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This Week in PLoS: May 4, 2009

In PLoS Computational Biology this week, scientists from the Hungarian Academy of Sciences in Budapest describe a method to predict the disordered binding regions of intrinsically unstructured/disordered proteins. "Our method targets the essential feature of these regions: they behave in a characteristically different manner in isolation than bound to their partner protein," the authors write. Testing their method on several hundred proteomes, they showed that disordered binding sites increased with the complexity of the organism and that the length distribution of binding sites gravitated toward shorter segments.

In work published in PLoS Genetics, researchers studied the evolution of Segregation Distorter (SD) genes in Drosophila melanogaster. Performing a large screen for SD chromosomes in African populations of D. melanogaster, they found a new SD chromosome type, SD-Mal, which is native to Africa and has a "perfect transmission advantage and lacks recombination over much of the chromosome." They say that this new chromosome swept rapidly across sub-Saharan Africa sometime within the last 3,000 years. These findings show that selfish gene complexes evolve continuously to evade suppression by other genes in the genome and to compete with one another for a place in the population," they write in the author summary.

French scientists have studied the evolution of the vertebrate forebrain using gene expression analysis in lampreys, a model organism for this type of work. In a paper in PLoS One, they looked at the embryonic expression patterns of 43 genes encoding transcription factors or signaling molecules involved in cell proliferation, stem cell-ness, neurogenesis, patterning, and regionalization in the developing forebrain. Comparisons with model organisms showed pattern conservation "likely to reflect shared features present in the vertebrate ancestors. They also point to changes in signaling systems -- pathways which control the growth and patterning of the neuroepithelium -- which may have been crucial in the evolution of forebrain anatomy at the origin of vertebrates," they say in the abstract.

Also in PLoS One, scientists used FISH, sequence alignment, phylogenetic reconstruction, and recombination detection analyses to compare the evolution of human and chimp versions of members of the double homeobox gene family on the Y chromosome. They found the existence of all copies in a common ancestor, and comparative analysis revealed that Y-chromosomal DUX genes and circumjacent beta-satellites evolved together. Importantly, they add, "the acquisition of complete ORFs in human copies might relate to evolutionary advantageous functions indicating neo-functionalization."

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.