linkstream2 microblog

New life for old bones https://www.sciencemag.org/content/349/6246/358.summary An explosion in ancient DNA research. Water & heat hard on DNA, creating a northern bias

Rock-paper-scissors may explain evolutionary ‘games’
http://news.sciencemag.org/biology/2015/05/rock-paper-scissors-may-explain-evolutionary-games-nature How aggressive, cooperative & deceptive behaviors can coexist

QT:{{”
“The hand game “rock-paper-scissors” is a classic way to settle playground disputes, with rock smashing scissors, scissors cutting paper, and paper covering rock. But it turns out that nature plays its own versions of the game, and mathematicians and biologists have used it to study everything from human societies to bacteria in a petri dish. Now, researchers have found that when players change their strategies on the fly, a stable pattern arises in which each of the three weapons gains and loses popularity in turn. The discovery could shed light on how living creatures maintain competing strategies in the struggle for existence.

When applied to biology, rock-paper-scissors blossoms from a two-person children’s game into a complex dance among multiple players. Certain lizards, for example, use three competing
strategies—aggression, cooperation, and deception—to win mates, with each tactic beating one and losing to another—just like rock, paper, and scissors. For the lizards, winning the game equates to making babies.
…
Inspired by computer simulations of a related game, two
mathematicians—Steven Strogatz and Danielle Toupo of Cornell University—decided to get to the root of what happens when players switch strategies midgame. “I thought it was fascinating, and I wanted to find a mathematical model that would describe this in its simplest form,” Strogatz says. They went back to basics, studying the pure equations instead of complicated computer simulations.”
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A New Initiative on Precision Medicine
http://www.nejm.org/doi/full/10.1056/NEJMp1500523 Notable: focus on #cancergenomics & mention of endophenotypes & #QS data

Francis S. Collins, M.D., Ph.D., and Harold Varmus, M.D.
N Engl J Med 2015; 372:793-795February 26, 2015DOI: 10.1056/NEJMp1500523

QT:{{”
“These features make efforts to improve the ways we anticipate, prevent, diagnose, and treat cancers both urgent and promising. Realizing that promise, however, will require the many different efforts reflected in the President’s initiative. To achieve a deeper understanding of cancers and discover additional tools for molecular diagnosis, we will need to analyze many more cancer genomes. ….
The cancer-focused component of this initiative will be designed to address some of the obstacles that have already been encountered in “precision oncology”: unexplained drug resistance, genomic
heterogeneity of tumors, insufficient means for monitoring responses and tumor recurrence, and limited knowledge about the use of drug combinations.
…
The initiative’s second component entails pursuing research advances that will enable better assessment of disease risk, understanding of disease mechanisms, and prediction of optimal therapy for many more diseases, with the goal of expanding the benefits of precision medicine into myriad aspects of health and health care.

The initiative will encourage and support the next generation of scientists to develop creative new approaches for detecting, measuring, and analyzing a wide range of biomedical information — including molecular, genomic, cellular, clinical, behavioral, physiological, and environmental parameters. Many possibilities for future applications spring to mind: today’s blood counts might be replaced by a census of hundreds of distinct types of immune cells; data from mobile devices might provide real-time monitoring of glucose, blood pressure, and cardiac rhythm; genotyping might reveal particular genetic variants that confer protection against specific diseases…
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#Chromatin…shapes the mutational landscape of cancer
http://www.nature.com/nature/journal/v518/n7539/full/nature14221.html Low DNase correlates w/ high SNVs in melanoma. True generally?

The most incompressible metal Os at… >750 GPa
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14681.html Surprisingly, core rather than valence electrons affected by pressure

Endosymbiotic origin & differential loss of eukaryotic
geneshttp://www.nature.com/nature/journal/v524/n7566/full/nature14963.html For Euks, horizontal transfer is episodic (v continuous)

DeconRNASeq…framework for #deconvolution of heterogeneous tissue samples http://bioinformatics.oxfordjournals.org/content/29/8/1083.long “App note” w/ very concise code snippet

30 lines of R?

[Population] genetics of Mexico by @cdbustamante lab
http://www.sciencemag.org/content/344/6189/1280.abstract Has groups as divergent from each other as Europeans v Asians

QT:{{”
We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians.
Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country.

The genetics of indigenous Mexicans exhibit substantial geographical structure, some as divergent from each other as are existing populations of Europeans and Asians.
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Analysis of #LOF variants & 20 risk factor phenotypes in 8.6K individuals identifies loci [both well known & new]
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3270.html

NATURE GENETICS | LETTER

Analysis of loss-of-function variants and 20 risk factor phenotypes in 8,554 individuals identifies loci influencing chronic disease

Alexander H Li,
Alanna C Morrison,
Christie Kovar,
L Adrienne Cupples,
Jennifer A Brody,
Linda M Polfus,
Bing Yu,
Ginger Metcalf,
Donna Muzny,
Narayanan Veeraraghavan,
Xiaoming Liu,
Thomas Lumley,
Thomas H Mosley,
Richard A Gibbs
& Eric Boerwinkle

#SingleCell chromatin accessibility
http://www.nature.com/nature/journal/v523/n7561/full/nature14590.html >1.6k ATAC-seq expts; many on @ENCODE_NIH cell lines H1, GM12878 & K562