Biology subjects

Goetz, F. W.

Publications and source records attributed to Goetz, F. W..

5 recordsLinked to original sources

bioRxiv2023

A rapid, inexpensive, non-lethal method for detecting disseminated neoplasia in a bivalve

Disseminated neoplasia (DN) is a form of cancer in bivalve molluscs that has been reported in some cases to be a transmissible cancer. Neoplastic cells are highly proliferative, and infection is often lethal. Some commercially valuable bivalve species (mussels, cockles, soft-shell clams, oysters) are affected by outbreaks of disseminated neoplasia, making disease diagnosis and mitigation an important issue in aquaculture and ecological restoration efforts. Here we describe a minimally invasive, non-lethal method for high-throughput screening for disseminated neoplasia in basket cockles (Clinocardium nuttallii). Basket cockles are native to the North American Pacific coast from California to Alaska. There is recent concern from some Coast Salish Tribes regarding an observed long-term decline in cockle populations in Puget Sound, WA. This has led to increased interest in monitoring efforts and research to improve our understanding of the mechanisms of observed basket cockle population dynamics, including assessing prevalence of disease, such as disseminated neoplasia. The rapid, non-lethal hemolymph smear screening method presented here to diagnose DN in adult C. nuttallii can be applied at field sites at low financial cost, and in a validation study of 29 animals the results were identical to that of the gold standard method, tissue histology. Due to the similar morphology of DN in different bivalves, this method can likely be generally applied for use in any bivalve species.

cell biology↗

bioRxiv2022

Dynamic DNA methylation contributes to carryover effects and beneficial acclimatization in geoduck clams

Given the rapidly changing global climate, there is a growing need to understand the acclimatory basis of animal response to environmental change. To investigate the role of DNA methylation in environmental acclimatization, we generated a reference genome and surveyed the physiology and DNA methylomes of juvenile geoduck clams, Panopea generosa, under differing seawater pH regimes. Juveniles were initially exposed to one of three seawater pH conditions, followed by ambient common-garden conditions, then a second reciprocal exposure to ambient pH or pH 7.4. Within 10 days of the initial low pH exposure, juvenile clams showed decreased shell size relative to ambient pH with corresponding differential DNA methylation. Following four months of ambient common-garden conditions, juveniles initially exposed to low pH compensatorily grew larger, with DNA methylation indicative of these phenotypic differences, demonstrating epigenetic carryover effects persisted months after initial exposure. Functional enrichment analysis of differentially methylated genes revealed regulation of signal transduction through widespread changes in the Wnt signaling pathways that influence cell growth, proliferation, tissue and skeletal formation, and cytoskeletal change. After 10 days of secondary exposure to pH 7.4, naive juvenile clams were more sensitive to low pH compared to those initially exposed, showing reduced growth and having nearly a 2-fold greater change in DNA methylation. Collectively, this new genomic resource and coordinated phenotypic and methylomic response support that epigenetic mechanisms underlie acclimatization to provide beneficial phenotypes.

genomics↗

bioRxiv2020

Ctenophore immune cells produce chromatin traps in response to pathogens and NADPH-independent stimulus

The formation of extracellular DNA traps (ETosis) is a first response mechanism by specific immune cells following exposure to microbes 1,2. Initially characterized in vertebrate neutrophils, cells capable of ETosis have been discovered recently in diverse non-vertebrate taxa 3 4-6. To assess the conservation of ETosis between evolutionarily distant non-vertebrate phyla, we observed and quantified ETosis using the model ctenophore Mnemiopsis leidyi and the oyster Crassostrea gigas. Here we report that ctenophores - thought to have diverged very early from the metazoan stem lineage 7-10- possess immune cell types capable of phagocytosis and ETosis. We demonstrate that both Mnemiopsis and Crassostrea immune cells undergo ETosis after exposure to diverse microbes and chemical agents that stimulate ion flux. Our results support ETosis as an evolutionarily ancient metazoan defense against pathogens.

evolutionary biology↗

bioRxiv2020

The rise and fall of the ancient northern pike master sex determining gene

Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies. Here, we traced back the evolution of sex determination in an entire clade of vertebrates and uncovered that the northern pike (Esox lucius) master sex-determining gene initiated from a 65 to 90 million-year-old gene duplication and remained sex-linked on undifferentiated sex chromosomes for at least 56 million years. Contrasting with its ancient origin, we identified several independent species- or population-specific transitions of sex determination mechanisms in this lineage, including an unexpected complete and recent Y-chromosome loss in some North American northern pike populations. These findings highlight the diversity of the evolutionary fates of master sex-determining genes and raise the importance of careful considerations of population demographic history in sex determination studies. Our study also puts forward the hypothesis that occasional sex reversals and genetic bottlenecks provide a non-adaptive explanation for sex determination transitions.

evolutionary biology↗

bioRxiv2020

RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data

The study of sex determination and sex chromosome organisation in non-model species has long been technically challenging, but new sequencing methodologies are now enabling precise and high-throughput identification of sex-specific genomic sequences. In particular, Restriction Site-Associated DNA Sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software designed to specifically search for sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analyzed a published dataset of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyze new RAD-Seq datasets from 15 fish species spanning multiple systematic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in non-model species and outperforms the commonly used RAD-Seq analysis software STACKS. RADSex in speed, resource usage, ease of application, and visualization options. Furthermore, our analysis of new datasets from 15 species provides new insights on sex determination in fish.

bioinformatics↗