Tonight we discussed various project options that would utilize next gen sequencing. We have to submit 500 word abstracts on why we deserve a MiSeq system.  We came to the conclusion that it is extremely important that we emphasize the citizen science movement and community projects.  If we have a MiSeq system at BioC, we would be able to open it up to other DIYers, subsidizing the cost of runs, growing the DIY community, and allowing for continual data collection.  We would make the data open source allowing for all to analyze the data including our own very talented computer programmers!

We came up with multiple project ideas:

1. Bioluminescence: Mapping unknown luciferase pathway genes.

2. Barcoding Dandelions: This would all for folks of all ages to collect dandelions from all over, isolate the dna, and correlate the genome sequence to the location in which the dandelions were found.  This could also be used to track herbicide resistance etc...

3. Monitor Invasive Species: Sequence hypervariable regions of invasive species and monitor generations over time.  

4. Microbiome/Oral Microbiome: Map the microbiome of insect species - find bacteria that digests plants etc... and/or the microbiome of the mouth. Determine what bacterial populations are present in the mouth - compare between different people/ages/demographics etc... use a way to potentially treat/monitor disease.

5. Soil Bacteria: Isolating new bacteria from soil in order to find new antibiotics and/or bacteria that have enzymes to digest biomasses

6. Phage: Map the phageome in the Bay Area and find novel phage that could be used for medical treatments such as against human bacterial infections.

7. Isolate and sequence hydrocarbon degrading bacteria from gas station soils and Gulf coast samples. [Patrik]

Proposals:

Hydrocarbon degraders (Patrik D'haeseleer)

We propose a community/citizen science project to study the bacterial community composition of hydrocarbon contaminated soils, isolate bacterial degraders of polycyclic aromatic hydrocarbons, and produce draft sequence one selected bacterial isolate.

Participants will collect hydrocarbon contaminated soils near gas stations. We will also use our contacts with DIYbio groups and hackerspaces in the Gulf coast to obtain oil contaminated sand, soil, and wetlands sediment, and a freshly collected tarball. We will extract DNA using a FastDNA spin kit for soil (MP Biomedicals), and perform amplicon sequencing of the V4 region of the 16S SSU rRNA (Caparosa et al. ISME J., 2012), using barcodes to multiplex multiple samples per MiSeq run.

Selected samples will be enriched for polycyclic aromatic hydrocarbons (PAHs) by inoculating them on autoclaved garden soil supplemented with a small amount of naphthalene, and characterized using 16S rRNA sequencing.. (Napthalene is relatively low in toxicity, and readily available in the form of traditional moth balls, and we will publish the protocol for this experiment online for other DIYbio groups to replicate.)

Isolates will be derived from the initial samples and enrichment cultures, identified by 16S sequencing. , and tested for naphthalene degrading activity. A final isolate will be selected for draft de novo sequencing. Genome assembly and analysis will be performed using the publicly accessible RAST and IMG platforms, followed by metabolic network analysis and curation on SRI Logic’s Pathway Tools.

These experiments will cover several workshops taught at BioCurious. One workshop will focus on sampling of contaminated soils, 16S amplification and sequencing. A second workshop will focus on streaking and characterizing isolates, following the framework of the Introductory College Level Experience in Microbiology (http://qb3.berkeley.edu/synberc/iclem.html) summer program at the Joint BioEnergy Institute. A third workshop will focus on genome assembly and analysis. Although these workshops will be open to amateurs of all stripes, each activity will also be performed by some of the highly experienced members at BioCurious, so we get both community involvement, and at least some high-quality results.