Biology subjects

Deshpande, K.

Publications and source records attributed to Deshpande, K..

7 recordsLinked to original sources

bioRxiv2026

A large-scale crowd-sourced annotated acoustic dataset of Indian fauna

Global rates of biodiversity loss warrant conservation action and monitoring at large geographic scales. Conservation technologies such as acoustic monitoring in conjunction with deep learning now enable us to monitor wildlife simultaneously across space and time. However, for a significant proportion of biodiversity in tropical regions, we cannot yet rely on automated recognition approaches because we lack acoustic templates to robustly train deep learning algorithms. In this paper, we relied on a novel participatory approach, enlisting researchers, conservation practitioners, and nature enthusiasts to create a unique crowd-sourced, open-access dataset of acoustic annotations across taxonomic groups for biodiversity in India. Our dataset comprises 3311 minutes of strongly labelled data (bounding boxes or annotations for a species vocalization) and 2504 minutes of weakly labelled data (indicating the presence of a species within an audio file but lacking bounding boxes) for 518 species across India, spanning 25 of 36 states and union territories. We present metadata and code for data processing and highlight the strengths of a participatory approach to biodiversity monitoring.

ecology↗

bioRxiv2024

PEARL: Protein Eluting Alginate with Recombinant Lactobacilli

Engineered living materials (ELMs) made of bacteria in hydrogels have shown considerable promise for therapeutic applications through controlled and sustained release of complex biopharmaceuticals at low costs and with reduced wastage. While most therapeutic ELMs use E. coli due to its large genetic toolbox, most live biotherapeutic bacteria in development are lactic acid bacteria due to native health benefits they offer. Among these, lactobacilli form the largest family of probiotics with therapeutic potential in almost all sites of the body with a microbiome. A major factor limiting the use of lactobacilli in ELMs is their limited genetic toolbox. In this study, we build upon our recent work to expand the genetic programmability of probiotic Lactiplantibacillus plantarum WCFS1 for protein secretion and encapsulate it in a simple, cost-effective, and biocompatible core-shell alginate bead to develop an ELM. We demonstrate the controlled release of recombinant proteins, even up to 14 days from this ELM, thereby terming it PEARL - Protein Eluting Alginate with Recombinant Lactobacilli. Notably, lactobacillus encapsulation offered benefits like bacterial containment, protein release profile stabilization, and metabolite-induced cytotoxicity prevention. These findings demonstrate the mutual benefits of combining recombinant lactobacilli with alginate for the controlled and sustained release of proteins.

bioengineering↗

bioRxiv2023

Polyimide-Based Flexible Multi-Electrode Arrays: Synthesis, Microfabrication, and in-vivo Validation

Neurological disorders such as epilepsy, Parkinsons disease, are rising globally, with conditions like drug-resistant epilepsy affecting millions of patients for whom traditional pharmacological treatments are ineffective. Implantable neural devices have shown great promise in managing these conditions, but their accessibility is limited due to high costs and the availability of suitable biocompatible materials.Thin film implantable neural interfaces hold immense promise over conventional clinical electrodes, offering higher resolution, flexibility, and improved integration with neural tissue. However, their widespread use, especially for flexible interfaces, is limited by the lack of customizable and medical grade materials. We report a novel synthesis method for ISO 10993-11 compliant polyamic acid that enables the fabrication of biocompatible polyimide films tailored for neural implants. Using this material, we developed 4 and 32 channel depth and surface electrodes, including custom whole brain ECoG arrays. These were implanted in the laforin knockout mice, a validated model of drug-resistant epilepsy, to monitor spontaneous seizures. Both acute and 12 day recordings demonstrated mechanical flexibility, long term stability, and excellent biocompatibility. This study presents a clinically safe material platform and a complete fabrication pathway for building thin film neural interfaces, paving the way for broader clinical use in applications such as epilepsy monitoring and stereo EEG.

bioengineering↗

bioRxiv2023

Nucleotide-protocell interactions: A reciprocal relationship in prebiotically pertinent environments

Spontaneous interactions between nucleotides and lipid membranes are likely to have played a prominent role in the emergence of life on Earth. However, the effect of nucleotides on the physicochemical properties of model protocellular membranes is relatively less understood. To this end, we aimed to discern the effect of canonical nucleotides on the properties of single-chain amphiphile membranes under prebiotically relevant conditions of multiple wet-dry cycles. Furthermore, the change in critical aggregation concentration of the membranes, and their stability in the presence of nucleotides, was also investigated in Astrobiologically analogue environments. We report that different nucleotides, lipid headgroups, and the ionic makeup of the system affect lipid-nucleotide interactions, which in turn can modulate the effect of nucleotides on the membranes. Specifically, oleic acid membranes seemingly showed an increase in the critical aggregation concentration, and an increase in the stability against prebiotically relevant selection pressures, in the presence of certain nucleotides. Our work has implications for understanding how nucleotides might have shaped the protocellular landscape of the prebiotic Earth.

biochemistry↗

bioRxiv2021

Accurate detection of RNA stem-loops in structurome data reveals widespread association with protein binding sites

RNA molecules are known to fold into specific structures which often play a central role in their functions and regulation. In silico folding of RNA transcripts, especially when assisted with structure profiling (SP) data, is capable of accurately elucidating relevant structural conformations. However, such methods scale poorly to the swaths of SP data generated by transcriptome-wide experiments, which are becoming more commonplace and advancing our understanding of RNA structure and its regulation at global and local levels. This has created a need for tools capable of rapidly deriving structural assessments from SP data in a scalable manner. One such tool we previously introduced that aims to process such data is patteRNA, a statistical learning algorithm capable of rapidly mining big SP datasets for structural elements. Here, we present a reformulation of patteRNAs pattern recognition scheme that sees significantly improved precision without major compromises to computational overhead. Specifically, we developed a data-driven logistic classifier which interprets patteRNAs statistical characterizations of SP data in addition to local sequence properties as measured with a nearest neighbor thermodynamic model. Application of the classifier to human structurome data reveals a marked association between detected stem-loops and RNA binding protein (RBP) footprints. The results of our application demonstrate that upwards of 30% of RBP footprints occur within loops of stable stem-loop elements. Overall, our work arrives at a rapid and accurate method for automatically detecting families of RNA structure motifs and demonstrates the functional relevance of identifying them transcriptome-wide.

genomics↗

bioRxiv2020

Subventricular zone adult mouse neural stem cells and human glioblastoma stem cells require insulin receptor for self-renewal

The insulin receptor (IR) is an evolutionarily conserved signaling protein that regulates development and cellular metabolism. IR signaling regulates neurogenesis in Drosophila; however, a specific role for the IR in maintaining adult neural stem cells (NSCs) in mammals has not been investigated. We show that conditionally deleting the IR reduces adult NSCs of the subventricular zone by [~]70% accompanied by a corresponding increase in progenitors. IR deletion produced hyposmia due to aberrant olfactory bulb neurogenesis. Interestingly, hippocampal neurogenesis was not perturbed nor were hippocampal dependent behaviors. Highly aggressive proneural and mesenchymal glioblastomas (GBMs) had high IR/insulin-like growth factor (IGF) pathway gene expression, and isolated glioma stem cells had an aberrantly high ratio of IR:IGF1R receptors. Moreover, IR knockdown inhibited proneural and mesenchymal GBM tumorsphere growth. Altogether, these data demonstrate that the IR is essential for a subset of normal NSCs as well as for brain tumor cancer stem cell self-renewal.

neuroscience↗

bioRxiv2019

Environmental influences on acoustic divergence in Rhinolophus bats of the Western Ghats-Sri Lanka region

According to the acoustic adaptation hypothesis, environmental and biogeographic factors such as atmospheric humidity can influence divergence of acoustic signals and speciation in high duty-cycle echolocating bats (e.g. Rhinolophus sp.), although this remains disputed. In this study we tested the hypothesis that Resting Frequency (RF) would decrease with increasing humidity along a large latitudinal gradient (6{degrees}-21{degrees} N), for four Rhinolophus species with different evolutionary histories, in the Western Ghats-Sri Lanka (WGSL) region. We conducted acoustic recordings and compiled published information on RFs of stationary Rhinolophus indorouxi, R. rouxi, R. beddomei, and R. lepidus from 40 roosts in 18 localities of the WGSL. These data comprised of recordings made with different devices and with different settings. Hence, due to the unknown measurement error involved in the recorded RFs, it was not possible to conduct conventional regression analyses to test our hypotheses. Hence, we qualitatively assessed effects of Relative Humidity (RH) and other environmental variables by interpreting only the sign, but not the magnitude of the RF responses (from the slopes of generalized least squares regression models). We also tested how RF and RH varied across biogeographic zones, and with bat body size. RFs of the Miocene-diverged species R. indorouxi and R. rouxi were higher at lower RH, as expected. In contrast, RF of the Pleistocene-diverged species R. beddomei and R. lepidus were higher at higher RH. Elevation and rainfall also emerged as important predictors of RF variation in these species. Bat body size differed in dry and humid regions of the WGSL. RF variation was not consistent across biogeographic zones. The cryptic, phonically differentiated sibling species R. indorouxi and R. rouxi co-occurred only in mid-elevation zones along the Western Ghats escarpment. The variable but significant influences of humidity and correlated factors on RF suggest the importance of environmentally mediated acoustic divergence in different Rhinolophus species in the WGSL. We propose some hypotheses on interacting effects of environmental and phylogenetic factors on acoustic divergence in Rhinolophus bats of the WGSL. These ideas could be further tested with phylogenetic and acoustic studies, as more consistent and comparable data on these species become available in the future.

ecology↗