https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000095
reawakened pseudogenes useful against HIV
Posts Tagged ‘pseudogene’
Reawakening Retrocyclins: Ancestral Human Defensins Active Against HIV-1
April 25, 2020Recent Loss of Vitamin C Biosynthesis Ability in Bats
April 22, 2020https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027114 no gulo in fruit bats
The GULO Pseudogene and Its Implications for Common Descent | Evolution News
February 6, 2020https://evolutionnews.org/2012/02/gulo_shared_mut/
vitamin C biosyn.
Mystery RNA spawns gene-activating peptides : Nature News
March 2, 2019https://www.nature.com/news/2010/100715/full/news.2010.356.html
QT:[[”
It should be possible to scan the genome for sequences encoding peptides shorter than 100 amino acids, says Mark Gerstein, a computational biologist at Yale University in New Haven, Connecticut, but sorting through the many ‘hits’ to determine which are functional is likely to be much more difficult.
Meanwhile, Gerstein notes that the polished rice peptides could also have implications for how we view pseudogenes, which have long been thought to be defunct relics of protein-coding genes. Pseudogenes often contain many signals that would stop protein synthesis and, as a result, could only encode short amino-acid chains. “Maybe this would provide a new way for pseudogenes to have some sort of function,” he says.
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Jim Simons, the Numbers King
January 27, 2018Jim Simons, the Numbers King
https://www.NewYorker.com/magazine/2017/12/18/jim-simons-the-numbers-king Highlights the new @FlatironInst & one of its new hires, Nick Carriero, who co-wrote the original Yale pseudogene pipeline, PseudoPipe (Pseudogene.org/pseudopipe) HT @Anne_Churchland
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“Our discussion turned to the Flatiron Institute. Renaissance’s computer infrastructure, he said, had been a central part of its success. At universities, Simons said, coding tends to be an erratic process. He said of the graduate students and postdocs who handled such work, “Some of them are pretty good code writers, and some of them are not so good. But then they leave, and there’s no one to maintain that code.” For the institute, he has hired two esteemed coders from academia: Carriero, who had led my tour, had been recruited from Yale, where he had developed the university’s high-performance computing capabilities for the life sciences; Ian Fisk had worked at cern, the particle-physics laboratory outside Geneva. Simons offered them greater authority and high salaries. “They’re the best of the breed,” he said. Carriero and Fisk sometimes consult with their counterparts at Renaissance about technical matters.
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Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. – PubMed – NCBI
October 30, 2017Comparative…3D chromosomal architecture identifies a novel fetal Hb reg. element http://GenesDev.cshlp.org/content/31/16/1704.abstract #Pseudogene shifts v. promotor
Mechanisms underlying structural variant formation in genomic disorders : Nature Reviews Genetics : Nature Publishing Group
April 1, 2017Mechanisms underlying #SV formation in…disorders
http://www.Nature.com/nrg/journal/v17/n4/abs/nrg.2015.25.html Highlights importance of repeats in creating genomic plasticity
Nat Rev Genet. 2016 Apr;17(4):224-38. doi: 10.1038/nrg.2015.25. Epub 2016 Feb 29.
Mechanisms underlying structural variant formation in genomic disorders. Carvalho CM, Lupski JR
pseudogenes that might have saved us !
March 20, 2017#Pseudogenes that might have saved us!
http://www.sciencedaily.com/releases/2012/06/120604155554.htm?fb_ref=.T829TjfxGmI.like&fb_source=home_oneline Interesting link to infectious disease for pseudo-siglecs 13 & 17
QT:{{”
“”In a small, restricted population, a single mutation can have a big effect, a rare allele can get to high frequency,” said senior author Ajit Varki, MD, professor of medicine and cellular and molecular medicine and co-director of the Center for Academic Research and Training in Anthropogeny at UC San Diego. “We’ve found two genes that are non-functional in humans, but not in related primates, which could have been targets for bacterial pathogens particularly lethal to newborns and infants. Killing the very young can have a major impact upon reproductive fitness. Species survival can then depend upon either resisting the pathogen or on eliminating the target proteins it uses to gain the upper hand.”
In this case, Varki, who is also director of the UC San Diego Glycobiology Research and Training Center, and colleagues in the United States, Japan and Italy, propose that the latter occurred. Specifically, they point to inactivation of two sialic acid-recognized signaling receptors (siglecs) that modulate immune responses and are part of a larger family of genes believed to have been very active in human evolution.
Working with Victor Nizet, MD, professor of pediatrics and pharmacy, Varki’s group had previously shown that some pathogens can exploit siglecs to alter the host immune responses in favor of the microbe. In the latest study, the scientists found that the gene for Siglec-13 was no longer part of the modern human genome, though it remains intact and functional in chimpanzees, our closest evolutionary cousins. The other siglec gene — for Siglec-17 — was still expressed in humans, but it had been slightly tweaked to make a short, inactive protein of no use to invasive pathogens.”
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Pseudogene derived chimeric CEL-HYB protein
March 14, 2017Recombined allele of..lipase gene CEL & its #pseudogene CELP confers susceptibility to..pancreatitis
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3249.html CEL-HYB chimera
Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia
February 13, 2017Genome expansion via lineage splitting…in the cicada endosymbiont Hodgkinia http://www.PNAS.org/content/112/33/10192.abstract Host lifecycle partially enables split
linkstream2 microblog 