Biology subjects

Pradhan, S. K.

Publications and source records attributed to Pradhan, S. K..

3 recordsLinked to original sources

bioRxiv2026

Asymmetric biparental but inefficient horizontal transmission of paralysis-causing sigmavirus in Queensland fruit fly

Insects are associated with diverse RNA viruses, including vertically transmitted viruses that form persistent infections without apparent symptoms. One of the first documented vertically transmitted viruses is sigmavirus (Rhabdoviridae) affecting fitness of Drosophila. Sigmaviruses and related rhabdoviruses have also been detected in pest fruit flies and other arthropods. However, their prevalence, transmission, tissue localisation and fitness effects remain poorly known, despite their potentially common infections in diverse hosts. We investigated Sigmavirus tryoni (BtSV) prevalence, load, transmission across multiple generations and host effects in Queensland fruit fly (Bactrocera tryoni), Australias most significant horticultural pest, which carries BtSV at low prevalence (13.7%) across field populations. We detected BtSV in 6 of 12 laboratory populations (prevalence 12.5% to 80.4%) where it was transmitted biparentally within embryos. Although incomplete, maternal transmission was more reliable and resulted in higher BtSV load than paternal transmission. Paternally transmitted BtSV was almost entirely lost after two generations. BtSV became detectable in most uninfected individuals cohabiting with infected flies, but this resulted in a low load that was subsequently transmitted to only few offspring. BtSV occurred across developmental stages, digestive and reproductive tissues, albeit its viral load was lower in reproductive tissues when received paternally than maternally, and lower in testes than ovaries. Furthermore, BtSV-infected individuals suffered paralysis and mortality when exposed to high CO2 concentrations, a Rhabdoviridae effect previously reported for several Drosophila species, a muscid fly and mosquitoes. Our study suggests that sigmavirus transmission dynamics and fitness effects may apply broadly to arthropod hosts and affect their management.

evolutionary biology↗

bioRxiv2025

Future flooding tolerant rice germplasm: resilience afforded beyond Sub1A gene

Developing high-yielding, flood-tolerant rice varieties is essential for enhancing productivity and livelihoods in flood-prone ecologies. We explored genetic avenues beyond the well-known SUB1A gene to improve flood resilience in rice. We screened a collection of 6,274 elite genotypes from IRRIs germplasm repository for submergence and stagnant flooding tolerance over multiple seasons and years. This rigorous screening identified 89 outstanding elite genotypes, among which thirty-seven exhibited high submergence tolerance, surpassing the survival rate of SUB1A introgression genotypes by 40-50%. Thirty-five genotypes showed significant tolerance to stagnant flooding, and 17 demonstrated dual tolerance capabilities, highlighting their adaptability to varying flood conditions. The genotypes identified have a broader genetic diversity and harbor 86 key QTLs and genes related to traits such as grain quality, grain yield, herbicide resistance, and various biotic and abiotic traits, highlighting the richness of the identified elite collection. Besides germplasm, we introduce an innovative breeding approach called Transition from Trait to Environment (TTE). TTE leverages a parental pool of high-performing genotypes with complete submergence tolerance to drive population improvement and enable genomic selection in the flood breeding program. Our approach of TTE achieved a remarkable 65% increase in genetic gain for submergence tolerance, with the resulting fixed breeding genotypes demonstrating exceptional performance in flood-prone environments of India and Bangladesh. The elite genotypes identified herein represent invaluable genetic resources for the global rice research community. By adopting the TTE approach, which is trait agonistic, we establish a robust framework for developing more resilient genotypes using advanced breeding tools. Plain Language SummaryTo address climate challenges, an urgent focus is necessary to identify and develop flood-tolerant rice varieties, particularly for flood-prone ecosystems across Asia and Africa. We screened 6,274 elite genotypes from IRRIs germplasm and identified 89 promising lines with improved tolerance to submergence and stagnant flooding. Among these, 37 demonstrated 40-50% greater submergence tolerance than SUB1A introgression lines, 35 exhibited stagnant flooding tolerance, and 17 showed dual tolerance. These genotypes contain 86 key QTLs and genes associated with yield, grain quality, and biotic and abiotic tolerance traits. A new breeding strategy, the Transition from Trait to Environment (TTE) approach, was developed. We achieved a genetic gain of 65% for submergence tolerance in rice using this method. The newly identified germplasm provides invaluable genetic resources for the global rice research community to develop flood-tolerant rice genotypes. Core ideas The SUB1A gene, enabling rice to survive underwater for 14 days, marked a significant breakthrough. We have identified elite genotypes with submergence tolerance significantly surpassing the SUB1A gene-mediated tolerance. The diverse elite genotypes identified harbor 86 key genes and QTLs that affect various traits positively. Developed a unique breeding strategy for implementing population improvement in challenging environments. The new breeding strategy demonstrated a genetic gain of 65% for submergence tolerance.

plant biology↗

bioRxiv2025

Super-resolution compatible DNA labeling technique reveals chromatin mobility and organization changes during differentiation

Chromatin dynamics play a crucial role in cellular differentiation, yet tools for studying global chromatin mobility in living cells remain limited. Here, we developed a novel probe for the metabolic labeling of chromatin and tracking its mobility during neural differentiation. The labeling system utilizes a newly developed silicon rhodamine-conjugated deoxycytidine triphosphate (dCSiRTP). We show that this dCTP is efficiently delivered into living human induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) via a synthetic transporter (SNTT1). Using correlative confocal microscopy and stimulated emission depletion (STED) super-resolution microscopy, we quantified the sizes of labeled chromatin domains. Time lapse super-resolution microscopy combined with single particle tracking revealed that chromatin mobility decreases during the transition from iPSCs (pluripotent state) to NSCs and neurons (differentiated state). This reduction in mobility correlates with the differentiation state, suggesting a role for chromatin dynamics in cellular plasticity. Concomitant mechanistic insights obtained from MNase digestion assays, chromatin compaction and histone modification analyses revealed a decrease in chromatin accessibility during neuronal differentiation, indicating that chromatin adopts a more constrained and compacted structure. These findings provide new insights into chromatin regulation during neurogenesis.

cell biology↗