Biology subjects

Joseph, M.

Publications and source records attributed to Joseph, M..

14 recordsLinked to original sources

bioRxiv2026

GpsB acts as an adapter for MacP-mediated activation of class A penicillin-binding protein aPBP2a in Streptococcus pneumoniae, independently of MacP phosphorylation

Regulation of class A penicillin-binding proteins (aPBPs) in peptidoglycan biosynthesis is incompletely understood in Gram-positive bacteria. One example is activation of aPBP2a by GpsB and phosphorylated MacP in the ovoid-shaped pathogen, Streptococcus pneumoniae. We set out to examine whether phosphorylation of Thr residues other than Thr32 contributed to MacP activation of aPBP2a. We also wanted to determine whether GpsB and MacP activation of aPBP2a were related. Here we report that MacP was phosphorylated about equally at Thr32 and Thr56 in physiological and biochemical assays. However, based on transformation and growth assays, phosphorylation of MacP was not required for aPBP2a activation. A structure-function analysis confirmed that most of the MacP cytoplasmic domain, which was predicted by AlphaFold3 to be disordered, was not required for aPBP2a activation. These analyses further identified amino acids in the MacP transmembrane domain and the aPBP2a juxtamembrane region, as well as a variant of the GpsB-binding motif in the membrane-proximal cytoplasmic region of MacP, required for aPBP2a activation. Together, these results support a tripartite model in which GpsB acts as an adapter for activation of aPBP2a by MacP. Finally, additional interaction, Tn-seq, and growth assays suggested other modes of direct or indirect regulation of aPBP2a activity.

microbiology↗

bioRxiv2026

immunoPETE: A DNA-based integrated B-cell and T-cell receptor profiling platform

The vast diversity of B and T cell receptors generated through the recombination of Variable (V), Diversity (D), and Joining (J) gene segments plays a critical role in adaptive immunity. Profiling immune repertoires at the DNA level provides a robust and stable approach to capture the clonal composition of these receptors. immunoPETE is an assay designed to target recombined human T-cell Receptor Beta (TRB), T-cell Receptor Delta (TRD), and Immunoglobulin Heavy (IGH) chain genes directly from genomic DNA. Simultaneous profiling of B and T cell receptor chains in a single reaction provides internally normalized clone counts and facilitates the study of B-T cell interactions. Full-length amplicon consensus sequences representative of original template DNA molecules are accurately reconstructed using Unique Molecular Identifiers (UMIs). An in-house pipeline compiles VDJ rearrangements from the Complementarity-Determining Region 3 (CDR3) of TRB, TRD and IGH chains into comprehensive readouts at cell-level resolution. In this study, we describe the immunoPETE end-to-end workflow, followed by a comprehensive benchmarking of its performance in adaptive immune profiling. Where applicable, we used both natural and contrived samples and characterized the assays accuracy, linearity, and reproducibility across several metrics: retrieving CDR3 sequences, determining B and T cell ratios, total cell count, yield, fraction of functional rearrangements, clonal diversity, composition of dominant clones, pairwise similarity, and V/J gene usage frequencies. Furthermore, we assessed its quantitative limits concerning the total number of lymphocytes and the detection of rare clones. As an example of its applications, we show that adding immune biomarkers extracted from immunoPETE data to clinical factors improves prediction of progression-free survival in a cohort of non-muscle invasive bladder cancer (NMIBC) patients. Finally, we discuss the broad applications of immunoPETE in the study of aging, cancers, infections, and autoimmune disorders with reference to select published studies.

immunology↗

bioRxiv2025

Improving a removal model for evaluating density changes in a widespread invasive species

Invasive species pose a significant threat to native ecosystems. Effective management of invasive species requires accurate abundance estimates through time, particularly at large spatial scales. Traditional methods of abundance estimation from management data, such as camera trap studies and harvest data, face challenges due to variations in sampling protocols and effort standardization. We propose an extension to a previously calibrated removal model by integrating into an Integrated Population Model (IPM) and incorporating multiple removal techniques. The model utilizes management and land cover data, both of which are readily available in many invasive species systems. We evaluate the model with a simulation study, then apply it to management data on wild pigs (Sus scrofa). Simulations showed that the model performs well across a wide range of densities and population trajectories. Density estimates were the most biased when effort and density were low and sharpshooting or fixed wing aircraft were used to conduct removals. We discuss the advantages and limitations of using removal models for invasive species management, how the model performs with respect to previous removal modeling efforts, how performance might be improved through changes to data management practices, and the models potential to inform decision-making processes for invasive species management. Data availabilityThe data for this manuscript is available from Dryad (http://datadryad.org/share/gFz3ClanB-8yPB5lQ1x-dl1JqI07CP3SX92P-9UyfaU). The code for this manuscript will is available from Zenodo (10.5281/zenodo.15784366).

ecology↗

bioRxiv2025

A connexin 43 targeting peptide prevents blood vessel neointima formation

The gap junction protein connexin 43 (Cx43) is associated with human pathological vascular smooth muscle cell (SMC) proliferation and neointima formation. We previously identified mitogen-activated protein kinase (MAPK) phosphorylation of Cx43 results in binding with the cell cycle protein cyclin E, facilitating neointima formation in mice. However, the specific nature of these interactions and their relevance to human disease have not been elucidated. Using an ex vivo human saphenous vein model of neointima formation, we identified increased MAPK-phosphorylated Cx43 and cyclin E in explant tissues. We used peptide arrays to define a cyclin E-Cx43 binding region and generated CycliCx, a stearate-linked Cx43 phospho-mimetic peptide. In human coronary artery SMC, CycliCx inhibits platelet-derived growth factor-BB (PDGF-{beta})-induced changes in Cx43 trafficking and interactions with cyclin E, and stimulation of proliferation. RNAseq analysis identified CycliCx significantly inhibits PDGF-{beta}-induced proliferative pathways in SMC by limiting PDGF-{beta}-induced early G1/S phase cell cycle progression transcripts. Finally, we show CycliCx limits neointima formation in mice in vivo and in ex vivo human saphenous vein explants. Our data provide strong evidence for selective targeting of Cx43 as a viable therapeutic strategy for preventing neointimal formation in humans.

physiology↗

bioRxiv2024

STRIPAK controls cell-cell communication by promoting cytoneme biogenesis through the membrane-sculpting function of Slik.

Cytonemes are signaling filopodia that facilitate long-range cell-cell communication by forming synapses between cells. Initially discovered in Drosophila for transporting morphogens during embryogenesis, they have since been identified in mammalian cells and recently implicated in carcinogenesis. Yet, despite their importance, the mechanisms controlling cytoneme biogenesis remain elusive. Here, we demonstrate that the Ser/Thr kinase Slik drives remote cell proliferation by promoting cytoneme formation. We discovered that this function depends on the coiled-coil domain of Slik (SlikCCD), which directly sculpts membranes into tubules. Importantly, Slik plays paradoxical roles in cytoneme biogenesis. While its membrane-sculpting activity promotes cytoneme formation, it is counteracted by its kinase activity, which enhances actin association with the plasma membrane via Moesin phosphorylation. In vivo, SlikCCD enhances formation of cytonemes in one epithelial layer of the wing disc to promote cell proliferation in an adjacent layer. Finally, we found that this function relies on the STRIPAK complex, which controls cytoneme formation and governs proliferation at a distance by regulating Slik association with the plasma membrane. Our study unveils the first family of kinases that directly sculpts membranes, a function crucial for cytoneme-mediated control of cell proliferation.

cell biology↗

bioRxiv2023

Preserving endothelial integrity in human saphenous veins during preparation for coronary bypass surgery

ObjectiveWhile multiple factors influence coronary artery bypass graft success rates, preserving saphenous vein endothelium during surgery may improve patency. Standard methods of saphenous vein graft preparation in heparinized saline (saline) solutions result in endothelial loss and damage. Here we investigated the impact of preparing saphenous graft vessels in heparinized patient blood (blood) vs saline on cellular health and survival. MethodsSaphenous vein tissues from a total of 23 patients undergoing coronary artery bypass graft surgery were split into 2 treatment groups, 1) standard preparation using saline and 2) preparation using blood. Immediately following surgery, excess tissue was fixed for analysis. Level of endothelial coverage, oxidative stress marker 4-hydroxynonenal (4HNE), and oxidative stress protective marker nuclear factor erythroid 2-related factor 2 (NRF2) expression were evaluated. ResultsIn saline patient veins, histological analysis revealed a broken or absent luminal layer, suggesting a loss of endothelial cell (EC) coverage. Luminal cell coverage was notably preserved in blood-treated samples. Immunofluorescent staining of endothelial markers vascular endothelial cadherin (VE-cadherin) and endothelial nitric oxide (eNOS) identified a significant improvement in endothelial coverage in the blood group compared to saline. Although in both treatment groups EC expressed 4HNE indicating a similar level of oxidative stress, EC stored in blood solutions expressed higher levels of the protective transcription NRF2. ConclusionsOur data indicate that maintaining and preparing saphenous vein tissues in solutions containing heparinized blood helps preserve the endothelium and promotes vein graft health. This has the potential to improve long-term outcomes in patients. Central MessageDuring coronary artery bypass grafting, preparation of saphenous veins with heparinized saline damages the endothelium and increases oxidative stress. Heparinized blood preparation limits this endothelial loss and damage. Perspectives StatementSaphenous vein grafts are prone to failure through neointimal hyperplasia or thrombosis. Endothelial damage and loss are thought to be major contributing factors to graft failure. Here we find that preparation and preservation of saphenous vein grafts with patients own heparinized blood is sufficient to ensure endothelial preservation and protect vessels from oxidative stress compared with heparinized saline. These changes may increase long-term graft patency rates.

physiology↗

bioRxiv2023

The mechanics of bronchoconstriction cause airway epithelial damage and inflammation by excess crowding-induced extrusion

Asthma is deemed an inflammatory disease, yet the defining diagnostic symptom is mechanical bronchoconstriction. We previously discovered a conserved process that drives homeostatic epithelial cell death in response to mechanical cell crowding called cell extrusion(1, 2). Here, we show that the pathological crowding of a bronchoconstrictive attack causes so much epithelial cell extrusion that it damages the airways, resulting in inflammation and mucus secretion. While relaxing airways with the rescue treatment albuterol did not impact these responses, inhibiting live cell extrusion signaling during bronchoconstriction prevented all these symptoms. Our findings propose a new etiology for asthma, dependent on the mechanical crowding of a bronchoconstrictive attack. Our studies suggest that blocking epithelial extrusion, instead of ensuing downstream inflammation, could prevent the feed-forward asthma inflammatory cycle.

cell biology↗

bioRxiv2023

Chromosomal Duplications of MurZ (MurA2) or MurA (MurA1), Amino Acid Substitutions in MurZ (MurA2), and Absence of KhpAB Obviate the Requirement for Protein Phosphorylation in Streptococcus pneumoniae D39

GpsB links peptidoglycan synthases to other proteins that determine the shape of the respiratory pathogen Streptococcus pneumoniae (pneumococcus; Spn) and other low-GC Gram-positive bacteria. GpsB is also required for phosphorylation of proteins by the essential StkP(Spn) Ser/Thr protein kinase. Here we report three classes of frequently arising chromosomal duplications ({approx}21-176 genes) containing murZ (MurZ-family homolog of MurA) or murA that suppress {Delta}gpsB or {Delta}stkP. These duplications arose from three different repeated sequences and demonstrate the facility of pneumococcus to modulate gene dosage of numerous genes. Overproduction of MurZ or MurA alone or overexpression of MurZ caused by {Delta}khpAB mutations suppressed {Delta}gpsB or {Delta}stkP phenotypes to varying extents. {Delta}gpsB and {Delta}stkP were also suppressed by MurZ amino-acid changes distant from the active site, including one in commonly studied laboratory strains, and by truncation or deletion of the homolog of IreB(ReoM). Unlike in other Gram-positive bacteria, MurZ is predominant to MurA in pneumococcal cells. However, {Delta}gpsB and {Delta}stkP were not suppressed by {Delta}clpCP, which did not alter MurZ or MurA amounts. These results support a model in which regulation of MurZ and MurA activity, likely by IreB(Spn), is the only essential requirement for protein phosphorylation in exponentially growing D39 pneumococcal cells.

microbiology↗

bioRxiv2022

Extracellular ATP drives pancreatic cancer cell invasion via purinergic receptor-integrin interactions

Pancreatic ductal adenocarcinoma (PDAC) is a cancer of unmet clinical need. Given the elevated ATP levels seen in PDAC, the purinergic axis represents an attractive therapeutic target. Mediated in part by highly druggable extracellular proteins, it plays essential roles in fibrosis, inflammation response and immune function. We have analysed the PDAC purinome using publicly available databases to discern which members may impact patient survival. We identified P2RY2 to be the purinergic gene with the strongest association to hypoxia, the highest cancer cell specific expression and the strongest impact on overall survival. Invasion assays using a 3D spheroid model revealed P2Y2 to be critical in facilitating invasion driven by extracellular ATP. Using genetic modification or pharmacological strategies we identify the mechanism of this ATP-driven invasion to require direct protein-protein interactions between P2Y2 and V integrins. Using DNA-PAINT super-resolution fluorescence microscopy, we found that P2Y2 regulates the amount and distribution of integrin V in the plasma membrane. This work highlights a novel GPCR-integrin interaction in cancer invasion and its potential for therapeutic targeting.

cancer biology↗

bioRxiv2022

Roles of RodZ and Class A PBP1b in the Assembly and Regulation of the Peripheral Peptidoglycan Elongasome in Ovoid-Shaped Cells of Streptococcus pneumoniae D39

RodZ of rod-shaped bacteria functions to link MreB filaments to the Rod peptidoglycan (PG) synthase complex that moves circumferentially perpendicular to the long cell axis, creating hoop-like sidewall PG. Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus; Spn) that lack MreB, use a different modality for peripheral PG elongation that emanates from the midcell of dividing cells. Yet, S. pneumoniae encodes a RodZ homolog similar to RodZ in rod-shaped bacteria. We show here that the helix-turn-helix and transmembrane domains of RodZ(Spn) are essential for growth at 37{degrees}C. {Delta}rodZ mutations are suppressed by {Delta}pbp1a, mpgA(Y488D), and {Delta}khpA mutations that suppress {Delta}mreC, but not {Delta}cozE. Consistent with a role in PG elongation, RodZ(Spn) co-localizes with MreC and aPBP1a throughout the cell cycle and forms complexes and interacts with PG elongasome proteins and regulators. Depletion of RodZ(Spn) results in aberrantly shaped, non-growing cells and mislocalization of elongasome proteins MreC, PBP2b, and RodA. Moreover, Tn-seq reveals that RodZ(Spn), but not MreCD(Spn), displays a specific synthetic-viable genetic relationship with aPBP1b, whose function is unknown. We conclude that RodZ(Spn) acts as a scaffolding protein required for elongasome assembly and function and that aPBP1b, like aPBP1a, plays a role in elongasome regulation and possibly peripheral PG synthesis. Graphical Summary O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/494439v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@f1cfb9org.highwire.dtl.DTLVardef@17cac68org.highwire.dtl.DTLVardef@1af20borg.highwire.dtl.DTLVardef@108d83c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike

The interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the ACE2 receptor on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, the N-terminal domain (NTD) and S2 subunits of Spike. To fully understand how these mutations affect the antigenicity of Spike, we have isolated and characterized neutralizing antibodies targeting epitopes beyond the already identified RBD epitopes. Using recombinant Spike as a sorting bait, we isolated >100 Spike-reactive monoclonal antibodies from SARS-CoV-2 infected individuals. ~45% showed neutralizing activity of which ~20% were NTD-specific. None of the S2-specific antibodies showed neutralizing activity. Competition ELISA revealed that NTD-specific mAbs formed two distinct groups: the first group was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Importantly, mutations present in B.1.1.7 Spike frequently conferred resistance to neutralization by the NTD-specific neutralizing antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes need to be considered when investigating antigenic drift in emerging variants.

immunology↗

bioRxiv2021

Cortico-amygdalar connectivity and externalizing/internalizing behavior in children with neurodevelopmental disorders

BackgroundExternalizing and internalizing behaviors are common and contribute to impairment in children with neurodevelopmental disorders (NDDs). Associations between externalizing or internalizing behaviors and cortico-amygdalar connectivity have been found in children with and without clinically significant internalizing/externalizing behaviors. This study examined whether such associations are present across children with different NDDs. MethodsMulti-modal neuroimaging and behavioral data from the Province of Ontario Neurodevelopmental Disorders (POND) Network were used. POND participants aged 6-18 years with a primary diagnosis of autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD) or obsessive-compulsive disorder (OCD), as well as typically developing children (TDC) with T1-weighted, resting-state fMRI or diffusion weighted imaging and parent-report Child Behavioral Checklist (CBCL) data available, were analyzed (n range=157-346). Associations between externalizing or internalizing behavior and cortico-amygdalar structural and functional connectivity indices were examined using linear regressions, controlling for age, gender, and image-modality specific covariates. Behavior-by-diagnosis interaction effects were also examined. ResultsNo significant linear associations (or diagnosis-by-behavior interaction effects) were found between CBCL-measured externalizing or internalizing behaviors and any of the connectivity indices examined. Post-hoc bootstrapping analyses indicated stability and reliability of these null results. ConclusionsThe current study provides evidence in favour of the absence of a shared linear relationship between internalizing or externalizing behaviors and cortico-amygdalar connectivity properties across a transdiagnostic sample of children with various NDDs and TDC. Detecting shared brain-behavior relationships in children with NDDs may benefit from the use of different methodological approaches, including incorporation of multi-dimensional behavioral data (i.e. behavioral assessments, neurocognitive tasks, task-based fMRI) or clustering approaches to delineate whether subgroups of individuals with different brain-behavior profiles are present within heterogeneous cross-disorder samples.

neuroscience↗

bioRxiv2020

Population dynamics and neuronal polyploidy in the developing neocortex

SUMMARYThe mammalian neocortex is composed of different subtypes of neurons which are generated during embryogenesis by sequential differentiation of neural progenitors. While molecular mechanisms that control neuronal production in the developing neocortex have been extensively studied, the dynamics and absolute numbers of the different progenitor and neuronal populations are still poorly characterized. Here we describe a medium throughput approach based on flow cytometry and well known identity markers of cortical subpopulations to collect quantitative data over the course of mouse neocortex development. We collected a complete dataset in a physiological developmental context on two progenitor and two neuron populations, including relative proportions and absolute numbers. Our study reveals unexpected numbers of progenitors. In addition, we discovered that a fraction of neurons in the developing mouse neocortex are polyploid.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2019

Sex differences in Variability of Brain Structure Across the Lifespan

Several brain disorders exhibit sex differences in onset, presentation, and prevalence. Increased understanding of the neurobiology of sex-based differences across the lifespan can provide insight into potential disease risk and protective mechanisms. We focused on sex-related differences in variability, which may be indicative of both disease vulnerability and resilience. In n=3,069 participants, from 8-95 years of age, we first analyzed the variance ratio in females vs. males of cortical surface area and global and subcortical volumes for discrete brain regions, and found widespread greater variability in males. In contrast, variance in cortical thickness was similar for males and females. Multivariate analysis that accounts for structural covariance supported variance ratio findings. Findings were present from early life and stable with age. We then examined variability among brain regions by sex. We found significant age-by-sex interactions across neuroimaging metrics, whereby in very early life males had reduced among-region variability compared to females, while in very late life this was reversed. Overall, our findings of greater regional variability but less among-region variability in males in early life may aid our understanding of sex-based risk for neurodevelopmental disorders. In contrast, our findings in late life may provide a potential sex-based risk mechanism for dementia.

neuroscience↗