Biology subjects

Shankar, S.

Publications and source records attributed to Shankar, S..

26 records · Page 2Linked to original sources

bioRxiv2020

Synergistic Coding of Human Odorants in the Mosquito Brain

The yellow fever mosquito Aedes aegypti employs olfaction to locate humans. We applied neural activity mapping to define the molecular and cellular logic of how the mosquito brain is wired to detect two human odorants that are attractive when blended together. We determined that the human breath volatile carbon dioxide (CO2) is detected by the largest unit of olfactory coding in the antennal lobe of the mosquito brain. Synergistically, CO2 detection gates pre-synaptic calcium signaling in olfactory sensory neuron axon terminals that innervate unique antennal lobe regions tuned to the human sweat odorant L-(+)-lactic acid. We propose that simultaneous detection of the signature human volatiles CO2 and L-(+)-lactic acid disinhibits a multimodal olfactory network for hunting humans in the mosquito brain.

neuroscience↗

bioRxiv2020

Predicting Adverse Drug Reactions of Two-drug Combinations using Structural and Transcriptomic Drug Representations to Train a Artificial Neural Network

Adverse drug reactions (ADRs) are pharmacological events triggered by drug interactions with various sources of origin including drug-drug interactions. While there are many computational studies that explore models to predict ADRs originating from single drugs, only a few of them explore models that predict ADRs from drug combinations. Further, as far as we know, none of them have developed models using transcriptomic data, specifically the LINCS L1000 drug induced gene expression data to predict ADRs for drug combinations. In this study we use the TWOSIDES database as a source of ADRs originating from two-drug combinations. 34,549 common drug pairs between these two databases were used to train an artificial neural network (ANN), to predict 243 ADRs that were induced by at least 10% of the drug pairs. Our model predicts the occurrence of these ADRs with an average accuracy of 82% across a multi fold cross validation. Source Code and input dataset used in this study can be found at: https://bitbucket.org/ishita98/prediction-of-adr/src/master/

bioinformatics↗

bioRxiv2019

BTK operates a phospho-tyrosine switch to regulate NLRP3 inflammasome activity

Activity of the NLRP3 inflammasome, a critical mediator of inflammation (1), is controlled by accessory proteins (2, 3), post-translational modifications (4, 5), cellular localization (6, 7) and oligomerization (8). How these factors relate, is unclear. We show that the established drug target, Brutons Tyrosine Kinase (BTK) (2, 9), integrates several levels of NLRP3 regulation: BTK phosphorylation of four conserved tyrosine residues, by neutralizing the charge of a polybasic linker region, weakens the interaction of NLRP3 with Golgi phospholipids and may thus guide NLRP3 cytosolic localization. BTK activity also promotes NLRP3 oligomerization and subsequent formation of inflammasomes. As NLRP3 tyrosine modification ultimately also impacts on IL-1{beta} release, we propose BTK-mediated, charge-switch-based NLRP3 regulation as a novel and therapeutically tractable step in the control of inflammation. One Sentence SummaryMulti-phosphorylation of NLRP3 by Brutons tyrosine kinase modulates NLRP3 cellular localization, inflammasome assembly, and IL-1{beta} release.

immunology↗

bioRxiv2019

An updated antennal lobe atlas for the yellow fever mosquito Aedes aegypti

The yellow fever mosquito Aedes aegypti is a prolific vector of arboviral and filarial diseases that largely relies on its sense of smell to find humans. To facilitate in-depth analysis of the neural circuitry underlying Ae. aegypti olfactory-driven behaviors, we generated an updated in vitro atlas for the antennal lobe olfactory brain region of this disease vector using two independent neuronal staining methods. We performed morphological reconstructions with replicate fixed, dissected and stained brain samples from adult male and female Ae. aegypti of the LVPib12 genome reference strain and determined that the antennal lobe in both sexes is comprised of approximately 80 discrete glomeruli. Guided by landmark features in the antennal lobe, we found 63 of these glomeruli are stereotypically located in spatially invariant positions within these in vitro preparations. A posteriorly positioned, mediodorsal glomerulus denoted MD1 was identified as the largest spatially invariant glomerulus in the antennal lobe. Spatial organization of glomeruli in a recently field-derived strain of Ae. aegypti from Puerto Rico was conserved, despite differences in antennal lobe shape relative to the inbred LVPib12 strain. This model in vitro atlas will serve as a useful community guide and resource to improve antennal lobe annotation and anatomically map projection patterns of neurons expressing target genes in this olfactory center. It will also facilitate the development of chemotopic maps of odor representation in the mosquito antennal lobe to decode the molecular and cellular basis of Ae. aegypti attraction to human scent and other chemosensory cues. Author SummaryThe olfactory system of the yellow fever mosquito Aedes aegypti is highly tuned for the detection of human odorants, as well as other chemical cues influencing host and food-search behavior, egg-laying and mating. To provide insights into the neuroanatomical organization of the olfactory system of this globally important disease vector, we have generated an updated in vitro atlas for the primary smell processing center of the Ae. aegypti brain, called the antennal lobe. These new guide maps facilitate systematic interrogation of antennal lobe morphology and naming of associated substructures in dissected brain samples of this species labeled with two common neural staining methods. We report that landmark features of the Ae. aegypti antennal lobe morphology and spatial organization appear conserved between mosquito sexes and across geographically divergent strains of this mosquito species. An improved understanding of Ae. aegypti antennal lobe neuroanatomy and how attractive or repellent odorant stimuli are encoded in this brain center has the potential to rapidly accelerate reverse engineering of synthetic chemical blends that effectively lure, confuse or repel this major disease vector.

neuroscience↗

bioRxiv2019

A low-cost and easy-to-use cell preservation reagent for 4{ring}C or room temperature sample storage

Current biospecimen storage and preservation methods no longer meet the demands of basic research and clinical diagnostics. Biospecimen preservation methodology has not advanced to accommodate cutting edge molecular analysis technologies that target single cells and full-length transcripts. Traditional methods, such as flash freezing and formalin-fixed paraffin-embedding (FFPE), were designed to provide information on cell structure and spatial relationships in whole tissues. These methods, however, do not maintain the integrity of proteins and nucleic acids. In this proof-of-concept study we examine preservation mechanisms utilized in nature for survival during cold seasons or periods of drought. Plants, brine shrimp, and tardigrades rely on components such as disaccharides or intrinsically disordered proteins to maintain cellular structure and biological activity in the settings of these environmental stresses. Our study demonstrates that these reagents aid in mammalian cell preservation for at least one week when a sample is stored in solution at 4{degrees}C, or as a dried sample in a low humidity desiccator.

pathology↗

bioRxiv2019

PROTEINATOR: Web-UI exploring repurposing hypotheses of PROTEIN InhibiTORs based on protein interactions

PROTEINATOR is the first version of a staggered, multi-paradigm and extensible drug repurposing platform, focusing on a novel data analytic and integration strategy to find repurposing candidates that have potential to modulate targets through protein-protein interactions. The UI was created as an explorer to find indirect drugs for a protein of interest. PROTEINATOR is developed as a web application that lets researchers search for alternate drugs for a protein of interest, based on the proteins direct interaction with a another druggable protein. This unique tool provides researchers exploring specific implicated protein(s) (in the context of drug development), alternate, plausible routes to modulation by listing proteins that interact with the protein of interest that have reported inhibitors. It is a search engine to identify indirect drugs through connecting various databases, thus avoiding multiple steps and avoiding any manual errors. Using a representative set of databases, 112083 number of indirect drug interactions are discovered that are potential modulators of proteins, detailed annotations of which are provided in the UI. PROTEINATOR is freely available at http://www.proteinator.in.

bioinformatics↗

bioRxiv2018

Karyopherin Kap114p regulates TATA-binding protein-mediated transcription

Gene expression is regulated by nuclear accessibility of transcription factors controlled by transport receptors and competitive inhibitors. Multiple karyopherin-{beta}s (Kap-{beta}s) facilitate nuclear import of yeast TATA-binding protein (yTBP). However, only Kap114p suppresses temperature-sensitive yTBP mutations, suggesting Kap114p executes undefined non-transport functions. We show that yTBP preferably binds Kap114p with an affinity three orders of magnitude higher than other Kap-{beta}s facilitating yTBP nuclear import. Our crystal structure of Kap114p reveals an extensively negatively-charged concave surface, accounting for high-affinity basic-protein binding. Furthermore, we biochemically demonstrate that two intra-HEAT-repeat inserts act as regulatory TBP-binding domains carried by TBP-associated factor 1 (TAF1-TAND), suppressing binding of yTBP with DNA and the transcription factor IIA. Remarkably, dual-knockout of Kap114 and TAF1-TAND in yeast synergistically suppresses cell growth. Our study reveals that Kap114p has a dual function that modulates the nuclear localization and activity of yTBP, illuminating how the nuclear transport machinery regulates yTBP-mediated transcription.

cell biology↗

bioRxiv2017

An Essential Role for Argonaute 2 in EGFR-KRAS Signaling in Pancreatic Cancer Development

KRAS and EGFR are known essential mediators of pancreatic cancer development. In addition, KRAS and EGFR have both been shown to interact with and perturb the function of Argonaute 2 (AGO2), a key regulator of RNA-mediated gene silencing. Here, we employed a genetically engineered mouse model of pancreatic cancer to define the effects of conditional loss of AGO2 in KRASG12D-driven pancreatic cancer. Genetic ablation of AGO2 does not interfere with development of the normal pancreas or KRASG12D-driven early precursor pancreatic intraepithelial neoplasia (PanIN) lesions. Remarkably, however, AGO2 is required for progression from early to late PanIN lesions, development of pancreatic ductal adenocarcinoma (PDAC), and metastasis. AGO2 ablation permits PanIN initiation driven by the EGFR-RAS axis, but rather than progressing to PDAC, these lesions undergo profound oncogene-induced senescence (OIS). Loss of Trp53 (p53) in this model obviates the requirement of AGO2 for PDAC development. In mouse and human pancreatic tissues, increased expression of AGO2 and elevated co-localization with RAS at the plasma membrane is associated with PDAC progression. Furthermore, phosphorylation of AGO2Y393 by EGFR disrupts the interaction of wild-type RAS with AGO2 at the membrane, but does not affect the interaction of mutant KRAS with AGO2. ARS-1620, a G12C-specific inhibitor, disrupts the KRASG12C-AGO2 interaction specifically in pancreatic cancer cells harboring this mutant, demonstrating that the oncogenic KRAS-AGO2 interaction can be pharmacologically targeted. Taken together, our study supports a biphasic model of pancreatic cancer development: an AGO2-independent early phase of PanIN formation reliant on EGFR-RAS signaling, and an AGO2-dependent phase wherein the mutant KRAS-AGO2 interaction is critical to prevent OIS in PanINs and allow progression to PDAC.

cancer biology↗