Travis C. Glenn
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View article: Wastewater Genomic Surveillance Captures SARS-CoV-2 Early Detection, Cryptic Transmission, and Variant Dynamics
Wastewater Genomic Surveillance Captures SARS-CoV-2 Early Detection, Cryptic Transmission, and Variant Dynamics Open
Wastewater-based epidemiology (WBE) addresses key biases and limitations in clinical surveillance by providing widespread, population-level coverage, capturing subclinical infections, and mitigating gaps and low rates in clinical testing. …
View article: Evidence of positive selection and a novel phylogeny among five subspecies of song sparrow (<i>Melospiza melodia</i>) in Alaska
Evidence of positive selection and a novel phylogeny among five subspecies of song sparrow (<i>Melospiza melodia</i>) in Alaska Open
Local adaptation occurs when populations evolve traits in response to local environmental challenges. Isolated island populations often experience different selection pressures than their mainland counterparts, which enables the study of h…
View article: Amplicon sequencing detects, identifies, and quantifies minority variants in mixed-species infections of <i>Cryptosporidium</i> parasites
Amplicon sequencing detects, identifies, and quantifies minority variants in mixed-species infections of <i>Cryptosporidium</i> parasites Open
Cryptosporidium is a globally endemic parasite genus with over 40 recognized species. While C. hominis and C. parvum are responsible for most human infections, human cases involving other species have also been reported. Furthermore, there…
View article: Hidden decay of live trees in a tropical rain forest
Hidden decay of live trees in a tropical rain forest Open
The trunks of forest trees store massive amounts of carbon, but fungi actively and invisibly decay wood inside even seemingly healthy trees. Wood‐decay fungi are responsible for the loss of stored carbon in living trees, and they make tree…
View article: New T2T assembly of Cryptosporidium parvum IOWA II annotated with Legacy-Compatible Gene identifiers
New T2T assembly of Cryptosporidium parvum IOWA II annotated with Legacy-Compatible Gene identifiers Open
Cryptosporidium parvum is a significant pathogen causing gastrointestinal infections in humans and animals. It is spread through ingesting contaminated food and water. Despite its global health significance, generating a C. parvum genome s…
View article: Duplex PCR assay to determine sex and mating status of <i>Ixodes scapularis</i> (Acari: Ixodidae), vector of the Lyme disease pathogen
Duplex PCR assay to determine sex and mating status of <i>Ixodes scapularis</i> (Acari: Ixodidae), vector of the Lyme disease pathogen Open
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 for Lyme disease, a disease caused b…
View article: Amplicon sequencing detects, identifies, and quantifies minority variants in mixed-species infections of <i>Cryptosporidium</i> parasites
Amplicon sequencing detects, identifies, and quantifies minority variants in mixed-species infections of <i>Cryptosporidium</i> parasites Open
Cryptosporidium is a globally endemic parasite genus with over 40 recognized species. While C. hominis and C. parvum are responsible for most human infections, human cases involving other species have also been reported. Furthermore, there…
View article: Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing Open
Multiple displacement amplification (MDA) outperforms conventional PCR in long fragment and whole‐genome amplification, making it attractive to couple MDA with long‐read sequencing of samples with limited quantities of DNA to obtain improv…
View article: Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life
Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life Open
The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data…
View article: Deciphering Transcription in<i>Cryptosporidium parvum</i>: Polycistronic Gene Expression and Chromatin Accessibility
Deciphering Transcription in<i>Cryptosporidium parvum</i>: Polycistronic Gene Expression and Chromatin Accessibility Open
Once considered rare in eukaryotes, polycistronic mRNA expression has been identified in kinetoplastids and, more recently, green algae, red algae, and certain fungi. This study provides comprehensive evidence supporting the existence of p…
View article: A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis
A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis Open
View article: Enriching the future of public health microbiology with hybridization bait capture
Enriching the future of public health microbiology with hybridization bait capture Open
SUMMARY 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. Howev…
View article: Duplex PCR assay to determine sex and mating status of<i>Ixodes scapularis</i>(Acari: Ixodidae), vector of the Lyme disease pathogen
Duplex PCR assay to determine sex and mating status of<i>Ixodes scapularis</i>(Acari: Ixodidae), vector of the Lyme disease pathogen Open
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 disea…
View article: Preparation of SARS-CoV-2 Particles in Raw Wastewater Samples for Sequencing on Illumina Platforms Using an ARTIC V4.1 Tiled Amplicon Approach v1
Preparation of SARS-CoV-2 Particles in Raw Wastewater Samples for Sequencing on Illumina Platforms Using an ARTIC V4.1 Tiled Amplicon Approach v1 Open
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 a…
View article: Preparation of SARS-CoV-2 Saliva Samples Using an ARTIC V4.1 Tiled Amplicon Approach for Sequencing on Illumina Platforms v1
Preparation of SARS-CoV-2 Saliva Samples Using an ARTIC V4.1 Tiled Amplicon Approach for Sequencing on Illumina Platforms v1 Open
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 …
View article: Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater
Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater Open
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 SAR…
View article: Evidence of positive selection and a novel phylogeny among five subspecies of song sparrow (<i>Melospiza melodia</i>) in Alaska
Evidence of positive selection and a novel phylogeny among five subspecies of song sparrow (<i>Melospiza melodia</i>) in Alaska Open
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 …
View article: Whole Genome Targeted Enrichment and Sequencing of Human-Infecting Cryptosporidium spp.
Whole Genome Targeted Enrichment and Sequencing of Human-Infecting Cryptosporidium spp. Open
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 fece…
View article: GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING <i>CRYPTOSPORIDIUM</i> spp.
GENOME TARGETED ENRICHMENT AND SEQUENCING OF HUMAN-INFECTING <i>CRYPTOSPORIDIUM</i> spp. Open
Cryptosporidium spp. are parasites that cause severe illness in vulnerable human populations. Obtaining pure and sufficient Cryptosporidium DNA from clinical and environmental samples is a challenging task. Oocysts shed in available fecal …
View article: The repetitive genome of the<i>Ixodes ricinus</i>tick reveals transposable elements have driven genome evolution in ticks
The repetitive genome of the<i>Ixodes ricinus</i>tick reveals transposable elements have driven genome evolution in ticks Open
Ticks are obligate blood-feeding parasites associated with a huge diversity of diseases globally. The hard tick Ixodes ricinus is the key vector of Lyme borreliosis and tick-borne encephalitis in Western Eurasia. Ixodes ticks have large an…
View article: Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny
Testing the mettle of METAL: A comparison of phylogenomic methods using a challenging but well-resolved phylogeny Open
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 us…
View article: A new chromosome-level genome assembly and annotation of<i>Cryptosporidium meleagridis</i>
A new chromosome-level genome assembly and annotation of<i>Cryptosporidium meleagridis</i> Open
Cryptosporidium spp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants and immunosuppressed populations as well as animals. Although most human Cryptosporidium infections are cause…
View article: “Evaluating the Benefits and Limits of Multiple Displacement Amplification with Whole-Genome Oxford Nanopore Sequencing”
“Evaluating the Benefits and Limits of Multiple Displacement Amplification with Whole-Genome Oxford Nanopore Sequencing” Open
Multiple Displacement Amplification (MDA) outperforms conventional PCR in long fragment and whole genome amplification which makes it attractive to couple with long-read sequencing of samples with limited quantities of DNA to obtain improv…
View article: Long-term gut colonization with ESBL-producing<i>Escherichia coli</i>in participants without known risk factors from the southeastern United States
Long-term gut colonization with ESBL-producing<i>Escherichia coli</i>in participants without known risk factors from the southeastern United States Open
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, Ge…
View article: Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture
Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture Open
GITDs are among the most common causes of death in adult and young horses in the United States (US). Previous studies have indicated a connection between GITDs and the equine gut microbiome. However, the low taxonomic resolution of the cur…
View article: The gut-brain axis mediates bacterial driven modulation of reward signaling
The gut-brain axis mediates bacterial driven modulation of reward signaling Open
We concluded from these data that a HF-type microbiota is sufficient to alter appetitive feeding behavior and that bacteria to reward communication is mediated by the vagus nerve.
View article: New T2T assembly of<i>Cryptosporidium parvum</i>IOWA annotated with reference genome gene identifiers
New T2T assembly of<i>Cryptosporidium parvum</i>IOWA annotated with reference genome gene identifiers Open
Cryptosporidium parvum is a significant pathogen causing gastrointestinal infections in humans and animals, that is spread through the ingestion of contaminated food and water. Despite its global impact on public health, generating a C. pa…
View article: A chromosome 16 deletion conferring a high sucrose phenotype in soybean
A chromosome 16 deletion conferring a high sucrose phenotype in soybean Open
View article: Phylogeography of the blacklegged tick (<i>Ixodes scapularis</i>) throughout the USA identifies candidate loci for differences in vectorial capacity
Phylogeography of the blacklegged tick (<i>Ixodes scapularis</i>) throughout the USA identifies candidate loci for differences in vectorial capacity Open
The blacklegged tick ( Ixodes scapularis ( Journal of the Academy of Natural Sciences of Philadelphia , 1821, 2 , 59)) is a vector of Borrelia burgdorferi sensu stricto ( s.s .) ( International Journal of Systematic Bacteriology , 1984, 34…
View article: Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex
Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex Open