Biology subjects

Pandit, S.

Publications and source records attributed to Pandit, S..

17 recordsLinked to original sources

bioRxiv2026

Does herbivore diversity increase induced phytochemical diversity? Testing the pathway co-activation hypothesis

The mechanistic link between multiple herbivory and phytochemical diversity as an emergent plant trait is poorly understood. Because alternative, interacting biosynthetic pathways enable high specificity of induced plant responses to different herbivores, we hypothesized that multi-species herbivory increases phytochemical diversity by simultaneously activating mutually-antagonistic response pathways. We tested this hypothesis using a dual-herbivory experiment with phloem-feeding aphids and leaf-chewing caterpillars on cabbage seedlings, combined with untargeted metabolomics. To isolate plant responses to herbivore identities from responses to damage levels, we equalized herbivory pressures across treatments. The underlying mechanism was tested using similar applications of the respective defense phytohormones. Phytochemical richness increased under dual-herbivory relative to single-species herbivory. Phytochemical evenness (2D diversity) increased from caterpillar-only to dual-herbivory. Phytohormone applications produced similar effects, supporting the hypothesized mechanism. Analyses of glucosinolate levels and whole-metabolome shifts were consistent with prevalent, but not exclusive, antagonistic JA-SA crosstalk, explaining the increased phytochemical evenness under combined exposures. The demonstrated general mechanistic basis suggests a broad positive relationship between phytochemical and herbivore diversity across plant-herbivore systems. Using a theoretical simulation model, we extend our two-species hypothesis to the community level. The ecological effects of herbivore-induced plasticity in phytochemical diversity may ultimately cascade through communities and food web interactions.

plant biology↗

bioRxiv2026

Peptidyl Protease Inhibitors Block ERM-BP Function and Suppress Entamoeba Encystation

Entamoeba encystation process is a crucial developmental process that support to parasite persistence and disease transmission, yet the molecular mechanisms governing this stage conversion remain poorly understood and represent an attractive opportunity for therapeutic intervention. The Encystation Regulatory Motif-Binding Protein (ERM-BP), a transcription factor and key regulator of encystation, therefore represents a promising target for anti-amoebic drug development to prevent disease transmission. In the present study, we applied a target-based drug discovery approach to screen small molecules that can block the activity of ERM-BP, with a particular focus on the Cys-198 residue of this protein, which is functionally important. A library comprising 100 compounds including broad-spectrum nicotinamidase inhibitors and cysteine-reactive electrophiles were screened against ERM-BP by Protein thermal shift assays (PTSA). Thirty-six compounds bound to wild-type ERM-BP while analysis using the C198A mutant narrowed the candidates to three compounds exhibiting Cys-198-dependent interactions. These three peptidyl protease inhibitors, PFMK (Z-Ala-Phe-FMK), LEK (Z-Leu-EK), and EBLL (Ethylbenzyl-Leu-Lys) binds to ERM-BP-WT and abolishes the DNA-binding activity of ERM-BP in a concentration-dependent way. Cellular evaluation further revealed distinct activity of PFMK, LEK and EBLL on trophozoite growth and PFMK and EBLL reduced encystation efficiency significantly, produced irregular, and structurally defective cysts, which fails to excyst to trophozoites, whereas LEK had no significant effects on encystation efficiency or cyst morphology. Altogether, these findings identify peptidyl protease inhibitors PFMK and EBLL as promising compounds to target ERM-BP and block the Entamoeba encystation, providing a framework for developing therapeutics targeting parasite differentiation and encystation.

microbiology↗

bioRxiv2025

Deciphering the Population Ecology of Blossom Midge, Contarinia maculipennis Felt: An Emerging Threat to Tuberose Cultivation in India

The blossom midge Contarinia maculipennis is a devastating pest of ornamental and vegetable crops, yet its population ecology remains poorly understood. This study employs an age-stage two-sex life table model to analyze its life history with additional focus on below-ground soil environment. Tuberose (Agave amica), a newly identified host, was selected for study. The average fecundity of C. maculipennis was 39.13 eggs, with an intrinsic rate of increase (r) of 0.137, and a mean generation time (T) of 19.73 days. The population doubling time was 5.05 days, with the highest survival rate observed in the first instar larvae (0.95), and the lowest in the adult stage (< 0.38). The population doubling time was 5.05 days. Survival was highest in first-instar larvae (0.95) and lowest in adults (< 0.38). Life expectancy peaked at age zero (e0 =15.57 days) and decreased with pivotal age. The reproductive value (Vx) peaked between 13 and 19 days post-field appearance. Pupal development was fastest, with a significantly higher adult-emergence recorded in sandy clay loam soil (9.67 days); however pupal development and adult-emergence were severely impacted in black cotton and marshy soils. Moderate soil moisture (20%) favored pupation and eclosion rate, while dry (10%) and saturated (30%) soils hindered pupation and emergence. Population projections over 90 days, starting with 133 eggs, estimated an adult population of 3,80738. These findings highlight pupal and adult stages as critical targets for management. Soil type and moisture strongly influence population dynamics, with strategies such as maintaining dry conditions between rows, deep ploughing to bury pupae, and mass trapping recommended for effective control. These insights offer practical strategies for the sustainable management of C. maculipennis.

ecology↗

bioRxiv2024

Extracellular ISG15 triggers ISGylation via a type-I interferon independent mechanism to regulate host response during virus infection

Type-I interferons (IFN) induce cellular proteins with antiviral activity. One such protein is Interferon Stimulated Gene 15 (ISG15). ISG15 is conjugated to proteins during ISGylation to confer antiviral activity and regulate cellular activities associated with inflammatory and neurodegenerative diseases and cancer. Apart from ISGylation, unconjugated free ISG15 is also released from cells during various conditions, including virus infection. The role of extracellular ISG15 during virus infection was unknown. We show that extracellular ISG15 triggers ISGylation and acts as a soluble antiviral factor to restrict virus infection via an IFN-independent mechanism. Specifically, extracellular ISG15 acts post-translationally to markedly enhance the stability of basal intracellular ISG15 protein levels to support ISGylation. Furthermore, extracellular ISG15 interacts with cell surface integrin (5{beta}1 integrins) molecules via its RGD-like motif to activate the integrin-FAK (Focal Adhesion Kinase) pathway resulting in IFN-independent ISGylation. Thus, our studies have identified extracellular ISG15 protein as a new soluble antiviral factor that confers IFN-independent non-canonical ISGylation via the integrin-FAK pathway by post-translational stabilization of intracellular ISG15 protein.

immunology↗

bioRxiv2024

Unravelling Antibody-Induced Mechanical Stability of Antigen: Insights from Single-Molecule Studies

The intricate nature of antigen-antibody interactions plays a pivotal role in immunological responses. Despite the multitude of ligand-binding sites on antigens, the influence of antibodies on their mechanical stability remains elusive. This study elucidates the impact of IgM, the largest antibody isotype, on the mechanical stability of protein L, a bacterial superantigen, using single-molecule magnetic tweezers and steered molecular dynamics. Our findings reveal a concentration-dependent elevation in mechanical stability induced by IgM, as demonstrated by prolonged unfolding dwell times. Through steered molecular dynamics simulations, we elucidate the distinct mechanical responses of protein L binding interfaces at various IgM complex states, highlighting their synergistic effect on IgM dimer complex stability. Notably, this enhanced response stems from the altered unfolding pathway of protein L upon IgM interaction, providing significant insights into the generic mechanisms governing antibody-induced mechanical stability of antigenic substrates in physiological conditions, shedding light on the underlying folding dynamics and molecular mechanics of antigen-antibody interaction.

biophysics↗

bioRxiv2023

Trophic microRNA: Precursor and mature microRNA ingestion downregulates the target transcripts and hampers larval development in Plutella xylostella

MicroRNAs (miRNAs) are post-transcriptional gene regulators. In the miRNA pathways cytoplasmic part, the miRNA is processed from a hairpin-structured precursor (pre-miRNA) to a double-stranded (ds) mature RNA and ultimately to a single-stranded mature miRNA. In insects, ingesting these two ds forms can regulate the target gene expression; this inspired the trophic miRNAs use as a functional genomics and pest management tool. However, systematic studies enabling comparisons of pre- and mature forms, dosages, administration times, and instar-wise effects on target transcripts and phenotypes, which can help develop a miRNA administration method, are unavailable due to the different focuses of the previous investigations. We investigated the impact of trophically delivered Px-let-7 miRNA on the Brassicaceae pest, Plutella xylostella, to compare the efficacies of its pre- and ds-mature forms. Continuous feeding on the miRNA-supplemented diet suppressed expressions of FTZ-F1 and E74, the target ecdysone pathway genes. Both the pre-let-7 and mature let-7 miRNA forms similarly downregulated the target transcripts in all four larval instars. Pre-let-7 and let-7 ingestions decreased P. xylostellas larval mass and instar duration and increased mortality in all instars, exhibiting adverse effects on larval growth and development. Pre-miRNA processing Dicer-1 was upregulated upon pre-let-7 ingestion, indicating the miRNA uptake by the midgut cells. The scrambled sequence controls did not affect the target transcripts, suggesting the sequence-specific targeting by the mature miRNA and hairpin cassettes non-involvement in the target downregulation. This work provides a framework for miRNA and target gene function analyses and potentiates the trophic miRNAs utility in pest management.

ecology↗

bioRxiv2023

Role of the osaA gene in Aspergillus fumigatus development, secondary metabolism and virulence.

Aspergillus fumigatus is the leading cause of aspergillosis, associated with high mortality rates, particularly in immunocompromised individuals. In search of novel genetic targets against aspergillosis, we studied the WOPR transcription factor OsaA. Deletion of the osaA gene resulted in colony growth reduction. Conidiation is also influenced by osaA; both osaA deletion and overexpression resulted in a decrease in spore production. Wild-type expression levels of osaA are necessary for expression of the conidiation regulatory genes brlA, abaA and wetA. In addition, osaA is necessary for normal cell wall integrity. Furthermore, deletion of osaA resulted in a reduction in the ability of A. fumigatus to adhere to surfaces, decreased thermotolerance, as well as increased sensitivity to oxidative stress. Metabolomics analysis indicated that osaA deletion or overexpression led to alterations in the production of multiple secondary metabolites, including gliotoxin. This was accompanied by changes in the expression of genes in the corresponding secondary metabolite gene clusters. These effects could be, at least in part, due to the observed reduction in the expression levels of the veA and laeA global regulators when the osaA locus was altered. Importantly, our study shows that osaA is indispensable for virulence in both the neutropenic and corticosteroid-immunosuppressed mouse models.

microbiology↗

bioRxiv2023

Molecular Dynamics studies of Long Neurotoxins against nAChR provide key insights towards design of therapeutic peptides for Dyskinesia

Peptide-based drugs are widely used as therapeutic products that exhibit strong binding affinities with high specificity and low toxicity. To develop novel therapeutics against severe involuntary muscle movement and trembling disorder (Dyskinesia), the study explored the design of peptides that could target the nicotine acetylcholine receptor (nAChR) as antagonistic leads. The work aimed to suggest that the pharmacological interaction of snake venom toxins and its associated peptides with nAChRs could be exploited as plausible solutions for PD. Molecular docking and Molecular dynamics exercises were carried out using long chain neurotoxins (-BTx, 1NTN) to analyze the efficacies of their binding to nAChRs, with both the entire toxin and short peptide moieties. The study demonstrated that the novel-peptide (F8J2D7) system appears to possess better affinity with the nAChR than the entire toxin, which is a first step towards designing peptide-based drugs from snake venom proteins that could facilitate further research in the peptide-engineering and drug designing prospects for various neurodegenerative diseases.

bioinformatics↗

bioRxiv2023

Eggplant's chlorogenic acid provides resistance against the tropical armyworm

Lepidopteran pests are the major crop devastators. Farmers have to resort to heavy synthetic pesticide application for their control. It increases the pesticide residue contamination on produce and causes health hazards. Synthetic pesticides also endanger beneficial insects and pollute the environment. Therefore, the use of safe and eco-friendly botanicals as biopesticides is rapidly increasing. Despite their high demand, only a few botanicals are commercially available. Consequently, biopesticide discovery research boomed in the last decade. Spodoptera litura Fabricius (armyworm) is a polyphagous multi-insecticide-resistant lepidopteran pest. It is a serious concern for several commercially important crops. In this study, we employed a chemical ecology approach to discover a biopesticide against it. As a biopesticide source, we explored secondary metabolite-rich Solanum melongena L. (eggplant), one of the armyworms hosts. We found that the armyworm larvae show differential occurrence on seven eggplant varieties; the Himalayan eggplant variety RC-RL-22 (RL22) showed no armyworm infestation. When reared in a no-choice condition on RL22, larval mortality was two-fold higher, and mass was three-fold lower than the varieties showing high infestation. We tested whether RL22s secondary metabolite(s) were associated with this hampered larval performance. Using LC-ESI-QTOF-based non-targeted metabolomics of eggplant varieties, we identified candidate metabolites. 5-O-caffeoylquinic acid (chlorogenic acid; CGA) showed a strong negative correlation (r= -0.88; p= 0.008) with the larval performance. CGA-spiked (average physiological concentration) artificial diet (CGA-AD)-fed larvae showed a three-fold mass reduction and two-fold mortality increase than the control artificial diet (AD)-fed larvae; pupation and eclosion also significantly reduced (1.3-fold and 1.4-fold, respectively) in the CGA-ingested larvae. We used a reverse genetics approach to assess the in planta insecticidal potential of CGA. When RL22s CGA biosynthesis gene hydroxycinnamoyl-CoA quinate transferase (SmHQT) was silenced using virus-induced gene silencing (VIGS), CGA levels decreased by three-fold. This CGA depletion rendered RL22 two-fold armyworm-susceptible than controls. Foliar CGA application restored RL22s armyworm resistance. Overall, this study showed that CGA exhibits larvicidal properties against the armyworm. It is also safe for beneficial organisms. CGA is a well-known dietary supplement and an antioxidant for humans. Thus, it is safe for human consumption. Together, high CGA-containing varieties can be used to reduce the armyworm infestation risk. CGA is a promising biopesticide candidate for the field trial phase against the lepidopteran pests, especially armyworm. If successful, it can be integrated into the pest control measures.

plant biology↗

bioRxiv2023

Sniffer beetles: Odor imaging reveals congeneric herbivores identify their congeneric hostplants based on differential olfactory perceptions

Hostplant location and conspecific aggregation on the hostplant are the key behaviors of several herbivore insect species. The cues used by insects for host identification and aggregation initiation have been researched mainly using a single hostplant species. The chemical repertoire of plants, including volatile and non-volatile secondary metabolites, is critical in mediating these processes. In natural ecosystems, often several closely related plant species co-occur. Despite these related plant species similar chemical repertoires, insects proficiently locate their hosts. How they resolve such complex chemical cues is understudied. To study the basis of such resolution, we used five commonly co-occurring Ipomoea spp. as hostplants and four Chiridopsis spp. (beetles) as their herbivores. In this wild sympatric system from the Western Ghats of India, monophagous, biphagous, and oligophagous Chiridopsis spp. are specialist herbivores of different Ipomoea species. We studied the chemistry of these beetles stringent host-specificity by determining the roles of chemical cues in hostplant location and aggregation. We analyzed beetles hostplant preferences vis-a-vis hostplant volatile blends. We found plant volatiles as the primary hostplant identification cues. Using GC-MS/-FID and SPME headspace analyses, we characterized odor blends of the five Ipomoea spp. and identified putative attractants and repellents for each Chiridopsis sp. using multivariate statistics. We determined their attractant or deterrent natures using behavioral assays and ascertained their perception by the antennal olfactory receptors using electroantennography. Beetles responded to these compounds only when they were delivered via their hostplant odor blends. Beetles did not respond when these compounds were given singularly or via non-host odor blends. We infer that these semiochemicals attractant, repellent, or neutral characters are associated with the hostplants volatile blend-the matrix. We integrated the multi-source data to visualize this in-flight odor perception by representing odor as color variations or odor images. Odor imaging revealed beetles differential olfactory perception of different hostplants and indicated how a beetle distinguishes between two closely-related plant species. Additionally, it showed a different olfactory perception of the same hostplant by different closely-related beetle species, suggesting they have evolved to recognize the same odor using different components. Our work demonstrates that the hostplants odor blend matrix is crucial; beetles do not respond to attractants/ repellents without it. Together, the closely-related plant species form an ideal system to understand how insects perceive subtle differences between hosts and non-host cues in nature. This investigation also underlines the relevance of studying entire odor blends over individual compounds.

ecology↗

bioRxiv2022

Maximization of Energy Recovery from Starch Processing Wastewater by Thermophilic Dark Fermentation Coupled with Microbial fuel Cell Technology

Utilization of organic wastewater for hydrogen production has dual advantages of clean energy generation and bioremediation which is sustainable for a longer period. To maximize the energy recovery from starch rich wastewater, a two stage system comprising of thermophilic dark fermentation coupled with microbial fuel cell was employed. A single parameter optimization strategy was implemented for the operation of the batch system. The maximum cumulative hydrogen production obtained was 2.56 L L-1 with a 48 % reduction in COD under the optimal conditions of 35 g L-1 initial substrate concentration (COD), temperature 60 oC, and pH 6.5. The H2 yield and H2 production rate were 6.8 mol H2/kg CODreduced and 731.3 mL L-1 h-1 respectively. The effect of the organic loading rate (OLR) on H2 production rate was studied in a continuous stirred tank reactor (CSTR). A maximum hydrogen production rate of 913 mL L-1 h-1 was observed at an OLR of 5.6 g L- 1 h-1. Effluent recycle played an important role in the improvement of H2 production. A maximum H2 production rate of 1224 mL L-1 h-1 was observed at a recycle ratio of 0.6. Power density of 4.2 W m-3 was observed with MFC using the dark fermentative spent media neutralized with carbonate buffer at an optimal pH of 7. A total COD reduction of 86% was observed.

bioengineering↗

bioRxiv2022

Chemical ecology of Himalayan eggplant variety's antixenosis: Identification of geraniol as an oviposition deterrent against the eggplant shoot and fruit borer

O_LIEggplant (Solanum melongena) suffers severe losses due to a multi-insecticide resistant lepidopteran pest, shoot and fruit borer (SFB, Leucinodes orbonalis). Heavy and combinatorial application of pesticides for SFB control renders eggplant risky for human consumption. C_LIO_LIWe observed that 1) ovipositing SFB females can find even solitary plants of susceptible varieties and 2) they do not oviposit on Himalayan eggplant variety RC-RL-22 (RL22). We hypothesized that the olfactory cues influence ovipositing females host choice. C_LIO_LITo find these cues, leaf volatile blends of seven eggplant varieties were profiled using GCMS. Seven compounds were present in >2.5-fold concentrations in RL22 than the other varieties. In choice assays, oviposition deterrence efficacies of these candidate compounds were independently tested by their foliar application on SFB-susceptible varieties. Complementation of geraniol, which was exclusively found in RL22, reduced oviposition (>90%). To validate geraniols role in RL22s SFB-deterrence, we silenced RL22s geraniol synthase gene using virus-induced gene silencing. Geraniol biosynthesis suppression rendered RL22 SFB-susceptible; foliar geraniol application on the geraniol synthase-silenced plants restored oviposition deterrence. C_LIO_LIWe infer that geraniol is RL22s SFB oviposition deterrent. The use of natural compounds like geraniol, which influence the chemical ecology of oviposition can reduce the load of hazardous larvicidal pesticides. C_LI

plant biology↗

bioRxiv2022

Nipsnap1- A Regulatory Factor Required for Long-Term Maintenance of Non-Shivering Thermogenesis

The molecular activation of non-shivering thermogenesis (NST) has strong potential to combat obesity and metabolic disease. However, the mechanisms surrounding the maintenance of NST once it is fully activated, remain unexplored. Here, we present 4-Nitrophenylphosphatase Domain and Non-Neuronal SNAP25-Like 1 (Nipsnap1) as a critical regulator of long-term thermogenic maintenance in brown adipose tissue (BAT). Nipsnap1 localizes to the mitochondrial matrix and increases its transcript and protein levels in response to both chronic cold and {beta}3 adrenergic signaling. Through the generation of BAT-specific Nipsnap1 knockout mice (N1-KO), we show that these mice are unable to sustain activated energy expenditure and fail to protect their body temperature in the face of an extended cold challenge. Mechanistically, we demonstrate that Nipsnap1 integrates with lipid metabolism and BAT-specific ablation of Nipsnap1 leads to severe defects in {beta}-oxidation capacity. Our findings identify Nipsnap1 as a potent regulator of long-term NST maintenance.

molecular biology↗

bioRxiv2021

Lack of authentic atrial fibrillation in commonly used murine atrial fibrillation models

The mouse is a useful preclinical species for evaluating disease etiology due to the availability of a wide variety of genetically modified strains and the ability to perform disease-modifying manipulations. In order to better characterize atrial fibrillation (AF), we profiled several commonly used murine AF models. We initially evaluated a pharmacological model of acute carbachol (CCh) treatment plus atrial burst pacing in C57BL/6 mice. In an effort to observe micro-reentrant circuits indicative of authentic AF, we employed optical mapping imaging in isolated mouse hearts. While CCh reduced atrial refractoriness and increased atrial tachyarrhythmia vulnerability, the left atrial (LA) excitation patterns were rather regular without reentrant circuits or wavelets. Therefore, the atrial tachyarrhythmia resembled high frequency atrial flutter, not typical AF per se. We next examined both a chronic angiotensin II (Ang II) infusion model and the surgical model of transverse aortic constriction (TAC), which have both been reported to induce atrial and ventricular structural changes that serve as a substrates for micro-reentrant AF. Although we observed some extent of atrial remodeling such as fibrosis or enlarged LA diameter, burst pacing-induced atrial tachyarrhythmia vulnerability did not differ from control mice in either model. This again suggested that an AF-like pathophysiology is difficult to demonstrate in the mouse. To continue searching for a valid murine AF model, we studied mice with a cardiac-specific deficiency (KO) in liver kinase B1 (Cardiac-LKB1), which has been reported to exhibit spontaneous AF. Indeed, the electrocardiograms (ECG) of conscious Cardiac-LKB1 KO mice exhibited no P waves and had irregular RR intervals, which are characteristics of AF. Histological evaluation of Cardiac-LKB1 KO mice revealed dilated and fibrotic atria, again consistent with AF. However, atrial electrograms and optical mapping revealed that electrical activity was limited to the sino-atrial node area with no electrical conduction into the atrial myocardium beyond. Thus, Cardiac-LKB KO mice have severe atrial myopathy or atrial standstill, but not AF. In summary, the atrial tachyarrhythmias we observed in the four murine models were distinct from typical human AF, which often exhibits micro- or macro-reentrant atrial circuits. Our results suggest that the four murine AF models we examined are poor representations of human AF, and raise a cautionary note about the use of any murine model to study AF.

physiology↗

bioRxiv2020

Effects of a combined enrichment intervention on the behavioural and physiological welfare of captive Asiatic lions (Panthera leo persica)

The endangered Asiatic lion (Panthera leo persica) is currently distributed as a single wild population of 670 individuals and [~]400 captive animals globally. Although the captive lions are major hope for the species long-term conservation through repatriation, their welfare status and management practises need research attention. To this end, we tested the efficacy of feeding, sensory and manipulable enrichment interventions on the welfare of Asiatic lions at the conservation breeding centre of Sakkarbaug Zoological Garden, Gujarat. We adopted a holistic approach by measuring physiological and behavioural responses of 35 captive Asiatic lions, divided into control (n=16) and test (n=19) groups. The test subjects approached feeding devices first and manipulable devices for a longer duration. Manipulable devices were used homogenously with two significant time peaks, but sensory devices were used sporadically throughout the day with no discernible peak usage. The control subjects remained unchanged in all welfare parameters compared to their pre-treatment levels. However, post-enrichment behavioural assessments showed higher behaviour diversity (95% increase from the baseline period), reduced enclosure zone bias (40.25% reduction) and aberrant repetitive behaviours (80.68%) in test samples. Similarly, faecal corticosterone measures showed lower stress levels in test samples (58% decrease), confirming significant improvement in all welfare indices than control groups. These results have universal applicability to assess welfare indices of other captive species in Indian zoos. We hope that the results will encourage zoo managers and regulatory agencies to improve animal welfare practices.

animal behavior and cognition↗

bioRxiv2020

Sero-prevalence and risk factors of leptospirosis in commercial cattle herds of Rupandehi district, Nepal

Nepal has an agrarian-based economy where the livestock sector contributes about 12 percent to the national GDP. Rupandehi district is one of the largest dairy pocket areas in the nation, but the disease, such as leptospirosis, posed a negative impact on their production and productivity. Despite the economic importance of cattle leptospirosis, the disease is concerned for the peoples occupational risk and food safety. Although leptospirosis is a priority zoonosis in Nepal, the effective implementation of the control program lacks both in animal and human health. A cross-sectional study was conducted to estimate the prevalence and identify associated risk factors of cattle leptospirosis from March 2019 to April 2020. Altogether, 206 cattle herds located in all the sixteen local levels of the district were visited. The owners were interviewed to record the cattle management systems information and their knowledge of the zoonotic diseases. A total of 383 cattle serum samples were collected, and an indirect antibody ELISA was performed to estimate the infection status of leptospirosis in the cattle herds. All the data were analyzed by Open epi and R software for the descriptive and analytical study. Bivariate and multivariable logistic regression was applied to assess the potential herd level and animal level risk factors. Out of seven potential herd-level risk factors, the purchased cattle herds (OR: 7.2, 95% CI: 1.24-136.5, p=0.025) and cattle with herd size >10 (OR: 14.92, 95% CI: 2.61-283.38, p=0.025) were identified as significant risk factors for leptospirosis. At the animal level, the cattle taken for grazing in pastureland accessed by the community dog was a significant risk factor (OR: 4.16, 95% CI: 1.13-14.06, p=0.034). Surprisingly, none of the farmers had heard about leptospirosis before. The outcome of this research could be an epidemiological insight in control of priority zoonosis to protect the livestock economy and reduce their negative impact on public health.

scientific communication and education↗

bioRxiv2018

Atomic Resolution Mechanism of Ligand Binding to a Solvent Inaccessible Cavity in T4 Lysozyme

Ligand binding sites in proteins are often localized to deeply buried cavities, inaccessible to bulk solvent. Yet, in many cases binding of cognate ligands occurs rapidly. An intriguing system is presented by the L99A cavity mutant of T4 Lysozyme (L99A T4L) that rapidly binds benzene (~106 M-1 s-1). Although the protein has long served as a model system for protein thermodynamics and crystal structures of both free and benzene-bound L99A T4L are available, the kinetic pathways by which benzene reaches its solvent-inaccessible binding cavity remain elusive. The current work, using extensive molecular dynamics simulation, achieves this by capturing the complete process of spontaneous recognition of benzene by L99A T4L at atomistic resolution. A series of multi-microsecond unbiased molecular dynamics simulation trajectories unequivocally reveal how benzene, starting in bulk solvent, diffuses to the protein and spontaneously reaches the solvent inaccessible cavity of L99A T4L. The simulated and high-resolution X-ray derived bound structures are in excellent agreement. A robust four-state Markov model, developed using cumulative 60 {micro}s trajectories, identifies and quantifies multiple ligand binding pathways with low activation barriers. Interestingly, none of these identified binding pathways required large conformational changes for ligand access to the buried cavity. Rather, these involve transient but crucial opening of a channel to the cavity via subtle displacements in the positions of key helices (helix4/helix6, helix7/helix9) leading to rapid binding. Free energy simulations further elucidate that these channel-opening events would have been unfavorable in otherwise ligand-inactive wild type T4L. Taken together, by integrating experiments, these simulations provide unprecedented mechanistic insights into complete ligand recognition process in a buried cavity. By illustrating the power of subtle helix movements in opening up multiple pathways for ligand access, this work offers an alternate view of ligand recognition mechanism in a solvent-inaccessible cavity, contrary to common perception of single dominant pathway for ligand binding.

biophysics↗