Biology subjects

Browne, W. E.

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

6 recordsLinked to original sources

bioRxiv2024

Reproductive success of inbred strain MV31 of the ctenophore Mnemiopsis leidyi in a self-sustaining inland laboratory culture system

Ctenophores are an attractive lineage for studying animal evolution due to their early divergence from other metazoans. Among Ctenophora, Mnemiopsis leidyi is a model system for developmental, cellular, molecular genetic, and evolutionary studies. Until recently, many of these studies were conducted on wild-caught animals, limiting access to researchers on the coast. Here we present significant advancements towards culturing M. leidyi in laboratories without coastal access, enabling its wider use as an experimental and genetic model system. We detail updated feeding regimes that take advantage of co-culturing Brachionus rotifers with Apocyclops copepods, and quantify the reproductive output of our M. leidyi lab strain on this diet. Our updated feeding regime maintains reproductive fitness comparable to wild-caught individuals. Importantly, we have eliminated the logistical complexities and costs of regularly feeding live larval fish to M. leidyi. Our updated protocols make it feasible to maintain continuous ctenophore cultures independent of access to both coastal populations of wild M. leidyi and larval fish culturing facilities.

zoology↗

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

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↗

bioRxiv2020

Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama

The formation of the Isthmus of Panama and final closure of the Central American Seaway (CAS) provides an independent calibration point for examining the rate of DNA substitutions. This vicariant event has been widely used to estimate the substitution rate across mitochondrial genomes and to date evolutionary events in other taxonomic groups. Nuclear sequence data is increasingly being used to complement mitochondrial datasets for phylogenetic and evolutionary investigations; these studies would benefit from information regarding the rate and pattern of DNA substitutions derived from the nuclear genome. To estimate this genomewide neutral mutation rate (), genotype-by-sequencing (GBS) datasets were generated for three transisthmian species pairs in Alpheus snapping shrimp. Using a Bayesian coalescent approach (G-PhoCS) applied to 44,960 GBS loci, we estimated to be 2.64E-9 substitutions/site/year, when calibrated with the closure of the CAS at 3 Ma. This estimate is remarkably similar to experimentally derived mutation rates in model arthropod systems, strengthening the argument for a recent closure of the CAS. To our knowledge this is the first use of transisthmian species pairs to calibrate the rate of molecular evolution from GBS data.

evolutionary 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↗

bioRxiv2019

Krüppel-like factor gene function in the ctenophore Mnemiopsis suggests an ancient role in promoting cell proliferation in metazoan stem cell niches

The Kruppel-like factor (Klf) gene family encodes for transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation, and development in bilaterians. While Klf genes have been shown to functionally specify various cell types in non-bilaterian animals, their role in early diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis results in abnormal development of several organs including the pharynx, tentacle bulbs, and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation. Summary StatementUsing CRISPR/Cas9 genome editing and morpholino oligonucleotide knockdown, this study shows that tissues derived from the endoderm are dependent upon Klf5 ortholog expression for proper development and patterning in the ctenophore Mnemiopsis leidyi.

developmental biology↗