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 10: / Line 9: @@
 ===[[Freezing -80 Stocks]]===
 ===[[Freezing Aliquots]]===
-===[[Plasmid Purification]]===
-===[[Creating Competent E. coli Cells]]===
 ===[[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]]===
-''The protocols for digest and ligation are from New England Biolab's "NEB Cloner" tool:'' http://nebcloner.neb.com/#!/redigest.
+===[[Creating Competent E. coli Cells]]===
+===[[Transformation]]===
+===[[Transformation — non-competent E. coli]]===
+===[[Gibson Assembly]]===
+===[[SOE PCR (Splicing by Overlap-Extension)]]===
+===[[Qubit dsDNA Broad Range Assay]]===
-'''Digestion: (1.5hrs)'''
+===[[Preparing Sanger Sequencing (Eurofins)]]===
+===[[Preparing Plasmid Sequencing (plasmidsaurus)]]===
-Prior to digesting DNA, be sure to purify the DNA amplified with Q5 polymerase to remove excess primers. Do this with the Zymogen DNA Clean and Concentrator Kits above the microwave.
+===[[Creating Lac- E. coli Mutants]]===
-Beforehand, turn on 37 degrees water bath and 65 degrees (for ligation heat inactivation). Calculate how much DNA you will need to add in order to digest 1ug. You can store this DNA in the -20 freezer for later use.
-#Go to the cloner tool link: http://nebcloner.neb.com/#!/redigest.
+== ''Streptococcus pneumoniae'' protocols ==
-#Simply select your digestion enzymes from dropdown menu for either a single or double restriction enzyme digestion. The buffer efficiency for each of the enzymes will be listed for the available NEB buffer options.
+===[[Dual Layer Assays]]===
-##Be aware of star* activity next to listed efficiency, indicating that the buffer may alter specificity of restriction enzymes. See baseball card binder for more information on star activity between pairs of restriction enzymes and their most efficient buffers.
+===[[Streptococcus DNA Extraction - Genome Prep]]===
-#Click on "Detailed Protocol" at the top middle of the page to see reagents and corresponding volumes to add to each reaction.
-Incubate reactions in a 1.5mL microcentrifuge tube for at least 1 hour.
+===[[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)]]===
-Between the digestion and ligation steps, '''purify (with the DNA Clean and Concentrator Kit) both the insert and plasmid vector DNA to remove restriction enzymes'''.
+== ''Streptococcus mutans'' protocols ==
+===[[Streptococcus mutans Growth]]===
+===[[Streptococcus mutans Transformation]]===
-'''Ligation: (0.5hrs)'''
+===[[Streptococcus mutans Transformation Media Recipe (SMUR)]]===
-''Navigate to the NEBioCalculator:'' https://nebiocalculator.neb.com/#!/ligation .
+== ''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]]===
-#There are three values to insert into the calculator.
+===[[Rehydrating New Primers]]===
-##Insert length in bp:
-##Vector DNA length
-##Vector DNA mass: enter 50ng.
-Go with the (3:1) insert:vector ratio values. Based on the amount of ng DNA resulting from the calculation, determine the appropriate volume of DNA to add to the ligation. BE SURE TO USE THE T4 DNA LIGASE (With 10X Ligase Buffer) protocol on NEB's Website: https://www.neb.com/protocols/1/01/01/dna-ligation-with-t4-dna-ligase-m0202
+===[[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]]===
-Thaw and resuspend ligase buffer at room temperature prior to performing reaction.
+== Phage protocols ==
+===[[Media and Passaging]]===
+===[[Plaque Assays with Soft Agar]]===
+===[[Serial Dilutions of Phage]]===
+===[[Calculating Virus Titre]]===
+===[[Measuring Burst Size]]===
-The exact volumes of vector and insert to add to the ligation reaction will depend on results from the NEBioCalculator.
+== [[Interactions Protocols]] ==
-#Add 2uL of 10X Ligase Buffer to a 0.6mL tube.
+===[[Zone of Inhibition Assay]]===
-#Add XX amount of insert
-#Add XX amount of vector
-#Add 1uL of T4 Ligase
-#Fill remaining volume with molecular grade water (in 4 degree fridge) to 20uL.
-#Gently mix the reaction by gently pipetting up and down.
-#Allow reaction to run for 10 minutes at room temperature.
-#Heat inactivate at 65 degrees for 10 minutes.
-#Either proceed to transformation, or store DNA in -20 degrees.
-===[[Transformation]]===
+== [[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.
-== Phyllosphere protocols ==
+*Journey to the Micro Cosmos
+**3 stars! Short 10 minute episodes about cool microbes.
-===[[Creating Sterile Agar Plates]]===
+== [[Waste Disposal]] ==
-===[[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'']]===
-===[[Measuring Light with HOBO Data Loggers]]===
-===[[Inoculation of ''Arabidopsis thaliana'' with Microbes]]===
+== [[Working with GitHub]]==
-===[[Removal and DNA Extraction of Phyllosphere Microbes]]===
-===[[ARISA]]===
-== ''Streptococcus pneumoniae'' protocols ==
-===[[Dual Layer Assays]]===
-===[[Streptococcus DNA Extraction]]===
 == ''Streptococcus suis'' protocols ==
+===[[Streptococcus suis Transformation]]===
 ===[[Measuring Absorbance in Streptococcus]]===
 ===[[Streptococcus DNA Extraction]]===
@@ Line 87: / Line 136: @@
 ===[[Measuring Competence : Fixation and Flow Cytometry]]===
-== [[Remote Molecular Biology]] ==
+== ''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]]===
-== [[Effect of Laboratory Protocols on Student Learning]] ==
+== 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 ==

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