A5008546456- Vector-borne infectious diseases
- Viral Infections and Vectors
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Insect symbiosis and bacterial influences
- Identification and Quantification in Food
- Zoonotic diseases and public health
- Wildlife Ecology and Conservation
- Mosquito-borne diseases and control
- Antimicrobial Resistance in Staphylococcus
- Mycobacterium research and diagnosis
- Tuberculosis Research and Epidemiology
- Yersinia bacterium, plague, ectoparasites research
- Species Distribution and Climate Change
- Plant and animal studies
- Animal Disease Management and Epidemiology
- Evolution and Genetic Dynamics
- SARS-CoV-2 and COVID-19 Research
- Herpesvirus Infections and Treatments
- Environmental DNA in Biodiversity Studies
- Bacteriophages and microbial interactions
- Ichthyology and Marine Biology
- Bacterial Identification and Susceptibility Testing
- RNA and protein synthesis mechanisms
- Plant Diversity and Evolution
SUNY Downstate Health Sciences University
2016-2025
State University of New York
2018-2023
Genomics (United Kingdom)
2022-2023
Brooklyn College
2023
Faculty of Public Health
2022-2023
Genomic Health (United States)
2020-2022
American Museum of Natural History
2012-2021
Fordham University
2006-2018
Columbia University
2007-2012
Barnard College
2011-2012
The panoply of microorganisms and other species present in our environment influence human health disease, especially cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, Gowanus Canal, public parks. Nearly half (48%) does match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, eukaryotic taxa, which were enriched for harmless genera associated skin...
Abstract Background Despite being one of the most studied families within Carnivora, phylogenetic relationships among members bear family (Ursidae) have long remained unclear. Widely divergent topologies been suggested based on various data sets and methods. Results We present a fully resolved phylogeny for ursids ten complete mitochondrial genome sequences from all eight living two recently extinct species, European cave ( Ursus spelaeus ) American giant short-faced Arctodus simus ). The...
For more than a century, the origin of metazoan animals has been debated. One aspect this debate centered on what hypothetical “urmetazoon” bauplan might have been. The morphologically most simply organized animal, placozoan Trichoplax adhaerens, resembles an intriguing model for one several hypotheses: placula hypothesis. Clear support basal position Placozoa would aid in resolving key issues metazoan-specific inventions (including, example, head–foot axis, symmetry, and coelom) determine...
It is now widely accepted that novel infectious disease can be a leading cause of serious population decline and even outright extinction in some invertebrate vertebrate groups (e.g., amphibians). In the case mammals, however, there are still no well-corroborated instances such diseases having caused or significantly contributed to complete collapse species. A point endemic Christmas Island rat (Rattus macleari): although it has been argued its disappearance ca. AD 1900 may have partly...
The use of DNA barcodes for the identification described species is one least controversial and most promising applications barcoding. There no consensus, however, as to what constitutes an appropriate standard barcoding efforts simply attempt pair a query sequence with reference sequences deem successful if it falls within bounds some pre-established cutoffs using genetic distance. Since Renaissance, biological classification schemes have relied on diagnostic characters identify place species.
The global trade in wildlife has historically contributed to the emergence and spread of infectious diseases. United States is world's largest importer products, yet minimal pathogen surveillance precluded assessment health risks posed by this practice. This report details findings a pilot project establish methodology for zoonotic agents confiscated products. Initial from samples collected at several international airports identified parts originating nonhuman primate (NHP) rodent species,...
A novel result of the current research is development and implementation a unique functional phylogenomic approach that explores genomic origins seed plant diversification. We first use 22,833 sets orthologs from nuclear genomes 101 genera across land plants to reconstruct their phylogenetic relationships. One more salient results resolution some enigmatic relationships in phylogeny, such as placement Gnetales sister rest gymnosperms. In using this approach, we were also able identify...
Blacklegged ticks (Ixodes scapularis) are one of the most important pathogen vectors in United States, responsible for transmitting Lyme disease and other tick-borne diseases. The structure a host's microbial community has potential to affect ecology evolution host. We employed high-throughput sequencing 16S rRNA gene V3-V4 hypervariable regions first study investigate tick microbiome across all developmental stages (larvae, nymphs, adults). In addition field-collected life stages, newly...
ABSTRACT The arginine catabolic mobile element (ACME) is the largest genomic region distinguishing epidemic USA300 strains of methicillin-resistant Staphylococcus aureus (MRSA) from other S. strains. However, functional relevance ACME to infection and disease has remained unclear. Using phylogenetic analysis, we have shown that modular segments were assembled into a single genetic locus in epidermidis then horizontally transferred common ancestor an extremely recent event. Acquisition one...
Background. The community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic in the United States is attributed to spread of USA300 clone. An CA-MRSA closely related has occurred northern South America (USA300 Latin-American variant, USA300-LV). Using phylogenomic analysis, we aimed understand relationships between these 2 epidemics.
The Great American Biotic Interchange (GABI) was greatly influenced by the completion of Isthmus Panama and impacted composition modern faunal assemblages in Americas. However, contribution preceding events has been comparatively less explored, even though early immigrants fossil records are evidence for waif dispersals. cricetid rodents subfamily Sigmodontinae a classic example species-rich South radiation resulting from an episode North invasion. Here, we provide temporal spatial framework...
Abstract The common bed bug ( Cimex lectularius ) has been a persistent pest of humans for thousands years, yet the genetic basis bug’s basic biology and adaptation to dense human environments is largely unknown. Here we report assembly, annotation phylogenetic mapping 697.9-Mb genome, with an N50 971 kb, using both long short read technologies. A RNA-seq time course across all five developmental stages male female adults generated 36,985 coding noncoding gene models. most pronounced change...
Understanding the emergence of novel viruses requires an accurate and comprehensive annotation their genomes. Overlapping genes (OLGs) are common in have been associated with pandemics but still widely overlooked. We identify characterize ORF3d, a OLG SARS-CoV-2 that is also present Guangxi pangolin-CoVs not other closely related or bat-CoVs. then document evidence ORF3d translation, its protein sequence, conduct evolutionary analysis at three levels: between taxa (21 members Severe acute...
Excessive ingestion of mercury—a health hazard associated with consuming predatory fishes—damages neurological, sensory-motor and cardiovascular functioning. The mercury levels found in Bigeye Tuna ( Thunnus obesus ) bluefin tuna species maccoyii , orientalis thynnus ), exceed or approach permissible by Canada, the European Union, Japan, US, World Health Organization. We used DNA barcodes to identify sushi samples analysed for demonstrate that ability cryptic market place allows regulatory...
Summary S taphylococcus aureus has evolved as a pathogen that causes range of diseases in humans. There are two dominant modes evolution thought to explain most the virulence differences between strains. First, genes may be acquired from other organisms. Second, mutations cause changes regulation and expression genes. Here we describe an evolutionary event which transposition IS element direct impact on gene resulting hypervirulence. Whole‐genome analysis methicillin‐resistant . ( MRSA )...
Extinctions and declines of large marine vertebrates have major ecological impacts are critical concern in environments. The Caribbean monk seal, Monachus tropicalis, last definitively reported 1952, was one the few mammal species to become extinct historical times. Despite its importance for understanding evolutionary biogeography southern phocids, relationships M. tropicalis two living critically endangered seals not been resolved. In this study we present first molecular data derived from...
Abstract The conservation of humpback dolphins, distributed in coastal waters the Indo‐West Pacific and eastern Atlantic Oceans, has been hindered by a lack understanding about number species genus ( Sousa ) their population structure. To address this issue, we present combined analysis genetic morphologic data collected from beach‐cast, remote‐biopsied museum specimens throughout known range. We extracted sequence 235 samples extant populations explored mitochondrial control region four...
Ancient DNA sequences are able to offer valuable insights into molecular evolutionary processes, which not directly accessible via modern DNA. They particularly suitable for the estimation of substitution rates because their ages provide calibrating information in phylogenetic analyses, circumventing difficult task choosing independent calibration points. The obtained from such datasets have typically been high, falling between estimated pedigrees and species phylogenies. Many these...
Background The international wildlife trade is a key threat to biodiversity. Temporal genetic marketplace monitoring can determine if regulation efforts such as the Convention on International Trade in Endangered Species (CITES) are succeeding. Protected under CITES effective 1997, sturgeons and paddlefishes, producers of black caviar, flagship species. Methodology/Principal Findings We test whether has limited amount fraudulent caviar reaching marketplace. Using mitochondrial DNA-based...
Background. Blacklegged ticks (Ixodes scapularis) are important disease vectors in the United States, known to transmit a variety of pathogens humans, including bacteria, protozoa, and viruses. Their importance as vector necessitates reliable comparable methods for extracting microbial DNA from ticks. Furthermore, explore population genetics or genomics this tick, appropriate extraction techniques needed both its microbes. Although few studies have investigated different isolation ticks,...
Abstract Little is known about the population structure of vancomycin-resistant Enterococcus faecium (VR Efm ) in Latin America (LATAM). Here, we provide a complete genomic characterization 55 representative American VR recovered from 1998–2015 5 countries. The LATAM structured into two main clinical clades without geographical clustering. Using genomes, reconstructed global by including 285 genomes 36 countries spanning 1946 to 2017. In contrast previous studies, our results show an early...