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Biology subjects

Dixit, S.

Publications and source records attributed to Dixit, S..

At least 19 recordsLinked to original sources

Sequential Sampling as a Computational Principle of Episodic Memory

Visual perception unfolds through sequential eye movements, yet computational models of episodic memory typically assume that event representations already exist. Here, we propose that sequential gaze sampling does not simply supply memory with visual information, but contributes to the construction and organisation of episodic representations. We introduce a computational model in which successive fixations are integrated into an evolving internal representation, subsequently stored in associative memory and later retrieved through partial reinstatement of the original sampling trajectory. Within to-be-remembered elements, successive samples support progressive individuation; between elements, more frequent transitions strengthen relational binding. As sampling proceeds, internal representations become progressively lower-dimensional while retaining information about where samples were taken and when they occurred in the sequence. Sampling history also remains embedded in the resulting representation: changing the order of otherwise identical samples alters both the representation itself and element-specific retrieval. At retrieval, reinstating more of the original sampling trajectory improves access to specific elements, while competition is strongest when memories share both semantic category and sampling history. Finally, an exploratory generative readout shows that regions sampled during encoding are reconstructed more faithfully than unsampled regions. Together, these findings suggest that sequential sampling provides a candidate computational process through which episodic representations are constructed, shaping their subsequent storage and retrieval.

neuroscience↗

Integrative Network Analysis Reveals Organizational Principles of the Endocannabinoid System

BackgroundThe endocannabinoid system (ECS) is a complex signaling network that regulates diverse physiological processes, including pain, mood, metabolism, and immune response, through coordinated interactions among receptors, enzymes, and lipid-derived ligands. Despite extensive research on individual ECS components, the systems-level organization and network resilience of the ECS remain underexplored. Here, we present a systems-level analysis of the ECS that integrates protein-protein and protein-chemical interactions into a unified network framework. MethodsWe constructed integrated ECS networks that combine protein-protein and protein-chemical interactions, utilizing data from multiple public databases. Network analyses were performed in Python using NetworkX to assess molecular connectivity and interaction topology. We utilized centrality measures to identify major hubs, employed community detection algorithms to examine the clustering of nodes, and performed targeted perturbations by sequentially removing the top-ranked nodes based on degree and betweenness centrality to assess network robustness. ResultsCentrality analyses identified the primary cannabinoid receptors, cannabinoid receptor 1 (CNR1) and cannabinoid receptor 2 (CNR2), as major hubs with extensive connectivity to endogenous and exogenous ligands. Non-canonical receptors, including transient receptor potential vanilloid 1 (TRPV1) and G-protein coupled receptor 55 (GPR55), also emerged as highly ranked nodes across multiple centrality measures, underscoring their integrative roles within the ECS signaling pathway. Community detection revealed biologically meaningful modules centered around receptor and metabolic clusters, with CNR1, CNR2, anandamide (AEA), 2-arachidonoylglycerol (2-AG), and major phytocannabinoids maintaining key network connectivity. Perturbation analyses demonstrated that removal of top hubs, particularly CNR1, caused pronounced losses in edge connectivity and disrupted signaling pathways among cannabinoids. However, the redistribution of influence toward CNR2 and GPR55 under multi-node removal conditions revealed compensatory plasticity and resilience within the ECS network. ConclusionThis systems-level study highlights the hierarchical and robust architecture of the ECS. The identification of hub nodes, functional communities, and compensatory mechanisms provides insight into how the ECS maintains signaling integrity in the face of perturbation. These findings establish a network-based framework for studying cannabinoid biology and may inform future therapeutic strategies targeting the ECS and its interacting molecular pathways.

systems biology↗

Evaluating zero-shot prediction of protein design success by AlphaFold, ESMFold, and ProteinMPNN

De novo protein design has enabled the creation of proteins with diverse functionalities that are not found in nature. Despite recent advances, experimental success rates remain inconsistent and context-dependent, posing a bottleneck for broader applications of de novo design. To overcome this, structure and sequence prediction models have been applied to assess design quality prior to experimental testing to save time and resources. In this study, we aimed to determine the extent to which AlphaFold2, Protein MPNN, and ESMFold can discriminate between experimentally successful and unsuccessful designs. For this, we curated a benchmark dataset of 614 experimentally characterized de novo designed monomers from 11 different design studies between 2012 and 2021. All predictive models demonstrated moderate ability to discriminate experimental successes (expressed, soluble, monomeric, and fold into the intended design structure) from failures, with many failed designs having better confidence metrics than successful designs. Among all computational models evaluated, ESMFold average pLDDT yielded the best individual performance at distinguishing between successful and unsuccessful designs. A logistic regression model combining all confidence metrics provided only modest improvement over ESMFold pLDDT alone. Overall, these results show that these models can serve as an initial filtering strategy prior to experimental validation; however, their utility at accurately predicting experimental successful designs remains limited without task-specific training.

bioinformatics↗

Alpha-2-Macroglobulin mitigates mitochondrial dysfunction and neuronal apoptotic responses in pesticide-induced neurotoxicity

Persistent and repetitive application of pesticides has been linked to adverse effects on human metabolism and the onset of various disorders. Commonly used pesticides, such as carbamates (e.g., Aldicarb, ALD) and organophosphates (e.g., Chlorpyrifos, CPF), are widely applied in potato cultivation and household pest control. Chronic exposure to these substances has been implicated in the early onset of neurodegenerative disorders. Alpha-2-macroglobulin (A2M), a protein known for its regulatory role in oxidative stress, participates in multiple biological processes. Despite its significance, the role of A2M in mitigating mitochondrial-induced neuronal apoptosis triggered by pesticide interference remains poorly understood. This study explores the involvement of A2M in SH-SY5Y neuroblastoma cells exposed to pesticides, focusing on its impact on mitochondrial enzyme expression, inflammatory cytokines, neuronal apoptotic and anti-apoptotic proteins, and the activation of the Nrf2 signaling pathway. Comparative analyses of control and pesticide-exposed SH-SY5Y cells revealed that A2M positively modulates neuronal stress responses. Western blot profiling demonstrated that A2M upregulates anti-apoptotic proteins such as Bcl-2 and Nrf2, while downregulating pro-apoptotic markers, including Bax, Caspase-3, and Caspase-9. Biochemical assays showed that A2M enhances mitochondrial enzyme activity, particularly complexes I and III, while mitigating the reactive oxygen species (ROS) generated by ALD and CPF exposure. Furthermore, A2M was found to reduce DNA damage caused by pro-inflammatory cytokines, which are exacerbated by mitochondrial oxidative stress. These findings highlight the pivotal role of A2M in attenuating pesticide-induced neuronal toxicity through the regulation of mitochondrial function and inhibition of neuronal apoptosis. Research HighlightsO_LIThis study is the first to report the interaction between human alpha-2-macroglobulin and neuronal apoptotic markers in pesticides mediated neurotoxicity. C_LIO_LIThe study found that treatment of alpha-2-macroglobulin promotes the proliferation of Nrf2 pathway during oxidative stress in neuronal cells. C_LIO_LIThis research reveals that alpha-2-macroglobulin modulates oxidative stress in mitochondrial enzyme complexes and during mitochondrial dysfunction. C_LIO_LIThe study confirms that treatment of alpha-2-macroglobulin significantly alleviates pro inflammatory cytokines during pesticides mediated neurotoxicity. C_LIO_LIThis research provides new theoretical basis and molecular targets for the treatment of neurodegenerative diseases during early preclinical stages, offering broad application prospects. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/661925v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1acb2baorg.highwire.dtl.DTLVardef@109ead0org.highwire.dtl.DTLVardef@171f0borg.highwire.dtl.DTLVardef@1f745b1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Modeling tissue-resident macrophage development from mouse pluripotent stem cells

Tissue-resident macrophages (TRMs) are innate immune cells that participate in tissue development, homeostasis, and immune surveillance. Extensive efforts have been made to recapitulate TRM development from pluripotent stem cells (PSCs) in vitro to study molecular and cellular mechanisms of TRM development and to create cellular models of disease. However, available PSC models of mouse TRM development exhibit low overall efficiencies of TRM generation, produce heterogeneous off-target populations, and rely upon undefined media components, thus limiting their reproducibility, scalability, and widespread application as an experimental platform for TRM biology. To address these important limitations, we developed an efficient and reproducible protocol to faithfully recapitulate the stepwise differentiation of mouse PSCs (epiblast stem cells) into unspecialized, proliferative TRMs through the pro-definitive hematopoietic program under defined conditions. These immature TRMs can stably integrate into developing mouse neural organoids in vitro and acquire features of microglia. In addition, PSC-derived immature TRMs can stably engraft into the lung niche in vivo and adopt alveolar macrophage characteristics. This new platform for modeling mouse TRM development represents a powerful experimental model system for studying TRM function and dysfunction in development and disease.

developmental biology↗

Large-scale discovery, analysis, and design of protein energy landscapes

All folded proteins continuously fluctuate between their low-energy native structures and higher energy conformations that can be partially or fully unfolded. These rare states influence protein function, interactions, aggregation, and immunogenicity, yet they remain far less understood than protein native states. Although native protein structures are now often predictable with impressive accuracy, conformational fluctuations and their energies remain largely invisible and unpredictable, and experimental challenges have prevented large-scale measurements that could improve machine learning and physics-based modeling. Here, we introduce a multiplexed experimental approach to analyze the energies of conformational fluctuations for hundreds of protein domains in parallel using intact protein hydrogen-deuterium exchange mass spectrometry. We analyzed 5,778 domains 28-64 amino acids in length, revealing hidden variation in conformational fluctuations even between sequences sharing the same fold and global folding stability. Site-resolved hydrogen exchange NMR analysis of 13 domains showed that these fluctuations often involve entire secondary structural elements with lower stability than the overall fold. Computational modeling of our domains identified structural features that correlated with the experimentally observed fluctuations, enabling us to design mutations that stabilized low-stability structural segments. Our dataset enables new machine learning-based analysis of protein energy landscapes, and our experimental approach promises to reveal these landscapes at unprecedented scale.

biophysics↗

AI, citizen science, and the 2024 eclipse emphasize the importance of light for bird behavior

On April 8th 2024, a total solar eclipse disrupted light-dark cycles for North American birds during the lead-up to spring reproduction. Compiling over 10,000 community observations and AI analyses of nearly 100,000 vocalizations, we found that bird behavior was significantly affected by these few minutes of unexpected afternoon darkness. More than half of wild bird species changed their biological rhythms, with many producing a dawn chorus in the aftermath of the eclipse. This natural experiment demonstrates the power of technology-enabled and public science projects to understand our natural world. Further, it underscores the power of light in structuring animal behavior: even when night lasts for just four minutes, robust behavioral changes ensue.

animal behavior and cognition↗

"Decoding Mobile Genetic Elements, Virulence Factors, and Antibiotic Resistance Genes Driving Biofilm Formation in MRSA via Network Analysis"

This study aimed to analyze the genome of the Methicillin-resistant Staphylococcus aureus (MRSA) strain d1418m22 through whole-genome sequencing (WGS) and comprehensive bioinformatics analysis with six references strains. De novo assembly resulted in 61 scaffolds with a total genome size of 2.78 Mb. Functional annotation revealed 2,625 predicted genes, including those involved in metabolism, cellular processes, and virulence. Comparative genomic analysis identified 20 antibiotic resistance genes, including those conferring resistance to beta-lactams, fluoroquinolones, and aminoglycosides. In addition, 21 virulence factors (VFs) were identified, including Panton-Valentine leukocidin (PVL) and various enterotoxins. The presence of staphylococcal cassette chromosome mec (SCCmec) type IVa and mobile genetic elements (MGEs), such as prophages and transposons, underscored the role of horizontal gene transfer (HGT) in the evolution and transmission of resistance and virulence factors. Interaction network analysis identified key hub genes involved in various cellular processes, including biofilm formation. This comprehensive genomic analysis provides valuable insights into the genetic makeup of MRSA strain d1418m22, contributing to a better understanding of its pathogenicity and potential public health implications. Six reference MRSA strains were isolated from (MRSA-AMRF4 and MRSA-AMRF5) eye infections, (MRSA and MRSA-15) wound pus, (VMRSA-WC071, and VMRSA-WC081) urine samples. The analysis identified resistance genes, virulence factors, GC content, ANI values, and SCCmec elements, which were found to be similar to those present in the resistant MRSA d1418m22 strain genome.

genomics↗

Conformational changes, excess area, and elasticity of the Piezo protein-membrane nanodome from coarse-grained and atomistic simulations

The mechanosensitive ion channels Piezo 1 and 2 induce a curved protein-membrane nanodome that flattens with increasing membrane tension{gamma} . The tension-induced flattening of the nanodome is associated with Piezo activation and driven by the energy{gamma}{Delta} A where {Delta}A is the excess area of the curved nanodome relative to its planar projected area. Based on extensive coarse-grained and atomistic simulations of membrane-embedded Piezo 1 and 2 proteins, we report here an excess area {Delta}A for the Piezo protein-membrane nanodome of about 40 nm2 in tensionless membranes, and a half-maximal reduction of {Delta}A at tension values of about 3 to 4 mN/m, which is within the range of experimentally determined values for the half-maximal activation of Piezo 1. In line with recent experimental investigations of Piezo proteins in cell membranes and membrane vesicles, the membrane-embedded Piezo proteins adopt conformations in our simulations that are significantly less curved than the protein conformation in the detergent micelles of cryo-EM structures. An elasticity analysis of the nanodome shapes and protein conformations obtained from our simulations leads to an elastic model for Piezo activation that distinguishes the different energy components of the protein and the membrane in the tension-induced flattening of the nanodome.

molecular biology↗

A mouse organoid platform for modeling cerebral cortex development and cis-regulatory evolution in vitro

Natural selection has shaped the gene regulatory networks that orchestrate the development of the neocortex, leading to diverse neocortical structure and function across mammals, but the molecular and cellular mechanisms driving phenotypic changes have proven difficult to characterize. Here, we develop a reproducible protocol to generate neocortical organoids from mouse epiblast stem cells (EpiSCs) that gives rise to diverse cortical cell types, including distinct classes of excitatory neurons (pre-plate, deep-layer, and upper-layer) and glia (oligodendrocyte precursor cells, myelinating oligodendrocytes, astrocytes, ependymal cells). Cortical organoids develop with similar kinetics to the mouse cortex in vivo and begin to exhibit features of maturation in glia and neuronal cell types relatively rapidly compared to human brain organoids. Using this new protocol, we generated cortical organoids from F1 hybrid EpiSCs derived from crosses between standard laboratory mice (C57BL/6J) and four wild-derived mouse strains from distinct sub-species spanning [~]1M years of evolutionary divergence. This allowed us to comprehensively map cis-acting transcriptional regulatory variation across developing cortical cell types using scRNA-seq. We identify hundreds of genes that exhibit dynamic allelic imbalances during cortical neurogenesis, providing the first insight into the developmental mechanisms underpinning changes in cortical structure and function between mouse strains. These experimental methods and cellular resources represent a powerful new platform for investigating mechanisms of gene regulation in the developing cerebral cortex.

developmental biology↗

A General Framework for Characterizing Optimal Communication in Brain Networks

Communication in brain networks is the foundation of cognitive function and behavior. A multitude of evolutionary pressures, including the minimization of metabolic costs while maximizing communication efficiency, contribute to shaping the structure and dynamics of these networks. However, how communication efficiency is characterized depends on the assumed model of communication dynamics. Traditional models include shortest path signaling, random walker navigation, broadcasting, and diffusive processes. Yet, a general and model-agnostic framework for characterizing optimal neural communication remains to be established. Our study addresses this challenge by assigning communication efficiency through game theory, based on a combination of structural data from human cortical networks with computational models of brain dynamics. We quantified the exact influence exerted by each brain node over every other node using an exhaustive multi-site virtual lesioning scheme, creating optimal influence maps for various models of brain dynamics. These descriptions show how communication patterns unfold in the given brain network if regions maximize their influence over one another. By comparing these influence maps with a large variety of brain communication models, we found that optimal communication most closely resembles a broadcasting model in which regions leverage multiple parallel channels for information dissemination. Moreover, we show that the most influential regions within the cortex are formed by its rich-club. These regions exploit their topological vantage point by broadcasting across numerous pathways, thereby significantly enhancing their effective reach even when the anatomical connections are weak. Our work provides a rigorous and versatile framework for characterizing optimal communication across brain networks and reveals the most influential brain regions and the topological features underlying their optimal communication.

neuroscience↗

Evaluating polarizable biomembranesimulations against experiments

Owing to the increase of available computational capabilities and the potential for providing more accurate description, polarizable molecular dynamics force fields are gaining popularity in modelling biomolecular systems. It is, however, crucial to evaluate how much precision is truly gained with the increased cost and complexity of the simulation. Here, we leverage the NMRlipids open collaboration and Databank to assess the performance of available polarizable lipid models--the CHARMM-Drude and the AMOEBA-based parameters--against high-fidelity experimental data and compare them to the top-performing non-polarizable models. While some improvement in the description of ion binding to membranes is observed in the most recent CHARMM-Drude parameters, and the conformational dynamics of AMOEBA-based parameters are excellent, the best non-polarizable models tend to outperform their polarizable counterparts for each property we explored. The identified shortcomings range from inaccuracies in describing the conformational space of lipids to excessively slow conformational dynamics. Our results provide valuable insights for further refinement of polarizable lipid force fields and for selecting the best simulation parameters for specific applications.

biophysics↗

Governing principles of transcriptional logic out of equilibrium

Cells face a myriad of environments and signaling cues. In order to survive, adapt, and desvelop, cells respond to external and internal stimuli, by tightly regulating transcription. Transcriptional regulation involves combinatorial binding of a repertoire of transcription factors (TFs) to DNA, which often results in switch-like binary outputs, akin to logic gates. Recent experimental studies have demonstrated that transcription factor binding to DNA often involves energy expenditure, thereby driving the system out of equilibrium. The governing mechanistic principles of transcriptional logic out of equilibrium remain elusive. To this end, we employ a simple two-input model of transcription that explicitly considers the non-equilibrium binding of TFs to DNA. This simple model can accommodate both equilibrium and non-equilibrium mechanisms and allows for a comparative study of logic operations obtained in the two regimes. We find that, out of equilibrium, the regulatory function of two transcription factors gets altered in a mutually exclusive manner. Such behavior allows non-equilibrium regimes to recreate all the logic operations seen in equilibrium and create new logic operations inaccessible in equilibrium. Our findings demonstrate that cells attain a wider range of decision-making abilities by expending energy.

biophysics↗

Genetic Gains in IRRIs Rice Salinity Breeding and Elite Panel Development as a Future Breeding Resource

Genetic gain is a crucial parameter to check the breeding programs success and help optimize future breeding strategies for enhanced genetic gains. In this work, IRRIs historical data from the Philippines and Bangladesh of the salinity breeding program was used to estimate the genetic gains and identify the best lines based on higher breeding values for yield as a future genetic resource. Two-stage mixed-model approach accounting for experimental design factors and pedigrees was adopted to obtain the breeding values for yield and estimate genetic trends under the salinity conditions. A positive genetic trend of 0.1% per annum with a yield advantage of 1.52 kg/ha for the Philippines and 0.31% per annum with a yield advantage of 14.02 kg/ha for Bangladesh datasets was observed. For the released varieties, genetic gain was 0.12% per annum with a yield advantage of 2.2 kg/ha/year and 0.14% per annum with a yield advantage of 5.9 kg/ha/year, respectively. Further, based on higher breeding values for grain yield, a core set of the top 145 genotypes with higher breeding values of >2400 kg/ha in the Philippines and >3500 kg/ha in Bangladesh with a selection accuracy >0.4 were selected for formulating the elite breeding panel as a future breeding resource. Conclusively, higher genetic gains are pivotal in IRRIs rice salinity breeding program, which requires a holistic breeding approach with a major paradigm shift in breeding strategies to enhance genetic gains. Key MessageEstimating genetic gains and formulating a future salinity elite breeding panel for rice pave the way for developing better high-yielding salinity tolerant lines with enhanced genetic gains.

genetics↗

When Neural Activity Fails to Reveal Causal Contributions

Neuroscientists rely on distributed spatio-temporal patterns of neural activity to understand how neural units contribute to cognitive functions and behavior. However, the extent to which neural activity reliably indicates a units causal contribution to the behavior is not well understood. To address this issue, we provide a systematic multi-site perturbation framework that captures time-varying causal contributions of elements to a collectively produced outcome. Applying our framework to intuitive toy examples and artificial neuronal networks revealed that recorded activity patterns of neural elements may not be generally informative of their causal contribution due to activity transformations within a network. Overall, our findings emphasize the limitations of inferring causal mechanisms from neural activities and offer a rigorous lesioning framework for elucidating causal neural contributions.

neuroscience↗

Automated Protein Affinity Optimization using a 1D-CNN Deep Learning Model

Functional biologics design is a multi-objective optimization problem often with competing design objectives. We report on a novel deep learning based protein sequence prediction framework, ZymeSwapNet, that can be customized to handle a wide range of quantifiable design objectives, a current limitation of traditional protein design methods. We train a simple convolutional neural network (1D-CNN) on nonredundant curated protein crystal structures, using a set of geometric and topological features that describes a local protein environment, to predict the likelihood of each amino acid type for residue sites in the design region. While the model can be directly used to rank templates derived from mutagenesis campaigns, we extend the scope by developing a sequence/mutation generator that optimizes the desired multivariate distribution using a Monte-Carlo sampling. Using a case study - the design of a stable heterodimeric Fc (HetFc) antibody domain - we show that we can further include a Metropolis criterion to bias the sampling to enhance features such as the heterodimeric binding specificity, in addition to original sampling objective of enhancing stability. We demonstrate that ZymeSwapNet can generate stable HetFc designs, within minutes that had taken several rounds of rational structure and physical force-field based modeling attempts.

bioengineering↗

Temporal Regulation of Organelle Biogenesis

Organelle abundance is tightly regulated in eukaryotic cells in response to external stimuli. The underlying mechanisms responsible for this regulation remains less understood. Time-lapse imaging of fluorescently labelled organelles allow for counting individual organelle copies at a single-cell level. These experiments contain information about the time evolution of distribution of organelle number across a population of cells. To tap onto such data, we build upon a recently proposed kinetic model of organelle biogenesis that explicitly incorporates de novo synthesis, fission, fusion and degradation of organelles. Different limits of this general model correspond to distinct mechanisms of organelle biogenesis. We compute the first two moments of organelle number distribution for these different mechanisms. Interestingly, different mechanisms of biogenesis lead to qualitatively distinct temporal behavior of cell-to-cell variability (noise), thereby allowing us to discern between these mechanisms. Notably, noise in temporal organelle abundance exhibits strikingly more complex behaviour as compared to the steady state. Our modeling framework paves the way for extracting quantitative information about the dynamics of organelle biogenesis from time-lapse experiments that can measure organelle abundance at single-molecule resolution.

systems biology↗

Cell type-specific assessment of cholesterol distribution in models of neurodevelopmental disorders

Most nervous system disorders manifest through alterations in neuronal signaling based on abnormalities in neuronal excitability, synaptic transmission, and cell survival. However, such neuronal phenotypes are frequently accompanied - or even caused - by metabolic dysfunctions in neuronal or non-neuronal cells. The tight packing and highly heterogenous properties of neural, glial and vascular cell types pose significant challenges to dissecting metabolic aspects of brain disorders. Perturbed cholesterol homeostasis has recently emerged as key parameter associated with sub-sets of neurodevelopmental disorders. However, approaches for tracking and visualizing endogenous cholesterol distribution in the brain have limited capability of resolving cell type-specific differences. We here develop tools for genetically-encoded sensors that report on cholesterol distribution in the mouse brain with cellular resolution. We apply these probes to examine sub-cellular cholesterol accumulation in two genetic mouse models of neurodevelopmental disorders, Npc1 and Ptchd1 knock-out mice. While both genes encode proteins with sterol-sensing domains that have been implicated in cholesterol transport, we uncover highly selective and cell type-specific phenotypes in cholesterol homeostasis. The tools established in this work should facilitate probing sub-cellular cholesterol distribution in complex tissues like the mammalian brain and enable capturing cell type-specific alterations in cholesterol flow between cells in models of brain disorders.

neuroscience↗