Biology subjects

Yadav, S. K.

Publications and source records attributed to Yadav, S. K..

12 recordsLinked to original sources

bioRxiv2026

CardioChrom Reconstructs the Human Cardiac Virtual Epigenome from Single-Nucleus Transcriptomes

Background: Matched epigenomic profiling remains scarce in human heart failure, limiting regulatory interpretation of single-nucleus ribonucleic acid (RNA) sequencing data. We developed CardioChrom, a cardiac-specialized framework that reconstructs chromatin accessibility, histone H3 lysine 27 acetylation (H3K27ac), and histone H3 lysine 27 trimethylation (H3K27me3) from single-nucleus RNA profiles. Methods: CardioChrom was developed using same-nucleus human heart datasets jointly measuring RNA with chromatin accessibility by assay for transposase-accessible chromatin (ATAC), H3K27ac, or H3K27me3, with donor-separated development and leave-one-cell-type-out testing. Frozen models were evaluated in 10-donor and 23-sample external human heart cohorts. Histone reconstruction was benchmarked against measured profiles and a Transformer. The models were then applied without refitting to an RNA-only cohort of 43 donors with heart failure with preserved ejection fraction (HFpEF). Results: Across unseen cardiac cell types, CardioChrom increased area under the precision-recall curve by 0.0109 relative to within-cell-type RNA shuffling in 11 of 12 cell types and increased area under the receiver operating characteristic curve by 0.0179 in all 12. CardioChrom exceeded controls in both external cohorts and matched or exceeded the Transformer across 6 prespecified histone metrics. In HFpEF, 3,581 donor-level pathway-layer associations met global false discovery rate, sex-adjustment, and leave-one-donor-out robustness criteria. Endothelial cells showed prominent reconstructed histone-associated changes involving coagulation, inflammation, hypoxia, and profibrotic signaling. Von Willebrand factor expression and its reconstructed regulatory states were consistently reduced, and all 6 linked candidate cis-regulatory elements were classified as repressed. Motif-supported TF-cCRE-gene hypotheses were generated in endothelial cells and fibroblasts. Conclusions: CardioChrom extends RNA-only human heart failure cohorts toward cell-type-resolved virtual epigenomic and regulatory analysis while distinguishing predictions from direct measurements.

bioinformatics↗

bioRxiv2026

Biofunctional 2D Graphitic Carbon Nitride-Hydrogel Heterointerfaces for Electrochemical Detection of Interleukin-6 toward Septic Cardiomyopathy Diagnostics in Clinical Biofluids

Interleukin-6 (IL-6) is a key pro-inflammatory cytokine closely associated with sepsis progression and septic cardiomyopathy (SCM), a severe clinical condition characterized by acute cardiac dysfunction and high mortality in critically ill patients. Rapid and sensitive monitoring of IL-6 in clinical biofluids is therefore crucial for early diagnosis, disease prognosis, and timely therapeutic intervention in emergency healthcare settings. Herein, we report a biofunctional, label-free electrochemical aptasensor based on a graphitic carbon nitride-incorporated chitosan hydrogel-modified gold screen-printed electrode (MCH/Apt-IL-6/g-C3N4@CS/Au-SPE) for ultrasensitive detection of IL-6 in clinical biofluids. The electroactive g-C3N4@CS hydrogel heterointerface was engineered via electrostatic interactions between the negatively charged surface functionalities of two-dimensional graphitic carbon nitride (g-C3N4) and the protonated amino groups (-NH3+) of chitosan (CS), yielding a porous, conductive, and biocompatible sensing matrix with enhanced aptamer immobilization and accelerated electron-transfer kinetics. Biocompatibility evaluation using MTT assay and confocal fluorescence imaging demonstrated that the hydrogel maintained excellent cellular compatibility at 5 mg/mL, preserving normal cytoskeletal organization, mitochondrial integrity, and nuclear morphology, while higher concentrations induced cellular stress responses. Under optimized experimental conditions, the developed aptasensor exhibited outstanding analytical performance with an ultrawide linear detection range from 1 fg/mL to 10 ng/mL, a high sensitivity of 2.162 A/[log10(ng/mL)] cm-2, a low detection limit of 0.460 pg/mL, and excellent linearity (R2 = 0.979). In addition, the sensor demonstrated remarkable selectivity toward common biological interferents, including ascorbic acid, cysteine, glucose, glycine, and urea, together with excellent reproducibility (RSD = 1.139%). Validation studies performed in spiked human serum samples further confirmed the reliability and practical applicability of the proposed sensing platform for rapid clinical analysis. Owing to its label-free detection strategy, disposable electrode format, high sensitivity, and favorable biocompatibility, the developed g-C3N4-hydrogel heterointerface-based aptasensor represents a promising next-generation platform for early septic cardiomyopathy diagnostics, inflammatory biomarker monitoring, and point-of-care electrochemical biosensing applications.

bioengineering↗

bioRxiv2026

BCG vaccination mitigates tau pathology and restores cognitive function in PS19 mice.

Retrospective studies in patients with non-muscle invasive bladder cancer (NMIBC) have reported a significant reduction in Alzheimers disease (AD) incidence (12-78%) among Bacillus Calmette-Guerin (BCG) recipients versus controls. To investigate the underlying mechanisms, we evaluated BCG in the PS19 mouse model of tauopathy. We found that BCG administration reduced hippocampal phospho-tau and microgliosis while preserving neuronal markers. In vivo volumetric T2-MRI demonstrated attenuation of brain atrophy accompanied by increased glutamate-weighted CEST-MRI signals. Functionally, BCG-treated mice showed improved performance in the novel object recognition test (NORT), as well as improved body-weight maintenance and survival. Transcriptomic profiling of the hippocampus revealed near complete normalization of the PS19 disease-associated gene expression signature towards that of healthy controls. Flow cytometric profiling of brain myeloid populations demonstrated a reduction in activated resident microglia, but total microglia cells remain elevated. Moreover, an increase of the co-stimulatory marker CD80 on the recruited peripheral myeloid cells ensues following BCG treatment. Consistent with this shift in myeloid state, primary brain myeloid cells from BCG-treated mice also exhibited enhanced phagocytosis of FITC-labeled tau fibrils and increased lactate production. Together, these findings indicate that BCG induces systemic and CNS myeloid cell reprogramming that limits neuroinflammation, enhances tau clearance, and rescues cognitive and neurodegenerative phenotypes in a tauopathy model. BCG is a safe, readily available therapy that merits consideration as a preventive agent against dementia. One sentence summaryBCG therapy prevents tauopathy in PS19 mouse model.

neuroscience↗

bioRxiv2025

Antiphospholipid syndrome (APS) is a platelet factor 4 (PF4)-centric immunothrombotic disorder

Antiphospholipid syndrome (APS) is an immunothrombotic disorder, frequently attributed to autoantibodies that bind {beta}2-glycoprotein I ({beta}2GPI). A study showed that the platelet-specific chemokine, platelet factor 4 (PF4), binds to {beta}2GPI, enhancing recognition of {beta}2GPI by APS antibodies. APS antibodies induce the release of neutrophil extracellular traps (NETs), webs of decondensed chromatin that bind both PF4 and {beta}2GPI. We propose that PF4 bridges {beta}2GPI to NETs (and other PF4-targeted polyanions), leading to the formation of prothrombotic PF4:{beta}2GPI:NET immunotargets in APS. Dynamic light-scattering studies of isolated IgGs from four patients with triple-positive APS show formation of PF4:{beta}2GPI:NET complexes that bind APS antibodies. NETs released in a microfluidic system bound {beta}2GPI, but only in the presence of PF4, forming a multimolecular APS antigenic target. Whole blood infused through a photochemically-injured, endothelium-lined microfluidic channel formed platelet-, fibrin-, and complement-rich thrombi that bound APS antibody only in the presence of PF4. Thrombi were reduced in size if either ADAMTS13 or DNase1 was infused. In a murine APS model, wildtype and transgenic mice expressing platelet human PF4 {+/-} Fc{gamma}RIIA developed more intense neutrophil rolling along veins, and more extensive thrombus formation following laser injury to cremaster arterioles and venules, whereas mice lacking PF4 did not. Three antigenically distinct anti-hPF4 monoclonal antibodies blocked thrombosis in vitro, and neutrophil rolling and thrombosis in vivo. Our studies provide new insights into the basis of APS that has mechanistic parallels to other known PF4 immunothrombotic disorders and offer potential diagnostic and non-anticoagulant therapeutic strategies for clinical management. Key pointsO_LIPF4 enhances {beta}2GPI binding to NETs and these complexes are central to APS immunothrombosis. C_LIO_LIAnti-PF4 monoclonal antibodies block APS immunothrombosis in microfluidic and murine studies. C_LI

cell biology↗

bioRxiv2025

Redefined Strategies to generate Conditional miR-141/200c miRNA cluster Knockout mice to eliminate confounding neo cassettes

MicroRNAs (miRNAs) of the miR-200 family specifically miR-141 and miR-200c regulate neurogenesis, differentiation, and epithelial-mesenchymal transitions in development. Dysregulation of these miRNAs is associated with several diseases including cancer and stroke. The Mirc13tm1Mtm/Mmjax mouse line, which targets the miR-141/200c cluster, was originally generated and described by Park et al. 2012 as a knockout-first, reporter-tagged insertion with conditional potential (conditional-ready) mouse line. Harnessing its full potential requires a two-step breeding process: breeding with FLP mice to excise the lacZ/neo cassette, then breeding with Cre to delete the floxed miRNA cluster (Park, et al. 2012). However, many studies either bypassed removal of the lacZ/Neo cassettes and treated the mouse line as Mirc13 knockouts or bred directly with Cre mouse lines, which could lead to unpredictable recombination and genotypes. Here we show that retention of the lacZ/Neo cassette is associated with reduced expression of the neighboring genes Ptpn6, Phb2 and Atn1 in the olfactory bulb, and that these genes are expressed normally once the cassette is excised. We therefore recommend a validated two-step FLPo-then-Cre breeding plan for this line, together with case-by-case allele validation for other knockout-first, reporter-tagged mouse lines.

neuroscience↗

bioRxiv2025

Molecular mechanism for cargo-mediated initiation of kinesin-1 activation

Kinesin-1 is a dynamic heterotetrameric assembly of two heavy and two light chains (KHC and KLC) that mediates microtubule-based intracellular transport of many different cargoes. The complex adopts a compact, autoinhibited state that is activated by cargo-adaptor proteins containing specific short linear peptide motifs (SLiMs). These motifs interact with the tetratricopeptide repeat (TPR) domains of the KLCs. The mechanism coupling SLiM recognition to activation-associated conformational changes in the complex is unknown. Here we combine protein design, computational modelling, biophysical analysis, and electron microscopy to examine the structural and mechanistic consequences of SLiM binding to the KLC-TPR domain within the complete heterotetrameric holoenzyme. We show that coiled coil 1 (CC1) of the KHC docks KLC TPR domains in the autoinhibited complex, forming the shoulder feature observed in electron microscopy. Disrupting this interaction or binding an activating SLiM dislocates the TPR shoulder, freeing the motor domains and promoting transition between its closed, inactive, and open states. Opening the kinesin-1 complex facilitates binding to the microtubule-associated kinesin-1 cofactor, MAP7. Therefore, cargo-mediated dislocation of the TPR shoulder serves as a key initial step in kinesin-1 activation, allosterically linking cargo binding to motor dynamics.

biochemistry↗

bioRxiv2024

Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma

Immune checkpoint inhibitors (ICIs) have heralded a remarkable shift in cancer care, significantly extending survival for advanced cancer patients. However, despite their remarkable clinical successes, a substantial majority of patients fail to achieve a lasting response to ICIs. To address this challenge and gain insights into the complex landscape of the tumor microenvironment (TME), we conducted an extensive analysis using single-cell RNA sequencing (scRNA; [~]216K cells across 39 samples) and single-nucleus transposase-accessible chromatin sequencing (snATAC; [~]43K cells from 15 samples) in a metastatic melanoma cohort. This systematic approach delineates 14 distinct cell types and 55 cell subtypes, including the identification of 15 transcriptional hallmarks of malignant cells. Through correlation analysis of cell subtype proportions, we unveiled six distinct clusters associated with varying tumor responses. Particularly intriguing was the identification of the mature DC enriched in immunoregulatory molecules (mregDC) subtype exhibiting correlations with naive T and B cells, forming an anti-tumor program that underscores the importance of multiple immune cell types in mediating anti-tumor immunity. Notably, we found that mregDC abundance represents a good prognostic predictor of progression-free survival (PFS) in the context of ICI treatment, and when combined with the TCF7+/- CD8 T cell ratio, it reliably predicts patient PFS across treatments beyond ICI. We validated our findings using an independent cohort of 274 ICI-treated melanoma samples analyzed using tissue-level expression. We next compared mregDCs and conventional dendritic cell types 1 and 2 (cDC1 and cDC2) using transcriptome signature, differentiation trajectory, interactome, cytokine milieu, and epigenome landscape analyses. This comparative analysis shed light on the unique attributes of mregDCs within the TME. Finally, we investigated cell type/subtype-specific genes, pathways, immune response enrichment, and ligand-receptor interactions closely associated with the proportions of mregDCs within the TME. These molecular and cellular insights, with their critical roles in enhancing the immune response against cancer, offer valuable prospects for predicting the efficacy of ICI regimens, and potentially guiding the selection of rational combinatorial therapies.

cancer biology↗

bioRxiv2023

Unravelling the novel genetic diversity and marker-trait associations of corn leaf aphid resistance in wheat using microsatellite markers

The study was conducted to identify novel simple sequence repeat (SSR) markers associated with resistance to corn aphid (CLA), Rhopalosiphum maidis L. in 48 selected bread wheat (Triticum aestivum L.) and wild wheat (Aegilops spp. & T. dicoccoides) genotypes during two consecutive cropping seasons (2018-19 and 2019-20). A total of 51 polymorphic markers containing 143 alleles were used for the analysis. The frequency of the major allele ranged from 0.552 (Xgwm113) to 0.938 (Xcfd45, Xgwm194 and Xgwm526), with a mean of 0.731. Gene diversity ranged from 0.116 (Xgwm526) to 0.489 (Xgwm113), with a mean of 0.354. The polymorphic information content (PIC) value for the SSR markers ranged from 0.107 (Xgwm526) to 0.370 (Xgwm113) with a mean of 0.282. The results of the STRUCTURE analysis revealed the presence of four main subgroups in the populations. Analysis of molecular variance (AMOVA) showed that the between-group difference was around 37% of the total variation contributed to the diversity by the whole germplasm, while 63% of the variation was attributed between individuals within the group. A general linear model (GLM) was used to identify marker-trait associations, which detected a total of 23 and 27 significant new marker-trait associations (MTAs) at the p < 0.01 significance level during the 2018-19 and 2019-20 crop seasons, respectively. The findings of this study have important implications for the identification of molecular markers associated with CLA resistance. These markers can increase the accuracy and efficiency of aphid-resistant germplasm selection, ultimately facilitating the transfer of resistance traits to desirable wheat genotypes.

molecular biology↗

bioRxiv2023

High prevalence of Bovine Tuberculosis reported in Cattle and Buffalo of Eastern Nepal

Livestock farming, specifically of cattle and buffalo, is crucial to Nepals economy, with more than 66% of the population involved in agriculture and animal husbandry. Animal tuberculosis (TB) caused by Mycobacterium bovis is a chronic disease that affects these animals and results in economic losses due to reduced milk and meat productivity, fertility and mortality. M. bovis also infects humans, non-human primates, goats and other mammals, and can afflict both cattle and buffalo. Our study is a part of routine surveillance of prevalent diseases, including M. bovis, in cattle and buffalo. We collected blood samples (n=400, 100 samples from each district) from selected eastern districts of Nepal. We used a Rapid Bovine TB Test Kit to test these samples for presence of M. bovis. Of the 400 samples collected, 74 animals (18.75%) tested positive for M. bovis, with the majority of positive samples coming from cattle (n=71, 17.75%) and only three from buffalo (<1%). Among the screened breeds of cattle and buffalo, Holstein Friesian cattle (HF) (n=43, 58%), Jersey-cross cattle (JX) (n=20, 27%), Local buffalo (n=8, 10.8%) and Murra breed buffalo (n=3, 4.1%) were found to carry M. bovis. The majority (50%) of infected animals were between 3-6 years old. Morang (n= 24 positive in cattle; n=1 positive in buffalo) and Jhapa (n= 22 positive in cattle; n=2 positive in buffalo) had the highest prevalence of M. bovis, while all the positive cases in Sunsari (n=19) and Udaypur (n=6) were in cattle. The fact that over 18% of the samples tested positive for M. bovis is of great concern. It is critical to thoroughly test animal products from these livestock prior to human consumption. To prevent and mitigate M. bovis-related infections in Nepal, a more comprehensive screening strategy coupled with more effective animal husbandry practices needs to be adapted.

microbiology↗

bioRxiv2020

Reduced nuclear lamin A/C enhances cancer cell squeezing through rigid barriers, does not facilitate endothelial crossing, and impairs experimental metastasis

The mechanisms by which the nuclear lamina of tumor cells controls their migration and survival are poorly understood. Lamin A and its variant lamin C are key nuclear lamina proteins that control nucleus stiffness and chromatin conformation. Downregulation of lamin A/C levels in two metastatic lines, B16F10 melanoma and E0771 breast carcinoma, facilitated cell squeezing through rigid pores, elevated nuclear deformability and reduced heterochromatin. Unexpectedly, the transendothelial migration of both cancer cells in vitro and in vivo, through lung capillaries, was not elevated by lamin A/C knockdown. Both cancer cells with lamin A/C knockdown grew normally in primary tumors and in vitro on rigid surfaces. Strikingly, however, both lamin A/C deficient melanoma and breast cancer cells grew poorly in 3D spheroids expanded in soft agar cultures. Experimental lung metastasis of both lamin A/C knockdown cells was also markedly reduced. Taken together, our results suggest that high content of lamin A/C in multiple cancer cells promotes cancer cell survival and ability to generate lung metastasis without compromising cancer cell emigration from lung vessels.

cancer biology↗

bioRxiv2020

Unexpected free fatty acid binding pocket in the cryo-EM structure of SARS-CoV-2 spike protein

COVID-19, caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), represents a global crisis. Key to SARS-CoV-2 therapeutic development is unraveling the mechanisms driving high infectivity, broad tissue tropism and severe pathology. Our cryo-EM structure of SARS-CoV-2 spike (S) glycoprotein reveals that the receptor binding domains (RBDs) tightly and specifically bind the essential free fatty acid (FFA) linoleic acid (LA) in three composite binding pockets. The pocket also appears to be present in the highly pathogenic coronaviruses SARS-CoV and MERS-CoV. Lipid metabolome remodeling is a key feature of coronavirus infection, with LA at its core. LA metabolic pathways are central to inflammation, immune modulation and membrane fluidity. Our structure directly links LA and S, setting the stage for interventions targeting LA binding and metabolic remodeling by SARS-CoV-2. One Sentence SummaryA direct structural link between SARS-CoV-2 spike and linoleic acid, a key molecule in inflammation, immune modulation and membrane fluidity.

biochemistry↗

bioRxiv2019

Conversion of a defensive toxin-antitoxin system into an offensive T6SS effector in Burkholderia

Bacteria use various kinds of toxins to either inhibit the growth of co-habiting bacteria or when needed control their own growth. Here we report that Burkholderia and certain other bacteria have altered the potential defensive function of Tox-REase-5 domain containing toxins into offensive function. The Burkholderia gladioli strain NGJ1 encodes such toxins as type VI secretion system (T6SS) effectors (Tse) and potentially deploys them to kill co-habiting rice endophytic bacteria. Notably, the immunity (Tsi) proteins associated with Tse effectors demonstrate functional similarity with the antitoxin of type II toxin-antitoxin (TA) system. Genome analysis of diverse bacteria revealed that various Tse orthologs are either encoded as TA or T6SS effectors. In addition, potential evolutionary events associated with conversion of TA into T6SS effectors have been delineated. Our results indicate that the transposition of IS3 elements has led to the operonic fusion of certain T6SS related genes with TA genes resulting in their conversion into T6SS effectors. Such a genetic change has enabled bacteria to utilize novel toxins to precisely target co-habiting bacteria.

microbiology↗