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]]===
+===[[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]]===
-.	Turn on heat block to 42 degrees.
+===[[Streptococcus mutans Transformation Media Recipe (SMUR)]]===
-.	Turn on shaking water bath to 37 degrees.
-.	Spray a beaker with ethanol, go get ice from the second floor imaging room (across from lab).
-.	Label 1 1.5mL microfuge tubes with for each of your experimental groups. (3 tubes for pUC18, pUC18-Empty, water 1 Control). From the -80 freezer: get enough competent cells to transfer 250 uL cells in each of the previously labeled experimental group tubes. Each freezer tube has 100uL cells. For negative control (water) you can use 100uL cells.
-.	Transfer 250uL of bacterial cells to each of your ligated and empty plasmid microfuge tubes. Transfer 100uL to the water tube. Spin for 5 minutes at 10,000 rpm at 4 degrees C. This will cause the bacterial cells to collect in a pellet at the bottom of your tube.
+== ''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]]===
-.	Remove the supernatant without disrupting the bacterial pellets. Add 25 µL of ice cold 1x TSS buffer/tube (10uL for the water tube) and resuspend the cells by flicking the tube gently, then place the tubes on ice. [TSS buffer is LB with detergents and salts which will permeabilize cell membranes, allowing the plasmid to enter the bacterial cells].
+===[[Rehydrating New Primers]]===
-.	Add 10µL (25ng) of ligated plasmid DNA to the cells in ligated plasmid group. Also add 25ng of empty vector to the cells in the empty vector tubes. Add 10uL of sterile water to the negative control tubes. Place back on ice. As you add these small volumes, mix gently with tip of your pipette.
+===[[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! ==
-.	Allow the cells to incubate for 40 minutes on ice. Do not mix the tubes during this incubation period.
+*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.
-.	After 40 mins, carry the ice bucket to a heat block pre-heated to 42 degrees and heat shock the cells for exactly 45 seconds, then immediately return the tubes to ice for 2 minutes. Add 250 ml of room temperature LB to each of your tubes.
+*This Week in Virology
+**By Vincent Racaniello
-.	Incubate your microfuge tubes with cells in ‘floaties’ for one hour in the shaking water bath, set to 37°C. Make sure tubes are completely shut.
+*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.
-.	After 60 minutes, plate cells. If you so choose, you can divide the volume of ~250µL LB/cells/DNA mixture into a plate of 10µL, 100µL, and the rest of the volume in order to see which volume grows the optimal amount of cells. Spread plates with sterile beads, and then pour used beads into white container with funnel (by the sink).
+*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 65: / 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