Biology subjects

Verma, B.

Publications and source records attributed to Verma, B..

11 recordsLinked to original sources

bioRxiv2026

RiboWin: A computational framework to identify non-canonical open reading frames

Abstract Ribosome profiling is widely used to map translation across the genome, yet current sORF discovery pipelines are constrained by their reliance on annotated protein coding regions and by treating biological replicates primarily as tools for quantification rather than as strict filters for reproducibility. This results in two major issues, the systematic exclusion of pseudogene derived loci from analysis and the generation of extremely large candidate sets in which true translation events are difficult to distinguish from noise. To overcome these limitations, a five-stage framework was developed that expands the search space to include pseudogene loci while enforcing dual biological replicate concordance as a hard binary filter. When applied to four human cell lines with matched replicates and benchmarked against existing tools, the framework produces dramatically smaller and more reliable candidate sets, reducing thousands to millions of predicted sORFs down to a small number of high confidence concordant loci. Across HeLa cell cycle conditions, a limited set of unique concordant sORFs was identified spanning multiple transcript classes including upstream ORFs, retained introns, and nonsense mediated decay transcripts, along with a pseudogene derived candidate. Notably, the pseudogene encoded sORF RPL26P19 was detected consistently in HeLa cells but missed or inconsistently identified by existing tools, while a separate pseudogene sORF from UBE3AP2 was observed specifically in normal primary cell types and absent in HeLa. Both candidates were later found to be supported by entries in OpenProt, even though this was not known during the analysis, which gives added confidence that the results are genuine and not biased by prior expectations. Overall, these findings suggest that pseudogenes are not just inactive remnants in the genome but can act as real, functional sources of translated sORFs in a cell type specific manner. At the same time, it becomes clear that most current tools are not designed to detect these signals effectively. This highlights the need for approaches that both broaden the regions being searched and apply stricter reproducibility checks, so that truly meaningful translation events can be identified more reliably.

bioinformatics↗

bioRxiv2026

Cofilin Suppresses Tau-Induced Defects in Dense-Core Granule Formation and Aβ-Induced Neurodegeneration

Intracellular neurofibrillary tangles formed from hyperphosphorylated tau and extracellular amyloid plaques containing aggregated A{beta}-peptides, specific cleavage products of the Amyloid Precursor Protein (APP), are the primary histopathological hallmarks of Alzheimers Disease (AD), the leading cause of dementia in humans. However, the initiating steps that lead to these pathologies and early neurodegeneration, and the mechanisms by which tau- and A{beta}-induced effects might be linked remain unclear. Using the prostate-like secondary cell (SC) in Drosophila, we recently showed that A{beta} modulates normal APP- and membrane-associated protein aggregation in the dense-core granule (DCG) compartments of the regulated secretory pathway by interfering with subsequent membrane:DCG dissociation. This disrupts endolysosomal trafficking and propagates the resulting endolysosomal defects to other cells that endocytose the secreted abnormal DCG proteins. Here we show that overexpressing human tau also disrupts DCG aggregation and membrane:DCG dissociation inside SC secretory compartments, leading to increased endolysosomal targeting of these compartments. In a genetic screen, we find that knockdown of cofilin, which encodes an actin-severing protein required for dynamic remodelling of microfilaments, generates a similar phenotype. Consistent with this, overexpression of Cofilin, which is known to suppress tau-induced neurodegeneration in flies, reduces tau-induced DCG defects in SCs. Indeed, we find that Cofilin overexpression also suppresses A{beta}-induced degeneration in the fly eye. We conclude that membrane:DCG aggregate dissociation in DCG compartments is disrupted by both tau- and A{beta}-induced genetic changes that are relevant to AD, and this partially involves inhibition of actin cytoskeleton dynamics. Increasing actin remodelling activity can suppress neurodegeneration induced by both tau and A{beta}, suggesting that this process provides an important functional link between them that might be targeted therapeutically.

neuroscience↗

bioRxiv2026

Rab11-exosome biogenesis regulators mediate Aβ-induced intercellular propagation of endolysosomal trafficking defects and neurodegeneration

Alzheimer's Disease (AD) is characterised by two histopathological hallmarks, intracellular tau-containing neurofibrillary tangles and extracellular amyloid plaques containing {beta}-amyloid (A{beta}), a specific cleavage product of Amyloid Precursor Protein (APP). Initiation of A{beta}-induced neuronal pathology, however, has been postulated to involve intracellular events affecting endolysosomal trafficking that can propagate between cells. Recent studies in non-neuronal Drosophila secondary cells (SCs) have revealed that A{beta} interferes with APP-regulated protein aggregation events, which package signalling molecules into insoluble dense-core granules (DCGs) during normal regulated secretion, inducing endolysosomal defects that are transferred to other cells. Here, using SCs, we show that knockdown of the gene encoding accessory ESCRT-III protein Chmp5, which selectively regulates the formation of intraluminal vesicles (ILVs) inside SC DCG compartments that are subsequently released as Rab11-exosomes, inhibits propagation of A{beta}-induced endolysosomal trafficking defects. Furthermore, knocking down Chmp5 or other accessory ESCRT-III genes also suppresses A{beta}-induced, neurodegeneration-dependent morphological defects in the Drosophila eye. We conclude that genes controlling the Rab11-exosome biogenesis pathway play a key role in both A{beta}-induced endolysosomal trafficking defects associated with aberrant regulated secretion and cellular events leading to neurodegeneration. Our findings indicate these processes are linked and may suggest new target pathways for future development of AD therapeutics.

neuroscience↗

bioRxiv2026

Dengue virus-induced thrombocytopenia is mediated by dysregulation of the RUNX1-MYH9 axis

Dengue virus (DENV) infection causes an acute febrile illness that is usually self-limiting but can become fatal. Thrombocytopenia, or a decrease in circulating platelets, is a major clinical feature of dengue and is strongly associated with the progression to dengue hemorrhagic fever and dengue shock syndrome. In this report, MYH9, a cytoskeletal protein involved in platelets maturation and release, was found to be down-regulated in DENV-infected Huh7 cell lines. The expression of RUNX1, an important transcription factor involved in megakaryopoiesis, was also decreased following DENV-infection. In-silico analysis identified three potential RUNX1 transcription-factor binding site in the promoter-region of MYH9 gene. We therefore investigated whether RUNX1 regulates MYH9 expression during DENV-infection. Luciferase-assay and ChIP assays showed that DENV-infection affect the binding of RUNX1 to the MYH9 promoter, providing insight into the molecular basis underlying the reduced expression of MYH9 expression. Furthermore, the megakaryocyte differentiation markers GATA1, ITGB3, and MYH9 were upregulated in PMA-induced K562-cells. However, DENV infection downregulated these genes and increased the expression of apoptosis marker gene CYCS. These findings suggest that the dengue affects megakaryopoiesis through multiple mechanisms, potentially reducing platelets production while also promoting platelets destruction. Additionally, Fluorescence and electron microscopy revealed that functional defects of MYH9 may affects megakaryopoiesis biogenesis. Overall, this study provides insights into the molecular mechanisms contributing to thrombocytopenia during DENV infection.

molecular biology↗

bioRxiv2024

Biotin based Northern Blotting (BiNoB): A Robust and Efficient Alternative

Advancements in sequencing technology have led to the emergence of diverse types of regulatory RNAs. Differential transcript levels regulate cellular processes and influence disease severity. Identifying these variations through reliable methods is crucial for understanding their regulatory roles and disease mechanisms. Northern blotting, which used to be considered the gold standard for differential expression analysis, poses challenges due to various limitations associated with RNA quality, integrity, radioactivity, reagents, and the expenses associated with it. In this study, we employed a biotin-based Northern blotting approach, BiNoB, which offers advantages over traditional methods. In this study, we comprehensively targeted various RNA types, making this technique a versatile tool for RNA detection. Additionally, we conducted a comparison between 3-end labeled probes, which were labeled in-house, and 5-end labeled probes, which were commercially obtained. Remarkably, the results revealed significantly increased sensitivity with 3-end labeled probes. Furthermore, we prepared an in-house buffer and compared its performance with the commercially available ULTRAhyb buffer, which exhibited comparable sensitivity, indicating that the in-house buffer is a cost-effective alternative. Intriguingly, our findings showed that as little as 1{micro}g of total RNA proved to be adequate for the detection of small RNAs like tRNAs and their derived fragments.

molecular biology↗

bioRxiv2024

APP and β-amyloid modulate protein aggregation and dissociation from recycling endosomal and exosomal membranes

Secretory proteins frequently aggregate into non-soluble dense-core granules (DCGs) in recycling endosome-like compartments prior to release. By contrast, aberrantly processed A{beta}-peptides derived from Amyloid Precursor Protein (APP) form pathological amyloidogenic aggregations in late-stage Alzheimers Disease (AD) after secretion. By examining living Drosophila prostate-like secondary cells, we show both APP and A{beta}-peptides affect normal DCG biogenesis. These cells generate DCGs and secreted nanovesicles called Rab11-exosomes within enlarged recycling endosomes. The fly APP homologue, APP-like (APPL), associates with Rab11-exosomes and the compartmental limiting membrane, from where its extracellular domain controls protein aggregation. Proteolytic release of this membrane-associated domain permits aggregates to coalesce into a large central DCG. Mutant A{beta}-peptide expression, like Appl loss-of-function, disrupts this assembly step and compartment motility, and increases lysosomal targeting, mirroring pathological events reported in early-stage AD. Our data therefore reveal a physiological role for APP in membrane-dependent protein aggregation, which when disrupted, rapidly triggers AD-relevant intracellular pathologies.

cell biology↗

bioRxiv2023

HiTaxon: A hierarchical ensemble framework for taxonomic classification of short reads

Whole microbiome DNA and RNA sequencing (metagenomics and metatranscriptomics) are pivotal to determining functional roles within microbial communities. A key challenge in analysing these complex datasets, typically composed of tens of millions of short reads, is accurately classifying reads to their taxon of origin. Traditional reference-based short-read classification tools are compromised by reference database biases, leading to interest in classifiers leveraging machine learning (ML) algorithms. While ML classifiers have shown promise, they still lag reference-based tools in species-level classification. To address this performance gap, attention has turned to approaches that incorporate the hierarchical structure of taxonomic classifications, albeit with limited results. Here we introduce HiTaxon, a hierarchical framework for creating ensembles of reference-dependent and ML classifiers. HiTaxon facilitates data collection and processing, reference database construction and model training to streamline ensemble creation. We show that databases created by HiTaxon improve the species-level performance of reference-dependent classifiers, while reducing their computational overhead. Additionally, through exploring hierarchical methods for HiTaxon, we highlight that our custom hierarchical ML approach improves species-level classification relative to traditional strategies. Finally, we demonstrate the improved performance of our hierarchical ensemble over current state-of-the-art classifiers in species classification using datasets comprised of either simulated or experimentally-derived reads.

bioinformatics↗

bioRxiv2022

Planar cell polarity: intracellular asymmetry and supracellular gradients of Dachsous

The slope of a supracellular molecular gradient has long been thought to orient and coordinate planar cell polarity (PCP). Here we demonstrate and measure that gradient. Dachsous (Ds) is a conserved and elemental molecule of PCP; Ds forms intercellular bridges with another cadherin molecule, Fat (Ft), an interaction modulated by the Golgi protein Four- jointed (Fj). Using genetic mosaics and tagged Ds we measure Ds in vivo in membranes of individual cells over a whole metamere of the Drosophila abdomen. We find: 1. A supracellular gradient that rises from head to tail in the anterior compartment (A) and then falls in the posterior compartment (P). 2. There is more Ds in the front than the rear membranes of all cells in the A compartment, except that compartments most anterior and most posterior cells. There is more Ds in the rear than in the front membranes of all cells of the P compartment 3. The loss of Fj removes intracellular asymmetry anteriorly in the segment and reduces it elsewhere. Additional experiments show that Fj makes PCP more robust. Using Dachs (D) as a molecular indicator of polarity, we confirm that opposing gradients of PCP meet slightly out of register with compartment boundaries.

developmental biology↗

bioRxiv2022

Bifidobacterium longum attenuates ovariectomy-induced bone loss via modulating the Immunoporotic Breg-Treg-Th17 cell axis

Discoveries in the last few years have emphasized the existence of an enormous breadth of communication between osteo-immune system. These discoveries fuel novel approaches for the treatment of several bone-pathologies including osteoporosis, an inflammatory bone anomaly affecting more than 500 million people globally. Bifidobacterium longum (BL) is preferred probiotic of choice due to its varied immunomodulatory potential in alleviating various inflammatory diseases. Here, we evaluate the effect of BL in ovariectomy (ovx)-induced post-menopausal osteoporotic mice model. Our in vitro findings reveal that BL suppresses the differentiation and functional activity of RANKL-induced osteoclastogenesis in both mouse bone marrow cells and human PBMCs. Our in vivo data clearly establish that BL exhibits osteoprotective potential via modulating the "immunoporotic" Breg-Treg-Th17 cell-axis. Furthermore, {micro}CT and bone mechanical strength data support that BL supplementation significantly enhanced bone mass and strength, and improved microarchitecture in ovx mice. Remarkably, alteration in frequencies of CD19+CD1dhiCD5+ Bregs, CD4+Foxp3+IL-10+ Tregs, and CD4+Ror{gamma}t+IL-17+ Th17 immune cells in distinct lymphoid organs along with serum-cytokine data (enhanced anti-osteoclastogenic cytokines IFN-{gamma} and IL-10 and reduced osteoclastogenic-cytokines IL-6, IL-17, and TNF-) strongly support the immunomodulatory potential of BL. Altogether our findings establish a novel osteo-protective and immunoporotic potential of BL in augmenting bone health under osteoporotic conditions.

immunology↗

bioRxiv2021

Regulatory B cells (Bregs) inhibit osteoclastogenesis and prevent bone loss in osteoporotic mice model

Increasing evidences in recent years have suggested that regulatory B cells (Bregs) are crucial modulator in various inflammatory disease conditions. However, the role of Bregs in case of postmenopausal osteoporosis remains unknown. Also, no study till date have ever investigated the significance of Bregs in modulating osteoclastogenesis. In the present study, we for the first time examined the anti-osteoclastogenic potential of Bregs under in vitro conditions and we observed that Bregs suppressed RANKL mediated osteoclastogenesis in bone marrow cells in a dose dependent manner. We further elucidated the mechanism behind the suppression of osteoclasts differentiation by Bregs and found that Bregs inhibit osteoclastogenesis via IL-10 production. To further confirm the bone health modulating potential of Bregs we employed post-menopausal osteoporotic mice model. Remarkably, our in vivo data clearly suggest a significant reduction (p < 0.01) in both CD19+IL-10+ and CD19+CD1dhiCD5+IL-10+ B10 Bregs in case of osteoporotic mice model. Moreover, our serum cytokine data further confirms the significant reduction of IL-10 levels in osteoporotic mice. Taken together, the present study for the first time unravels and establish the unexplored role of regulatory B cells in case of osteoporosis and provide new insight into Bregs biology in the context of post-menopausal osteoporosis.

immunology↗

bioRxiv2020

Lactobacillus rhamnosus attenuates bone loss and maintains bone health by skewing Treg-Th17 cell balance in Ovx mice

Osteoporosis is a systemic-skeletal disorder characterized by enhanced fragility of bones leading to increased rates of fractures and morbidity in large number of populations. Probiotics are known to be involved in management of various-inflammatory diseases including osteoporosis. But no study till date had delineated the immunomodulatory potential of Lactobacillus rhamnosus (LR) in bone-health. In the present study, we examine the effect of probiotic-LR on bone-health in osteoporotic (Ovx) mice model. We observed that administration of LR attenuated bone-loss in Ovx mice. Both the cortical and trabecular bone-content of LR treated group was significantly higher than Ovx-group. Remarkably, the percentage of osteoclastogenic-CD4+Ror{gamma}t+Th17 cells at distinct immunological sites such as BM, spleen, LN and PP were significantly reduced, whereas the percentage of anti-osteoclastogenic-CD4+Foxp3+Tregs and CD8+Foxp3+Tregs were significantly enhanced in LR-treated group thereby resulting in inhibition of bone-loss. The immunomodulatory-role of LR was further supported by serum-cytokine data with a significant reduction in proinflammatory-cytokines (IL-6, IL-17 and TNF-) along with enhancement in anti-inflammatory-cytokines (IL-10, IFN-{gamma}) in LR treated-group. Altogether, the present study for the first time establishes the osteoprotective role of LR on bone-health, thus highlighting the potential of LR in the treatment and management of various bone related diseases including osteoporosis.

immunology↗