Biology subjects

Pradhan, S.

Publications and source records attributed to Pradhan, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

An improved deep learning model for immunogenic B epitope prediction

The recognition of B epitopes by B cells of the immune system initiates an immune response that leads to the production of antibodies to combat bacterial and viral infections. Computational methods for predicting the epitopes on antigens have shown promising results in the development of subunit vaccines and therapeutics. Recently, the use of protein language models (pLMs) for epitope prediction has led to a substantial increase in prediction accuracy. However, further improvements in precision are necessary for practical applications. Here, we develop and evaluate a series of models using different combinations of features and feature fusion techniques on a curated independent test set. Our results show that the models that use protein embeddings along with structural features are better at predicting both linear and conformational B epitopes when compared to a baseline model that uses only protein embeddings as features. Additionally, we show that the embeddings of ESM-2, an evolutionary scale model, likely capture T-B reciprocity.

bioinformatics↗

bioRxiv2025

Huntingtin preserves mitochondrial genome integrity in neurons, which is impaired in Huntingtons disease

Huntingtin (HTT) function is enigmatic, as the native protein plays critical roles in neuronal health, while mutant HTT (mHTT), carrying an expanded polyglutamine stretch, triggers neurotoxicity and contributes to the pathogenesis of Huntingtons disease (HD). We recently found that HTT is part of a nuclear transcription-coupled DNA repair (TCR) complex with DNA repair enzymes including polynucleotide-kinase-3-phosphatase (PNKP). This complex resolves DNA lesions during transcription to maintain genome integrity, while in HD, mHTT impairs the activity of this complex, resulting in accumulation of DNA lesions. Using molecular, cellular biology and computational methods, we find that HTT has a role in assembling a functional DNA repair complex in mitochondria. Together with mitochondrial RNA polymerase and transcription factors, HTT resolves mitochondrial DNA lesions to preserve mitochondrial genome integrity and function. Pathogenic mHTT impairs this activity, resulting in persistent DNA lesions and reduced mitochondrial function in HD. Importantly, restoring activity of this complex in a Drosophila HD model through ectopic HTT or PNKP expression significantly improves mitochondrial genome integrity and ameliorates motor deficits. HIGHLIGHTSO_LIHTT organizes a functional, multifactorial mitochondrial DNA repair complex C_LIO_LIMutant HTT impairs the mitochondrial DNA repair complex causing DNA damage accumulation C_LIO_LIHTT-associated repair complex resolves mitochondrial DNA lesions and DNA integrity C_LIO_LIRestoring repair activity in HD flies rescues mitochondrial DNA integrity and motor defects C_LI

neuroscience↗

bioRxiv2025

Matrix compliance regulates cellular and nuclear confinement of fibroblasts in tunable protein-based hydrogel microenvironments

The extracellular matrix (ECM) influences cellular behavior, fate, and various mechanisms underlying homeostasis, development, and disease. Biophysical and biochemical properties of the ECM are known to affect three-dimensional (3D) cellular behavior, and phenotype that regulate a wide range of pathological conditions. Tunable biomimetic hydrogels are extensively employed to regulate cellular dynamics in defined 3D microenvironments, enabling detailed investigation of cell-matrix interactions. This study aims to establish the relationship between varying hydrogel properties (adhesivity, degradability, porosity, and stiffness, hereby collectively referred to as matrix compliance) and fibroblast morphology at the cellular and nuclear levels. Poly(ethylene glycol diacrylate)-fibrinogen (PF)-based hydrogels were fabricated and their matrix properties were tuned using two different non-degradable co-monomers of varying molecular weights and concentrations. NIH3T3 mouse fibroblasts were cultured in 3D hydrogels for 10 days and their cellular and nuclear morphology was analyzed via confocal imaging. Cells in degradable, soft, porous, and adhesive hydrogels displayed higher degree of spreading, higher cell density, longer protrusions, and elongated and larger nuclei compared to those in less degradable, stiffer, less porous, and less adhesive hydrogels. Matrix compliance conjointly regulated cell density, protrusion length, and protrusion frequency (collectively referred to as cellular confinement) and nuclear volume (referred to as nuclear confinement). These results highlight the complex interplay and interdependence of these cellular and nuclear morphological features as regulated by engineered tunable matrices, providing guidance for future studies of 3D cell behavior in novel biomaterials. Statement of significanceBiomimetic tunable hydrogels are commonly used to support, and control, three-dimensional (3D) cellular behavior to recapitulate various developmental processes and disease states. Specific biophysical and biochemical characteristics of the extracellular matrix (ECM) can be modeled using these hydrogels by controlling the compositions and crosslinking mechanisms. Using this approach, the behavior of cells in 3D hydrogel matrices can be correlated with the matrix properties, thereby providing mechanistic insights into cell-matrix interactions. This study assesses the variations in the morphological features of fibroblasts encapsulated in 3D protein-based hydrogel matrices with varying crosslinking mechanisms. Our results reveal the combinatorial role of matrix adhesivity, degradability, porosity, and stiffness in regulating cellular and nuclear confinement of fibroblasts in 3D microenvironments. Overall, this study elucidates how matrix characteristics influence cellular behavior, serving as a practical guide for researchers developing innovative biomaterial matrices for 3D cell culture applications.

bioengineering↗

bioRxiv2025

Historical Contingency Shapes Toxin Resistance in a Specialist Avian Predator

Adaptations to toxic diets can cascade through ecosystems, altering physiology, species interactions, and trophic dynamics. To uncover the molecular basis of toxin resistance in the black-headed grosbeak (Pheucticus melanocephalus), a specialist predator of cardiotonic steroid-defended monarch butterflies (Danaus plexippus), we investigated the evolution of target-site insensitivity in the toxins molecular target - the Na,K-ATPase. Functional assays of engineered Na,K-ATPases revealed that resistance in grosbeaks arises from a non-additive interaction between a substitution at position 111 (Q111E) and up to six nearby amino acid changes in the first extracellular loop of the protein. Using resurrected ancestral proteins, we show that the earliest of these six substitutions to evolve (V113L) altered the functional effects of Q111E, such that Q111E alone became maladaptive. Only after the accumulation of additional permissive substitutions could Q111E confer resistance, highlighting how intramolecular epistatic interactions and historical contingency constrained the evolutionary path to adaptation. Our phylogenetic analysis of Na,K-ATPase sequences from 360 birds further revealed that several of the specific grosbeak substitutions--particularly at sites 112, 114, and 116--show strong signatures of co-evolution with changes at site 111 across the avian tree, supporting the hypothesis that resistance evolves through repeated, interacting changes. Together, these results reveal the molecular mechanisms of convergent evolution of toxin resistance and demonstrate how genetic background can shape evolutionary outcomes across trophic levels.

evolutionary biology↗

bioRxiv2025

Oncogenic virus hijacks SOX18 pioneer function to enhance viral persistence

Kaposis sarcoma herpesvirus (KSHV) establishes lifelong oncogenic infection in lymphatic endothelial cells (LECs) by ensuring episomal maintenance of its genome via the viral protein LANA. Efficient viral genome maintenance typically involves host DNA replication and episome tethering, but the extent of cell-type-specific regulation remains unclear. Here, we identify that KSHV hijacks the pioneering function of the endothelial-specific transcription factor SOX18 to facilitate persistence of viral episomes. Upon infection, LANA co-opts SOX18 to recruit the SWI/SNF chromatin-remodeling complex via its ATPase subunit BRG1, enhancing chromatin accessibility and enabling efficient viral genome persistence. Disruption of SOX18 or BRG1--genetically or pharmacologically--leads to reduced episome load and attenuated hallmarks of virus infection. This work highlights how viruses can harness lineage-specific transcriptional regulators to establish persistent nuclear retention of their episome into the host genome.

molecular biology↗

bioRxiv2025

Molecular and biological characterization of a distinct species of Lolavirus infecting different accessions of seashore paspalum, a turfgrass, widely grown in the United States

Seashore paspalum (Paspalum sp.), is an economically significant grass used in golf courses, sports fields, and landscaping in the United States. A novel Lolavirus, tentatively named paspalum latent virus (PaLV), was identified for the first time in seashore paspalum plants from the USDA National Plant Germplasm System (NPGS) using high-throughput sequencing. Three complete genome sequences of PaLV from different Paspalum accessions, with a length of 6,995 nucleotides (nt), not including the poly(A) tail, were obtained by Rapid Amplification of cDNA Ends and Sanger sequencing. Phylogenetic analysis based on the replicase protein sequences from the Alphaflexiviridae family revealed that PaLV grouped with the Lolavirus genus, with the closest relative being Lolium latent virus (LoLV). PaLV shares less than 72% nt identity to the replicase and coat protein genes of LoLV, which demarks PaLV as a new species and the second member of the genus. Furthermore, the coat protein region showed intense negative selection pressure and low spatially structured diversity. Host range analysis of PaLV showed that wheat, corn, sorghum, and Lolium are systemic hosts of PaLV. A one-step RT-PCR technique was developed to reliably detect PaLV infection.

pathology↗

bioRxiv2025

Intergenerational control of ribosomes under dietary restriction

Cells adjust their proteome to their environment. Most prominently, ribosome expression scales near linearly with the cellular growth rate to provide sufficient translational capacity while preventing metabolically wasteful ribosomal excess. In microbes, such proteome adjustments can passively perpetuate through symmetric cell division. However, in animals, a passive propagation is hindered by the separation between soma and germline. This separation raises the crucial question whether the proteome of animals is reset at every generation or can be propagated from parent to offspring despite this barrier. We addressed this question by exploring the intergenerational effects of dietary restriction in C. elegans, combining proteomics and live imaging. While most proteins showed no intergenerational regulation, ribosomal proteins remained reduced in offspring after maternal dietary restriction. When offspring of dietarily restricted mothers were raised under improved dietary conditions, this reduced ribosome content delayed their growth until normal ribosomal protein levels were restored. Soma-specific maternal inhibition of mTORC1 signalling replicated these effects, while other growth-reducing perturbations, such as reduced insulin signalling or maternal ribosome depletion, did not impact offspring ribosomes. Thus, mTORC1 signalling bridges across the soma-germline divide to regulate ribosome levels of the next generation, likely priming the offspring for the anticipated demand in protein synthesis.

physiology↗

bioRxiv2024

Knockdown-resistance (kdr) mutations in Indian Aedes aegypti populations: lack of recombination among haplotypes bearing V1016G, F1534C, and F1534L kdr alleles

BackgroundKnockdown resistance (kdr) mutations in the voltage-gated sodium channel (VGSC) gene are a key mechanism of insecticide resistance in mosquitoes. In Asian Aedes aegypti populations two main VGSC haplogroups with kdr mutations have been identified: one carrying the F1534C mutation and another with V1016G and/or S989P mutations. Functional studies have demonstrated that these three mutations on a single haplotype confer up to a 1100-fold increase in pyrethroid resistance, underscoring the need to monitor these triple mutations within distinct populations. This study investigates the prevalence of kdr mutations in Indian populations and explores the linkage association between these mutations and two distinct conserved types of introns located between exons 20 and 21. MethodsAe. aegypti specimens collected from eight different locations were genotyped for kdr alleles and intron (between exons 20 and 21) haplotypes using PCR-based assays. Representative samples underwent DNA sequencing of VGSC regions. ResultsFive kdr mutations namely S989P, V1016G, T1520I, F1534C, and F1534L, were identified, each exhibiting varying distribution and frequencies across different geographical regions. Two distinct and stably-diverged intron haplotypes, designated as intron-A and intron-B, were identified between exons 20 and 21. Seven haplotypes, including two wild-type variants, were observed among Indian populations. The kdr-bearing haplotypes can be classified into three distinct haplogroups: haplogroup G (V1016G with/or without S989P and with intron-A), haplogroup L (F1534L and intron-A), and haplogroup C (F1534C with/or without T1520I and with intron-B). Importantly, no evidence of recombination within Indian populations was detected among these three haplogroups. ConclusionsFive kdr mutations were identified in the VGSC of Indian Ae. aegypti populations, each showing a definitive linkage with one of the two types of intron haplotypes. The lack of recombination among haplogroups bearing 1016G with 989P, 1534C and 1534L mutations suggests that the most potent insecticide resistance haplotype, bearing the triple kdr mutation, is currently absent. This finding has significant operational implications, as it may indicate that current vector control measures remain effective against these populations, potentially delaying the emergence of highly resistant phenotypes

zoology↗

bioRxiv2024

Scrutinized lipid utilization disrupts Amphotericin-B responsiveness in clinical isolates of Leishmania donovani

The management of Leishmania donovani (LD), responsible for fatal visceral leishmaniasis (VL), faces increasing challenges due to rising drug-unresponsiveness, leading to increasing treatment failures. While hypolipidemia characterizes VL, LD, a cholesterol auxotroph, relies on host lipid scavenging for its intracellular survival. The aggressive pathology, in terms of increased organ parasite load, observed in hosts infected with antimony-unresponsive-LD (LD-R) as compared to their sensitive counterparts (LD-S), highlights LD-Rs heightened reliance on host lipids. Here we report that LD-R-infection promotes fluid-phase endocytosis in the host, selectively accumulating neutral lipids while excluding oxidized-LDL. LD-R enhances the fusion of endocytosed LDL-vesicles with its phagolysosomal membrane and inhibits cholesterol mobilization from these vesicles by suppressing NPC-1. This provides LD-R amastigotes with excess lipids, supporting their rapid proliferation and membrane synthesis. This excess LDL-influx leads to an eventual accumulation of neutral lipid droplets around LD-R amastigotes, thereby increasing their unresponsiveness towards Amphotericin-B, a second-line amphiphilic antileishmanial. Notably, VL patients showing relapse with Amphotericin-B treatment exhibited significantly lower serum LDL and cholesterol than cured cases. Treatment with Aspirin, a lipid droplet blocker, reduced lipid droplets around LD-R amastigotes, restoring Amphotericin-B responsiveness.

microbiology↗

bioRxiv2024

Chromatin remodeler BRG1 recruits huntingtin to repair DNA double-strand breaks in neurons

Persistent DNA double-strand breaks (DSBs) are enigmatically implicated in neurodegenerative diseases including Huntingtons disease (HD), the inherited late-onset disorder caused by CAG repeat elongations in Huntingtin (HTT). Here we combine biochemistry, computation and molecular cell biology to unveil a mechanism whereby HTT coordinates a Transcription-Coupled Non-Homologous End-Joining (TC-NHEJ) complex. HTT joins TC-NHEJ proteins PNKP, Ku70/80, and XRCC4 with chromatin remodeler Brahma-related Gene 1 (BRG1) to resolve transcription-associated DSBs in brain. HTT recruitment to DSBs in transcriptionally active gene- rich regions is BRG1-dependent while efficient TC-NHEJ protein recruitment is HTT-dependent. Notably, mHTT compromises TC-NHEJ interactions and repair activity, promoting DSB accumulation in HD tissues. Importantly, HTT or PNKP overexpression restores TC-NHEJ in a Drosophila HD model dramatically improving genome integrity, motor defects, and lifespan. Collective results uncover HTT stimulation of DSB repair by organizing a TC-NHEJ complex that is impaired by mHTT thereby implicating dysregulation of transcription-coupled DSB repair in mHTT pathophysiology. Highlights* BRG1 recruits HTT and NHEJ components to transcriptionally active DSBs. * HTT joins BRG1 and PNKP to efficiently repair transcription related DSBs in brain. * Mutant HTT impairs the functional integrity of TC-NHEJ complex for DSB repair. * HTT expression improves DSB repair, genome integrity and phenotypes in HD flies.

neuroscience↗

bioRxiv2024

Genome-wide Identification of the Laccase Gene Family in White Jute (Corchorus capsularis): Potential Targets for Lignin Engineering in Bast Fiber

Jute (Corchorus spp.) is an important industrial bast fibre crop valued for its lignocellulosic fibres, yet the molecular basis of fibre lignification remains unexplored. Laccase (EC 1.10.3.2) is a key enzyme catalysing the final steps of lignin polymerisation. A genome-wide analysis of white jute (Corchorus capsularis) identified 32 putative laccase genes (CcaLACs) that were phylogenetically grouped into six clades. Expression profiling revealed predominant expression in phloem tissue (16 genes), followed by leaf (8) and xylem/root tissues (4). Several CcaLACs showed progressive upregulation from early growth to harvest stages. Homology with Arabidopsis laccases highlighted candidate genes involved in lignification, which were further supported by transcriptomic and qRT-PCR analyses. Notably, key CcaLACs showed significantly reduced expression in dlpf (deficient lignified phloem fibre), a low-lignin white jute mutant. CcaLAC expression was also responsive to abiotic stresses, including abscisic acid and copper. MicroRNA target prediction identified Ath-miR397a and Ath-miR397b as potential regulators of multiple CcaLACs. Structural and subcellular analyses revealed conserved motifs, transmembrane domains, and diverse cellular localisation. Gene ontology analysis linked CcaLACs to lignin and phenylpropanoid biosynthesis. Among them, CcaLAC28 and CcaLAC32 emerged as strong candidate genes associated with phloem fibre lignification, representing promising targets for future functional validation towards developing low-lignin jute varieties.

plant biology↗

bioRxiv2024

Distinct structural and functional heterochromatin partitioning of lamin B1 and B2 revealed using genome-wide Nicking Enzyme Epitope targeted DNA sequencing.

A genome-wide chromatin profiling technology, named as Nicking Enzyme Epitope targeted DNA sequencing (NEED-seq) in which antibody-targeted controlled nicking by Nt.CviPII-pGL is used to study specific protein-DNA complexes. NEED-seq is performed in situ in formaldehyde fixed cells, allowing for both visual and genomic resolution of epitope bound chromatin. When applied to nuclei, NEED-seq yielded genome-wide chromatin associated proteins and histone post-translational modifications (PTMs). NEED-seq of lamin B1/B2 demonstrated their association with heterochromatin. Lamin B1 and B2 associated domains (LAD) segregated to three different states, and states with stronger LAD correlated with heterochromatic marks. Hi-C analysis displayed A and B compartment with equal lamin B1/B2 distribution, although methylated DNA remained high in B compartment. LAD clustering with Hi-C resulted in subcompartments, with lamin B1-B2 partitioning to facultative and constitutive heterochromatin respectively and were associated with neuronal development. Thus, lamin B1 and B2 have structural and functional partitioning in mammalian nucleus. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/603107v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@44c36forg.highwire.dtl.DTLVardef@7ab1adorg.highwire.dtl.DTLVardef@126e99eorg.highwire.dtl.DTLVardef@1b38bd7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract: Model depicting association of lamin B1 and B2 in A (facultative heterochromatin) and B (constitutive heterochromatin) compartmentalization. C_FIG

genomics↗

bioRxiv2024

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A

Continued advances in variant effect prediction are necessary to demonstrate the ability of machine learning methods to accurately determine the clinical impact of variants of unknown significance (VUS). Towards this goal, the ARSA Critical Assessment of Genome Interpretation (CAGI) challenge was designed to characterize progress by utilizing 219 experimentally assayed missense VUS in the Arylsulfa-tase A (ARSA) gene to assess the performance of community-submitted predictions of variant functional effects. The challenge involved 15 teams, and evaluated additional predictions from established and recently released models. Notably, a model developed by participants of a genetics and coding bootcamp, trained with standard machine-learning tools in Python, demonstrated superior performance among sub-missions. Furthermore, the study observed that state-of-the-art deep learning methods provided small but statistically significant improvement in predictive performance compared to less elaborate techniques. These findings underscore the utility of variant effect prediction, and the potential for models trained with modest resources to accurately classify VUS in genetic and clinical research.

genetics↗

bioRxiv2024

Effects of Exercise Frequency on Aortic Calcification in Hyperlipidemic Mice

Cardiovascular disease risk is associated with coronary artery calcification and is mitigated by regular exercise. However, the optimal regimen (activity level and frequency) for benefitting cardiovascular health is not clear. The surface area of calcium deposits, in addition to the quantity of calcium mineral, is a key factor in the risk of plaque rupture in humans due to compliance mismatch of edges with surrounding distensible tissue resulting in debonding. We previously found that aortic PET tracer uptake, a marker of mineral surface area, was reduced in hyperlipidemic (Apoe-/-) mice that underwent treadmill exercise, especially those in the low-speed (12.5 meters/min) regimen. To test the optimal exercise frequency on cardiovascular health, hyperlipidemic mice with baseline aortic calcification were subjected to none, 3- or 5-day/week treadmill regimen (12.5 meters/min for 30 min/day) for 5 weeks. MicroPET/microCT imaging and echocardiography were performed before and after the 5-week study. Results show that aortic calcification significantly progressed in all 3 groups, and 18F-NaF uptake increased in the control and 3-day groups, but not in the 5-day group. As for cardiac function, left ventricular (LV) systolic function was not affected but LV mass and wall thickness decreased in the 5-day group, suggesting cardiac remodeling. Skeletal bone density assessed at lumbar vertebrae shows that bone density decreased in all 3 groups. These findings suggest that, in mice with underlying calcific atherosclerosis, low-speed exercise and a frequency of 5 days/week is optimal for benefitting cardiovascular health.

physiology↗

bioRxiv2024

Whole genome assembly of the Little Millet (Panicum sumatrense) genome: A climate resilient crop species

Little millet (Panicum sumatrense) belongs to one of the largest genera, Panicum comprising of 500 species that are distributed especially in tropical and sub-tropical Asia as well as Africa. This is a climate resilient crop that has the ability to adapt to adverse growing conditions, especially drought. Added to this is the better nutritional profile of little millet, which has higher iron and fibre contents as compared with rice. These characteristics make it an important crop species that would be pivotal for ensuring food security. Generating genomic resources for the species is significant and will have implications in crop improvement. Therefore, in the present study we report the de novo whole genome sequence of P. sumatrense. Long read sequencing and Hi-C based scaffolding resulted in a total of 279 scaffolds with N50 of 7.8Mb. The genome was annotated to predict protein coding genes and orthologous groups were analysed after comparison with various plant genomes. This high-quality genome assembly can be a valuable resource as future reference for genomic studies in this crop and related crop species.

genomics↗

bioRxiv2024

Pathogen infection induces sickness behaviors by recruiting neuromodulatory systems linked to stress and satiety in C. elegans

When animals are infected by a pathogen, peripheral sensors of infection signal to the brain to coordinate a set of adaptive behavioral changes known as sickness behaviors. While the pathways that signal from the periphery to the brain have been intensively studied in recent years, how central circuits are reconfigured to elicit sickness behaviors is not well understood. Here we find that neuromodulatory systems linked to stress and satiety are recruited upon infection to drive sickness behaviors in C. elegans. Upon chronic infection by the bacterium Pseudomonas aeruginosa PA14, C. elegans decrease their feeding behavior, then display reversible bouts of quiescence, and eventually die. The ALA neuron and its neuropeptides FLP-7, FLP-24, and NLP-8, which control stress-induced sleep in uninfected animals, promote the PA14-induced feeding reduction. However, the ALA neuropeptide FLP-13 instead acts to delay quiescence and death in infected animals. Cell-specific genetic perturbations show that the neurons that release FLP-13 to delay quiescence in infected animals are distinct from ALA. A brain-wide imaging screen reveals that infection-induced quiescence involves ASI and DAF-7/TGF-beta, which control satiety-induced quiescence in uninfected animals. Our results suggest that a common set of neuromodulators are recruited across different physiological states, acting from distinct neural sources and in distinct combinations to drive state-dependent behaviors.

neuroscience↗

bioRxiv2023

De novo assembly of the whole genome of Moth bean (Vigna aconitifolia), an underutilized Vigna species of India

As a fast-growing legume species, moth bean (Vigna aconitifolia) has a unique habit of sustaining in conditions of higher temperatures and drought. This grain legume is also valued for it seeds which have one of the highest contents of proteins amongst all grain legumes. This plant can be a rich source of genomic resources, which can be applied to improve abiotic stress response in allied grain legumes and also help understand the biological processes governing their overall development. Here we generate a de novo genome assembly of Vigna aconitifolia using PacBio High-Fidelity reads and Hi-C sequencing data, with a total size of 409 Mb and contig N50 of more than 30Mb. We also annotated the genome for repeat sequences, found that the moth bean genome comprises of about 54% of repetitive sequences, and predicted 36950 protein-coding genes. Using the available RNA-Seq data for moth bean, we have developed a differential expression profile for various tissues of moth bean using the whole genome as a reference and identified simple sequence repeats that could be developed into viable molecular markers. This nascent study will provide insight into the identification of agronomically important genes and accelerate the genetic improvement of moth bean as well as other legume crops.

genomics↗

bioRxiv2023

Viral attachment blocking chimera composed of DNAorigami and nanobody inhibits Pseudorabies Virusinfection in vitro

Antivirals are indispensable tools that can be targeted at viral domains directly or indirectly at cellular domains to obstruct viral infections and reduce pathogenicity. Despite their transformative use in healthcare, antivirals have been clinically approved to treat only 10 of the more than 200 known pathogenic human viruses. Additionally, many virus functions are intimately coupled with host cellular processes, which present challenges in antiviral development due to the limited number of clear targets per virus, necessitating an extensive insight into these molecular processes. Compounding this challenge, many viral pathogens have evolved to evade effective antivirals. We hypothesize that a Viral Attachment Blocking Chimera (VirABloC) composed of a viral binder and a bulky scaffold that sterically blocks interactions between a viral particle and a host cell may be suitable for the development of antivirals agnostic to the extravirion epitope that is being bound. We test this hypothesis by modifying a nanobody that specifically recognizes a non-essential epitope presented on the extra virion surface of Pseudorabies virus strain 486 with a 3-dimensional wireframe DNA origami structure [~]100 nm in diameter. The nanobody switches from having no inhibitory properties (tested up to 50 {micro}M) to 4.2 {+/-} 0.9 nM IC50 when conjugated with the DNA origami scaffold. Mechanistic studies support that inhibition is mediated by the non-covalent attachment of the DNA origami scaffold to the virus particle, which obstructs the attachment of the viruses onto host cells. These results support the potential of VirABloC as a generalizable approach to developing antivirals.

biophysics↗