A5003440200- Gut microbiota and health
- Vibrio bacteria research studies
- Oral microbiology and periodontitis research
- Probiotics and Fermented Foods
- Salivary Gland Disorders and Functions
- Bacteriophages and microbial interactions
- Clostridium difficile and Clostridium perfringens research
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Listeria monocytogenes in Food Safety
- Immune Response and Inflammation
- Antibiotic Resistance in Bacteria
- Image Processing Techniques and Applications
- Food Security and Health in Diverse Populations
- Endoplasmic Reticulum Stress and Disease
- Bacterial biofilms and quorum sensing
- Evolution and Genetic Dynamics
- Genomics and Chromatin Dynamics
- Drug Transport and Resistance Mechanisms
- Mycobacterium research and diagnosis
- Pediatric health and respiratory diseases
- Single-cell and spatial transcriptomics
- Industrial Vision Systems and Defect Detection
- RNA and protein synthesis mechanisms
- Aquaculture disease management and microbiota
Cornell University
2017-2025
Chan Zuckerberg Initiative (United States)
2024
Ithaca College
2023
Saint Meinrad Seminary and School of Theology
2019
Clinical Orthopaedics and Related Research
2019
National Institute of Arthritis and Musculoskeletal and Skin Diseases
2019
National Institute of Allergy and Infectious Diseases
2019
National Institutes of Health
2019
Hospital for Special Surgery
2019
Broad Institute
2015-2016
Aneuploidy decreases cellular fitness, yet it is also associated with cancer, a disease of enhanced proliferative capacity. To investigate one mechanism by which aneuploidy could contribute to tumorigenesis, we examined the effects on genomic stability. We analyzed 13 budding yeast strains that carry extra copies single chromosomes and found all aneuploid exhibited or more forms instability. Most displayed increased chromosome loss mitotic recombination, as well defective DNA damage repair....
Abstract Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics the functional diversity, but resolving role of individual cells in throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation Concatenation PCR), a new technique that links genes phylogenetic markers uncultured single cells, providing hundreds thousands with costs comparable to one genomic library...
Abstract The gut microbiome harbors a ‘silent reservoir’ of antibiotic resistance (AR) genes that is thought to contribute the emergence multidrug-resistant pathogens through horizontal gene transfer (HGT). To counteract spread AR, it paramount know which organisms harbor mobile AR and engage in HGT. Despite methods characterize overall abundance gut, technological limitations short-read sequencing have precluded linking bacterial taxa specific genetic elements (MGEs) encoding genes. Here,...
An increase in plastic waste and its release into the environment has led to health concerns over microplastics (MPs) environment. The intestinal mucosal layer is a key defense mechanism against ingested MPs, preventing migration of particles other parts body. MP through mucus challenging study due difficulties obtaining intact layers for testing numerous formulations, shapes, sizes microplastics. Previous studies have primarily used from animals, hydrogel models, samples body as...
Silencing within the yeast ribosomal DNA (rDNA) repeats protects integrity of this highly repetitive array by inhibiting hyperrecombination and repressing transcription from foreign promoters. Using affinity purification combined with sensitive mixture mass spectrometry, we have analyzed protein interaction network involved in suppressing homologous recombination rDNA locus. We show that Net1 Sir2 subunits RENT (regulator nucleolar silencing telophase exit) complex, Fob1, which recruits to...
Infectious diseases are economically detrimental to aquaculture, and with continued expansion intensification of the importance managing infectious will likely increase in future. Here, we use evolution virulence theory, along examples, identify aquaculture practices that might lead increased pathogen virulence. We eight common theory predicts may favor toward higher Four related intensive operations, four others specifically disease control. Our intention is make managers aware these risks,...
The metagenome of the gut microbiome encodes tremendous potential for biosynthesizing and transforming small-molecule metabolites through activities enzymes expressed by intestinal bacteria. Accordingly, elucidating this metabolic network is critical understanding how microbiota contributes to health disease. Bile acids, which are first biosynthesized in liver, modified commensal bacteria into secondary bile regulate myriad host processes, including lipid metabolism, glucose immune...
Phylogenetic distance, shared ecology, and genomic constraints are often cited as key drivers governing horizontal gene transfer (HGT), although their relative contributions unclear. Here, we apply machine learning algorithms to a curated set of diverse bacterial genomes tease apart the importance specific functional traits on recent HGT events. We find that content accurately predicts network [area under receiver operating characteristic curve (AUROC) = 0.983], performance improves further...
Multiple Sclerosis (MS) is a complex disease of the CNS thought to require an environmental trigger. Gut dysbiosis common in MS, but specifically causative species are unknown. To address this knowledge gap, we used sensitive and quantitative PCR detection show that people with MS were more likely harbor greater abundance epsilon toxin (ETX)-producing strains C. perfringens within their gut microbiomes compared healthy controls (HC). patient-derived isolates produced functional ETX had...
The exchange of mobile genetic elements (MGEs) facilitates the spread functional traits including antimicrobial resistance within bacterial communities. Tools to spatially map MGEs and identify their hosts in complex microbial communities are currently lacking, limiting our understanding this process. Here we combined single-molecule DNA fluorescence situ hybridization (FISH) with multiplexed ribosomal RNA-FISH enable simultaneous visualization both taxa. We mapped bacteriophage (AMR)...
The mucus layer lining the gastrointestinal tract is essential for gut health, providing a protective barrier against pathogens while maintaining symbiosis with microbiome. Its disruption hallmark of diseases like ulcerative colitis. While glycan foraging by bacteria thought to initiate disruption, its impact on structural properties remains poorly understood, largely due lack physiologically relevant models. To address this gap, we developed method collect human-cell-derived that closely...
Changes in neuronal activity modify the structure of dendritic spines and alter function protein composition synapses. Regulated degradation postsynaptic density (PSD) proteins by ubiquitin-proteasome system is believed to play an important role activity-dependent synaptic remodeling. Stimulating vitro vivo induces ubiquitination GKAP/SAPAP Shank, major scaffold PSD. However, specific ubiquitin ligases that regulate have not been identified. Here we identify RING finger-containing TRIM3 as a...
Large-scale studies of human gut microbiomes have revealed broad differences in composition across geographically distinct populations. Yet, examining impacts microbiome on various health outcomes typically focus single populations, posing the question whether compositional between populations translate into susceptibility. Using germ-free mice humanized with samples from 30 donors representing three countries, we observe robust susceptibility to Citrobacter rodentium, a model for...
The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It been suggested that acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for conferring all classes However, only subset confers clinically relevant antibiotics, and, although these gene profiles are well-characterized common pathogens, less is known about their taxonomic associations and transfer potential within diverse...
Bile acids (BA) are among the most abundant metabolites produced by gut microbiome. Primary BAs in liver converted bacterial 7-α-dehydroxylation into secondary BAs, which can differentially regulate host health via signaling based on their varying affinity for BA receptors. Despite importance of health, regulation and role diet modulating this process is incompletely defined. Understanding could lead to dietary guidelines that beneficially shift metabolism. Dietary fiber regulates microbial...