Skip to main content
Premium Trial:

Request an Annual Quote

Genome Biology Papers on Parasite Impacts in Gut, Lung Microenvironment Interactions, More

Researchers at the University of Pennsylvania and elsewhere describe gut microbiome features in individuals from Cameroon, including participants carrying helminth worm parasites. Using targeted 16S ribosomal RNA gene sequencing, metagenomic sequencing, imaging-based blood and intestinal pathogen analyses, blood serum immune tests, and other analyses, the team considered factors related to gut microbiome and parasite patterns in 575 individuals from pastoralist, agro-pastoralist, and hunter-gatherer backgrounds in Cameroon, uncovering gut microbial communities that varied with subsistence methods and were distinct from those found in individuals from an urban environment in the US. In hunter-gatherer participants, for example, the authors saw a rise in intestinal parasites, particularly helminth worms transmitted by soil, that appeared to coincide with higher gut microbial diversity and an uptick in immune features such as proinflammatory cytokines.

A Stanford University-led team looks at the cell types and cellular interactions that occur in the microenvironment surrounding newly resected primary non-small-cell lung tumors, using RNA sequencing on flow-sorted malignant, stromal, and immune cells to put together the "Lung Tumor Microenvironment Interactome," or LTMI. That LTMI resource includes information on differential expression patterns and other informative features in mapped microenvironment cells, the researchers say, providing insights into cross-talk between these cell types as well as cell-type specific features that appear to correspond to better or worse outcomes. From their proof-of-principle analyses of lung adenocarcinoma cells, for example, the authors suggest that LTMI may serve as a "resource for generating hypotheses concerning tumor-microenvironment interactions that may have prognostic and therapeutic relevance."

Finally, a team from France presents a nanopore sequencing-based approach called FORK-seq for mapping DNA replication in the budding yeast model organism Saccharomyces cerevisiae. The researchers used the method — which involves sequencing and quantifying the incorporation of the synthetic thymine analog bromodeoxyuridine (BrdU) after pulse-chase experiments in S. cerevisiae cells — to profile nearly 59,000 of these BrdU-labeled replication tracks, uncovering more than 4,900 replication initiation and nearly 4,500 replication termination events. Based on their findings, the authors argue that "this high-resolution genome-wide method represents a major step forward compared to current single-molecule methods and will likely transform this research field."