Author Archives: Tattooed Science

Scratch spaces

I get torn between putting out work here, on github and on google+ . I think each site serves a slightly different purpose. Github for code, google+ for a narrower audience, and here maybe for a scratch space for writing … Continue reading

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Primers working!!!

So I am wrangling with getting these literature based PKS I primers working for my PhD project. Finally success!!! PKS I Primers degKS2F 5’-GCIATGGAYCCICARCARMGIVT  degKS2R 5’- GTICCIGTICCRTGISCYTCIAC 760 bp fragment Schirmer, A., R. Gadkari, C. D. Reeves, F. Ibrahim, E. F. DeLong, … Continue reading

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Returned from Parashants

Just got back from an amazing time in the Parashants! Will post an update shortly.

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Figshare – GC content compared to genome size

For those that are interested in opensource science I am over on figshare as well. Just posted GC content and genome size plot from some data I mined from NCBI awhile back. http://figshare.com/articles/GC_Content_vs_Genome_Size_of_4231_Bacteria_Genomes/97275    

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Sunday: A Swarm of Cave Pools

I like this sketch I did. This shows the spatial relationship between several cave pools in cross section to the geologic structures in the area. The numbers with the arrows are the strikes of the flowstone and rimstone dams. The … Continue reading

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Optimizing PCR reactions for gene amplification Part II

Here is a slightly modified one for those troublesome genes that won’t amplify or if you get lots of smearing. Basic Master Mix recipe for AmpliTAQ gold for 15 µL reaction (volumes in µL)H2O 9.5710x PCR Buffer 1.5100x BSA 0.125Forward … Continue reading

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Trees! and some field work

I’ve been working on this thing here This shows the effect of different alignment programs on the same 16S data set. Pretty neat. I am going out on Saturday to the Ojito Wilderness area to do a strat section on … Continue reading

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