Biology subjects

Pandeya, A.

Publications and source records attributed to Pandeya, A..

5 recordsLinked to original sources

bioRxiv2026

HiC-LEGO: Biologically Guided High-Resolution 3D Genome Reconstruction Preserves Chromatin Organization at Kilobase Resolution

Three-dimensional (3D) chromosome reconstruction from Hi-C contact maps remains challenging because genome organization is hierarchical and fine-resolution models must reconcile local structure with chromosome-scale constraints. Here we present HiC-LEGO, a domain-aware hierarchical framework integrating ensemble chromatin domains with graph-based structural learning and progressive chromosome assembly. By combining ensemble domain selection with hierarchical reconstruction, HiC-LEGO reduces dependence on individual domain definitions while maintaining local organization during chromosome-scale assembly. Across five human cell lines at 5-kb resolution, HiC-LEGO achieves higher reconstruction concordance than evaluated state-of-the-art methods while better preserving domain organization. At 1-kb resolution, HiC-LEGO reconstructs complete GM12878 chromosome 8 and recovers close spatial proximity between an epigenomically supported distal MYC enhancer and its promoter. Reconstructions from 5-kb Micro-C data show that 249 experimentally defined RCMC microcompartment interactions at the Ppm1g locus occupy compact 3D configurations. In the breast cancer dataset, HiC-LEGO reconstructs structures that maintain stable TAD organization across healthy breast, primary tumors, and liver metastases, while revealing greater inter-patient structural heterogeneity in malignant pleural effusion samples. Pore-C validation shows that experimentally observed multi-way contacts spanning 1-5 Mb are enriched in compact reconstructed configurations across all 23 chromosomes. Thus, HiC-LEGO preserves regulatory interactions, disease-associated chromatin organization and higher-order spatial relationships beyond pairwise contact-map concordance.

bioinformatics↗

bioRxiv2025

Estimation of stature from hand length and hand breadth in undergraduate medical students: An anthropometric study

BackgroundStature, a determinant that aids in personal identification, can be estimated using measurements of various body parts. This study measured the length and breadth of hands and the height of the participants, aiming to develop linear regression equations for stature estimation. MethodsThis is a cross-sectional descriptive study in which 195 medical students aged 18 to 24 were enrolled, and measurement of stature was done by stadiometer and hand length and breadth by vernier calliper, after an informed written consent was obtained. ResultsMean stature was higher in males (170.24{+/-}5.79 cm) as compared to females (159.01{+/-}7.261 cm). Mean length and breadth of both right and left hands were also found to be higher in males when compared with females. With a standard error of estimates of 5.083 cm and an R2 of 0.648, the multiple linear regression analysiss model summary concluded that R is .805, indicating a strong positive association between stature estimation and hand dimensions. ConclusionsHand length and hand breadth together may be a powerful predictor of stature, as indicated by the greater R value when compared to regression coefficients derived for other body parts. A variable entity, height is influenced by genetics and nutritional status. Future studies can be done taking these factors into consideration and also including a larger population size.

systems biology↗

bioRxiv2024

A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa

BackgroundOrganization of the eukaryotic genome is essential for proper function, including gene expression. In metazoans, chromatin loops and Topologically Associated Domains (TADs) organize genes into transcription factories, while chromosomes occupy nuclear territories in which silent heterochromatin is compartmentalized at the nuclear periphery and active euchromatin localizes to the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation typified by heterochromatic centromeres and telomeres independently clustering at the nuclear membrane, while interspersed heterochromatic loci aggregate across Megabases of linear genomic distance to loop chromatin in TAD-like structures. However, the role of individual heterochromatic loci in normal genome organization and function is unknown. ResultsWe examined the genome organization of a Neurospora strain harboring a [~]47.4 kilobase deletion within a temporarily silent, facultative heterochromatic region, as well as the genome organization of a strain deleted of a 110.6 kilobase permanently silent constitutive heterochromatic region. While the facultative heterochromatin deletion minimally effects local chromatin structure or telomere clustering, the constitutive heterochromatin deletion alters local chromatin structure, the predicted three-dimensional chromosome conformation, and the expression of some genes, which are qualitatively repositioned into the nucleus center, while increasing Hi-C variability. ConclusionsOur work elucidates how an individual constitutive heterochromatic region impacts genome organization and function. Specifically, one silent region indirectly assists in the hierarchical folding of the entire Neurospora genome by aggregating into the "typical" heterochromatin bundle normally observed in wild type nuclei, which may promote normal gene expression by positioning euchromatin in the nucleus center.

genomics↗

bioRxiv2020

Extracellular histones trigger disseminated intravascular coagulation by lytic cell death

Histones are cationic nuclear proteins that are essential for the structure and functions of eukaryotic chromatin. However, extracellular histones trigger inflammatory responses and contribute to death in sepsis by unknown mechanisms. We recently reported that inflammasome activation and pyroptosis trigger coagulation activation through a tissue factor (TF)-dependent mechanism. Here, we show that histones trigger coagulation activation in vivo as evidenced by coagulation parameters and fibrin deposition in tissues. However, histone-induced coagulopathy was neither dependent on caspase 1/11 and gasdermin D (GSDMD), nor on TLR2 and TLR4, as deficiency of these genes in mice did not protect against histone-induced coagulopathy. Incubation of histones with macrophages induced lytic cell death and phosphatidylserine (PS) exposure, which is required for TF activity, a key initiator of coagulation. Neutralization of TF diminished histone-induced coagulation. Our findings reveal lytic cell death as a novel mechanism of histone-induce coagulation activation and thrombosis. Key PointsO_LIHistones trigger DIC in a tissue factor dependent mechanism C_LIO_LIHistones induce tissue factor activation through lytic cell death C_LI

immunology↗

bioRxiv2017

A Web-resource for Nutrient Use Efficiency related Genes, QTLs, and microRNA in important cereals and model plants

Cereals are the key contributors to global food security. Genes involved in uptake (transport), assimilation and utilization of macro- and micro-nutrients are responsible for their content in grain and straw. Although many cereal genomic databases are available, currently there is no cohesive web-resource of manually curated nutrient use efficiency (NtUE) related genes and QTLs, etc. In this study, we present a web-resource containing information on NtUE related genes/QTLs and the corresponding available microRNAs for some of these genes in four major cereal crops [wheat (Triticum aestivum), rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare)], two alien species (Triticum urartu and Aegilops tauschii) related to wheat, and two model species including Brachypodium distachyon and Arabidopsis thaliana. Gene annotations integrated in the current web-resource were collected from the existing databases and the available literature. The primary goal of developing this web-resource is to provide descriptions of the NtUE related genes and their functional annotation. MicroRNA targeting some of the NtUE related genes and the quantitative trait loci (QTLs) for NtUE related traits are also included. The available information in the web-resource should help the users to readily search the desired information.\n\nWeb-resource URLhttp://bioclues.org/NtUE/

bioinformatics↗