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<center>
<center>
=Equipment=
=Equipment=
</center>
</center>
==Dionex IC==
==Dionex IC==
::Overview
::'''[[Richard Lab:IC overview|Overview]]'''
::Eluent Preparation
::'''[[Richard Lab:IC eluents|Eluent Preparation]]'''
::[[Richard Lab:IC standards|Standard Preparation]]
::'''[[Richard Lab:IC standards|Standard Preparation]]'''
==Dionex ASE==
==Dionex ASE==
::Overview
::'''[[Richard Lab:ASE overview|Overview]]'''
==Anaerobic Chamber==
==Anaerobic Chamber==
::'''[[Richard Lab:anaerobic chamber|Overview]]'''
==YSI Analyzer==
::'''[[YSI 2700 Select Biochemistry Analyzer|Overview]]
::'''[[Quantification of glucose]]


<center>
<center>
=Methods=
=Methods=
</center>
</center>
==Biomass Protocols==
::'''[[Silage protocols|Silage Protocols]]'''
::'''[[Biomass compositional analysis|Biomass Compositional Analysis]]'''
::'''[[Richard_Lab:_NDF|NDF (Neutral Detergent Fiber) Determination]]'''
::'''[[Richard_Lab:ADF|ADF (Acid Detergent Fiber) Determination]]'''
::'''[[Richard_Lab:ADL|ADL (Acid Detergent Lignin) Determination]]'''
::'''[[Richard Lab:Dilute-acid pretreatment|Dilute-Acid Pretreatment of Biomass]]'''
::'''[[Richard Lab:Enzymatic Hydrolysis of Biomass|Enzymatic Hydrolysis of Biomass]]'''
::'''[[Quantification of glucose|Quantification of Glucose]]'''
::'''[[Richard Lab:SSCF|Simultaneous Saccharification and Co-Fermentation (SSCF)]]'''
::'''[[SSF Ethanol production]]'''
::'''[[Acidification of C and N Samples using Tartic Acid]]'''
==Enzymatic Screens and Assays==
::'''[[Feruloyl Esterase Protocols|Ferulic Acid Esterase Protocols]]'''
::'''[[Laccase Protocols]]'''
::'''[[Xylanase Protocols]]'''
::'''[[Beta-galactosidase assay|Beta-galactosidase (LacZ) Assay]]'''
::'''[[Beta-galactosidase Screen]]
::'''[[Beta-glucuronidase protocols|Beta-glucuronidase (GusA) Protocols]]'''
::'''[[Cellulase assays]]'''
==Molecular/Synthetic Biology==
==Molecular/Synthetic Biology==


::'''[[Richard Lab:Amplified Insert Assembly|Amplified Insert Assembly]]'''
::'''[[Richard Lab:Bio-Brick Formats|Bio-Brick Formats]]'''
::'''[[Richard Lab:PCR|PCR Protocols]]'''
::'''[[Richard Lab:Site Directed Mutagenesis| Site Directed Mutagenesis]]'''
::'''[[Miniprep/GET_buffer | Plasmid Extraction]]'''
::'''[[Miniprep/GET_buffer | Plasmid Extraction]]'''
::'''[[DNA Quantification]]'''
::'''[[DNA Quantification]]'''
::'''[[Ethanol_precipitation_of_nucleic_acids | DNA Concentration]]'''
::'''[[Ethanol_precipitation_of_nucleic_acids | DNA Concentration]]'''
 
::'''[[DNA Synthesis from Oligos|DNA Synthesis]]'''
::'''[[DNA Synthesis from Oligos]]'''
::'''[[Richard_Lab:Restriction_Digest | Restriction Digestion]]'''
 
::'''[[Richard_Lab:Restriction_Digest | Bio-Brick Digest]]'''
 
::'''[[Partial Restriction Digest]]'''
::'''[[Partial Restriction Digest]]'''
::'''[[Richard_Lab:_Agarose_Gel_Electrophoresis| Agarose Gel Electrophoresis]]'''
::'''[[Richard_Lab:_Agarose_Gel_Electrophoresis| Agarose Gel Electrophoresis]]'''
::'''[[Polyacrylamide Gel Electrophoresis]]'''
::'''[[Polyacrylamide Gel Electrophoresis]]'''
::'''[[DNA_Gel_extraction | Gel Extraction of DNA]]'''
::'''[[DNA_Gel_extraction | Gel Extraction of DNA]]'''
::'''[[Richard_Lab:Ligation|Ligation]]'''
::'''[[Richard_Lab:Ligation|Ligation]]'''
 
::'''[[In vitro modification of DNA for L. plantarum|Preparation of Shuttle-vectors for transformation]]'''
::'''[[Transforming Lactococcus lactis]]'''
::'''[[Richard_Lab:Preparing_electrocompetent_cells|Making Electro-competent ''E. coli'']]'''
::'''[[Richard Lab:Electroporation of E. coli|Electro-transformation of ''E. coli'']]'''
::'''[[Richard Lab:Electroporation of E. coli|Electro-transformation of ''E. coli'']]'''
::'''[[Lactobacillus transformation (Speer 2012)|Electro-transformation of ''L. Plantarum'']]'''
::'''[[Chromosomal Integration]]'''


::'''Electro-transformation of Lactobacillus'''
==Manure Storage and Emissions Analysis==
 
::'''[[Richard_Lab:Preparing_electrocompetent_cells|Making Electro-competent Cells]]'''
 
::'''Promoter Probing'''
 
==Biomass Composition Analysis==
 
::'''[[Richard_Lab:_NDF|NDF (Neutral Detergent Fiber)]]'''
 
::'''[[Richard_Lab:ADF|ADF (Acid Detergent Fiber)]]'''
 
::'''[[Richard_Lab:ADL|ADL (Acid Detergent Lignin)]]'''
 
::'''Acetyl Bromide Lignin Analysis'''
 
::'''TMAH Lignin Analysis'''


::'''[[Richard Lab:Gas_Flux|Measuring and Analyzing Gas-Flux from a Surface]]'''
::'''[http://www.abe.psu.edu/bioconversion/biofilters_setup.ppt Setting Up Biofilters in the Field].
::'''Formatting Data from Data Logger'''
:::*The following is a set of [http://www.abe.psu.edu/bioconversion/temperature/instructions.htm instructions on how to use macros] to transform a data set from [http://www.abe.psu.edu/bioconversion/temperature/config1.htm configuration 1] to [http://www.abe.psu.edu/bioconversion/temperature/config2.htm configuration 2].
::'''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.


==Manure Storage and Emissions Analysis==
==Compost Analysis==
 
::'''[[Chemical Oxygen Demand]]'''
====Measuring and Analyzing Gas-Flux from a Surface====
::'''[[Compost Pile Monitoring]]'''
*gaseous emission data is collected using a [http://www.abe.psu.edu/bioconversion/gas_sampling.ppt static flux chamber and a photoacoustic sensor].
::'''[[CO2 Respiration]]'''
*an [http://www.abe.psu.edu/bioconversion/programPAS.xls Excel program] is then used to extract relevant data (from the continuous data collected by the photoacoustic sensor every minute). The same program also calculates the flux of selected gases from the tested surface, using Pedersen's equation (2001).
::'''[[Manure and Compost Sampling Preparation Protocols]]'''
*selected data are copied and pasted as values into a compiled data set
::'''[[Acidification of compost with 0.5 N HCl]]'''
*a regression analysis is performed to evaluate the effect of time, biofilter treatment, and other input variables on the flux level of each analyzed gas: ammonia, methane, carbon dioxide, nitrous oxide and water vapor. The Sagata Regression Pro software (ltd) is used: go to regression > pick inputs > pick outputs > chose data types (categorical or continuous) > chose regression model (to evaluate interactions create input variables made of factors evaluate for interaction amongst them, multiplied by each other) > go to output, get response vs. factors for preliminary graphs > choose indicative title for the output sheet > click ok.
::'''[[Free Air Space Testing Procedure]]'''
*the statistical analysis output is interpreted: the first Anova table shows possible treatment effect. The "term significance" table shows effect of individual factors (or interactions).
 
====Method used to set up biofilters on a surface in the field====
[http://www.abe.psu.edu/bioconversion/biofilters_setup.ppt How biofilters are set up].
 
====To Reconfigure data from data logger into a compatible format====
*The following is a set of [http://www.abe.psu.edu/bioconversion/temperature/instructions.htm instructions on how to use macros] to transform a data set from [http://www.abe.psu.edu/bioconversion/temperature/config1.htm configuration 1] to [http://www.abe.psu.edu/bioconversion/temperature/config2.htm configuration 2].
 
 
Back to [[Richard_Lab | Richard Lab]]
Back to [[Richard_Lab | Richard Lab]]

Latest revision as of 13:35, 10 January 2012

Back to Richard Lab Main Page

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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