Biology subjects

Gurung, A.

Publications and source records attributed to Gurung, A..

6 recordsLinked to original sources

bioRxiv2026

Metabarcode and transcriptome datasets of Pinus sylvestris to assess fungal phyllosphere and disease dynamics.

Understanding how host-microbiome interactions influence tree disease is critical for understanding forest resilience. Here, we present foliar microbiome ITS2 metabarcoding transcriptomic datasets from Pinus sylvestris to investigate susceptibility to Dothistroma needle blight (DNB), a globally important foliar disease caused by Dothistroma septosporum. We hypothesised that host genotype shapes foliar microbial communities and their interactions, thereby influencing disease outcomes. Samples were collected from a progeny-provenance field trial in the south of Scotland representing a broad spectrum of disease susceptibilities. The dataset comprises ITS2 metabarcoding samples from 200 genotypes across three timepoints and RNAseq samples from 48 genotypes across two timepoints. Sampling captured key stages of pathogen exposure and disease progression. Both standardised and bespoke protocols were used for nucleotide extraction, sequencing, and quality control, including multiple negative and positive controls. These datasets, available in the European Nucleotide Archive (project accession PRJEB88228), enable analysis of temporal dynamics in foliar fungal communities, host-microbiome transcriptional responses, and genotype-dependent variation in disease susceptibility.

bioinformatics↗

bioRxiv2026

A decade of disease survey data in a progeny-provenance trial: Dothistroma needle blight in Scots pine

Longitudinal data on disease susceptibility in forest trees are rare but essential for understanding host-pathogen dynamics and genetic variation in susceptibility traits. We present a long-term multisite common garden dataset quantifying susceptibility of Scots pine (Pinus sylvestris) to Dothistroma needle blight. The dataset comprises annual disease assessments collected from the same trees across 11 years, spanning 168 families and 21 Scottish provenances. This design enables partitioning of genetic and environmental sources of variation, evaluation of temporal stability in host response, and estimation of variance components and narrow-sense heritability of susceptibility. The data support analyses of phenotypic plasticity, provenance-level responses, and interactions between disease susceptibility and other adaptive traits. This resource will facilitate predictive modelling of host susceptibility under current and future environmental conditions.

ecology↗

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↗

bioRxiv2024

Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts

Single-cell RNA sequencing is revolutionizing our understanding of cell state dynamics, allowing researchers to observe the progression of individual cells transcriptomic profiles over time. Among the computational techniques used to predict future cellular states, RNA velocity has emerged as a predominant tool for modeling transcriptional dynamics. RNA velocity leverages the mRNA maturation process to generate velocity vectors that predict the likely future state of a cell, offering insights into cellular differentiation, aging, and disease progression. Although this technique has shown promise across biological fields, the performance accuracy varies depending on the RNA velocity method and dataset. We established a comparative pipeline and analyzed the performance of five RNA velocity methods on three datasets based on local consistency, method agreement, identification of driver genes, and robustness to sequencing depth. This benchmark provides a resource for scientists to understand the strengths and limitations of different RNA velocity methods.

bioinformatics↗

bioRxiv2023

One Health Assessment of an Urban Temporary Settlement Reveals Gut Microbiome Serving as Antimicrobial Resistance Gene Reservoir

Antimicrobial resistance (AMR) is an emerging and growing global health challenge that could result in 10.2 million deaths annually by 2050. The unrestricted and haphazard use of antibiotics is contributing to the rapid emergence and spread of AMR, and the problem is exacerbated by release of untreated waste water from high-risk sources like hospitals into rivers. Bacteria often develop resistance through horizontal gene transfer mechanism and gut flora can act as a source for new Antimicrobial Resistance Genes (ARG). Upcoming methods like metagenomics can identify the resistance profile (AMR) of gut microbiome, and detect bacterial infections that otherwise go unnoticed. Our study focused on understanding the presence of AMR mutations and gene transfer dynamics in human, animal and environmental samples collected in one of the temporary settlements of Kathmandu (Nepal) using One Health approach. Current AMR reporting based on clinical cases is limited and does not provide information on specific pathogen and associated AMR genes-our study is an effort to contribute information to fulfill this gap. Twenty-one samples were collected from a temporary settlement in Thapathali (Kathmandu), which included fecal samples from birds (n=3) and humans (n=14), and environmental samples (n=4). Microbiological assessment was carried out based on 16S sequence metagenomic analysis using MiSeq (Illumina, USA). Taxonomic classification on obtained 16S sequences were determined by using Metaphlan 2 and Qiime 2 bioinformatics tools. ShortBRED was used to classify ARG and virulence factors, and WAFFLE was used for horizontal gene transfer event prediction. The network analysis was carried out using Gephi v0.9 and the ResistoXplorer web tool to identify ARG in the collected samples. Prevotella spp. was the dominant gut microbiome in humans. We detected diverse phages and viruses, including Stx-2 converting phages. 72 virulence factors and 53 ARG subtypes were detected, with poultry samples having the highest number of subtypes. The cluster and network analysis showed a strong association between gut microbiome and ARG, which was also supported by Horizontal Gene Transfer (HGT) analysis. One-Health interface showed ARG dynamics and revealed gut microbiomes of humans and animals serving as a reservoir for the circulating ARG.

genomics↗

bioRxiv2022

Cell-Type-Specific Epigenetic Priming of Gene Expression in Nucleus Accumbens by Cocaine

A hallmark of addiction is the ability of drugs of abuse to trigger relapse after periods of prolonged abstinence. Here, we describe a novel epigenetic mechanism whereby chronic cocaine exposure causes lasting chromatin and downstream transcriptional modifications in the nucleus accumbens (NAc), a critical brain region controlling motivation. We link prolonged withdrawal from cocaine to the depletion of the histone variant H2A.Z, coupled to increased genome accessibility and latent priming of gene transcription, in D1 dopamine receptor-expressing medium spiny neurons (D1 MSNs) that relates to aberrant gene expression upon drug relapse. The histone chaperone ANP32E removes H2A.Z from chromatin, and we demonstrate that D1 MSN-selective Anp32e knockdown prevents cocaine-induced H2A.Z depletion and blocks cocaines rewarding actions. By contrast, very different effects of cocaine exposure, withdrawal, and relapse were found for D2-MSNs. These findings establish histone variant exchange as an important mechanism and clinical target engaged by drugs of abuse to corrupt brain function and behavior.

molecular biology↗