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====== Marine Microbiology Methods Page ======
 
This site contains some common methods/protocols in microbial ecology.  The material originates from many different places and some of it may be taken directly from other sources.  I try to give credit where I can, but don't always explicitly state my source. So please use caution. The information is not intended for distribution and was written as a document for internal use only.

The manual currently has the following content :





===== CHAPTER 1 - Bootcamp =====
 
  * [[Bootcamp:Pipette School]]





===== CHAPTER 2 - DNA extraction and quantification =====
 
  * [[DNA extraction:DNA extraction from seawater - John Paul]]
  * [[DNA extraction:DNA extraction from seawater - Lee Kerkoff]]	
  * [[DNA extraction:DNA extraction from anaerobic cultures - Amy Callaghan]]	
  * [[DNA extraction:DNA purification by CsCl centrifugation]]
  * [[DNA extraction:Agarose gel electrophoresis]]
  * [[DNA extraction:Dissolved DNA using HOECHST 33258]]	




===== CHAPTER 3 - Community Analysis =====

  * [[Community Analsyis:TRFLP]]
  * [[Community Analsyis:DGGE]]
  * [[Community Analsyis:SIP]]
  * [[Community Analsyis:Purification of DNA from CsCl fractions]]

===== CHAPTER 4 - Field Work =====
 
  * [[Cruises:Cleaning carboys]]
  * [[Cruises:Chlorophyll a (Welschmeyer method)]]	
  * [[Cruises:Primary productivity]]	
  * [[Cruises:Whole cell RubisCO assay - Tabita]]



===== CHAPTER 5 - Phytoplankton culture =====
 
  * [[Phytoplankton:Phytoplankton glassware]]	
  * [[Phytoplankton:Media and Cultures]]
  * [[Phytoplankton:SN Medium]]





===== CHAPTER 6 - Gene expression by mRNA analysis=====
 
  * [[Gene Expression:Gene expression Introduction]]	
  * [[Gene Expression:RNAse free working with RNA]]
  * [[Gene Expression:Making glassware RNAse free]]	
  * [[Gene Expression:RNA electrophoresis – formaldehyde gel]]	
  * [[Gene Expression:RNA extraction from SW using RNEasy]]	
  * [[Gene Expression:Reagent for riboprobing]]
  * [[Gene Expression:Making a 35S labeled riboprobe]]	
  * [[Gene Expression:Hybridizing filters using riboprobes]]	
  * [[Gene Expression:Stripping riboprobes from DNA filters]]	
  * [[Gene Expression:Cleaning the Dot-Blotter]]
  * [[Gene Expression:RNA Loading Buffer]]	
  * [[Gene Expression:Quantitative PCR]]	
  * [[Gene Expression:Optimizing Primers for SYBR qPCR]]
  * [[Gene Expression:Nuclease QC assay for TaqMan qPCR probes]]	








===== CHAPTER 7 - PCR and Cloning =====
 
  * [[Cloning:Commonly used Primers and Probes]]
  * [[Cloning:TA cloning]]
  * [[Cloning:A-tailing old PCR products for TA cloning]]
  * [[Cloning:Blunt-end cloning]]
  * [[Cloning:QIAquick PCR purification protocol]]
  * [[Cloning:Inverse PCR]]
  * [[Cloning:Competent Cells]]






===== CHAPTER 8 - Manipulation of HMW DNA =====
 
  * [[Genomics:Preparation of dialysis bags]]
  * [[Genomics:DNA containing agar plugs]]
  * [[Genomics:Partial digestion of DNA in agar plugs]]
  * [[Genomics:Colony Filter Arrays]]




===== CHAPTER 9 - Media =====
 
  * [[Media:LB]]
  * [[Media:Terrific Broth]]
  * [[Media:SOB]]
  * [[Media:SOC]]
  * [[Media:2xYT]]
  * [[Media:ASWJP]] (Paul)
  * [[Media:ASW]] (Wyman)	
  * [[Media:Seawater with instant ocean]] 


===== CHAPTER 10 - Viruses =====
 
  * [[Viruses:SYBR-Gold viral direct counts]]
  * [[Viruses:Prophage induction]]
  * [[Viruses:Cyanophage enumeration]]








===== CHAPTER 11 - Anaerobic Microbiology =====

  * [[Anaerobic Microbiology:How to build a degassing station - Neil Q. Wofford]]
  * [[Anaerobic Microbiology:Cleaning glassware]]
  * [[Cysteine Sulfide (2.5%)]]
  * [[Anaerobic Microbiology:BT Medium]]
  * [[Anaerobic Microbiology:SL-10A Trace Metal Solution]]
  * [[Anaerobic Microbiology:Selenite Tungstate Solution]]
  * [[Anaerobic Microbiology:Resazurin Solution]]
  * [[Anaerobic Microbiology:MS3 Salt Mix]]
  * [[Anaerobic Microbiology:SL-10 Trace Element solution]]
  * [[Anaerobic Microbiology:VB-1 Vitamin Solution]]
  * [[Anaerobic Microbiology:Trace Metal Solution - Widdel et al.]]

===== CHAPTER 12 - Miscellaneous Methods =====

  * Plasmid prep using alkaline lysis	
  * Plasmid prep using SV minipreps	
  * [[Miscellaneous:Colony lift]]
  * Bacterial production by 3H Leucine	







===== CHAPTER 13 - Buffers/Reagents/Solutions =====

  * [[Buffers and Reagents:0.5 M EDTA]]
  * [[Buffers and Reagents:Ethidium Bromide]]
  * [[Buffers and Reagents:IPTG]]
  * [[Buffers and Reagents:β-mercaptoethanol (BME)]]
  * [[Buffers and Reagents:Phosphate Buffered Saline (PBS)]]
  * [[Buffers and Reagents:1 M Potassium Acetate pH 7.5]]
  * [[Buffers and Reagents:3 M Sodium Acetate]]
  * [[Buffers and Reagents:10 % SDS]]
  * [[Buffers and Reagents:100 % TCA]]
  * [[Buffers and Reagents:1 M Tris]]
  * [[Buffers and Reagents:X-Gal]]
  * [[Buffers and Reagents:DAPI]]

  * [[Buffers and Reagents:SSC]]
  * [[Buffers and Reagents:TE]]
  * [[Buffers and Reagents:STE]]
  * [[Buffers and Reagents:TAE]]
  * [[Buffers and Reagents:TBE]]

  * [[Buffers and Reagents:1 M DTT (dithiothreitol)]]
  * [[Buffers and Reagents:Gel loading buffers]]
  * [[Buffers and Reagents:Antibiotics]]
  * [[Buffers and Reagents:HOECHST 33258]]
  * [[Buffers and Reagents:Phenol]]

  * [[Buffers and Reagents:Proteinase K]]