Biology subjects

Sharma, V.

Publications and source records attributed to Sharma, V..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

Supraorbital whiskers act as wind-antennae in rat anemotaxis

We know little about mammalian anemotaxis, wind-sensing. Recently, however, Hartmann and colleagues showed whisker-based anemotaxis in rats. To investigate how whiskers sense airflow, we tracked whisker tips in anesthetized or cadaver rats under no airflow, low airflow and high (fan-blowing) airflow. Whisker tips showed little movement under no airflow conditions and all whisker tips moved during high airflow. Low airflow conditions - most similar to naturally occurring wind stimuli - engaged whisker tips differentially. Most whiskers moved little, the long supraorbital whisker showed maximal displacement and , A1, {beta}, and {gamma} whiskers also showed movements. The long supraorbital whisker differs from other whiskers in its exposed dorsal position, upward bending, length and thin diameter. Ex vivo extracted long supraorbital whiskers also showed exceptional airflow displacement, suggesting whisker-intrinsic biomechanics mediate the unique airflow-sensitivity. Micro computed tomography revealed that the ring-wulst - the follicle structure receiving the most sensitive afferents - was more complete/ closed in supraorbital and other wind-sensitive whiskers than in non-wind-sensitive whiskers, suggesting specialization of the supraorbital for omni-directional sensing. We localized and targeted the cortical supraorbital whisker representation in simultaneous Neuropixels recordings with D/E-row whisker barrels. Responses to wind-stimuli were stronger in the supraorbital whisker representation than in D/E-row barrel cortex. We assessed the behavioral significance of whiskers in an airflow-sensing paradigm. We observed that rats spontaneously turn towards airflow stimuli in complete darkness. Selective trimming of wind-responsive whiskers diminished airflow turning responses more than trimming of non-wind-responsive whiskers. Lidocaine injections targeted to supraorbital whisker follicles also diminished airflow turning responses compared to control injections. We conclude that supraorbital whiskers act as wind antennae. New and NoteworthyAnimals rely on sensory processing of airflow (anemotaxis) to guide navigation and survival. We examined mechanisms of rat anemotaxis by combining whisker tracking, biomechanical analysis, micro computed tomography of follicle structure, Neuropixels recordings in the barrel field, behavior of airflow turning and whisker interference by trimming and lidocaine injections. This diversity of methods led to a coherent pattern of results. Whiskers greatly differ in their airflow sensitivity and strongly wind-responsive whiskers - in particular long supraorbital whiskers - determine behavioral responses to airflow stimuli in rats.

neuroscience↗

bioRxiv2022

Understanding the mechanism of Trikatu in type 2 diabetes mellitus and lipid-related metabolic disorders: A network pharmacology approach

ObjectiveTrikatu is an Indian polyherbal formulation comprising three herbs, i.e., Zingiber officinale, Piper longum, and Piper nigrum. It is traditionally used to treat metabolic disorders such as type 2 diabetes mellitus (T2DM), dyslipidemia, and obesity. However, its mechanism of action remains unknown. This study aims to explore the underlying therapeutic mechanism of Trikatu in T2DM and lipid metabolic disorders using network pharmacology (NP). MethodsTrikatu phytochemicals were retrieved from various databases and screened on the basis of druglikeness and oral bioavailability (>30%) score. Putative targets of the bioactive phytochemicals were identified using TargetNet, Similarity Ensemble Approach, and Swiss Target Prediction databases. Protein-protein interaction (PPI) network of overlapping targets of phytochemicals and metabolic disorders was constructed using NetworkAnalyst 3.0. The Bioactive Phytochemical-Target-Pathway (BP-T-P) network was constructed using cytoscape v3.8.2, and the key targets of Trikatu were analyzed by Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. ResultsTwenty bioactive phytochemicals and 102 targets of Trikatu were identified. PPI network and enrichment analysis showed that 51 targets of Trikatu phytochemicals such as RXRA, STAT3 and ESR1, GSK3B, TNF, NOS2/3 regulate pathways like insulin resistance, steroid hormone biosynthesis, regulation of lipolysis in adipocytes, adipocytokine & cGMP-PKG signalling pathways, arachidonic acid metabolism and bile secretion. The results were validated by molecular docking which showed that RXRA, STAT3 and ESR1 strongly interact with their ligands alpha gurjunene, beta-sitosterol, piperlongumine, genistein and E-beta carotene, respectively. ConclusionHence, the multiple target and multiple pathway approach of Trikatu can be further explored in pharmacokinetics / Pharmacodynamics studies.

bioinformatics↗

bioRxiv2022

Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex

Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane1. Here we show that in ciliates, the membrane curvature is provided by a supercomplex containing all four respiratory chain components. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-megadalton assembly. Due to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and cristae tubulation. Our findings explain how the architecture of the native I-II-III2-IV2 supercomplex reflects the functional specialization of bioenergetics by shaping the membrane.

biochemistry↗

bioRxiv2022

Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I

Respiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 [A] long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.

biophysics↗

bioRxiv2022

APOE ϵ2 vs APOE ϵ4 dosage shows sex-specific links to hippocampus-default network subregion co-variation

Alzheimers disease and related dementias (ADRD) are marked by intracellular tau aggregates in the medial-temporal lobe (MTL) and extracellular amyloid aggregates in the default network (DN). Here, we sought to clarify ADRD-related co-dependencies between the MTLs most vulnerable structure, the hippocampus (HC), and the highly associative DN at a subregion resolution. We confronted the effects of APOE {varepsilon}2 and {varepsilon}4, rarely investigated together, with their impact on HC-DN co-variation regimes at the population level. In a two-pronged decomposition of structural brain scans from [~]40,000 UK Biobank participants, we located co-deviating structural patterns in HC and DN subregions as a function of ADRD family risk. Across the disclosed HC-DN signatures, recurrent deviations in the CA1, CA2/3, molecular layer, fornixs fimbria, and their cortical partners related to ADRD risk. Phenome-wide profiling of HC-DN co- variation expressions from these population signatures revealed male-specific associations with air-pollution, and female-specific associations with cardiovascular traits. We highlighted three main factors associated with brain-APOE associations across the different gene variants: happiness, and satisfaction with friendships, and with family. We further showed that APOE {varepsilon}2/2 interacts preferentially with HC-DN co-variation patterns in estimating social lifestyle in males and physical activity in females. Our findings reinvigorate the often-neglected interplay between APOE {varepsilon}2 dosage and sex, which we have linked to fine-grained structural divergences indicative of ADRD susceptibility.

neuroscience↗

bioRxiv2022

Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations

Multiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 [A] resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including [~]70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated transmembrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.

biochemistry↗

bioRxiv2021

Intramolecular interactions enhance the potency of gallinamide A analogs against Trypanosoma cruzi

Gallinamide A, a metabolite of the marine cyanobacterium Schizothrix sp., selectively inhibits cathepsin L-like cysteine proteases. We evaluated potency of gallinamide A and 23 synthetic analogs against intracellular Trypanosoma cruzi amastigotes and the cysteine protease, cruzain. We determined the co-crystal structures of cruzain with gallinamide A and two synthetic analogs at [~]2[A]. SAR data revealed that the N-terminal end of gallinamide A is loosely bound and weakly contributes in drug-target interactions. At the C-terminus, the intramolecular {pi}-{pi} stacking interactions between the aromatic substituents at P1 and P1 restrict the bioactive conformation of the inhibitors, thus minimizing the entropic loss associated with target binding. Molecular dynamics simulations showed that in the absence of an aromatic group at P1, the substituent at P1 interacts with tryptophan-184. The P1-P1 interactions had no effect on anti-cruzain activity whereas anti-T. cruzi potency increased by [~]5-fold, likely due to an increase in solubility/permeability of the analogs.

molecular biology↗

bioRxiv2021

Preservation of neural synchrony at peak alpha frequency via global synaptic scaling compensates for white matter structural decline over adult lifespan

We propose that preservation of functional integration, estimated from measures of neural synchrony, is a key neurocompensatory mechanism associated with healthy human ageing. To support this proposal, we demonstrate how phase-locking at peak alpha frequency from Magnetoencephalography (MEG) data is invariant over lifespan in a large cohort of human participants, aged 18-88 years. Using empirically derived connection topologies from diffusion tensor imaging (DTI) data, we create an in-silico model of whole-brain alpha dynamics. We show that enhancing inter-areal coupling can cancel the effect of increased axonal transmission delay associated with age-related degeneration of white matter tracts and thus, preserve neural synchrony. Together with analytical solutions for non-biological all-to-all connection scenarios, our model establishes the theoretical principles by which frequency slowing with age, frequently observed in the alpha band in diverse populations, can be viewed as an epiphenomenon of the underlying neurocompensatory mechanisms.

neuroscience↗

bioRxiv2021

Horn trophy seized in illegal wildlife trade assigned to swamp buffalo using a combined morphometric and DNA based approach in wildlife forensics in India

The illegal wildlife trade has threatened the existence of many extant wild animal species throughout the world. While dealing with the illegal wildlife trade of horns, we face problems of not having a proper protocol and lack of reference database to assign the species for proper implementation of wildlife laws. In one such condition, a horn trophy suspected to be of a wild buffalo was seized by authorities and sent to us for species identification. We used a combined approach of morphological and DNA analysis to ascertain the seized horns species. The two measurements, circumference at the base (CAB) and length on the front curve (LOFC) were measured for the seized and other horns of different bovid species, showing morphological resemblance with the seized horn. The 3-D scatter plot, generated by the values of CAB, LOFC and CAB/ LOFC, differentiated the different bovid species into distinct clusters and placed the seized horn in the proximity of domestic buffaloes. The Bayesian evolutionary analysis of the partial D-loop gene (521bp) placed the seized horn in a clade with swamp buffaloes. Since swamp buffaloes are domestic buffaloes, both these approaches concluded the same results. Hence, the current protocol developed may also be used to differentiate among wild buffalo, domestic buffalo, Cattle, Wild yak, Gaur and Takin using a combined approach of morphometric and DNA-based analysis, which may be used to deal with illegal wildlife trade of different bovid species at the world level.

zoology↗

bioRxiv2021

Fast and cost-effective age estimation in Bengal tiger and Asiatic lion: applicability of cementum analysis method

Age estimation methods, through cementum analysis, for wild animals are rarely developed in Southeast Asian Countries. In the present study, we describe the applicability of the cementum analysis technique for developing a fast ({+/-}19 hours) and cost-effective age estimation method for Bengal tiger (Panthera tigris tigris) and Asiatic lion (Panthera leo persica) using incisor tooth. The I2 and I3 incisor teeth from the right mandible of a tiger and I2 and I3 from the left maxilla of a lion were used in the study. The longitudinal sections of the tooth were made using a low cost hand grinding technique on sand papers followed by decalcification and staining with hematoxylin. The cementum layers were counted under the microscope at 100X or 200X magnifications. Two cementum layers were observed in each of the I2 and I3 incisor tooth of tiger and six cementum layers were observed in each of the I2 and I3 incisor teeth of lion. The permanent incisors in tiger and lion erupt between 12-14 months; hence, we added 1 year to the counted number of cementum layers to estimate the final age of tiger and lion incisors. The absolute age of tiger and lion incisors was estimated to be of 2+1 years and 6+1 years, respectively. The same number of cementum layers in both incisors respective to the tiger and lion were observed. Therefore, we suggest (i) undertake the blind test and (ii) collect incisor teeth from naturally died or killed individuals for strengthening the database on the age of the wild population. This optimized method may be suitable for many carnivore species, applicable in wildlife forensic studies and can be used by researchers with minimum expertise, time, and funds requirements throughout the world.

zoology↗

bioRxiv2021

Avian haemosporidians (Plasmodium and Haemoproteus) in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India and their phylogenetic relationships with other lineages of the world

The avian haemosporidians (Plasmodium and Haemoproteus) are widely distributed and may affect the host populations from body damage at individual level to the extinction of a population. The knowledge about their status may help in future avifauna conservation plans. Hence, we examined the avian haemosporidians status, in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India, and their phylogenetic relationships with other known lineages of the world. We used the common genetic marker (Cytochrome b gene fragment of 479 bp) with information on the geographic distribution of parasite and host species available at MalAvi database. The prevalence of avian haemosporidians, from northern, eastern, and southern parts of India and phylogenetic genetic analysis of lineages was carried out to know the genetic relatedness among them at local and world level. The MCC tree revealed six Haemosporidian lineages in which one was common (H_MSP01) and five were unique (H_CYOPOL01, H_CHD01, H_CYORUB01, H_EUMTHA01, and P_GEOCIT01). The avian host richness Index was 2.0852. 9.9%, prevalence of Haemosporidian infection was found in 111 DNA samples belonging to 6 host species. The Haemoproteus prevalence was found to be 9.0 % across five host species (Phylloscopus trochiloides, Cyornis poliogenys, C. hainanus dialilaemus, C. rubeculoides, Eumiyas thalassinus) and Plasmodium prevalence was 0.9% in Geokichla citrina. Spatial phylogeny at global level showed H_MSP01 lineage, found in different host species in India, was genetically related to H. pallidus lineages (COLL2 and PFC1) in parts of Africa, Europe, North America, Malaysia, and Philippines. The Plasmodium lineage (P_GEOCIT01) was related to PADOM16 in Egypt with poor sequence similarity (93.89%). The statistical analysis suggested that the haemosporidians host species distribution range was directly and significantly associated with the altitude, minimum temperature, and relative humidity. H_MSP01 distribution was in accordance with H. pallidus having a wide geographic and host range.

genetics↗

bioRxiv2021

ZRC3308 monoclonal antibody cocktail shows protective efficacy in Syrian hamsters against SARS-CoV-2 infection

We have developed a monoclonal antibody (mAb) cocktail (ZRC-3308) comprising of ZRC3308-A7 and ZRC3308-B10 in the ratio 1:1 for COVID-19 treatment. The mAbs were designed to have reduced immune effector functions and increased circulation half-life. mAbs showed good binding affinities to non-competing epitopes on RBD of SARS-CoV-2 spike protein and were found neutralizing SARS-CoV-2 variants B.1, B.1.1.7, B.1.351, B.1.617.2 and B.1.617.2 AY.1 in vitro. The mAb cocktail demonstrated effective prophylactic and therapeutic activity against SARS-CoV-2 infection in Syrian hamsters. The antibody cocktail appears to be a promising candidate for the prophylactic use and for therapy in early COVID-19 cases which have not progressed to severe disease.

microbiology↗

bioRxiv2021

Social isolation is linked to classical risk factors of Alzheimer's disease-related dementias

Alzheimers disease and related dementias is a major public health burden - compounding over upcoming years due to longevity. Recently, clinical evidence hinted at the experience of social isolation in expediting dementia onset. In 502,506 UK Biobank participants and 30,097 participants from the Canadian Longitudinal Study of Aging, we revisited traditional risk factors for developing dementia in the context of loneliness and lacking social support. Across these measures of subjective and objective social deprivation, we have identified strong links between individuals social capital and various indicators of Alzheimers disease and related dementias risk, which replicated across both population cohorts. The quality and quantity of daily social encounters had deep connections with key aetiopathological factors, which represent 1) personal habits and lifestyle factors, 2) physical health, 3) mental health, and 4) societal and external factors. Our population-scale assessment suggest that social lifestyle determinants are linked to most neurodegeneration risk factors, highlighting them promising targets for preventive clinical action.

neuroscience↗

bioRxiv2021

The m6A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay

The role m6A modifications have increasingly been associated with diverse set of roles in modulating viruses and influencing the outcomes of viral infection. Here we report that the landscape of m6A deposition is drastically shifted during KSHV (Kaposi Sarcoma Associated herpesvirus) lytic infection for both viral and host transcripts. In line with previous reports, we also saw an overall decrease in host methylation in favor of viral mRNA along with 5 hypomethylation and 3 hypermethylation. During KSHV lytic infection, a major shift in overall mRNA abundance is driven by the viral endoribonuclease SOX, which induces the decay of greater than 70% of transcripts. Here, we reveal that Interlukin-6 (IL-6) mRNA, a well-characterized SOX-resistant transcript, is m6A modified during lytic infection. Furthermore, we show that this modification falls within the IL-6 SOX Resistance Element (SRE), an RNA element in IL-6 3 UTR that was previously shown to be sufficient for protection from SOX cleavage. We show that the presence of this m6A modification is essential to confer SOX resistance to the IL-6 mRNA. We next show that this modification recruits the m6A reader YTHDC2 and found that YTHDC2 is necessary for the escape of the IL-6 transcript. These results shed light on how the host cell has evolved to use RNA modifications to circumvent viral manipulation of RNA fate during KSHV infection.

microbiology↗

bioRxiv2021

Effects of sub-threshold transcutaneous auricular vagus nerve stimulation on cerebral blood flow

BackgroundTranscutaneous auricular vagus nerve stimulation (taVNS) has shown promise as a non-invasive alternative to vagus nerve stimulation (VNS) with implantable devices, which has been used to treat drug-resistant epilepsy and treatment-resistant depression. Prior work has used functional MRI to investigate the brain response to taVNS, and more recent work has also demonstrated potential therapeutic effects of high-frequency sub-threshold taVNS in rheumatoid arthritis. However, no studies to date have measured the effects of high-frequency sub-threshold taVNS on cerebral blood flow (CBF). Objective/HypothesisThe objective of this study was to determine whether high-frequency (20 kHz) sub-threshold taVNS induces significant changes in CBF. MethodsArterial spin labeling (ASL) MRI scans were performed on 20 healthy subjects in a single-blind placebo-controlled repeated measures experimental design. The ASL scans were performed before and after 15 minutes of either sub-threshold taVNS treatment or a sham control. ResultstaVNS induced significant changes in CBF in the superior posterior cerebellum that were largely localized to bilateral Crus I and Crus II. Post hoc analyses showed that the changes were driven by a treatment-related decrease in CBF. ConclusionsFifteen minutes of high-frequency sub-threshold taVNS can induce sustained CBF decreases in the bilateral posterior cerebellum in a cohort of healthy subjects. This study lays the foundation for future studies in clinical popluations to assess whether similar effects can be observed and are related to treatment outcomes.

neuroscience↗

bioRxiv2021

Artemisinin acts by inhibiting Plasmodium falciparum Ddi1, a retropepsin, resulting into the accumulation of ubiquitinated proteins

Reduced sensitivity of the human malaria parasite, Plasmodium falciparum, to Artemisinin and its derivatives (ARTs) threatens the global efforts towards eliminating malaria. ARTs have been shown to cause ubiquitous cellular and genetic insults, which results in the activation of the unfolded protein response (UPR) pathways. The UPR restores protein homeostasis, which otherwise would be toxic to cellular survival. Here, we interrogated the role of DNA-damage inducible protein 1 (PfDdi1), a unique proteasome-interacting retropepsin in mediating the actions of the ARTs. We demonstrate that PfDdi1 is an active A2 family protease that hydrolyzes ubiquitinated substrates. We further show that treatment with ARTs lead to the accumulation of ubiquitinated proteins in the parasites and blocks the destruction of the ubiquitinated substrates by PfDdi1. Besides, whereas the PfDdi1 is predominantly localised in the cytoplasm, exposure of the parasites to ARTs leads to DNA fragmentation and increased recruitment of the PfDdi1 into the nucleus. Furthermore, Ddi1 knock-out Saccharomyces cerevisiae cells are more suceptible to ARTs and the PfDdI1 protein robustly restores the corresponding functions in the knock-out cells. Together, these results show that ARTs act by inducing DNA and protein damage, and impairing the damage recovery by inhibiting the activity of PfDdi1, an essential ubiquitin-proteasome retropepsin.

cell biology↗

bioRxiv2021

RNA silencing by CRISPR in plants does not require Cas13

RNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation and expanded function including anti-viral immunity. Here, we report the use of CRISPR-Cas13 in plants to reduce both viral and endogenous RNA. Unexpectedly, we discovered that crRNA designed to guide Cas13 could, in the absence of the Cas13 protein, cause substantial reduction in RNA levels as well. We demonstrate Cas13-independent guide-induced gene silencing (GIGS) in three plant species, including stable transgenic Arabidopsis. We determined that GIGS utilizes endogenous RNAi machinery despite the fact that crRNA are unlike canonical triggers of RNAi such as miRNA, hairpins or long double-stranded RNA. These results suggest that GIGS offers a novel and flexible approach to RNA reduction with potential benefits over existing technologies for crop improvement. Our results demonstrate that GIGS is active across a range of plant species, evidence similar to recent findings in an insect system, which suggests that GIGS is potentially active across many eukaryotes.

plant biology↗

bioRxiv2021

High-resolution structure and dynamics of mitochondrial complex I - insights into the proton pumping mechanism

Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is a 1 MDa membrane protein complex with a central role in energy metabolism. Redox-driven proton translocation by complex I contributes substantially to the proton motive force that drives ATP synthase. Several structures of complex I from bacteria and mitochondria have been determined but its catalytic mechanism has remained controversial. We here present the cryo-EM structure of complex I from Yarrowia lipolytica at 2.1 [A] resolution, which reveals the positions of more than 1600 protein-bound water molecules, of which [~]100 are located in putative proton translocation pathways. Another structure of the same complex under steady-state activity conditions at 3.4 [A] resolution indicates conformational transitions that we associate with proton injection into the central hydrophilic axis. By combining high-resolution structural data with site-directed mutagenesis and large-scale molecular dynamics simulations, we define details of the proton translocation pathways, and offer new insights into the redox-coupled proton pumping mechanism of complex I.

biochemistry↗