A5063853901- Gut microbiota and health
- Genomics and Phylogenetic Studies
- SARS-CoV-2 detection and testing
- Clostridium difficile and Clostridium perfringens research
- Fish biology, ecology, and behavior
- Gastrointestinal motility and disorders
- Evolution and Genetic Dynamics
- Microbial Community Ecology and Physiology
- Evolution and Paleontology Studies
- Bacteriophages and microbial interactions
- Fish Ecology and Management Studies
- Genetic diversity and population structure
- Metabolomics and Mass Spectrometry Studies
- Viral gastroenteritis research and epidemiology
- SARS-CoV-2 and COVID-19 Research
- Environmental DNA in Biodiversity Studies
- Vaccine Coverage and Hesitancy
- Radio Astronomy Observations and Technology
- Astrophysics and Cosmic Phenomena
- Molecular Biology Techniques and Applications
- Microscopic Colitis
- Mathematical and Theoretical Epidemiology and Ecology Models
- Healthcare Systems and Technology
- Plant Parasitism and Resistance
- Higher Education and Employability
Massachusetts Institute of Technology
2023-2024
Dalhousie University
2022
North Carolina State University
2018-2021
HM Prison Service
2019
Stanford University
2016
University of Pennsylvania
2011-2013
Roche (United Kingdom)
1975
Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from truth, often dramatically, because these experiments are biased toward detecting some taxa over others. This experimental bias makes taxon or gene abundances measured by different protocols quantitatively incomparable can lead spurious conclusions. We propose a mathematical model for how distorts community based on properties of real...
We present constraints on cosmological and astrophysical parameters from high-resolution microwave background maps at 148 GHz 218 made by the Atacama Cosmology Telescope (ACT) in three seasons of observations 2008 to 2010. A model primary secondary foreground is fit map power spectra lensing deflection spectrum, including contributions both thermal Sunyaev-Zeldovich (tSZ) effect kinematic (kSZ) effect, Poisson correlated anisotropy unresolved infrared sources, radio correlation between tSZ...
Clostridioides difficile is a bacterial pathogen that causes range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against difficile. Disease mediated by two large toxins expression their genes induced upon nutrient depletion via alternative sigma factor TcdR. Here, we use tcdR mutants in strains omics...
To survive, plants and animals must continually defend against pathogenic microbes that would invade disrupt their tissues. Yet they do not attempt to extirpate all microbes. Instead, tolerate even encourage the growth of commensal microbes, which compete with pathogens for resources via direct inhibition. We argue hosts have evolved cooperate commensals in order enhance pathogen resistance this competition provides. briefly describe between within host, consider how natural selection might...
We present a detection of the Sunyaev–Zel'dovich (SZ) decrement associated with luminous red galaxy (LRG) sample Sloan Digital Sky Survey. The SZ data come from 148 GHz maps equatorial region made by Atacama Cosmology Telescope. LRG is divided luminosity into four bins, and estimates for central temperature are calculated through stacking process. detect account bias signal due to weak radio sources. use numerical simulations relate observed Y200 clustering properties halo mass. also...
Human challenge trials (HCTs) have been proposed as a means to accelerate SARS-CoV-2 vaccine development. We identify and discuss 3 potential use cases of HCTs in the current pandemic: evaluating efficacy, converging on correlates protection, improving understanding pathogenesis human immune response. outline limitations find that are likely be most useful for candidates currently preclinical stages conclude that, while limited their application, there scenarios which would extremely...
Abstract Measurements of biological communities by marker-gene and metagenomic sequencing are biased: The measured relative abundances taxa or their genes systematically distorted from true values because each step in the experimental workflow preferentially detects some over others. Bias can lead to qualitatively incorrect conclusions makes measurements different protocols quantitatively incomparable. A rigorous understanding bias is therefore essential. Here we propose, test, apply a...
Abstract Differential-abundance (DA) analyses enable microbiome researchers to assess how microbial species vary in relative or absolute abundance with specific host environmental conditions, such as health status pH. These typically use sequencing-based community measurements that are taxonomically biased measure some more efficiently than others. Understanding the effects taxonomic bias has on results of a DA analysis is essential for achieving reliable and translatable findings; yet...
Abstract Habitat fragmentation and population declines call for informed management of many endangered species. The dominant paradigm such focuses on avoiding deleterious inbreeding effects in separated populations, by facilitating migration to maintain connectivity between them, an approach epitomized the “one migrant per generation” rule. We show that this fails take into account two important factors. First, it ignores inherent trade-off: maintaining within-population genetic diversity is...
Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools make accurate about microbial communities and their functions. More discussion is needed the current state analysis required overcome hurdles preventing development implementation predictive analyses. We summarize ideas generated by participants Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from presentations that...
Abstract Adaptations may require multiple mutations that are beneficial only in combination. To adapt, a lineage must acquire individually neutral or deleterious before gaining the combination, thereby crossing plateau valley, respectively, mapping from genotype to fitness. Spatial population structure can facilitate and valley by allowing lineages survive longer produce more mutants. Here, we analyze adaptation across two-mutation an asexual is subdivided into discrete subpopulations,...
Abstract Background Clostridioides difficile is an enteric pathogen historically known to cause hospital associated (HA)-infections in humans. A major risk factor for CDI humans antibiotic usage as it alters the gut microbiota and there a loss of colonization resistance against C. . In recent years has been increase community (CA)- infection that does not have same factors HA-CDI. Potential sources CA-CDI proposed include animals, food, water, environment, however these remain poorly...
Introductory paragraph Clostridioides difficile is a bacterial pathogen that causes range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against . Disease mediated by two large toxins expression their genes induced upon nutrient depletion via alternative sigma factor TcdR. Using tcdR mutants in strains , we...
This protocol details our workflow for performing concentration and total nucleic acid extraction from wastewater influent the purposes of untargeted RNA DNA sequencing viruses present in wastewater. In this protocol, 200 mL raw is concentrated to a final volume 400 uL using InnovaPrep Concentrating Pipette Select. Prior concentration, sample treated with Tween 20 sonicated dissociate viral particles solids matrix. The then centrifuged remove larger solids. pellet discarded, supernatant...
This protocol details our workflow for performing concentration and total nucleic acid extraction from wastewater influent the purposes of untargeted RNA DNA sequencing viruses present in wastewater. Protocol overview: 200 mL raw is concentrated to a final volume 400 uL using InnovaPrep Concentrating Pipette Select. Prior concentration, sample treated with Tween 20 sonicated dissociate viral particles solids matrix. The then centrifuged pellet larger solids. discarded, supernatant filtered...
This protocol details our workflow for performing concentration and total nucleic acid extraction from aggregated airplane waste the purposes of untargeted RNA DNA sequencing viruses present in wastewater. Protocol overview: In this protocol, 40 mL is concentrated to a final volume 400 uL using InnovaPrep Concentrating Pipette Select. Prior concentration, sample treated with Tween 20 sonicated dissociate viral particles solids wastewater matrix. The filtered 0.45 um PES 75 mm filtration...
This protocol details our workflow for performing concentration and total nucleic acid extraction from wastewater primary sludge (settled solids) the purposes of untargeted RNA DNA sequencing viruses present in wastewater. Protocol overview: In this protocol, 20 mL is concentrated to a final volume 400 uL using InnovaPrep Concentrating Pipette Select. Prior concentration, sample treated with Tween sonicated dissociate viral particles solids matrix. The then centrifuged remove larger solids....