Biology subjects

Moore, P. J.

Publications and source records attributed to Moore, P. J..

15 recordsLinked to original sources

bioRxiv2026

Conserved genes with variable expression and function: Vasa, Piwi, and Dnmt1 in Oncopeltus fasciatus gametogenesis

The production of gametes is one of the universal processes of life and given millennia of evolution many of the core genes involved are expected to be highly refined and resistant to change. Here we examine the pattern of expression and functionally characterize three genes widely involved in gametogenesis: Vasa, Piwi, and Dnmt1. We examine their cellular location during both oogenesis and spermatogenesis in Oncopeltus fasciatus, a hemipteran insect, using fluorescent in situ hybridization chain reaction. In females, expression of Piwi was restricted to the trophocytes, but Vasa and Dnmt1 were expressed in developing ooctyes as well as the trophoctyes. In males, Piwi was expressed in the testis germline stem cells (GSCs), but Vasa and Dnmt1 expression was absent from these cells. Additionally, Piwi and Vasa were expressed in secondary spermatogonia and spermatocytes while Dnmt1 was predominantly expressed in the primary spermatogonia. We also functionally characterized their necessity for gametogenesis after RNAi-mediated gene expression knockdown. Vasa was not required for oogenesis but was required during spermatogenesis. Piwi and Dnmt1 were required for both oogenesis and spermatogenesis. These results were in contrast to their requirement for these processes from other organisms, which highlight the unexpected variation found in the processes and suggest that conservation depends on the level at which genes are examined: sequence, expression, or phenotypic and biochemical function. This suggests there is a more nuanced evolutionary story of conserved, yet plastic, gametogenic gene set in Metazoa that deserves further study across more organisms.

evolutionary biology↗

bioRxiv2025

Anaerobic microbiota facilitate pathogen access to the airway epithelium in a novel co-culture model of colonization

Chronic rhinosinusitis (CRS) is a prevalent condition characterized by mucus stasis, persistent inflammation, and infection of the paranasal sinuses. It often involves the bacterium Pseudomonas aeruginosa, especially in individuals with cystic fibrosis or a history of antibiotic use. While P. aeruginosa is a known opportunistic pathogen that employs a diverse array of virulence factors to cause airway infections, its ability to thrive in the sinonasal environment is also likely influenced by its local microbial ecology. For instance, anaerobic bacterial genera, such as Streptococcus, Veillonella, and Prevotella, are also commonly found in CRS and may contribute to P. aeruginosa persistence. Here we sought to test the hypothesis that anaerobes promote P. aeruginosa colonization of the upper airways, specifically through degradation of mucin glycoproteins that decorate the epithelial surface. Using a novel dual oxic-anoxic culture platform termed DOAC, we co-cultured Calu-3 epithelial cells with a CRS-derived anaerobic microbial community. We observed increased expression of inflammatory marker genes and degradation of mucin glycoproteins, along with enhanced P. aeruginosa colonization of the epithelial surface after anaerobe pre-treatment. Furthermore, mucins isolated from anaerobe-treated Calu-3 cells promoted greater P. aeruginosa attachment to microtiter plates in vitro compared to intact mucins. These results suggest that anaerobic microbiota may shape the sinonasal environment in a way that favors P. aeruginosa persistence, offering new insights into CRS pathogenesis and potential therapeutic targets to disrupt detrimental bacterial interactions in chronic airway disease. IMPORTANCEThe prevalence and abundance of strict and facultative anaerobic bacteria in chronic sinusitis as detected by culture-independent sequencing has renewed interest in their potential role(s) in disease onset, progression, and treatment. However, reductionist study of interactions between anaerobic microbiota and the host has been limited by the lack of laboratory models compatible with their conflicting oxygen demands. The significance of this work lies in the use of a novel co-culture platform, termed DOAC, to interrogate anaerobe interactions with the airway epithelium. We use this platform to show that anaerobic CRS microbiota elicit a pro-inflammatory response, degrade mucin glycoproteins, and promote mucosal colonization by the canonical CRS pathogen, Pseudomonas aeruginosa. This work highlights highlight a potential role of anaerobic microbiota in conditioning the sinonasal environment to favor pathogen colonization.

microbiology↗

bioRxiv2025

Intestinal enteroendocrine cell subtype differentiation and hormone production in zebrafish

Enteroendocrine cells (EECs) are rare sensory cells in the intestinal epithelium that coordinate digestive physiology by secreting a diverse repertoire of peptide hormones. These hormones are the main effectors of EEC function, and their characterization requires direct observation by mass spectrometry due to the specialized protein cleavage and posttranslational modifications that yield their mature forms. Based on the distinct subset of hormones they predominantly secrete, EECs can be categorized into subtypes. How each EEC subtype is specified, however, remains poorly understood. Here we describe EEC subtype differentiation and hormone production in the zebrafish. Using single-cell RNA sequencing data, we identified EEC progenitors and six EEC subtypes in zebrafish and revealed that their expression profiles are consistent across larval and adult stages. Mass spectrometry analysis of isolated zebrafish EECs identified highly processed peptides derived from 18 of 21 hormone coding genes expressed by EECs, yielding a catalog of >400 unique EEC hormone peptides. We assembled reporters for zebrafish EEC subtypes to test the lineage relationships between EEC subtypes and the EEC progenitor population, which expresses neurogenin3. Despite its essential role in mammalian EEC differentiation, we found that selective cytotoxic ablation of neurogenin3+ cells in zebrafish only reduced a subset of EEC subtypes. Finally, we discovered that selective ablation of ghrelin+ EECs reduced a different subset of EEC subtypes, together suggesting that neurogenin3+ and ghrelin+ cells serve as distinct precursors for separate EEC subtypes. We anticipate these observations and resources will facilitate future studies in the zebrafish to discern the developmental biology, physiology, and endocrinology of EEC subtypes.

developmental biology↗

bioRxiv2024

Embryological insights into the evolution of genome regulation using haploid and diploid whiteflies, Bemisia tabaci

The whitefly, Bemisia tabaci, is a hemipteran with a haplodiploid sex determination system, which provides a natural experiment for examining genome function in haploid and diploid embryos. Yet the embryogenesis of B. tabaci remains understudied. Our previous work has established a possible role of DNA methyltransferase 1 (Dnmt1) in genome stability. In this study we used maternal RNA interference (RNAi) and immunohistochemistry to study the complex dynamics between DNMT1 and ploidy during embryogenesis. We found that both haploid and diploid B. tabaci have a similar developmental timeline to other holometabolous insects. We also found that, like other obligatory haploid insects, ploidy does not affect developmental timing, suggesting that maternal factors play a greater role than ploidy in developmental timing. For embryos with reduced expression of Dnmt1, we found that the loss of DNMT1 disrupts blastoderm development and affects nuclei morphology in both haploid and diploid embryos. Our results suggest that DNMT1 is required for blastoderm development.

developmental biology↗

bioRxiv2023

Dmnt1 and Wnt in the production of oocytes

The function of methylation in insects and the DNA methyltransferase (Dnmt) genes that influence methylation remains uncertain. We used RNAi to reduce the gene expression of Dnmt1 within the whitefly Bemisia tabaci, a hemipteran species that relies on Dnmt1 for proper gametogenesis. We then used RNA-seq to test an a priori hypothesis that meiosis related genetic pathways would be perturbed. We generally did not find an overall effect on meiosis related pathways. However, we found that genes in the Wnt pathway, genes associated with the entry into meiosis in vertebrates, were differentially expressed. Our results are consistent with Dnmt1 knockdown influencing specific pathways and not causing general transcriptional response. This is a finding that is also seen with other insect species. We also characterized the methylome of B. tabaci and assessed the influence of Dnmt1 knockdown on cytosine methylation. This species has methylome characteristics comparable to other hemipterans regarding overall level, enrichment within gene bodies, and bimodal distribution of methylated/non-methylated genes. Very little differential methylation was observed, and difference of methylation were not associated with differences of gene expression. The effect on Wnt presents an interesting new candidate pathway for future studies.

genomics↗

bioRxiv2023

takeout gene expression is associated with temporal kin recognition

A key component of parental care is avoiding killing and eating your own offspring. Many organisms commit infanticide but switch to parental care at the time when their own offspring would be expected, known as temporal kin recognition. It is unclear how such indirect kin recognition is so common across taxa. One possibility is that temporal kin recognition can be achieved by altering a simple mechanism, such as co-opting the regulation of timing and feeding in other contexts. Here we determine whether takeout, a gene implicated in coordinating feeding, influences temporal kin recognition in the roundneck sexton beetle, Nicrophorus orbicollis. We find that takeout expression is not associated with non-parental feeding changes resulting from hunger, or in the general switch to the full parental care repertoire. However, beetles that accepted and provided care to their offspring had a higher takeout expression than beetles that committed infanticide. Together, these data support the idea that the evolution of temporal kin recognition may be enabled by co-option of mechanisms that integrate feeding behaviour in other contexts.

animal behavior and cognition↗

bioRxiv2023

The critical role of Dmnt1 during spermatogenesis is not predictable, but knockdown does cause pervasive differential transcription.

Cytosine methylation and its machinery influence the gene expression of many eukaryotes; however, insects are an exception to this general tenet despite many lineages retaining methyltransferases and methylated genomes. Here, we tested the a priori hypothesis that perturbed genetic pathways will be associated with meiosis using transcriptomics because previous our work using Oncopeltus fasciatus shows that gametogenesis is interrupted at meiosis following knockdown of DNA methyltransferase 1 (Dnmt1). Testes, which are almost exclusively contain gametes at varying stages of development, were sampled at 7-days and 14-days following knockdown of Dmnt1 using RNAi. Using microscopy, we found actively dividing spermatocysts were reduced at both sampling points. However, we found limited support of perturbation for our predicted cell cycle and meiotic pathways and only at 14-days. We found that Gene Ontology terms had no preferential enrichment for meiosis-associated genes. Following our a priori tests, we used the full dataset to uncover further candidate pathways influenced by Dnmt1 knockdown. Very few genes were differentially expressed at 7-days, but nearly half were at 14-days. We did not find strong candidate pathways for how Dnmt1 knockdown was achieving its effect through Gene Ontology term overrepresentation analysis. Given the evidence from microscopy, we propose Dnmt1 knockdown results in condensed nuclei after mitosis-meiosis transition and then cellular arrest. This explanation posits that differential gene expression is a product of comparing healthy to arrested cells and is not a targeted response.

genomics↗

bioRxiv2022

Oxytocin/vasopressin system of insects influences parental care in males but not females

AO_SCPLOWBSTRACTC_SCPLOWParental care is thought to evolve through modification of behavioral precursors, which predicts that the mechanistic changes occur in the genes underlying those traits. The duplicated gene system of oxytocin/vasopressin has been broadly co-opted across vertebrates to influence parenting, from a pre-duplication ancestral role in water balance. It remains unclear whether co-option of these genes for parenting is limited to vertebrates. Here, we experimentally tested for associations between inotocin gene expression and water balance, parental acceptance of offspring, and active parenting in the subsocial beetle Nicrophorus orbicollis, to test whether a single copy homologue, inotocin, has similarly been co-opted for parental care in a species with elaborate parenting. As expected, inotocin was associated with water balance in both sexes. Inotocin expression increased around sexual maturation in both males and females, although more clearly in males. Finally, we found that expression of inotocin was not associated with acceptance of larvae but was associated with a transition to male but not female parenting. Moreover, level of offspring provisioning behavior and gene expression were positively correlated in males but uncorrelated in females. Our results suggest a broad co-option of this system for parenting that may have existed prior to gene duplication, and that inotocin may be associated with flexibility in parenting behavior. IO_SCPLOWMPACTC_SCPLOW SO_SCPLOWUMMARYC_SCPLOWOxytocin/vasopressin are amongst the most studied neuropeptides in vertebrates, influencing water balance, mating interactions, and most notably, social bonding. This gene pair evolved from a duplication in the vertebrate lineage of an ancestral vasopressin-like gene. Are the multiple social effects in vertebrates due to this duplication, or are social influences also ancestral? Here, we demonstrate that, in a biparental social beetle with a single copy, inotocin is associated with social interactions between fathers and offspring as well as being associated with the ancestral role of water balance in both males and females. In vertebrates, both oxytocin and vasopressin have been shown to impact social interactions in both sexes, although often showing sex-specificity in their action within species. Our results suggest that this system may have been co-opted for parenting prior to gene duplication and may facilitate flexibility in caring behavior.

evolutionary biology↗

bioRxiv2021

A global dataset of seaweed net primary productivity

Net primary productivity (NPP) plays a pivotal role in the global carbon balance, but estimating the NPP of underwater habitats remains a challenging task. Seaweeds (marine macroalgae) form the largest and most productive underwater vegetated habitat on Earth. Yet, little is known about the distribution of their NPP at large spatial scales, despite more than 70 years of local-scale studies being scattered throughout the literature. We present a global dataset containing NPP records for 242 seaweed species at 419 individual sites distributed on all continents from the intertidal to 55 m depth. All records are standardized to annual aerial carbon production (g C m-2 yr-1) and are accompanied by detailed taxonomical and methodological information. The dataset presented here provides a basis for local, regional and global comparative studies of the NPP of underwater vegetation, and is pivotal for achieving a better understanding of the role seaweeds play in the global coastal carbon cycle.

ecology↗

bioRxiv2021

Anaerobic microbiota facilitate P. aeruginosa access to airway epithelia in a novel co-culture model of colonization

Strict and facultative anaerobic bacteria are widely associated with both acute and chronic airway disease. However, their potential role(s) in disease pathophysiology remain poorly understood due to inherent limitations of existing models and conflicting oxygen demands between anaerobes and host cells. To overcome these limitations, we optimized a dual oxic-anoxic culture (DOAC) platform that maintains an oxygen-limited microenvironment at the epithelial interface while host cells are oxygenated basolaterally. This approach enables host-bacterial co-culture for [~]24h, and here we demonstrate its utility via two applications. First, we show that anaerobe challenge results in epithelial mucus degradation, inflammatory marker gene expression, and enhanced pathogen colonization. Second, we combine DOAC with single cell RNA sequencing (scRNAseq) to reveal a cell type-specific transcriptional response of the airway epithelium to anaerobe infection. Together, these data illustrate the versatility of DOAC while revealing new insights into anaerobe-host interactions and their mechanistic contributions to airway disease pathophysiology.

microbiology↗

bioRxiv2020

Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of epithelial cell types are susceptible to infection, ciliated cells are the predominant cell target of SARS-CoV-2. The host protease TMPRSS2 was required for infection of these cells. Importantly, remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. Induction of interferon responses within infected cells was rare and there was significant heterogeneity in the antiviral gene signatures, varying with the burden of infection in each cell. We also found that heavily infected secretory cells expressed abundant IL-6, a potential mediator of COVID-19 pathogenesis.

microbiology↗

bioRxiv2020

The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus

Given the importance of DNA methylation in protection of the genome against transposable elements and transcriptional regulation in other taxonomic groups, the diversity in both levels and patterns of DNA methylation in the insects raises questions about its function and evolution. We show that the maintenance DNA methyltransferase, DNMT1, affects meiosis and is essential to fertility in milkweed bugs, Oncopeltus fasciatus, while DNA methylation is not required in somatic cells. Our results support the hypothesis that Dnmt1 is required for the transition of germ cells to gametes in O. fasciatus and that this function is conserved in male and female gametogenesis. They further suggest that DNMT1 has a function independent of DNA methylation in germ cells. Our results raise the question of how a gene so critical in fitness across multiple insect species can have diverged widely across the insect tree of life.

evolutionary biology↗

bioRxiv2019

More than DNA methylation: does pleiotropy drive the complex pattern of evolution of Dnmt1?

DNA methylation is an important chromatin modification that can stably alter gene expression in cells and maintain genome integrity in plants and vertebrates. The function of DNA methylation outside of these well-studied systems, however, is unclear. Insects, in particular, represent an understudied group. Variation in the level of DNA methylation and gains and losses in the maintenance methyltransferase, DNMT1, across the insect tree of life suggests that there is much we dont understand about DMNT1 function and evolution. One constant across the studies examining patterns of Dnmt1 expression in insects is that expression is consistently high in reproductive tissues compared to somatic tissue. The explanation for this has been that DNMT1 is required in tissues that have high levels of cell division. Our previous study found that downregulation of Dnmt1 expression in the milkweed bug Oncopeltus fasciatus results in the expected reduction of DNA methylation, no global changes in gene expression reflecting changes in DNA methylation, and the loss of the ability to produce viable oocytes. Here, we show that females treated with ds-Dnmt1 RNA during larval development have a more extreme phenotype; they lack oocytes entirely but develop a normal somatic ovary. Our results indicate a specific role for DNMT1 in the formation of gametes and are consistent with data from other systems, including Tribolium castaneum, a species does not have DNA methylation. We propose that DNMT1 has multiple functional roles in addition to methylating DNA, which explains its complex patterns of evolution, and suggests that previous inferences of causation from associations are premature.

evolutionary biology↗

bioRxiv2018

Gene-regulatory independent functions for insect DNA methylation

The function of cytosine (DNA) methylation in insects remains unknown. Here we provide evidence for the functional role of the maintenance DNA methyltransferase 1 (Dnmt1) in an insect using experimental manipulation. Through RNA interference (RNAi) we successfully post-transcriptionally knocked down Dnmt1 in ovarian tissue of the hemipteran Oncopeltus fasciatus (the large milkweed bug). Individuals depleted for Dnmt1, and subsequently DNA methylation, failed to reproduce. Eggs were inviable and declined in number, and nuclei structure of follicular epithelium was aberrant. Depletion of DNA methylation did not result in changes in gene or transposable element expression revealing an important function of DNA methylation seemingly not contingent on gene expression. Our work provides direct experimental evidence for a functional role of Dnmt1 and DNA methylation independent of gene expression in insects.

genetics↗

bioRxiv2017

Early developmental morphology reflects independence from parents in social beetles

The variation in degree of offspring dependence in parents where parental care has evolved is striking, from feeding independence at birth to complete dependence on parents for all nutritional resources. This presents an evolutionary puzzle. Why lose the ability to feed as a contingency when parents may die or abandon broods? Comparisons of altricial and precocial vertebrates suggest that there may be life-history and developmental costs to early independence1-3. The generality of this beyond vertebrates is unclear, but we can extend the comparison as invertebrate species also vary in the level of independence in early life-history stages. For example, larvae of several burying beetle species (Nicrophorus), a genus in which parents regurgitate pre-digested food to begging larvae, have lost the ability to self-feed thus creating complete parental dependency for first instars4. Here, we ask whether variation in dependency amongst burying beetles is related to heterochrony in development of a more complex morphological structures. We show that the rate of development and allometry of mandibles of precocial larvae that can self-feed from birth are the same as those in altricial larvae that cannot survive without parenting. Instead, self-feeding is associated with shape variation in mandibles. In altricial species first instar larvae have smooth mandibles, whereas in precocial species mandibles are serrated. Later instars, which can self-feed in all species, have serrated mandibles. Serrations on teeth generally function to \"grip and rip\"5, whereas smooth blades function more to puncture6, and broods of altricial but not precocial Nicrophorus larvae show evidence for siblicide. We therefore suggest that altricial first-instar mandibles function more as weapons than feeding tools when released from self-feeding. This study presents a novel coevolution between developmental timing and parenting potentially mediated by sibling competition.

evolutionary biology↗