Emily K. Cope
A5012356079- Sinusitis and nasal conditions
- Gut microbiota and health
- Nasal Surgery and Airway Studies
- Pediatric health and respiratory diseases
- Asthma and respiratory diseases
- Clostridium difficile and Clostridium perfringens research
- Mycobacterium research and diagnosis
- Oral microbiology and periodontitis research
- Bacterial biofilms and quorum sensing
- Allergic Rhinitis and Sensitization
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Tryptophan and brain disorders
- Scientific Computing and Data Management
- Respiratory and Cough-Related Research
- Probiotics and Fermented Foods
- Antimicrobial Peptides and Activities
- Tracheal and airway disorders
- Legionella and Acanthamoeba research
- Genetics, Bioinformatics, and Biomedical Research
- Crystallization and Solubility Studies
- Eosinophilic Esophagitis
- Air Quality and Health Impacts
- Cystic Fibrosis Research Advances
- Indoor Air Quality and Microbial Exposure
Northern Arizona University
2014-2024
North Carolina State University
2023
Flagstaff Medical Center
2022
York College of Pennsylvania
2020
University of California, San Francisco
2013-2017
Translational Genomics Research Institute
2017
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Silver carbenes may represent novel, broad-spectrum antimicrobial agents that have low toxicity while providing varying chemistry for targeted applications. Here, the bactericidal activity of four silver carbene complexes (SCCs) with different formulations, including nanoparticles (NPs) and micelles, was tested against a panel clinical strains bacteria fungi are causative many skin soft tissue, respiratory, wound, blood, nosocomial infections. MIC, MBC multidose experiments were conducted...
Chronic rhinosinusitis (CRS) is a heterogeneous disease characterized by persistent sinonasal inflammation and sinus microbiome dysbiosis. The basis of this heterogeneity poorly understood. We sought to address the hypothesis that limited number compositionally distinct pathogenic bacterial microbiota exist in CRS patients invoke discrete immune responses clinical phenotypes patients. Sinus brushings from with (n = 59) healthy individuals 10) collected during endoscopic surgery were analyzed...
The role of microbiota in sinonasal inflammation can be further understood by targeted sampling healthy and diseased subjects. We compared the middle meatus (MM) inferior (IM) healthy, allergic rhinitis (AR), chronic rhinosinusitis (CRS) subjects to characterize intrasubject, intersubject, intergroup differences.Subjects were recruited office, characterized into AR, CRS groups. Endoscopically-guided swab samples obtained from MM IM bilaterally. Bacterial sequencing V3-V4 region 16S ribosomal...
In this study we examined changes to the human gut microbiome resulting from an eight-week intervention of either cardiorespiratory exercise (CRE) or resistance training (RTE). Twenty-eight subjects (21 F; aged 18–26) were recruited for our CRE and 28 (17 18–33) RTE study. Fecal samples profiling collected twice weekly during pre-intervention phase (three weeks), (eight post-intervention weeks). Pre/post VO2max, three repetition maximum (3RM), body composition measurements conducted. Heart...
Recent studies have demonstrated alterations in the gut microbiota composition mice modeling Alzheimer’s disease (AD) pathologies; however, these only included up to 4 time points. Our study is first of its kind characterize a transgenic AD mouse model, fortnightly, from weeks age 52 age, quantify temporal dynamics microbial that correlate with development pathologies and host immune gene expression.
Cigarette smokers and those exposed to second hand smoke are more susceptible life threatening infection than non-smokers. While much is known about the devastating effect tobacco exposure has on human body, less of commensal commonly found pathogenic bacteria respiratory tract, or tract microbiome. Chronic rhinosinusitis (CRS) a common medical complaint, affecting 16% US population with an estimated aggregated cost $6 billion annually. Epidemiologic studies demonstrate correlation between...
Abstract The sinonasal microbiome remains poorly defined, with our current knowledge based on a few cohort studies whose findings are inconsistent. Furthermore, the variability of sinus across geographical divides unexplored. We characterize and its variations in both health disease using 16S rRNA gene sequencing 410 individuals from world. Although microbial ecology is highly variable between individuals, we identify core comprised Corynebacterium , Staphylococcus Streptococcus Haemophilus...
Chronic type 2 (T2) inflammatory diseases of the respiratory tract are characterized by mucus overproduction and disordered mucociliary function, which largely attributed to effects IL-13 on common epithelial cell types (mucus secretory ciliated cells). The role rare cells in airway T2 inflammation is less clear, though tuft have been shown be critical initiation immunity intestine. Using bulk single-cell RNA sequencing epithelium mouse modeling, we found that expanded programmed toward...
Abstract Background Upper small intestinal dietary lipids activate a gut-brain axis regulating energy homeostasis. The prebiotic, oligofructose (OFS) improves body weight and adiposity during metabolic dysregulation but the exact mechanisms remain unknown. This study examines whether alterations to microbiota following OFS treatment improve lipid-sensing regulate food intake in high fat (HF)-fed rats. Results In rats fed HF diet for 4 weeks, supplementation decreased meal size within 2 days,...
Epithelial remodeling is a histopathologic feature of chronic inflammatory airway diseases including rhinosinusitis (CRS). Cell-type shifts and their relationship to CRS endotypes severity are incompletely described.
A series of N-heterocyclic carbene silver complexes have been synthesized and tested against the select group bio-safety level 3 bacteria Burkholderia pseudomallei, mallei, Bacillus anthracis, methicillin-resistant Staphylococcus aureus Yersinia pestis. Minimal inhibitory concentrations, minimal bactericidal killing assays demonstrated exceptional efficacy these potentially weaponizable pathogens.
BackgroundThe length of time that people with HIV on antiretroviral therapy (ART) viral load suppression will be able to continue before developing rebound is unknown. We aimed investigate the rate first in have achieved initial ART, determine factors associated rebound, and use these estimates predict long-term durability suppression.MethodsThe UK Collaborative Cohort (UK CHIC) Study an ongoing multicentre cohort study brings together a standardised format data attending clinics around UK....
Recent evidence has highlighted important associations between obstructive sleep apnea and the microbiome. Although intricacies of pathophysiologic mechanisms are not well understood, available suggests a bidirectional relationship microbiota composition. Sleep fragmentation, intermittent hypoxia, hypercapnia all play significant roles in altering microbiome, initial shown that alterations affect patterns. Animal model strongly supports idea microbiome mediates disease states associated with...
Chronic rhinosinusitis (CRS) is a common inflammatory disease of the sinonasal cavity mediated, in part, by polymicrobial communities bacteria. Recent molecular studies have confirmed importance Streptococcus pneumoniae and nontypeable Haemophilus influenzae (NTHi) CRS. Here, we hypothesize that interaction between S. NTHi mixed-species cause change bacterial virulence gene expression. We examined CRS as model human to validate these interactions. Clinical strains were grown mono- co-culture...
The respiratory tract is a complex system that inhabited by niche-specific communities of microbes including bacteria, fungi, and viruses. These microbial assemblages are in constant contact with the mucosal immune play critical role airway health homeostasis. Changes composition diversity microbiota frequently observed patients chronic inflammatory diseases rhinosinusitis (CRS), cystic fibrosis, allergy, asthma. While bacterial microbiome upper lower airways has been focus many recent...
This study offers a novel description of the sinonasal microbiome, through an unsupervised machine learning approach combining dimensionality reduction and clustering. We apply our method to International Sinonasal Microbiome Study (ISMS) dataset 410 sinus swab samples. propose three main "microbiotypes" or "states": first is