Thanks for the response. To answer some of your questions: I'll be graduating with a MSc in chemical engineering and biotechnology this summer and am doing my thesis project in a molecular biology lab, so I'm comfortable with all techniques required. I've read a number of papers on both 16S RNA analysis and DNA tests for meat product species identification. As for scientific value, I don't have any illusions or want anyone to have any: There's none. I think something can be scientifically uninteresting but still worth doing though.

In vivo cloning is strictly regulated where I live, so sequencing would be performed on PCR products. The 16S RNA gene(s) would be amplified and sequenced from the near beginning. Using universal primers 27F and 1492 R gives an amplicon size of ~1500 bp. An amplicon size/sequence read of the 600 first bp are enough to cover hypervariable regions V1-V3 (an overview of the E. coli 16S RNA sequence is shown by Baker and Cowan, 2003: http://www.sciencedirect.com/science/article/pii/S0167701203002276).

I don't know why I mentioned 16S RNA when talking about meat, thanks for catching that mistake. For animal samples, species-specific DNA may be detected by amplification of species-specific sequences or identification may be attempted amplification and sequencing of the cytochrome b gene. See for example http://library-resources.cqu.edu.au/JFS/PDF/vol_48/iss_1/JFS2002128_481.pdf

I agree that culturing environmental samples might be challenging. "Just a few" would be exactly my goal, but I understand people might not find that interesting enough. Analysis of meat samples seems like a simpler and perhaps more interesting prospect. Sample material is easily available, and the methods may be of a bit wider interest. Everyone wants to know what they're eating, right? As recent events in Europe show, food companies and the government can not necessarily be trusted to guarantee the content of processed food products.

Actually, I think the cost estimates are about right for primer and sequencing costs. As mentioned, I'm discussing ideas for a *small* project. Single-read sequencing costs about €4/reaction, so for €200 you'd get about 50 sequencing reactions (not including shipping, but there's a collection point nearby). For the same amount you would get a fair selection of primers which should be enough to last for several hundred reactions each. Mind you, I would not be looking to cover all costs of running a hobby lab - just the project-specific expenses. So PCR reagents, purification kits etc. would not be included. I already spent quite a lot of money on that, but there's not so much left now.

Here's some relevant papers, for anyone who's curious:

Weisburg et al. 1991: 16S ribosomal DNA amplification for phylogenetic study. http://jb.asm.org/content/173/2/697.full.pdf+html

Klindworth et al. 2013: Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. http://nar.oxfordjournals.org/content/41/1/e1.full?sid=e66b42ac-a309-47cf-8cd1-94e1229a098e

Lahiff et al. 2001: Species-specific PCR for the identification of ovine, porcine and chicken species in meta and bone meal (MBM). http://www.ncbi.nlm.nih.gov/pubmed/11284433

Lago et al. 2011: Authentication of species in meat products by genetic techniques. http://link.springer.com/article/10.1007%2Fs00217-010-1417-1?LI=true#page-1


Regards,
Jarle P

kl. 15:02:57 UTC+1 torsdag 21. mars 2013 skrev jarlemag følgende:

Hi. For a while now, I've been thinking of a couple of molecular biology hobby projects regarding species identification of both microbial samples and consumer meat I would like to try.
However, the costs for primer synthesis and sequencing reactions can be, while not too bad, a bit of a strain on a student budget.
So, do you think there would be a willingness or interest in the DIY community to crowd-fund small investigative projects? Already owning basic equipment, as I do, I figure that for a couple hundred $/€, one can do a fair bit of interesting stuff. I imagine about $300-$500 is a reasonable cost range for a small project, but I might of course cover parts of the costs myself, thus decreasing the funding goal for contributions.

Possible projcects I have in mind are:
 *Culturing environmental microbial followed by 16S RNA analysis. What (culturable) organisms live in different places?
 *Testing and evaluating PCR methods for  DIY species identification of meat. (this was discussed on the mailing list a little while ago). Could also include 16S RNA sequencing.

What do you think? Is it worth trying to start a KickStarter for something like this? It would of course have more details than the above descriptions, with article references and an experimental plan to be followed. Results would be made available on OpenWetware

Best regards,

Jarle Pahr

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