Biology subjects

Antony, B.

Publications and source records attributed to Antony, B..

6 recordsLinked to original sources

bioRxiv2026

Insect olfaction-inspired biohybrid sensor array for selective airborne pheromone detection and early monitoring of invasive Rhynchophorus ferrugineus

The red palm weevil, Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae), is a globally invasive quarantine pest threatening palm cultivation across 49 countries and inflicting annual economic losses estimated at over USD 100 million. Weevil larvae burrow into palm trunks, causing progressive internal structural damage that rarely produces visible external symptoms until lethal injury has occurred, rendering early detection exceptionally challenging. In the absence of effective early-warning surveillance technologies, tens of thousands of infested palm trees have been removed across major palm-cultivation regions in the Middle East and Mediterranean basin. Rapid, sensitive detection of volatile organic compounds (VOCs) emitted by weevil colonies and infested palm trees therefore represents a critical unmet need for timely pest surveillance and intervention. Existing artificial gas sensors lack the chemical selectivity required to discriminate among structurally similar VOCs, and no validated field-deployable early-detection platform has been established to date. Here, we report a portable biohybrid sensor array that mimics insect olfaction by exploiting two classes of diagnostic chemical signatures: the male-released aggregation pheromone (4RS,5RS)-4-methylnonan-5-ol (ferrugineol) and ethyl ester volatile blends emitted by weevil-infested palm trees. The R. ferrugineus odorant receptor RferOR1 was stabilised in lipid nanodiscs and co-immobilised with two in vivo-synthesised odorant-binding proteins (RferOBP1768 and RferOBP23) on quartz crystal microbalance (QCM) transducers to construct the biohybrid sensing platform. The sensor array achieved selective detection of airborne ferrugineol at a limit of detection of approximately 60 parts per billion (ppb) under field conditions, distinguishing infested from healthy palms. OBP- and OR-functionalised sensors retained full functional activity for 12 and 7 months, respectively, under ambient storage, confirming operational robustness and shelf life suitable for long-term field deployment. This work translates the molecular architecture of the insect olfactory system into a practical, field-validated chemical sensor platform with direct applicability to early-stage R. ferrugineus infestation monitoring and sustainable integrated pest management. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/744605v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@596c4org.highwire.dtl.DTLVardef@ed5336org.highwire.dtl.DTLVardef@f2229borg.highwire.dtl.DTLVardef@bdf1ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Ommochrome pathway knockout via CRISPR/Cas9 reveals sex-linked eye pigmentation and establishes a heritable genome-editing platform in Rhynchophorus ferrugineus

The red palm weevil, Rhynchophorus ferrugineus, is the most economically destructive palm pest worldwide, threatening livelihoods, food security, and ecosystems across 49 countries. Weevil management currently relies predominantly on chemical insecticides, raising significant environmental and public health concerns. Despite its global agricultural importance, genetic approaches to pest management and the mechanistic basis of genome-editing strategies in Rhynchophorus remain largely unexplored. Here, we employed CRISPR/Cas9 genome editing to disrupt the R. ferrugineus ommochrome biosynthetic pathway -- a multi-enzymatic metabolic cascade that converts tryptophan into ommochrome pigments, including brown, yellow, and red pigments. We targeted two key pathway components: the ATP-binding cassette transporter white and the heme peroxidase cardinal. Both genes were ubiquitously expressed, with peak expression levels in the gut, fat body, and head. Elevated transcript levels were observed across early, mid, and late pupal stages and in 0-, 1-, and 2-day-old adult males and females, consistent with the progression of eye pigmentation throughout the R. ferrugineus life cycle. Embryonic microinjection of a single guide RNA (sgRNA)-Cas9 ribonucleoprotein complex targeting white produced in the Generation-0 (G0) adults with a distinct, white-eyed phenotype with a brownish outer margin, in contrast to the black eyes of wild-type adults. Genome-edited cardinal mutant adults displayed a translucent, brownish-white-eyed phenotype, with white streaks that gradually transitioned to a persistent translucent reddish-brown eye coloration. Mutations in both genes were confirmed in G0 adults by genomic DNA sequencing. Mutant adults were crossed to generate heterozygous G1 (+/-), G2 (-/-, -/+, and +/+), and G3 lines (-/-) with genotypes verified as carrying 2-, 3-, 9-, and 13-nucleotide deletions. A stable, heritable eye-color phenotype was established in homozygous knockout (-/-) G3 lines for both white and cardinal, confirmed by unambiguous indel (insertions/deletions) genotyping. Inheritance analysis revealed that both genes are X-linked, following a classical Mendelian sex-linked pattern: paternal alleles are transmitted exclusively to daughters, while maternal alleles are inherited equally by both daughters and sons. This study establishes the first fully homozygous knockout strain in R. ferrugineus and, by characterizing sex-linked inheritance in a coleopteran system, advances our understanding of how CRISPR/Cas9 can be efficiently applied to destructive palm weevil species. The present study represents the first report of CRISPR/Cas9 genome editing in any weevil (Curculionidae), using white and cardinal as marker genes. These findings provide a valuable platform for functional genomics and genome engineering in R. ferrugineus and offer a translational framework for genome editing in the invasive South American palm weevil, R. palmarum, laying a solid foundation for the development of gene-drive strategies aimed at sustainable palm weevil population control.

zoology↗

bioRxiv2025

HAVEN: Hierarchical Attention for Viral protEin-based host iNference

It is crucial to accurately predict hosts of viruses to understand and anticipate human infectious diseases that originate from animals. There is a lack of versatile models that handle out-of-distribution factors such as unseen hosts and viruses. We develop a machine learning model for predicting the host infected by a virus, given only the sequence of a protein encoded by the genome of that virus. Our approach, HAVEN, is the first to apply to multiple hosts and to generalize to unseen hosts and viruses. HAVEN is a transformer-based architecture coupled with hierarchical self-attention that can accept sequences of highly diverse lengths. We integrate HAVEN with a prototype-based few-shot learning classifier to predict rare classes. We demonstrate the accuracy, robustness, and generalizability of HAVEN through a comprehensive series of experiments. In particular, we show that HAVEN can achieve a median AUPRC of 0.67 while predicting common hosts. Moreover, HAVEN retains this AUPRC value even for rare hosts (median prevalence as low as 0.09%). Our model performs on par with state-of-the-art foundation models, which are 65 to 5, 000 times larger in size, and outperforms them in identifying hosts of SARS-CoV-2 variants of concern.

bioinformatics↗

bioRxiv2023

Predicting Pseudomonas aeruginosa drug resistance using artificial intelligence and clinical MALDI-TOF mass spectra

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used in clinical microbiology laboratories for bacterial identification but its use for prediction of antimicrobial resistance (AMR) remains limited. Here, we used MALDI-TOF MS with artificial intelligence (AI) approaches to successfully predict AMR in Pseudomonas aeruginosa, a priority pathogen with complex AMR mechanisms. The highest performance was achieved for modern {beta}-lactam/{beta}-lactamase inhibitor drugs, namely ceftazidime/avibactam and ceftolozane/tazobactam, with area under the receiver operating characteristic curve (AUROC) of 0.86 and 0.87, respectively. As part of this work, we developed dynamic binning, a feature engineering technique that effectively reduces the high-dimensional feature set and has wide-ranging applicability to MALDI-TOF MS data. Compared to conventional methods, our approach yielded superior performance in 10 of 11 antimicrobials. Moreover, we showcase the efficacy of transfer learning in enhancing the performance for 7 of 11 antimicrobials. By assessing the contribution of features to the models prediction, we identified proteins that may contribute to AMR mechanisms. Our findings demonstrate the potential of combining AI with MALDI-TOF MS as a rapid AMR diagnostic tool for Pseudomonas aeruginosa.

microbiology↗

bioRxiv2023

Reverse chemical ecology approach for sustainable palm tree protection against invasive palm weevils

The reverse chemical ecology approach facilitates sustainable plant protection by identifying odorant receptors (ORs) tuned to odorants, especially the volatile molecules emitted from host plants that insects use for detection. A few studies have explored such an approach to develop sustainable pest management programs, especially in host-specialized insect species. We revealed the molecular mechanism of host plant detection of a destructive, invasive insect pest of palm trees (Arecaceae), the Asian palm weevil (Rhynchophorus ferrugineus), by deorphanizing an OR (RferOR2) tuned to several palm-emitted odors. We found that RferOR2 responded explicitly to several ecologically relevant palm-emitted odors and significantly to palm esters when transgenically expressed in Drosophila olfactory neurons. We mapped RferOR2 expression in the R. ferrugineus genome and found that odor specificity is likely to develop equally in both sexes. We inferred that the semiochemicals that attract palm weevils to a palm tree might aid in weevil control efforts by improving attraction, enticing many palm weevils to the traps. We demonstrate that including synthetic palm volatiles in pheromone-based mass trapping has a synergistic effect on pheromones, resulting in significantly increased weevil catches. We proved that insect OR deorphanization could aid in the identification of novel behaviorally active volatiles for inclusion in pest management. These results suggest that targeting RferOR2 may help design receptor antagonists that can interfere with weevil host-searching behavior in sustainable pest management applications. SignificanceAsian and South American palm weevils are tremendously important agricultural pests primarily adapted to palm trees and cause severe destruction, threatening sustainable palm cultivation worldwide. The host plant selection of these weevils is mainly attributed to functional specialization of odorant receptors that detect palm-derived volatiles. We unraveled the intricacies of weevil-palm tree communication by deorphanizing an odorant receptor tuned to natural palm-emitted odors. We used palm ester volatiles, which produced a significant response in the functional studies, and proved their synergistic effect on the pheromone coinciding with increased weevil catches in the field. We revealed that insect odorant receptor deorphanization could help identify novel behaviorally active volatiles (reverse chemical ecology) for sustainable palm protection.

ecology↗

bioRxiv2020

Pheromone receptor of the globally invasive quarantine pest of the palm tree, the red palm weevil (Rhynchophorus ferrugineus)

Palm trees are of immense economic, sociocultural, touristic and patrimonial significance all over the world, and date palm-related knowledge, traditions and practices are now included in UNESCOs list of the Intangible Cultural Heritage of Humanity. Of all the pests that infest these trees, the red palm weevil (RPW), Rhynchophorus ferrugineus (Olivier) is its primary enemy. The RPW is a category-1 quarantine insect pest that causes enormous economic losses in the cultivation of palm trees worldwide. The RPW synchronizes mass gathering on the palm tree for feeding and mating, regulated by a male-produced pheromone composed of two methyl-branched compounds, (4RS,5RS)-4-methylnonan-5-ol (ferrugineol) and 4(RS)-methylnonan-5-one (ferrugineone). Despite the importance of odorant detection in long-range orientation towards palm trees, palm colonization and mating, nothing regarding the molecular mechanisms of pheromone detection in this species is known. In this study, we report the identification and characterization of the first RPW pheromone receptor, RferOR1. Using gene silencing and functional expression in Drosophila olfactory receptor neurons, we demonstrate that RferOR1 is tuned to both ferrugineol and ferrugineone and binds five other structurally related molecules. We reveal the lifetime expression of RferOR1, which correlates with adult mating success irrespective of age, a factor that could explain the wide distribution and spread of this pest. As palm weevils are challenging to control based on conventional methods, elucidation of the mechanisms of pheromone detection opens new routes for mating disruption and the early detection of this pest via the development of pheromone receptor-based biosensors.

neuroscience↗