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)]] ===
+=== [[Detailed Lab Task Descriptions]] ===
 == General microbiology protocols ==
@@ Line 11: / Line 13: @@
 ===[[Gradient PCR]]===
 ===[[Running DNA Gels]]===
+===[[Running SDS-PAGE Gels]]===
+===[[Western Blot]]===
 ===[[Protein Purification]]===
+===[[Protein Sample Concentration]]===
-===[[Sample Concentration]]===
+===[[Fixing Cells for Microscope/Flow Cytometry Work]]===
 == Cloning and gene manipulation ==
@@ Line 19: / Line 23: @@
 ===[[Plasmid Purification]]===
 ===[[Digest and Ligation]]===
+===[[Gel Purification]]===
 ===[[Creating Competent E. coli Cells]]===
 ===[[Transformation]]===
+===[[Transformation — non-competent E. coli]]===
 ===[[Gibson Assembly]]===
-===[[Creating Lac- E. coli Mutants]]===
+===[[SOE PCR (Splicing by Overlap-Extension)]]===
+===[[Qubit dsDNA Broad Range Assay]]===
-== Arabidopsis protocols ==
+===[[Preparing Sanger Sequencing (Eurofins)]]===
+===[[Preparing Plasmid Sequencing (plasmidsaurus)]]===
-===[[Creating Sterile Agar Plates]]===
+===[[Creating Lac- E. coli Mutants]]===
-===[[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]]===
-===[[Removal and DNA Extraction of Phyllosphere Microbes]]===
-===[[ARISA]]===
-===[[Measuring ''A. thaliana'' Phenotype using FIJI]]===
-===[[DNeasy PowerSoil Protocol]]===
-'''Before you Begin:'''
+== ''Streptococcus pneumoniae'' protocols ==
+===[[Dual Layer Assays]]===
+===[[Streptococcus DNA Extraction - Genome Prep]]===
-:Note: Upon arrival of the kit the CD2 solution should be stored at 2–8°C upon arrival. All other reagents and kit components should be stored at room temperature (15-25°C).
+===[[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]]===
-'''Material:'''
+===[[Streptococcus mutans Transformation Media Recipe (SMUR)]]===
-•  Quick-Start Protocol for the DNeasy PowerSoil Pro Kit as published in the
+== ''Myxococcus xanthus'' protocols ==
-May 2019 DNeasy® PowerSoil® Pro Kit Guide as seen here www.qiagen.com/HB-2495. The safety data sheet can be found here: www.qiagen.com/safety.
+===[[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]]===
-•   Before starting ensure that the PowerBead Pro Tubes rotate freely in the centrifuge without rubbing. If Solution CD3 has precipitated, heat at 60°C until precipitate dissolves. Perform all centrifugation steps at room temperature (15-25°C).
+===[[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]]===
-'''Protocol:'''
+== Phage protocols ==
+===[[Media and Passaging]]===
+===[[Plaque Assays with Soft Agar]]===
+===[[Serial Dilutions of Phage]]===
+===[[Calculating Virus Titre]]===
+===[[Measuring Burst Size]]===
-.	Spin the PowerBead Pro Tube briefly to ensure that the beads have settled at the bottom. Add up to 250 mg of soil and 800 pl of Solution CD1. Vortex briefly to mix.
+== [[Interactions Protocols]] ==
+===[[Zone of Inhibition Assay]]===
-.	Secure the PowerBead Pro Tube horizontally on a Vortex Adapter for 1.5-2 ml tubes (cat. no. 13000-V1-24). Vortex at maximum speed for 10 min. Note: If using the Vortex Adapter for more than 12 preps simultaneously, increase the vortexing time by 5-10 min.
+== [[Remote Molecular Biology]] ==
-:a.	For more information about other bead beating methods, see the “Protocol: Detailed" section of DNeasy® Power Soil® Pro Kit Handbook.
-.	Centrifuge the PowerBead Pro Tube at 15,000 x g for 1 min.
+== [[Effect of Laboratory Protocols on Student Learning]] ==
+== Interesting Podcasts to Listen to When Doing Lab Work! ==
-.	Transfer the supernatant to a clean 2 ml Microcentrifuge Tube (provided).
-:a.	Expect 500-600 pl. The supernatant may still contain some soil particles.
-.	Add 200 ul of Solution CD2 and vortex for 5 s.
-.	Centrifuge at 15,000 xg for 1 min at room temperature. Avoiding the pellet, transfer up to 700 ul of supernatant to a clean 2 ml Microcentrifuge Tube (provided).
-:a.  Expect 500-600 ul.
-.	Add 600 ul of Solution CD3 and vortex for 5 s.
-.	Load 650 ul of the lysate onto an MB Spin Column and centrifuge at 15,000 x g for 1 min.
-.	Discard the flow-through and repeat step 8 to ensure that all of the lysate has passed through the MB Spin Column.
-.  Carefully place the MB Spin Column into a clean 2 ml Collection Tube (provided). Avoid splashing any flow-through onto the MB Spin Column.
-.  Add 500 ul of Solution EA to the MB Spin Column. Centrifuge at 15,000 x g for 1 min.
-. Discard the flow-through and place the MB Spin Column back into the same 2 ml Collection Tube.
+*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.
-. Add 500 ul of Solution C5 to the MB Spin Column. Centrifuge at 15,000 x g for 1 min.
+*This Week in Virology
+**By Vincent Racaniello
-. Discard the flow-through and place the MB Spin Column into a new 2 ml Collection Tube (provided).
+*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.
-. Centrifuge at up to 16,000 x g for 2 min. Carefully place the MB Spin Column into a new 1.5 ml Elution Tube (provided).
+*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.
-. Add 50-100 ul of Solution C6 to the center of the white filter membrane.
+*Journey to the Micro Cosmos
+**3 stars! Short 10 minute episodes about cool microbes.
-. Centrifuge at 15,000 x g for 1 min. Discard the MB Spin Column. The DNA is now ready for downstream applications.
+== [[Waste Disposal]] ==
-:Note: We recommend storing the DNA frozen (-30 to -15°C or -90 to -65°C) as Solution Co does not contain EDTA. To concentrate DNA, please refer to the Troubleshooting Guide.
+== [[Working with GitHub]]==
-== ''Streptococcus pneumoniae'' protocols ==
-===[[Dual Layer Assays]]===
-===[[Streptococcus DNA Extraction]]===
-===[[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 suis'' protocols ==
@@ Line 119: / Line 136: @@
 ===[[Measuring Competence : Fixation and Flow Cytometry]]===
-== [[Interactions Protocols]] ==
+== ''Arabidopsis thaliana'' protocols ==
-===[[Zone of Inhibition Assay]]===
-== [[Remote Molecular Biology]] ==
+===[[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]] ==
-== Interesting Podcats to Listen to When Doing Lab Work! ==
 == Cambridge protocols ==
@@ Line 133: / Line 160: @@
 === [[expression]] ===
 === [[lysis and immobilization]] ===
 ==[[Bio320 Microbe Species Wikipedia Pages]]==

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