A5028399086- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Antibiotic Resistance in Bacteria
- Gut microbiota and health
- Probiotics and Fermented Foods
- Microbial Metabolism and Applications
- Spaceflight effects on biology
- Infection Control and Ventilation
- Plant Pathogens and Fungal Diseases
- Vibrio bacteria research studies
- Legionella and Acanthamoeba research
- Bacterial Identification and Susceptibility Testing
- Bacterial biofilms and quorum sensing
- Genetics, Bioinformatics, and Biomedical Research
- Bacteriophages and microbial interactions
- Indoor Air Quality and Microbial Exposure
- Coral and Marine Ecosystems Studies
- Actinomycetales infections and treatment
- SARS-CoV-2 detection and testing
- Space Exploration and Technology
- Diphtheria, Corynebacterium, and Tetanus
- Olfactory and Sensory Function Studies
- Planetary Science and Exploration
- COVID-19 epidemiological studies
- COVID-19 and healthcare impacts
University of California, Davis
2015-2024
Lawrence Berkeley National Laboratory
2021
Joint Genome Institute
2021
University of Oregon
2020
West Virginia University
2019
Virginia Tech
2019
Methodist University
2019
University of California Davis Medical Center
2019
University of Technology Sydney
2014
Rega Institute for Medical Research
2007-2010
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable automating all steps in the process de novo from Illumina data. Results: A5-miseq can produce high-quality microbial assemblies on a laptop computer without any parameter tuning. does this by adapter trimming, quality filtering, error correction, contig and scaffold generation detection misassemblies. Unlike original A5 pipeline,...
Most scientific endeavors require science process skills such as data interpretation, problem solving, experimental design, writing, oral communication, collaborative work, and critical analysis of primary literature. These are the fundamental upon which conceptual framework expertise is built. Unfortunately, most college departments lack a formalized curriculum for teaching undergraduates skills. However, evidence strongly suggests that explicitly early in their education may enhance...
The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to ecosystem level underpins health Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, individual microbial symbionts consortia significantly relevant taxa, little is known about their interactions with vast majority host species. We outline priorities strengthen our current knowledge host-microbiome how they shape argue that such advances will...
We found no significant difference in cycle threshold values between vaccinated and unvaccinated persons infected with severe acute respiratory syndrome coronavirus 2 Delta, overall or stratified by symptoms. Given the substantial proportion of asymptomatic vaccine breakthrough cases high viral levels, interventions, including masking testing, should be considered settings elevated disease 2019 transmission.
The envelope protein from vesicular stomatitis virus (VSV) has become an important tool for gene transfer and therapy. It is widely used mainly because of its ability to mediate entry into all cell types tested date. Consistent with the broad tropism virus, receptor VSV thought be a ubiquitous membrane lipid, phosphatidylserine (PS). However, evidence this hypothesis indirect incomplete. Here, we have examined potential interaction PS at plasma in more detail. Measurements surface levels...
Background Modern advances in sequencing technology have enabled the census of microbial members many natural ecosystems. Recently, attention is increasingly being paid to residents human-made, built ecosystems, both private (homes) and public (subways, office buildings, hospitals). Here, we report results characterization ecology a singular environment, International Space Station (ISS). This ISS sampling involved collection analysis (via 16S rDNA PCR) 15 surfaces sampled by swabs onboard...
There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance presence and infectivity this virus on environmental surfaces, especially hospital setting, remains less clear.
The "gamification" of science has gained a lot traction in recent years, and games that convey scientific concepts or themes are increasingly popular. While number existing touch on microbiology, very few consider the beneficial (as opposed to detrimental) aspects microbes. We designed board game called "Gut Check: Microbiome Game" fill this gap. is meant be both educational as well challenging fun. Here we discuss development game, some logistics context, offer suggestions for others...
Background. While significant attention has been paid to the potential risk of pathogenic microbes aboard crewed spacecraft, non-pathogenic in these habitats have received less consideration. Preliminary work demonstrated that interior International Space Station (ISS) a microbial community resembling those built environments on Earth. Here we report results sending 48 bacterial strains, collected from Earth, for growth experiment ISS. This project was component Project MERCCURI (Microbial...
Streptococcus pyogenes is a very important human pathogen, commonly associated with skin or throat infections but can also cause life-threatening situations including sepsis, streptococcal toxic shock syndrome, and necrotizing fasciitis. Various studies involving typing molecular characterization of S. have been published to date; however next-generation sequencing (NGS) provide comprehensive collection an organism’s genetic variation. In this study, the genomes nine isolates pharyngitis...
Abstract We found no significant difference in cycle threshold values between vaccinated and unvaccinated, asymptomatic symptomatic groups infected with SARS-CoV-2 Delta. Given the substantial proportion of vaccine breakthrough cases high viral levels, interventions, including masking testing, should be considered for all settings elevated COVID-19 transmission.
Legionella pneumophila is a Gram-negative, facultative intracellular pathogen and the causative agent of Legionnaires' disease, severe pneumonia in humans. Analysis sequenced genomes revealed gene with variable number tandem repeats (VNTRs), whose varies between strains. We examined strain distribution this among collection 108 clinical, environmental hot spring serotype I Twelve variants were identified, but no correlation was observed repeat units clinical The encoded protein contains...
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking expensive undertaking, has become much easier for research labs with access to standard molecular biology computational tools. However, there are confusing variety options available DNA library preparation inexperience bioinformatics can pose significant barrier entry many who may be interested in genomics. objective the present study was design, test, troubleshoot, publish simple, comprehensive workflow...
Testing surfaces in school classrooms for the presence of SARS-CoV-2, virus that causes COVID-19, can provide public-health information complements clinical testing. We monitored SARS-CoV-2 RNA five schools (96 classrooms) Davis, California (USA) by collecting weekly surface-swab samples from classroom floors and/or portable high-efficiency particulate air (HEPA) units (n = 2,341 swabs). Twenty-two tested positive, with qPCR cycle threshold (Ct) values ranging 36.07-38.01. Intermittent...
Objective: The emergence of extended-spectrum β-lactamase (ESBL)-producing bacteria is now a critical concern. ESBL-producing Klebsiella pneumonia constitutes one the most common multidrug-resistant groups gram-negative involved in nosocomial infections worldwide. In this study we report on molecular characterization through whole genome sequencing an K. pneumoniae strain, LAU-KP1, isolated from stool sample patient admitted for gastrointestinal procedure/surgery at Lebanese Amrican...
With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in disease 2019 (COVID-19), corporate entities, federal, state, county and city governments, universities, school districts, places worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, other building owners occupants have an opportunity to reduce potential for transmission through built environment (BE) mediated pathways. Over last decade, substantial...
Abstract Background Qualitative and quantitative variability in gene expression represents the substrate for external conditions to exert selective pressures natural selection. Current technologies allow some forms of genetic variation, such as DNA mutations polymorphisms, be determined accurately on a comprehensive scale. Other components variability, stochastic events cellular transcriptional translational processes, are less well characterized. Although potentially important, relative...
As focus for exploration of Mars transitions from current robotic explorers to development crewed missions, it remains important protect the integrity scientific investigations at Mars, as well Earth's biosphere any potential harmful effects returned martian material. This is discipline planetary protection, and Committee on Space Research (COSPAR) maintains consensus international policy guidelines how this implemented. Based National Aeronautics Administration (NASA) European Agency (ESA)...
Enveloped virus vectors are used in a wide variety of applications. We have discovered that treatment cultured cells with phosphatidylserine (PS) liposomes can increase vector infection by up to 20-fold. This effect does not abrogate receptor requirements, is specific PS compared other phospholipids, and limited enveloped viruses. Furthermore, the enhancement occur through increases levels or binding, indicating fusion enhanced. The easily generated, store well, allow enhanced cell types.
Abstract Background Bacterial genomes harbour a large number of tandem repeats, yet the possible phenotypic effects those found within coding region genes are only beginning to be examined. Evidence exists from other organisms that these repeats can involved in evolution new genes, gene regulation, adaptation, resistance environmental stresses, and avoidance immune system. Results In this study, we have investigated presence variability copy intragenic tandemly repeated sequences genome...
Abstract During the water crisis in Flint, Michigan, USA (2014–2015), 2 outbreaks of Legionnaires' disease occurred Genesee County, Michigan. We compared whole-genome sequences 10 clinical Legionella pneumophila isolates submitted to a laboratory County during second outbreak with 103 collected following year. documented genetically diverse range L. strains across and isolates. Isolates belonging 1 clade (3 isolates, 3 from Flint hospital, isolate residence, reference Paris strain) had high...
ABSTRACT Here, we present the complete genome of extreme thermophile, Dictyoglomus thermophilum H-6-12 (phylum Dictyoglomi ), which consists 1,959,987 bp.