Biology subjects

Tripathi, L.

Publications and source records attributed to Tripathi, L..

7 recordsLinked to original sources

bioRxiv2026

Comparative transcriptomic analysis of cassava genotypes under extended photoperiodism across flowering stages

Cassava (Manihot esculenta Crantz) is a major staple crop across tropical and subtropical regions. Despite advances in genomic selection, delayed, non-flowering, and asynchronous flowering remain key bottlenecks in breeding programs. To better understand the molecular basis of flowering-time variation, we performed RNA sequencing across three genotypes with contrasting flowering phenotypes (early, late, and non-flowering) sampled at three developmental stages under contrasting light regimes in field conditions (natural light and three-hour night-break with white light). Comparative transcriptomic analysis revealed distinct gene expression patterns associated with flowering responses. Genotype comparisons with no light supplementation revealed stage-specific enrichment of biological processes. Light supplementation was associated with changes in the expression of key components of photoperiodic and circadian regulation, as well as pathways involved in flowering-time integration and hormone and sugar-related signaling. These findings suggest that coordinated changes across multiple biological pathways regulate flowering behavior in cassava. The candidate genes and expression patterns reported provide a foundation for functional studies and advance our understanding of molecular mechanisms governing flowering-time regulation in cassava.

plant biology↗

bioRxiv2026

Uncovering phenotypic diversity and cell-type-specific prefrontal cortex calcium dynamics in rat fentanyl self-administration

BACKGROUNDThe proliferation of the potent synthetic opioid fentanyl has exacerbated the ongoing crisis of substance use disorder and associated overdose deaths, yet the neurobiological mechanisms that underlie individual vulnerability to addiction and relapse remain poorly understood, particularly in the context of fentanyl use. The prefrontal cortex (PFC) has been identified as a key brain structure important for cognitive functions impacted in addiction, including inhibitory control of behavior and association of drug experience with specific cues, contexts, or actions. Although the heterogenous neuronal composition of the PFC complicates attribution of addiction-related behavioral regulation to specific cortical cell types and circuits, application of cell-type-specific methods in translationally relevant rodent models have begun to elucidate the key neural substrates of opioid addiction. METHODSWe used an intermittent access fentanyl self-administration (IntA SA) model to characterize individual variation and sex differences in addiction vulnerability in male and female rats. Longitudinal wireless fiber photometry recording was used to track calcium activity patterns in intratelencephalic (IT) neurons of the prelimbic cortex across acquisition of self-administration, escalation of fentanyl intake, extinction training, and cue-induced reinstatement of fentanyl seeking. RESULTSWe found that our fentanyl IntA SA paradigm produces distinct low- and high-risk addiction severity phenotypes and that female rats exhibited a greater propensity for high-risk classification, which was characterized by abundant and consistent fentanyl intake, robust responsiveness to conditioned and discriminative fentanyl-associated cues, and high levels of fentanyl-seeking during periods of drug unavailability, extinction training, and a cue-induced reinstatement test. Fiber photometry recordings revealed dynamic encoding of fentanyl-associated stimuli by prelimbic IT neurons across the IntA SA paradigm with event-related calcium transients observed in association with lever presses, fentanyl infusions, and presentation of conditioned and discriminative cues. CONCLUSIONSOur data indicate that fentanyl IntA SA is a translationally relevant paradigm that enables investigation of phenotypic diversity and the role of sex in fentanyl addiction. Longitudinal cell-type-selective calcium recordings revealed dynamic representation of fentanyl-associated stimuli by IT neurons of the prelimbic cortex consistent with a role for this cortical subpopulation in addiction-related behaviors.

neuroscience↗

bioRxiv2026

Expanding the repertoire of suicidal germination stimulants for control of parasitic weeds

Witchweeds (Striga spp.) are parasitic plants that severely constrain cereal production across sub-Saharan Africa, threatening food security for millions of people (Runo and Kuria, 2018). Striga infection begins when dormant seeds germinate in response to host-derived biomolecules, primarily strigolactones which plants emit to regulate shoot branching and to communicate with beneficial microbes. This obligate dependence on host signals can be exploited for Striga control through suicidal germination, whereby strigolactone-like compounds induce parasite germination in the absence of a host. Although this strategy proved highly effective during Striga eradication efforts in the United States using ethylene gas as a Striga germination inducer (Eplee, 1975; Iverson et al., 2011), its deployment in Africa has been limited by capacity to synthesize cost-effective strigolactone-like Striga germination inducers. Here, we show that structure-guided in silico screening of chemical libraries using AlphaFold2-modeled receptor-ligand interactions improve the efficiency and likelihood of identifying previously unknown strigolactone analogs. Using this approach, we identify a structurally simple synthetic lactone scaffold that induces Striga germination at nanomolar concentrations. These results present new avenues for the development of strigolactone analogs and support revisiting suicidal germination as a practical Striga control strategy in Africa.

plant biology↗

bioRxiv2025

Overexpression of MusaVicilin Gene for Disease Resistance in Banana

Banana Xanthomonas wilt (BXW) disease, caused by Xanthomonas vasicola pv. musacearum, is a major constraint to banana production in East and Central Africa. All cultivated banana varieties are susceptible, with the wild progenitor Musa balbisiana being the only known source of complete resistance. Limitations in classical breeding have prompted the exploration of molecular genetic tools, such as genetic modification, to develop resistant cultivars. Comparative transcriptomic analyses revealed a five-fold upregulation of MusaVicilin gene in M. balbisiana (BB genome) compared to the BXW- susceptible Pisang Awak when challenged with the pathogen, suggesting its role in defense. This study investigated whether constitutive overexpression of the MusaVicilin gene cloned from M. balbisiana could enhance resistance to BXW in the susceptible Sukali Ndiizi cultivar (AAB genome). Transgenic events were developed with the MusaVicilin gene under the control of the constitutive CaMV 35S promoter. These events exhibited enhanced disease resistance compared with non-transgenic control plants. The overexpression of MusaVicilin highlights its potential as a candidate gene for engineering resistance to BXW in susceptible cultivars. Moreover, MusaVicilin could serve as a valuable component in gene stacking strategies aimed at developing durable, disease-resistant banana varieties.

synthetic biology↗

bioRxiv2023

Transgenic expression of Arabidopsis ELONGATION FACTOR-TU RECEPTOR (AtEFR) gene in banana enhances resistance to Banana Xanthomonas Wilt disease

Banana Xanthomonas wilt (BXW) caused by Xanthomonas campestris pv. musacearum (Xcm) is a severe bacterial disease devastating banana production in East and Central Africa, where banana is cultivated as a staple crop. Classical breeding of banana is challenging because the crop is clonally propagated and has limited genetic diversity. Thus, genetic engineering serves as a viable alternative for banana improvement. Several studies have shown that interfamily transfer of the elongation factor Tu receptor gene (AtEFR) from Arabidopsis thaliana to other plant families can increase broad-spectrum resistance against bacterial diseases. In this study, transgenic events of banana cultivar dwarf Cavendish expressing the AtEFR gene were generated and evaluated for resistance against Xcm under greenhouse conditions. The transgenic banana events were responsive to the EF-Tu-derived elf18 peptide and exhibited enhanced resistance to BXW disease compared to non-transgenic control plants. This study suggests that the functionality of AtEFR is retained in banana with the potential of enhancing resistance to BXW disease under field conditions.

plant biology↗

bioRxiv2020

Network Modeling and Inference of Peroxisome Proliferator-Activated Receptor Pathway in High fat diet-linked Obesity

Systems biology aims to understand how holistic systems theory can be used to explain the observable living system characteristics, and mathematical modeling tools have been successful in understanding the intricate relationships underlying cellular functions. Lately, researchers have been interested in understanding molecular mechanisms underlying obesity, which is a major health concern worldwide and has been linked to several diseases. Various mechanisms such as peroxisome proliferator-activated receptors (PPARs) are known to modulate obesity-induced inflammation and its consequences. In this study, we have modeled the PPAR pathway using a Bayesian model and inferred the sub-pathways that are potentially responsible for the activation of the output processes that are associated with high fat diet (HFD)-induced obesity. We examined a previously published dataset from a study that compared gene expression profiles of 40 mice maintained on HFD against 40 mice fed with chow diet (CD). Our simulations have highlighted that GPCR and FATCD36 sub-pathways were aberrantly active in HFD mice and are therefore favorable targets for anti-obesity strategies. We further cross-validated our observations with experimental results from the literature. We believe that mathematical models such as those presented in the present study can help in inferring other pathways and deducing significant biological relationships.

bioinformatics↗

bioRxiv2020

Genome sequence of the banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and its symbionts

The banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervos a we developed a k-mer based deduplication pipeline to remove genomic scaffolds derived from the assembly of haplotigs (allelic variants assembled as separate scaffolds). To demonstrate the usefulness of this pipeline, we applied it to the recently generated assembly of the aphid Myzus cerasi, reducing the duplication of conserved BUSCO genes by 25%. Phylogenomic analysis of P. nigronervos a, our improved M. cerasi assembly, and seven previously published aphid genomes, spanning three aphid tribes and two subfamilies, reveals that P. nigronervos a falls within the tribe Macrosiphini, but is an outgroup to other Macrosiphini sequenced so far. As such, the genomic resources reported here will be useful for understanding both the evolution of Macrosphini and for the study of P. nigronervosa. Furthermore, our approach using low cost, high-quality, Illumina short-reads to generate complete genome assemblies of understudied aphid species will help to fill in genomic black spots in the diverse aphid tree of life.

genomics↗