Biology subjects

Kumari, N.

Publications and source records attributed to Kumari, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Gasdermin E couples mitochondrial stress to STING-driven neuronal pyroptosis during Chandipura virus encephalitis

Neurotropic RNA viruses are major causes of fatal encephalitis worldwide, yet how infected neurons transition from antiviral defense to inflammatory cell death is not well characterized. Chandipura virus (CHPV), an emerging neurotropic rhabdovirus, causes acute, rapidly progressive encephalitis with high case fatality in children, but the mechanisms underlying its neuropathogenesis remain poorly defined. Here, we demonstrate that CHPV suppresses canonical RNA virus sensing early but subsequently switches to a mitochondria-driven innate immune program that culminates in inflammatory cell death. Early infection of neuronal cells with CHPV was marked by reduced levels of the mitochondrial antiviral adaptor protein, MAVS and attenuation of type I and III interferon responses. As infection progressed, mitochondrial dysfunction promoted accumulation of mtROS, mitochondrial accumulation of cleaved GSDME and cytosolic mtDNA release, triggering STING activation, which coincided with robust neuroinflammation and pyroptotic cell death. Pharmacological inhibition or genetic silencing of STING markedly attenuated inflammatory signaling, prevented pyroptotic membrane rupture and protected neurons from cell death without significantly affecting viral replication. In contrast, GSDME depletion reduced both viral replication and neuronal death. Notably, GSDME depletion markedly attenuated STING phosphorylation, while STING depletion also reduced GSDME activation, revealing functional coupling between these pathways during CHPV-induced neuronal injury. Collectively, our findings identify a mitochondria-GSDME-STING axis linking early immune evasion to neuroinflammation during CHPV infection, revealing a previously unrecognized mechanism of inflammatory neuronal death in viral encephalitis and highlighting STING as a potential therapeutic target in certain CNS viral infections.

immunology↗

bioRxiv2026

γLinolenic Acid Induces a Vitamin D Receptor-Independent Mineralization Program by Activating CaMKII--SMAD2/3 Pathway in Calvarial Osteoblasts

Vitamin D receptor (VDR) signaling is essential for osteoblast maturation and skeletal mineralization, yet the intracellular mechanisms linking VDR activity to matrix production remain poorly defined. Here, we show that vdr-/- calvarial osteoblasts initiate differentiation but fail to complete the transition to a mature, mineralizing state, exhibiting suppressed late-stage markers such as Dmp1, Phex, and Col1a1 and defective nodule formation both in vivo and in vitro. Transcriptomic profiling revealed a SMAD network imbalance, with elevated inhibitory SMADs and attenuated phosphorylation of both SMAD1/5/9 and SMAD2/3. Whereas SMAD1/5/9 activation was preserved in vivo and restored by exogenous BMP2 in vitro, consistent with in vivo paracrine BMP availability, reduced SMAD2/3 phosphorylation persisted in both contexts, indicating a cell-autonomous defect. Mechanistically, vdr-/- osteoblasts displayed impaired intracellular Ca2+ dynamics and diminished CaMKII activation, with VDR/RXR occupancy detected near the Camk2g locus. Pharmacological CaMKII inhibition (KN-93) recapitulated the phenotype, reducing SMAD2/3 phosphorylation and mineralization and establishing CaMKII as an upstream regulator of SMAD2/3. A milk-based diet rescued skeletal defects in vdr-/- mice in a calcium-independent manner and selectively restored CaMKII-SMAD2/3 signaling. Metabolomic profiling identified the omega-6 fatty acid y-linolenic acid (GLA) as an elevated circulating mediator; exogenous GLA restored Ca2+ flux, CaMKII activation, SMAD2/3 phosphorylation, matrix production, and mineralization, without reactivating Runx2, Sp7, or BMP-SMAD1/5/9 signaling, and dependent on CaMKII activity. These findings reveal a VDR-independent, GLA-inducible CaMKII-SMAD2/3 mineralization program, positioning metabolic modulation of calcium signaling as a strategy to restore osteoblast function under impaired vitamin D signaling.

physiology↗

bioRxiv2026

"Editing the conserved IPA1-TB1 regulatory module reshapes plant architecture and enhances tillering in wheat

Plant architecture is a major determinant of yield potential in cereal crops, where tiller number directly influences spike production and grain yield. The transcriptional regulators Ideal Plant Architecture 1 (IPA1) and Teosinte Branched1 (TB1) constitute a conserved genetic module controlling axillary bud activity and branching in grasses; however, their functional contribution to wheat architecture remains largely unexplored. Here, we employed CRISPR/Cas9-mediated genome editing to investigate the roles of TaIPA1 and TaTB1 in regulating tillering in hexaploid wheat (Triticum aestivum L.). Comparative genomic analysis identified conserved IPA1 orthologs across the wheat A, B, and D sub-genomes, with strong conservation of the SQUAMOSA-binding protein domain. Sequencing analysis confirmed targeted mutations, including nucleotide substitutions and insertions that generated frameshift mutations and premature stop codons. Genome-edited lines exhibited enhanced tillering compared with wild-type plants. Several TaIPA1 mutant lines produced up to two-fold higher tiller numbers, while TaTB1 knockout lines showed earlier tiller initiation and [~]50% increased tillering. Notably, enhanced tillering was associated with increased grain weight without affecting spikelet number per spike. Together, these results demonstrate that the conserved TaIPA1-TaTB1 regulatory module plays a pivotal role in shaping wheat plant architecture. Targeted manipulation of this pathway using CRISPR/Cas9 provides a promising strategy for optimizing tillering and developing high-yielding wheat ideotypes.

molecular biology↗

bioRxiv2026

Structure-Activity Mapping of Intraperitoneal mRNA-LNPs: Decoupling Tumor and Liver Biodistribution in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) remains difficult to treat with nucleic acid therapeutics because efficient intratumoral delivery is limited and off-target liver accumulation is common. Here, we developed a structure-activity map for intraperitoneally administered mRNA lipid nanoparticles (mRNA-LNPs) to identify formulation features that improve delivery to pancreatic tumors while reducing liver expression. A full-factorial library of 48 mRNA-LNP formulations was generated by varying ionizable lipid, sterol, phospholipid, and PEG-lipid components. Formulations were characterized for size, polydispersity, zeta potential, and encapsulation, then evaluated in an orthotopic KPC8060 pancreatic tumor model after intraperitoneal administration of firefly luciferase mRNA-loaded LNPs. Biodistribution was assessed by Rhodamine B fluorescence and functional delivery by luciferase expression 12 h after dosing. Lipid composition strongly influenced both physicochemical properties and in vivo performance. G0-C14-based formulations produced the smallest and most homogeneous particles, whereas FTT5-containing formulations were generally larger. Across the 48-formulation library, mRNA expression and nanoparticle biodistribution varied significantly among tumor, pancreas, liver, and spleen. Statistical, decision-tree, and predictive modeling analyses identified composition rules associated with organ-selective delivery. High tumor expression was associated primarily with G0-C14 combined with DSPC and {beta}-sitosterol, whereas liver expression was favored by C12-200 or DLin-MC3-DMA with DOPE and DSPE-PEG. Notably, a G0-C14/DSPC/DSPE-PEG formulation emerged as a lead candidate, producing a greater than 6-fold increase in tumor luciferase signal relative to the library median while reducing liver exposure by approximately 60%. Histopathology showed no treatment-related liver or lung toxicity. These findings define actionable formulation rules for tuning intraperitoneal mRNA-LNP delivery in PDAC and support further development of tumor-selective mRNA therapeutics for pancreatic cancer.

bioengineering↗

bioRxiv2026

TRACKING EVOLUTIONARY COSTS OF IMMUNE ADAPTATION AGAINST SINGLE VERSUS COINFECTING PATHOGENS

Immunity against pathogens is costly and can adversely affect fitness through resource allocation or physiological trade-offs. Infection by multiple pathogens may further worsen the effects if hosts require the activation of multiple immune responses, which in turn can elevate the overall immunological costs. Poor body condition and stressful environments can also exacerbate these trade-offs. In this study, we experimentally tested these possibilities using Tribolium castaneum populations that were evolving against either a single or a set of coinfecting bacterial pathogens. Contrary to our expectations, none of these evolved beetles showed any measurable trade-offs between pathogen resistance vs major fitness traits, such as reproduction or lifespan. Instead, they appeared to increase reproductive success and resistance to starvation, suggesting improved body condition that could mask underlying fitness costs. However, evolved beetles showed reduced quinone production, an externally secreted antimicrobial defence, indicating trade-offs between internal vs external immunity. Finally, we identified reproductive costs only under limited resource availability, but not under suboptimal resource quality, suggesting that trade-offs can be highly condition-dependent. Overall, this study provides a unique comparison across pathogens and infection types, highlighting the importance of analysing variation in life-history traits within relevant ecological contexts to understand fitness costs of evolving immunity.

evolutionary biology↗

bioRxiv2025

Neuromodulation of Swarming Behavior in C. elegans: Insights into the Conserved role of Calsyntenins

Collective animal behaviors arise from a complex interplay between internal physiological states and external environmental cues. In Caenorhabditis elegans, favorable conditions promote dispersal, while stressors like food scarcity or overcrowding trigger aggregation. Here, we describe a distinct behavior termed as swarming, where C. elegans move and feed in aggregates despite abundant food availability. While environmental factors have been implicated in this behavior, the underlying genetic and molecular mechanisms remain unclear. We identify a novel role for the conserved calsyntenin protein CASY-1 in regulating swarming. Through genetic, behavioral, and optogenetic approaches, we show that CASY-1 functions in sensory neurons to modulate the neuropeptide pigment-dispersing factor (PDF) signaling. Mutants in casy-1 show impaired PDF-1 signaling and reduced inhibition of the serotonin pathway, a known regulator of social behaviors. This dysregulation, along with its associated mechanosensory and foraging defects, likely contributes to the swarming phenotype. Our findings reveal a putative neuromodulatory pathway critical for swarming behavior in C. elegans.

neuroscience↗

bioRxiv2025

Fluctuation structure predicts genome-wide perturbation outcomes

Pooled single-cell perturbation screens represent powerful experimental platforms for functional genomics, yet interpreting these rich datasets for meaningful biological conclusions remains challenging. Most current methods fall at one of two extremes: either opaque deep learning models that obscure biological meaning, or simplified frameworks that treat genes as isolated units. As such, these approaches overlook a crucial insight: gene co-fluctuations in unperturbed cellular states can be harnessed to model perturbation responses. Here we present CIPHER (Covariance Inference for Perturbation and High-dimensional Expression Response), a conceptual framework leveraging ideas from linear response in statistical physics to model transcriptome-wide perturbation outcomes using gene co-fluctuations in unperturbed cells. We validated our approach on synthetic regulatory networks before applying it to 29 large-scale single-cell genetic perturbation datasets covering 19,003 perturbations and over 6.26M cells. Our work robustly recapitulated genome-wide responses to single and double perturbations by exploiting baseline gene covariance structure. Importantly, eliminating gene-gene covariances, while retaining gene-intrinsic variances, i.e. mean-field conditions, dramatically reduced model performance by several folds across multiple metrics, demonstrating the rich information stored within baseline fluctuation structures. Benchmarked against recent deep learning and linear baselines, CIPHER matched or exceeded the best-performing approaches with fitting a single parameter. Moreover, gene-gene correlations transferred successfully across independent studies of the same cell type, revealing stereotypic fluctuation structures. We further extended CIPHER to the inverse problem of identifying true driver perturbations, where it achieved high performance across both genetic and chemical perturbation screens through uncertainty-aware Bayesian inference. We further used CIPHER to nominate drivers of therapy resistance in melanoma and pancreatic cancer, validating its top predictions experimentally. Finally, most genome-wide responses propagated through the covariance matrix along approximately 1-3 independent and global gene modules, consistent with a low-rank structure of the underlying gene regulatory network, which we show can enable the framework's success. We have also created a package called cipher-perturb, available on PyPI, to apply the framework to any dataset, accompanied by a detailed website (https://goyallab.github.io/CIPHERWebsite/). Our study underscores the importance of theoretically-grounded models in capturing complex biological responses, highlighting fundamental design principles encoded in cellular fluctuation patterns.

systems biology↗

bioRxiv2025

Phytofabrication of gold nanoparticles (AuNPs) via Wedelia chinensis Internodal extract: Characterization, Antioxidant, Antimicrobial, Hemolytic assay and Methylene Dye degradation properties

Wedelia chinensis is a medicinal herb of Asteraceae family. Preliminary phytochemical screening of internodal extract was done by using its aqueous, methanolic and ethanolic extracts. Preliminary phytochemical screening showed the presence of several pharmaceutically important compounds such as alkaloids, tannins, anthraquinons, saponins, flavonoids, terpenoids, phenols, etc. Aqueous internodal extract was used for the biosynthesis of gold nanoparticles. The characterization of gold nanoparticles were done by using a range of analytical techniques, such as energy-dispersive X-ray spectroscopy (EDS, EDX), X-ray diffraction (XRD), transmission electron microscopy (TEM), dynamic light scattering (DLS), Fourier transformed infrared spectroscopy (FTIR), scanning electron microscopy (SEM). The stability and other characteristics were ascertained using a UV-Vis spectrophotometer. The plasmon resonance occurred at the wavelength of 530 nm, thus showing the formation of gold nanoparticles. X-ray diffraction demonstrated the existence of Au-rich (fcc) phases in gold nanoparticles. FTIR analysis clearly indicated the participation of active constituents of internodal extract in the conversion of gold ions into AuNPs. DLS showed the size distribution (99.71 nm) of the suspended particles. There was variations in the sizes and shapes of the nanoparticles. The zeta potential of synthesized AuNPs was observed as -5.12 mV, thus showing the stability of the synthesized nanoparticles. In TEM study, uniform distribution of nanoparticles was seen with some agglomerates and average size of nanoparticles was observed in between 30-40 nm. The antioxidant potential of internodal extract was slightly higher than the synthesized gold nanoparticles. The green-synthesized AuNPs along with antibiotics demonstrated strong synergistic effect against several bacterial strains such as Escherichia coli and Bacillus subtilis. Gold nanoparticles showed good hemolytic activity against rat erythrocytes (90%). Gold nanoparticles also showed catalytic activity that reduces methylene blue at low concentration (1 mg). Highlights[tpltrtarr] Internodal extracts showed the presence of several active constituents in preliminary phytochemical screening. [tpltrtarr]Internodal extract was used for the synthesis of gold nanoparticles in one step process. [tpltrtarr]Synergistic action of AuNPs and antibiotics were reported against many pathogenic bacterial strains. [tpltrtarr]AuNPs showed its potential as antioxidant. [tpltrtarr]Hemolytic effect of nanoparticles was reported on rat blood sample. [tpltrtarr]Nanoparticles showed dye reducing activity thus enhancing its application in the purification of water bodies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/660090v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@12a27e3org.highwire.dtl.DTLVardef@a0d1b6org.highwire.dtl.DTLVardef@28178aorg.highwire.dtl.DTLVardef@216935_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig.C_FLOATNO Graphical abstract of AuNPs C_FIG

plant biology↗

bioRxiv2025

Biofabrication of gold nanoparticles (GNPs) synthesized from Dillenia indica leaves with their anticancer, antibacterial, and antioxidant activities.

In this study, we describe the cytotoxic and antibacterial capabilities of gold nanoparticles (GNPs) synthesized from Dillenia indica leaves. Here, we used an environmentally friendly method to synthesize GNPs and then characterized them using techniques such as transmission electron microscopy (TEM), dynamic light scattering (DLS), UV-visible spectroscopy, XRD, and Fourier transform infrared spectroscopy. The Surface Plasmon Resonance of GNPs was identified by an absorption peak at 533 nm in the UV-visible spectroscopic studies. The biosynthesized GNPs had an average size of 83 nm and were spherical in shape, according to TEM examination. Its interesting to note that the biosynthesized GNPs exhibited antibacterial action against a variety of bacterial isolates, both Gram-positive and negative. By using an MTT assay, growth inhibition and the cytotoxic effect of the synthesized GNPs against Daltons lymphoma cell lines were also evaluated.

plant biology↗

bioRxiv2025

Inhalable Perfluorocarbon Nanocapsules for RNA-based Immunotherapeutic Treatment of Lung Metastases

Inhalation RNA therapy offers to transform treatment of pulmonary diseases, yet mucus trapping, immune clearance, and navigation of heterogeneous lung tissue architecture still prevents RNA from reaching its target cells. Here, we develop perfluorocarbon (PFC) RNA nanocapsules that show negligible immune clearance, minimal inflammatory response, and efficient mucus transport, while passively homing to lung epithelial and tumor cells. After a single aerosolized dose in orthotopic lung metastasis model, more than 60% of tumor cells and most type II alveolar and bronchial epithelial cells internalized the nanocapsules, with observed pulmonary retention exceeding 48 h. The nanocapsule provoke negligible cytokine release, enabling repeated dosing. Treatment with therapeutic miR34-a suppresses metastatic outgrowth, potentiates anti-tumor immunity, and almost doubles median survival relative to control paclitaxel chemotherapy. By combining unique PFC disposition with RNA versatility, the delivery platform overcomes the main biological barriers for inhalable RNA medicines and opens a translatable path for treating diverse pulmonary diseases.

bioengineering↗

bioRxiv2025

JNK2 pathway in colonocytes enhances gut barrier integrity in response to microbial acetate.

Weaning involves a nutritional shift from fat-rich milk to carbohydrate-based solid food, reshaping metabolism, microbiota, and gut immune tolerance. While dairy remains a component of the human diet beyond weaning, the impact of continued milk supplementation on gut epithelial homeostasis remains poorly understood. Here, using a mouse model, we show that continued milk-based feeding post-weaning promotes intestinal barrier function by enriching the commensal bacterium Dubosiella newyorkensis, which produces acetate to activate epithelial JNK2 signaling. This pathway enhances barrier integrity and suppresses inflammation induced by mild Dextran Sodium Sulphate (DSS) treatment. In contrast, feeding a lard-based high-fat diet or transient pharmacologic inhibition of JNK2 induces epithelial P38 activation, resulting in barrier disruption and inflammation. Importantly, the beneficial effects of milk were observed only if initiated during the weaning period, when the microbiome is in a metastable transitional state. Initiation of the same intervention two weeks after weaning led to P38 activation and inflammatory responses. These findings highlight the microbiome-dependent, stage-specific effects of diet and underscore the importance of early-life nutritional interventions for long-term gut health.

physiology↗

bioRxiv2025

Exploration of the Anticancer Activity of Selaginella bryopteris-derived Silver Nanoparticles

AbstractOvarian cancer is characterized by chronic hormonal imbalances and associated symptoms like irregular menstruation, fertility problems and abdominal discomfort. Poly ADP-ribose polymerases (PARPs) are proteins that play a crucial role in DNA repair pathways like base excision repair (BER). PARP family proteins exhibit catalytic activities which facilitate the transport of ADP-ribose to targeted proteins. Inhibition of PARP proteins in cancer cells with BRAC1/2 gene mutations impairs the process of Single Strand Break (SSBs) repairs followed by Double Strand Breaks (DSBs), stalling replication, leading to apoptosis. PARP1 protein inhibition is an innovative therapeutic approach in cancer treatment. Commercially available drugs like Olaparib and Rucaparib are used as PARP1 inhibitors to treat ovarian cancer, however the development of effective new therapeutic drugs is urgently needed to overcome drug toxicity and resistance. In this study, we synthesized silver nanoparticles (AgNPs) from the leaf extract of Selaginella bryopteris demonstrating their cytotoxic nature against the ovarian cancer SKOV-3 cell line, with an IC50 value of 7.81{micro}g/ml. We also observed cell death in cancer cells with an ROS upsurge induced by S. bryopteris AgNPs. Our findings also elaborate on the role of Rhamnetin, a S. bryopteris phytochemical that exhibits active site targeting of PARP-1 residues.

biochemistry↗

bioRxiv2024

Enhanced Sampling Simulations of RNA-peptide Binding using Deep Learning Collective Variables

Enhanced sampling (ES) simulations of biomolecular recognition such as binding of small molecules to proteins and nucleic acids targets, protein-protein association, and protein-nucleic acids interactions have been gaining significant attention in the simulation community due to their ability to sample long timescale processes. However, a key challenge in implementing collective variable (CV)-based enhanced sampling methods is the selection of appropriate CVs that can distinguish the systems metastable states and, when biased, can effectively sample these states. This challenge is particularly acute when simulating the binding of a flexible molecule to a conformationally rich host molecule, such as the binding of a peptide to an RNA. In such cases, a large number of CVs are required to capture the conformations of both the host and the guest, as well as the binding process. In our work, we employed the recently developed Deep Targeted Discrimination Analysis (DeepTDA) method to design CVs for the study of the binding of a cyclic peptide, L22 to a TAR RNA of HIV as a prototypical system. These CVs were used in the on-the-fly probability-based enhanced sampling and well-tempered metadynamics simulations to sample reversible binding and unbinding of L22 peptide to the TAR RNA target. The enhanced sampling simulations revealed multiple binding and unbinding events, which enabled the calculation of the free energy surface for the peptide binding process. Our results demonstrate the potential of the DeepTDA method for designing CVs to study complex biomolecular recognition processes.

biophysics↗

bioRxiv2024

Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson's disease

Neuronal alpha-synucleinopathies, including Parkinson's disease (PD) and dementia with Lewy bodies (DLB), lack disease-modifying therapies. We developed a Drosophila model for identifying novel glial-based therapeutic targets for alpha-synucleinopathies. In this model, human alpha-synuclein is expressed in neurons and individual genes are independently knocked down in glia. We performed a forward genetic screen, knocking down the entire Drosophila kinome in glia in alpha-synuclein expressing flies. Among the top hits were five genes (Ak1, Ak6, Adk1, Adk2, and awd) involved in adenosine metabolism. Knockdown of each gene increased brain adenosine levels, improved locomotor dysfunction, reduced alpha-synuclein oligomer levels, and rescued neurodegeneration. We determined that the mechanism of neuroprotection requires adenosine signaling through the neuronal adenosine receptor (AdoR) in Drosophila. These experiments support glial adenosine as a novel therapeutic target in PD.

neuroscience↗

bioRxiv2023

Elucidation of the essentiality of lumazine synthase (RibH) for Mycobacterium tuberculosis survival and discovery of potent inhibitors for enhanced antimycobacterial therapy

Tuberculosis (TB) continues to be a global health crisis, necessitating urgent interventions to address drug resistance and improve treatment efficacy. In this study, we validate the indispensable role of lumazine synthase (RibH), a vital enzyme in the riboflavin biosynthetic pathway, in the survival of Mycobacterium tuberculosis (M. tb) using a CRISPRi-based conditional gene knockdown strategy. We show that genetic and functional ablation of RibH in M. tb cannot be compensated by exogenous supply of Riboflavin, or co-factors Flavin Adenine Dinucleotide (FAD) or Flavin Mononucleotide (FMN). Capitalizing on the essentiality of RibH, we employ a high-throughput molecular docking approach to screen [~]600,000 compounds and identify inhibitors of RibH. Through in vitro screening of 55 shortlisted compounds, we discover 3 inhibitors that exhibit potent antimycobacterial activity. These compounds effectively also eradicate intracellular M. tb during macrophage infection and prevent the resuscitation of the nutrient-starved persister bacteria. Moreover, these 3 compounds synergistically enhance the bactericidal effect of first-line anti-TB drugs, Isoniazid and Rifampicin. Corroborating with the in silico predicted high docking scores along with favorable ADME and toxicity profiles, all 3 compounds demonstrate exceptional binding affinity towards purified lumazine synthase enzyme in vitro, and display an acceptable safety profile in mammalian cells, with a high selective index. By providing mechanistic evidence for the essentiality of RibH in M. tb survival, and discovering potent RibH inhibitors with outstanding antimycobacterial activity, our study contributes to the development of superior TB treatment strategies and advances the global fight against this devastating disease.

microbiology↗

bioRxiv2023

BrainProt(™) 3.0: Understanding Human Brain Diseases using comprehensively curated & Integrated OMICS datasets

BrainProt 3.0 is an integrative and simplified omics-based knowledge base of the human brain and its associated diseases. The current version of BrainProt includes six domains, which provide simplified, robust, and comprehensive data visualization to understand the human brain and its diseases/disorders based on proteomics, transcriptomics, public data curation, and integration strategies. Firstly, the HBDA (Human Brain Disease Atlas), index and navigator of BrainProt provides a resource table for 56 brain diseases. Secondly, Brain Disease Marker Curator (BDMC) and Brain Disease Drug Finder (BDDF) include a total of 20,202 diseases associated genes, more than 1,30,000 Chemical Target interactions, and around 2,145 Clinical Trial Information for more than 50 Brain Diseases. Thirdly, Brain Disease Transcriptome Map (BDTM) and Brain Disease Proteome Map (BDPM) integrate multi-omics data for 11 and 6 alarming brain diseases respectively. Currently, these two domains feature an expressional profile of 52 datasets, information of 1,868 samples, 3,657 DEPs, and 6,256 DEGs. Lastly, BrainProt also modifies and integrates the proteome and phosphoproteome data of the Inter-hemispheric Brain Proteome Map (IBPM). Overall, BrainProt is the first knowledgebase that connects different omics level information of brain diseases and provides a powerful scoring-based ranking platform to select and identify brain disease-associated markers, along with exploration of clinical trials, and drugs/chemical compounds to accelerate the identification of new disease markers and novel therapeutic strategies. The objectives of BrainProt are to support and follow the footsteps of the HBPP (Human Brain Proteome Project) by integrating different datasets to unravel the complexity of Human Brain and its associated diseases.

neuroscience↗

bioRxiv2022

Uracil-DNA glycosylase efficiency is modulated by substrate rigidity

Uracil DNA-glycosylase (UNG) is a base excision repair enzyme that removes the highly mutagenic uracil lesion from DNA by a base flipping mechanism. UNG excision efficiency depends on DNA sequence, yet the underlying principles that dictate UNG substrate specificity have remained elusive. Here, we show that UNG efficiency is dictated by the intrinsic local deformability of the substrate sequence around the uracil. UNG specificity constants (kcat/KM) and DNA flexibilities were measured for an engineered set of DNA substrates containing AUT, TUA, AUA, and TUA motifs. Time-resolved fluorescence spectroscopy, NMR imino proton exchange measurements, and molecular dynamics simulations of the bare DNA indicated significant differences in substrate flexibilities. A strong correlation between UNG efficiency and substrate flexibility was observed, with higher kcat/KM values measured for more flexible strands. DNA bending and base flipping were observed in simulations, with more frequent uracil flipping observed for the more bendable sequences. Experiments show that bases immediately adjacent to the uracil are allosterically coupled and have the greatest impact on substrate flexibility and resultant UNG activity. The finding that substrate flexibility controls UNG efficiency has implications in diverse fields, including the genesis of mutation hotspots, molecular evolution, and understanding sequence preferences of emerging base editors.

biophysics↗

bioRxiv2021

Identification and Characterization of novel mutants of Nsp13 Protein among Indian SARS-CoV-2 isolates.

SARS-CoV-2, the causative agent of COVID-19 has mutated rapidly which enabled them to adapt and evade the immune system of the host. Emerging SARS-CoV-2 variants with crucial mutations pose a global challenge in context of therapeutic drugs and vaccines being developed globally. There are currently no specific therapeutics or vaccines available to combat SARS-CoV-2 devastation. In view of this, the current study aimed to identify and characterize the mutations found in the Nsp13 of SARS-CoV-2 in Indian isolates. Non-structural protein, Nsp13 protein sequences from Indian isolates were analyzed by comparing with the first reported Severe acute respiratory syndrome Corona Virus-2 (SARS-CoV-2) protein sequence from Wuhan, China. Out of 825 Nsp13 protein sequences, a total of 38 mutations were observed among Indian isolates. Our data show that mutations in Nsp13 at various positions (H164Y, A237T, T214I, C309Y, S236I, P419S, V305E, G54S, H290Y, P53S, A308Y, and A308Y) have a significant impact on the proteins stability and flexibility. Also, the impact of Nsp13 mutations on the protein function were predicted based on PROVEAN score that includes 15 mutants as neutral and 23 mutants as deleterious effect. Furthermore, B-cell epitopes contributed by Nsp13 were identified using various predictive immunoinformatic tools. Immunological Parameters of Nsp13 such as antigenicity, allergenicity and toxicity were evaluated to predict the potential B-cell epitopes. The predicted peptide sequences were correlated with the observed mutants. Our predicted data showed that there are seven high rank linear epitopes as well as 18 discontinuous B-cell epitopes based on immunoinformatic tools. Moreover, it was observed that out of total 38 identified mutations among Indian SARS-CoV-2 Nsp13 protein, four mutant residues at position 142 (E142), 245 (H245), 247 (V247) and 419 (P419) are localised in the predicted B cell epitopic region. Altogether, the results of the present in-silico study might help to understand the impact of the identified mutations in Nsp13 protein on its stability, flexibility and function.

bioinformatics↗