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Introduction
I make DNA tools and genomic resources to answer a broad range of questions with relevance to environmental health.
Skills and Expertise
Education
January 1991 - May 1997
Publications
Publications (610)
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model or...
Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconser...
The diversity of available 2(nd) and 3(rd) generation DNA sequencing platforms is increasing rapidly. Costs for these systems range from < $100,000 to more than $1,000,000, with instrument run times ranging from minutes to weeks. Extensive trade-offs exist among these platforms. I summarize the major characteristics of each commercially available p...
Cryptosporidium spp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants, immunosuppressed populations and many animals. Although most human Cryptosporidium infections are caused by C. parvum and C. hominis, there are several other human-infecting species including C. meleagridis, which are c...
Public health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to...
Ticks are a major health threat to humans and other animals, through direct damage, toxicoses, and transmission of pathogens. An estimated half a million people are treated annually in the United States of America for Lyme disease, a disease caused by the bite of a black-legged tick ( Ixodes scapularis Say) infected with the bacterial pathogen Borr...
This protocol describes how to prepare purified SARS-CoV-2 RNA from raw wastewater samples for short-read sequencing. The initial targeted amplification utilizes the commercially available IDT ARTIC V4.1 tiled amplicon panel, followed by amplification with IDT custom-ordered fusion primers that follow the same amplicon scheme, allowing for further...
This protocol describes how to prepare purified SARS-CoV-2 RNA from positive saliva samples for short-read sequencing. The initial targeted amplification utilizes the commercially available IDT ARTIC V4.1 tiled amplicon panel, followed by amplification with IDT custom-ordered fusion primers that follow the same amplicon scheme, allowing for further...
During the COVID-19 pandemic, the detection and sequencing of SARS-CoV-2 from wastewater proved to be a valuable tool in assessing trends at the community level. Several whole genome enrichment methods have been proposed for sequencing SARS-CoV-2 from the mixed wastewater community, but there is little consensus on the most appropriate sequencing m...
Antimicrobial resistance (AMR) is an urgent global public health threat, affecting human health, veterinary care, agricultural production, and ecological systems. Effectively combating AMR requires a better understanding of how the genes that confer resistance are distributed and move among bacteria, hosts, and the environment. New methods are need...
Numerous pharmaceutical and industrial chemicals are classified as endocrine‐disrupting chemicals (EDCs) that interfere with hormonal homeostasis, leading to developmental disorders and other pathologies. The synthetic estrogen 17α‐ethynylestradiol (EE2) is used in oral contraceptives and other hormone therapies. EE2 and other estrogens are inadver...
Under local adaptation, populations evolve traits in response to the local environment. Isolated island populations often experience different selection pressures than their mainland counterparts, which enables the study of how phenotypes and genotypes respond to different selection regimes. We used a group of five phenotypically differentiated sub...
Cryptosporidium spp. are protozoan parasites that cause severe illness in vulnerable human populations. Obtaining pure Cryptosporidium DNA from clinical and environmental samples is challenging because the oocysts shed in contaminated feces are limited in quantity, difficult to purify efficiently, may derive from multiple species, and yield limited...
Cryptosporidiosis— caused by several Cryptosporidium species— is typically diagnosed by microscopic examination of clinical fecal samples. Single-marker PCR has permitted species and subtype classification. However, single-marker approaches restrict our understanding of the entire genome in this obligately sexual organism. Thus, associations betwee...
Genome-scale sequencing is important in the study of infectious diseases, but preparing DNA samples for such sequencing can be constrained by the need for specialized equipment, expensive reagents, and higher input DNA than is readily available. Cryptosporidium oocysts are shed into feces, making it difficult and expensive to purify and yielding li...
The evolutionary histories of different genomic regions typically differ from each other and from the underlying species phylogeny. This makes species tree estimation challenging. Here, we examine the performance of phylogenomic methods using a well-resolved phylogeny that nevertheless contains many difficult nodes, the species tree of living birds...
We evaluated gut carriage of extended spectrum beta lactamase producing Enterobacteriaceae (ESBL-E) in southeastern U.S. residents without recent in-patient healthcare exposure. Study enrollment was January 2021-February 2022 in Athens, Georgia, U.S. and included a diverse population of 505 adults plus 50 child participants (age 0-5). Based on cult...
Simple Summary
Gastrointestinal tract disorders (GITDs) are a serious problem for both adult and young horses. In many cases, the sources of these disorders are unknown, and a link with alterations of the gastrointestinal (GI) microbiome (i.e., GI dysbiosis) is suspected. New alternatives to conventional amplicon sequencing are needed to decipher t...
Key message
Sucrose in soybean seeds is desirable for many end-uses. Increased sucrose contents were discovered to associate with a chromosome 16 deletion resulting from fast neutron irradiation.
Abstract
Soybean is one of the most economically important crops in the United States. A primary end-use of soybean is for livestock feed. Therefore, gen...
The blacklegged tick, (Ixodes scapularis Say 1821) is a vector of Borrelia burgdorferi sensu stricto (s.s.) Johnson et al. 1984, the causative bacterial agent of Lyme disease, part of a slow-moving epidemic of Lyme borreliosis spreading across the northern hemisphere. Well-known geographic differences in the vectorial capacity of these ticks are as...
The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspeci...
Ixodes spp. and related ticks transmit prevalent infections, although knowledge of their biology and development of anti-tick measures have been hindered by the lack of a high-quality genome. In the present study, we present the assembly of a 2.23-Gb Ixodes scapularis genome by sequencing two haplotypes within one individual, complemented by chromo...
The Gulf Coast tick, Amblyomma maculatum, inhabits the Southeastern states of the USA bordering the Gulf of Mexico, Mexico, and other Central and South American countries. More recently, its U.S. range has extended West to Arizona and Northeast to New York state and Connecticut. It is a vector of Rickettsia parkeri and Hepatozoon americanum. This t...
Total mercury (THg) concentrations were measured in wild alligators inhabiting a coastal marsh in southern Louisiana, to determine the tissue distribution of THg among various body organs and tissue compartments. Concentrations of THg in claws and dermal tail scutes were compared to those in blood, brain, gonad, heart, kidney, liver, and skeletal m...
Avian influenza (AI) is a zoonotic disease that will likely be involved in future pandemics. Because waterbird movements are difficult to quantify, determining the host-specific risk of Eurasian-origin AI movements into North America is challenging. We estimated relative rates of movements, based on long-term evolutionary averages of gene flow, bet...
Avian influenza (AI) is an emerging zoonotic disease that will likely be involved in future pandemics. Because waterbird movements are difficult to quantify, determining the host-specific risk of Eurasian-origin AI movements into North America is challenging. We estimated relative rates of movements, based on long-term evolutionary averages of gene...
The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal ( Anas crecca ) complex is a Holarctic species of dabbling duck currently categorized as three subspe...
Finding, characterizing, and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive, and cost‐effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples....
The prevalence of antibiotic resistance genes (ARGs) can be driven by direct selection from antibiotic use and indirect selection from substances such as heavy metals (HMs). While significant progress has been made to characterize the influence of HMs on the enrichment and dissemination of ARGs in the environment, there is still much we do not know...
Finding, characterizing, and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive, and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples....
Triatominae are the largest radiation of haematophagous species within the true bugs (Hemiptera) and the sole vectors of Trypanosoma cruzi Chagas, the causative agent of Chagas disease, a neglected human disease that affects millions. We used a combined ultraconserved element (UCE) and ribosomal dataset from ethanol‐preserved and pinned specimens i...
We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome of L. monocytogenes. Our a...
• Sharks are a priority for conservation because numerous species, including small‐sized coastal species, are being heavily exploited by commercial and recreational fisheries. Understanding the genetic population structure of sharks is key to effective management, maximizing their evolutionary potential in a rapidly changing environment and prevent...
Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic metho...
We have developed an open-source tool ( https://github.com/swarnalilouha/Haplo-ST ) that provides allele-based subtyping of L. monocytogenes isolates at the whole-genome level. Along with allelic profiles, this tool also generates allele sequences and identifies paralogs, which is useful for phylogenetic tree reconstruction and deciphering relation...
We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome of L. monocytogenes . Our...
To meet growing global food demand, producers are actively searching for ways tocrop yield. One way to boost yield is to reduce arthropod damage. However, insecticides are becoming less effective and can have detrimental effects on human health and the environment. Learning how to harness natural pest control is one way to reduce arthropod damage t...
Selenium represents an essential trace nutrient that is necessary for biological functions. Deficiencies can induce disease, but excess can induce toxicity. Selenium deficiency is a major concern in underdeveloped countries, while also posing as a toxic pollutant in waterways surrounding landfills, agricultural areas, and fossil fuel production sit...
Chagas disease is a zoonosis that affects several million people and is caused by the parasite Trypanosoma cruzi, which is mainly transmitted through the feces of triatomine bugs. Within triatomines, several Rhodnius species have been found inhabiting palms, and certain factors such as palm species and location have been related to the abundance an...
Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans‐Beringian distribution, where Asian and North A...
A reliable and standardized classification of Listeria monocytogenes ( Lm ) is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS) based approaches for strain characterization either lack standardization, rendering them less suitable for data exchange, or are not freely available. Thus,...
Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co‐selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relat...
Rhodnius pallescens is the principal vector of Chagas disease in Panama. Recently a dark chromatic morph has been discovered in the highlands of Veraguas Province. Limited genetic studies have been conducted with regards to the population structure and dispersal potential of Triatominae vectors, particularly in R. pallescens. Next generation sequen...
MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to bird...
Most of the research efforts involving the bovine gastrointestinal microbiota have focused on cattle’s forestomach, particularly the rumen, so information concerning the bovine fecal microbiota is more scarce, especially in young beef cattle. The present study was performed to evaluate the ruminal and fecal microbiotas of beef calves as they reache...
The song sparrow, Melospiza melodia , is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species' pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We...
Phellinus noxius is a root-decay pathogen with a pan-tropical/subtropical distribution that attacks a wide range of tree hosts. For this study, genomic sequencing was conducted on P. noxius isolate P919-02W.7 from Federated States of Micronesia (Pohnpei), and its gene expression profile was analyzed using different host wood (Acer, Pinus, Prunus, a...
Crocodilians are an economically, culturally, and biologically important group. To improve researchers' ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro...
The song sparrow, Melospiza melodia , is one of the most widely distributed species of songbirds found in North America. It has been used in a wide range of behavioral and ecological studies. This species’ pronounced morphological and behavioral diversity across populations makes it a favorable candidate in several areas of biomedical research. We...
Key message
Protein content of soybean is critical for utility of soybean meal. A fast-neutron-induced deletion on chromosome 12 was found to be associated with increased protein content.
Abstract
Soybean seed composition affects the utility of soybean, and improving seed composition is an essential breeding goal. Fast neutron radiation introduces...
S. Heidelberg is a clinically important serovar, linked to foodborne illness and among the top 5 serovars isolated from poultry in the United States and Canada. Acquisition of new genetic material from the microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heid...
Background:
Triatomine bugs are vectors of the protozoan parasite Trypanosoma cruzi, which causes Chagas disease. Rhodnius pallescens is a major vector of Chagas disease in Panama. Understanding the microbial ecology of disease vectors is important in the development of vector management strategies that target vector survival and fitness. In this...
Next-generation DNA sequencing (NGS) offers many benefits, but major factors limiting NGS include reducing costs of: 1) start-up (i.e., doing NGS for the first time); 2) buy-in (i.e., getting the smallest possible amount of data from a run); and 3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in...
Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR p...
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it...
Crocodilians are an economically, culturally, and biologically important group. To improve researchers' ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus , from Illumina short read data from genomic libraries and in vitro...
Our previous study showed heritable reproductive toxicity in the nematode Caenorhabditis elegans after multigenerational exposure to AgNO3 and silver nanoparticles (Ag-NPs). The aim of this study was to determine whether such inheritable effects are correlated with induced germline mutations in C. elegans. Individual C. elegans lineages were expose...
Environmental contaminants, such as the trace element selenium (Se), are a continuing concern to species worldwide due to their potential pathophysiological effects, including their influence on the stress response mediated through glucocorticoids (GCs; stress hormones). Environmental concentrations of Se are increasing due to anthropogenic activit...
The chicken gastrointestinal tract harbors taxa of microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich en...
Background: Oil palm plantation establishment in Colombia has the potential to impact Chagas disease transmis-sion by increasing the distribution range of Rhodnius prolixus. In fact, previous studies have reported Trypanosoma cruzi natural infection in R. prolixus captured in oil palms (Elaeis guineensis) in the Orinoco region, Colombia. The aim of...
A study was conducted to examine the effects of supplementing beef calves during their suckling phase (popularly known as creep feeding) with supplements that contained or did not contain the enzyme xylanase. Forty-two cow-calf pairs were divided into three groups and assigned to one of three treatments for a period of 105 days, as follows: (1) No...
Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. Most NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. I...
Molecular ecologists have used genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from individuals being studied (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently. Here, we present...
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncert...
Bromate (BrO3-) is a water disinfection byproduct (DBP) previously shown to induce nephrotoxicity in vitro and in vivo. We recently showed that inhibitors of DNA methyltransferase 5-aza-2'-deoxycytidine (5-Aza) and histone deacetylase trichostatin A (TSA) increased BrO3- nephrotoxicity whereas altering the expression of the cyclin-dependent kinase...