Talk:CH391L/S12/Bioprospecting

David M. Truong 16:24, 30 January 2012 (EST):If anyone else has examples of Genes/proteins used today found by prospecting, please add it and put a sentence description

• Ben Slater 17:27, 3 February 2012 (EST):Under Cellulosic Biomass degrading genes found in Cow Rumen, you say "These microbes cannot be cultured in lab." Given that the vast majority of life can't be cultured in a lab, I was wondering about what potential exists for different culturing conditions that would allow this to change. What obstacles are blocking us from a wider array of culturable microbes, and is it possible to bypass these barriers? Increasing the pool of bioprospecting sources seems like it would be very helpful, as you never know what crazy thing nature has already invented that we can hijack.

David M. Truong 20:23, 4 February 2012 (EST): Ben, that's an interesting question. Like I mentioned, there are many microbial species living in the vastness of the world's oceans. These microbes have often adapted to incredibly harsh conditions, such as different energy sources such as hydrogen sulfide and/or higher ocean pressures without the need for light. That's not even including organisms on land, that for whatever reason, don't grow well in lab. Although it is tempting to identify a new general culture protocol for these "other" organisms, it might be more prudent to focus on a case by case basis, purely by need. For instance, the recently infamous GFAJ-1 microbe (the arsenic microbe), is also an extremophile and was specially cultured in higher pH. It is interesting because, maybe it uses arsenic in it's DNA (most likely not). But if there is an interesting microbe found in another interesting enviroment, say Mars for example, I think people would definitely focus on that. This isn't the most straight-forward response, but let me get back to you on this.

Jeffrey E. Barrick 11:56, 5 February 2012 (EST):Sometimes microbes require certain "growth factors" that might be vitamins or quorum sensing molecules produced by other microbe that they are "used to" living with. In certain cases supplementing agar plates with the compounds has enabled them to be grown in lab [1]. Another reason that things are often "unculturable" is that they have adapted to grow very slowly (but efficiently) and we are not patient enough in lab, or they get overgrown by other bacteria int he same soil samples that are microbial "weeds" before they have a chance to form colonies.

• Jeffrey E. Barrick 11:56, 5 February 2012 (EST): I think Dave has a great point in his article that even with all the diversity in nature, evolution only produces things that are "good enough". While often much better than anything we can currently create in the lab de novo, they are not optimal. In many cases nothing may have evolved to do what we want at all.

• Jeffrey E. Barrick 11:56, 5 February 2012 (EST): Maybe you should point out that one difficulty with bioprospecting by the random cloning approaches is that it only works when one fairly short piece of DNA has all the genes required for a function. Often one has to computationally look for gene clusters that you can recognize (as in the case of polyketide synthase genes[2]), amplify with degenerate primers specifically to those genes, and move multiple genes around and screen them to find new functions.

• James L. Bachman 13:20, 5 February 2012 (EST) Under Limitations you said that using emPCR on short-reads will introduce bias, what exactly do you mean by bias in this context and how is that physically done?

References

1. Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, and Breznak JA. New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol. 2004 Aug;70(8):4748-55. DOI:10.1128/AEM.70.8.4748-4755.2004 |
2. Seow KT, Meurer G, Gerlitz M, Wendt-Pienkowski E, Hutchinson CR, and Davies J. A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms. J Bacteriol. 1997 Dec;179(23):7360-8. DOI:10.1128/jb.179.23.7360-7368.1997 |