Posts Tagged ‘evolution’

A Big Bang model of human colorectal tumor growth : Nature Genetics : Nature Research

June 7, 2017

Big Bang model of…tumor growth, v. slow #evolution under selection #Cancer is born w/ key mutations all there

Andrea Sottoriva,
Haeyoun Kang,
Zhicheng Ma,
Trevor A Graham,
Matthew P Salomon,
Junsong Zhao,
Paul Marjoram,
Kimberly Siegmund,
Michael F Press,
Darryl Shibata
& Christina Curtis

Nature Genetics 47, 209–216 (2015) doi:10.1038/ng.3214

Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution: Cell

February 4, 2017

Temporal Collateral Sensitivity in Tumor…Evolution Drug-fitness landscape illuminates transiently vulnerable state

Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution

Boyang Zhao
Joseph C. Sedlak
Raja Srinivas
Pau Creixell
Justin R. Pritchard
Bruce Tidor
Douglas A. Lauffenburger
Michael T. Hemann

The Ascent of Mammals – Scientific American

July 4, 2016

The Ascent of #Mammals Overview of their slow growth & coexistence w. dinosaurs, not just advent after KT asteroid

Identification of neutral tumor evolution across cancer types : Nature Genetics : Nature Publishing Group

February 27, 2016

Neutral tumor #evolution across #cancer types Initial burst of driver events followed by random mutations

Boutros PC…., van der Kwast T, Bristow RG* (2015) “Spatial genomic heterogeneity within localized, mult i-focal prostate cancer” Nature Genetics 47(7):736-745 (PMID: 26005866)

January 25, 2016

Spatial genomic heterogeneity w/in…prostate #cancer WGS analysis of many sites suggests divergent tumor evolution

Boutros…, van der Kwast, Bristow (2015) “Spatial genomic
heterogeneity within localized, multi-focal prostate cancer” Nature Genetics 47(7):736-745 (PMID: 26005866)

This work represents the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcomes at the level of whole-genome sequencing (WGS). Five patients, with index tumors of Gleason score 7, were subjected to a WGS protocol with spatial sampling of 23 distinct tumor regions to assess intraprostatic heterogeneity. In their analysis, Boutros et al, discovered recurrent amplification of MYCL, which is associated with TP53 loss. This finding is one of the first clear functional distinctions between MYC family members in prostate cancer and suggests that MYCL amplification may be preferentially localized in the index lesion. Overall, the authors believe their results are useful in the development of prognostic biomarkers that are necessary to achieve personalized prostate cancer medicine. It is important to note that such diagnostic biopsy protocols can miss regions of more aggressive cancers resulting in the patient being under-staged.

PLOS Computational Biology: Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations

December 18, 2015

Folding by Chaperones Accelerates Evolutionary Dynamics Multiscale models link NT mutations, PPIs & cell populations

Punctuated equilibrium in the large-scale evolution of programming languages | Journal of The Royal Society Interface

September 22, 2015

Punctuated equilibrium in the large-scale #evolution of #programming languages Clustering groups these into trees

Punctuated equilibrium in the large-scale evolution of programming languages
Sergi Valverde, Ricard V. Solé

Did natural selection make the Dutch the tallest people on the planet?

June 16, 2015

Did natural #selection make the Dutch the tallest people on the
planet? Height spurt in last century not all nurture

“This study drives home the message that the human population is still subject to natural selection,” says Stephen Stearns, an evolutionary biologist at Yale University who wasn’t involved in the study. “It strikes at the core of our understanding of human nature, and how malleable it is.” It also confirms what Stearns knows from personal experience about the population in the northern Netherlands, where the study took place: “Boy, they are tall.”

“For many years, the U.S. population was the tallest in the world. In the 18th century, American men were 5 to 8 centimeters taller than those in the Netherlands. Today, Americans are the fattest, but they lost the race for height to northern Europeans—including Danes, Norwegians, Swedes, and Estonians—sometime in the 20th century.

Just how these peoples became so tall isn’t clear, however. Genetics has an important effect on body height: Scientists have found at least 180 genes that influence how tall you become. Each one has only a small effect, but together, they may explain up to 80% of the variation in height within a population. Yet environmental factors play a huge role as well. The children of Japanese immigrants to Hawaii, for instance, grew much taller than their parents. Scientists assume that a diet rich in milk and meat played a major role.

The Dutch have become so much taller in such a short period that scientists chalk most of it up to their changing environment. As the Netherlands developed, it became one of the world’s largest producers and consumers of cheese and milk. An increasingly egalitarian distribution of wealth and universal access to health care may also have helped.”

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

May 25, 2015

Mtn gorilla genomes reveal…impact of long-term…inbreeding Pop. variation so low that very deleterious SNPs purged

Science 10 April 2015:
Vol. 348 no. 6231 pp. 242-245
DOI: 10.1126/science.aaa3952

Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding

Yali Xue1,*,
Javier Prado-Martinez2,*,
Peter H. Sudmant3,*,

Tomas Marques-Bonet2,12,
Chris Tyler-Smith1,†,
Aylwyn Scally13,†

Comparative genomics reveals insights into avian genome evolution and adaptation

May 16, 2015

Comparative #genomics reveals insights into avian…#evolution Less repeats & dups in birds; woodpecker, an exception

Science 12 December 2014:
Vol. 346 no. 6215 pp. 1311-1320
DOI: 10.1126/science.1251385

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang1,2,*,†,
Cai Li1,3,*,
Avian Genome Consortium§,
Erich D. Jarvis20,†,
M. Thomas P. Gilbert3,56,†,
Jun Wang1,55,57,58,59,†