when referring... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase expression... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> `In plate` / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony `in situ` (in plate) transformation with minimal... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/`rescue` from counter selection... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media amendments Preparation: Generally, prepare 30 50 mL of solution in a 50 mL conical tube. Then, filter sterilize solutions by pushing them through a 50 mL syringe... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Aphid Care and Protocols Rearing and Caring for Aphid Species Protocols and Primers <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Re engineering the ribosome for efficient selenoprotein synthesis SUPPLIES: Equipment:... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computer Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for your science... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computing Environment Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Lactobacillus `Firm 5` The Lactobacillus `Firm 5` clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Fluctuation Tests Introduction This protocol is for doing a Luria Delbr... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Getting Started with Lab Techniques General molecular lab techniques Engineering: A Primer to Get You Started General microbiology lab techniques... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Intracellular Reactive Oxygen Species (ROS) This procedure is commonly utilized to quantify ROS. For more information about limitations associated with this... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Leafhopper Care and Protocols Rearing and Caring for Leafhopper Species Leafhopper species are kept in BugDorms (BugDorm 4F3030 and 4F2222). We have the following... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Learn Biocomputing General Resources / Courses Software Carpentry https://software carpentry.org/lessons/ Code Academy https://www.codecademy.com/ edX Computer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media Recipes When making media, make sure the autoclave bin you`re using contains water (DI or tap) at least half an inch deep to help prevent excess water loss... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Introduction This protocol was inspired (after failed site directed mutagenesis attempts using Quikchange) by the protocol listed here at the Colgate website here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by `twitching`. 1L Final Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> PA: Lac Papillation Agar Make 10 Minimal A Salts. 10 Minimal A Salts 1L Component MW 80 g Potassium Phosphate (dibasic) K2HPO... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Burst Size of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates Overnight stock of permissive bacterial host... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator Gel Electrophoresis 50 TAE (Tris Acetate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 1416: 4 hydroxybenzoic acid medium (for JJ 1b, Bacillus sp.) 1L 4L Component 4.25 g 17.0 g Potassium Phosphate (dibasic) K2HPO4 trihydrate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> ABMS: Acinetobacter Minimal Succinate Courtesy of the Averhoff lab, with modifications for available reagents. To make standard ABMS, combine the following pre sterilized... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blood Heart Infusion Agar Heart Infusion Agar supplemented with sterile Sheep`s Blood. Used for the cultivation of fastidious organisms (Bee gut microbiome species... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.5L 5L Component MW 2.67 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> M9 Minimal Medium 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MC: Minimal Citrate Prepared the same as MG: Minimal Glucose with the following changes: No glucose 4.5 g/L Sodium Citrate (trisodium, dihydrate) <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> S2 Used for Acinetobacter Recipe for 900mL (Autoclave in three separate bottles 300mL each) Bottle 1 (Erlenmeyer flask: 300mL) 300mL Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Special Media <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Stab Agar Making agar stabs for storage and transport of bacterial strains. 1L Component 10 g Tryptone 5 g Yeast extract 10 g Sodium... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 1 L flask: 500 mL Component 5 g Tryptone 500 mg Yeast Extract 2.5 g NaCl 8 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified double stranded DNA product from template DNA. In addition to the template, the reactions... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strain Database Table Description Barrick lab strains are stored in a database on UT Box, accessible after login via this link. column example description... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Which polymerase is right for me? Types of polymerase NEB polymerases may be purchased from the NEB freezer, which is located in the Biomedical Research Supply Core... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> _... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> UV mutagenesis of Bacteria Determination of Optimal UV treatment This procedure is used to determine optimal treatment which will be used for library generation.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Pseuodmonas syringae (PSY) Pseudomonas syringae (PSY) comprises many species of bacteria that live on or within different plant species, as noted... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia marcescens Serratia marcescens is a gram negative pathogenic bacteria known for its distinctive red pigmentation. While it is not found in... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Vibrio natriegens (Vmax) Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Legend: Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Animations Saves a series of generated images to GIF, Flash, video, HTML, or PDF (LaTeX) formats. Installation install.packages(`animation`) library(animation)... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR Note: Once you... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Characteristics of the E. coli Genome The Origin of DNA Replication ( oriC ) is not at position zero (0... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Research Listen to an introduction to our synthetic biology research:Evolution and Engineering Bee Guts (EBRC in Translation Podcast) Watch a public... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Science Quotations The price of a metaphor is eternal vigilance. ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Images for use on other pages... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Software Also check out our GitHub code repositories: http://plannotate.barricklab.org pLannotate (Plasmid Annotation)Automated annotation of engineered... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Subtle Grammatical Usage Notes aka Common mistakes when writing scientific papers and grants. Usage Alternate / Alternative Alternate means `every other... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki Administrator Group Set GROUP JeffreyBarrick Set ALLOWTOPICCHANGE TWikiAdminGroup (Note: Set the members of TWiki Administrator Group in GROUP... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Local TWiki Preferences favicon: Attach a favicon.ico to a web`s WebPreferences or add a FAVICON setting to WebPreferences Set FAVICON ///favicon... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> asdasdf JeffreyBarrick 20 Jun 2009 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .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 wk0a504iaux... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blue Oyster Mushrooms Total Elapsed Time: ~10 days <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> RNA Structure Mutual Information Overview: What do these programs do? information between columns in a sequence alignment of structured RNAs can provide evidence... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Bar of TopMenuSkin Top bar of TopMenuSkin, replacing WebTopBar. var twTopMenuBarCloseTimer null; var twTopMenuBarTimerMsec 1000; function twToggleTopMenuBar... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The University of Texas at Austin :: iGEM Team The Barrick lab sponsored and mentored the UT Austin iGEM team from 2012 2025 when we were located at The University... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To be filled out later.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki`s Lab web The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the faster 1 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Contact Research Publications Team Protocols Reference Software UT Austin Mol Biosciences... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> /Lab The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Statistics for Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Menu of Lab Web This topic defines the menu structure of the Lab web, used by the TopMenuSkin . Barrick Lab Homepage Contact Information... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the verbose 1 . <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> Number of topics: 305 <--/patternSearchResultCount--> | ||||||||
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Revision 12001-08-08 - PeterThoeny
Results from Lab web retrieved at 02:07 (GMT)<--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Autoclave Sterilization Overview Autoclaves heat their contents to 121... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Genetic Code (NCBI Translation Table 11) AAs FFLLSSSSYY CC WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts M M MMMM M Base1 TTTTTTTTTTTTTTTTCCCCCCCCC... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemical List Fisher supplied item name item # size/qty CAS Chemalert storage code Agar BP1423 2 2 kg 9002 18 0 gray... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Coding 101: Best Practices for Writing Software Build Your Development Suite To code effectively, you need an appropriate development setup. We recommend at least... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Attach graphics to be used throughout the site here. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Contact Information Jeffrey E. Barrick, PhD John A. Hannah Distinguished ProfessorDepartment of Microbiology, Genetics, Immunology Department... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Education 2006 Ph.D, Molecular Biophysics and Biochemistry (MB B), Yale University 2001 B.S., Chemistry, California Institute of Technology. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General guidelines for sorting bacteria with fluorescence activated cell sorting (FACS) FACS is a powerful tool for high throughput analysis and manipulation of complex... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Former Front Page Images Genome dynamics in experimental evolution Read article at NRG Flying Spaghetti Monster meet syntheticbiology? Caffeine addicted E. coliSupport... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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! <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> How to clean glassware LTEE flasks and lids LTEE glassware... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Handling High Molecular Weight DNA Introduction Long read sequencing, such as Oxford Nanopore or PacBio sequencing, is becoming increasingly important for genome... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Naturally Transformable Bactera Acinetobacter baylyi ADP1 Overview History Physiology Molecular Biology Natural Competence Deinococcus radiodurans R1 Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Journal Club Archive April 13, 2015 Dacia : Reijns, Martin A M, Harriet Kemp, James Ding, Sophie Marion de Proc... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Lab Rules UNDER CONSTRUCTION <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Interested in research in the Barrick lab? We are always looking for outstanding undergraduate students, graduate students, and postdocs who are interested in experimental... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lab Notebook Best Practices Notebook Setup Preferred Platform: Benchling Electronic Notebooks Have an administrator add you to the Barrick Lab organization on Benchling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To Do Receive equipment and find locations to store items EHS inspection Find out about material sample transfer process CraigBarnhart 09 Feb 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Links Advice for graduate students (Saw this linked by Cooper) for Young Scientists (Andrew Hendry) Serial Mentor (Claus Wilke`s Blog... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bioinformatics Master List This page is a master list of bioinformatics software frequently used in the lab, and their purposes. It also includes additional notes... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570007/ <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Megaprimer whole plasmid cloning aka MEGAWHOP cloning aka Overlap Extension PCR cloning We describe two approaches to MEGAWHOP in this protocol page. Approach... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Michael Hammerling Michael Hammerling MichaelHammerling 22 Nov 2011 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Microplate Reader Quick Start Best Practices 1 Follow typical best practice for experimental design. Utilize technical replicates from the same biological sample... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Space for temporary attachments... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: News Archive August 2014: Graduate student Michael Hammerling is awarded a UT Graduate School Named Continuing Fellowship. April 2014: Graduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Past Barrick Lab Members Devin Lake Lucio Navarro Vibhav Iyengar Anna Grove Krisha Chaudhari Korin Jones Dr. Patrick Lariviere Dr. Dennis Mishler Alexa Morton Cameron... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Phenol/chloroform extraction Extracting genomic bacterial DNA from pellet with phenol/chloroform with a combined EtOH precipitation step for salt/SDS/small nucleic... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Presentation List 2010 03 17 MSU GEDD Next Gen.pdf: 2010 03 17 MSU GEDD Next Gen.pdf <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Previous Research Leafhoppers: Evolution and Biochemistry of Natural Nanoparticles Leafhopper and SEM image of brochosomes on its wing Leafhoppers... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Custom Primer Design Overview While there are tools available for automatically designing primers (such as the Primer BLAST) often specialized PCR applications, such... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> (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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Day 1: Plating the Mixed Population 1. Find microsatellite containing strains in the 80... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Allelic exchange using pKOV or pKOV style vectors Before beginning part 1: design primers 1 Insert should be ~1kb with approximately 500bp on either side of mutation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Using Emulsions to Select by Yield Background Evolution in suspension culture proceeds by selecting for those strains that grow most rapidly, quickly depleting the... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Mutation Rates from Genome Resequencing Motivation: You have re sequenced several genomes after a mutation accumulation or adaptive evolution experiment. How do... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Materials Description Cat # Price Qiagen RNeasy Protect Bacteria Mini Kit (50) 74524 $386.00 Invitrogen Superscript Plus Indirect cDNA Labeling... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Evolution Experiments Introduction An evolution experiment typically consists of evolving one or more ancestor strains in laboratory culture and assessing the types... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Competition Assays for Evolvability Lines Serial transfer of 3.5 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Label Templates Templates for printing labels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strains Deleterious Mutations (UV Mutation Accumulation) Strain Fitness Ara relative to REL607 Marker Fitness Ara relative to Ara #8211; Designation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Primer Extension or Oligo Overlap Extension To stitch together large DNA templates from oligonucleotide fragments. Using Klenow Fragment (3 5 exo... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Pulsed Field Gel Electrophoresis Mapping Purpose: To validate mutations predicted from whole genome re sequencing and possibly discover rearrangements through repetitive... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Gel Electrophoresis Overview Gel electrophoresis separates DNA fragments based on size. Electric current moves the negatively charged DNA through the gel, which slows... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Total Alkaline Digest of Embedded RNA Linkages Materials 0.2 N Sodium Hydroxide (NaOH) Molarity and Normality are related by N nM For example... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Protocol Updates Needed this page on DNA sequencing needs to be updated and be made more for the general public than to the lab General guide for sorting... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 16S rRNA Sequencing to Identify Unknown Microbes Ever wonder what that contaminant in your culture is? Need to accurately identify an environmental isolate? Overview... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Purifying 6xHis Tagged Proteins from E. Coli by Immobilized Metal Affinity Chromatograpy (IMAC) under Native Conditions SUPPLIES: Equipment: Nutator or Rocking... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Overview ADP1 Resources Genome Sequences type strain (GenBank Format) In general, use this genome as a reference when referring... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase expression... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> `In plate` / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony `in situ` (in plate) transformation with minimal... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/`rescue` from counter selection... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media amendments Preparation: Generally, prepare 30 50 mL of solution in a 50 mL conical tube. Then, filter sterilize solutions by pushing them through a 50 mL syringe... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Aphid Care and Protocols Rearing and Caring for Aphid Species Protocols and Primers <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SeanLeonard 14 Sep 2017 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Re engineering the ribosome for efficient selenoprotein synthesis SUPPLIES: Equipment:... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computer Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for your science... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Computing Environment Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Lactobacillus `Firm 5` The Lactobacillus `Firm 5` clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Fluctuation Tests Introduction This protocol is for doing a Luria Delbr... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Getting Started with Lab Techniques General molecular lab techniques Engineering: A Primer to Get You Started General microbiology lab techniques... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Intracellular Reactive Oxygen Species (ROS) This procedure is commonly utilized to quantify ROS. For more information about limitations associated with this... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Leafhopper Care and Protocols Rearing and Caring for Leafhopper Species Leafhopper species are kept in BugDorms (BugDorm 4F3030 and 4F2222). We have the following... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Learn Biocomputing General Resources / Courses Software Carpentry https://software carpentry.org/lessons/ Code Academy https://www.codecademy.com/ edX Computer... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Media Recipes When making media, make sure the autoclave bin you`re using contains water (DI or tap) at least half an inch deep to help prevent excess water loss... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Introduction This protocol was inspired (after failed site directed mutagenesis attempts using Quikchange) by the protocol listed here at the Colgate website here... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by `twitching`. 1L Final Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> PA: Lac Papillation Agar Make 10 Minimal A Salts. 10 Minimal A Salts 1L Component MW 80 g Potassium Phosphate (dibasic) K2HPO... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Burst Size of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates Overnight stock of permissive bacterial host... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator Gel Electrophoresis 50 TAE (Tris Acetate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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 ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 1416: 4 hydroxybenzoic acid medium (for JJ 1b, Bacillus sp.) 1L 4L Component 4.25 g 17.0 g Potassium Phosphate (dibasic) K2HPO4 trihydrate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> ABMS: Acinetobacter Minimal Succinate Courtesy of the Averhoff lab, with modifications for available reagents. To make standard ABMS, combine the following pre sterilized... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blood Heart Infusion Agar Heart Infusion Agar supplemented with sterile Sheep`s Blood. Used for the cultivation of fastidious organisms (Bee gut microbiome species... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.5L 5L Component MW 2.67 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> M9 Minimal Medium 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> MC: Minimal Citrate Prepared the same as MG: Minimal Glucose with the following changes: No glucose 4.5 g/L Sodium Citrate (trisodium, dihydrate) <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> S2 Used for Acinetobacter Recipe for 900mL (Autoclave in three separate bottles 300mL each) Bottle 1 (Erlenmeyer flask: 300mL) 300mL Component... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Special Media <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Stab Agar Making agar stabs for storage and transport of bacterial strains. 1L Component 10 g Tryptone 5 g Yeast extract 10 g Sodium... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 1 L flask: 500 mL Component 5 g Tryptone 500 mg Yeast Extract 2.5 g NaCl 8 g... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified double stranded DNA product from template DNA. In addition to the template, the reactions... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Strain Database Table Description Barrick lab strains are stored in a database on UT Box, accessible after login via this link. column example description... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Which polymerase is right for me? Types of polymerase NEB polymerases may be purchased from the NEB freezer, which is located in the Biomedical Research Supply Core... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> _... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> UV mutagenesis of Bacteria Determination of Optimal UV treatment This procedure is used to determine optimal treatment which will be used for library generation.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Pseuodmonas syringae (PSY) Pseudomonas syringae (PSY) comprises many species of bacteria that live on or within different plant species, as noted... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia marcescens Serratia marcescens is a gram negative pathogenic bacteria known for its distinctive red pigmentation. While it is not found in... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Working with Vibrio natriegens (Vmax) Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Legend: Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Animations Saves a series of generated images to GIF, Flash, video, HTML, or PDF (LaTeX) formats. Installation install.packages(`animation`) library(animation)... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR Note: Once you... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Characteristics of the E. coli Genome The Origin of DNA Replication ( oriC ) is not at position zero (0... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Research Listen to an introduction to our synthetic biology research:Evolution and Engineering Bee Guts (EBRC in Translation Podcast) Watch a public... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Science Quotations The price of a metaphor is eternal vigilance. ... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Images for use on other pages... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab :: Software Also check out our GitHub code repositories: http://plannotate.barricklab.org pLannotate (Plasmid Annotation)Automated annotation of engineered... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Subtle Grammatical Usage Notes aka Common mistakes when writing scientific papers and grants. Usage Alternate / Alternative Alternate means `every other... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki Administrator Group Set GROUP JeffreyBarrick Set ALLOWTOPICCHANGE TWikiAdminGroup (Note: Set the members of TWiki Administrator Group in GROUP... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Local TWiki Preferences favicon: Attach a favicon.ico to a web`s WebPreferences or add a FAVICON setting to WebPreferences Set FAVICON ///favicon... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> asdasdf JeffreyBarrick 20 Jun 2009 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .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 wk0a504iaux... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Blue Oyster Mushrooms Total Elapsed Time: ~10 days <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> RNA Structure Mutual Information Overview: What do these programs do? information between columns in a sequence alignment of structured RNAs can provide evidence... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Bar of TopMenuSkin Top bar of TopMenuSkin, replacing WebTopBar. var twTopMenuBarCloseTimer null; var twTopMenuBarTimerMsec 1000; function twToggleTopMenuBar... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> The University of Texas at Austin :: iGEM Team The Barrick lab sponsored and mentored the UT Austin iGEM team from 2012 2025 when we were located at The University... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> To be filled out later.... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> TWiki`s Lab web The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> .within page container{ display: flex; flex wrap: wrap; / allows stacking when narrow / gap: 1rem; / space between blocks / background... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the faster 1 <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Barrick Lab Contact Research Publications Team Protocols Reference Software UT Austin Mol Biosciences... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> /Lab The 1 web of TWiki. TWiki is a Web Based Collaboration Platform for the Enterprise. <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Statistics for Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> Top Menu of Lab Web This topic defines the menu structure of the Lab web, used by the TopMenuSkin . Barrick Lab Homepage Contact Information... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> See also the verbose 1 . <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> <--/twikiTopRow--> 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... <--/twikiSummary--> <--/twikiBottomRow--> <--/patternSearchResult--> Number of topics: 305 <--/patternSearchResultCount--> |
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