Archive for the 'SciLit' Category

A naturally occurring variant of the human prion protein completely prevents prion disease : Nature : Nature Publishing Group

August 14, 2015

Natural variant of the…#prion protein [G127V] completely
prevents…disease
http://www.nature.com/nature/journal/v522/n7557/full/nature14510.html Under pos. selection for kuru afflicted

QT:{{”
A novel PrP variant, G127V, was under positive evolutionary selection during the epidemic of kuru—an acquired prion disease epidemic of the Fore population in Papua New Guinea—and appeared to provide strong protection against disease in the heterozygous state2. Here we have investigated the protective role of this variant and its interaction with the common, worldwide M129V PrP polymorphism. V127 was seen exclusively on a M129 PRNP allele. We demonstrate that transgenic mice expressing both variant and wild-type human PrP are completely resistant to both kuru…”
“}}

seasonal effects on gene expression

August 9, 2015

Widespread [25% genes] seasonal…expression reveals [circ]annual differences in…immunity, relevant for vaccination http://www.nature.com/ncomms/2015/150512/ncomms8000/full/ncomms8000.html

In addition to circadian rhythms, batch effects, now consider seasonal effects on gene expression

High-throughput DNA sequence data compression

August 9, 2015

DNA sequence…#compression
http://bib.oxfordjournals.org/content/16/1/1.full Nice review comparing approaches on 2 axes: classic v Nextgen & reference-based v -free

Not much on LD-based approaches

Zexuan Zhu
Yongpeng Zhang
Zhen Ji
Shan He
Xiao Yang

Brief Bioinform (2015) 16 (1): 1-15.doi: 10.1093/bib/bbt087
First published online: December 3, 2013

L1 – Somatic – Brain – Single cell DNA

August 7, 2015

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements http://www.sciencedirect.com/science/article/pii/S0896627314011374 Somatic events from #neuron #singlecell WGS

Ancient DNA Holds Clues to Gene Activity in Extinct Humans

August 3, 2015

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

David Gokhman,
Eitan Lavi,
Kay Prüfer,
Mario F. Fraga,
José A. Riancho,
Janet Kelso,
Svante Pääbo,
Eran Meshorer,
and Liran Carmel

Science 2 May 2014: 523-527.Published online 17 April 2014

http://www.sciencemag.org/content/344/6181/245.summary

PLOS Genetics: 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

August 2, 2015

QT:{{”
While enriched with ENCODE biochemical annotations, much of the short-lived constrained sequences we identify are not detected by models optimized for wider pan-mammalian conservation. Constrained DNase 1 hypersensitivity sites, promoters and untranslated regions have been more evolutionarily stable than long noncoding RNA loci which have turned over especially rapidly. By contrast, protein coding sequence has been highly stable, with an estimated half-life of over a billion years (d1/2 = 2.1–5.0). From extrapolations we estimate that 8.2% (7.1–9.2%) of the human genome is presently subject to negative selection and thus is likely to be functional, while only 2.2% has maintained constraint in both human and mouse since these species diverged.
“}}

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004525

New lives for old: evolution of pseudoenzyme function illustrated by iRhoms : Abstract : Nature Reviews Molecular Cell Biology

August 2, 2015

– pseudoenzyme

http://www.nature.com/nrm/journal/v13/n8/abs/nrm3392.html

Genome-wide identification of pseudogenes capable of disease-causing gene conversion. – PubMed – NCBI

August 2, 2015

http://www.ncbi.nlm.nih.gov/pubmed/16671097

Is evolution Darwinian or/and Lamarckian?

August 2, 2015

QT:{{”
Various forms of stress-induced mutagenesis are tightly regulated and comprise a universal adaptive response to environmental stress in cellular life forms. Stress-induced mutagenesis can be construed as a quasi-Lamarckian phenomenon because the induced genomic changes, although random, are triggered by environmental factors and are beneficial to the organism.
“}}

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781790/

BMC Genomics | Full text | Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

July 31, 2015

[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential http://www.biomedcentral.com/1471-2164/16/113