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 about processes.



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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



760 bp fragment

Schirmer, A., R. Gadkari, C. D. Reeves, F. Ibrahim, E. F. DeLong, and C. R. Hutchinson. 2005. Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta. Appl Environ Microbiol 71:4840-4849.

Master mix for one reaction (bring up to 15 uL total with DNA and water)

in uL

H2O 6.00

PCR Buffer 1.5

DNTP 1.5

BAS 0.14

Primers 0.15 each

Taq 0.1

MgCl 2.4

DMSO 1.4 ***I typically don’t use DMSO so swap in water here)

GEL!!!! The first well in each line is the positive control



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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.



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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 circle in the lower right is an equal hemisphere projection. The lines are best thought of as planes sitting inside a hollow hemisphere. This is one way to represent different geologic features as planes.

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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 9.57
10x PCR Buffer 1.5
100x BSA 0.125
Forward Primer 0.1
Reverse Primer 0.1
TAQ 0.15
MgCl2 1.5
DMSO 1.5

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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 a mesa. I want to show folks what a geosciences notebook looks like.

Sunday will be some data from Lechuguilla Cave (one of the places I work in)

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