Biology subjects

Mohan, V.

Publications and source records attributed to Mohan, V..

13 recordsLinked to original sources

bioRxiv2026

Vesicular pseudopodia define the fusion site on large secretory vesicles of the Drosophila salivary glands

Large secretory vesicles (LSVs) pose a scaling problem for regulated exocytosis. Their micron-scale dimensions greatly increase the vesicular membrane surface area, making productive engagement between the vesicular and target membrane fusion machinery unlikely. Here, we show that vesicular pseudopodia define the fusion sites of LSVs in Drosophila larval salivary glands. Focused ion beam scanning electron microscopy revealed that most LSVs project polarized pseudopodia that interconnect neighboring vesicles and orient toward the apical membrane. Exposed pseudopodia were frequently observed at the apical surface and associated with narrow fusion pores, indicating that fusion occurs at these structures. Three-dimensional correlative light and electron microscopy showed that the I-BAR protein Missing in Metastasis (MIM) selectively localizes to exposed pseudopodia. Proteomic analysis based on a MIM pull-down assay identified exocyst components, including Sec15, which localizes to pseudopodia and persists at fusion sites throughout secretion. Finally, the tetraspanin Tsp42Ee marked complementary apical fusion domains and was required for efficient exocytosis. Our findings support a model in which prepatterned vesicular and apical membrane domains coordinate efficient exocytosis. SummaryRegulated exocytosis of large secretory vesicles is facilitated by vesicular pseudopodia and an apical fusion domain that spatially organizes membrane tethering and fusion during secretion.

cell biology↗

bioRxiv2025

Hippo signalling regulates the nuclear behaviour and DNA dwell times of YAP and TEAD to control transcription

Over the past two decades, genetic and proteomic screens have enabled the discovery and elucidation of the Hippo pathway as a complex signalling network that controls tissue growth and cell fate and which is of major importance for human cancers. Despite these advances, our understanding of how Hippo signalling regulates transcription is less clear. To address this, we used live microscopy approaches to study the nuclear behaviour of the major transcription effectors of the human Hippo pathway, YAP and TEADs. Our experiments revealed that TEADs are a major determinant of YAPs nuclear biophysical behaviour, whilst YAP only has a minor influence on TEAD behaviour. Acute chemical inhibition of Hippo signalling stimulated an increase in the DNA residence time of both YAP and TEAD1. Consistently, YAP and TEAD1 bound DNA for longer periods in cells with high intrinsic YAP/TEAD activity (induced trophoblast stem cells) than in cells with low intrinsic YAP/TEAD activity (induced pluripotent stem cells). TEAD1 bound the genome on a broad range of timescales, and this is extended substantially in nuclear condensates. Finally, single molecule tracking experiments revealed that a fusion protein encoded by a cancer-associated YAP allele exhibits substantially different nuclear biophysical behaviour than either YAP or TEAD1. These live microscopy experiments reveal that Hippo signalling regulates transcription at least in part by influencing the DNA dwell times of both YAP and TEAD.

cell biology↗

bioRxiv2024

Energy efficiency and sensitivity benefits in a motion processing adaptive recurrent neural network

Motion processing is a key function for the survival of many organisms and is initially implemented in the primary visual cortex (V1) and the middle temporal area (V5/MT) of the primate visual cortex. Advances in machine learning approaches have led to the development of motion processing neural networks that have elucidated several aspects of this process. However, it remains unclear how adaptation, a canonical function of sensory processing, influences motion processing. In this study, we developed two recurrent neural networks to study motion processing: MotionNet-R, a baseline model, and AdaptNet, a model that employs adaptive mechanisms inspired by biological systems. Both networks were trained on natural image sequences to estimate motion vectors. We found that both networks developed response properties that resembled those of neurons found in areas V1 and MT, e.g., speed tuning, and AdaptNet recapitulated the motion aftereffect phenomenon (i.e., the waterfall illusion). We show that the emergent computational properties that implement the phenomenon in AdaptNet confirm previous theoretical hypotheses. Further, we compared the performance of the two networks and found that AdaptNet processed motion more efficiently, operationalized as reduced activation. While AdaptNet incurred reduced accuracy in response to prolonged constant input, it was both more accurate and sensitive in response to changes in motion input. These results are consistent with theoretical explanations of adaptation as neural property that supports metabolic efficiency and increased sensitivity to change in the environment. Our findings provide novel insights into the neural mechanisms underlying motion adaptation and highlight the potential advantages of adaptive neural networks in modelling biological processes.

neuroscience↗

bioRxiv2024

High throughput single-cell proteomics of in-vivo cells

Single-cell mass spectrometry-based proteomics (SCP) can resolve cellular heterogeneity in complex biological systems and provide a system-level view of the proteome of each cell. Major advancements in SCP methodologies have been introduced in recent years, providing highly sensitive sample preparation methods and mass spectrometric technologies. However, most studies present limited throughput and mainly focus on the analysis of cultured cells. To enhance the depth, accuracy, and throughput of SCP for tumor analysis, we developed an automated, high-throughput pipeline that enables the analysis of 1,536 single cells in a single experiment. This approach integrates low-volume sample preparation, automated sample purification, and LC-MS analysis with the Slice-PASEF method. Integration of these methodologies into a streamlined pipeline led to a robust and reproducible identification of more than 3000 proteins per cell. We applied this pipeline to analyze tumor macrophages in a murine lung metastasis model. We identified over 1,800 proteins per cell, including key macrophage markers and [~]500 differentially expressed proteins between tumor and control macrophages. PCA analysis successfully separated these populations, revealing the utility of SCP in capturing biologically relevant signals in the tumor microenvironment. Our results demonstrate a robust and scalable pipeline poised to advance single-cell proteomics in cancer research.

biochemistry↗

bioRxiv2023

Identification of resistance mechanisms to small-molecule inhibition of TEAD-regulated transcription

The Hippo tumour suppressor pathway controls transcription by regulating nuclear abundance of YAP and TAZ, which activate transcription with the TEAD1-TEAD4 DNA-binding proteins. Recently, several small-molecule inhibitors of YAP and TEADs have been reported, with some now entering clinical trials for different cancers. Here, we investigated the cellular response to TEAD palmitoylation inhibitors, using a combination of genomic and genetic strategies. Genome-wide CRISPR/Cas9 screens identified genes that modulate the cellular response to TEAD inhibition, including members of the Hippo, MAPK and JAK-STAT signaling pathways. By exploring gene expression programs of mutant cells, we found that MAPK pathway hyperactivation confers resistance to TEAD inhibition by reinstating expression of a subset of YAP/TEAD target genes. Consistent with this, combined inhibition of TEAD and the MAPK protein MEK, synergistically blocked proliferation of several mesothelioma and lung cancer cell lines and more potently reduced the growth of patient-derived lung cancers in vivo. Collectively, we reveal mechanisms by which cells can overcome small-molecule inhibition of TEADs and potential strategies to enhance the anti-tumor activity of emerging Hippo pathway targeted therapies.

cancer biology↗

bioRxiv2022

Reactive Bergmann glia play a central role in Spinocerebellar ataxia inflammation via the JNK pathway

The spinocerebellar ataxias (SCAs) are devastating neurological diseases characterized by progressive cerebellar incoordination. While neurons bear the brunt of the pathology, a growing body of evidence suggests that glial cells are also affected. It has, however, been difficult to understand the role of glia, given the diversity of subtypes, each with their individual contributions to neuronal health. Using human SCA autopsy samples we have discovered that Bergmann glia--the radial glia of the cerebellum, which form intimate functional connections with cerebellar Purkinje neurons--display inflammatory JNK-dependent c-Jun phosphorylation. This phosphorylation defines a signaling pathway not observed in other activated glial populations, providing an opportunity to specifically isolate the role of Bergmann glia in SCA inflammation. Turning to an SCA1 mouse model as a paradigmatic SCA, we demonstrate that inhibiting the JNK pathway reduces Bergmann glia inflammation accompanied by improvements in the SCA1 phenotype both behaviorally and pathologically. These findings demonstrate the causal role for Bergmann glia inflammation in SCA1 and point to a novel therapeutic strategy that could span several ataxic syndromes where Bergmann glia inflammation is a major feature. Significance StatementWe have identified a Bergmann-glia specific signaling pathway that contributes to cerebellar degeneration in the spinocerebellar ataxias. This pathway is defined by activation of JNK that phosphorylates the transcription factor c-Jun leading to the release of IL-1{beta} and potentially other cytokines from Bergmann glia. Inhibiting c-Jun phosphorylation with pharmacological JNK inhibition could serve as therapeutic approach to treating cerebellar degeneration.

neuroscience↗

bioRxiv2022

The L1 Cell Adhesion Molecule Constrains Dendritic Spine Density through Ankyrin Binding in Pyramidal Neurons of the Mouse Cerebral Cortex

A novel function for L1 cell adhesion molecule and its interaction with Ankyrin, an actin-spectrin adaptor protein, was identified in constraining dendritic spine density on pyramidal neurons in the mouse neocortex. In an L1-null mouse mutant increased spine density was observed on apical but not basal dendrites of pyramidal neurons in diverse cortical areas (prefrontal cortex layer 2/3, motor cortex layer 5, visual cortex layer 4).The Ankyrin binding motif (FIGQY) in L1s cytoplasmic domain was critical for spine formation, as demonstrated by increased spine density in the prefrontal cortex of a mouse mutant (L1YH) harboring a tyrosine to histidine mutation in this motif, which disrupts L1-Ankyrin association. This mutation is a known variant in the human L1 syndrome. In both mutants mature mushroom spines rather than immature spines were predominant. L1 was detected in spines and dendrites of wild-type prefrontal cortical neurons by immmunostaining. L1 coimmunoprecipitated with Ankyrin B (220 kDa) from cortical lysates of wild-type but not L1YH mice. Spine pruning assays in cortical neuron cultures from wild-type and L1YH mutant mice showed that the L1-Ankyrin interaction mediated spine retraction in response to the class 3 Semaphorins, Sema3F and to a lesser extent Sema3B. These ligands also induce spine pruning through other L1 family adhesion molecules, NrCAM and Close Homolog of L1 (CHL1), respectively. This study provides insight into the molecular mechanism of spine regulation and underscore the potential for this adhesion molecule to regulate cognitive and other L1-related functions that are abnormal in the L1 syndrome.

neuroscience↗

bioRxiv2022

iPheGWAS : an intelligent computational framework to integrate and visualise genome-phenome wide association studies

Estimating the genetic correlations by LDSC is computationally demanding and visualising multiple GWAS results along with their genetic relationships is restricted. This study developed iPheGWAS, a novel approach which applied hierarchical clustering to GWAS summary statistics to (i) calculate their genetic relatedness, and (ii) enable three-dimensional visualisation of multiple ordered GWAS plots. Simulation and real-world data analysis demonstrated that when investigating genetic relationships among multiple phenotypes, iPheGWAS can deliver comparable results with LDSC but with 8 times faster computational speed. It can also provide novel findings in studying genetically-correlated comorbidities, such as mental illness and rheumatoid arthritis.

bioinformatics↗

bioRxiv2021

Semaphorin3F Drives Dendritic Spine Pruning through Rho-GTPase Signaling

Dendritic spines of cortical pyramidal neurons are initially overproduced then remodeled substantially in the adolescent brain to achieve appropriate excitatory balance in mature circuits. Here we investigated the molecular mechanism of developmental spine pruning by Semaphorin 3F (Sema3F) and its holoreceptor complex, which consists of immunoglobulin-class adhesion molecule NrCAM, Neuropilin-2 (Npn2), and PlexinA3 (PlexA3) signaling subunits. Structure-function studies of the NrCAM-Npn2 interface showed that NrCAM stabilizes binding between Npn2 and PlexA3 necessary for Sema3F-induced spine pruning. Using a mouse neuronal culture system, we identified a dual signaling pathway for Sema3F-induced pruning, which involves activation of Tiam1-Rac1-PAK1-3 -LIMK1/2-Cofilin1 and RhoA-ROCK1/2-Myosin II in dendritic spines. Inhibitors of actin remodeling impaired spine collapse in the cortical neurons. Elucidation of these pathways expands our understanding of critical events that sculpt neuronal networks and may provide insight into how interruptions to these pathways could lead to spine dysgenesis in diseases such as autism, bipolar disorder, and schizophrenia.

neuroscience↗

bioRxiv2020

South Asian patient population genetics reveal strong founder effects and high rates of homozygosity - new resources for precision medicine

Population-scale genetic studies can identify drug targets and allow disease risk to be predicted with resulting benefit for management of individual health risks and system-wide allocation of health care delivery resources. Although population-scale projects are underway in many parts of the world, genetic variation between population groups means that additional projects are warranted. South Asia has a population whose genetics is the least characterized of any of the worlds major populations. Here we describe GenomeAsia studies that characterize population structure in South Asia and that create tools for economical and accurate genotyping at population-scale. Prior work on population structure characterized isolated population groups, the relevance of which to large-scale studies of disease genetics is unclear. For our studies we used whole genome sequence information from 4,807 individuals recruited in the health care delivery systems of Pakistan, India and Bangladesh to ensure relevance to population-scale studies of disease genetics. We combined this with WGS data from 927 individuals from isolated South Asian population groups, and developed a custom SNP array (called SARGAM) that is optimized for future human genetic studies in South Asia. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of homozygosity that approach 100 times that seen in outbred populations. We describe founder effects that increase the power to associate functional variants with disease processes and that make South Asia a uniquely powerful place for population-scale genetic studies.

genomics↗

bioRxiv2020

In-vitro evaluation of Pseudomonas fluorescens antibacterial activity against Listeria spp. isolated from New Zealand horticultural environments

Beneficial bacteria with antibacterial properties are an attractive alternative to chemical-based antibacterial or bactericidal agents. The aim of our study was to source such bacteria from horticultural produce and environments and to explore the mechanisms of their antimicrobial properties. Four strains of Pseudomonas fluorescens were isolated that possessed antibacterial activity against the pathogen Listeria monocytogenes. These strains (PFR46H06, PFR46H07, PFR46H08 and PFR46H09) were tested against L. monocytogenes (n=31), L. seeligeri (n=1) and L. innocua (n=1) isolated from seafood and horticultural sources, and two L. monocytogenes from clinical cases (Scott A and ATCC 49594, n=2). All Listeria strains were inhibited by the three strains PFR46H07, PFR46H08 and PFR46H09 with average zones of inhibition of 14.8, 15.1 and 18.2 mm, respectively, with PFR46H09 having significantly more inhibition than the other two (p<0.05). PFR46H06 showed minimal inhibition towards the L. seeligeri and L. innocua isolates and no inhibition towards most of the L. monocytogenes isolates. In order to investigate the functional protein differences between these strains, all four strains were subjected to whole cell lysate proteomics; data are available via ProteomeXchange with identifier PXD019965. We found significant differences in the peptide profiles and protein summaries between these isolates. The total number of proteins identified was 1781 in PFR46H06, 2030 in PFR46H07, 2228 in PFR46H08 and 1994 in PFR46H09. We paid special attention to secretion system proteins as these play a main role in the defense mechanisms of bacteria, particularly those of the type VI secretion system (T6SS) and found that they varied significantly (p<0.001) among the four isolates. PFR46H06 and PFR46H07 possessed the fewest secretion system structural proteins (12 and 11 respectively) while PFR46H08 and PFR46H09 each had 18. PFR46H09, which showed the greatest antimicrobial effect, had nine T6SS proteins compared to just four in the other three strains.

microbiology↗

bioRxiv2019

Identifying suitable Listeria innocua strains as surrogates for Listeria monocytogenes for horticultural products

We conducted a laboratory-based study testing nine Listeria innocua strains independently and a cocktail of 11 Listeria monocytogenes strains. The aim was to identify suitable L. innocua strain(s) to model L. monocytogenes in inactivation experiments. Three separate inactivation procedures and a hurdle combination of the three were employed: thermal inactivation (55{degrees}C), UV-C irradiation (245 nm) and chemical sanitiser (Tsunami 100, a mixture of acetic acid, peroxyacetic acid and hydrogen peroxide). The responses were strain dependent in the case of L. innocua with different strains responding differently to different regimes. L. innocua isolates generally responded differently to the L. monocytogenes cocktail and had different responses among themselves. In the thermal inactivation treatment, inactivation of all strains including the L. monocytogenes cocktail plateaued after 120 minutes. Chemical sanitiser, inactivation could be achieved at concentrations of 10 and 20 ppm with inactivation increasing with contact time up to 8 minutes, beyond which there was no significant benefit. Although most of the L. innocua strains in the study responded similarly to L. monocytogenes when subjected to a single inactivation treatment, when the treatments were applied as hurdle, all L. innocua strains except PFR16D08 were more sensitive than the L. monocytogenes cocktail. PFR16D08 almost matched the resistance of the L. monocytogenes cocktail but was much more resistant to the individual treaments. A cocktail of two L. innocua strains (PFR 05A07 and PFR 05A10) had the closest responses to the hurdle treatment to those of the L. monocytogenes cocktail and is therefore recommended for hurdle experiments.\n\nImportanceOwing to researcher safety risks it is often difficult to use actual pathogens, such as Listeria monocytogenes, to explore different inactivation procedures under field conditions. Organisms that are closely related to the pathogen but without its virulence are therefore used as surrogates for the actual pathogen. However, this assumes that the surrogate will behave in a similar manner to the pathogen and it is difficult to predict the responses of the surrogate compared to the actual pathogen. This study compares the responses of individual and combined \"cocktails\" of strains of non-pathogenic Listeria innocua to different inactivation procedures when compared to the response of a cocktail of L. monocytogenes. Our study highlights the importance of evaluating a number of strains when choosing surrogates.

microbiology↗

bioRxiv2017

Penetrance of polygenic obesity susceptibility loci across the body mass index distribution: an update on scaling effects.

A growing number of single nucleotide polymorphisms (SNPs) have been associated with body mass index (BMI) and obesity, but whether the effect of these obesity susceptibility loci is uniform across the BMI distribution remains unclear. We studied the effects of 37 BMI/obesity-associated SNPs in 75,230 adults of European ancestry along BMI percentiles using conditional quantile regression (CQR) and meta-regression (MR) models. The effects of 9 SNPs (24%) increased significantly across the sample BMI distribution including, FTO (rs1421085, p=8.69x10-15), PCSK1 (rs6235, p=7.11x10-06), TCF7L2 (rs7903146, p=9.60x10-06), MC4R (rs11873305, p=5.08x10-05), FANCL (rs12617233, p=5.30x10-05), GIPR (rs11672660, p=1.64x-04), MAP2K5 (rs997295, p=3.25x10-04), FTO (rs6499653, p=6.23x10-04) and NT5C2 (rs3824755, p=7.90x10-04). We showed that such increases stem from unadjusted gene interactions that enhanced the effects of SNPs in persons with high BMI. When 125 height-associated were analyzed for comparison, only one (<1%), IGF1 (rs6219, p=1.80x10-04), showed effects that varied significantly across height percentiles. Cumulative gene scores of these SNPs (GS-BMI and GS-Height, respectively) showed that only GS-BMI had effects that increased significantly across the sample distribution (BMI: p=7.03x10-37, Height: p=0.499). Overall, these findings underscore the importance of gene-gene and gene-environment interactions in shaping the genetic architecture of BMI and advance a method to detect such interactions using only the sample outcome distribution.

genetics↗