Biology subjects

Vaughn, J.

Publications and source records attributed to Vaughn, J..

6 recordsLinked to original sources

bioRxiv2025

Comparative Analysis of Tick Microbiomes in Remnant and Reconstructed Prairie Ecosystems

The ecological processes that shape tick-associated microbial communities are not fully understood. Ticks harbor diverse microbial communities that include both symbiotic and pathogenic bacteria, and these microbes can influence tick physiology, vector competence, and pathogen transmission. We evaluated bacterial microbiome diversity and composition in two medically important tick species, Amblyomma americanum and Dermacentor variabilis, collected from remnant and reconstructed tallgrass prairies in central Missouri between 2020 and 2023. Using 16S rRNA gene amplicon sequencing, we characterized microbial communities from 200 pooled tick samples and assessed patterns in alpha diversity, beta diversity, and differential abundance across tick species and prairie types. Microbiome diversity and composition differed strongly between tick species, with D. variabilis exhibiting higher alpha diversity than A. americanum and clear species-specific clustering in beta diversity analyses. In contrast, differences between remnant and reconstructed prairies were modest. Differential abundance testing revealed Rickettsia to be enriched in A. americanum and Francisella in D. variabilis, consistent across prairie types. Species-level screening further showed that A. americanum primarily harbored low virulent Rickettsia, whereas D. variabilis more frequently carried pathogenic Rickettsia species. Prairie restoration status did not significantly predict Rickettsia type, although a higher proportion of potentially pathogenic lineages was observed in reconstructed sites. These findings indicate that tick species identity is the primary determinant of microbiome structure in prairie ecosystems, with habitat context exerting secondary influences. Our results underscore the importance of incorporating microbiome ecology into medical entomology and suggest that land management practices may subtly shape vector-microbe interactions relevant to disease risk.

ecology↗

bioRxiv2025

Genomic Characterization of Novel Endophyte Strains from Tall Fescue Shows Genome Fragmentation Post-Hybridization

Interspecific hybridization in fungi has gained attention for its role in fungal evolution and potential commercial applications. Successful hybridization can enhance fitness and facilitate adaptation to new ecological niches. However, the genomic consequences of hybridization in fungi remain poorly understood. Epichloe is a genus of fungi that includes both non-hybrid and hybrid species, with the hybrids forming through parasexual hybridization and reproducing asexually. Some Epichloe hybrids are of commercial significance, as they colonize Lolium arundinaceum (Schreb.) Darbysh., a crucial forage and turf grass species. In this study, we sought to generate high-quality genome assemblies for two previously uncharacterized Epichloe hybrid strains, both of which are similar to Epichloe sp. FaTG-3. We aimed to characterize their genomes and examine the effects of parasexual interspecific hybridization on fungal genome structure. Our results reveal that the genomes of both strains are rich in AT-rich blocks and repetitive elements. Upon comparison with putative progenitor genomes, we observed significant fragmentation and rearrangement. Despite the genomic instability, more than 85% of gene homologs from each progenitor species were retained. This study demonstrates that while parasexual hybridization dramatically alters genome structure, it does not significantly affect gene content.

genomics↗

bioRxiv2025

Long-Read Low-Pass Sequencing for High-Resolution Trait Mapping

Accelerating crop improvement is critical to meeting food security demands in a changing climate. Long-read sequencing offers advantages over short-reads in resolving structural variations (SVs) and aligning to complex genomes, but its high cost has limited adoption in breeding programs. Here we develop a high-throughput, scalable approach for long-read low-pass (LRLP) sequencing and variant analysis with PacBio HiFi reads, and apply it to trait mapping in a complex tetraploid peanut (Arachis hypogaea) genome multi-parent advanced generation intercross. We analyze LRLP using both a single reference genome and a pangraph, using both proprietary and open-source tools to analyze SVs and coverage. An increased number of variants are consistently called for LRLP data compared to short-read data. At 1.63x average depth, LRLP sequencing covered 55% of the genome and 58% of gene space, outperforming 1.68x depth short-read low-pass sequencing, which achieved only 17% and 11%, respectively. Enhanced data retention after filtering for probabilistic misalignment and an [~]8.5x decrease in cost per value further demonstrated LRLPs efficacy. Our results highlight LRLP sequencing as a scalable, cost-effective tool for high-resolution trait mapping, with transformative potential for plant breeding and broader genomic applications.

genetics↗

bioRxiv2022

Evaluating instruments for assessing healthspan: a multi-center cross-sectional study on health-related quality of life (HRQL) and frailty in the companion dog

Developing valid tools that assess key determinants of canine healthspan such as frailty and health-related quality of life (HRQL) is essential to characterizing and understanding aging in dogs. Additionally, because the companion dog is an excellent translational model for humans, such tools can be applied to evaluate gerotherapeutics and investigate mechanisms underlying longevity in both dogs and humans. In this multi-center, cross sectional study, we investigated the use of a clinical questionnaire (Canine Frailty Index; CFI; Banzato et al., 2019) to assess frailty and an owner assessment tool (VetMetrica HRQL) to evaluate HRQL in 451 adult companion dogs. Results demonstrated validity of the tools by confirming expectations that frailty and HRQL deteriorate with age. CFI scores were significantly higher (higher frailty) and HRQL scores significantly lower (worse HRQL) in old dogs ([≥] 7 years of age) compared to young dogs ([≥] 2 and < 6 years of age). Body size (small < 25lbs or large > 50lbs) was not associated with CFI or total HRQL score. However, older, larger dogs showed faster age-related decline in HRQL scores specific to owner-reported activity and comfort. Findings suggest that the clinician-assessed CFI and owner-reported VetMetrica HRQL are useful tools to evaluate two determinants of healthspan in dogs: the accumulation of frailty and the progressive decline in quality of life. Establishing validated tools that operationalize the assessment of canine healthspan is critical for the advancement of geroscience and the development of gerotherapeutics that benefit both human and veterinary medicine. Graphical abstractGraphical summary of the design, results, and conclusions of the study. O_FIG O_LINKSMALLFIG WIDTH=179 HEIGHT=200 SRC="FIGDIR/small/500746v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1d70950org.highwire.dtl.DTLVardef@a4748borg.highwire.dtl.DTLVardef@df6892org.highwire.dtl.DTLVardef@14a7aed_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2019

Relating anthropometric indicators to brain structure in 2-month-old Bangladeshi infants growing up in poverty: a pilot study

Anthropometric indicators, including stunting, underweight, and wasting, have previously been associated with poor neurocognitive outcomes. This link may exist because malnutrition and infection, which are known to affect height and weight, also impact brain structure according to animal models. However, a relationship between anthropometric indicators and brain structural measures has not been tested yet, perhaps because stunting, underweight, and wasting are uncommon in higher-resource settings. Further, with diminished anthropomorphic growth prevalent in low-resource settings, where biological and psychosocial hazards are most severe, one might expect additional links between measures of poverty, anthropometry, and brain structure. To begin to examine these relationships, we conducted an MRI study in 2-3-month-old infants growing up in the extremely impoverished urban setting of Dhaka, Bangladesh. The sample size was relatively small because the challenges of investigating infant brain structure in a low-resource setting needed to be realized and resolved before introducing a larger cohort. Initially, fifty-four infants underwent T1 sequences using 3T MRI, and structural images were segmented into gray and white matter maps, which were carefully evaluated for accurate tissue labeling by a pediatric neuroradiologist. Gray and white matter volumes from 29 infants (79 {+/-} 10 days-of-age; F/M = 12/17), whose segmentations were of relatively high quality, were submitted to semi-partial correlation analyses with stunting, underweight, and wasting, which were measured using height-for-age (HAZ), weight-for-age (WAZ), and weight-for-height (WHZ) scores. Positive semi-partial correlations (after adjusting for chronological age and sex and correcting for multiple comparisons) were observed between white matter volume and HAZ and WAZ; however, WHZ was not correlated with any measure of brain volume. In examining the role of poverty, no associations were observed between income-to-needs or maternal education and brain volumetric measures, suggesting that risk factors previously linked with poverty were not associated with total brain tissue volume pre- or peri-natally in this sample. Overall, these results provide the first link between diminished anthropomorphic growth and white matter volume in infancy. Challenges of conducting a developmental neuroimaging study in a low-resource country are described.

neuroscience↗

bioRxiv2018

Mechanisms of Host Cell Binding and Neurotropism of Zika Virus

Zika virus (ZIKV) recently emerged in the Western Hemisphere with previously unrecognized or unreported clinical presentations. Here, we identify two distinct binding mechanisms of ancestral and emergent ZIKV strains featuring the envelope (E) protein residue ASN154 and viral phosphatidylserine (PS). Short (20-mer) peptides representing the region containing ASN154 from strains PRVABC59 (Puerto Rico 2015) and MR_766 (Uganda 1947) were exposed to neuronal cells and fibroblasts, expecting interactions to be representative of ZIKV E protein/cell interactions, and bound MDCK or Vero cells and primary neurons significantly above a scrambled PRVABC59 control peptide. Peptides also significantly inhibited Vero cell adsorption by ZIKV strains MR_766 and PRVABC59, indicating that we have identified a binding mechanism of ancestral African ZIKV strains and emergent Western Hemisphere strains.\n\nPretreatment of ZIKV MR_766 and PRVABC59 with the PS-binding protein annexin V significantly inhibited replication of PRVABC59, but not MR_766, suggesting that Western hemisphere strains are additionally utilizing PS-mediated entry to infect host cells. Taken together, these data indicate that we have identified an ancestral binding mechanism of ZIKV, and a secondary binding mechanism utilized by Western Hemisphere strains.

microbiology↗