Richard Lab:protocols

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(Molecular/Synthetic Biology)
Current revision (15:35, 10 January 2012) (view source)
(Compost Analysis)
 
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Back to [[Richard_Lab | Richard Lab]]
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Back to [[Richard_Lab | Richard Lab Main Page]]
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<center>
=Equipment=
=Equipment=
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::'''[[Richard Lab:ASE overview|Overview]]'''
::'''[[Richard Lab:ASE overview|Overview]]'''
==Anaerobic Chamber==
==Anaerobic Chamber==
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::'''[[Richard Lab:anaerobic chamber|Overview]]'''
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==YSI Analyzer==
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::'''[[YSI 2700 Select Biochemistry Analyzer|Overview]]
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::'''[[Quantification of glucose]]
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<center>
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=Methods=
=Methods=
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==Molecular/Synthetic Biology==
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==Biomass Protocols==
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::'''[[Richard Lab:New Standard Assembly| New Standard Assembly]]'''
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::'''[[Silage protocols|Silage Protocols]]'''
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::'''[[Biomass compositional analysis|Biomass Compositional Analysis]]'''
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::'''[[Richard_Lab:_NDF|NDF (Neutral Detergent Fiber) Determination]]'''
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::'''[[Richard_Lab:ADF|ADF (Acid Detergent Fiber) Determination]]'''
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::'''[[Richard_Lab:ADL|ADL (Acid Detergent Lignin) Determination]]'''
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::'''[[Richard Lab:Dilute-acid pretreatment|Dilute-Acid Pretreatment of Biomass]]'''
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::'''[[Richard Lab:Enzymatic Hydrolysis of Biomass|Enzymatic Hydrolysis of Biomass]]'''
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::'''[[Quantification of glucose|Quantification of Glucose]]'''
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::'''[[Richard Lab:SSCF|Simultaneous Saccharification and Co-Fermentation (SSCF)]]'''
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::'''[[SSF Ethanol production]]'''
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::'''[[Acidification of C and N Samples using Tartic Acid]]'''
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::'''[[Richard Lab:Bio-Brick Formats|Bio-Brick Formats]]'''
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==Enzymatic Screens and Assays==
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::'''Richard Lab PCR Protocols'''
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::'''[[Feruloyl Esterase Protocols|Ferulic Acid Esterase Protocols]]'''
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::'''[[Laccase Protocols]]'''
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::'''[[Xylanase Protocols]]'''
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::'''[[Beta-galactosidase assay|Beta-galactosidase (LacZ) Assay]]'''
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::'''[[Beta-galactosidase Screen]]
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::'''[[Beta-glucuronidase protocols|Beta-glucuronidase (GusA) Protocols]]'''
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::'''[[Cellulase assays]]'''
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==Molecular/Synthetic Biology==
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::'''[[Richard Lab:Amplified Insert Assembly|Amplified Insert Assembly]]'''
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::'''[[Richard Lab:Bio-Brick Formats|Bio-Brick Formats]]'''
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::'''[[Richard Lab:PCR|PCR Protocols]]'''
::'''[[Richard Lab:Site Directed Mutagenesis| Site Directed Mutagenesis]]'''
::'''[[Richard Lab:Site Directed Mutagenesis| Site Directed Mutagenesis]]'''
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::'''[[Miniprep/GET_buffer | Plasmid Extraction]]'''
::'''[[Miniprep/GET_buffer | Plasmid Extraction]]'''
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::'''[[DNA Quantification]]'''
::'''[[DNA Quantification]]'''
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::'''[[Ethanol_precipitation_of_nucleic_acids | DNA Concentration]]'''
::'''[[Ethanol_precipitation_of_nucleic_acids | DNA Concentration]]'''
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::'''[[DNA Synthesis from Oligos|DNA Synthesis]]'''
::'''[[DNA Synthesis from Oligos|DNA Synthesis]]'''
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::'''[[Richard_Lab:Restriction_Digest | Restriction Digestion]]'''
::'''[[Richard_Lab:Restriction_Digest | Restriction Digestion]]'''
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::'''[[Partial Restriction Digest]]'''
::'''[[Partial Restriction Digest]]'''
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::'''[[Richard_Lab:_Agarose_Gel_Electrophoresis| Agarose Gel Electrophoresis]]'''
::'''[[Richard_Lab:_Agarose_Gel_Electrophoresis| Agarose Gel Electrophoresis]]'''
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::'''[[Polyacrylamide Gel Electrophoresis]]'''
::'''[[Polyacrylamide Gel Electrophoresis]]'''
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::'''[[DNA_Gel_extraction | Gel Extraction of DNA]]'''
::'''[[DNA_Gel_extraction | Gel Extraction of DNA]]'''
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::'''[[Richard_Lab:Ligation|Ligation]]'''
::'''[[Richard_Lab:Ligation|Ligation]]'''
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::'''[[In vitro modification of DNA for L. plantarum|Preparation of Shuttle-vectors for transformation]]'''
::'''[[In vitro modification of DNA for L. plantarum|Preparation of Shuttle-vectors for transformation]]'''
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::'''[[Transforming Lactococcus lactis]]'''
::'''[[Richard_Lab:Preparing_electrocompetent_cells|Making Electro-competent ''E. coli'']]'''
::'''[[Richard_Lab:Preparing_electrocompetent_cells|Making Electro-competent ''E. coli'']]'''
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::'''[[Richard Lab:Electroporation of E. coli|Electro-transformation of ''E. coli'']]'''
::'''[[Richard Lab:Electroporation of E. coli|Electro-transformation of ''E. coli'']]'''
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::'''[[Lactobacillus transformation (Speer 2012)|Electro-transformation of ''L. Plantarum'']]'''
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::'''[[Preparation of Lactobacillus Competent Cells|Making Electro-competent ''L. plantarum'']]'''
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::'''[[Chromosomal Integration]]'''
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::'''[[Electrotransformation of Lactobacillus plantarum|Electro-transformation of ''L. Plantarum'']]'''
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::'''Chromosomal Integration'''
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==Enzymatic Screens and Assays==
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::'''[[Feruloyl Esterase Protocols|Ferulic Acid Esterase Protocols]]'''
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::'''[[Laccase Protocols]]'''
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::'''Xylanase Plate Screen'''
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::'''Xylanase Assay'''
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==Biomass Analysis==
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::'''[[Mini-Silo Sampling|Mini-Silo Sampling]]'''
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::'''[[Richard_Lab:_NDF|NDF (Neutral Detergent Fiber)]]'''
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+
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::'''[[Richard_Lab:ADF|ADF (Acid Detergent Fiber)]]'''
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::'''[[Richard_Lab:ADL|ADL (Acid Detergent Lignin)]]'''
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::'''Acetyl Bromide Lignin Analysis'''
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::'''TMAH Lignin Analysis'''
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::'''[[Richard Lab:Enzymatic Hydrolysis of Biomass|Enzymatic Hydrolysis of Biomass]]'''
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::'''Quantification of Glucose'''
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==Manure Storage and Emissions Analysis==
==Manure Storage and Emissions Analysis==
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::'''BOD, moisture and VS content'''
::'''BOD, moisture and VS content'''
:::*Organic matter samples are analyzed according to the following instructions for [http://www.abe.psu.edu/bioconversion/biofilter_characterization/BOD.htm BOD (Biological Oxygen Demand)] and [http://www.abe.psu.edu/bioconversion/biofilter_characterization/moisture_and_VS.htm moisture and Volatile Solids (organic matter) content] analysis.
:::*Organic matter samples are analyzed according to the following instructions for [http://www.abe.psu.edu/bioconversion/biofilter_characterization/BOD.htm BOD (Biological Oxygen Demand)] and [http://www.abe.psu.edu/bioconversion/biofilter_characterization/moisture_and_VS.htm moisture and Volatile Solids (organic matter) content] analysis.
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==Compost Analysis==
==Compost Analysis==
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::'''[[Manure and Compost Sample Preparation|Manure and Compost Sample Preparation]]'''
 
::'''[[Chemical Oxygen Demand]]'''
::'''[[Chemical Oxygen Demand]]'''
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::'''[[Compost Pile Monitoring]]'''
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::'''[[CO2 Respiration]]'''
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::'''[[Manure and Compost Sampling Preparation Protocols]]'''
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::'''[[Acidification of compost with 0.5 N HCl]]'''
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::'''[[Free Air Space Testing Procedure]]'''
Back to [[Richard_Lab | Richard Lab]]
Back to [[Richard_Lab | Richard Lab]]

Current revision

Back to Richard Lab Main Page

Contents

Equipment

Dionex IC

Overview
Eluent Preparation
Standard Preparation

Dionex ASE

Overview

Anaerobic Chamber

Overview

YSI Analyzer

Overview
Quantification of glucose

Methods

Biomass Protocols

Silage Protocols
Biomass Compositional Analysis
NDF (Neutral Detergent Fiber) Determination
ADF (Acid Detergent Fiber) Determination
ADL (Acid Detergent Lignin) Determination
Dilute-Acid Pretreatment of Biomass
Enzymatic Hydrolysis of Biomass
Quantification of Glucose
Simultaneous Saccharification and Co-Fermentation (SSCF)
SSF Ethanol production
Acidification of C and N Samples using Tartic Acid

Enzymatic Screens and Assays

Ferulic Acid Esterase Protocols
Laccase Protocols
Xylanase Protocols
Beta-galactosidase (LacZ) Assay
Beta-galactosidase Screen
Beta-glucuronidase (GusA) Protocols
Cellulase assays

Molecular/Synthetic Biology

Amplified Insert Assembly
Bio-Brick Formats
PCR Protocols
Site Directed Mutagenesis
Plasmid Extraction
DNA Quantification
DNA Concentration
DNA Synthesis
Restriction Digestion
Partial Restriction Digest
Agarose Gel Electrophoresis
Polyacrylamide Gel Electrophoresis
Gel Extraction of DNA
Ligation
Preparation of Shuttle-vectors for transformation
Transforming Lactococcus lactis
Making Electro-competent E. coli
Electro-transformation of E. coli
Electro-transformation of L. Plantarum
Chromosomal Integration

Manure Storage and Emissions Analysis

Measuring and Analyzing Gas-Flux from a Surface
Setting Up Biofilters in the Field.
Formatting Data from Data Logger
BOD, moisture and VS content

Compost Analysis

Chemical Oxygen Demand
Compost Pile Monitoring
CO2 Respiration
Manure and Compost Sampling Preparation Protocols
Acidification of compost with 0.5 N HCl
Free Air Space Testing Procedure

Back to Richard Lab

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