Biology subjects

Vandepas, L. E.

Publications and source records attributed to Vandepas, L. E..

5 recordsLinked to original sources

bioRxiv2023

Phylogenetic and protein structure analyses provide insight into the evolution and diversification of the CD36 domain 'apex' among scavenger receptor class B proteins across Eukarya

The cluster of differentiation 36 (CD36) domain defines the characteristic ectodomain associated with scavenger receptor class B (SR-B) proteins. In bilaterians, SR-Bs play critical roles in diverse biological processes including innate immunity functions such as pathogen recognition and apoptotic cell clearance, as well as metabolic sensing associated with fatty acid uptake and cholesterol transport. While previous studies suggest this protein family is ancient, SR-B diversity across Eukarya has not been robustly characterized. We analyzed SR-B homologs identified from the genomes and transcriptomes of 165 diverse eukaryotic species. The presence of highly conserved amino acid motifs across major eukaryotic supergroups supports the presence of a SR-B homolog in the last eukaryotic common ancestor (LECA). Our comparative analyses of SR-B protein structure identifies the retention of a canonical asymmetric beta barrel tertiary structure within the CD36 ectodomain across Eukarya. We also identify multiple instances of independent lineage-specific sequence expansions in the apex region of the CD36 ectodomain -- a region functionally associated with ligand-sensing. We hypothesize that a combination of both sequence expansion and structural variation in the CD36 apex region may reflect the evolution of SR-B ligand sensing specificity between diverse eukaryotic clades. Significance StatementSR-Bs are well-described in bilaterians, however the diversity and evolution of this ancient receptor protein family is poorly understood across Eukarya. Our analyses reveal a conserved beta barrel tertiary structure across eukaryotic SR-Bs that correlates with the presence of an intramolecular tunnel. In contrast, the putative ligand-sensing region associated with the apex of the protein can be highly divergent in both sequence and structure within and between taxa. Our data confirm the antiquity of the SR-B receptor protein family in Eukaryota and improve characterization of SR-B diversity outside of Metazoa. We hypothesize that eukaryotic SR-B diversity may be used as a model to explore receptor protein evolution driven by lineage-specific ligand specificity.

evolutionary biology↗

bioRxiv2023

Multiple lineages of transmissible neoplasia in the basket cockle (Clinocardium nuttallii) with repeated horizontal transfer of mitochondrial DNA

Transmissible cancers are clonal lineages of neoplastic cells able to infect multiple hosts, spreading through populations in the environment as an infectious disease. Transmissible cancers have been identified in Tasmanian devils, dogs, and bivalves. Several lineages of bivalve transmissible neoplasias (BTN) have been identified in multiple bivalve species. In 2019 in Puget Sound, Washington, USA, disseminated neoplasia was observed in basket cockles (Clinocardium nuttallii), a species that is important to the culture and diet of the Suquamish Tribe as well as other tribes with traditional access to the species. To test whether disseminated neoplasia in cockles is a previously unknown lineage of BTN, a nuclear locus was amplified from cockles from Agate Pass, Washington, and sequences revealed evidence of transmissible cancer in several individuals. We used a combination of cytology and quantitative PCR to screen collections of cockles from eleven locations in Puget Sound and along the Washington coastline to identify the extent of contagious cancer spread in this species. Two BTN lineages were identified in these cockles, with one of those lineages (CnuBTN1) being the most prevalent and geographically widespread. Within the CnuBTN1 lineage, multiple nuclear loci support the conclusion that all cancer samples form a single clonal lineage. However, the mitochondrial alleles in each cockle with CnuBTN1 are different from each other, suggesting mitochondrial genomes of this cancer have been replaced multiple times during its evolution, through horizontal transmission. The identification and analysis of these BTNs are critical for broodstock selection, management practices, and repopulation of declining cockle populations, which will enable continued cultural connection and dietary use of the cockles by Coast Salish Tribes.

cancer biology↗

bioRxiv2023

Flow cytometry methods for targeted isolation of ctenophore cells

Cell suspension fluidics, such as flow cytometry (FCS) and fluorescence-activated cell sorting (FACS), facilitates the identification and precise separation of individual cells based on phenotype. Since its introduction, flow cytometry has been used to analyze cell types and cellular processes in diverse non-vertebrate taxa, including cnidarians, molluscs, and arthropods. Ctenophores, which diverged very early from the metazoan stem lineage, have emerged as an informative clade for the study of metazoan cell type evolution. We present standardized methodologies for flow cytometry-mediated identification and analyses of cells from the model ctenophore Mnemiopsis leidyi that can also be applied to isolate targeted cell populations. Here we focus on the identification and isolation of ctenophore phagocytes. Implementing flow cytometry methods in ctenophores allows for fine scale analyses of fundamental cellular processes conserved broadly across animals, as well as potentially revealing novel cellular phenotypes and behaviors restricted to the ctenophore lineage.

cell biology↗

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↗

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↗