Biology subjects

Newton, I.

Publications and source records attributed to Newton, I..

11 recordsLinked to original sources

bioRxiv2026

Skeletons in the closet: The importance of actin in alphavirus replication

The ability of the bacterial endosymbiont Wolbachia pipientis to block arboviruses in its mosquito host may be impinged by host genetic variation, leading to reduced efficacy in field releases. Across a large collection of Drosophila lines carrying natural genetic variation, we found that viral replication varied greatly in the absence of Wolbachia. However, the introduction of the symbiont reduced viral load in each background to similar levels, near the limit of detection. Therefore, Wolbachia-mediated viral blocking is seemingly robust against host genetic background. A genome-wide association study harnessing the variation in the viral loads across the Wolbachia-free set identified rhoGAP18B and betaCOP as host factors that contribute to SINV replication; furthermore, the gene products of which seemingly interact with each other in the context of cytoskeletal dynamics. These results shed light on host requirements for SINV replication and suggest possible avenues by which Wolbachia may encroach upon them during blocking.

microbiology↗

bioRxiv2025

Nested Connections: Local Phage and Broad Plasmid Sharing in the Honey Bee Mobilome

Honey bees rely on bacterial symbionts for their nutritional needs and for protection against invading pathogens. Genetic diversity among strains within the colony has the potential to impact symbiont function and subsequently the benefits that honey bees receive from them. Mobilized genes vectored by mobile genetic elements (MGEs) like phages, transposons, conjugative elements and plasmids, are known to rapidly alter bacterial phenotypes. We identified phages and plasmids in genomes of the symbiont Bombella apis between two colonies, with the goal of understanding which MGEs contribute to strain diversification as well as MGE distribution across colonies and between microbial species. Interestingly, we found some B. apis strains carry plasmids while all harbor a diversity of integrated phages, with only one phage clusters conserved across all. Identified B. apis phages are not found outside of the Bombella and Saccaribacter species, suggesting some host specificity for these MGEs. Of the five plasmids discovered, two appear to be phage-plasmids with high similarity to phages found in previously sequenced B. apis genomes. Interestingly, three plasmids in B. apis shared significant average nucleotide identity with known plasmids from acetic acid bacteria isolated from flowers, plants, and fermented foods. This result suggests that B. apis has acquired MGEs, either vertically or horizontally, from plant- and fermented-food associated AABs. Overall, our findings suggest that MGE content varies between colonies and has the potential to shape genetic and phenotypic variation between strains.

microbiology↗

bioRxiv2025

Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly

Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiomes have been central models for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi- kingdom interactions. Stingless bees, highly eusocial managed bees that rely on yeast for larval development, offer a valuable complementary system to study microbiome assembly, and within an eco-evolutionary framework. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of stingless bee microbiome assembly. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also actively maintained through highly selective bacterial-fungal interactions. Our findings uncover multi-layered mechanisms shaping an eusocial insect microbiome, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.

microbiology↗

bioRxiv2023

Manipulation of the nucleoscaffold potentiates cellular reprogramming kinetics

Somatic cell fate is an outcome set by the activities of specific transcription factors and the chromatin landscape and is maintained by gene silencing of alternate cell fates through physical interactions with the nuclear scaffold. Here, we evaluate the role of the nuclear scaffold as a guardian of cell fate in human fibroblasts by comparing the effects of transient loss (knockdown) and mutation (progeria) of functional Lamin A/C, a core component of the nuclear scaffold. We observed that Lamin A/C deficiency or mutation disrupts nuclear morphology, heterochromatin levels, and increases access to DNA in lamina-associated domains. Changes in Lamin A/C were also found to impact the mechanical properties of the nucleus when measured by a microfluidic cellular squeezing device. We also show that transient loss of Lamin A/C accelerates the kinetics of cellular reprogramming to pluripotency through opening of previously silenced heterochromatin domains while genetic mutation of Lamin A/C into progerin induces a senescent phenotype that inhibits the induction of reprogramming genes. Our results highlight the physical role of the nuclear scaffold in safeguarding cellular fate.

cell biology↗

bioRxiv2021

Heightened virulence of Yersinia is associated with decreased function of the YopJ protein

Despite the maintenance of YopP/J alleles throughout the human-pathogenic Yersinia lineage, the benefit of YopP/J-induced phagocyte death for Yersinia pathogenesis in animals is not obvious. To determine how sequence divergence of YopP/J has impacted Yersinia virulence, we examined protein polymorphisms in this Type III secreted effector protein across 17 Yersinia species, and tested the consequences of polymorphism in a murine model of sub-acute systemic yersiniosis. Our evolutionary analysis revealed that codon 177 has been subjected to positive selection - the Y. enterocolitica residue had been altered from a leucine to a phenylalanine in nearly all Y. pseudotuberculosis and Y. pestis strains examined. Despite being a minor change, as both leucine and phenylalanine have hydrophobic side chains, reversion of YopJF177 to the ancestral YopJL177 variant yielded a Y. pseudotuberculosis strain with enhanced cytotoxicity towards macrophages, consistent with previous findings. Surprisingly, expression of YopJF177L in the mildly attenuated ksgA- background rendered the strain completely avirulent in mice. Consistent with this hypothesis that YopJ activity indirectly relates to Yersinia pathogenesis in vivo, ksgA- strains lacking functional YopJ failed to kill macrophages but actually regained virulence in animals. Also, treatment with the anti-apoptosis drug suramin prevented YopJ-mediated macrophage cytotoxicity and enhanced Y. pseudotuberculosis virulence in vivo. Our results demonstrate that Yersinia-induced cell death is detrimental for bacterial pathogenesis in this animal model of illness, and indicate that positive selection has driven YopJ/P and Yersinia evolution towards diminished cytotoxicity and increased virulence, respectively.

microbiology↗

bioRxiv2020

Adaptive evolution in DNMT2 supports its role in the dipteran immune response

Eukaryotic nucleic acid methyltransferase (MTase) proteins are essential mediators of epigenetic and epitranscriptomic regulation. DNMT2 belongs to a large, conserved family of DNA MTases found in many organisms, including holometabolous insects like fruit flies and mosquitoes, where it is the lone MTase. Interestingly, despite its nomenclature, DNMT2 is not a DNA MTase, but instead targets and methylates RNA species. A growing body of literature suggest DNMT2 mediates the host immune response against a wide range of pathogens, including RNA viruses. Evidence of adaptive evolution, in the form of positive selection, can often be found in genes that are engaged in conflict with pathogens like viruses. Here we identify and describe evidence of positive selection that has occurred at different times over the course of DNMT2 evolution within dipteran insects. We identify specific codons within each ortholog that are under positive selection, and find they are restricted to four distinct domains of the protein and likely influence substrate binding, target recognition, and adaptation of unique intermolecular interactions. Additionally, we describe the role of the Drosophila-specific host protein IPOD, in regulating the expression and/or function of fruit fly DNMT2. Finally, heterologous expression of these orthologs suggest that DNMT2s role as an antiviral is host dependent, indicating a requirement for additional host-specific factors. Collectively, our findings highlight the adaptive evolution of DNMT2 in Dipteran insects, underscoring its role as an important, albeit non-canonical, regulator of host-pathogen interactions in mosquitoes and fruit flies.

microbiology↗

bioRxiv2020

Wolbachia and virus alter the host transcriptome at the interface of nucleotide metabolism pathways

Wolbachia is a maternally transmitted bacterium that manipulates arthropod and nematode biology in myriad ways. The Wolbachia strain colonizing Drosophila melanogaster creates sperm-egg incompatibilities and protects its host against RNA viruses, making it a promising tool for vector control. Despite successful trials using Wolbachia-transfected mosquitoes for Dengue control, knowledge of how Wolbachia and viruses jointly affect insect biology remains limited. Using the Drosophila model, transcriptomics and gene expression network analyses revealed pathways with altered expression and splicing due to Wolbachia colonization and virus infection. Included are metabolic pathways previously unknown to be important for Wolbachia-host interactions. Additionally, Wolbachia-colonized flies exhibit a dampened transcriptomic response to virus infection, consistent with early blocking of virus replication. Finally, using Drosophila genetics, we show Wolbachia and expression of nucleotide metabolism genes have interactive effects on virus replication. Understanding the mechanisms of pathogen blocking will contribute to the effective development of Wolbachia-mediated vector control programs.

microbiology↗

bioRxiv2020

A bacterial symbiont protects honey bees from fungal disease

Fungi are the leading cause of insect disease, contributing to the decline of wild and managed populations1,2. For ecologically and economically critical species, such as the European honey bee (Apis mellifera), the presence and prevalence of fungal pathogens can have far reaching consequences, endangering other species and threatening food security3,4,5. Our ability to address fungal epidemics and opportunistic infections is currently hampered by the limited number of antifungal therapies6,7. Novel antifungal treatments are frequently of bacterial origin and produced by defensive symbionts (bacteria that associate with an animal/plant host and protect against natural enemies 89. Here we examined the capacity of a honey bee-associated bacterium, Bombella apis, to suppress the growth of fungal pathogens and ultimately protect bee brood (larvae and pupae) from infection. Our results showed that strains of B. apis inhibit the growth of two insect fungal pathogens, Beauveria bassiana and Aspergillus flavus, in vitro. This phenotype was recapitulated in vivo; bee brood supplemented with B. apis were significantly less likely to be infected by A. flavus. Additionally, the presence of B. apis reduced sporulation of A. flavus in the few bees that were infected. Analyses of biosynthetic gene clusters across B. apis strains suggest antifungal production via a Type I polyketide synthase. Secreted metabolites from B. apis alone were sufficient to suppress fungal growth, supporting this hypothesis. Together, these data suggest that B. apis protects bee brood from fungal infection by the secretion of an antifungal metabolite. On the basis of this discovery, new antifungal treatments could be developed to mitigate honey bee colony losses, and, in the future, could address fungal epidemics in other species.

microbiology↗

bioRxiv2019

Normal human lymph node T follicular helper cells and germinal center B cells accessed via fine needle aspirations

Germinal centers (GC) are critically important for the maturation of the antibody response and the generation of memory B cells, which are the basis for long-term protection from pathogens. Germinal centers only occur in lymphoid tissue, such as lymph nodes, and are not present in blood. Therefore, cells of the germinal center, including GC B cells and GC T follicular helper (TFH) cells, are not well-studied in humans under normal healthy conditions, due to the limited availability of healthy lymph node samples. We used a minimally invasive, routine clinical procedure, lymph node fine needle aspirations (LN FNAs), to obtain lymph node cells from healthy human subjects to establish benchmarks of GC cells under noninflammatory conditions. This study of 50 lymph nodes demonstrates that human LN FNAs are a safe and feasible technique for immunological research, and defines benchmarks for human GC biology. The findings indicate that assessment of the GC response via LN FNAs will have application to the study of human vaccination, allergy, and autoimmune disease.

immunology↗

bioRxiv2018

Social communication between microbes colonizing the social honey bee Apis mellifera

The European honey bee (Apis mellifera) is a charismatic species that plays a critical role in the pollination of agriculturally important crops and native flora. One emerging field of research is that of the host-associated honey bee microbiome: a group of bacterial phylotypes consistently found within the honey bee, which may play critical roles such as protection from pathogens and nutrient acquisition. In other model systems, host-associated microbial communities are known to participate in a form of bacterial communication known as quorum sensing. This type of communication allows bacteria to sense their environment and respond with changes in gene expression, controlling a number of factors including virulence, biofilm formation, and cell motility. Here, we have investigated the production of a specific quorum sensing molecule by honey bee microbes in vivo and in vitro. We specifically focused on the inter-species signaling molecule, autoinducer-2 (AI-2). We identified the production of AI-2 by both the entire community (using honey bee gut homogenates) and by cultured isolates, using a Vibrio harveyi biosensor. By comparing newly emerged and adult bees, we showed this signal is likely coming from the core microbial community. Finally, using honey bee specific bacterial isolates, we identified changes in biofilm production when isolates are exposed to increased levels of exogenous AI-2. Altogether, these data provide multiple lines of evidence for the presence of quorum sensing inside the honey bee host. The effect of AI-2 on biofilm formation by honey bee specific bacteria identifies one potential avenue for quorum sensing to affect host health.\n\nAuthor summaryMicrobial communities associate with every animal on the planet and can have dramatic effects on the health of their host. The honey bee is one such animal, home to a characteristic community of bacteria, which may provide various benefits. Here, we show that these microbes are producing quorum sensing molecules which could support interactions between bacterial members and facilitate host colonization.

microbiology↗

bioRxiv2017

Delayed activation of the DNA replication licensing system in Lgr5(+) intestinal stem cells

During late mitosis and early G1, replication origins are licensed for replication by binding to double hexamers of MCM2-7. Here, we investigate how licensing and proliferative commitment are coupled in the small-intestinal epithelium. We developed a method for identifying cells in intact tissue containing DNA-bound MCM2-7. Interphase cells above the transit-amplifying compartment had no DNA-bound MCM2-7, but still expressed MCM2-7 protein, suggesting that licensing is inhibited immediately upon differentiation. Strikingly, we found most proliferative Lgr5(+) stem cells are in an unlicensed state. This suggests that the elongated cell-cycle of intestinal stem-cells is caused by an increased G1 length, characterised by dormant periods with unlicensed origins. Significantly, the unlicensed state is lost In Apc mutant epithelium, which lacks a functional restriction point, causing licensing immediately upon G1 entry. We propose that the unlicensed G1 of intestinal stem cells creates a temporal window when proliferative fate decisions can be made.

cell biology↗