linkstream2 microblog

https://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.
“]]

Jim 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

QT:{{”
“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…3D chromosomal architecture identifies a novel fetal Hb reg. element http://GenesDev.cshlp.org/content/31/16/1704.abstract #Pseudogene shifts v. promotor

Genome expansion via lineage splitting…in the cicada endosymbiont Hodgkinia http://www.PNAS.org/content/112/33/10192.abstract Host lifecycle partially enables split

Eat, pray, #Latin
http://www.NewYorker.com/culture/cultural-comment/eat-pray-latin “An undead language, a ghost shadowing…our words, a zombie…in sentences,” viz pseudolanguage!

QT:{{”
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]. “}}

http://proteopedia.org/wiki/index.php/Pseudoenzyme

– pseudoenzyme

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

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

http://www.nature.com/nrm/journal/v15/n11/full/nrm3884.html

NATURE REVIEWS MOLECULAR CELL BIOLOGY | ANALYSIS
William H. Hudson
& Eric A. Ortlund
Nature Reviews Molecular Cell Biology 15, 749–760 (2014) doi:10.1038/nrm3884

BRAF #Pseudogene Functions as a Competitive Endogenous RNA; [Shows it] induces Lymphoma [after alteration, in mice]
http://www.cell.com/cell/abstract/S0092-8674(15)00244-5

Cell. 2015 Apr 9;161(2):319-32. doi: 10.1016/j.cell.2015.02.043. Epub 2015 Apr 2.

Karreth FA1, Reschke M1, Ruocco A1, Ng C1, Chapuy B2, Léopold V1, Sjoberg M3, Keane TM3, Verma A4, Ala U1, Tay Y1, Wu D5, Seitzer N1, Velasco-Herrera Mdel C3, Bothmer A1, Fung J1, Langellotto F6, Rodig SJ7, Elemento O4, Shipp MA2, Adams DJ3, Chiarle R8, Pandolfi PP9.

Abstract
Research over the past decade has suggested important roles for pseudogenes in physiology and disease. In vitro experiments
demonstrated that pseudogenes contribute….