What we’re reading: readings for DNA Day, estimating Ne, and open-sourced data visualization

Microfiche Reader on Level 7

As we head into the weekend, here’s a few things we’ve noticed that might be worth your screen-time.

In the journals

Sixty years ago Thursday, Nature published three papers that unravelled (ha!) the molecular structure of DNA. They’re freely available online. But here’s the paper from that archive you mignt not know about already, which was published almost 70 years ago:

Avery, O.T., MacLeod, C.M. & McCarty, M. 1979. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. The Journal of Experimental Medicine 79: 137–159.

Griffith found that mice injected subcutaneously with a small amount of a living R culture derived from Pneumococcus Type II together with a large inoculum of heat-killed Type III (S) cells frequently succumbed to infection … The fact that the R strain was avirulent and incapable by itself of causing fatal bacteremia and the additional fact that the Type III cells contained no viable organisms brought convincing evidence that the R forms growing under these conditions had newly acquired the capsular structure and biological specificity of Type III pneumococci.

Macbeth, G.M., Broderick, D., Buckworth, R.C. & Ovenden, J.R. 2013. Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: A case study on Spanish mackerel (Scomberomorus commerson). G3: Genes|Genomes|Genetics 3: 709–717. doi: 10.1534/g3.112.005124.

A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or nonbreeding immigrants from genetically separate populations. … When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were greater than 24,000.

In the news

Grad student stipends aren’t exactly geared towards a life of luxury—at Southern Fried Science, they’re doing a series of posts providing advice for life on the stipend. (Via Scicurious, who adds her own thoughts.)

Trevor Bedford is building a pretty neat online library of his own science visualizations. We especially like the coalescent simulation.

Ken Wissoker, the editorial director of Duke University Press talks about the future of academic publishing, and doesn’t sound too worried.

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About Jeremy Yoder

Jeremy Yoder is an Assistant Professor of Biology at California State University, Northridge. He also blogs at Denim and Tweed, and tweets under the handle @jbyoder.
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