Biology subjects

Davis, D. D.

Publications and source records attributed to Davis, D. D..

4 recordsLinked to original sources

bioRxiv2026

Genomics and CT imaging reveal diversity in silk genes and gland morphology of webspinners

Webspinners (Insecta: Embioptera) are an unusual insect order that are known for their subsocial behavior and prolific silk-production. Due to their unique foreleg silk glands, and spider-like ability to produce silk throughout their entire life cycle, webspinners are hypothesized to have evolved silk independently from other arthropod lineages. To date, there are no reference-quality genomes available for the order, preventing the study of their silk gene origination and diversification. Here, we assembled PacBio HiFi reference genomes and characterized the silk genes present in two webspinner species, Aposthonia ceylonica and Oligotoma nigra. The genomes reveal multiple full-length copies of the primary Embioptera silk gene, e-fibroin, that have undergone both ancestral and recent gene duplications within the group. For both species, all e-fibroin paralogs show the presence of complex repeat units consisting of multiple exons and introns that are remarkably homogenized across each gene. We also used CT-scanning of the internal silk glands to provide details concerning the localization of silk production in foreleg tarsi, and interspecific morphology. Article summaryThis study introduces the first high-quality genomes for webspinners, enabling new research on silk for evolutionary biologists and materials scientists alike. The authors sequenced two embiopteran species, Aposthonia ceylonica and Oligotoma nigra, to compare silk genes and gland structure using micro-computed tomography, an imaging method that shows internal anatomy in detail. They found multiple copies of the primary silk gene in both species that likely arose from multiple duplication events at different evolutionary times. These silk genes exhibit unusual gene structure with hierarchically organized repeat units that are highly homogenized within a gene. The findings show that silk genes have a complex evolutionary history in webspinners and provide a foundation for studying silk diversity within the order, and in the broader context of insect silk.

evolutionary biology↗

bioRxiv2025

Exposure of male mice to nicotine leads to metabolic dysfunction in their male and female offspring

Paternal exposure to nicotine has been linked to altered metabolic phenotypes in offspring, yet the underlying mechanisms and sex-specific outcomes remain elusive. In this study, we investigated the effects of paternal nicotine exposure on glucose metabolism, and adipose tissue and liver transcriptomic profiles in male and female offspring. Despite no differences in body weight during early postnatal life, female offspring displayed lower fasting glucose and reduced glucose levels during glucose tolerance tests, without alterations in insulin sensitivity. These effects were accompanied by decreased circulating insulin and upregulation of genes involved in the insulin signaling pathway in gonadal white adipose tissue (gWAT), consistent with enhanced glucose uptake capacity. In contrast, male offspring showed no overt changes in glucose tolerance or insulin sensitivity, despite reduced plasma insulin and glucagon levels. In male offspring, liver transcriptomic analyses revealed downregulation of glucagon signaling, insulin resistance, and PPAR pathways, suggesting impaired fasting adaptation and reduced hepatic catabolic capacity. Collectively, these findings demonstrate that paternal nicotine exposure induces sex-dependent metabolic reprogramming, with pronounced effects on glucose homeostasis in females and transcriptional signatures of reduced fasting resilience in males. These results identify the liver and adipose tissue as key targets of paternal nicotine exposure in the offspring and underscore the need for longitudinal studies to determine whether these alterations predispose offspring to metabolic disease across the lifespan.

pharmacology and toxicology↗

bioRxiv2025

Whole genome assembly and annotation of the acorn weevil, Curculio nanulus (Coleoptera: Curculionidae)

The acorn weevil Curculio nanulus (Coleoptera: Curculionidae) is a seed predator that lays its eggs inside developing acorns and hickory nuts in the western United States. The female weevil uses her elongated rostrum to excavate a hole into the seed, creating a protected site for oviposition. Natural history traits among Curculio species--such as host-specificity and variation in larval diapause--suggest a dynamic evolutionary relationship with their host plants. These traits are best studied through a comparative genomic framework, but such analyses cannot currently be undertaken due to the lack of whole genome assemblies for Curculio species. To address this gap, we generated a whole genome assembly for C. nanulus using PacBio HiFi sequencing. The resulting assembly is [~]1.5 Gbp in length, with high contiguity (contig N50 = 7.7 Mbp) and gene completeness (USCO score: 97.46%). To enable comparative analysis, we also assembled the genome of the pecan weevil, Curculio caryae, using publicly available PacBio HiFi reads. For both species, we annotated repetitive elements and protein-coding genes, and compared these features with those of other weevil genomes. Our results reveal a marked expansion of repetitive elements within Curculio and its close relatives. These genomic resources provide a foundation for investigating seed predation, co-speciation, and host-parasite evolutionary dynamics in Curculio and related taxa, as well as their impacts on forest ecology.

genomics↗

bioRxiv2024

African origin haplotype protective for Alzheimer's disease in APOEϵ4 carriers: exploring potential mechanisms

APOE{varepsilon}4 is the strongest genetic risk factor for Alzheimers disease (AD) with approximately 50% of AD patients carrying at least one APOE{varepsilon}4 allele. Our group identified a protective interaction between APOE{varepsilon}4 with the African-specific A allele of rs10423769, which reduces the AD risk effect of APOE{varepsilon}4 homozygotes by approximately 75%. The protective variant lies 2Mb from APOE in a region of segmental duplications (SD) of chromosome 19 containing a cluster of pregnancy specific beta-1 glycoprotein genes (PSGs) and a long non-coding RNA. Using both short and long read sequencing, we demonstrate that rs10423769_A allele lies within a unique single haplotype inside this region of segmental duplication. We identified the protective haplotype in all African ancestry populations studied, including both West and East Africans, suggesting the variant has an old origin. Long-read sequencing identified both structural and DNA methylation differences between the protective rs10423769_A allele and non-protective haplotypes. An expanded variable number tandem repeat (VNTR) containing multiple MEF2 family transcription factor binding motifs was found associated with the protective haplotype (p-value = 2.9e-10). These findings provide novel insights into the mechanisms of this African-origin protective variant for AD in APOE{varepsilon}4 carriers and supports the importance of including all ancestries in AD research.

genetics↗