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=== [[Lab Floor Plan (with list of materials)]] === | |||
== | === [[Detailed Lab Task Descriptions]] === | ||
== General microbiology protocols == | == General microbiology protocols == | ||
Line 11: | Line 10: | ||
===[[Freezing Aliquots]]=== | ===[[Freezing Aliquots]]=== | ||
===[[Competition Assays]]=== | ===[[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]]=== | |||
===[[SOE PCR (Splicing by Overlap-Extension)]]=== | |||
===[[Qubit dsDNA Broad Range Assay]]=== | |||
===[[Preparing Sanger Sequencing (Eurofins)]]=== | |||
===[[Preparing Plasmid Sequencing (plasmidsaurus)]]=== | |||
===[[Creating Lac- E. coli Mutants]]=== | |||
== ''Streptococcus pneumoniae'' protocols == | |||
===[[Dual Layer Assays]]=== | |||
===[[Streptococcus DNA Extraction - Genome Prep]]=== | |||
===[[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 mutans'' protocols == | |||
===[[Streptococcus mutans Growth]]=== | |||
===[[Streptococcus mutans Transformation]]=== | |||
===[[Streptococcus mutans Transformation Media Recipe (SMUR)]]=== | |||
== ''Myxococcus xanthus'' protocols == | |||
===[[Media Protocols]]=== | |||
===[[Culture Cells from a Frozen Stock]]=== | |||
===[[Making a Broth Culture from an Agar Plate]]=== | |||
===[[Updated Liquid Biological Waste Disposal Protocol (BSL1)]]=== | |||
===[[Generating Frozen Stocks of Strains]]=== | |||
===[[Measure Absorbance of M. xanthus Culture]]=== | |||
===[[Generate St Curve for OD600 to Cells/mL conversion]]=== | |||
===[[Development Assay on Agarose Plates]]=== | |||
===[[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]]=== | |||
===[[Plate Colonies Using CTTSA]]=== | |||
===[[Electroporation and Plating of M. xanthus transformants]]=== | |||
===[[M. xanthus genomic DNA extraction with Zymo (yellow) kit]]=== | |||
===[[Image Analysis in Fiji]]=== | |||
===[[Prepping a Submerged Culture]]=== | |||
===[[Heat Fixing and Staining]]=== | |||
===[[Propidium Iodide Staining on Agar Plates]]=== | |||
===[[Spore Assay]]=== | |||
== Phage protocols == | |||
===[[Media and Passaging]]=== | |||
===[[Plaque Assays with Soft Agar]]=== | |||
===[[Serial Dilutions of Phage]]=== | |||
===[[Calculating Virus Titre]]=== | |||
===[[Measuring Burst Size]]=== | |||
== [[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]] == | |||
== [[Working with GitHub]]== | |||
== ''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]]=== | |||
== ''Arabidopsis thaliana'' protocols == | |||
===[[Creating Sterile Agar Plates]]=== | ===[[Creating Sterile Agar Plates]]=== | ||
===[[ | ===[[Sterile Seeding Protocol]]=== | ||
===[[Germination Protocol for ''Arabidopsis thaliana'' Seeds in Non-Sterile Experiments]]=== | ===[[Germination Protocol for ''Arabidopsis thaliana'' Seeds in Non-Sterile Experiments]]=== | ||
===[[Growth Stage Phenotype Definitions]]=== | ===[[Growth Stage Phenotype Definitions]]=== | ||
===[[Growth Conditions for ''Arabidopsis thaliana'']]=== | ===[[Growth Conditions for ''Arabidopsis thaliana'']]=== | ||
===[[Measuring Light with HOBO Data Loggers]]=== | ===[[Measuring Light with HOBO Data Loggers]]=== | ||
===[[Inoculation of ''Arabidopsis thaliana'' with Microbes]]=== | ===[[Inoculation of ''Arabidopsis thaliana'' with Microbes]]=== | ||
===[[Removal and DNA Extraction of Phyllosphere Microbes]]=== | ===[[Removal and DNA Extraction of Phyllosphere Microbes]]=== | ||
===[[ARISA]]=== | ===[[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]]=== | |||
== | == 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 == | == Getting started with MediaWiki == |
Latest revision as of 11:06, 19 June 2024
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
SOE PCR (Splicing by Overlap-Extension)
Qubit dsDNA Broad Range Assay
Preparing Sanger Sequencing (Eurofins)
Preparing Plasmid Sequencing (plasmidsaurus)
Creating Lac- E. coli Mutants
Streptococcus pneumoniae protocols
Dual Layer Assays
Streptococcus DNA Extraction - Genome Prep
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 mutans protocols
Streptococcus mutans Growth
Streptococcus mutans Transformation
Streptococcus mutans Transformation Media Recipe (SMUR)
Myxococcus xanthus protocols
Media Protocols
Culture Cells from a Frozen Stock
Making a Broth Culture from an Agar Plate
Updated Liquid Biological Waste Disposal Protocol (BSL1)
Generating Frozen Stocks of Strains
Measure Absorbance of M. xanthus Culture
Generate St Curve for OD600 to Cells/mL conversion
Development Assay on Agarose Plates
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
Plate Colonies Using CTTSA
Electroporation and Plating of M. xanthus transformants
M. xanthus genomic DNA extraction with Zymo (yellow) kit
Image Analysis in Fiji
Prepping a Submerged Culture
Heat Fixing and Staining
Propidium Iodide Staining on Agar Plates
Spore Assay
Phage protocols
Media and Passaging
Plaque Assays with Soft Agar
Serial Dilutions of Phage
Calculating Virus Titre
Measuring Burst Size
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
Working with GitHub
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
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
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.