Biology subjects

Puri, D.

Publications and source records attributed to Puri, D..

12 recordsLinked to original sources

bioRxiv2026

Genome-wide multi-layered epigenomic profiling across human aging

Aging is characterized by highly reproducible alterations across multiple layers of the epigenetic landscape, including DNA methylation, chromatin accessibility, and histone modifications. However, it remains unclear to what extent these age-associated changes are interconnected and coordinated coherently. To investigate the genome-wide distribution and interplay of age-associated epigenetic alterations, we generated whole-genome bisulfite sequencing (WGBS) data from blood samples of 120 healthy donors. Integration with ATAC-seq data revealed no clear relationship between age-related changes in DNA methylation and chromatin accessibility. We further examined the association of these alterations with age-dependent changes in CTCF occupancy and histone modifications, including H3K27ac, H3K27me3, H3K4me1, H3K4me3, and H3K9me3, but observed very little corresponding changes in chromatin states. Collectively, our integrative genome-wide analysis revealed only limited association between age-associated epigenetic alterations in DNA methylation, chromatin accessibility, and histone modifications, arguing against a broadly coordinated remodeling of the aging epigenome.

genomics↗

bioRxiv2026

Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging

Aging of the immune system is associated with chronic inflammation and impaired immune function, yet the regulatory mechanisms underlying these changes remain incompletely understood. Here, we generated paired single-cell transcriptomic and chromatin accessibility profiles from peripheral blood mononuclear cells of young and old healthy donors to characterize immune aging at single-cell resolution. Using an integrative computational framework for multi-omic single-cell analysis, we detected pronounced age-associated changes in T cells, including loss of naive CD8+ T cells and expansion of differentiated memory and effector populations. Aging was accompanied by increased inflammatory signaling and reduced oxidative phosphorylation programs. Enhancer-based gene regulatory network analyses identified a reduced role of TCF7 and increased activity of inflammatory regulators, including FOSL2, in aged T cells. Integration with genetic association and eQTL datasets further supported the functional relevance of age-associated regulatory regions and their target genes.

bioinformatics↗

bioRxiv2026

Rapid Isolation and Genomic Characterization of Sewage-Derived Bacteriophages Targeting Multidrug-Resistant Avian Pathogenic Escherichia coli in Poultry

Antimicrobial resistance (AMR) in Escherichia coli is a major threat to global poultry production, particularly for controlling colibacillosis caused by avian pathogenic E. coli (APEC). Intensive antibiotic use has accelerated the emergence of multidrug-resistant (MDR) strains, undermining treatment efficacy and facilitating zoonotic transmission of resistance genes. This study evaluated bacteriophage therapy as a targeted, antibiotic-independent strategy to control MDR E. coli in Nepalese poultry systems. Seventeen E. coli isolates were obtained from commercial broiler and local-breed chicken farms. Using the double-layer agar method, 18 lytic phages were isolated from three urban sewage samples, infecting eight isolates. Real Time PCR screening revealed extensive AMR profiles in six isolates; one broiler-derived strain (EcI8) harbored 30 resistance genes, including carbapenemases, ESBLs, aminoglycoside, quinolone, and last-resort antibiotic determinants associated with class 1 and 3 integrons. Purified phages were whole-genome sequenced and all of them belonged to the genera Tequatrovirus, Phapecoctavirus, Vequintavirus, and Gamaleyavirus--lineages previously used in veterinary and human phage therapy. Several exhibited broad host ranges (up to seven isolates) and lacked detectable virulence or resistance genes; they also encoded potent lytic enzymes, including endolysins, holins, spanins, and transglycosylases. Notably, one Phapecoctavirus (PG7) showed close similarity to established APEC-infecting phages. These findings demonstrate that sewage can be a readily accessible source of safe, therapeutically relevant phages targeting highly resistant poultry E. coli. Phage cocktails and derived enzybiotics delivered through drinking water or feed offer a scalable alternative for preventing and treating colibacillosis, reducing antibiotic dependence, and mitigating zoonotic AMR risks. This study establishes a rapid, reproducible pipeline for local phage isolation and genomic validation, supporting field deployment of tailored phage-based interventions in resource-limited poultry systems.

microbiology↗

bioRxiv2025

The lac operon in uropathogenic Escherichia coli enhances intracellular growth by enabling host glycan utilization

The lac operon in Escherichia coli has been used as a model of gene regulation throughout biology since its characterization in the early 1960s. Despite the myriad of biotechnology applications that arose from characterization of the lac system, the explanation for the importance of a functional lac operon in normal bladder colonization by uropathogenic E. coli remains unknown given that the prototypical substrate, lactose, is not normally known to be readily available within the urinary tract. Here, we identified a unique uropathogenic clinical isolate (5.3r) that has a two codon deletion in the LacY permease, leading to impaired {beta}-galactoside metabolism and attenuation of development of critical intracellular bacterial communities (IBCs) in which UPEC replicates to high numbers, and then disseminates during urinary tract infection. Further, we show that expression of a functional lacY permease gene is sufficient to rescue defects in IBC size and number in 5.3r. In addition, we demonstrate that UPEC are able to utilize the disaccharide galactose {beta}-1,4 N-acetylglucosamine (LacNAc) - which appears as the terminal glycan in a subset of the glycoproteins that decorate the apical surface of bladder epithelial cells - as a sole carbon source in a lac system dependent manner. These data suggest that the lac operon is important to the growth and development of intracellular E. coli through metabolism of host bladder cell glycans.

microbiology↗

bioRxiv2025

NSD1 governs H3K36me2-mediated DNA methylation and drives differentiation of human iPSCs by regulating HIDEN lncRNA expression

Epigenetic regulatory mechanisms, which include histone modifications and DNA methylation, play a central role in development and aging. Dimethylation of H3K36, deposited mainly by the histone methyltransferase NSD1, occurs predominantly in intergenic regions and recruits the DNA methyltransferase DNMT3A to facilitate DNA methylation. Haploinsufficiency of NSD1 results in the overgrowth disorder Sotos syndrome in vivo, which is associated with aberrant DNA methylation signatures and an enhanced epigenetic age. To understand the mechanisms by which NSD1 may regulate development, differentiation and diseases, we generated human iPSC lines deficient in functional NSD1 (NSD1-KO). NSD1-KO cells exhibit a substrate-specific decrease in proliferation, reduced H3K36me2 levels and extensive DNA hypomethylation. Notably, the loss of functional NSD1 altered the differentiation potential of iPSCs, with aberrant endodermal and mesodermal lineage commitment. Further analysis revealed that NSD1 might drive endodermal differentiation by regulating the expression of an endodermal lncRNA HIDEN by mechanisms independent of the regulation of DNA methylation. Our NSD1-KO iPSC lines partially recapitulate the DNA methylation defects associated with NSD1-related disorders. Additionally, we uncovered a novel mechanism by which NSD1 may regulate endodermal differentiation of human iPSCs.

cell biology↗

bioRxiv2025

Protamine expression in somatic cells condenses chromatin and disrupts transcription without altering DNA methylation

Protamines play a crucial role in nuclear condensation during spermiogenesis, a process that involves significant chromatin remodeling and the replacement of histones. While much research has focused on the function of protamines in sperm development and fertility, their effects in non-sperm cells remain largely unexplored. In this study, we investigated the impact of overexpressing murine and human protamine 1 and 2 (PRM1 and PRM2) on nuclear architecture, histone eviction, DNA methylation, and transcription in HEK293T cells and mesenchymal stromal cells (MSCs). Overexpression of protamines resulted in nuclear condensation; particularly PRM1 showed notable enrichment in nucleoli, and cells exhibited cell cycle abnormalities. Immunofluorescence staining indicated a significant reduction in specific histone modifications (H3K9me3, H3K4me1, and H3K27Ac) in response to protamine expression, especially in MSCs. Interestingly, despite these changes in nuclear organization, the methylome remained largely stable. However, expression of protamines significantly diminished transcription, particularly of the ribosomal genes, upon PRM1 expression. Our studies indicate that PRM1 and PRM2 condense distinct genomic regions in somatic cells, resulting in widespread silencing of gene expression.

cell biology↗

bioRxiv2023

Escherichia coli sister cells dynamically organize developmental rosettes

Rosettes are self-organizing, circular multicellular communities that initiate developmental processes, like organogenesis and embryogenesis, in complex organisms. Their formation results from the active repositioning of adhered sister cells and is thought to distinguish multicellular organisms form unicellular ones. Though common in eukaryotes, this multicellular behavior has not been reported in bacteria. In this study, we discovered that Escherichia coli forms rosettes by active sister cell repositioning. After division, sister cells "fold" to actively align at the 2- and 4-cell stages of clonal division, thereby producing rosettes with characteristic quatrefoil configuration. Analysis revealed folding follows an angular random walk, comprised of [~]1-{micro}m strokes and directional randomization. We further showed that this motion was produced by the flagellum, the extracellular tail whose rotation generates swimming motility. Rosette formation was found to require de novo flagella synthesis suggesting it must balance the opposing forces of Ag43 adhesion and flagellar propulsion. We went on to show that proper rosette formation was developmentally required for subsequent morphogenesis of multicellular chains, rpoS expression, and formation of hydrostatic clonal-chain biofilms. Moreover, we discovered self-folding rosette-like communities in the standard motility assay, indicating this behavior may be general to hydrostatic environments. This study establishes that self-organization of developmental rosettes is a cross-kingdom multicellular behavior. Our findings indicate the potential of targeting bacterial rosettes to interrupt biofilms or reduce their antibiotic tolerance.

systems biology↗

bioRxiv2023

Poor biosafety and biosecurity practices and haphazard antibiotics usage in poultry farms in Nepal hindering antimicrobial stewardship

Poultry industry in Nepal has experienced remarkable growth in the last decade, but farm biosafety and biosecurity measures are often overlooked by farmers due to lack of knowledge or to save cost. As a result, farms often suffer from sporadic and regular outbreaks of many zoonotic diseases such as highly pathogenic avian influenza (HPAI), impacting production and creating public health challenges. Poor farm management practices, including overuse of antibiotics for prophylaxis and therapeutics, can complicate the spread of poultry diseases by creating and enhancing antimicrobial resistance (AMR) that is threating to both, poultry, and human health. We assessed biosafety, biosecurity risks and AMR stewardship in sixteen poultry farms located in four districts (Ramechhap, Nuwakot, Sindhupalchowk, and Kavre) surrounding densely populated Kathmandu valley. Risk assessment and AMR stewardship evaluation questionnaire were administered to formulate biosafety and biosecurity compliance matrix (BBCM). Risk assessment checklist assessed facility operations, personnel and standard operating procedures, water supply, cleaning and maintenance, rodent/pest control and farm record keeping. Oral and cloacal samples from the poultry were collected, pooled, and screened for eight poultry pathogens using Polymerase Chain Reaction (PCR) tests. Based on BBCM, we identified one of the farms in Sindhupalchowk (Farm 4) having the most (BBCM score= 67%) and a farm in Kavre (Farm 3) to having the least (BBCM score= 12%) biosafety and biosecurity compliance. Although most of the farms (61.6%) followed general poultry farming practices, only half had clean and well-maintained farms. Personal safety standard procedure compliance (BBCM score = 42.4%) and rodent control (BBCM score = 3.1%) were the biggest gaps. At least one of either bacterial or viral pathogen was detected in all farms. Mycoplasma gallisepticum was the most common disease detected in all but one farm, followed by Mycoplasma synoviae. Although more than half of the farmers considered AMR a threat, over 26% of them used antibiotics as a preventive measure and 81% did not consider withdrawal period for antibiotics prior to processing of their meat products. Additionally, antibiotics classified as Watch and Restrict by the WHO were frequently used by the farmers to treat bacterial infections in their farms. Lack of awareness and inadequate enforcement of regulations have exacerbated the risk of disease transmission in farms and compromised antimicrobial stewardship.

microbiology↗

bioRxiv2022

Musleblind-1 regulates microtubule cytoskeleton in C. elegans mechanosensory neuron through tubulin mRNAs

Regulation of microtubule cytoskeleton is fundamental for the development and maintenance of neuronal architecture. Recent studies have shown that regulated RNA processing is also critical for the establishment and maintenance of neural circuits. In a genetic screen using mechanosensory neurons of C. elegans, we identified a mutation in muscleblind-1 as a suppressor of loss of kinesin-13 family microtubule destabilizing factor klp-7. Muscleblind-1(MBL-1) is an RNA-binding protein that regulates the splicing, localization, and stability of RNA. We found that mbl-1 is required cell-autonomously for axon growth and synapse formation in the posterior lateral microtubule (PLM) neuron. Loss of mbl-1 affects stability and plus-end-out organization of microtubules in the anterior process of PLM. These defects are also accompanied by abnormal axonal transport of the synaptic protein RAB-3 and loss of gentle touch sensation in mbl-1 mutant. Our data showed that mbl-1 is genetically epistatic to mec-7 ({beta} tubulin) and mec-12 (a tubulin) for axon growth. The immunoprecipitation of MBL-1 pulls down the mec-7, mec-12, and sad-1 mRNAs. Additionally, the mbl-1 mutants show a reduction in the level and stability of mec-7 and mec-12 transcripts. Independently, mbl-1 is epistatic to sad-1 for synapse formation. Our work elucidated a previously unknown link between RNA binding protein and cytoskeletal machinery for the development and maintenance of the nervous system.

neuroscience↗

bioRxiv2022

Screening Avian Pathogens in Eggs from Commercial Hatcheries in Nepal- an Effective Poultry Disease Surveillance Tool

BackgroundCommercial hatcheries play an important role in the overall poultry value chain-providing small to large poultry farmers with day old chicks. Any outbreak in such hatcheries can spread diseases to other farms. Regular screening of major avian pathogens, along with strict bio-security measures, can prevent spread of diseases in hatcheries. Newcastle Disease Virus (NDV), Infectious Bronchitis Virus (IBV), Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), Infectious Bursal Disease Virus (IBDV) and Influenza A Virus (IAV) are among the most prevalent poultry diseases which can be detected in egg albumin. MethodWe retrospectively (August 2020-August 2021, except October 2020) analyzed diagnostic results for six selected avian pathogens (NDV, IBV, MS, MG, IBDV and IAV) on eggs (n=4343) received from eleven major commercial poultry hatcheries located in the five adjoining districts of Kathmandu, Nepal. Albumin from 10% randomly selected eggs from each hatchery were tested for the six avian pathogens using multiplex PCR. ResultMajority (7/11, 64%) of the poultry hatcheries had at least one of the six pathogens present. We detected at least one avian pathogen in nine out of eleven months (82%) of screening. Except for IBDV, we found one or more of the other major avian pathogens-Influenza A (IAV) (n=4 times) and Mycoplasma gallisepticum (MG) (n=4 times) were detected the most, followed by Newcastle Virus (NDV) (n=3 times). Infectious bronchitis virus (IBV) were detected twice, and Mycoplasma synoviae (MS) was detected once. ConclusionIn a resource strapped country like Nepal, poultry disease outbreak investigation in particular and surveillance in general are challenging. Meanwhile, poultry production is highly impacted by disease outbreaks often triggered by poor bio-security and lack of pathogen screening practices. Our molecular screening tests have picked up major poultry pathogens present throughout the year in eggs collected from hatcheries. Influenza A was detected at 4 different incidences throughout the year, which is of concern to both human and animal health. Quick systematic screening of eggs at key distribution points (hatcheries) for major avian pathogens is an effective surveillance tool for early disease detection and containment of outbreaks.

microbiology↗

bioRxiv2022

Autophagy-cell death balance is maintained by Polycomb-mediated regulation during stem cell differentiation

Autophagy is a conserved cytoprotective process, aberrations in which, lead to numerous degenerative disorders. While the cytoplasmic components of autophagy have been extensively studied, the epigenetic regulation of autophagy genes, especially in stem cells, is less understood. Deciphering the epigenetic regulation of autophagy genes becomes increasingly relevant given the therapeutic benefits of small-molecule epigenetic inhibitors in novel treatment modalities. We observe that, during retinoic acid-mediated differentiation of mouse embryonic stem cells (mESCs), autophagy is induced, and identify the Polycomb enzyme EZH2 as a regulator of this process. In mESCs, EZH2 represses several autophagy genes including the autophagy regulator Dram1. EZH2 facilitates the formation of a bivalent chromatin domain at the Dram1 promoter, which allows the expression of the gene and induction of autophagy during differentiation, while still retaining the repressive H3K27me3 mark. EZH2 inhibition leads to loss of the bivalent domain, and a consequential "hyper- expression" of Dram1, with extensive cell death. This study shows that Polycomb group proteins help maintain an autophagy-cell death balance during stem cell differentiation, in part, by regulating the expression of the Dram1 gene.

cell biology↗

bioRxiv2021

Foxd3 controls heterochromatin-mediated silencing of repeat elements in mouse embryonic stem cells and represses the 2-cell transcription program

Repeat element transcription plays a vital role in early embryonic development. Expression of repeats such as MERVL characterises mouse embryos at the 2-cell stage, and defines a 2-cell-like cell (2CLC) population in a mouse embryonic stem cell culture. Repeat element sequences contain binding sites for numerous transcription factors. We identify the forkhead domain transcription factor FOXD3 as a regulator of repeat element transcription in mouse embryonic stem cells. FOXD3 binds to and recruits the histone methyltransferase SUV39H1 to MERVL and major satellite repeats, consequentially repressing the transcription of these repeats by the establishment of the H3K9me3 heterochromatin modification. Notably, depletion of FOXD3 leads to the de-repression of MERVL and major satellite repeats as well as a subset of genes expressed in the 2-cell state, shifting the balance between the stem cell and 2-cell like population in culture. Thus, FOXD3 acts as a negative regulator of repeat transcription, ascribing a novel function to this transcription factor.

developmental biology↗