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 ==
+===[[Media Recipes]]===
+===[[Reagent Recipes]]===
+===[[Working with Antibiotics]]===
+===[[Freezing -80 Stocks]]===
+===[[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]]===
-== General microbiology protocols ==
+===[[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]]===
-== Phyllosphere protocols ==
-===Creating Sterile Agar Plates===
+== ''Streptococcus pneumoniae'' protocols ==
-====Version 1: Copied from ABRC's Seed Handling FAQ for Seed Handling====
+===[[Dual Layer Assays]]===
-'''Citation: ABRC Seed Handling FAQ PDF [https://abrc.osu.edu/sites/abrc.osu.edu/files/abrc_handling_seed_2013.pdf], accessed Sept. 23, 2018.'''
+===[[Streptococcus DNA Extraction - Genome Prep]]===
-. Add 4.31 g of Murashige and Skoog (MS) basal salt mixture and 0.5 g of 2-(N-Morpholino)
+===[[Streptococcus CRISPR-Cas9 Editing]]===
-ethanesulfonic acid (MES) to a beaker containing 0.8 L of distilled water and stir to dissolve.
+===[[Streptococcus Transformation]]===
-Add distilled water to final volume of 1 L. Check and adjust pH to 5.7 using 1M KOH.
+===[[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)]]===
-. Divide the media into two 1 L glass bottles, 500 mL in each. Add 5 g of agar granulated per
+== ''Streptococcus mutans'' protocols ==
-bottle. Keep the lid loose.
+===[[Streptococcus mutans Growth]]===
+===[[Streptococcus mutans Transformation]]===
-. Autoclave for 20 min at 121°C, 15 psi with a magnetic stirring device in the bottle.
+===[[Streptococcus mutans Transformation Media Recipe (SMUR)]]===
-. Place the bottles on a stir plate at low speed, and allow the agar medium to cool to 45-50°C
+== ''Myxococcus xanthus'' protocols ==
-(until the container can be held with bare hands).
+===[[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]]===
-. Starting from this step, perform all the steps in sterile conditions in a laminar flow hood. Add
+===[[Rehydrating New Primers]]===
-(optional) 1-2% sucrose and 1 mL Gamborg’s Vitamin Solution, stirring to evenly dissolve.
-Optional sucrose and vitamins should be added after autoclaving and only after the agar
-media cools, because vitamins are thermo-labile and 15-25% of the sucrose may be
-hydrolyzed to glucose and fructose at elevated temperatures. Plants grow more vigorously
-and quickly on media containing 1-2% of sucrose, however, fungal and bacterial
-contamination must be rigorously avoided by seed sterilization. Note that germination of
-some mutants might be delayed on sucrose-containing media.
-. Label the bottom of Petri plates with identification number or name, including the date.
+===[[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]]===
-. Pour enough media into plates to cover approximately half of the depth of the plate.
+== Phage protocols ==
+===[[Media and Passaging]]===
+===[[Plaque Assays with Soft Agar]]===
+===[[Serial Dilutions of Phage]]===
+===[[Calculating Virus Titre]]===
+===[[Measuring Burst Size]]===
-. Allow the plates to cool at room temperature for about an hour to allow the agar to solidify.
+== [[Interactions Protocols]] ==
-If the plates are not to be used immediately, wrap them in plastic and store at 4°C
+===[[Zone of Inhibition Assay]]===
-(refrigerator temperature). Covered plates, boxes, or tubes with solidified agar can be stored
-for several weeks at 4°C in a container that prevents desiccation.
-NOTE: Our lab will likely be using Magnenta GA-7 plant culture boxes rather than petri dishes - if any changes to this protocol are necessary due to this difference, it will be addressed in Version 2 of this protocol.
+== [[Remote Molecular Biology]] ==
-===Sterilization and Germination Protocol for ''Arabidopsis thaliana'' Seeds in Gnotobiotic Experiments===
-====Version 1: Based on ABRC's Seed Handling FAQ for Seed Handling====
-Citation: ABRC Seed Handling FAQ PDF [https://abrc.osu.edu/sites/abrc.osu.edu/files/abrc_handling_seed_2013.pdf], accessed Sept. 23, 2018.
+== [[Effect of Laboratory Protocols on Student Learning]] ==
+== Interesting Podcasts to Listen to When Doing Lab Work! ==
-# Surface sterilize seeds in microcentrifuge tubes by soaking for 20 min in 50% household bleach with the addition of 0.05% Tween®20 detergent.
+*This Week in Microbiology
-# Remove all bleach residue by rinsing 5-7 times with sterile distilled water.
+**By Vincent Racaniello
-## Add 1 mL of sterile distilled water to epitube and invert once; remove water and continue 5 more times.
+**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.
-#For planting of individual seeds at low density, adhere one seed to the tip of a pipette using suction, then release seed onto the agar in desired location. For planting seeds at higher densities, mix seeds in sterile distilled water (or 0.1% cooled top agar), pour onto plate, and immediately swirl to achieve even distribution. Use a sterile pipet tip to adjust the distribution and remove excess water. Allow the water or top agar to dry slightly before placing lid onto plate.
-# Seal with Micropore paper tape to prevent desiccation, while allowing slight aeration.
-# Place the plates at 4°C for 3 days. This cold treatment, also called stratification, will improve the rate and synchrony of germination. The use of an extended cold treatment of approximately 7 days is especially important for freshly harvested seeds, which have more pronounced dormancy. An extended cold treatment is also necessary for certain natural accessions (e.g., Dobra-1, Don-0, Altai-5, Anz-0, Cen-0, WestKar-4). Cold treatment of dry seeds is usually not effective in breaking dormancy.
-## NOTE: Experiments will be conducted that will determine what amount of cold stratification leads to maximum synchrony in seed germination time for Col-0 ''Arabidopsis thaliana'' seeds.
-===Growing Conditions for ''Arabidopsis thaliana''===
+*This Week in Virology
+**By Vincent Racaniello
-===Inoculation of ''Arabidopsis thaliana'' with Microbes===
+*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.
-===Removal of Phyllosphere Microbes===
+*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.
-===Extraction of Phyllosphere Microbial DNA===
+*Journey to the Micro Cosmos
+**3 stars! Short 10 minute episodes about cool microbes.
-===ARISA Protocol===
+== [[Waste Disposal]] ==
-== ''Streptococcus pneumoniae'' protocols ==
+== [[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 ==

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