Posts Tagged ‘pseudogene’

Jim Simons, the Numbers King

January 27, 2018

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 ( HT @Anne_Churchland

“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.

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. – PubMed – NCBI

October 30, 2017

Comparative…3D chromosomal architecture identifies a novel fetal Hb reg. element #Pseudogene shifts v. promotor

Mechanisms underlying structural variant formation in genomic disorders : Nature Reviews Genetics : Nature Publishing Group

April 1, 2017

Mechanisms underlying #SV formation in…disorders 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! Interesting link to infectious disease for pseudo-siglecs 13 & 17

“”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.”

Pseudogene derived chimeric CEL-HYB protein

March 14, 2017

Recombined allele of..lipase gene CEL & its #pseudogene CELP confers susceptibility to..pancreatitis CEL-HYB chimera

Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia

February 13, 2017

Genome expansion via lineage splitting…in the cicada endosymbiont Hodgkinia Host lifecycle partially enables split

Eat, Pray, Latin – The New Yorker

August 19, 2016

Eat, pray, #Latin “An undead language, a ghost shadowing…our words, a zombie…in sentences,” viz pseudolanguage!

Pseudoenzyme – Proteopedia, life in 3D

August 2, 2015

Pseudoenzymes are proteins that cannot catalyze chemical reactions despite being clearly related structurally to functioning enzymes. Many enzyme families contain inactive members. For example, a number of human kinases lack at least one of the key amino acids necessary for catalysis of phosphate transfer [1]. Often pseudoenzymes still have biological roles, albeit non-catalytic. Some assist true enzymes in obtaining functional folds, some server as platforms for other proteins to interact, and some are escorts for proteins [2][3]. “}}

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

August 2, 2015

– pseudoenzyme

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

August 2, 2015