Main Page: Difference between revisions
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===[[Making a Broth Culture from an Agar Plate]]=== | ===[[Making a Broth Culture from an Agar Plate]]=== | ||
===[[Measure Absorbance of M. xanthus Culture]]=== | ===[[Measure Absorbance of M. xanthus Culture]]=== | ||
1. Turn on the spectrophotometer so it can warm up. | |||
2. Obtain one 13mm glass test tube for each sample that you want to measure density for, plus one to blank. | |||
3. Add 3mL of uncultured CTTYE growth media to the tube that will serve as your blank. | |||
4. Add 2.5mL of uncultured CTTYE to labeled sample test tubes, and add 0.5mL of bacterial culture to the correspondingly labeled tube. **Note, if your sample is particularly dilute, add 1mL culture and 2mL nutrient media for dilution** | |||
5. Blank the spectrophotometer with your blank tube. | |||
6. One at a time, vortex one tube of diluted culture, then immediately record the Absorbance value at 600nm. Repeat for each sample. | |||
7. Turn off the spectrophotometer if you are done and if no one else plans to use it relatively soon. | |||
8. To obtain OD600 from these Absorbance values, divide by a path length of 1.3cm (diameter of the test tubes). | |||
9. You can use the below equation to calculate cells/mL of your sample: | |||
Density (cells/mL) = 1.1x10^9 * (OD600) - 2.1x10^7 | |||
Note: for phenotype assays, use this cells/mL calculation to decide how to dilute or concentrate your sample accordingly. | |||
===[[Rehydrating New Primers]]=== | ===[[Rehydrating New Primers]]=== | ||
Revision as of 11:44, 25 May 2023
Lab Floor Plan (with list of materials)
Detailed Lab Task Descriptions
General microbiology protocols
Media Recipes
Reagent Recipes
Working with Antibiotics
Freezing -80 Stocks
Freezing Aliquots
Competition Assays
Generic PCR
Gradient PCR
Running DNA Gels
Running SDS-PAGE Gels
Western Blot
Protein Purification
Protein Sample Concentration
Fixing Cells for Microscope/Flow Cytometry Work
Cloning and gene manipulation
Commonly Used Plasmids
Plasmid Purification
Digest and Ligation
Gel Purification
Creating Competent E. coli Cells
Transformation
Transformation — non-competent E. coli
Gibson Assembly
Qubit dsDNA Broad Range Assay
Preparing Sanger Sequencing (Eurofins)
Preparing Plasmid Sequencing (plasmidsaurus)
Creating Lac- E. coli Mutants
Arabidopsis thaliana protocols
Creating Sterile Agar Plates
Sterile Seeding Protocol
Germination Protocol for ''Arabidopsis thaliana'' Seeds in Non-Sterile Experiments
Growth Stage Phenotype Definitions
Growth Conditions for ''Arabidopsis thaliana''
Measuring Light with HOBO Data Loggers
Inoculation of ''Arabidopsis thaliana'' with Microbes
Removal and DNA Extraction of Phyllosphere Microbes
ARISA
Measuring ''A. thaliana'' Phenotype using FIJI by Hand
DNeasy PowerSoil Protocol
Fiji Measurement
Making Boxes
Growing ''A. thaliana'' for Seed Harvest
Growing ''A. thaliana'' in Cut Pipet Tips
Streptococcus pneumoniae protocols
Dual Layer Assays
Streptococcus DNA Extraction
Streptococcus CRISPR-Cas9 Editing
Streptococcus Transformation
Streptococcus Growth Curve Protocol
Streptococcus Growth Curve and Cell Count in Liquid Media
Log Phase Growth Curve and Cell Count in Liquid Media
Streptococcus Bacteriocin (Dual Layer) Assays - Original
Streptococcus Bacteriocin (Dual Layer) Assays - Early Producer
Streptococcus Bacteriocin (Dual Layer) Assays - Light and Normal Target Lawns
Streptococcus Bacteriocin (Dual Layer) Assays - Finding Producer-Resistant Target Bacteria
Streptococcus Bacteriocin (Dual Layer) Assays - Finding Producer-Resistant Target Bacteria (6-well plate version)
Streptococcus suis protocols
Streptococcus suis Transformation
Measuring Absorbance in Streptococcus
Streptococcus DNA Extraction
Streptococcus Competence Induction
Peptide Synthesis
Peptide Cleavage
Mass Spectrometery
Plate Reader Assay and Growth Curve
Measuring Competence : Fixation and Flow Cytometry
Streptococcus mutans protocols
Streptococcus mutans Growth
Streptococcus mutans Transformation
Myxococcus xanthus protocols
Media Protocols
Culture Cells from a Frozen Stock
Making a Broth Culture from an Agar Plate
Measure Absorbance of M. xanthus Culture
1. Turn on the spectrophotometer so it can warm up.
2. Obtain one 13mm glass test tube for each sample that you want to measure density for, plus one to blank.
3. Add 3mL of uncultured CTTYE growth media to the tube that will serve as your blank.
4. Add 2.5mL of uncultured CTTYE to labeled sample test tubes, and add 0.5mL of bacterial culture to the correspondingly labeled tube. **Note, if your sample is particularly dilute, add 1mL culture and 2mL nutrient media for dilution**
5. Blank the spectrophotometer with your blank tube.
6. One at a time, vortex one tube of diluted culture, then immediately record the Absorbance value at 600nm. Repeat for each sample.
7. Turn off the spectrophotometer if you are done and if no one else plans to use it relatively soon.
8. To obtain OD600 from these Absorbance values, divide by a path length of 1.3cm (diameter of the test tubes).
9. You can use the below equation to calculate cells/mL of your sample:
Density (cells/mL) = 1.1x10^9 * (OD600) - 2.1x10^7
Note: for phenotype assays, use this cells/mL calculation to decide how to dilute or concentrate your sample accordingly.
Rehydrating New Primers
PCR Amplification from Genome
Ligation of PCR product into TOPO 2.1 vector
Transform competent E. coli cells
Colony PCR to confirm correct insert
Plasmid Isolation with BioBasic Miniprep Kit
EcoRI digest of plasmid
Phage protocols
Preparing the Soft Agar
Preparing the Plates
Serial Dilutions of Phage
Pouring the Plaques
Calculating Virus Titre
Notes and Troubleshooting
Interactions Protocols
Zone of Inhibition Assay
Remote Molecular Biology
Effect of Laboratory Protocols on Student Learning
Interesting Podcasts to Listen to When Doing Lab Work!
- This Week in Microbiology
- By Vincent Racaniello
- 5 stars! Amazing podcast to learn all about different types of microbiology research! This podcast goes pretty in depth into different current scientific papers so it is a great way to learn about current research.
- This Week in Virology
- By Vincent Racaniello
- Ologies
- By Alie Ward
- 5 stars! Great all around podcast made for a more general audience. There are many different episodes on scientific topics including Environmental Microbiology, Mathematical Biology, and much much more. This is a great podcast to explore different careers and listen to some amazing speakers.
- Overheard at National Geographic
- By National Geographic
- 4 stars! Great podcast to hear about the many wonders of the world. It also has shorter episodes and is a great way to learn about the world.
- Journey to the Micro Cosmos
- 3 stars! Short 10 minute episodes about cool microbes.
Waste Disposal
Cambridge protocols
Storage buffer
transformation of R5(2)-mCh-FL-BST and
expression
lysis and immobilization
Bio320 Microbe Species Wikipedia Pages
Getting started with MediaWiki
Consult the User's Guide for information on using the wiki software.