Crowdfunding small-scale projects

[jarlemag]

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

[Josiah Zayner]

You can start a Kickstarter for basically anything. That is your choice.

Here are the questions:

What skills and knowledge do you possess that would make people believe that you could accomplish one of the projects you propose?

Have you done literature searches? Environmental sampling and identifying species is constantly being done. What are you doing different and what will you add?

What part of the 16S do you plan to sequence? In which way do you plan to sequence this(through PCR products? cloning?)?

16S is prokaryotic what do you plan on sequencing for meats?

What would this add the the general knowledge of science or the DIYBio community?

Your budget seems low. For $300 - $500 I doubt you could culture and sequence more than a handful of bacterial strains probably very few if you have never done it before.

If someone had a very well thought out and planned research proposal and the skills to accomplish it. I think the DIYBio community would be supportive. As to how supportive I do not know.

[jarlemag]

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

[John Griessen]

On 03/21/2013 02:03 PM, jarlemag wrote:
> 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?

Crowd funders seem to want something tangible mostly, and for the low priced deliverables they will
donate, but want some trophy to show for it. You didn't mention you would productize anything, or offer diagnostic kits for sale,
so the crowd-funders might not come forth in droves.

[jarlemag]

Yes, I see your point. That would require some more work though, upping the project scale a bit. I don't feel able to commit to that. And I totally get that it's not tangible or interesting enough to attract $$$. So anyway, against better financial judgement, I just ordered a bunch of primers for both 16S RNA analysis and detection of horse and porcine meat. I'll make a post if anything interesting comes of it.

Thanks for the replies!

[mgaldzic]

Microryza.com maybe be a good choice for diybio projects with no tangible rewards to donors. 

Here in Seattle we're raising money to open HiveBio BioHacker Community Lab. https://www.microryza.com/projects/seattle-biohacker-space

It is going pretty well, there is just under a month left and we're at 36%

btw please help us out and post the link where you think someone interested might contribute. Also consider donating even very small donations help!

thanks,

mike

[Nathan McCorkle]

You could productize it by selling a meat ID service. 'Donate to my kickstarter and when it's funded send me a piece of meat/fish to be identified'

Possible problems for you to address:
Preserving a sample if needed
Shipping time could cause spoilage (preserve, ship with dry ice, only accept from people within a day or two shipping distance)

Would placing a meat slice in isoprop/eth-anol be ok for shipping, or would tissue-internal nucleases/bacteria screw this up?

23andme uses a buffer for shipping, but spit has a lot more surface area than a flesh chunk.

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[John Griessen]

On 03/21/2013 07:25 PM, mgaldzic wrote:
> Microryza.com maybe be a good choice for diybio projects with no tangible rewards to donors.
>
> Here in Seattle we're raising money to open HiveBio BioHacker Community
> Lab. https://www.microryza.com/projects/seattle-biohacker-space

.
.
.

even very
> small donations help!

Thanks for pointing out microryza.com, it does look like
they have attracted donors that don't require donor premiums
or a full product at a syndicated price.