Biology subjects

Koirala, D.

Publications and source records attributed to Koirala, D..

4 recordsLinked to original sources

bioRxiv2026

Management of Root-Knot Nematode-Fusarium Wilt Complex with different Bio-management methods in Tomato (Solanum lycopersicum L.) var Srijana

The root-knot nematode-Fusarium complex is a major constraint to protected tomato cultivation in Nepal, particularly on the widely grown Srijana hybrid, which lacks Mi-mediated nematode resistance. The present study was conducted to identify the most effective biocontrol agent, to identify the most effective Solanum rootstock, and to compare the overall efficacy of grafting versus biocontrol agents under polyhouse conditions. For the management of the root knot nematode-Fusarium complex, a pot experiment was set up in a completely randomized design at Pokhara, Kaski. Treatments comprised Trichoderma viride, Pseudomonas fluorescens, their half-dose combination, self-grafted Srijana, and four resistant rootstocks (S. sisymbriifolium, S. melongena, S. torvum, and VNRRs-10), together with nematode-only, Fusarium-only, complex (Nematode + Fusarium), and disease-free controls. Each plant was inoculated with approximately 2,000 nematode eggs, followed by 25 ml of 10^6 spores per ml of Fusarium seven days later to mimic the field complex. Plant growth parameters and nematode infestation data were recorded and analyzed via RStudio v. 2026.04.0. The root knot nematode-Fusarium complex caused significantly greater reductions in vegetative biomass than root knot nematode and Fusarium alone (20.32 gm vs 38.40 gm vs 51.32 gm) at 45 DAT. Single-agent biocontrol gave intermediate protection (T. viride 64.9%; P. fluorescens 47.9% nematode management efficiency), whereas combined T. viride + P. fluorescens treatment produced the highest vegetative biomass but the weakest nematode suppression (320 galls, reproduction factor: 38). Grafting onto S. torvum and S. melongena resulted in the greatest nematode suppression, achieving 97.9% and 93.6% management efficiency, respectively, while S. torvum alongside VNRRs-10 maintained the highest Fusarium suppression (92.5%). Overall resistant rootstocks consistently outperformed biological control in reducing disease severity. These findings indicate that grafting onto resistant solanum rootstocks, particularly S. torvum and S. melongena, was observed as the most effective strategy for managing the root knot nematode-Fusarium complex under protected cultivation, offering a viable chemical-free management option. Keywords: Root-Knot Nematode, Fusarium oxysporum, RKN-Fusarium-complex, Solanum torvum

pathology↗

bioRxiv2025

Template-based RNA structure prediction advanced through a blind code competition

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previously unreleased structures to tackle this challenge. The top three submitted algorithms achieved scores within statistical error of the winners of the recent CASP16 competition. Unexpectedly, the top Kaggle strategy involved a pipeline for discovering 3D templates, without the use of deep learning. We integrated this template-modeling pipeline and other Kaggle strategies to develop a single model RNAPro that retrospectively outperformed individual Kaggle models on the same test set. These results suggest a growing importance of template-based modeling in RNA structure prediction.

biophysics↗

bioRxiv2025

Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers

Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular. Here, we report quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs, however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, e.g., the nucleic-acid backbone bends or a base forms a non-standard hydrogen bond. These bends and non-canonical interactions are integral to form functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life-cycle, posing a future challenge for the community.

biophysics↗

bioRxiv2025

Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA

The Rev Response Element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 infection. However, our structural understanding of this crucial virological process remains limited. In this study, we determined several crystal structures of an intact RRE stem-loop II in two distinct conformations, performed negative-staining electron microscopy and molecular dynamics simulations, and revealed that this three-way junction RNA exhibits remarkable structural plasticity. Through in vitro Rev-binding and in vivo Rev-activity assays using various stem-loop II mutants designed to favor one of the conformers, we demonstrated that the structural plasticity of stem-loop II modulates Rev binding and oligomerization. Our findings illuminate emerging perspectives on RRE dynamics-based regulation of HIV-1 RNA nuclear export and provide a framework for developing anti-HIV drugs that target specific RRE conformations.

biophysics↗