Biology subjects

Sarkar, D.

Publications and source records attributed to Sarkar, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

A V-ATPase complex, required for biogenesis of a lysosome-related organelle (LRO) in Tetrahymena thermophila, disassembles during LRO maturation

Lysosome-related organelles (LROs) are a heterogeneous family of organelles found in many cell types, whose significant similarities to lysosomes include their acidification by vacuolar-type ATPases (V-ATPases). However, some organelles with hallmarks of LROs are nonetheless non-acidic. Here we investigate this poorly understood phenomenon using the ciliate Tetrahymena thermophila, which have prominent secretory LROs called mucocysts. Using three different approaches, we show that mature mucocysts, poised for exocytosis, are non-acidic. Nonetheless, a specific V-ATPase a-subunit is targeted to mucocysts and is indispensable for mucocyst biogenesis and secretion. Consistent with this, immature mucocysts in the cytoplasm appear to be transiently acidified. The stage specificity of acidification can be explained by our finding that several canonical V-ATPase subunits are present in the immature, but not mature, mucocysts. Our data argue that a mucocyst-specific V-ATPase complex is targeted to newly-forming mucocysts and subsequently disassembles at a late stage in Tetrahymena LRO maturation, and that this depends on the AP-3 trafficking adaptor.

cell biology↗

bioRxiv2024

Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila

Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a systematic exploration of parameters and computational controls, enabling us to infer functional gene associations from their co-expression patterns. To illustrate the power of this approach, we took advantage of new data regarding a previously studied pathway, the biogenesis of a secretory organelle called the mucocyst. Our untargeted clustering approach recovered over 80% of the genes that were previously verified to play a role in mucocyst biogenesis. Furthermore, we tested four new genes that we predicted to be mucocyst-associated based on their co-expression and found that knocking out each of them results in mucocyst secretion defects. We also found that our approach succeeds in clustering genes associated with several other cellular pathways that we evaluated based on prior literature. We present the Tetrahymena Gene Network Explorer (TGNE) as an interactive tool for genetic hypothesis generation and functional annotation in this organism and as a framework for building similar tools for other systems. Key PointsO_LIur approach integrates nearly 20-year-old microarray and contemporary RNA-seq datasets. C_LIO_LIrigorously compare co-expression clustering parametrization by way of computational controls. C_LIO_LICo-expression clustering identifies known and novel functionally associated genes in Tetrahymena. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/627356v2_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1dbe655org.highwire.dtl.DTLVardef@1ef09aaorg.highwire.dtl.DTLVardef@63b670org.highwire.dtl.DTLVardef@5e9209_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Ultra-high-throughput screening of antimicrobial combination therapies using a two-stage transparent machine learning model

Here, we present M2D2, a two-stage machine learning (ML) pipeline that identifies promising antimicrobial drug combinations, which are crucial for combating drug resistance. M2D2 addresses key challenges in drug combination discovery by predicting drug synergies using computationally generated drug-protein interaction data, thereby circumventing the need for expensive omics data. The model improves the accuracy of drug target identification using high-throughput experimental and computational methods via feedback between ML stages. M2D2s transparent framework provides mechanistic insights into drug interactions and was benchmarked against chemogenomics, transcriptomics, and metabolomics datasets. We experimentally validated M2D2 using high-throughput screening of 946 combinations of Food and Drug Administration (FDA)- approved drugs and antibiotics against Escherichia coli. We discovered synergy between a cerebrovascular drug and a widely used penicillin antibiotic and validated predicted mechanisms of action using genome-wide CRISPR inhibition screens. M2D2 offers a transparent ML tool for rapidly designing combination therapies and guides repurposing efforts while providing mechanistic insights.

systems biology↗

bioRxiv2024

Water-saving GC-MC model captures temporally differential enzymatic and transporter activities during C3-CAM transition

CAM (Crassulacean Acid Metabolism) plants reduce the water loss through transpiration in arid environments (Wickell et al., 2021), using an alternative pathway of carbon assimilation. To ensure food security, engineering CAM into C3 plants can be achieved by inverting the stomatal rhythm and the timing of major CO2 uptake from day to night. Identification of the metabolic enzymes and intra-cellular transporters, present in both C3 and CAM but having different differential temporal activities throughout the diel cycle (Yang et al., 2015; Heyduk et al., 2019) and quantitative estimations of the flux distributions along the biochemical trajectory of C3-to-CAM transition may help us to achieve the goal. Here, we simulate a constraint-based combined metabolic model of guard cell (GC) and mesophyll cell (MC), linking temporal fluctuations of temperature (T) and relative humidity (RH) throughout the diurnal cycle with osmolyte accumulation dependent stomatal opening, CO2 uptake and transpirational water loss. Starting with C3 metabolism, gradual increase in water-use efficiency (WUE) captures several known and new differential activities of metabolic enzymes, transporters, sugar-malate cycle etc. in GC and MC during C3-to-CAM transition.

systems biology↗

bioRxiv2024

Lessons from combined metabolic model of mesophyll and guard cells

Understanding of overall metabolisms of guard cell (GC) and mesophyll cell (MC), their possible interactions and roles in stomatal movement will help in designing crop plants with higher water use efficiencies. Although, previous constraint based modelling and analyses correctly predicted some known metabolic patterns of isolated C3 MC, GC and Crassulacean Acid Metabolism (CAM) MC, quantitative estimations of combined metabolism of GC and MC and detailed analysis of GC metabolism in CAM are still awaiting. A six phase diel combined model of GC and MC is constructed integrating existing models of two different cell types with necessary modifications guided by known physiology. It is used to predict the similarities and dissimilarities of GC and MC metabolisms. In addition to previously predicted results, analysis of this new two-cell model successfully shows higher activities of some experimentally observed C4 like enzymes in GC than MC in C3, the possible storage patterns of the osmolytes like K+, malate2-, sucrose etc., in CAM GC. Results also show different patterns of starch synthesis and accumulation, ATP production and utilization in GC and MC of C3 and CAM. This combined model integrates stomatal opening, gaseous exchange and GC-MC metabolisms. It is a significant step towards understanding and quantitative estimation of the whole leaf tissue metabolism linking gaseous exchange with environment. Significance statementOur time-resolved combined metabolic model of guard and mesophyll cells integrates stomatal opening, gaseous exchange and cellular metabolisms in C3, CAM and partial CAM conditions; their analyses provide quantitative estimations of metabolic fluxes, ATP production and utilization, and different metabolic patterns of starch synthesis and accumulation of both the cells. It is a significant step towards understanding and quantitative estimation of the whole leaf tissue metabolism linking gaseous exchange with environment and phloem loading.

systems biology↗

bioRxiv2024

Advancing thermostability of the key photorespiratory enzyme glycerate 3-kinase by structure-based recombination

As global temperatures rise, maintaining and improving crop yields will require enhancing the thermotolerance of crops. One approach for improving thermotolerance is using bioengineering to increase the thermostability of enzymes catalyzing essential biological processes. Photorespiration is an essential recycling process in plants that is integral to photosynthesis and crop growth. The enzymes of photorespiration are targets for enhancing plant thermotolerance as this pathway limits carbon fixation at elevated temperatures. Exploring inter-specific variation of the key photorespiratory enzyme glycerate kinase (GLYK) from various photosynthetic organisms, we found that the homolog from the thermophilic alga Cyanidioschyzon merolae was more thermotolerant than those from mesophilic plants, including Arabidopsis thaliana. To understand factors influencing thermotolerance of C. merolae GLYK (CmGLYK), we performed molecular dynamics simulations using AlphaFold-predicted structures, which revealed greater movement of loop regions of mesophilic plant GLYKs at higher temperatures compared to CmGLYK. Based on these simulations, a series of hybrid proteins were produced and analyzed. These hybrid enzymes contained selected loop regions from CmGLYK replacing the most highly mobile corresponding loops of AtGLYK. Two of these hybrid enzymes had enhanced thermostability, with melting temperatures increased by 6 {degrees}C. One hybrid with three grafted loops maintained higher activity at elevated temperatures. While this hybrid enzyme exhibited enhanced thermostability and a similar Km for ATP compared to AtGLYK, its Km for glycerate increased threefold. This study demonstrates that molecular dynamics simulation-guided structure-based recombination offers a promising strategy for enhancing thermostability of other plant enzymes.

biochemistry↗

bioRxiv2024

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We use molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceum model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.

biophysics↗

bioRxiv2024

Context-dependent acetylation of the virulence regulator PhoP accounts for carbon-source specific mycobacterial growth inhibition under acidic conditions

Mycobacterium tuberculosis PhoP is essential for intracellular survival and virulence of the tubercle bacilli. Genetic evidences coupled with biochemical studies uncover that PhoP affects various aspects of M. tuberculosis pathophysiology including pH sensing during intracellular adaptation and carbon source utilization. Building on this observation, herein we report essentiality of the phoP locus in carbon-source specific mycobacterial growth. Further, our results on mycobacterial growth in the presence of different carbon sources suggest accumulation of acetyl CoA, a metabolic intermediate which acetylates major transcription factors. To explore the mechanism, we examined in vivo acetylation of PhoP, and our results suggest a link between acetylation of PhoP and mycobacterial carbon source utilization. Using a genetic screening, we identified PhoP-specific mycobacterial acetylases. Our two major findings that (a) acidic conditions of growth inhibit PhoP acetylation, which represses PhoP regulon by interfering with DNA binding activity of the regulator and (b) mycobacteria expressing acetylation-defective PhoP shows growth inhibition, together suggest a role of acetylation on mycobacterial growth via carbon-source utilization. These results have implications on intracellular survival and growth program of mycobacteria under varying environmental cues.

microbiology↗

bioRxiv2024

Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973

Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth, Synechococcus elongatus UTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR/Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55 kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the WT. This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome to phenome relationships. ImportanceGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome editing tool and in this study we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.

synthetic biology↗

bioRxiv2024

3-epicaryoptin induces G2/M phase cell cycle arrest and apoptosis in human breast cancer cells by disrupting the microtubule network, an in vitro and in silico investigation

Breast cancer (BC) is a prevalent form of cancer observed in women across the globe, constituting over a quarter of all female BC cases. The treatment of BC continues to require significant efficacy, aiming to achieve high success rates while minimizing adverse effects on the body as a whole. In the current study, 3-epicaryoptin was tested for the molecular mechanism of its anti-cancer activity in the human breast cancer cell line, MCF-7. We investigated cell viability by MTT assay, cell cycle kinetics and apoptosis, immunofluorescence straining, molecular modelling, and ADMET profiling. MTT assay results showed that 3-epicaryoptin was found cytotoxic against MCF-7 cells with an IC50 value of 344.64 {micro}g mL-1 for 48 h. Flow cytometric analysis exhibited that 3-epicaryoptin halted the MCF-7 cells in the G2/M phase and subsequently induced apoptosis in a time-dependent manner. Our immunofluorescence studies indicated that 3-epicaryoptin inhibited microtubule polymerization in MCF-7 cells. Furthermore, molecular docking followed by molecular dynamics (MD) simulation studies demonstrated the ability of 3-epicaryoptin to interact with the tubulin protein at the colchicine binding pockets. Overall, our results suggest that 3-epicaryoptin can inhibit the proliferation of human breast cancer cells by depolymerizing of cellular microtubule networks, which causes cell cycle arrest and promotes apoptotic cell death. Therefore, it has been indicated that the natural product 3-epicaryoptin exhibited considerable promise as a potent therapeutic agent capable of inducing apoptosis in breast cancer cells.

cancer biology↗

bioRxiv2023

Structural Remodeling of Fungal Cell Wall Promotes Resistance to Echinocandins

The insufficient efficacy of existing antifungal drugs and the rise in resistance necessitate the development of new therapeutic agents with novel functional mechanisms1,2. Echinocandins are an important class of antifungals that inhibit {beta}-1,3-glucan biosynthesis to interfere with cell wall structure and function3,4. However, their efficacy is limited by the fungistatic activity against Aspergillus species and the trailing effect during clinical application. Here, we describe how echinocandins remodel the supramolecular assembly of carbohydrate polymers in the fungal cell wall in an unexpected manner, possibly resulting in a subsequent inhibition of the activity of these drugs. Solid-state nuclear magnetic resonance (ssNMR) analysis of intact cells from the human pathogenic fungus Aspergillus fumigatus showed that the loss of {beta}-1,3-glucan and the increase of chitin content led to a decrease in cell wall mobility and water-permeability, thus enhancing resistance to environmental stresses. Chitosan and -1,3-glucan were found to be important buffering molecules whose physical association with chitin maintained the wall integrity. These new findings revealed the difficult-to-understand structural principles governing fungal pathogens response to echinocandins and opened new avenues for designing novel antifungal agents with improved efficacy.

biophysics↗

bioRxiv2023

Protein semisynthesis underscores role of a conserved lysine in activation and desensitization of acid-sensing ion channels

Acid-sensing ion channels (ASICs) are trimeric ion channels that open a cation-conducting pore in response to proton binding. Excessive ASIC activation during prolonged acidosis in conditions such as inflammation and ischemia is linked to pain and stroke. A conserved lysine in the extracellular domain (Lys211 in mASIC1a) is suggested to play a key role in ASIC function. However, the precise contributions are difficult to dissect with conventional mutagenesis, as replacement of Lys211 with naturally occurring amino acids invariably changes multiple physico-chemical parameters. Here, we study the contribution of Lys211 to mASIC1a function using tandem protein-trans splicing (tPTS) to incorporate non-canonical lysine analogs. We conduct optimization efforts to improve splicing and functionally interrogate semisynthetic mASIC1a. In combination with molecular modeling, we show that Lys211 charge and side chain length are crucial to activation and desensitization, thus emphasizing that tPTS can enable atomic-scale interrogations of membrane proteins in live cells.

biophysics↗

bioRxiv2022

Glycyrrhizin, an inhibitor of HMGB1 induces autolysosomal degradation function and inhibits H. pylori infection

Helicobacter pylori a key agent for causing gastric complications is linked with peptic ulcer, gastritis, and in severe cases gastric cancer. In response to infection, host cells stimulate autophagy to maintain cellular homeostasis. However, H. pylori have evolved the ability to usurp the hosts autophagic machinery. High mobility group box1 (HMGB1), an alarmin molecule is a regulator of autophagy and its expression is augmented in gastric cancer and many other cancers. Therefore, this study aims to explore the role of glycyrrhizin (a known inhibitor of HMGB1) in autophagy during H. pylori infection. Human gastric cancer (AGS) cells were infected with H. pylori SS1 strain and further treatment was done with glycyrrhizin. Western blot was used to examine the expression levels of autophagy proteins. Autophagy and lysosomal activity were monitored by immunofluorescence. We have performed knockdown of HMGB1 to verify the effect of glycyrrhizin by siRNA transfection method. H. pylori-infection in vivo C56BL/6 mice model was established and the effect of glycyrrhizin treatment was studied. We found that the autophagy-lysosomal pathway was impaired due to a significant increase in lysosomal membrane permeabilization during H. pylori infection in AGS cells. Subsequently, glycyrrhizin treatment restored the lysosomal membrane integrity, accompanied by an increase in cathepsin B activity and reduction of ROS and inflammatory cytokine IL-8. The recovered lysosomal function enhanced autolysosome formation and concomitantly attenuated the intracellular H. pylori growth by eliminating the pathogenic niche from gastric cells. Additionally, glycyrrhizin treatment inhibited inflammation and improved gastric tissue damages in mice.

microbiology↗

bioRxiv2022

Convergence of two global regulators to coordinate expression of essential virulence determinants of Mycobacterium tuberculosis

Cyclic AMP (cAMP) is known to function as a global regulator of M. tuberculosis gene expression. Sequence-based transcriptomic profiling identified the mycobacterial regulon controlled by the cAMP receptor protein, CRP. In this study, we identified a new subset of CRP-associated genes including virulence determinants which are also under the control of a major regulator, PhoP. Our results suggest that PhoP as a DNA binding transcription factor, impacts expression of these genes, and phosphorylated PhoP promotes CRP recruitment at the target promoters. Further, we uncover a distinct regulatory mechanism involving CRP and PhoP on transcriptional control of these genes. While both these regulators influence gene expression, we show that activation of these genes requires direct recruitment of both PhoP and CRP at their target promoters. The most fundamental biological insight is derived from the inhibition of CRP binding at the regulatory regions in a PhoP-deleted strain owing to CRP-PhoP protein-protein interactions. Based on these results, a model is proposed suggesting how CRP and PhoP function as co-activators and contribute to activation of the essential pathogenic determinants. Together, these results uncover a novel mechanism where two interacting virulence factors impact expression of virulence determinants, have significant implications on TB pathogenesis.

microbiology↗

bioRxiv2022

Mycobacterial virulence regulator integrates cAMP homeostasis with stress response and virulence

Survival of M. tuberculosis within the host macrophages requires the bacterial virulence regulator PhoP, but the underlying reason remains unknown. cAMP is one of the most widely used second messengers, which impacts on a wide range of cellular responses in microbial pathogens including M. tuberculosis. Herein, we hypothesized that intra-bacterial cAMP level could be controlled by PhoP since this major regulator plays a key role in bacterial responses against numerous stress conditions. A transcriptomic analysis reveals that PhoP functions as a repressor of cAMP-specific phosphodiesterase (PDE) Rv0805, which hydrolyses cAMP. In keeping with these results, we find specific recruitment of the regulator within the promoter region of rv0805 PDE, and absence of phoP or ectopic expression of rv0805 independently accounts for elevated PDE synthesis leading to depletion of intra-bacterial cAMP level. Thus, genetic manipulation to inactivate PhoP-rv0805-cAMP pathway decreases cAMP level, stress tolerance and intracellular survival of the bacillus.

microbiology↗

bioRxiv2021

Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary-structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. We introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehy-drogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 [A] map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

biophysics↗

bioRxiv2021

Inhibition of LRRK2 kinase activity promotes anterograde axonal transport and presynaptic targeting of α-synuclein

Pathologic inclusions composed of -synuclein called Lewy pathology are hallmarks of Parkinsons Disease (PD). Dominant inherited mutations in leucine rich repeat kinase 2 (LRRK2) are the most common genetic cause of PD. Lewy pathology is found in the majority of individuals with LRRK2-PD, particularly those with the G2019S-LRRK2 mutation. Lewy pathology in LRRK2-PD associates with increased non-motor symptoms such as cognitive deficits, anxiety, and orthostatic hypotension. Thus, understanding the relationship between LRRK2 and -synuclein could be important for determining the mechanisms of non-motor symptoms. In PD models, expression of mutant LRRK2 reduces membrane localization of - synuclein, and enhances formation of pathologic -synuclein, particularly when synaptic activity is increased. -Synuclein and LRRK2 both localize to the presynaptic terminal. LRRK2 plays a role in membrane traffic, including axonal transport, and therefore may influence -synuclein synaptic localization. This study shows that LRRK2 kinase activity influences -synuclein targeting to the presynaptic terminal. We used the selective LRRK2 kinase inhibitors, MLi-2 and PF-06685360 (PF-360) to determine the impact of reduced LRRK2 kinase activity on presynaptic localization of -synuclein. Expansion microscopy (ExM) in primary hippocampal cultures and the mouse striatum, in vivo, was used to more precisely resolve the presynaptic localization of -synuclein. Live imaging of axonal transport of -synuclein-GFP was used to investigate the impact of LRRK2 kinase inhibition on -synuclein axonal transport towards the presynaptic terminal. Reduced LRRK2 kinase activity increases -synuclein overlap with presynaptic markers in primary neurons, and increases anterograde axonal transport of - synuclein-GFP. In vivo, LRRK2 inhibition increases -synuclein overlap with glutamatergic, cortico-striatal terminals, and dopaminergic nigral-striatal presynaptic terminals. The findings suggest that LRRK2 kinase activity plays a role in axonal transport, and presynaptic targeting of -synuclein. These data provide potential mechanisms by which LRRK2-mediated perturbations of -synuclein localization could cause pathology in both LRRK2-PD, and idiopathic PD.

neuroscience↗

bioRxiv2021

In-silico analysis: common biomarkers of NDs

Neurodegenerative disorders (NDs) are a class of rapidly rising devastating diseases and the reason behind are might be an improper function of related genes or a mutation in a particular gene or even could be autoimmune also. Parkinsons disease (PD), Multiple sclerosis (MS), Huntingtons disease (HD) are some of the NDs, and still, incurable fully. Apart from the similarities in symptoms, there are common genes that express somehow a differential manner in patients of PDs, MSs, and HDs. A total of 1197 differentially expressed genes (DEGs) are obtained by analyzing the chosen datasets. The protein interactions by STRING online tool and degree sorted hubs obtained through a plug-in in Cytoscape; Cyto-Hubba. Among the sorted hubs KRAS, CREB1, PIK3CA, JAK2 are the ones that are not only common to all the studied datasets of NDs but also in other neurological disorders like Alzheimers. The enriched pathways with biological process, molecular function, cellular component, and KEGG pathway details are obtained and analyzed using Enricher. This paper frames that the obtained hub genes could be potential biomarkers also and a need for further drug design for finding a possible cure.

neuroscience↗