Biology subjects

Jackson, E. W.

Publications and source records attributed to Jackson, E. W..

6 recordsLinked to original sources

bioRxiv2025

Automated, high-throughput in-situ hybridization of Lytechinus pictus embryos

Despite the reach of in situ hybridization (ISH) in developmental biology, it has rarely been used at scale. The major limitation has been the throughput of the assay, which typically relies upon labor intensive manual steps. The goal of this study was to develop a fully automated hybridization chain reaction (HCR) pipeline capable of large-scale gene expression pattern profiling, with dramatically reduced cost and effort, in the sea urchin Lytechinus pictus. Our resulting pipeline, which we term high throughput (HT)-HCR, can process 192 gene probe sets on whole-mount embryos within 32 hours. The unique qualities of the sea urchin embryo enabled us to automate the entire HCR assay in a 96-well plate format, and utilize highly miniaturized reaction volumes, a general purpose robotic liquid handler, and automated confocal microscopy. From this approach we produced high quality localization data for 101 target genes across three developmental stages of L. pictus. The results reveal the localization of previously undescribed physiological genes, as well as canonical developmental transcription factors. HT-HCR represents a log order increase in the rate at which spatial transcriptomic data can be resolved in the sea urchin. This study paves the way for localization of understudied genes and for sophisticated perturbation analysis. Summary StatementWe developed an automated high-throughput HCR pipeline to rapidly map expression of 101 genes in sea urchin embryos, enabling large-scale discovery of novel developmental gene expression patterns.

developmental biology↗

bioRxiv2024

Stable germline transgenesis using the Minos Tc1/mariner element in the sea urchin, Lytechinus pictus.

Stable transgenesis is a transformative tool in model organism biology. While the sea urchin is one of the oldest animal models in cell and developmental biology, it has relied on transient manipulations of wild animals, and has lacked a strategy for stable transgenesis. Here we build on recent progress to develop a more genetically tractable sea urchin species, Lytechinus pictus, to establish a robust transgene integration method. Three commonly used transposons (Minos, Tol2, piggyBac) were tested for non-autonomous transposition, using plasmids containing a polyubiquitin promoter upstream of a H2B-mCerulean nuclear marker. Minos was the only transposable element that resulted in significant expression past metamorphosis. F0 animals were raised to sexual maturity and spawned to determine germline integration, transgene inheritance frequency, and to characterize expression patterns of the transgene in F1 progeny. The results demonstrated transgene transmission through the germline, the first example of a germline transgenic sea urchin, and indeed of any echinoderm. This milestone paves the way for the generation of diverse transgenic resources that will dramatically enhance the utility, reproducibility, and efficiency of sea urchin research. Significance StatementTransgenic tools are essential for effective utilization of animal models. Despite being an established model for cell and developmental biology, the sea urchin has not previously benefited from transgenic technology. This study reports the generation of the first germline transgenic sea urchin and opens new avenues for this organism.

developmental biology↗

bioRxiv2022

The RNA Virome of Echinoderms

Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.

microbiology↗

bioRxiv2020

Diversity of sea star-associated densoviruses and transcribed endogenized viral elements of densovirus origin

A viral etiology of Sea Star Wasting Syndrome (SSWS) has been largely explored using metagenomics leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome, and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are however highly diverse and pervasive among eukaryotic organisms which we hypothesize may confound the association between densoviruses and SSWS in sea stars. To test this hypothesis and assess the association of densoviruses to SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study to SSaDV, the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained mostly endogenized densovirus elements similar to the NS1 gene, while >30 complete and near-complete densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the west coast of the United States and globally that are commonly associated with grossly normal (i.e. healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in wild sea stars confounds the original hypothesis that one densovirus was the etiologic agent of SSWD. ImportanceThe primary interest in sea star densoviruses, specifically SSaDV, has been their association with Sea Star Wasting Syndrome (SSWS), a disease that has decimated sea star populations across the west coast of the United States since 2013. The association of SSaDV to SSWS was originally drawn from metagenomic analyses concluding that it was (1) the only densovirus present in the metagenomic data and (2) the most likely viral candidate based on representation in symptomatic sea stars. We reassessed the original metagenomic data with additional genomic datasets and found that SSaDV was one of ten densoviruses present in the original dataset and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations.

genomics↗

bioRxiv2019

A highly prevalent and pervasive densovirus discovered among sea stars from the North American Atlantic Coast

Viral metagenomes prepared from tissues from Forbes sea star (Asterias forbesi) led to the discovery of a complete genome of a novel sea star densovirus (AfaDV). The genome organization of AfaDV and phylogenetic analysis place this virus among the Ambidensovirus genus in the subfamily Densoviridae, family Parvoviridae. AfaDV shares 78% nucleotide pairwise identity to the sea star associated densovirus (SSaDV), previously described as the putative causative agent of Sea Star Wasting Syndrome among sea stars from the Northwest Pacific. SSaDV was not found in specimens collected in this study, and the discovery of AfaDV might explain previous reports of SSaDV among sea stars from the Atlantic Coast. A qPCR assay was designed to assess tissue tropism, host specificity, and prevalence of AfaDV among wild populations of sea stars at five locations on the North American Atlantic Coast. AfaDV was detected in all three common sea star species (Asterias forbesi, Asterias rubens, and Henricia sp.) found in the region and was highly prevalent (80-100% of individuals tested, n=134), among populations collected at disparate sites 7 years apart. AfaDV was detected in the body wall, gonads, and pyloric caeca (digestive gland) of specimens but was not detected in their coelomic fluid. A significant difference in viral load was found between tissue types with the pyloric caeca having the highest viral load suggesting it is the primary site of viral replication in the animal. Further investigation of Asterias forbesi gonad tissue found germline cells (oocytes) to be virus positive suggesting a potential route of vertical transmission. Taken together, these observations show that the presence AfaDV is not an indicator of Sea Star Wasting Syndrome because AfaDV is a common constituent of these animals microbiome, regardless of health. These results broaden the understanding of echinoderm densoviruses outside the context of disease that suggest these viruses might form commensal or mutualistic relationships with their hosts.

microbiology↗

bioRxiv2018

Associations between Afrotropical bats, parasites, and microbial symbionts

Bats are among the most diverse animals on the planet and harbor numerous bacterial, viral, and eukaryotic symbionts. The interplay between bacterial community composition and parasitism in bats is not well understood and may have important implications for studies of similar systems. Here we present a comprehensive survey of dipteran and haemosporidian parasites, and characterize the gut, oral, and skin microbiota of Afrotropical bats. We identify significant correlations between bacterial community composition of the skin and dipteran ectoparasite prevalence across four major bat lineages, as well as links between the oral microbiome and malarial parasitism, suggesting a potential mechanism for host selection and vector-borne disease transmission in bats. In contrast to recent studies of host-microbe phylosymbiosis in mammals, we find no correlation between chiropteran phylogenetic distances and bacterial community dissimilarity across the three anatomical sites, suggesting that host environment is more important than shared ancestry in shaping the composition of bat-associated bacterial communities.\n\nSIGNIFICANCEAnimals rely on bacterial symbionts for numerous biological functions, such as digestion and immune system development. Increasing evidence suggests that host-associated microbes may play a role in mediating parasite burden. This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and parasite prevalence. This study provides a framework for future approaches to systems biology of host-symbiont interactions across broad taxonomic scales, emphasizing the interdependence between microbial symbionts and vertebrate health in the study of wild organisms and their natural history.

ecology↗