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Neupane, R.

Publications and source records attributed to Neupane, R..

8 recordsLinked to original sources
bioRxiv2026

Structural basis for emetine inhibition of ribosome translocation in Toxoplasma gondii

Apicomplexan parasites, including Toxoplasma gondii and Plasmodium falciparum, are major human pathogens that cause toxoplasmosis and malaria, respectively. The existing structures of T. gondii translational machinery are from empty ribosomes that lack several key components, including ribosomal protein RACK1 (Receptor for Activated C Kinase 1). Here, we used cryo-electron microscopy (cryoEM) to determine high-resolution structures of T. gondii ribosomal complexes, including a translating 80S ribosome bound to mRNA and tRNA. These structures reveal that RACK1 occupies the conserved binding site on the 40S subunit observed in other eukaryotic ribosomes. We also determined the architecture of the ribosomal P-stalk and identified the ribosomal proteins uL10 and uL11, which were not observed in previous T. gondii ribosome structures. In addition, we determined structures of the 80S ribosome bound to mRNA, tRNA, and the translation inhibitor emetine in two distinct conformational states. These snapshots reveal two mechanisms by which emetine inhibits the translocation step of mRNA translation: either by dislodging the mRNA from the E-site of the ribosome or by acting as a molecular glue within the E-site, thereby stalling translocation. Together, these findings provide new insights into the molecular basis of protein synthesis in apicomplexan parasites and establish a structural framework for the development of future antiparasitic therapeutics. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/740346v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@18b69d5org.highwire.dtl.DTLVardef@1d125e5org.highwire.dtl.DTLVardef@efc11org.highwire.dtl.DTLVardef@1c6d088_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗
bioRxiv2026

Drought escape as an adaptive strategy across an aridity gradient in wild sunflower

PremiseDrought is intensifying in many regions under climate change, affecting plant growth, phenology, and resource allocation. Plants cope with water limitation through strategies such as escape, avoidance, and tolerance, but how these strategies are reflected in trait variation across natural drought gradients remains poorly understood. We examined how drought-related traits vary across a drought gradient in wild sunflower (Helianthus annuus L.). MethodsWe conducted a common-garden experiment using 19 wild sunflower populations collected across Southern California spanning a climatic moisture deficit gradient. We quantified growth, phenology, morphology, biomass allocation, and physiological traits and evaluated their relationships with climatic moisture deficit and soil variables using regression and correlation analyses. ResultsPopulations from drier environments exhibited coordinated shifts in life-history strategy, combining faster growth, earlier flowering, and increased reproductive output. These changes were coupled with reduced allocation to roots and structural tissues and diminished investment in traits that buffer plant water status, as reflected in declines in relative water content and higher (less negative) leaf water potentials. Ordinal modeling further indicated that populations from drier environments had a greater probability of severe wilting under drought stress. Together, these patterns are consistent with a drought escape strategy rather than drought avoidance or drought tolerance. ConclusionOur results suggest that increasing aridity can favor integrated drought escape strategies characterized by rapid growth and early reproduction. These coordinated shifts reveal trade-offs between fast life-history strategies and investment in traits associated with drought resistance, highlighting how environmental gradients shape adaptive trait syndromes in wild plant populations.

evolutionary biology↗
bioRxiv2025

STUDY OF STRUCTURAL, PHYSICOCHEMICAL, DRUG-LIKENESS PROPERTIES OF URACIL AND FLUOROURACIL

Withdrawal StatementThe authors have withdrawn this manuscript because of significant conflict of interest and substantial ambiguity in the data interpretation that may lead to misrepresentation of the findings. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

biophysics↗
bioRxiv2024

Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans

Pantoea agglomerans is one of four Pantoea species for which strains have been reported in the United States to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected >300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Genome assemblies were generated for 87 P. agglomerans strains that showed a range in onion virulence phenotypes. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies identified two well-represented and well-supported P. agglomerans phylogroups. Strains causing severe symptoms on onion leaves and bulbs were only identified in Phylogroup II and encoded the HiVir biosynthetic cluster for the phytotoxin pantaphos, supporting the role of HiVir as a crucial pathogenicity factor. Using a MASH-based plasmid classification system, the P. agglomerans HiVir cluster was determined to be encoded in two distinct plasmid contexts: 1) as an accessory gene cluster on a conserved P. agglomerans plasmid (pAggl), or 2) on a mosaic cluster of plasmids common among onion strains (pOnion). Analysis of closed genomes of P. agglomerans revealed that the pOnion plasmids harbored alt genes responsible for encoding tolerance to the thiosulfinate defensive chemistry in Allium spp. Additionally, many of these pOnion plasmids harbored cop gene clusters, which confer resistance to copper. However, the pOnion plasmids encoded the HiVir cluster less frequently. We demonstrated that the pOnion plasmid pCB1C, encoding HiVir and alt clusters as well as an intact conjugative type IV secretion system (T4SS), can act as a natively mobilizable pathogenicity plasmid that transforms P. agglomerans Phylogroup I strains, including environmental strains, into virulent pathogens of onion. This work indicates a central role for plasmids and plasmid ecology in mediating P. agglomerans interactions with onion plants, with potential implications for onion bacterial disease management.

microbiology↗
bioRxiv2024

Evaluating machine learning algorithms to predict lameness in dairy cattle

Dairy cattle lameness represents one of the common concerns in intensive and commercial dairy farms. Lameness is characterized by gait-related behavioral changes in cows and multiple approaches are being utilized to associate these changes with lameness conditions including data from accelerometers, and other precision technologies. The objective was to evaluate the use of machine learning algorithms for the identification of lameness conditions in dairy cattle. In this study, 310 multiparous Holstein dairy cows from a herd in Northern Colorado were affixed with a leg-based accelerometer (Icerobotics(R) Inc, Edinburg, Scotland) to obtain the lying time (min/d), daily steps count (n/d), and daily change (n/d). Subsequently, study cows were monitored for 4 months and cows submitted for claw trimming (CT) were differentiated as receiving corrective claw trimming (CCT) or as being diagnosed with a lameness disorder and consequent therapeutic claw trimming (TCT) by a certified hoof trimmer. Cows not submitted to CT were considered healthy controls. A median filter was applied to smoothen the data by reducing inherent variability. Three different machine learning (ML) models were defined to fit each algorithm which included the conventional features (containing daily lying, daily steps, and daily change derived from the accelerometer), slope features (containing features extracted from each variable in Conventional feature), or all features (3 simple features and 3 slope features). Random forest (RF), Naive Bayes (NB), Logistic Regression (LR), and Time series (ROCKET) were used as ML predictive approaches. For the classification of cows requiring CCT and TCT, ROCKET classifier performed better with accuracy (> 90%), ROC-AUC (> 74%), and F1 score (> 0.61) as compared to other algorithms. Slope features derived in this study increased the efficiency of algorithms as the better-performing models included All features explored. However, further classification of diseases into infectious and non-infectious events was not effective because none of the algorithms presented satisfactory model accuracy parameters. For the classification of observed cow locomotion scores into severely lame and moderately lame conditions, the ROCKET classifier demonstrated satisfactory accuracy (> 0.85), ROC-AUC (> 0.68), and F1 scores (> 0.44). We conclude that ML models using accelerometer data are helpful in the identification of lameness in cows but need further research to increase the granularity and accuracy of classification.

animal behavior and cognition↗
bioRxiv2019

A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate.

RNA viruses are pervasive entities in the biosphere with significant impact in human health and economically important livestock. As strict cellular parasites, RNA viruses abuse host resources, redirecting them towards viral replication needs. Taking control of the cellular apparatus for protein production is a requirement for virus progression and diverse strategies of cellular mimicry and/or ribosome hijacking evolved to ensure this control. Especially in complex eukaryotes, translation is a sophisticated process, with multiple mechanisms acting on ribosomes and mRNAs. The initiation stage of translation is specially regulated, involving multiple steps and the engagement of numerous initiation factors some of them of high complexity. The use of structured RNA sequences, called Internal Ribosomal Entry Sites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5-UTR of a viral RNA assembles a functional translation initiation complex via an uAUG intermediate, redirecting the cellular machinery for protein production towards viral messengers. The IRES features a novel extended, multi-domain architecture, circling the 40S head, leveraging ribosomal sites not previously described to be exploited by any IRES. The structures and accompanying functional data, illustrate the importance of 5-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs. Given the large number of new viruses metagenomic studies have uncovered, the quantity and diversity of mechanisms for translation hijacking encrypted in viral sequences may be seriously underestimated. Exploring this diversity could reveal novel avenues in the fight against these molecular pathogens.

biochemistry↗
bioRxiv2019

The Israeli Acute Paralysis Virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.

The Colony Collapse Disorder or CCD is a multi-faceted syndrome decimating bee populations worldwide[1]. A group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD[2]. This family of viruses employ non-coding RNA sequences, called Internal Ribosomal Entry Site (IRES), to precisely exploit the host machinery for protein production. Using single-particle cryo-electron microscopy (cryo-EM) we have characterized at high resolution how the IRES of the intergenic region of the Israeli Acute Paralysis Virus (IAPV) captures and redirects translating ribosomes towards viral messengers. Through a series of six structures at nominal resolutions close to 3[A], we could reconstruct the trajectory of IAPV-IRES from an early small subunit recruitment to a final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. The presented structures will help guide on-going efforts directed towards fighting CCD through RNA-interference technology [3].

biophysics↗