Biology subjects

Midha, T.

Publications and source records attributed to Midha, T..

2 recordsLinked to original sources

bioRxiv2026

Genomic characterization and therapeutic potential of five broad-spectrum lytic bacteriophages against multidrug-resistant avian pathogenic Escherichia coli (APEC)

Colibacillosis, caused by Avian Pathogenic Escherichia coli (APEC), result in substantial economic losses in global poultry production. The emergence of multidrug-resistant (MDR) APEC poses zoonotic risks through horizontal transfer of antimicrobial resistance (AMR) genes. Bacteriophage therapy emerges as a safe alternative to antibiotherapy; however, comprehensive characterization of phages targeting MDR-APEC from diverse geographical regions remains limited. We isolated five lytic bacteriophages from poultry fecal samples collected from five Indian states and characterized them through morphological analysis, physiological stability testing, whole-genome sequencing, and in vivo efficacy assessment. Host range was determined against APEC isolates, and therapeutic potential was validated in Galleria mellonella infection model. All five phages showed Myovirus-like morphology and stability across physiologically relevant temperatures (up to 55-70{degrees}C) and pH conditions (3-11). Their genome size ranges from 170 to 356 kb, belonging to three distinct genera; Dhakavirus, Gaprivervirus, and Asteriusvirus. Genomic analysis confirmed absence of antimicrobial resistance, virulence, toxin, or lysogeny genes. 51 APEC strains were isolated, of which 23 (45.1%) were MDR. Individual phages lysed 37-51% of tested APEC and 17-39% of MDR strains. Three Escherichia phages (fBSZT1, fUAMT1, fPKPT2) significantly improved larval survival to 60-80% at MOI 10 in G. mellonella infection models compared to untreated controls. This study establishes a well-characterized phage bank targeting MDR-APEC strains, providing foundation for developing phage-based interventions to reduce antibiotic dependency and mitigate AMR transmission risks under One Health framework.

microbiology↗

bioRxiv2025

Kinetic mechanisms for the sequence dependence of transcriptional errors

The fidelity of template-dependent mRNA synthesis during transcription elongation is the primary determinant of accurate gene expression and the maintenance of functional RNA transcripts. However, the mechanisms governing transcription fidelity remain incompletely understood. While previous studies have characterized how error rates vary with nucleotide identity at upstream and downstream positions from the incorporation site, the comprehensive microscopic explanation of this sequence dependence has not been elucidated. In this study, we develop a novel theoretical approach that integrates transcription proofreading mechanisms and inhomogenous DNA sequence effects. Using first-passage analysis validated by Monte Carlo simulations, we quantitatively characterize nucleotide-specific error rates during RNA polymerase II transcription. The model accurately reproduces experimental error rates and predicts kinetic parameters influencing transcriptional fidelity. Analysis reveals nucleotide incorporation rates follow the hierarchy U<C<G<A, consistent with independent experimental observations. Notably, our model not only explains how the error rates depend on the nature of the base immediately down-stream (+1) but also predicts that the identity of the nucleotide at the second downstream position (+2) also plays an important role. Pyrimidines at position +2 contribute to lower error rates than purines, whereas the third downstream base (+3) has no effect. These previously unreported correlations are corroborated by bioinformatic analysis of existing datasets. In addition, using the BRCA1 gene as an example, we explore the physiological implications of sequence-dependent error rates, identifying an increased likelihood of premature stop codon errors. These findings clarify how DNA sequence context modulates nucleotide incorporation kinetics, advancing our understanding of transcriptional fidelity and its functional consequences.

biophysics↗