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]]===
+===[[Fixing Cells for Microscope/Flow Cytometry Work]]===
 == Cloning and gene manipulation ==
@@ Line 20: / Line 24: @@
 ===[[Digest and Ligation]]===
 ===[[Gel Purification]]===
-Using the NEB #T1020 Monarch Kit
-For a detailed protocol, or to download the full manual, visit www.neb.com/T1020
-BEFORE YOU BEGIN:
-*Add 4 volumes of ethanol (2 95%) to one volume of DNA Wash Buffer. (Needed to do the first time that the kit is used).
-*All centrifugation steps should be carried out at 16,000 xg (-13,000 RPM).
-*Please note: column holds 800 ul.
-PROTOCOL STEPS:
-# Run your digested DNA on an agarose gel. Use the 'wide combs' that will allow for more volume inside of them. Run the gel slowly (40-60 volts) for better band separation.
-# Weigh empty micro-centrifuge tubes, and write the weight on the outside of the tube.
-# Using the UV illuminator in Exx (across from Superlab), excise the DNA fragment from the agarose gel, taking care to trim excess agarose. Transfer to the 1.5 ml micro-centrifuge tube. Minimize exposure to UV light. Weigh the gel slice + micro-centrifuge tube and calculate the weight of just the agarose chunk. Agarose in a tube can be frozen at -20 and extracted later — this is a potential stopping point in the protocol.
-# Turn on the small water bath and set to 50°C. Put in the DNA Elution Buffer bottle, ensuring that it does not tip over in the water bath.
-# Add 4 volumes of Gel Dissolving Buffer to the gel slice (e.g., 400 ul buffer per 100 ul or 100 mg agarose).
-# Incubate the sample at 50°C, vortexing periodically until the gel slice is completely dissolved (generally 5-10 minutes). For DNA fragments > 8 kb, an additional 1.5 volumes of water should be added after the slice is dissolved to mitigate the tighter binding of larger pieces of DNA (e.g., 100 ul gel slice: 400 ul Gel Dissolving Buffer: 150ul water).
-# Insert column into collection tube and load sample onto the column with the mixture. Remember that the column can hold only 800ul maximum; you may need to load 800ul; spin; discard flow-through; load remaining liquid; spin again. Spin for 1 minute, then discard flow-through.
-# Re-insert column into collection tube. Add 200 ul DNA Wash Buffer and spin for 1 minute. Discarding flow-through.
-# Repeat step 5 by adding 200 ul DNA Wash Buffer and spin for 1 minute.
-# Transfer column to a clean 1.5 ml micro-centrifuge tube. Use care to ensure that the tip of the column does not come into contact with the flow-through. If in doubt, re-spin for 1 minute.
-# Add 6ul - 20ul of DNA Elution Buffer at 50°C to the center of the matrix. Wait for 1 minute, and spin for 1 minute to elute DNA. Molecular grade water (pH 7-8.5) can also be used to elute the DNA. Yield may slightly increase if a larger volume of DNA Elution Buffer is used, but the DNA will be less concentrated.
 ===[[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]]===
-== ''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]]===
 == ''Streptococcus pneumoniae'' protocols ==
 ===[[Dual Layer Assays]]===
-===[[Streptococcus DNA Extraction]]===
+===[[Streptococcus DNA Extraction - Genome Prep]]===
+===[[Streptococcus CRISPR-Cas9 Editing]]===
 ===[[Streptococcus Transformation]]===
 ===[[Streptococcus Growth Curve Protocol]]===
@@ Line 76: / Line 51: @@
 ===[[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 ==
@@ Line 88: / 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 102: / 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