Biology subjects

Biswas, D.

Publications and source records attributed to Biswas, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Identifying the source population of naturally recolonised rhinoceros (Rhinoceros unicornis) in Laokhowa-Burhachapori Wildlife Sanctuary, Assam, through multidisciplinary methods

Megaherbivore population recovery largely depends on restoring connectivity between fragmented protected areas to facilitate natural dispersal, gene flow, and range expansion. The Indian rhinoceros (Rhinoceros unicornis) has recovered from severe population decline in the past, but several populations remain spatially restricted. Recent conservation efforts and the expansion of protected areas in Assam have coincided with natural rhino recolonization in Laokhowa-Burhachapori Wildlife Sanctuary (WLS). This has occurred from nearby regions of Orang NP and Kaziranga NP after the species was locally extinct in the 1980s. Identifying the source population of these recolonised rhinos is crucial for managing this emerging metapopulation. We used non-invasive genetic sampling, genetic assignment and a landscape connectivity model to investigate the origin and potential movement routes of the recolonising rhinos. We identified eight unique individuals from Laokhowa-Burhachapori WLS and assigned them to the potential source population using Bayesian and frequency-based approaches against a reference dataset of 365 individual rhinos across the rhino-bearing areas of Assam. Habitat suitability was modelled using 161 spatially thinned presence points and eight environmental variables. We applied least-cost path (LCP) analysis to assess landscape resistance between protected area nodes. All eight recolonising rhinos were assigned to Orang NP with high Bayesian assignment probabilities (q = 0.97-0.99). The connectivity model identified two least-cost pathways, with the Orang NP-Laokhowa-Burhachapori WLS linkage showing lower landscape friction than the Kaziranga NP linkage. These findings provide genetic evidence that the recolonisation occurred through natural dispersal, most likely from Orang NP, and indicate that recent landscape restoration has re-established the structural connectivity across this floodplain. Maintaining these linkages will be essential to promote natural range expansion and the long-term persistence of Indian rhinoceros in Assam.

ecology↗

bioRxiv2026

Inbred and outcrossed Drosophila embryos diverge in stress defense and developmental maintenance during heat stress

Early embryos must mount stress defenses without compromising the developmental programs that drive morphogenesis, but whether genetic background alters this balance remains unclear. We compared cellularizing Drosophila melanogaster embryos from inbred and outcrossed backgrounds under control conditions and after acute or chronic heat-stress. Both backgrounds developed successfully and showed modest transcriptomic differences at 18{degrees}C. Heat stress at 32{degrees}C, however, sharply separated their phenotypic and transcriptional responses. Inbred embryos showed poor larval hatching after acute and chronic heat, and this deficit persisted through adult eclosion. Their transcriptomes exhibited a greater stress-response burden, with enrichment of proteostasis, DNA repair, mitochondrial maintenance, RNA processing, and metabolic remodeling programs. Outcrossed embryos retained substantially greater developmental survival and higher abundance of transcripts associated with development, adhesion, epithelial organization, signaling, transport, sensory responses, and morphogenesis. Background-dependent divergence was greatest during acute heat. Under chronic heat, background-dependent differences were fewer, with most overlapping those seen during acute heat and a smaller set detected only under chronic heat. Transcript-origin analysis further showed that acute outcrossed-biased genes were predominantly maternally derived and showed no enrichment for purely zygotic transcripts, whereas chronic outcrossed-biased genes contained a larger zygotic component. In summary, the less viable inbred background mounted the broader molecular stress signature, whereas the more viable outcrossed background retained greater abundance of development-associated transcripts. These findings identify genetic background as a major determinant of how embryonic heat responses are distributed between molecular stress defense and developmental gene expression.

genetics↗

bioRxiv2026

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets

The complement of tumor cell surface proteins, or "surfaceome", is a rich source of potential immunotherapy targets. To move beyond expression-based target discovery, we previously described "structural surfaceomics," combining crosslinking mass spectrometry (XL-MS) with surface protein biotinylation to identify conformation-selective targets. In our prior work, we applied this method to a single model of acute myeloid leukemia (AML), identifying active integrin beta-2 as a promising target. Here, we expand structural surfaceomics to identify additional immunotherapy targets and surface protein biology across additional models of AML, multiple myeloma, and prostate cancer, as well as donor peripheral blood mononuclear cells. Utilizing these models and different chemical crosslinkers, we compile an extensive database of 5,209 crosslinks. We characterize both shared and unique crosslink-based features, identifying 1,612 disease model-specific crosslinks, including 212 potentially defining tumor-specific conformations based on distance constraint violations relative to AlphaFold predictions. We further implement a suite of emerging modeling tools to predict tumor-specific protein structures. We probe crosslinking patterns suggesting multiple myeloma-specific CD48 and AML-specific integrin 1/{beta}4 heterodimer conformations. This work establishes a resource for cancer structural biology by implementation of structural surfaceomics. Our findings also point toward more realistic protein design models, potentially enabling systematic detection of targetable cancer-specific epitopes for next-generation immunotherapies.

cancer biology↗

bioRxiv2026

Paclitaxel sensitizes TRAIL (tumor necrosis factor-related apoptosis-inducing ligand)-resistant breast cancer cells towards TRAIL-mediated apoptosis

BackgroundThe ability of TRAIL to specifically induce apoptosis in cancer cells makes it a promising candidate to be an effective chemotherapeutic drug. But resistance to TRAIL treatment is a major obstacle. Finding combinatorial therapies that make resistant tumors more susceptible to TRAIL is an effective preclinical approach. In this work, we investigated the possibility that pre-treatment of paclitaxel may promote apoptosis in TRAIL-resistant breast cancer cells. MethodsIn silico analysis was done to investigate the binding affinity between TRAIL receptors (DR5 and DCR2) and paclitaxel via docking and MD simulation. To check whether any non-lethal dose of paclitaxel can modulate the expression of TRAIL receptors, qPCR was done in paclitaxel treated breast cancer cells. Next, paclitaxel was pre-administered to TRAIL-resistant MCF7 and MDA-MB-453 human breast cancer cells followed by rhTRAIL treatment. Cell viability and survival was evaluated using the MTT assay and colony formation assay, respectively. Immunoblot for caspase-3 was performed to study apoptosis. The expression level changes of DR5 and DCR2 were analyzed post-treatment using qPCR and immunoblot assay. ResultsIn silico analysis showed that paclitaxel can bind with higher stability to DCR2 in comparison to DR5 thereby changing the preference of TRAIL molecules towards DR5. Next, in cell line experiments we observed that administering a non-lethal dose of paclitaxel to MDA-MB-231 and MCF7 breast cancer cells resulted in no significant cell death but led to an increase in DR5 and a decrease in DCR2 expression at both the transcript and protein levels. Furthermore, in TRAIL-resistant MCF7 and MDA-MB-453 cells, pre-treatment with paclitaxel followed by rhTRAIL administration induced significant cell death due to paclitaxel induced increase in DR5 as well as decrease in DCR2 expression at both the transcript and protein levels. Moreover, long term survival of MDA-MB-453 cells was significantly lower when pretreated with paclitaxel and exposed to rhTRAIL compared to control, paclitaxel alone or rhTRAIL alone group. ConclusionThus, our study uncovers a novel therapeutic strategy to overcome TRAIL resistance underscoring the clinical potential of using a non-lethal dose of paclitaxel to modulate TRAIL receptor dynamics. Future research should be aimed at exploring the potentiality of using paclitaxel-based combinatorial approaches in crafting effective TRAIL therapies.

cancer biology↗

bioRxiv2026

Reactive Astrocytes Drive Extracellular Acidification to Mediate α-Synuclein Neurodegeneration

Astrocytes are increasingly recognized as key players in neurodegeneration1-3, yet the molecular mechanisms by which they drive disease remain elusive. Here, we uncover a fundamental pathway in which reactive astrocytes fuel neurodegeneration in -synucleinopathies--including Dementia with Lewy bodies and Parkinsons disease dementia--by acidifying the brains extracellular environment. We demonstrate that both human patient tissue and a gut-to-brain -synuclein mouse model exhibit accumulation of reactive astrocytes and extracellular acidosis. Mechanistically, we show that astrocytic lysosomal exocytosis releases acidic contents, driving a drop in pH that activates neuronal acid-sensing ion channel 1a (ASIC1a), resulting in neuronal loss and behavioral decline. Blocking this pathway--either by inhibiting astrocytic lysosomal exocytosis or genetically or pharmacologically targeting neuronal ASIC1a--mitigates pathology and rescues neurodegenerative phenotypes in vivo. These findings provide a conceptual advance by establishing a mechanistic link between glial inflammation, acid-base homeostasis, and neuronal vulnerability, and suggest that targeting astrocyte-driven acidification or ASIC1a signaling could offer new avenues for disease modification in -synucleinopathies.

neuroscience↗

bioRxiv2025

Synergy unleashed: Leishmania donovani GP63 paralogues cooperatively function to drive parasite infectivity at various pathogenic stages and regulate host survival mechanisms

Highly plastic genome of Leishmania is thought to underlie its remarkable ability to adapt to diverse host microenvironments, yet how this plasticity translates into dermal versus visceral persistence remains unclear. GP63, a zinc metalloprotease, is a well-established determinant of promastigote infectivity, particularly in cutaneous leishmaniasis. Despite this, its role in amastigote stage and in visceral disease caused by Leishmania donovani remains undefined. Here, using an integrated approach combining phylogenetics, CRISPR-mediated genome editing, and biochemical analyses, we demonstrate that GP63 paralogues in L. donovani have undergone independent evolutionary diversification to support visceral infection. While GP63-paralogues encoded on chromosome 10, previously implicated in cutaneous manifestation caused by L. major, were found severely truncated and dispensable in L. donovani, two distinct GP63-paralogues encoded on chromosome 28 and 31 were found essential to establish visceral infection. LdGP63_31 facilitates promastigote attachment to macrophages by promoting lipid raft engagement and complement inactivation, thereby enabling host entry and subsequent amastigote differentiation. LdGP63_28 is essential for intracellular amastigote survival by suppressing host inflammatory pyroptosis. Structural and enzymatic analyses revealed preferential host localization and substrate specificities, possibly resulting from distinct amino acid substitution within conserved motifs of these proteases, indicating independent evolutionary adaptations. Importantly, loss of the LdGP63_28 more severely impaired amastigote reinfection than loss of its counterpart LdGP63_31. Together, these findings reveal coordinated functional specialization of GP63-paralogues ensuring visceral adaptation.

microbiology↗

bioRxiv2025

How tp1, an indirect wing steering muscle, stabilizes Drosophila's flight

Flapping flight is inherently unstable, requiring Drosophila to fine-tune their wing motions on a milliseconds timescale. Pioneering studies have shown that the direct steering muscles, which attach to the wing hinge, are important for generating these rapid flight reflexes. Recent connectome data, however, reveal that indirect steering muscles or tension muscles, which alter the mechanics of the thorax, receive some of the same synaptic inputs from the sensory apparatus as the direct steering muscles. This discovery suggests that the indirect steering muscles may also be important for flight control. Here, we show that the indirect tergopleural muscles indeed contribute substantially to stabilization, particularly for large pitch perturbations. We find that for small perturbations (less than 1000 deg/s), flies modulate their wing stroke amplitude to generate lift-based corrective torques, a strategy that has been previously documented. For larger perturbations, however, we observe that Drosophila engage an additional wing degree of freedom--the wing pitch angle--to leverage additional lift and drag forces during the corrective maneuver. Quasi-steady aerodynamic simulations reveal that this strategy minimizes power consumption, anaolgous to how some mammals (including humans) adjust their steady-state gaits in a near energy-optimal manner. Using optogenetics and a control theory framework we demonstrate that the tergopleural muscle is activated by a proportional gain component of a nonlinear PI controller responsible for determining the wing pitch angle during large perturbations. A simplified torsional-spring model for the wing hinge captures the changes in the wing pitch dynamics observed during correction maneuvers by using the tergopleural muscle to adjust the rest angle of the wing. These findings provide a striking example of reflex strategy selection in time-critical behaviors and underscores the vital role of indirect steering muscles in flight stabilization.

neuroscience↗

bioRxiv2025

Common and distinct roles of AMPKγ isoforms in small-molecule activator-stimulated glucose uptake in mouse skeletal muscle

ObjectiveSmall-molecule activators targeting the allosteric drug and metabolite (ADaM) site of AMPK enhance insulin-independent glucose uptake in skeletal muscle and lower glucose in preclinical models of hyperglycemia. The regulatory AMPK{gamma} subunit plays a central role in energy sensing. While the skeletal muscle-selective {gamma}3 isoform is essential for AMP/ZMP-induced glucose uptake, it is dispensable for ADaM site-binding activators. We hypothesized that the predominant {gamma}1 isoform is required for ADaM site activator-stimulated glucose uptake in skeletal muscle. MethodsSingle-nucleus RNA sequencing (snRNA-seq) was performed on mouse and human skeletal muscle mapping AMPK subunit isoform distribution across resident cell types. To determine {gamma} isoform-specific requirements for activator-stimulated glucose uptake, skeletal muscle-specific inducible AMPK{gamma}1/{gamma}3 double knockout (im{gamma}1-/-/{gamma}3-/-) and single knockout (im{gamma}1-/- and im{gamma}3-/-) mice were generated. Ex vivo glucose uptake was measured following treatment with AICAR (AMP-mimetic) or MK-8722 (ADaM site activator), and in vivo MK-8722-induced blood glucose lowering was assessed. ResultssnRNA-seq revealed distinct AMPK isoform distribution: {gamma}1 was ubiquitously expressed, whereas {gamma}3 was enriched in glycolytic myofibers in both mouse and human skeletal muscle. Ex vivo, glucose uptake stimulated by either AICAR or MK-8722 was abolished in im{gamma}1-/-/{gamma}3-/- muscle, and MK-8722-induced blood glucose lowering was significantly blunted in vivo. AICAR but not MK-8722-stimulated muscle glucose uptake was abolished in im{gamma}3-/-, whereas both activators fully retained effects on glucose uptake and glucose lowering in im{gamma}1-/- mice. ConclusionsWhile {gamma}1 predominates in stabilizing the AMPK2{beta}2{gamma}1 complex, it is dispensable for AMPK activator-stimulated glucose uptake in skeletal muscle, whether mediated via the nucleotide-binding or ADaM site.

biochemistry↗

bioRxiv2025

Cell migration sculpts evolutionary dynamics favouring therapy resistance in lung cancer

The evolution of cancer undermines the long-term efficacy of therapy. In this study, we combine experimental, computational, and clinical data analysis to investigate factors influencing the competition of subclones in lung cancer. Lineage tracing reveals unexpected variation in the long-term fate of neutral subclones, with subclones arising near the edge of tumours being favoured. Low levels of cell migration and cell mixing lead to high cell densities in the interior of the tumour that suppress proliferation. Using agent-based modelling and in silico analysis we inferred the extent of cell mixing in human tumours from the TRACERx lung cancer study. This reveals correlations between Epithelial to Mesenchymal Transition (EMT), stromal fibroblasts and levels of cell mixing. Experimental analysis confirms that both TGF{beta}-driven EMT and stromal fibroblasts reduce the variability in subclone fate and promote subclone mixing. Moreover, mixing favours clonal sweeps by subclones resistant to therapy-induced cell killing. Together, these analyses demonstrate that EMT and stromal fibroblasts sculpt tumour evolution by promoting cell mixing and thereby favour the rapid dominance of therapy resistant subclones.

cancer biology↗

bioRxiv2025

Poly(ADP-ribose) Polymerase 1 Deficiency Attenuates Amyloid Pathology, Neurodegeneration, and Cognitive Decline in a Familial Alzheimer Disease Model

Poly(ADP-ribose) (PAR) polymerase-1 (PARP1) has been implicated in DNA damage responses and neuroinflammation in Alzheimers disease (AD), yet its role in amyloid-{beta} (A{beta}) pathology remains unclear. Here, we show that PARP1 activation drives A{beta} pathology and neurodegeneration. Using a sensitive ELISA, we observed significantly elevated PAR levels in the cerebrospinal fluid (CSF) of patients with mild cognitive impairment (MCI) and AD compared to controls. In vitro, oligomeric A{beta}1-42 activated PARP1 and induced DNA damage, while genetic or pharmacological inhibition of PARP1 conferred neuroprotection. In vivo, PARP1 knockout in the 5XFAD mouse model of amyloidosis led to reduced amyloid plaque burden, preserved synaptic and neuronal integrity, attenuated glial activation and neuroinflammation, and rescued cognitive deficits. Mechanistically, PARP1 deficiency decreased amyloid precursor protein (APP) and BACE1 levels, altered {gamma}-secretase complex composition, and enhanced A{beta} degradation via neprilysin. These findings position PARP1 as a critical mediator of A{beta} toxicity and neurodegeneration, suggesting its inhibition as a promising therapeutic strategy for AD. Significance StatementOur study identifies poly(ADP-ribose) (PAR) as an elevated biomarker in the cerebrospinal fluid of patients with mild cognitive impairment and Alzheimers disease, correlating with established markers of amyloid pathology. We demonstrate that PARP1, the enzyme responsible for PAR synthesis, is activated by neurotoxic A{beta}1-42 and mediates neuronal death, amyloid plaque formation, neuroinflammation, and cognitive deficits in a mouse model of AD. Importantly, genetic ablation of PARP1 not only protects neurons from A{beta} toxicity but also reduces amyloid burden by suppressing A{beta} production and enhancing its degradation. These findings highlight PARP1 as a critical regulator of amyloid pathology and neurodegeneration, and suggest that PARP1 inhibition may offer a promising therapeutic avenue for Alzheimers disease by simultaneously targeting multiple pathogenic mechanisms.

neuroscience↗

bioRxiv2025

AlphaCross-XL: a seamless tool for automated and proteome-scale map-ping of crosslinked peptides onto three-dimensional protein structures

Crosslinking mass spectrometry (XL-MS) is an exciting proteomics technology to capture native protein conformations in real time within biological systems. Historically, however, implementation of this technology has typically been limited to single purified recombinant proteins or in vitro assembled protein complexes. These limitations are associated with inherent challenges in XL-MS analysis, including extremely low abundance of crosslinked (XL) peptides and complex deconvolution of XL peptide-derived spectral data. However, impressive recent developments in computation and instrumentation have now made it feasible to address biological questions using proteome-wide XL-MS analysis. Although some XL mapping software tools exist, these require manual input of specific Protein Data Bank (PDB) structures at the single protein level, and do not function at the high throughput scale required to analyze datasets derived from thousands of proteins. To address this need, we therefore sought to develop a strategy enabling automated mapping of XL peptides onto the three-dimensional (3D) structures of proteins, at a proteome-wide scale. Herein we describe AlphaCross-XL, a first-in-class seamless computational tool for automated mapping of XL peptides onto the protein structures for intra-protein crosslinks and loop-links. The AlphaCross-XL software first retrieves protein structures from the AlphaFold Protein Structure Database and maps all the identified crosslinks onto the 3D structure. It also calculates the Euclidian distance between the crosslinked residues and reports the violated and satisfied crosslink distances based on a user-defined distance threshold, which is visually discriminated by color in PyMOL. Lastly, the tool also supports further validation of user-submitted protein structures, that can include any computer-predicted protein structure and experimentally derived protein structures (i.e., from PDB). AlphaCross-XL is available at https://github.com/sanjyotshenoy/alphacross-xl.

bioinformatics↗

bioRxiv2025

Distinct region-specific neutralization profiles of contemporary HIV-1 clade C against best-in-class broadly neutralizing antibodies

Broadly neutralizing antibodies (bnAb) have been clinically proven to be an excellent choice for HIV-1 prevention. However, the relative effectiveness of best-in-class bnAbs against regionally relevant circulating HIV-1 forms is not clear. In the present study, we compared the degree of neutralization sensitivity of contemporary HIV-1 Indian clade C with that of South African origin. Phylogenetic analysis revealed that these clade C viruses continue to evolve distinctly from one another. Env-pseudotyped viruses prepared using contemporary HIV-1 clade C env genes (N=115) obtained from nine geographically distinct sites in India (between 2020-2023) were found to be most sensitive to V3-directed bnAbs 10-1074 and BG18, and second generation CD4 binding site (CD4bs) directed bnAbs (VRC07, N6 and 1-18), however they were found to be significantly resistant to V1/V2 apex directed bnAbs. Moreover, we observed that the degree of sensitivity varied between contemporary Indian and South African clade C viruses. Differences in degree of neutralization susceptibility were associated with differences observed in key residues that form bnAb contact sites, gp120 loop lengths and the number of N-linked glycans in the V4 hypervariable region. Interestingly, the second generation CD4bs bnAbs (VRC07, N6, 1-18) showed neutralization of VRC01 and 3BNC117 resistant viruses but with 2-7-fold reduced potency compared to the VRC01 sensitive counterparts, likely due to the enrichment of resistance associated residues observed in loop D. Predictive analysis indicated that combination of BG18, N6 and PGDM1400 can provide over 95% neutralization coverage at 1g/mL of contemporary India clade C, an observation found to be distinct to that reported for the Africa clade C viruses. Taken together, we found distinct neutralization patterns and env signatures associated with resistance to key bnAbs. Our study highlights that towards achieving clinical effectiveness, both the complementarity of bnAb classes and the regionally relevant HIV forms need to be considered. Author summaryWhile the development of vaccines to prevent HIV infection remains a global priority, their potential effectiveness is limited by the extraordinarily diversified circulating forms of HIV-1. The prospect of best-in-class bnAbs as potential prevention option has been demonstrated in several studies including the Phase II Antibody Mediated Prevention (AMP) trial; however, to be broadly applicable, bnAbs will need to overcome the substantial variability of HIV env. The present study highlights that the contemporary HIV-1 clade C viruses are evolving to be less sensitive to the best-in-class bnAbs and HIV-1 clade C that predominates in India and South Africa vary in their degree of susceptibility to best-in-class clinically relevant bnAbs. This indicates differences in the antigenic properties between globally circulating HIV-1 clade C at a population level. Overall, the outcome of this study highlights the need for periodic assessment of sequence and neutralization profiles of the circulating regionally relevant HIV-1 forms towards prioritizing the bnAb combination suitable for effective intervention.

immunology↗

bioRxiv2024

Illumination mediates a switch in both active sensing and control in weakly electric fish

To execute sensory-guided behavior, the nervous system must manage uncertainty within multiple streams of information. There are two highly nonlinear mechanisms for achieving this: 1) sensory reweighting, an internal neural computation which places more emphasis on sensory information that exhibits the least uncertainty, e.g. in a Bayesian framework, and 2) active sensing, an overt behavior that seeks to improve the quality of sensory information before it enters the nervous system. Here we show that animals solve both of these nonlinear problems concurrently. We studied how the weakly electric glass knifefish Eigenmannia virescens alters its movement dynamics under parametric manipulations of illumination. We hypothesized a concomitant switch in both overt active sensing and internal multisensory reweighting. To test this, we varied illumination levels from 0.1 to 210 lx as fish tracked a moving refuge. We discovered that in a neighborhood of a critical threshold (on the order of 1 to 10 lx), small increases in illumination led to dramatic changes in both active sensing and multisensory control, specifically in 1) steep reductions in fish head and tail movements and 2) decreased refuge tracking phase lag. Outside of this threshold, large changes in illumination only caused small changes in active sensing and control. A control-theoretic model that dynamically modulates the weights of vision and electrosense due to illumination changes corroborates our findings. These findings underscore the complex, multipartite, nonlinear nature of locomotor control and the remarkable ability of the nervous system to execute multiple parallel strategies for managing sensory uncertainty.

animal behavior and cognition↗

bioRxiv2024

Protocol for muscle fiber type and cross-sectional areaanalysis in cryosections of whole lower mouse hindlimbs

We outline a robust, simple, and cost-effective method to simultaneously visualize all mouse lower hindlimb skeletal muscles. We describe procedures for orientating the whole lower hindlimb in gum tragacanth prior to freezing, simplifying the proceeding experimental steps, and enhancing the clarity and comprehensiveness of characterizations. We then detail steps for quantifying muscle fiber size and fiber type characteristics in a single cryosection using immunofluorescence and histochemistry. This protocol can be applicable for commonly used histological and (immuno) histochemical evaluations such muscle degeneration/regeneration, fibrosis, immune cell infiltration, enzymatic activity and glycogen content. HighlightsO_LIEmbedding and orientating mouse lower hindlimb in tragacanth before freezing enhances clarity and simplifies steps. C_LIO_LISimultaneously visualizing myofibers in different muscle compartments enables efficient and comprehensive evaluations of morphology and physiological characteristics. C_LIO_LISingle cryosection analysis of myofiber size and types with immunofluorescence. C_LIO_LIApplicable for evaluating muscle degeneration, fibrosis, and immune infiltration. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/608909v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@9d3fe4org.highwire.dtl.DTLVardef@1cdcc85org.highwire.dtl.DTLVardef@2e494eorg.highwire.dtl.DTLVardef@cebfc6_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Modeling of whole brain Electroencephalogram (EEG) in a spatially organized oscillatory network

In this study, we model high-dimensional Electroencephalogram signals in sleep stages, using a general trainable network of Hopf oscillators. The proposed architecture has two components: a layer of oscillators with lateral connections, and a complex valued feedforward network with and without a hidden layer. The output of the Hopf oscillators, whose dynamics is described in the complex domain, is fed as input to the feedforward network and the output predicts the EEG signals. The proposed network is trained in two stages: in the 1st stage, intrinsic frequencies of the oscillators and the lateral connections are trained whereas, in the 2nd stage, the complex-valued feed-forward network is trained. Reconstruction error obtained when there is a hidden layer in the feedforward network is an order of magnitude smaller than that obtained without a hidden layer. Also, it has been shown that during testing our model is able to generate EEG signals, whose spectral properties accurately describe the corresponding target signals. In the first, the oscillators do not have any spatial localization, whereas in the second the oscillators are spatially distributed in a spherical shell geometry. The model described can be interpreted as a stepping stone towards a large-scale model of brain dynamics.

neuroscience↗

bioRxiv2023

BrainProt(™) 3.0: Understanding Human Brain Diseases using comprehensively curated & Integrated OMICS datasets

BrainProt 3.0 is an integrative and simplified omics-based knowledge base of the human brain and its associated diseases. The current version of BrainProt includes six domains, which provide simplified, robust, and comprehensive data visualization to understand the human brain and its diseases/disorders based on proteomics, transcriptomics, public data curation, and integration strategies. Firstly, the HBDA (Human Brain Disease Atlas), index and navigator of BrainProt provides a resource table for 56 brain diseases. Secondly, Brain Disease Marker Curator (BDMC) and Brain Disease Drug Finder (BDDF) include a total of 20,202 diseases associated genes, more than 1,30,000 Chemical Target interactions, and around 2,145 Clinical Trial Information for more than 50 Brain Diseases. Thirdly, Brain Disease Transcriptome Map (BDTM) and Brain Disease Proteome Map (BDPM) integrate multi-omics data for 11 and 6 alarming brain diseases respectively. Currently, these two domains feature an expressional profile of 52 datasets, information of 1,868 samples, 3,657 DEPs, and 6,256 DEGs. Lastly, BrainProt also modifies and integrates the proteome and phosphoproteome data of the Inter-hemispheric Brain Proteome Map (IBPM). Overall, BrainProt is the first knowledgebase that connects different omics level information of brain diseases and provides a powerful scoring-based ranking platform to select and identify brain disease-associated markers, along with exploration of clinical trials, and drugs/chemical compounds to accelerate the identification of new disease markers and novel therapeutic strategies. The objectives of BrainProt are to support and follow the footsteps of the HBPP (Human Brain Proteome Project) by integrating different datasets to unravel the complexity of Human Brain and its associated diseases.

neuroscience↗

bioRxiv2023

Organisms employ a mode-switching strategy for solving the explore-vs-exploit problem

The inescapable link between sensing and movement generates a conflict between producing costly movements for gathering information ("explore") versus using previously acquired information to achieve a goal ("exploit"). Determining the optimal balance between explore and exploit is a computationally intractable problem, necessitating the use of heuristics. We looked to nature to measure and model the solutions used by organisms. Here we show that the electric fish Eigenmannia virescens uses a salience-dependent mode-switching strategy to solve the explore-exploit conflict during a refuge tracking task. The fish produced distinctive non-Gaussian (i.e., non-normal) distributions of movement velocities characterized by sharp peaks for slower, task-oriented "exploit" movements and broad shoulders for faster, "explore" movements. The measures of non-normality increased in relation to increased sensory salience. Data from ten phylogenetically diverse organisms, from amoebae to humans, revealed the same distinctive distribution of movement velocities that were also modulated in relation to sensory salience. We propose a state-uncertainty based mode-switching heuristic that (1) reproduces the distinctive velocity distribution, (2) rationalizes modulation by sensory salience, and (3) outperforms the classic persistent excitation approach while using less energy. This mode-switching heuristic provides insights to purposeful exploratory behaviors in organisms as well as a framework for more efficient state estimation and control of robots.

animal behavior and cognition↗

bioRxiv2023

A dynamic partitioning mechanism polarizes membrane protein distribution

The plasma membrane is widely regarded as the hub of the signal transduction network activities that drives numerous physiological responses, including cell polarity and migration. Yet, the symmetry breaking process in the membrane, that leads to dynamic compartmentalization of different proteins, remains poorly understood. Using multimodal live-cell imaging, here we first show that multiple endogenous and synthetic lipid-anchored proteins, despite maintaining stable tight association with the inner leaflet of the plasma membrane, were unexpectedly depleted from the membrane domains where the signaling network was spontaneously activated such as in the new protrusions as well as within the propagating ventral waves. Although their asymmetric patterns resembled those of standard peripheral "back" proteins such as PTEN, unlike the latter, these lipidated proteins did not dissociate from the membrane upon global receptor activation. Our experiments not only discounted the possibility of recurrent reversible translocation from membrane to cytosol as it occurs for weakly bound peripheral membrane proteins, but also ruled out the necessity of directed vesicular trafficking and cytoskeletal supramolecular structure-based restrictions in driving these dynamic symmetry breaking events. Selective photoconversion-based protein tracking assays suggested that these asymmetric patterns instead originate from the inherent ability of these membrane proteins to "dynamically partition" into distinct domains within the plane of the membrane. Consistently, single-molecule measurements showed that these lipid-anchored molecules have substantially dissimilar diffusion profiles in different regions of the membrane. When these profiles were incorporated into an excitable network-based stochastic reaction-diffusion model of the system, simulations revealed that our proposed "dynamic partitioning" mechanism is sufficient to give rise to familiar asymmetric propagating wave patterns. Moreover, we demonstrated that normally uniform integral and lipid-anchored membrane proteins in Dictyostelium and mammalian neutrophil cells can be induced to partition spatiotemporally to form polarized patterns, by optogenetically recruiting membrane domain-specific peptides to these proteins. Together, our results indicate "dynamic partitioning" as a new mechanism of plasma membrane organization, that can account for large-scale compartmentalization of a wide array of lipid-anchored and integral membrane proteins in different physiological processes.

cell biology↗