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This Week in PLOS: May 20, 2014

The Pseudomonas species found in lung microbiomes of individuals who've received lung transplants correspond with distinct clinical features in the transplant recipients, according to a PLOS One study. A University of Michigan-led team performed 16S ribosomal RNA sequencing and quantitative PCR analyses of bronchoscopy samples from 33 lung transplant recipients to identify microbial members of lung microbiomes. When they compared the microbe collections to one another and to those found in bronchoscopy samples from 26 transplant-free control individuals, the researchers saw symptom-associated transplant microbiomes that tended to contain either P. aeruginosa or P. fluorescens, including differences in microbiome diversity and the likelihood of acute infection.

A PLOS Genetics study reveals genetic patterns in the genomes of more than three dozen individuals from South Asia. A team involved in the Singapore Sequencing Indian Project did whole-genome sequencing on 38 Asian Indian individuals. The researchers detected genetic diversity across the South Indian genomes, which were compared to sequences generated for the 1,000 Genomes Project and Singapore Sequencing Malay Project. The data provided other population insights as well. For instance, it suggested that a subset of Asian Indian individuals have somewhat higher European admixture, while admixture from Neanderthal and Denisovan populations did not appear to be as recent for the Asian Indian group as for East Asians tested previously.

In PLOS Pathogens, National Institute of Allergy and Infectious Diseases researchers describe interactions between the papillomavirus and its host, identifying sites in the host genome where the viral protein E2 latches on to host chromatin with the help of a cellular protein called BRD4. Using ChIP-chip along with other approaches, the team identified parts of the host genomes dubbed "persistent E2 and BRD4-broad localized enrichments of chromatin" — sites shown to be associated with both papillomavirus replication and fragile sites in the human cervical cell genome.

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.