Biology subjects

Meek, S.

Publications and source records attributed to Meek, S..

9 recordsLinked to original sources

bioRxiv2026

Suidae iPSC-derived macrophages as models for investigating susceptibility and resilience to African swine fever virus

African swine fever virus (ASFV) causes a lethal haemorrhagic fever in pigs and spread of this disease threatens many pig species (Suidae) globally. By contrast, ASFV infections in the natural evolved hosts, the warthog and bushpig, are subclinical. The macrophage (M{varphi}) is the primary target of ASFV and species-dependent responses in M{varphi}s are presumed to influence disease susceptibility. In an attempt to model these differences in vitro, we generated transgene-regulated induced pluripotent stem cells (iPSCs) from domestic pig, wild boar, red river hog and warthog, and confirmed that their corresponding iPSC-derived M{varphi}s (iPSCdMs) supported infection and replication of ASFV. In contrast to the other species, however, warthog iPSCdMs did not induce interferon upon infection by either virulent or attenuated ASFV. iPSCdMs may therefore represent an experimental system to understand how ASFV infection of M{varphi}s contributes to disease and aid development of strategies to combat this economically and environmentally devastating pathogen.

developmental biology↗

bioRxiv2026

ExoFILT: Transfer learning for robust and accelerated analysis of exocytosis single-particle tracking data

MotivationUnderstanding constitutive exocytosis at the molecular level requires quantitative characterization of protein dynamics during the process. Single-particle tracking allows the measurement of protein dynamics in living cells. However, identifying bona fide exocytic events requires extensive manual annotation, limiting throughput and introducing personal biases that affect reproducibility. ResultsWe present ExoFILT, a deep learning-based classifier designed to identify exocytic events in single-particle tracking data, using the exocyst complex as a reference. Trained via transfer learning on simulated and experimental data, ExoFILT reduces the time required for manual annotation by ten-fold while improving measurement consistency across researchers. When applied to simultaneous dual-color time-lapse movies, ExoFILT enabled the systematic quantification of temporal relationships between exocytic proteins. The increased throughput uncovered distinct subpopulations of exocytic events with differential molecular composition (e.g., events with and without detectable levels of Sec1), underscoring the potential of ExoFILT to reveal mechanistic insights into exocytosis.

bioinformatics↗

bioRxiv2025

The cow udder is a potential mixing vessel for influenza A viruses

The incursion of high pathogenicity avian influenza A virus (IAV) into US dairy cows is unprecedented in the era of molecular diagnosis and pathogen sequencing. This raises questions over the likelihood of further outbreaks and whether dairy cattle could be a "mixing vessel" for novel strains of IAV. Using a panel of BSL2-safe reassortant viruses representing clade 2.3.4.4b H5 epizootic lineages circulating since 2020, we found that a cow B3.13 isolate displayed enhanced replication in cow mammary gland cells, along with increased viral polymerase activity and stronger interferon antagonism in cow cells compared to an earlier EA-2020-C genotype virus. However, multiple avian and mammalian IAV strains, including other clade 2.3.4.4b high pathogenicity genotypes, were replication competent in bovine cells, particularly those of the mammary gland, suggesting that there is a diverse circulating IAV pool with the potential to infect cows. Moreover, we show that cow mammary cells co-express -2,3 and -2,6 - linked sialic acids, and are susceptible to co-infection with human and avian IAVs. We conclude that the US cow influenza outbreak does not simply reflect a unique adaptation of the B3.13 genotype virus; rather, the bovine udder represents a permissive niche for IAV and a plausible site for reassortment, underscoring its potential role in generating novel influenza viruses with pandemic risk.

microbiology↗

bioRxiv2025

DNA Divers: volunteer-based eDNA capture for local and global marine biodiversity monitoring

Volunteer-based biodiversity recording is a powerful source of scalable data yet to be used to its full potential by the scientific community. Coastal ecosystems are varied and diverse, making it difficult for managers to identify flexible methods for monitoring biological components. Emerging technologies such as environmental DNA (eDNA) analysis are promising for measuring aquatic biodiversity, yet most management organizations lack personnel and capacity to collect molecular data. Here we investigate, together as professional and non-professional scientists, the efficacy of a quasi-passive eDNA capture technique. Volunteer SCUBA divers and snorkelers used low-cost materials, namely cotton medical gauze, to capture eDNA via swimming. We compared this method to conventional eDNA capture techniques in an aquarium and nature, collectively iterating the field and laboratory procedures to improve feasibility. With a small (< 30) network of volunteers, we detected 275 unique teleost and elasmobranch species from varied marine habitats spanning 90 degrees of latitude. The swimming motion of divers was more effective than stationary soaking and the fish communities sampled by divers were comparable to that of conventional eDNA samples. The ease of this technique matched by the eagerness and generosity of volunteers presents an untapped, viable approach for scaling multi-species marine eDNA monitoring as well as an avenue for improving science literacy. Data availabilityhttps://zenodo.org/records/14853820?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImYxMTlhODFiLTI3NGYtNDQ2Ni05MDYyLTIyOTlkNWVhY2FkNiIsImRhdGEiOnt9LCJyYW5kb20iOiIwYmZlMzJhMWU0YWZkM2ZhMWEwYTE0NmY0ZWM5YWZkNSJ9.0R7GJjVJLEuq-UJVKA1CcMT8LCTamv3GEvPl-5ItzP10pFRd-cAzAr_Q5ggjEewZUtByHjBu-eSegWWlLAx_Rw

ecology↗

bioRxiv2025

Continuum architecture dynamics of vesicle tethering in exocytosis

Essential for eukaryotic organisms, multiple copies of the exocyst complex tether each secretory vesicle to the plasma membrane (PM) in constitutive exocytosis. The exocyst higher-order structure (ExHOS) that coordinates the action of these multiple exocysts remains unexplored. We integrated particle-tracking, super-resolution microscopy and cryo-electron tomography in a model that time-resolves the continuum conformational landscape of the ExHOS and functionally annotates its different conformations. We found that 7 exocysts form flexible ring-shaped ExHOS that tether vesicles at <45 nm from the PM. The ExHOS, initially 19 nm in radius, rapidly expands while it pulls the vesicle towards the PM. Subsequently, the ExHOS stabilizes, securing the vesicle at [~]4 nm from the PM. After fusion, Sec18 mediates the ExHOS disassembly when its radius is 38 nm. By resolving the fundamental biophysical principles of tethering we bridged the gap between static isolated structures and the dynamic and multimeric nature of exocytosis.

cell biology↗

bioRxiv2023

p75NTR neurotrophin receptor function is redundant for development, growth and fertility in the rat.

The p75NTR neurotrophin receptor has positive and negative roles regulating cell survival in the nervous system. Unambiguous interpretation of p75NTR function in vivo has been complicated, however, by residual expression of alternate forms of p75NTR protein in initial p75NTR knock-out mouse models. As rats are the preferred rodent for studying brain and behaviour, and to simplify interpretation of the knock-out phenotype, we report here the generation of a mutant rat devoid of the p75NTR protein. TALEN-mediated recombination in embryonic stem cells (ESCs) was used to flank exon 2 of p75NTR with Lox P sites and produce transgenic rats carrying either un-recombined floxed p75NTREx2-fl, or recombined, exon-2 deleted p75NTREx2-{Delta} alleles. Crossing p75NTREx2-fl rats with a Cre-deleter strain efficiently removed exon 2 in vivo. Excision of exon 2 causes a frameshift after p75NTR Gly23 and eliminated p75NTR protein expression. Rats lacking p75NTR were healthy, fertile, and histological analysis did not reveal significant changes in cellular density or overall structure in their brains. Thus, p75NTR function appears largely dispensable for normal development, growth and basal homeostasis in the rat. The availability of constitutive and conditional p75NTREx2-{Delta} rats should, however, provide new opportunities to investigate specific roles of p75NTR upon injury and during regeneration.

genetics↗

bioRxiv2023

MeCP2 binds to methylated DNA independently of phase separation and heterochromatin organisation

Correlative evidence has suggested that DNA methylation promotes the formation of transcriptionally silent heterochromatin. Accordingly, the methyl-CpG binding domain protein MeCP2 is often portrayed as a constituent of heterochromatin. This interpretation has been reinforced by the use of mouse cells as an experimental system for studying the mammalian epigenome, as heterochromatin, DNA methylation and MeCP2 colocalise in prominent foci. The findings presented here revise this view. We show that focal localisation of MeCP2 in mice is independent of heterochromatin, as DNA methylation-dependent MeCP2 foci persist even when the signature heterochromatin histone mark H3K9me3 is absent and heterochromatin protein HP1 is diffuse. Contrary to the proposal that MeCP2 forms condensates at mouse heterochromatic foci via liquid-liquid phase transition, the short methyl-CpG binding domain, which lacks the disordered domains thought to be required for condensation, is sufficient to target foci in mouse cells. Importantly, we find that the formation of MeCP2 foci in mice is highly atypical, as they are indetectable in 14 out of 16 other mammalian species, including humans. Notably, MeCP2 foci are absent in Mus spretus which can interbreed with Mus musculus but lacks its highly methylated pericentric satellite DNA repeats. We conclude that MeCP2 has no intrinsic tendency to form nuclear condensates and its localisation is independent of heterochromatin formation. Instead, the distribution of MeCP2 in the nucleus is primarily determined by global DNA methylation patterns and is typically euchromatic.

cell biology↗

bioRxiv2021

Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock

Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. We explored how pluripotent stem cells (PSCs) can provide a limitless in vitro supply of genetically and experimentally tractable macrophages from livestock. Porcine and bovine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics of ex vivo primary macrophages. Pig PSCdMs were productively infected by Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and African Swine Fever Virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, Pig PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied in parental stem cells, or directly by lentiviral vector transduction. PSCs and differentiated derivatives therefore provide a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in livestock.

immunology↗

bioRxiv2020

Modulation of Aplnr signaling is required during the development and maintenance of the hematopoietic system

Apelin receptor (Aplnr/Agtrl1/Apj) marks a transient cell population during the differentiation of hematopoietic progenitor cells (HPCs) from pluripotent stem cells but the function of this signalling pathway during hematopoietic development both in vitro and in vitro is poorly understood. We generated an Aplnr-null mouse embryonic stem cell (mESC) line and demonstrated that they are significantly impaired in the production of HPCs indicating that the Aplnr pathway is required for their formation. Using Aplnr-tdTomato reporter mESCs we demonstrated that is expressed in a population of differentiating mesodermal cells committed to a hematopoietic and endothelial fate. Activation of this signaling pathway by the addition of the Apelin ligand to differentiating ESCs has no effect on the production of HPCs but the addition to ex vivo AGM cultures impaired the generation of long term reconstituting hematopoietic stem cells and appeared to drive myeloid differentiation. Taken together, our data suggest that the Aplnr pathway is required for the generation of cells that give rise to HSCs during development but its subsequent down regulation is required for their maintenance. HIGHLIGHTSO_LIHematopoietic differentiation is impaired in Aplnr-null ESCs C_LIO_LIAplnr-tdTomato reporter marks a subpopulation of ESC-derived mesoderm. C_LIO_LIAplnr signaling drives the maturation of lineage-committed myeloid progenitors C_LIO_LIIn AGM explant cultures HSC activity is reduced in the presence of Aplnr ligands. C_LI

developmental biology↗