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The blood DNA virome in 8,000 humans.
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and...
Library preparation methodology can influence genomic and functional predictions in human microbiome research.
Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparing WGS...
Scientists discover molecular predictors of toxic algal blooms that pose health risk, ecological and economic harm
La Jolla, California—September 19, 2024—A team of researchers from the J. Craig Venter Institute (JCVI), Scripps Institution of Oceanography at the University of California San Diego, and collaborators, have published a groundbreaking study on predicting harmful algal blooms (HABs) that contain high levels of the neurotoxin domoic acid. The study provides new insights into the mechanisms driving this type of HAB and offers potential solutions for predicting and mitigating their impacts....
Rescue of mutant fitness defects using in vitro reconstituted designer transposons in Mycoplasma mycoides.
With only hundreds of genes contained within their genomes, mycoplasmas have become model organisms for precise understanding of cellular processes, as well as platform organisms for predictable engineering of microbial functions for mission-critical applications. Despite the availability of "whole genome writing" in Mycoplasma mycoides, some traditional methods for genetic engineering are underdeveloped in mycoplasmas. Here we demonstrate two facile transposon-mediated approaches for...
Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells.
Functional genomics studies in minimal mycoplasma cells enable unobstructed access to some of the most fundamental processes in biology. Conventional transposon bombardment and gene knockout approaches often fail to reveal functions of genes that are essential for viability, where lethality precludes phenotypic characterization. Conditional inactivation of genes is effective for characterizing functions central to cell growth and division, but tools are limited for this purpose in...
Risks of mirror bacteria
In this study we discuss the feasibility and potential risks of creating an alternative form of life called mirror bacteria. We call upon the broader scientific community and policymakers to engage in discussion and to implement guardrails to avert this potentially severe threat from unfolding. All known life in the natural world is homochiral — DNA and RNA are composed of right-handed nucleotides, and proteins are made from left-handed amino acids. Mirror versions of these and other...
Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging.
Genome sequencing has established clinical utility for rare disease diagnosis. While increasing numbers of individuals have undergone elective genome sequencing, a comprehensive study surveying genome-wide disease-associated genes in adults with deep phenotyping has not been reported. Here we report the results of a 3-y precision medicine study with a goal to integrate whole-genome sequencing with deep phenotyping. A cohort of 1,190 adult participants (402 female [33.8%]; mean age, 54 y...
Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
Although biofilms have been shown to be reservoirs of pathogens, our knowledge of the microbial diversity in biofilms within critical areas, such as health care facilities, is limited. Available methods for pathogen identification and strain typing have some inherent restrictions. In particular, culturing will yield only a fraction of the species present, PCR of virulence or marker genes is mainly focused on a handful of known species, and shotgun metagenomics is limited in the ability to...
Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling.
The availability of genetically tractable organisms with simple genomes is critical for the rapid, systems-level understanding of basic biological processes. Mycoplasma bacteria, with the smallest known genomes among free-living cellular organisms, are ideal models for this purpose, but the natural versions of these cells have genome complexities still too great to offer a comprehensive view of a fundamental life form. Here we describe an efficient method for reducing genomes from these...
Launching the Global Community Cyberinfrastructure for Advanced Marine Microbial Research and Analysis (CAMERA)
Scientists and engineers at the University of California, San Diego and the J. Craig Venter Institute (JCVI) have flipped the virtual switch on the first cyberinfrastructure customized to serve the marine microbial metagenomics community. At the heart of the cyberinfrastructure is a new, high-performance computer and storage complex funded by the Gordon and Betty Moore Foundation and located in UC San Diego's Atkinson Hall, headquarters of the California Institute for Telecommunications and...