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Kulkarni, N.

Publications and source records attributed to Kulkarni, N..

11 recordsLinked to original sources

Active sensing movements by antennae enhance neural processing and plasticity for odour processing in the CNS in the honey bee Apis mellifera

Animals frequently move their sensory organs relative to dynamic environmental stimuli to maximize information acquisition, a behaviour known as active sensing. Recent studies show that insects adjust antennal movements according to the temporal structure and salience of olfactory signals, suggesting that antennae participate in active sensing. However, how these movements affect central olfactory processing remains unclear. To address this question, we trained honey bee foragers using a proboscis extension response (PER) protocol in which one odour (CS+) was paired with sucrose and another (CS-) with salt water. This training produces distinct antennal movements toward the two odours. Bees were subsequently tested with a series of concentrations of both CS+ and CS- odours. Antennae were either fixed or allowed to move freely during training and testing, while ectrophysiological recordings were made from the antennae and from the antennal lobes. Peripheral antennal responses across odour concentrations were not affected by whether the antennae were fixed or free. In contrast, antennal lobe projection neurons and local interneurons showed learning-related increases in responses to the CS+ odour, consistent with previous studies, and these increases were stronger in bees with freely moving antennae. Neural responses were also more variable, particularly at lower odour concentrations, when antennae could move, suggesting that response variability may contribute to plasticity. These results support the hypothesis that active antennal movements influence central processing of odour representations. Future studies comparing restrained bees with freely walking bees will help clarify the natural behavioural contexts in which antennal movements enhance olfactory sensing.

neuroscience↗

Binding affinities for 2D protein dimerization benefit from enthalpic stabilization

Dimerization underpins all macromolecular assembly processes both on and off the membrane. While the strength of dimerization, KD, is commonly quantified in solution (3D), many proteins like the soluble BAR domain-containing proteins also reversibly dimerize while bound to a membrane surface (2D). The ratio of dissociation constants, [Formula], defines a lengthscale that is essential for determining whether dimerization is more favorable in solution or on the membrane surface, particularly for these proteins that reversibly transition between 3D and 2D. While purely entropic rigid-body estimates of h apply well to transmembrane adhesion proteins, we show here using Molecular Dynamics simulations that even moderate flexibility in BAR domains dramatically alters the free energy landscape from 3D to 2D, driving enhanced selectivity and stability of the native dimer in 2D. By simulating BAR homodimerization in three distinct environments, 1) solution (3D), 2) bound to a lipid bilayer (2D), and 3) fully solvated but restrained to a pseudo membrane (2D), we show that both 2D environments induce backbone configurations that better match the crystal structure and produce more enthalpically favorable dimer states, violating the rigid-body estimates to drive h<<hRIGID. Remarkably, contact with an explicit lipid bilayer is not necessary to drive these changes, as the solvated pseudo membrane induces this same result. We show this outcome depends on the stability of the protein interaction, as a parameterization that produces exceptionally stable binding in 3D does not induce systematic improvements on the membrane. With h lengthscales calculated here that are well below a physiological volume-to-surface-area lengthscale, assembly will be dramatically enhanced on the membrane, which aligns with BAR domain function as membrane remodelers. Our approach provides simple metrics to move beyond rigid-body estimates of 2D affinities and assess whether conformational flexibility selects for enhanced stability on membranes.

biophysics↗

Molecular Glue-Design-Evaluator (MOLDE): An Advanced Method for In-Silico Molecular Glue Design

Protein function modulation using small molecule binding is an important therapeutic strategy for many diseases. However, many proteins remain undruggable due to lack of suitable binding pockets for small molecule binding. Proximity induced protein degradation using molecular glues has recently been identified as an important strategy to target undruggable proteins. Molecular glues were discovered serendipitously and as such currently lack an established approach for in-silico driven rationale design. In this work, we aim to establish an in-silico method for designing molecular glues. To achieve this, we leverage known molecular glue-mediated ternary complexes and derive a rationale for in-silico design of molecular glues. Establishing an in-silico rationale for molecular glue design would significantly contribute to the literature and accelerate the discovery of molecular glues for targeting previously undruggable proteins. Our work presented here and named as Molecular Glue-Designer-Evaluator (MOLDE) contributes to the growing literature of in-silico approaches to drug design in-silico literature.

bioinformatics↗

Olfactomedin-4+ neutrophils exacerbate intestinal epithelial damage and worsen host survival after Clostridioides difficile infection.

Neutrophils are key first responders to Clostridioides difficile infection (CDI). Excessive tissue and blood neutrophils are associated with worse histopathology and adverse outcomes, however their functional role during CDI remains poorly defined. Utilizing intestinal epithelial cell (IEC)-neutrophil co-cultures and a pre-clinical animal model of CDI, we show that neutrophils exacerbate C. difficile-induced IEC injury. We utilized cutting-edge single-cell transcriptomics to illuminate neutrophil subtypes and biological pathways that could exacerbate CDI-associated IEC damage. As such, we have established the first transcriptomics atlas of bone marrow (BM), blood, and colonic neutrophils after CDI. We found that CDI altered the developmental trajectory of BM and blood neutrophils towards populations that exhibit gene signatures associated with pro-inflammatory responses and neutrophil-mediated tissue damage. Similarly, the transcriptomic signature of colonic neutrophils was consistent with hyper-inflammatory and highly differentiated cells that had amplified expression of cytokine-mediated signaling and degranulation priming genes. One of the top 10 variable features in colonic neutrophils was the gene for neutrophil glycoprotein, Olfactomedin 4 (OLFM4). CDI enhanced OLFM4 mRNA and protein expression in neutrophils, and OLFM4+ cells aggregated to areas of severe IEC damage. Compared to uninfected controls, both humans and mice with CDI had higher concentrations of circulating OLFM4; and in mice, OLFM4 deficiency resulted in faster recovery and better survival after infection. Collectively, these studies provide novel insights into neutrophil-mediated pathology after CDI and highlight the pathogenic role of OLFM4+ neutrophils in regulating CDI-induced IEC damage. One Sentence SummaryUtilizing single-cell transcriptomics, IEC-epithelial co-cultures, and pre-clinical models of CDI, we have identified a subset of neutrophils that are marked by OLFM4 expression as pathogenic determinants of IEC barrier damage after CDI.

immunology↗

Episodic boundaries affect neural features of representational drift in humans

A core feature of episodic memory is representational drift, the gradual change in aggregate oscillatory features that supports temporal association of memory items. However, models of drift overlook the role of episodic boundaries, which indicate a shift from prior to current context states. Our study focuses on the impact of task boundaries on representational drift in the parietal and temporal lobes in 99 subjects during a free recall task. Using intracranial EEG recordings, we show boundary representations reset gamma band drift in the medial parietal lobe, selectively enhancing the recall of early list (primacy) items. Conversely, the lateral temporal cortex shows increased drift for recalled items but lacked sensitivity to task boundaries. Our results suggest regional sensitivity to varied contextual features: the lateral temporal cortex uses drift to differentiate items, while the medial parietal lobe uses drift-resets to associate items with the current context. We propose drift represents relational information tailored to a regions sensitivity to unique contextual elements. Our findings offer a mechanism to integrate models of temporal association by drift with event segmentation by episodic boundaries.

neuroscience↗

PROTAC-Design-Evaluator (PRODE) -- An Advanced Method for in-silico PROTAC design

PROTAC (proteolysis-targeting chimeras) is a rapidly evolving technology to target undruggable targets. The mechanism by which this happens is when a bifunctional molecule binds to a target protein and also brings in proximity an E3 ubiquitin ligase to trigger ubiquitination and degradation of the target protein. Yet in-silico driven approaches to design these hetero-bifunctional molecules that have the desired functional properties to induce proximity between the target protein and E3 ligase remains to be established. In this paper we present a novel in-silico method for PROTAC design and to demonstrate the validity of our approach. We show that for a BRD4-VHL PROTAC ternary complex known in the literature, we are able to reproduce the PROTAC binding mode, the structure of ternary complex formed therein and the free energy ({Delta}G) thermodynamics favoring ternary complexation through theoretical computational methodologies. Further, we demonstrate the use of Thermal Titration Molecule Dynamics (TTMD) to differentiate the stability of PROTAC mediated ternary complexes. We employ the proposed methodology to design a PROTAC for a new system of FGFR1-MDM2 to degrade the FGFR1 (Fibroblast growth factor receptor 1) which is overexpressed in cancer. Our work presented here and named as PROTAC-Designer-Evaluator (PRODE) contributes to the growing literature of in-silico approaches to PROTAC design and evaluation by incorporating the latest in-silico methods and demonstrates advancement over previously published PROTAC in-silico literature.

bioinformatics↗

Genetic variation associated with relative resistance in teak (Tectona grandis L. f.) against the leaf skeletonizer, Eutectona machaeralis Walker

BackgroundPhotosynthesizing tissue of teak (Tectona grandis L. f.) foliage is damaged by a host-specific insect pest called leaf skeletonizer (Eutectona machaeralis Walker) that severely eclipses annual growth increment and carbon sequestration of natural populations and plantation of teak. Gene-assisted selection of relatively resistant teak clones may efficiently control the damage in the populations and plantations. The present investigation aimed to identify genetic variation associated with relative resistance in teak against the pest. MethodThe investigation was carried out on 106 teak plus tree clones assembled at the National Teak Germplasm Bank from the Indian meta-population of teak. Resistance data were obtained recording the ocular damage caused by the pest to teak accessions for four years. Genotyping of the teak accessions was performed with 21 co-dominant markers and marker-trait association mapping was performed confirming the genetic structure of the germplasm bank and linkage disequilibrium (LD) among the marker loci. ResultsThe sampled teak accessions exhibited a low albeit highly admixed genetic structure (FST=0.07) and low level of LD (16.66%) among loci, making them suitable for high-resolution association analysis. A significant correlation (p[&le;]0.01, R2=0.67) was obtained between intra-specific heterozygosity and the relative resistance against the pest. A marker locus CCoAMT-1 representing the enzyme caffeoyl-CoA O-methyltransferase of phenylpropanoid pathway was also found significantly (p[&le;]0.05) associated with the relative resistance against the pest explaining 6.6% of the phenotypic variation (R2=0.066) through positive effect (0.57) on the trait. ConclusionsThe present work exhibited a significant correlation of intra-specific heterozygosity with relative resistance in teak against a pest. It is the first report on teak identifying genetic markers associated with relative resistance against the pest. The marker can be applied for the selection of resistant planting stock for breeding and commercial plantation. Further investigation can be performed to understand the expression level polymorphism linked with the resistance applying next-generation sequencing approaches.

plant biology↗

A New In-Silico Approach for PROTAC Design and Quantitative Rationalization of PROTAC mediated Ternary Complex Formation

Proteolysis-Targeting Chimeric Molecules (PROTAC) is a rapidly emerging technology for drug target protein degradation and drugging undruggable drug targets. There is a growing literature on in-silico approaches to the complex problem of PROTAC design, specifically the advantages of AI/ in-silico methods in the PROTAC Design Make Test Analyze (DMTA) cycle. Our work presented here aims to contribute to the growing literature of in-silico approaches to PROTAC design by incorporating and demonstrating incremental advancement over previously published methods. We use AI based generative methods for PRTOAC design and Molecular Dynamics to evaluate the stability of the ternary complex formed and ability of the PROTAC to hold the target protein and E3 ligase together stably. To quantify the performance of the PROTAC candidate, we also estimate computationally the PROTAC performance metrics routinely measured by the experimentalists in PROTAC assays. We use highly accurate absolute binding free energy calculations used traditionally in protein-ligand space for the PROTAC system. We calculate (Gibbs free energy change) {Delta}G for binary complex formation and ternary complex formation mediated by the PROTAC using Free Energy Perturbation - Thermodynamics Integration (FEP-TI) method which is benchmarked in literature with a root mean square error of 0.8 kcal/mol. We calculate {Delta}G for ternary and binary complexes and estimate whether {Delta}G for ternary is lower than the {Delta}G estimated for binary complexes. When the {Delta}G for ternary is lower than the binary it is inferred that ternary complexation is favoured over binary. Therefore, through these methods we can theoretical estimate {Delta}G measured by experimentalists in PROTAC assays such as Isothermal titration calorimetry (ITC) and Surface plasmon resonance (SPR) which capture the {Delta}G for ternary and binary complex formation mediated by the PROTAC. This method will help reduce time as well as costs of the PROTAC DMTA cycle and will accelerate early stage PROTAC drug discovery. As an illustrative application of our in-silico PROTAC design approach, we chose the target Fibroblast growth factor receptor 1(FGFR-1) which is a target approved drug for colorectal cancer. We report the findings and conclude with future research directions.

bioinformatics↗

Antimicrobials from a feline commensal bacterium inhibit skin infection by drug-resistant S. pseudintermedius.

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important emerging zoonotic pathogen that causes severe skin infections. To combat infections from drug-resistant bacteria, the transplantation of commensal antimicrobial bacteria as a therapeutic has shown clinical promise. We screened a collection of diverse staphylococcus species from domestic dogs and cats for antimicrobial activity against MRSP. A unique strain (S. felis C4) was isolated from feline skin that inhibited MRSP and multiple gram-positive pathogens. Competition experiments in mice showed that S. felis significantly reduced MRSP skin colonization and an antimicrobial extract from S. felis significantly reduced necrotic skin injury from MRSP infection. Fluorescence and electron microscopy revealed that S. felis antimicrobials disrupted bacterial but not eukaryotic cell membranes. LC/MS identified several S. felis phenol-soluble modulin beta (PSM{beta}) peptides that exhibited antimicrobial and anti-inflammatory activity. These findings indicate a feline commensal bacterium that could be utilized in bacteriotherapy against difficult-to-treat animal and human skin infections.

microbiology↗

Interfacial Water Molecules Make RBD of SPIKE Protein and Human ACE2 to Stick Together

A novel coronavirus (SARS-CoV-2; COVID-19) that initially originates from Wuhan province in China has emerged as a global pandemic, an outbreak that started at the end of 2019 which claims 431,192 (Date: 15th June 2020 (https://covid19.who.in) life till now. Since then scientists all over the world are engaged in developing new vaccines, antibodies, or drug molecules to combat this new threat. Here in this work, we performed an in-silico analysis on the protein-protein interactions between the receptor-binding (RBD) domain of viral SPIKE protein and human angiotensin-converting enzyme 2 (hACE2) receptor to highlight the key alteration that happened from SARS-CoV to SARS-CoV-2. We analyzed and compared the molecular differences between these two viruses by using various computational approaches such as binding affinity calculations, computational alanine, and molecular dynamics simulations. The binding affinity calculations show SARS-CoV-2 binds little more firmly to the hACE2 receptor than that of SARS-CoV. Analysis of simulation trajectories reveals that enhanced hydrophobic contacts or the van der Waals interaction play a major role in stabilizing the protein-protein interface. The major finding obtained from molecular dynamics simulations is that the RBD-ACE2 interface is populated with water molecules and interacts strongly with both RBD and ACE2 interfacial residues during the simulation periods. We also emphasize that the interfacial water molecules play a critical role in binding and maintaining the stability of the RBD/hACE2 complex. The water-mediated hydrogen bond by the bridge water molecules is crucial for stabilizing the RBD and ACE2 domains. The structural and dynamical features presented here may serve as a guide for developing new drug molecules, vaccines, or antibodies to combat the COVID-19 pandemic.

biophysics↗

Reproducible Bioinformatics Project: A community for reproducible bioinformatics analysis pipelines

BackgroundReproducibility of a research is a key element in the modern science and it is mandatory for any industrial application. It represents the ability of replicating an experiment independently by the location and the operator. Therefore, a study can be considered reproducible only if all used data are available and the exploited computational analysis workflow is clearly described. However, today for reproducing a complex bioinformatics analysis, the raw data and a list of tools used in the workflow could be not enough to guarantee the reproducibility of the results obtained. Indeed, different releases of the same tools and/or of the system libraries (exploited by such tools) might lead to sneaky reproducibility issues.\n\nResultsTo address this challenge, we established the Reproducible Bioinformatics Project (RBP), which is a non-profit and open-source project, whose aim is to provide a schema and an infrastructure, based on docker images and R package, to provide reproducible results in Bioinformatics. One or more Docker images are then defined for a workflow (typically one for each task), while the workflow implementation is handled via R-functions embedded in a package available at github repository. Thus, a bioinformatician participating to the project has firstly to integrate her/his workflow modules into Docker image(s) exploiting an Ubuntu docker image developed ad hoc by RPB to make easier this task. Secondly, the workflow implementation must be realized in R according to an R-skeleton function made available by RPB to guarantee homogeneity and reusability among different RPB functions. Moreover she/he has to provide the R vignette explaining the package functionality together with an example dataset which can be used to improve the user confidence in the workflow utilization.\n\nConclusionsReproducible Bioinformatics Project provides a general schema and an infrastructure to distribute robust and reproducible workflows. Thus, it guarantees to final users the ability to repeat consistently any analysis independently by the used UNIX-like architecture.

bioinformatics↗