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This Week in PLOS: Sep 10, 2012

A PLOS One study looks at the microbial communities living in water samples from aquariums housing ornamental fish from several pet shops in Rhode Island. Researchers from the Marine Biological Laboratory at Woods Hole, Brown University, and elsewhere used high-throughput 16S ribosomal RNA gene sequencing to identify bacterial members of microbial communities in water samples from two aquariums containing common goldfish and Chinese algae eater fish. The samples contained bacteria from some 30 phyla, though most of the 16S rRNA sequences seemed to stem from bacteria in four main phyla. And not all the bugs are believed to be innocuous: Based on their 16S rRNA analyses and PCR-based testing for several specific pathogens, the researchers found that the aquarium samples harbored sequences related to those found in 11 potentially pathogenic bacterial species. "Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans, and other species," the study's authors wrote.

An international team led by investigators from the University of Montreal has traced some cases of a heritable heart condition called congenital left-sided heart disease back to rare copy number changes. As they write in PLOS Genetics, the researchers assessed array-based copy number variant patterns in hundreds of individuals from dozens of families affected by left-sided congenital heart disease, comparing CNV profiles in the families with those found in almost 1,600 unaffected and unrelated controls. The search led to a set of rare inherited or de novo CNVs that were present only in the affected families. From this and other data, the team track down 25 genes suspected of contributing to left-sided congenital heart disease, including some genes associated with blood vessel production.

Meanwhile in PLOS Neglected Tropical Diseases, an international team reports on findings from a genome sequencing study that targeted the tough-to-culture malaria parasite species Plasmodium vivax. The researchers used Illumina's HiSeq 2000 to do relatively deep sequencing on P. vivax DNA from the red blood cells of malaria patients in Madagascar and Cambodia. By comparing these genomes to one another and to two more re-sequenced P. vivax genomes representing strains from other parts of the world, they were able to discern tens of thousands of variants across the malaria parasite's genome, demonstrating that many of the same alleles are found in P. vivax strains from very different regions. That, say study authors, "could be consistent with a high level of gene flow among parasite strains distributed throughout the world." For more information on the study, check out our sister publication GenomeWeb Daily News.

The Scan

US Supports Patent Waivers

NPR reports that the Biden Administration has announced its support for waiving intellectual property protections for SARS-CoV-2 vaccines.

Vaccines Versus Variants

Two studies find the Pfizer-BioNTech SARS-CoV-2 vaccine to be effective against viral variants, and Moderna reports on booster shots to combat variants.

CRISPR for What Ails You

The Wall Street Journal writes that CRISPR-based therapies could someday be used to treat common conditions like heart attacks.

Nature Papers Review Integration of Single-Cell Assay Data, Present Approach to Detect Rare Variants

In Nature this week: review of ways to integrate data from single-cell assays, and more.