A5049826494- Gut microbiota and health
- Video Analysis and Summarization
- Genomics and Phylogenetic Studies
- Natural Language Processing Techniques
- Bacteriophages and microbial interactions
- Protein Tyrosine Phosphatases
- Analytic and geometric function theory
- Microbial Community Ecology and Physiology
- Holomorphic and Operator Theory
- CAR-T cell therapy research
- Probiotics and Fermented Foods
- Ethics in Clinical Research
- Advanced Harmonic Analysis Research
- Virus-based gene therapy research
- interferon and immune responses
- Barrier Structure and Function Studies
- Axon Guidance and Neuronal Signaling
- Amoebic Infections and Treatments
- Hematological disorders and diagnostics
- Advanced Topics in Algebra
- Melanoma and MAPK Pathways
- Antimicrobial Peptides and Activities
- Neuroblastoma Research and Treatments
- Antimicrobial agents and applications
- Veterinary Equine Medical Research
University of Pennsylvania
2023-2025
Denver Zoo
2023
Taylor University
2022
Northwestern University
2018-2022
William & Mary
2014-2018
Williams (United States)
2017-2018
University of Ulster
2000
The ubiquitous use of antimicrobial chemicals may have undesired consequences, particularly on microbes in buildings. This study shows that the taxonomy and function indoor dust are strongly associated with chemicals—more so than any other feature Moreover, we identified links between chemical concentrations culturable bacteria cross-resistant to three clinically relevant antibiotics. These findings suggest humans be influencing microbial species genes found indoors through addition removal...
The built environment contains a variety of microorganisms, some which pose critical human health risks (e.g., hospital-acquired infection, antibiotic resistance dissemination). We uncovered combination complex biological functions that may play role in bacterial survival under the presumed selective pressures model environment—the International Space Station—by using an approach to compare pangenomes strains from two clinically relevant species ( B. cereus and S. aureus ) isolated both...
Environmental surveillance is a critical tool for combatting public health threats represented by the global COVID-19 pandemic and continuous increase of antibiotic resistance in pathogens. With its power to detect entire microbial communities, metagenomics-based methods stand out addressing need. However, several hurdles remain be overcome order generate actionable interpretations from metagenomic sequencing data infection prevention. Conceptually technically, we focus on viability...
Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial 496 showerheads collected from continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of diversity. Although a large fraction observed variation composition could not be explained,...
In the course of studying virome protozoan parasites, we identified small circular genomes resembling viruses, which turned out to be contaminants from an RNA purification kit. We report their sequences here so others can detect possible contamination in samples by aligning them these targets.
We previously reported that the pseudophosphatase MK-STYX (mitogen activated kinase phosphoserine/threonine/tyrosine binding protein) dramatically increases number of what appeared to be primary neurites in rat pheochromocytoma (PC-12) cells; however, question remained whether these MK-STYX-induced outgrowths were bona fide neurites, and formed synapses. Here, we report microtubules microfilaments, components cytoskeleton are involved formation present outgrowths. In addition, response nerve...
The rat pheochromocytoma PC12 cell line is a widely used system to study neuronal differentiation for which sustained activation of the extracellular signaling related kinase (ERK) pathway required. Here, we investigate function MK-STYX [MAPK (mitogen-activated protein kinase) phosphoserine/threonine/tyrosine-binding protein] in differentiation. member MAPK phosphatase (MKP) family, generally responsible dephosphorylating ERKs. However, lacks catalytic activity due absence nucleophilic...
Abstract Background Effective surveillance of microbial communities in the healthcare environment is increasingly important infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but currently challenged by several limitations: (1) they not powerful enough extract valid signals out background noise for low-biomass samples, (2) do distinguish between viable and nonviable organisms, (3) reveal load quantitatively. An additional practical challenge...
Closely related species are typically assumed to demonstrate similar phenotypes driven by underlying conserved genotypes. When monitoring for the effect of antimicrobials on types that may be selected for, this assumption prove incorrect, and identification additional genetic markers necessary.
Decades of effort have yielded highly effective antiviral agents to treat HIV, but viral strains evolved resistance each inhibitor type, focusing attention on the importance developing new classes. A particularly promising target is HIV capsid, function which can be disrupted by potent inhibitors that persist long term in treated subjects. Studies with such contributed an evolving picture role capsid itself-the inhibitors, like certain protein (CA) amino acid substitutions, disrupt...
Abstract Seasonal influenza virus predominantly evolves through antigenic drift, marked by the accumulation of mutations at sites. Because vaccines are frequently updated, though their efficacy may still be limited due to strain mismatches. Despite high levels viral diversity observed across populations, most human studies reveal intrahost diversity, leaving origin population-level unclear. Previous show host characteristics, such as immunity, might affect within-host evolution. Here we...
Medically and industrially important genes can be recovered from microbial communities by high-throughput sequencing, but precise annotation is often limited to characterized their relatives. Cloning a metagenome en masse into an expression host produce functional metagenomic library, directly connecting functions, sequence-naive cultivation-independent method discover novel genes.
Identifying variant forms of gene clusters interest in phylogenetically proximate and distant taxa can help to infer their evolutionary histories functions. Conserved may differ by only a few genes, but these small differences turn induce substantial phenotypes, such as the formation pseudogenes or insertions interrupting regulation. Particularly microbial genomes metagenomic assemblies become increasingly abundant, unsupervised grouping similar, not necessarily identical, into consistent...
Veterinary literature on diseases in binturong (Arctictis binturong) is often limited to case series or reports without population-level information. Morbidity and mortality data were collected from North American institutions through survey completion submission of medical records. Responses included information about 74 individuals (37 males, 30 females, 7 unknown neonates) representing 22 institutions, 1986 2019. Antemortem available 39 individuals, postmortem 53 individuals. Eighteen had...
Amoebiasis is a significant protozoal disease of reptiles causing nonspecific clinical signs including diarrhea, anorexia, and lethargy. It frequently results in acute death. Investigation the pathophysiology amoebiasis has been hampered by inability to accurately identify amoeba species level using conventional techniques. This study reviewed reptile medical records from Wildlife Conservation Society's archives 1998 2017. Amoebae were identified histologically 54 cases 31 different species....
ABSTRACT Functional metagenomic libraries, physical bacterial libraries which allow the high-throughput capture and expression of microbiome genes, have been instrumental in sequence-naïve cultivation-independent discovery novel genes from microbial communities. Preparation these is limited by their high DNA input requirement low cloning efficiency. Here, we describe a new method, METa assembly, for extremely efficient functional library preparation. We apply tagmentation to soil gut...
Abstract Effective surveillance of microbial communities in the healthcare environment is increasingly important infection prevention. However, current workflows are insufficient for proper risk assessment. Upon evaluating and optimizing techniques, we recommend best practices introduce a well-structured workflow metagenomics-based environmental that appropriate low-biomass samples, distinguishes viability, quantitative. The was developed using representative microbiome sample, which created...
Abstract Motivation Identifying gene clusters of interest in phylogenetically proximate and distant taxa can help to infer phenotypes interest. Conserved may differ by only a few genes, which be biologically meaningful, such as the formation pseudogenes or insertions interrupting regulation. These qualities allow for unsupervised clustering similar into bins that provide population-level understanding genetic variation clusters. Results We developed GeneGrouper, command-line tool uses...
Mitogen‐activated protein kinases (MAPKs) are essential players in important neuronal signaling pathways including development, plasticity, survival, learning, and memory. The inactivation of MAPKs is tightly controlled by MAPK phosphatases (MKPs), which also regulators these processes. There compelling evidence that a unique catalytically inactive member the MKP family, MK‐STYX (mitogen activated kinase phosphoserine/threonine/tyrosine binding protein), regulator processes such as neurite...
Background: Cultivation of targeted pathogens has been long recognized as a gold standard for healthcare surveillance. However, there is an emergent need to characterize all viable microorganisms in facilities understand the role that both clinical and nonclinical play healthcare-associated infections. Metagenomic sequencing allows detection entire microbial communities, contrast identification by cultivation. Widespread application metagenomic impeded part because sensitivity specificity...