Biology subjects

Francis, A.

Publications and source records attributed to Francis, A..

16 recordsLinked to original sources

bioRxiv2026

Preclinical characterization of immune responses induced by a candidate gonococcal native Outer Membrane Vesicle vaccine

BackgroundNeisseria gonorrhoeae poses significant public health challenges due to multidrug-resistant gonorrhoeic and severe reproductive health complications of untreated infection. No vaccine is licensed to prevent gonorrhea. However, the meningococcal outer membrane vesicle (OMV)-containing vaccine, 4CMenB, provides moderate cross-protection against gonorrhea. We have recently demonstrated that immunization with gonococcal OMV accelerates clearance of gonococcal infection in mice compared with 4CMenB. MethodsTo gain insight into possible mechanisms of protection of gonococcal OMV, we evaluated the immunogenicity of GonoVac, a candidate native OMV (nOMV) vaccine against gonorrhea, in mice and rabbits. Three doses of GonoVac were administered intramuscularly from 0.15 to 5 {micro}g in mice, and four doses were used to immunize rabbits at 50 {micro}g per dose, formulated with or without aluminum hydroxide (Al(OH)3). Systemic and mucosal antibody responses were evaluated by enzyme-linked immunosorbent assay (ELISA) and serum bactericidal assay (SBA). Cellular responses were assessed by enzyme-linked immunosorbent spot (ELISpot). ResultsImmunization with GonoVac formulated with and without Al(OH)3 induced significantly higher levels of gonococcal serum and vaginal IgG, and serum bactericidal antibodies, compared with 4CMenB, which induced no serum killing activity. Serum bactericidal activity of GonoVac correlated with anti-gonococcal IgG and IgG2a levels. Serum IgA levels were minimal. Cellular immune responses were higher in mice receiving GonoVac/Al(OH)3 compared with GonoVac alone. Immunogenicity was similar for GonoVac produced in a bioreactor and shake flasks. ConclusionGonoVac elicits robust and functional immune responses in mice and rabbits compared with 4CMenB, supporting its further development as a promising candidate vaccine against gonorrhea. ImportanceGonorrhea, caused by Neisseria gonorrhoeae, remains a significant global health concern, disproportionately affecting populations in low- and middle-income countries (LMICs), particularly women. The emergence of multidrug-resistant strains of N. gonorrhoeae has raised the concern of untreatable gonorrhea, underscoring the urgent need for effective preventive measures. Although there is no licensed vaccine against gonorrhea, the meningococcal OMV-based vaccine, 4CMenB, is partially effective against the disease and has been recommended for use in high-risk groups. In this article, we build on previous findings of enhanced efficacy of gonococcal OMV vaccine candidates compared with 4CMenB in the mouse gonococcal infection model to demonstrate the superior anti-gonococcal immunogenicity of a gonococcal OMV-based candidate vaccine (GonoVac) compared with 4CMenB. GonoVac elicits robust immunity in mice, inducing antibodies that are able to kill gonococci, whereas 4CMenB does not. The findings highlight the potential of GonoVac as a promising vaccine candidate for the prevention of gonorrhea worldwide.

immunology↗

bioRxiv2026

Resident cardiac macrophages are not required for normal atrioventricular node conduction

Resident cardiac macrophages are understood to facilitate atrioventricular (AV) node conduction because they purportedly couple to AV node myocytes via connexin43 (Cx43) containing gap junctions. We tested this mechanism using biophysical modelling, high-resolution imaging of mouse and human AV conduction tissue, and pharmacological macrophage depletion. In silico, coupling macrophage membrane phenotypes to HCN4+ AV node myocytes imposed an electrotonic load that suppressed pacemaking and promoted conduction slowing, including stable 2:1 block in strand simulations. Anatomically, HCN4-defined components of the mouse AV conduction axis were essentially devoid of Cx43 and overlap of CD68+ macrophages and Cx43 was negligible in both mouse AV node and human penetrating bundle. Finally, near-complete macrophage depletion with CSF1R inhibition (PLX5622) did not alter AV electrical activity in vivo or ex vivo. Together, these data argue against a physiologically relevant role for Cx43-mediated macrophage-myocyte electrical coupling in normal AV node function. HIGHLIGHTSO_LIModelling predicts that AV node automaticity and conduction would be suppressed if macrophages coupled to AV node myocytes C_LIO_LIThe mouse AV conduction axis is essentially devoid of Cx43, currently considered responsible for macrophage-AV node myocyte coupling C_LIO_LIOverlap of macrophages and Cx43 expression is not discernible in the Cx43-expressing human distal AV node C_LIO_LIMacrophage depletion by CSF1R inhibition does not impact AV electrical activity in vivo or ex vivo C_LI

physiology↗

bioRxiv2025

Cell-Type-Specific Transcriptomic Signatures in Prefrontal Cortex Reveal lncRNA-mediated Gene Silencing and Enhancer Activities Contributing to the Pathophysiology of Major Depressive Disorder

Long non-coding RNAs (lncRNAs) have emerged as pivotal epigenetic regulators that influence chromatin structure, gene expression, and various cellular processes. We conducted a comprehensive transcriptomic analysis to explore the regulatory roles of lncRNAs in gene expression across major cell types. Based on the cell type abundance as predicted by CIBERSORTx, the gene expression deconvolution of lncRNAs and mRNAs obtained from nonpsychiatric control (n=41) and MDD (n=59) subjects was carried out using bMIND. LncRNA regulatory activity and functional enrichment analysis were assessed in each cell type. Interactions between lncRNAs and transcription factors and RNA-binding proteins, as well as their associations with DNA and RNA, were obtained from the RNA Interactome Database. The protein-protein interactions of lncRNA-regulated mRNAs and the associations between genes and psychiatric disorders were sourced from STRING network PsyGeNET databases, respectively. We observed a prevalence of inhibitory neurons in the control group and a higher proportion of excitatory neurons within the MDD group. A significant dysregulation of lncRNAs and mRNAs, characterized by distinct gene-silencing activity of lncRNAs, was observed, potentially facilitated through chromatin modifications in excitatory and inhibitory neurons, as well as enhancer activity of specific lncRNAs in both neuronal and glial cell types. Functional analyses of the silenced neuronal genes highlighted the involvement of cell adhesion molecules and stress-related signaling in MDD, indicating disrupted neuron-glia interactions. The enhancer activity of lncRNAs indicated the positive regulation of genes involved in Hippo signaling and neurodegeneration. This work uniquely highlights the cell-type-specific roles of lncRNAs and their contributions to MDD pathophysiology. HIGHLIGHTSO_LIComprehensive cell-type-specific transcriptomic analysis of dorsolateral prefrontal cortex in MDD subjects. C_LIO_LIDistinct gene-silencing activity of lncRNAs in excitatory and inhibitory neurons. C_LIO_LIEnhancer activity of specific lncRNAs in both neuronal and glial cell types. C_LIO_LICritical roles of lncRNAs and associated cellular functions in the pathophysiology of MDD. C_LI

genomics↗

bioRxiv2025

Anti-amyloid antibody equilibrium binding to Aβ aggregates from human Alzheimer disease brain

ImportanceAnti-amyloid immunotherapy is used to treat Alzheimer disease (AD) with moderate benefits and potentially serious side effects due to amyloid related imaging abnormality with effusions/edema (ARIA-E). Different anti-amyloid antibodies have different in vitro binding characteristics to different synthetic A{beta} aggregates, leading to the assumption that they bind different species in the human brain. Lecanemab is hypothesized to bind "protofibrils," but these are not well-characterized in human brain. It is also unknown how binding differences correlate with ARIA-E rates. The APOE {varepsilon}4 allele increases ARIA-E risk, but how it affects antibody binding characteristics is unknown. ObjectivesTo determine whether anti-amyloid antibodies bind different species of human brain A{beta} and whether these binding properties to human brain A{beta} explains ARIA-E rates. DesignCross-sectional study of 18 postmortem human brains. SettingSingle tertiary care hospital. ParticipantsDeceased patients with AD and cerebral amyloid angiopathy (CAA). Main Outcomes and MeasuresEquilibrium binding constants (KD) and total A{beta} binding (Bmax) of recombinant aducanumab, lecanemab, and donanemab equivalents to human brain soluble and insoluble amyloid plaque-enriched and CAA-enriched A{beta} aggregates. ResultsLecanemab did not bind with greater affinity to the soluble fraction of A{beta} compared to aducanumab. All three antibodies were bound essentially identical quantities of A{beta} across the 18 cases and fractions (Pearsons r 0.84 - 0.97). Antibody preference for plaque vs CAA A{beta} did not differ in soluble fractions but differed slightly in insoluble extracts. The APOE {varepsilon}4 allele led to a more soluble antibody-accessible A{beta} pool in a dose-dependent manner for all three antibodies. Conclusions and RelevanceThe lecanemab binding target in human brain is unlikely to be distinctly "protofibrillar" compared to other antibodies. Differences in antibody preference for plaque vs CAA A{beta} are unlikely to fully explain differences in ARIA-E rates. The APOE {varepsilon}4 allele may plausibly increase ARIA-E risk by making antibody-accessible A{beta} more soluble. These results have implications for improving the safety and efficacy of current and future anti-amyloid antibody therapies.

neuroscience↗

bioRxiv2025

Endurance exercise remodels pulmonary vein sleeve myocytes and promotes a proarrhythmic atrial substrate

BACKGROUNDAtrial fibrillation (AF) susceptibility is heightened in endurance athletes but the underlying mechanisms are incompletely understood. Because pulmonary vein (PV) myocyte triggers are critical determinants of AF, we investigated PV electrophysiological remodelling in animal models of the athletes heart. METHODSThe following experiments were performed in canines and mice after 16 or 6 weeks, respectively, of daily exercise training (ExT), and compared to sedentary (Sed) controls: ECG recording, echocardiography, pharmacological autonomic block, extrastimulus pacing, multielectrode array mapping, monophasic and intracellular action potential (AP) recording with custom-designed pattern recognition analysis, histology, RNAseq and spatial in situ transcriptomics. RESULTSAF propensity was significantly increased in ExT animals. Mapping studies identified heightened rotational activity in the PV-left atrial (LA) junction of ExT vs. Sed canines in vivo, and enhanced automaticity, triggered activity and AP duration variability ex vivo in ExT canines and mice. Intracellular recordings in mouse PV cardiomyocytes determined at least six AP subtypes with increased frequency of pacemaker-like APs in ExT PV, concomitant with increased expression of pacemaking HCN4, Cav1.3 and Cav3.1 channels. PV spontaneous excitability was also significantly enhanced. Subcellular resolution spatial transcriptomics in mouse PV-LA identified diffuse ion channel remodelling and activation of established AF-promoting pro-inflammatory and pro-fibrotic cytokines and chemokines in ExT PV cardiomyocytes. Conduction slowing in the ExT PV-LA junction was attributable to: gap junction remodelling, reduced Na+ channel expression and increased extracellular matrix deposition with enhanced myofibroblast number and proximity to PV cardiomyocytes. CONCLUSIONSEndurance exercise elicits proarrhythmic electro-anatomical remodelling of the PV-LA junction with enhanced pacemaking ion channel expression and immune-inflammatory pathway activation in PV myocytes as prominent contributors. CLINICAL PERSPECTIVEO_ST_ABSWhat is new?C_ST_ABSO_LIThis work is the first demonstration that endurance training results in proarrhythmic electrophysiological remodelling of PV sleeve myocytes and extracellular matrix deposition in the PV-LA junction. C_LIO_LIWe register electrical and molecular heterogeneity of the PV-LA junction at single cell and subcellular resolution, and for the first time identify the molecular events that underlie increased proarrhythmic activity of the trained PV. These include enhanced pacemaking ion channel expression (e.g., HCN4, Cav1.3, and Cav3.1), pro-inflammatory cytokine activation (e.g., TNF, IL-6), increased myofibroblasts and extracellular matrix deposition. C_LI What are the clinical implications?O_LIWe identify the molecular determinants of PV proarrhythmic activity in the trained heart and present new therapeutic targets for AF prevention in athletes. C_LIO_LIOur findings provide mechanistic rationale for the efficacy of pulmonary vein isolation for AF in athletes. C_LI

physiology↗

bioRxiv2024

Structural and Mechanistic Bases for Resistance of the M66I Capsid Variant to Lenacapavir

Lenacapavir (LEN) is the first in class viral capsid protein (CA) targeting antiretroviral for treating multi-drug-resistant HIV-1 infection. Clinical trials and cell culture experiments have identified resistance associated mutations (RAMs) in the vicinity of the hydrophobic CA pocket targeted by LEN. The M66I substitution conferred by far the highest level of resistance to the inhibitor compared to other RAMs. Here we investigated structural and mechanistic bases for how the M66I change affects LEN binding to CA and viral replication. The high-resolution X-ray structure of the CA(M66I) hexamer revealed that the {beta}-branched side chain of Ile66 induces steric hindrance specifically to LEN thereby markedly reducing the inhibitor binding affinity. By contrast, the M66I substitution did not affect binding of Phe-Gly (FG)-motif-containing cellular cofactors CPSF6, NUP153, or SEC24C, which engage the same hydrophobic pocket of CA. In cell culture the M66I variant did not acquire compensatory mutations or replicate in the presence of LEN. Analysis of viral replication intermediates revealed that HIV-1(M66I CA) predominantly formed correctly matured viral cores, which were more stable than their wildtype counterparts. The mutant cores stably bound to the nuclear envelope but failed to penetrate inside the nucleus. Furthermore, the M66I substitution markedly altered HIV-1 integration targeting. Taken together, our findings elucidate mechanistic insights for how the M66I change confers remarkable resistance to LEN and affects HIV-1 replication. Moreover, our structural findings provide powerful means for future medicinal chemistry efforts to rationally develop second generation inhibitors with a higher barrier to resistance. IMPORTANCELenacapavir (LEN) is a highly potent and long-acting antiretroviral that works by a unique mechanism of targeting the viral capsid protein. The inhibitor is used in combination with other antiretrovirals to treat multi-drug-resistant HIV-1 infection in heavily treatment-experienced adults. Furthermore, LEN is in clinical trials for preexposure prophylaxis (PrEP) with interim results indicating 100 % efficacy to prevent HIV-1 infections. However, one notable shortcoming is a relatively low barrier of viral resistance to LEN. Clinical trials and cell culture experiments identified emergent resistance mutations near the inhibitor binding site on capsid. The M66I variant was the most prevalent capsid substitution identified in patients receiving LEN to treat muti-drug resistant HIV-1 infections. The studies described here elucidate the underlying mechanism by which the M66I substitution confers a marked resistance to the inhibitor. Furthermore, our structural findings will aid future efforts to develop the next generation of capsid inhibitors with enhanced barriers to resistance.

microbiology↗

bioRxiv2024

CanDrivR-CS: A Cancer-Specific Machine Learning Framework for Distinguishing Recurrent and Rare Variants

MotivationMissense variants play a crucial role in cancer development, and distinguishing between those that frequently occur in cancer genomes and those that are rare may provide valuable insights into important functional mechanisms and consequences. Specifically, if common variants confer growth advantages, they may have undergone positive selection across different patients due to similar selection pressures. Moreover, studies have demonstrated the significance of rare mutations that arise as resistance mechanisms in response to drug treatment. This highlights the importance of understanding the role of both recurrent and rare variants in cancer. In addition to this, most existing tools for variant prediction focus on distinguishing variants found in normal and disease populations, often without considering the specific disease contexts in which these variants arise. Instead, they typically build predictors that generalise across all diseases. Here, we introduce CanDrivR-CS, a set of cancer-specific gradient boosting models designed to distinguish between rare and recurrent cancer variants. ResultsWe curated missense variant data from the International Cancer Genome Consortium (ICGC). Cancer-type-specific models significantly outperformed a baseline pan-cancer model, achieving a maximum leave-one-group-out cross-validation (LOGO-CV) F1 score of up to 90% for CanDrivRSKCM (Skin Cutaneous Melanoma) and 89% for CanDrivR-SKCA (Skin Adenocarcinoma), compared to 79.2% for the baseline model. Notably, DNA shape properties consistently ranked among the top features for distinguishing recurrent and rare variants across all cancers. Specifically, recurrent missense variants frequently occurred in DNA bends and rolls, potentially implicating regions prone to DNA replication errors and acting as mutational hotspots. Availability and ImplementationAll training and test data, and Python code are available in our CanDrivR-CS GitHub repository: https://github.com/amyfrancis97/CanDrivR-CS.

genomics↗

bioRxiv2024

DrivR-Base: A Feature Extraction Toolkit For Variant Effect Prediction Model Construction

MotivationRecent advancements in sequencing technologies have led to the discovery of numerous variants in the human genome. However, understanding their precise roles in diseases remains challenging due to their complex functional mechanisms. Various methodologies have emerged to predict the pathogenic significance of these genetic variants. Typically, these methods employ an integrative approach, leveraging diverse data sources that provide critical insights into genomic function. Despite the abundance of publicly available data sources and databases, the process of navigating, extracting, and pre-processing features for machine learning models can be daunting. Furthermore, researchers often invest substantial effort in feature extraction, only to later discover that these features lack informativeness. ResultsIn this paper, we present DrivR-Base, an innovative resource that efficiently extracts and integrates molecular information (features) for single nucleotide variants from a wide range of databases and tools, including AlphaFold, ENCODE, and Variant Effect Predictor. The resulting features can be used as input for machine learning models designed to predict the pathogenic impact of human genome variants in disease. Moreover, these feature sets have applications beyond this, including haploinsufficiency prediction and the development of drug repurposing tools. We describe the resources development, practical applications, and potential for future expansion and enhancement. Availability and ImplementationDrivR-Base source code is available at https://github.com/amyfrancis97/DrivR-Base.

bioinformatics↗

bioRxiv2024

Altered Socio-Affective Communication and Amygdala Development in mice with Protocadherin10-deficient Interneurons

Autism Spectrum Disorder (ASD) is a group of neurodevelopmental conditions associated with deficits in social interaction and communication, together with repetitive behaviors. The cell adhesion molecule Protocadherin10 (Pcdh10) has been implicated in the etiology of ASD. Pcdh10 is expressed in the nervous system during embryonic and early postnatal development and has been linked to neural circuit formation. Here, we show strong expression of Pcdh10 in the ganglionic eminences and in the basolateral complex of the amygdala at mid and late embryonic stages, respectively. Both inhibitory and excitatory neurons expressed Pcdh10 in the basolateral complex at perinatal stages and genes linked to vocalization behavior were enriched in Pcdh10- expressing neurons in adult mice. To further investigate the involvement of Pcdh10 in neurodevelopment with relevance to ASD, and to assess the functional and behavioral consequences of loss of Pcdh10 in basolateral amygdala interneurons, we combined a ubiquitous and a conditional Pcdh10 knockout mouse model. Conditional knockout of Pcdh10 reduced the number of interneurons in the basolateral complex. Both models exhibited altered developmental trajectories of socio-affective communication through isolation-induced ultrasonic vocalizations in neonatal pups, characterized by increased emission rates in heterozygous pups. Furthermore, acoustic call features were affected and heterozygous conditional knockout pups emitted calls characterized by reduced peak frequencies but increased frequency modulation. Additionally, we identified distinct clusters of call subtypes with specific developmental trajectories, suggesting the vocalization repertoire is extensive and dynamic during early life. The nuanced alterations in socio-affective communication at the level of call emission rates, acoustic call features, and clustering of call subtypes were primarily seen in heterozygous pups of the conditional knockout and less prominent in the ubiquitous Pcdh10 knockout, suggesting that changes in anxiety levels associated with Gsh2-lineage interneurons might drive the observed behavioral effects. Together, this demonstrates that loss of Pcdh10 specifically in interneurons contributes to behavioral alterations in socio-affective communication with relevance to ASD.

neuroscience↗

bioRxiv2023

Elasticity of the HIV-1 Core Facilitates Nuclear Entry and Infection

HIV-1 infection requires passage of the viral core through the nuclear pore of the cell, a process that depends on functions of the viral capsid 1,2. Recent studies have shown that HIV- 1 cores enter the nucleus prior to capsid disassembly 3-5. Interactions with the nuclear pore complex are necessary but not sufficient for nuclear entry, and the mechanism by which the viral core traverses the comparably sized nuclear pore is unknown. Here we show that the HIV-1 core is highly elastic and that this property is linked to nuclear entry and infectivity. Using atomic force microscopy-based approaches, we found that purified wild type cores rapidly returned to their normal conical morphology following a severe compression. Results from independently performed molecular dynamic simulations of the mature HIV-1 capsid also revealed its elastic property. Analysis of four HIV-1 capsid mutants that exhibit impaired nuclear entry revealed that the mutant viral cores are brittle. Suppressors of the mutants restored elasticity and rescued infectivity and nuclear entry. Elasticity was also reduced by treatment of cores with the capsid-targeting compound PF74 and the antiviral drug lenacapavir. Our results indicate that capsid elasticity is a fundamental property of the HIV-1 core that enables its passage through the nuclear pore complex, thereby facilitating infection. These results provide new insights into the mechanisms of HIV-1 nuclear entry and the antiviral mechanisms of HIV-1 capsid inhibitors.

biophysics↗

bioRxiv2023

A Connectome of the Male Drosophila Ventral Nerve Cord

Animal behavior is principally expressed through neural control of muscles. Therefore understanding how the brain controls behavior requires mapping neuronal circuits all the way to motor neurons. We have previously established technology to collect large-volume electron microscopy data sets of neural tissue and fully reconstruct the morphology of the neurons and their chemical synaptic connections throughout the volume. Using these tools we generated a dense wiring diagram, or connectome, for a large portion of the Drosophila central brain. However, in most animals, including the fly, the majority of motor neurons are located outside the brain in a neural center closer to the body, i.e. the mammalian spinal cord or insect ventral nerve cord (VNC). In this paper, we extend our effort to map full neural circuits for behavior by generating a connectome of the VNC of a male fly.

neuroscience↗

bioRxiv2023

Labellable phylogenetic networks

AO_SCPLOWBSTRACTC_SCPLOWPhylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations), and non-tree-like "reticulate" processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes networks harder to infer from data, and more complicated to work with as mathematical objects. In this paper we define a new, large class of phylogenetic networks, that we call labellable, and show that they are in bijection with the set of "expanding covers" of finite sets. This correspondence is a generalisation of the encoding of phylogenetic forests by partitions of finite sets. Labellable networks can be characterised by a simple combinatorial condition, and we describe the relationship between this large class and other commonly studied classes. Furthermore, we show that all phylogenetic networks have a quotient network that is labellable.

evolutionary biology↗

bioRxiv2022

MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localized multicopper oxidase family enzymes LACCASES (LACs) catalyze the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem diameter. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing (miR397OX) and STTM397 chickpea lines showed sensitivity and tolerance, respectively, to drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to dry root rot. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and dry root rot in an agriculturally important crop chickpea.

plant biology↗

bioRxiv2022

Genome duplication and transposon mediated gene alteration shapes the pathogenicity of Rhizoctonia solani AG1-IA

Rhizoctonia solani AG1-IA is a polyphagous basidiomycete fungal pathogen that causes sheath blight disease in rice. In a high-quality genome assembly-based analysis, we report a recent whole genome duplication in R. solani AG1-IA. Duplicated syntenic gene blocks showed presence of district clusters of transposable elements (TEs), which introduced disruption in the continuity of synteny and caused alterations in gene structures. Genome duplication followed by TE-mediated gene structure alterations caused neofunctionalization of genes associated with pathogenicity, as experimentally shown by variation in expression patterns and their involvement during plant colonization. High throughput genome sequencing of forty-two rice field isolates of R. solani AG1-IA from different agro-climatic zones of India profiled the population genetic structure of the Indian isolates and classified those into three distinct groups and a subgroup of admixture, emphasizing exchange of genetic material under field conditions. Genetic diversity analysis of this population predicted the regions that are that are targets for diversifying and purifying selections. Experimental evidence showed that the genes undergoing diversifying and purifying selections were essential for pathogenicity. Together, our data and the analysis revealed profound impact of genome duplication and the transposable elements on genomic diversity and evolution that shaped the pathogenicity of R. solani AG1- IA.

evolutionary biology↗

bioRxiv2022

The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency

Early during preimplantation development and in heterogeneous mouse embryonic stem cells (mESC) culture, pluripotent cells are specified towards either the primed epiblast or the primitive endoderm (PE) lineage. Canonical Wnt signaling is crucial for safeguarding naive pluripotency and embryo implantation, yet the role and relevance of canonical Wnt inhibition during early mammalian development remains unknown. Here, we demonstrate that transcriptional repression exerted by Wnt/TCF7L1 promotes PE differentiation of mESCs and in preimplantation inner cell mass. Time-series RNA sequencing and promoter occupancy data reveal that TCF7L1 binds and represses genes encoding essential naive pluripotency factors and indispensable regulators of the formative pluripotency program, including Otx2 and Lef1. Consequently, TCF7L1 promotes pluripotency exit and suppresses epiblast lineage formation, thereby driving cells into PE specification. Conversely, deletion of Tcf7l1 abrogates PE differentiation without restraining epiblast priming. Taken together, our study underscores the importance of transcriptional Wnt inhibition in regulating lineage segregation in ESCs and preimplantation embryo development as well as identifies TCF7L1 as key regulator of this process.

developmental biology↗

bioRxiv2020

The connectome of the adult Drosophila mushroom body: implications for function

Making inferences about the computations performed by neuronal circuits from synapse-level connectivity maps is an emerging opportunity in neuroscience. The mushroom body (MB) is well positioned for developing and testing such an approach due to its conserved neuronal architecture, recently completed dense connectome, and extensive prior experimental studies of its roles in learning, memory and activity regulation. Here we identify new components of the MB circuit in Drosophila, including extensive visual input and MB output neurons (MBONs) with direct connections to descending neurons. We find unexpected structure in sensory inputs, in the transfer of information about different sensory modalities to MBONs, and in the modulation of that transfer by dopaminergic neurons (DANs). We provide insights into the circuitry used to integrate MB outputs, connectivity between the MB and the central complex and inputs to DANs, including feedback from MBONs. Our results provide a foundation for further theoretical and experimental work.

neuroscience↗