Protocols

Here is a list of all the procedures we used this summer. Each contains a description and list of materials required.

General Protocols

• Agarose Gel Electrophresis
• Bacterial Transformation
• Construction Techniques
• Gel Extraction
• LB Agar Plates
• Overnight Cultures
• PCR Purification
• Plasmid Purification (from E. coli)
• Preparing Chemically Competent Cells (E. coli)
• Preparing Glycerol Stocks (E. coli)
• Rehydration of Registry DNA
• Taq PCR Protocol
• Bacterial Genomic DNA Purification
• Site-Directed Mutagenesis

Electrochemistry Protocols

• Electorchemistry protocols (include agarose bead making)

Desulfurization

• Desulphuirzation assay protocol
• Catalase/ hpac assays

Decarboxylation

• Petrobrick/oleT assay protocols/ GC MS

Denitrogenation

Decatecholization

• Decateccholzation (xylE and incubation with the Petrobrick)

Transposon

Kill Switch

• Rhamnose, magnesium and manganese, kill gene assay (nuclease)

Bioreactor

• Bioreactor assays

Modeling

• Modelling validation experiments