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This Week in Genome Research: Oct 31, 2012

The microbial communities in people's mouths are more closely tied to environmental exposures than to genetics, according to a study published online in Genome Research. A University of Colorado, Boulder, team performed 16S ribosomal RNA sequencing on spit samples from more than 100 individuals, each of whom was tested up to three times over the course of a decade. Among the participants were 27 identical- and 18 non-identical twin pairs. Although the investigators saw similarities between younger twins' mouth microbiomes, that was less often the case for older twins, who were more apt to live apart. And while all of the individuals tested shared a core set of mouth microbiome components, the mouth microbiomes in non-identical twins were as similar to one another as those in identical twins.

The Tufts University School of Medicine's Tim van Opijnen and Andrew Camilli delve into relationships between genotype and phenotype for the bacterial pathogen Streptococcus pneumoniae. Using a high-throughput screening method that's based on transposon insertion sequencing, or Tn-seq, the researchers screened S. pneumoniae in 17 different carriage (in vitro) or infection (in vivo) situations that involved a range of carbon sources, stressors, and so on. In the process, they created a genotype-phenotype map representing more than 1,800 interactions. "We have generated a resource that provides detailed insight into the biology and virulence of S. pneumoniae," the pair writes, "and provided a road map for similar discovery in other microorganisms."

Finally, a study led by investigators at Kansas State University and Iowa State University takes a look at quantitative trait loci distribution in the maize genome. The team tallied up trait-associated SNPs in maize and looked at whether these tended to fall in genic or non-genic bits of the genome. Although variants affecting gene expression often turned up in non-genic parts of the maize genome, they were typically concentrated within a few thousand bases upstream of protein-coding genes. From these and other findings, the group concludes that "efficient, cost-effective genome-wide association studies in species with complex genomes can focus on genic and promoter regions."

The Scan

UK Funds to Stay Ahead of Variants

The UK has announced a further £29.3 million to stay on top of SARS-CoV-2 variants, the Guardian reports.

Push for Access

In a letter, researchers in India seek easier access to COVID-19 data, Science reports.

Not as Cold

Late-stage trial results are expected soon for an RNA-based vaccine that could help meet global demand as it does not require very cold storage, the New York Times writes.

Genome Research Papers on Microbes' Effects on Host Transfer RNA, Honeybee Evolution, Single-Cell Histones

In Genome Research this week: influence of microbes on transfer RNA patterns, evolutionary relationships of honeybees, and more.