Biology subjects

Mittal, P.

Publications and source records attributed to Mittal, P..

17 recordsLinked to original sources

bioRxiv2026

Glial Mutant Huntingtin Expression Initiates a Progressive Pathological Cascade Toward Neuronal Involvement in Drosophila

The mechanisms of involvement of glial cells in the progression of Huntingtons disease remain sparingly elucidated. Using the Drosophila melanogaster model, we investigated the temporal course of the disease pathogenesis induced by pan-glial expression of HTTex1pQ93 in comparison to the temporal course of pathology induced by pan-neuronal expression. Our behavioural data were supported by quantitative confocal microscopy, quantification of aggregate formation and its morphometry, Manders M2 colocalization index, and correlative holotomography. Expression of mHTT in glial cells led to developmental defects and subsequent delayed onset of motor dysfunction and death with increasing amounts of HTT and changes in the immunoreactivity of glial cells. In spite of the progressive increase in HTT accumulation, glial aggregates showed stability after their initial formation, while neuronal mHTT revealed distinct age-dependent remodelling of its aggregates. Importantly, there was an initial preference of glial mHTT for glial compartments followed by a progressively increasing number of HTT in the neurons with aging. Correlative holotomography provided spatial evidence of the neuronal association of HTT. Together, these findings demonstrate that glial mHTT establishes a distinct progressive pathological trajectory characterised by evolving glial pathology, increasing neuronal involvement, and delayed functional decline, highlighting glia as an active component of HD-like disease progression.

neuroscience↗

bioRxiv2026

Inverse Protocol Prediction from Spheroid Microscopy Imaging via Morphology-Aware Structured Learning

We introduce Inverse Protocol Prediction (IPP), which is a task of inferring experimental culture conditions directly from a single bright-field spheroid image. We formulate IPP as a structured multi-label prediction problem and propose a protocol-aware learning framework that integrates morphology extraction, multimodal representation learning, and dependency-aware inference. Morphometric descriptors derived from automated spheroid segmentation are fused with deep visual embeddings via a morphometry vision fusion module. To capture biological and procedural dependencies, we develop a Hierarchical Multi-Task Transformer that conditions predictions across protocol attributes. The framework is trained with domainadversarial supervision and morphology-preserving augmentation to improve robustness to acquisition variability. Hybrid convolution attention encoders achieve the best performance, reaching 95.7% multi-attribute accuracy. We further evaluate cross dataset transfer and temporal morphology forecasting. Results demonstrate that structured, dependency-aware modeling enables reliable reconstruction of experimental protocols from imaging alone, supporting reproducibility auditing and protocol validation in 3D cell culture systems.

bioinformatics↗

bioRxiv2026

Minimum inoculum of resistance assay for evaluating for anti-toxoplasmosis compounds that target phenyl alanine tRNA synthetase

Toxoplasma gondii is a globally important intracellular parasite, and treatment regimens are limited by the failure of drugs to target latent tissue cysts. Developing new candidates for treatment also needs to address the potential for resistance to arise. Here, we developed a Minimum Inoculum for Resistance (MIR) assay as a quantitative metric for evaluating inhibitors of T. gondii. The MIR assay, adapted from assays used in malaria drug discovery, measures the frequency for pre-existing resistance alleles by exposing different sized parasite populations to drug pressure. We profiled a series of bicyclic pyrrolidone analogs that inhibit phenylalanine tRNA synthetase (PheRS). We demonstrate that these inhibitors require higher inocula to lead to parasite resistance (up to > 108 parasites) in comparison with an inhibitor of DNA synthesis, and that MIR values vary across inhibitors with closely related chemical structures. Clonal analysis of resistant parasites emerging from MIR assays revealed both new and previously identified resistance conferring mutations in TgPheRS, and structural modeling revealed their potential impact the enzyme active site. The MIR assay provides a functional benchmark to compare new and existing inhibitors, allowing for rational prioritization of lead compounds with a high genetic barrier to resistance.

microbiology↗

bioRxiv2026

Ascites-Driven Modulation of Cell Phenotypes and Proteomes: Implications for Cancer Progression

BackgroundMore than 90% of advanced ovarian cancer patients develop malignant ascites, which describes a buildup of fluid in the peritoneal cavity caused by increased vascular permeability and obstructed lymphatic drainage. Malignant ascites contains spheroidal tumor cell clusters that contain stromal cells, cancer-associated fibroblasts, and blood cells. These spheroids promote peritoneal metastasis and treatment resistance, yet the phenotypic and proteomic changes of cells caused by the ascites environment remain poorly understood, as does its influence on ex vivo responses to chemotherapeutics in personalized medicine approaches. MethodsUsing mass spectrometry, we compared the proteome profiles of cell-free ascites to serum from ovarian cancer patients. We then analyzed the proteomes of immortalized cancer cells grown as monolayers or spheroids in either malignant ascites or standard cell culture medium. The effects of this fluid on the phenotype, molecular composition, and ex vivo chemotherapy responses of cancer cells were also investigated. ResultsProteome analysis revealed that cell-free ascites had higher levels of extracellular, secreted, and membrane proteins compared to serum. Ascites enhanced cell viability and spheroid formation in immortalized ovarian cancer cell lines more effectively than standard cell culture medium. Despite this altered baseline viability, growth of spheroids in ascites versus cell culture medium did not hinder chemotherapy response assessments, indicating the appropriateness of standard cell culture medium in ex vivo applications. The observed phenotypic changes of cells grown in ascites could not be recapitulated by adding chemokines or periostin to the cell culture medium, suggesting that additional factors are required. Notably, elevated levels of transglutaminase 2 were identified in SKOV-3 cells grown in ascites, indicating that ascites directly influences protein expression in cancer cells.

cancer biology↗

bioRxiv2026

Circulating miR-4532 is associated with loss of ambulation in dysferlinopathy

BackgroundLimb-girdle muscular dystrophies (LGMDs) are inherited myopathies characterized mainly by progressive weakness of the proximal muscles of the shoulder and pelvic girdle areas, leading to functional decline and eventual loss of independent ambulation. Dysferlinopathy (LGMD2B) is an autosomal recessive LGMD subtype, is caused by mutations in the DYSF gene that lead to lack of dysferlin which results in muscle death and chronic muscle fiber degeneration. Preservation of ambulation is a key clinical milestone, as loss of independent gait markedly reduces quality of life and complicates care management. Although patients often perceive functional decline before their initial clinical presentation, current clinical assessments typically detect disease progression after substantial muscle damage has occurred. MethodsIn this multigroup case-control study, we profiled plasma miRNAs from 49 genetically confirmed dysferlinopathy patients (24 ambulatory, 25 non-ambulatory) and 25 age- and sex-matched healthy controls. Total RNA was extracted from blood samples and hybridized to Affymetrix GeneChip miRNA 3.1 arrays. After quality control and filtering, differential expression analysis was performed using linear models for microarrays, adjusting for age and sex, with a false discovery rate cutoff of 10%. Results14 miRNAs were significantly altered between dysferlinopathy patients and controls. Notably, miR-4532 was upregulated in ambulatory patients relative to controls, whereas it was downregulated in non-ambulatory patients compared with ambulatory patients, although expression levels remained higher than in controls. Levels of miR-4532 were positively associated with circulating monocyte levels in ambulatory patients only. ConclusionThese results suggest that miR-4532 may be a circulating marker associated with ambulatory status in dysferlinopathy. Its known involvement in inflammatory signaling and muscle regeneration pathways underscores its potential as an early indicator for disease activity.

bioinformatics↗

bioRxiv2025

Geometric Characterization of Pediatric Multiple Sclerosis Lesion Morphology: A Cross-Sectional and Temporal Analysis using Differential Geometry

Pediatric-onset multiple sclerosis (POMS) involves aggressive inflammation and large lesions; however, its detailed shapes and structures remain poorly understood. Traditional volumetric metrics often overlook the complex geometry of these lesions. The main objective of this study is to develop a differential geometry-based framework to quantify the shape and structure of lesions in pediatric multiple sclerosis(MS) patients using longitudinal 3D FLAIR MRI. The goal was to identify reproducible lesion morphotypes and to track their evolution over time. Our approach sensitively tracked shape changes over time and revealed consistent progression patterns. Our findings suggest that geometric biomarkers offer a powerful new lens for decoding MS heterogeneity and tracking disease activity in the pediatric population.

neuroscience↗

bioRxiv2024

Bicyclic pyrrolidine inhibitors of Toxoplasma gondii phenylalanine t-RNA synthetase with antiparasitic potency in vitro and brain exposure

Previous studies have shown that bicyclic azetidines are potent and selective inhibitors of apicomplexan phenylalanine tRNA synthetase (PheRS), leading to parasite growth inhibition in vitro and in vivo, including in models of Toxoplasma infection. Despite these useful properties, additional optimization is required for the development of efficacious treatments of toxoplasmosis from this inhibitor series, in particular to achieve sufficient exposure in the brain. Here, we describe a series of PheRS inhibitors built on a new bicyclic pyrrolidine core scaffold designed to retain the exit-vector geometry of the isomeric bicyclic azetidine core scaffold while offering avenues to sample diverse chemical space. Relative to the parent series, bicyclic pyrrolidines retain reasonable potency and target selectivity for parasite PheRS vs. host. Further structure-activity relationship studies revealed that the introduction of aliphatic groups improved potency, ADME and PK properties, including brain exposure. The identification of this new scaffold provides potential opportunities to extend the analog series to further improve selectivity and potency and ultimately deliver a novel, efficacious treatment of toxoplasmosis. Lay abstractThe inhibition of protein synthesis in parasites has emerged as an attractive strategy to target parasitic diseases such as malaria, cryptosporidiosis, and toxoplasmosis. In this study, we report a new series of small molecules that inhibit the enzyme responsible for loading the amino acid phenylalanine onto its cognate tRNA in the parasite species Toxoplasma, directly upstream of protein synthesis. We show that small molecules in this new series inhibit Toxoplasma parasite growth at low concentrations, and that, orally administered to mice, these molecules achieve high concentrations in the brain, which hold promise for the treatment of forms of toxoplasmosis that result from parasitic brain infection.

microbiology↗

bioRxiv2023

p38-MAPK is prerequisite for the synthesis of SARS-CoV-2 protein

The inhibition of p38 mitogen-activated protein kinase (p38-MAPK) by small molecule chemical inhibitors was previously shown to impair severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) replication, however, mechanisms underlying antiviral activity remains unexplored. In this study, reduced growth of SARS-CoV-2 in p38- knockout Vero cells, together with enhanced viral yield in cells transfected with construct expressing p38, suggested that p38-MAPK is essential for the propagation of SARS-CoV-2. The SARS-CoV-2 was also shown to induce phosphorylation (activation) of p38, at time when transcription/translational activities are considered to be at the peak levels. Further, we demonstrated that p38 supports viral RNA/protein synthesis without affecting viral attachment, entry, and budding in the target cells. In addition, we demonstrated that long-term culture of SARS-CoV-2 in the presence of p38 inhibitor SB203580 does not easily select resistant viral mutants. In conclusion, we provide mechanistic insights on the regulation of SARS-CoV-2 replication by p38 MAPK.

microbiology↗

bioRxiv2023

BrainLM: A foundation model for brain activity recordings

AO_SCPLOWBSTRACTC_SCPLOWWe introduce the Brain Language Model (BrainLM), a foundation model for brain activity dynamics trained on 6,700 hours of fMRI recordings. Utilizing self-supervised masked-prediction training, BrainLM demonstrates proficiency in both fine-tuning and zero-shot inference tasks. Fine-tuning allows for the accurate prediction of clinical variables like age, anxiety, and PTSD as well as forecasting of future brain states. Critically, the model generalizes well to entirely new external cohorts not seen during training. In zero-shot inference mode, BrainLM can identify intrinsic functional networks directly from raw fMRI data without any network-based supervision during training. The model also generates interpretable latent representations that reveal relationships between brain activity patterns and cognitive states. Overall, BrainLM offers a versatile and interpretable framework for elucidating the complex spatiotemporal dynamics of human brain activity. It serves as a powerful "lens" through which massive repositories of fMRI data can be analyzed in new ways, enabling more effective interpretation and utilization at scale. The work demonstrates the potential of foundation models to advance computational neuroscience research.

neuroscience↗

bioRxiv2023

Exoribonuclease RNase R protects Antarctic Pseudomonas syringae Lz4W from DNA damage and oxidative stress

RNase R is a highly processive, 3 -5 exoribonuclease involved in RNA degradation, maturation, and processing in bacteria. In Pseudomonas syringae Lz4W, RNase R interacts with RNase E to form the RNA degradosome complex and is essential for growth at low temperature. RNase R is also implicated in general stress response in many bacteria. We show here that the deletion mutant of rnr gene (encoding RNase R) of P. syringae is highly sensitive to various DNA damaging agents and oxidative stress. RNase R is a multidomain protein comprised of CSD, RNB and S1 domains. We investigated the role of each domain of RNase R and its exoribonuclease activity in nucleic acid damage and oxidative stress response. Our results revealed that the RNB domain alone without its exoribonuclease activity is sufficient to protect against DNA damage and oxidative stress. We also show that the association of RNase R with the degradosome complex is not required for this function. Our study has discovered for the first time a hitherto unknown role of RNase R in protecting P. syringae Lz4W against DNA damage and oxidative stress. ImportanceBacterial exoribonucleases play a crucial role in RNA maturation, degradation, quality control and turnover. In this study, we have uncovered a previously unknown role of 3-5 exoribonuclease RNase R of P. syringae Lz4W in DNA damage and oxidative stress response. Here, we show that neither the exoribonuclease function of RNase R, nor its association with the RNA degradosome complex is essential for this function. Interestingly, in P. syringae Lz4W, hydrolytic RNase R exhibits physiological roles similar to phosphorolytic 3-5 exoribonuclease PNPase of E. coli. Our data suggest that during the course of evolution, mesophilic E. coli and psychrotrophic P. syringae have apparently swapped these exoribonucleases to adapt to their respective environmental growth conditions.

microbiology↗

bioRxiv2022

Evidence of kinesin motors involved in stable kinetochore assembly during early meiosis

The characteristic bi-lobed organization of the kinetochores observed during mitotic metaphase is a result of separation of the sister kinetochores into two clusters upon their stable end-on attachment to the microtubules emanating from opposite spindle poles. In contrast, during metaphase I of meiosis despite bi-orientation of the homologs, we observe that the kinetochores are linearly dispersed between the two spindle poles indicating that pole-distal and pole-proximal kinetochores are attached laterally and end-on, respectively to the microtubules. Colocalization studies of kinetochores and kinesin motors suggest that budding yeast kinesin 5, Cin8 and Kip1 perhaps localize to the end-on attached kinetochores while kinesin 8, Kip3 resides at all the kinetochores. Unlike mitosis in budding yeast, in meiosis, the outer kinetochores assemble much later after prophase I. From the findings including co-appearance of kinesin 5 and the outer kinetochore protein Ndc80 at the centromeres after prophase I and a reduction in Ndc80 level in Cin8 null mutant, we propose that kinesin motors are required for reassembly and stability of the kinetochores during early meiosis. Thus, this work reports yet another meiosis specific function of kinesin motor.

cell biology↗

bioRxiv2020

Hitchhiking on condensed chromatin promotes plasmid persistence in yeast without perturbing chromosome function

Equipartitioning by chromosome hitchhiking and copy number correction by DNA amplification are at the heart of the evolutionary success of the selfish yeast 2-micron plasmid. The present analysis reveals plasmid presence near centromeres and telomeres in mitotic cells, with a preference towards the latter. The observed correlation of plasmid missegregation with non-disjunction of rDNA and telomeres under Cdc14 inactivation, higher plasmid missegregation upon induced missegregation of chromosome XII but not chromosome III, requirement of condensin for plasmid stability and the interaction of the condensin subunit Brn1 with the plasmid partitioning system lend functional credence to condensed chromatin being favored for plasmid tethering. By homing to condensed/quiescent chromosome locales, and not over-perturbing genome homeostasis, the plasmid may minimize fitness conflicts with its host. Analogous persistence strategies may be utilized by other extrachromosomal selfish genomes, for example, episomes of mammalian viruses that also hitchhike on host chromosomes for their stable maintenance.

cell biology↗

bioRxiv2019

Meiosis-specific functions of kinesin motors in cohesin removal and maintenance of chromosome integrity in budding yeast

Kinesin motors provide the molecular forces at the kinetochore-microtubule interface and along the spindle to control chromosome segregation. During meiosis with the two rounds of microtubule assembly-disassembly, the roles of motor proteins remain unexplored. We observed that in contrast to mitosis Cin8 (kinesin 5) and Kip3 (kinesin 8) together are indispensable in meiosis. Examining the meiosis in cin8{triangleup} kip3{triangleup} cells, we detected chromosome breakage in the meiosis II cells. The double mutant exhibits delay in the cohesin removal and spindle elongation during anaphase I. Consequently, some cells abrogate meiosis II and form dyads while some, as they progress through meiosis II, cause defect in chromosome integrity. We believe that in the latter cells, an imbalance of spindle mediated force and simultaneous persistent cohesin on the chromosomes cause their breakage. We provide evidence that tension generated by Cin8 and Kip3 through microtubule cross-linking is essential for signaling efficient cohesin removal and maintenance of chromosome integrity during meiosis.\n\nSummaryMolecular motors generate forces that facilitate chromosome segregation. Unlike mitosis, in meiosis, two times chromosome segregation occur with twice microtubule assembly/disassembly. This work reports that the motor mediated forces are crucial for cohesin removal in meiosis and thus maintain genome integrity.

cell biology↗

bioRxiv2019

Comparative analysis of corrected tiger genome provides clues to their neuronal evolution

The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are very sensitive to errors in genome sequences and thus require accurate genomic assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger, which was also validated by resequencing of a Bengal tiger genome and transcriptome. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard, and using five different methods at three hierarchical levels i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing the signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to be significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behavior in tiger.

genomics↗

bioRxiv2018

Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth.

Modified nucleosides in tRNAs are critical for protein translation. N1-methylguanosine-37 and N1-methylinosine-37 in tRNAs, both located at the 3-adjacent to the anticodon, are formed by Trm5 and here we describe Arabidopsis thaliana AtTrm5 (At3g56120) as a Trm5 ortholog. We show that AtTrm5 complements the yeast trm5 mutant, and in vitro methylates tRNA guanosine-37 to produce N1-methylguanosine (m1G). We also show in vitro that AtTRM5 methylates tRNA inosine-37 to produce N1-methylinosine (m1I) and in Attrm5 mutant plants, we show a reduction of both N1-methylguanosine and N1-methylinosine. We also show that AtTRM5 is localized to the nucleus in plant cells. Attrm5 mutant plants have overall slower growth as observed by slower leaf initiation rate, delayed flowering and reduced primary root length. In Attrm5 mutants, mRNAs of flowering time genes are less abundant and correlated with delayed flowering. Finally, proteomics data show that photosynthetic protein abundance is affected in mutant plants. Our findings highlight the bifunctionality of AtTRM5 and the importance of the post-transcriptional tRNA modifications m1G and m1I at tRNA position 37 in general plant growth and development.

molecular biology↗

bioRxiv2018

Codon usage influences fitness through RNA toxicity

Many organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. To experimentally dissect the mechanisms of selection on synonymous sites, we expressed several hundred synonymous variants of the GFP gene in Escherichia coli, and used quantitative growth and viability assays to estimate bacterial fitness. Unexpectedly, we found many synonymous variants whose expression was toxic to E. coli. Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We identified RNA sequence determinants of toxicity, and evolved suppressor strains that can tolerate the expression of toxic GFP variants. Genome sequencing of these suppressor strains revealed a cluster of promoter mutations that prevented toxicity by reducing mRNA levels. We conclude that translation-independent RNA toxicity is a previously unrecognized obstacle in bacterial gene expression.\n\nSignificance statementSynonymous mutations in genes do not change protein sequence, but they may affect gene expression and cellular function. Here we describe an unexpected toxic effect of synonymous mutations in Escherichia coli, with potentially large implications for bacterial physiology and evolution. Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We hypothesize that the mechanism we identified influences the evolution of endogenous genes in bacteria, by imposing selective constraints on synonymous mutations that arise in the genome. Of interest for biotechnology and synthetic biology, we identify bacterial strains and growth conditions that alleviate RNA toxicity, thus allowing efficient overexpression of heterologous proteins.

synthetic biology↗

bioRxiv2018

Genome Sequence of Indian Peacock Reveals the Peculiar Case of a Glittering Bird

The unique ornamental features and extreme sexual traits of Peacock have always intrigued the scientists. However, the genomic evidence to explain its phenotype are yet unknown. Thus, we report the first genome sequence and comparative analysis of peacock with the available high-quality genomes of chicken, turkey, duck, flycatcher and zebra finch. The candidate genes involved in early developmental pathways including TGF-{beta}, BMP, and Wnt signaling pathway, which are also involved in feather patterning, bone morphogenesis, and skeletal muscle development, showed signs of adaptive evolution and provided useful clues on the phenotype of peacock. The innate and adaptive immune components such as complement system and T-cell response also showed signs of adaptive evolution in peacock suggesting their possible role in building a robust immune system which is consistent with the between species predictions of Hamilton-Zuk hypothesis. This study provides novel genomic and evolutionary insights into the molecular understanding towards the phenotypic evolution of Indian peacock.

genomics↗