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 Genomic DNA Purification
• 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
• Reviving Freeze-dried Bacterial Cultures from DMSZ
• Site-Directed Mutagenesis
• Taq PCR Protocol

Electrochemistry Protocols

• Electorchemistry protocols (include agarose bead making)

Desulfurization

• Desulfurization Assay
• Catalase assay
• HPAC assay

Decarboxylation

• Petrobrick/oleT assay protocols/ GC MS

Denitrogenation

• Organic Extraction
• Carbzazole Degradation Assay
• GC-MS Analysis

Decatecholization

• Decatecholization (xylE and incubation with the Petrobrick)

Transposon Mutant Library for Toxin Detection

• Transposon-Mediated Mutant Library Generation

Kill Switch

• Nuclease assay
• Magnesium circuit characterization
• Characterization of the mgtA circuit with S7 promoter

Bioreactor Assays

• Bacterial Growth Experiments

Belt Selection Tests:

• Hydrocarbon Test
• Tailings Test
• Bacteria Test
• Hydrocarbon Separation Test
• NA and Hexadecane Belt Skim Test

Modeling

• Modelling validation experiments