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This Week in PNAS: Feb 1, 2011

In this week's PNAS Early Edition, groups of researchers report the genome sequences for three ant species. A team led by investigators at Switzerland's University of Lausanne reports the Solenopsis invicta, also known as the fire ant, genome, which it assembled using "454 and Illumina sequencing reads obtained from a focal haploid male and his brothers." Another team presents a draft of the Pogonomyrmex barbatus, or red harvester ant, genome, which it sequenced via 454 pyrosequencing. Using 454 and Illumina sequencing, an international team assembled a draft Linepithema humile, or Argentine ant, genome, which it published online in PNAS this week.

Yale University's Allison Hansen and Nancy Moran report in this week's PNAS their discovery of two pea aphid genes — glutamine synthetase and glutamate synthase — that may work together and are up-regulated in bacteriocytes that contain Buchnera, a bacterial endosymbiont of the insect. By comparing "pea aphid gene expression between bacteriocytes and other body tissues" with RNA-seq and pathway analysis, Hansen and Moran found 26 genes that underlie amino acid synthesis that were upregualted in bacteriocytes, seven of which "fill the gaps of Buchnera's essential amino acid pathways," they write, adding that the ammonium nitrogen into glutamate cycle "may be a key source of nitrogen fueling the integrated amino acid metabolism of the aphid-Buchnera partnership."

Researchers at the University of California, Berkeley, report a 'reverse ecology' population genomic approach, which they've applied to the microbial eukaryote Neurospora crassa. This approach, the authors write, "is free of a priori assumptions about candidate adaptive alleles." By sequencing the transcriptomes of 48 Neurospora, the Berkeley team found "two cryptic and recently diverged populations" and, with its high-res chromosomal analysis, the team identified two genomic islands, which it says "may be the result of local adaptation to the 9°C difference in average yearly minimum temperature between these two populations."

A team led by investigators at Yale presents its identification of rare copy-number variants in patients with the congenital heart disease, heterotaxy, which it says "identify unique genes in left-right patterning." The team genotyped 262 individuals with heterotaxy and 991 controls and found a "two-fold excess of subjects with" rare copy-number variants among affected individuals in 61 genes, 22 of which have Xenopus orthologs. In its in situ hybridization investigations, the team found that seven of these 22 genes expressed in the ciliated left-right organizer showed "marked enrichment compared with 40 of 845 previously studied genes." In its Xenopus knockdown experiments, the team found that five of the candidates — NEK2, ROCK2, TGFBR2, GALNT11, and NUP188 — "strongly disrupted both morphological LR development and expression of pitx2, a molecular marker of LR patterning."

The Scan

Vaccine Update Recommended

A US Food and Drug Administration panel recommends booster vaccines be updated to target Omicron, CNBC reports.

US to Make More Vaccines for Monkeypox Available

The US is to make nearly 300,000 vaccine doses available in the coming weeks to stem the spread of human monkeypox virus, according to NPR.

Sentence Appealed

The Associated Press reports that Swedish prosecutors are appealing the sentence given to a surgeon once lauded for transplanting synthetic tracheas but then convicted of causing bodily harm.

Genome Biology Papers on COVID-19 Effector Genes, Virtual ChIP-seq, scDART

In Genome Biology this week: proposed COVID-19 effector genes, method to predict transcription factor binding patterns, and more.