Main Page: Difference between revisions

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.

Retrieved from "http://microbes.sites.haverford.edu/MEE_wiki/index.php?title=Main_Page&oldid=3424"

@@ Line 1: / Line 1: @@
+=== [[Lab Floor Plan (with list of materials)]] ===
-== Laboratory information ==
+=== [[Detailed Lab Task Descriptions]] ===
 == General microbiology protocols ==
@@ Line 11: / Line 10: @@
 ===[[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)]]===
-== Phyllosphere protocols ==
+===[[Creating Lac- E. coli Mutants]]===
-===[[Creating Sterile Agar Plates]]===
-===[[Sterilization and Germination Protocol for ''Arabidopsis thaliana'' Seeds in Gnotobiotic Experiments]]===
-===[[Germination Protocol for ''Arabidopsis thaliana'' Seeds in Non-Sterile Experiments]]===
-===[[Growth Stage Phenotype Definitions]]===
-===[[Growth Conditions for ''Arabidopsis thaliana'']]===
-===[[Inoculation of ''Arabidopsis thaliana'' with Microbes]]===
-===[[Removal and DNA Extraction of Phyllosphere Microbes]]===
-===[[ARISA]]===
 == ''Streptococcus pneumoniae'' protocols ==
 ===[[Dual Layer Assays]]===
-===[[Streptococcus DNA Extraction]]===
+===[[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]]===
-Bacterial Transformation/Competence Measurements:
+== ''Arabidopsis thaliana'' protocols ==
-Natural Transformation with pNZ8048 plasmid w/antibiotic resistance ONLY
-.	Grow S. suis strain in an overnight culture containing Todd-Hewitt broth (THB) at 37 °C.
+===[[Creating Sterile Agar Plates]]===
-.	When ready to start the transformation experiment, dilute overnight culture 1:40 in pre-warmed media (37°C with no shaking).
+===[[Sterile Seeding Protocol]]===
-.	After 1 hour, measure the optical density of the culture using the spectrophotometer (refer to the protocol to use this machine on the Laboratory WIKI). Assuming favorable O.D, remove 100 uL of sample from the main culture and place in 1.5 mL epi tube.
+===[[Germination Protocol for ''Arabidopsis thaliana'' Seeds in Non-Sterile Experiments]]===
-a.	Competence Development occurs with the following ranges of bacterial densities (O.D. 0.035 to 0.058) MAX EFFICIENCY (O.C. 0.042). MAKE SURE THE BACTERIA FALLS WITHIN THIS RANGE
+===[[Growth Stage Phenotype Definitions]]===
-.	Add 1.2 mg of pNZ8048 plasmid in EB buffer (10 mM Tris-Cl, pH 8.5) to the epi tube.
+===[[Growth Conditions for ''Arabidopsis thaliana'']]===
-.	Immediately afterwards, add 5 uL of synthetic peptide [FINAL - 250 mM].
+===[[Measuring Light with HOBO Data Loggers]]===
-.	Incubate at 37 °C for 2 hours.
+===[[Inoculation of ''Arabidopsis thaliana'' with Microbes]]===
-.	Prepare solid agar media by adding 12 g/L to the medium.  Add either chloramphenicol (5mg/mL) or spectinomycin (100 mg/mL) to the medium.
+===[[Removal and DNA Extraction of Phyllosphere Microbes]]===
-.	Following incubation, add dilute samples to the THB/agar/antibiotic plates.
+===[[ARISA]]===
-a.	Make sure to also dilute and add bacteria to an Antibiotic (-) control plate
+===[[Measuring ''A. thaliana'' Phenotype using FIJI by Hand]]===
-.	Count the number of colonies in one quadrant each plate. Multiply by 4 to get an estimate of the total number of bacteria on each plate.
+===[[DNeasy PowerSoil Protocol]]===
+===[[Fiji Measurement]]===
+===[[Making Boxes]]===
+===[[Growing ''A. thaliana'' for Seed Harvest]]===
+===[[Growing ''A. thaliana'' in Cut Pipet Tips]]===
-Natural Transformation with pNZ8048 plasmid w/antibiotic resistance and red fluorescence genes
+== Cambridge protocols ==
-.	Inoculate S. suis strain in an overnight culture containing Todd-Hewitt broth (THB) at 37 °C.
+=== [[Storage buffer]] ===
-.	When ready to start the transformation experiment, dilute overnight culture 1:40 in pre-warmed media (37°C with no shaking).
+=== [[transformation of R5(2)-mCh-FL-BST and ]] ===
-.	After 1 hour, measure the optical density of the culture using the spectrophotometer (refer to the protocol to use this machine on the Laboratory WIKI). Assuming favorable O.D, remove 100 uL of sample from the main culture and place in 1.5 mL epi tube.
+=== [[expression]] ===
-a.	Competence Development occurs with the following ranges of bacterial densities (O.D. 0.035 to 0.058) MAX EFFICIENCY (O.C. 0.042). MAKE SURE THE BACTERIA FALLS WITHIN THIS RANGE
+=== [[lysis and immobilization]] ===
-.	Add 1.2 mg of pNZ8048 plasmid in EB buffer (10 mM Tris-Cl, pH 8.5) to the epi tube as well as 5 uL of synthetic peptide [FINAL - 250 mM].
-.	Incubate at 37 °C for 2 hours.
-Measuring Competence – Fixation and Flow Cytometry
+==[[Bio320 Microbe Species Wikipedia Pages]]==
-The movement of Bio Safety 2 equipment/lab material MUST be well regulated. Since the Flow cytometer is located in _________, we need to take extra precautions to prevent contamination via infectious agents when transporting the S. suis samples out of lab.
-Fixation
-.	Centrifuge 1.5 ml epi tube to collect cells and aspirate supernatant
-a.	https://www.cellsignal.com/contents/resources-protocols/flow-cytometry-protocol-(flow)/flow
-.	Resuspend the pelleted cells in 0.5-1 ml 1X PBS. Add formaldehydepe [FINAL 4%]
-.	Allow mixture to sit for 15 minutes at room temperature to fix.
-.	Wash via centrifugation with excess 1x PBS. Discard supernatant and resuspend in 0.5-1 ml 1X PBS.
-Flow Cytometry  (Room : ______)
-.	Upon Fixation, run the Flow cytometer machine (Refer to the Flow cytometry protocal).
-.	Record
-a.	Total number of particulates
-b.	Total number of red particulates
 == Getting started with MediaWiki ==

Main Page: Difference between revisions

Latest revision as of 11:06, 19 June 2024

General microbiology protocols

Cloning and gene manipulation

Streptococcus pneumoniae protocols

Streptococcus mutans protocols

Myxococcus xanthus protocols

Phage protocols

Interesting Podcasts to Listen to When Doing Lab Work!

Streptococcus suis protocols

Arabidopsis thaliana protocols

Cambridge protocols

Getting started with MediaWiki

Navigation menu

Search