Biology subjects

Chandra, S.

Publications and source records attributed to Chandra, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Expandable DNA-origami rings as a nanomechanical platform for studying disordered nucleoporins

Phe-Gly-rich nucleoporins (FG-Nups) within the nuclear pore complex (NPC) form a diffusion barrier that controls the exchange of macromolecules between the nucleus and cytoplasm. The behaviors of these intrinsically disordered FG-Nups are fundamental to the NPC function but remain difficult to probe within the dynamic, native nuclear pore. To bridge this knowledge gap, here we build expandable DNA-origami rings with tunable elasticity and study FG-Nups site-specifically tethered in such mechanically responsive NPC mimics. The elastic deformation of DNA rings, measured by single-particle TEM, reveals the type (attraction or repulsion) and strength of FG-Nup interactions that shape the collective morphology of these unstructured proteins. Analyzing homotypic interactions of five FG-Nup species finds diverse FG-Nup behaviors that can be classified as repulsive/extended (Nsp1), moderately cohesive/extended (Nup62, Nup153, and Nup214), and strongly cohesive/compact (Nup98). Furthermore, we examine how FG-Nups' primary sequence, O-glycosylation, grafting density, and binding to nuclear transport receptors (NTRs) impact their biophysical state. For example, O-GlcNAcylation reduced FG-Nup cohesiveness, switching Nup98 from a collapsed state to more extended conformations. Our work thus elucidates spatially confined Nup-Nup and Nup-NTR interactions within an NPC-like nanopore, suggests a previously underappreciated role of FG-Nups in modulating NPC dilation, and establishes a generalizable method for studying multivalent interactions among disordered proteins.

biophysics↗

bioRxiv2026

Euchromatin Peripheral Organization Follows Anterograde Signalling Under Anaesthetic Stress

Anterograde and retrograde signalling establish bidirectional communication between the nucleus and chloroplasts. Retrograde signals from chloroplasts regulate nuclear gene expression while anterograde signals from the nucleus coordinate chloroplast development and maintain cellular homeostasis. How this bidirectional signalling framework extends beyond locus-specific regulation to shape the global spatial organization of nuclear chromatin across tissues remains unclear. Although anaesthesia can alter chromatin organisation, the role of chloroplast dysfunction in these changes remains unclear. Here, we investigate how chloroplast dysfunction and anaesthesia influence euchromatin and heterochromatin organisation in Solanum lycopersicum seedlings across tissues with contrasting photosynthetic competence. Using confocal and super-resolution radial fluctuation (SRRF) imaging with quantitative multiparameter analysis, we identify distinct, tissue-specific chromatin responses to chloroplast disruption and anaesthesia. Notably, anaesthesia induces distinct spatial chromatin changes across tissues that are independent of chloroplast dysfunction, suggesting a direct nuclear response to anaesthesia rather than a chloroplast-mediated retrograde effect. These findings highlight chromatin topology as a potential quantitative biomarker of cellular disruption and provide a framework for investigating anterograde chloroplast-nucleus coordination and stress-responsive nuclear organisation in plants.

plant biology↗

bioRxiv2026

Efficient Mitigation of Copper Induced Cellular Dysfunction Using Chitosan Based Iron Oxide Nanoparticles

Copper is an essential redox-active micronutrient, but agricultural soils are increasingly contaminated by copper from mining, industrial discharge, and intensive agrochemical use, pushing concentrations beyond levels plants can tolerate. Excess copper triggers Fenton-like reactive oxygen species (ROS) generation, mitochondrial dysfunction, and impaired growth. Existing mitigation strategies, such as soil amendments, phytoremediation, antioxidants, and different chelators, have been explored to reduce copper toxicity, but their effectiveness can be limited by immobilization, poor specificity, and environmental persistence. The present work introduces a nanoparticle-based strategy for the direct sequestration of excess copper coupled with protection against the oxidative damage caused by copper stress. Here, we report MPA-iron oxide nanoparticles (MIONPs), sequentially functionalized with chitosan, glutathione, and 3-mercaptopropionic acid, designed to simultaneously scavenge ROS, restore redox homeostasis, and chelate copper via surface thiol groups. MIONPs showed a significant increase in copper binding capacity over bare iron oxide nanoparticles (BIONPs) and, in copper-stressed Solanum lycopersicum seedlings, significantly improved germination and root/shoot growth, reduced intracellular ROS, restored mitochondrial membrane potential, and preserved nuclear integrity. This integrated design establishes MIONPs as a promising, dual-function nanoplatform for sustainable copper stress management in agriculture.

plant biology↗

bioRxiv2026

Mechanoresponsive modulation of nuclear pore complex structure and function by O-GlcNAc

Nuclear pore complexes (NPCs) control molecular exchange across the nuclear envelope, but how they tailor their selective permeability to meet the needs of specific cell types and/or environments remains poorly understood. We demonstrate that the strength of the NPC diffusion barrier differs across cell types, is particularly stringent in cultured neurons, and correlates with the O-linked N-acetylglucosamine (GlcNAc) modification of nucleoporins. Using conditional tools that specifically control nucleoporin GlcNAcylation, we show that GlcNAc modulates NPC permeability. Interestingly, nucleoporin GlcNAcylation is mechanosensitive, increasing in cells plated on stiff substrates, a condition where nuclear pores dilate. Indeed, we demonstrate that increasing or decreasing GlcNAcylation dilates and constricts NPCs, respectively. Further, O-linked N-acetylglucosamine transferase is recruited to modify NPCs upon their acute constriction during osmotic shock. Thus, cells employ GlcNAc to modulate steady-state NPC permeability in response to mechanical inputs and to counteract critical changes to their osmotic environment.

cell biology↗

bioRxiv2026

Interpreting GC content differences across populations at polymorphic sites

Recent studies have reported consistent inter-population differences in GC content at polymorphic sites in multiple species, including humans. Specifically, populations that experienced recent bottlenecks exhibit lower average GC content (GC%) at common polymorphic sites compared to non-bottlenecked groups--an observation previously interpreted as indication of rapid evolution of base composition. In this study, we investigate the evolutionary and technical factors driving these patterns across humans, mice, maize, and silkworm. We find that GC% at polymorphic sites is highly sensitive to the allele frequency threshold applied. Relaxing this threshold reduces inter-population differences to negligible levels in humans and significantly attenuates similar signals in other species. We further observe substantial GC% variation across allele frequency bins, a pattern driven by the differential abundance of different mutation types. We demonstrate that these observations are collectively driven by an interaction between demographic history and a universal excess of strong-to-weak mutations relative to weak-to-strong mutations, which is counteracted by GC-biased gene conversion (gBGC) over long evolutionary timescales. Forward-in-time simulations with realistic parameters recapitulate observed patterns of GC% variation across both populations and allele frequency bins. Overall, our findings reveal that the base composition at polymorphic sites is strongly shaped by the interaction between demographic history, mutation bias, and gBGC, and does not represent stable, genome-wide trends. Consequently, inter-population differences in GC content--especially at common variants--should not be interpreted as evidence of ongoing divergence in base composition or shifts in mutation patterns.

evolutionary biology↗

bioRxiv2026

Neuronal overexpression of Nrf2 reduces dystrophic neurites in 5XFAD Alzheimer's disease model mice

BackgroundThe hallmark lesions of the Alzheimers disease (AD) brain are amyloid plaques consisting of the {beta}-amyloid protein and neurofibrillary tangles comprised of hyperphosphorylated, aggregated tau protein, which both cause neuronal dysfunction and loss. One goal of neuroprotective therapies is to maintain normal neuronal function and survival in the presence of toxic pathologies such as plaques and tangles. A potential neuroprotective target is nuclear factor erythroid 2-related factor 2 (Nrf2) transcription factor, which regulates the expression of many antioxidant and detoxification genes. Nrf2 mRNA is decreased in AD brains, and deletion of the Nrf2 gene causes increased BACE1 and A{beta} production and worsened cognitive deficits in amyloid pathology mouse models. Overexpression of Nrf2 in astrocytes has been shown to be protective against neurodegeneration, but the role of Nrf2 is neurons is unclear. MethodsWe overexpressed Nrf2 from birth in neurons of 5XFAD amyloid pathology model mice using AAV8, hypothesizing that neuronal Nrf2 overexpression decreases cortical neuron loss and reduces plaque load by decreasing BACE1 levels. We quantified protein levels by immunoblot and neuropathology by immunofluorescent staining, using two-way ANOVA to measure differences between genotypes and AAV treatments. To assess genetic changes, we performed bulk mRNA seq. ResultsWhile neuronal overexpression of Nrf2 in 5XFAD mice did not prevent neuronal loss as measured by NeuN labeling, decrease neuroinflammation by Iba1 or GFAP labeling, or reduce amyloid load by A{beta} antibody or methoxy-XO4 staining, we show that increased Nrf2 expression reduces BACE1 protein levels, especially in swollen axonal dystrophic neurites around amyloid plaques. Other proteins that accumulate in dystrophic neurites were also reduced, indicating decreased dystrophic neurites overall. Immunoblot analysis suggested increased autophagy was unlikely to play a role, while bulk mRNA sequencing indicated changes in lipid metabolism and microtubule stability may have contributed to reduced dystrophic neurite formation. ConclusionsDystrophic neurites impair action potential conductance and contribute to tau seeding and spreading. Their reduction by neuronal Nrf2 overexpression may protect neurons against these pathologic changes. Further study of the mechanisms by which Nrf2 reduces dystrophic neurites may lead to therapeutic strategies that can limit neuritic damage caused by cerebral amyloid accumulation.

neuroscience↗

bioRxiv2026

Identification of Human Gut Microbiome Derived Peptides Targeting Biofilm Specific Lectin Proteins of Pseudomonas aeruginosa

The carbohydrate-binding proteins (LecA and LecB) present within the extracellular polymeric substance (EPS) matrix of Pseudomonas aeruginosa play an essential role in maintaining the structural integrity of the biofilms through interactions with the EPS polysaccharides. Therefore, targeting the above lectins can turn out to be one of the promising strategies for disrupting P. aeruginosa biofilms. In the current study, we investigated the potency of antimicrobial peptides (AMPs) produced by the human gut microbiome in targeting LecA and LecB proteins of P. aeruginosa. Initially, a comprehensive in-silico pipeline was developed to identify and characterize putative antibacterial and antibiofilm AMPs produced by the human gut microbiome. These AMPs were then subsequently studied for their interaction with the lectin proteins through molecular docking, MM-GBSA, residue analysis, and molecular dynamics (MD) simulation. Among the studied peptides, amp21 and amp24 exhibited the strongest interactions with the lectin protein, occupying binding sites overlapping with key active-site residues previously reported for raffinose binding. amp6, amp21, and amp24 were selected for in vitro validation based on the MD simulation results of both LecA and LecB proteins. The above selected peptides exhibited minimal hemolytic activity across the tested concentration range. amp21 and amp6 were non-toxic to mammalian cells while amp24 demonstrated cytotoxicity only at higher doses. amp21 was found to be the most potent AMP and inhibited the growth of P. aeruginosa by [~]60% at 50 {micro}g mL{square}{superscript 1}. amp6 and amp21 resulted in a significant disruption of P. aeruginosa biofilms. Membrane permeabilization assays and scanning electron microscopy revealed that amp6, amp21, and amp24 damaged the bacterial cell membranes apart from compromising the integrity of the biofilm EPS matrix. Lastly, through in-silico studies, we designed ultrashort peptides (USPs) from the lead AMPs. The USPs (amp21.4 and amp24.2) exhibit superior antibiofilm efficacy compared to their parent AMPs. These findings establish human-gut microbiome-derived AMPs as promising candidates to target P. aeruginosa biofilms via inhibition of lectin proteins.

microbiology↗

bioRxiv2025

Sequence context and methylation interact to shape germline mutation rate variation at CpG sites

A prominent example of sequence context-dependent mutation rate variation is the elevated transition rate at CpG sites, which is largely attributed to cytosine methylation. CpGs with different flanking sequences also exhibit mutation rate variation, but this variation is only partially correlated with context-specific methylation level. Here, we quantify the CpG mutation rate and mutagenic effect of methylation across sequence contexts. Using a regression framework that accounts for recurrent mutations, we analyze human polymorphisms from the gnomAD dataset to estimate mutation rates of unmethylated and methylated CpGs separately in each unique 4-mer or 6-mer context. We find that CpG mutation rate variation in the human genome is shaped by methylation at the focal cytosine, the flanking nucleotides, and interactions between them, suggesting distinct context-dependent mutation patterns for unmethylated and methylated cytosines. Our analysis further reveals that the context effects are driven by largely independent effects of upstream and downstream sequences. Notably, an upstream adenine markedly increases CpG mutation rates regardless of methylation status or downstream sequences. Furthermore, upstream and downstream sequences have similar effects in chimpanzee and rhesus macaque, indicating that some conserved, intrinsic sequence features shape CpG mutability. On the other hand, some inter-species differences, which are especially pronounced at methylated sites on the chimpanzee lineage, point to recent evolutionary changes, possibly in context-specificity of proteins governing DNA demethylation and repair processes. Author SummaryThe DNA sequence surrounding a nucleotide strongly influences how likely it is to mutate. An extreme example is the CpG dinucleotide: cytosines in CpGs mutate far more frequently than other sites in the human genome. This is related to DNA methylation, a chemical modification that occurs almost exclusively at CpGs in vertebrates and makes cytosines more prone to mutations. However, CpGs in different sequence contexts also vary in their mutation rates, and methylation level alone cannot explain this variation. To gain insight into what processes drive this variation, we estimate mutation rates for methylated and unmethylated CpGs in different sequence contexts using human genetic variation data. We find that methylation and neighboring bases interact to influence CpG mutation rates, and that the DNA sequence on either side of the CpG exerts largely independent effects. Extending our analysis to other primates reveals both conserved and species-specific patterns, with differences being especially pronounced at methylated sites on the chimpanzee lineage. Together, our results suggest that while intrinsic DNA sequence features underlie some conserved context effects on CpG mutation rate, inter-species differences may reflect recent evolutionary changes in the mechanisms that regulate DNA demethylation and repair.

genetics↗

bioRxiv2025

Protectin DX resolves fracture-induced postoperative pain in mice via neuronal signaling and GPR37-activated macrophage efferocytosis

Protectin DX (PDX) is a member of the superfamily of specialized pro-resolving mediators (SPMs) and exerts anti-inflammatory actions in animal models; but the specific signaling pathways involved in its actions have not been fully elucidated. Here we demonstrate the analgesic actions of PDX in a mouse model of tibial fracture-induced postoperative pain (fPOP) via activation of GPR37. Intravenous early-phase and late-phase treatment of PDX (100 ng/mouse) effectively alleviated fPOP. Compared to protectin D1/neuroprotectin D1, DHA, steroid, and meloxicam, PDX produced superior pain relief. While dexamethasone and meloxicam prolonged fPOP, PDX shortened the pain duration. The analgesic effects of PDX were abrogated in Gpr37-/- mice, which displayed deficits in fPOP resolution. PDX binds GPR37 and induces calcium responses in peritoneal macrophages. LC-MS-MS-based lipidomic analysis revealed that endogenous PDX levels were [~]10-fold higher than PD1 in muscle at the fracture site. PDX promotes macrophage polarization via GPR37-dependent phagocytosis and efferocytosis through calcium signaling in vitro, and it further enhances macrophage viability and efferocytosis in vivo via GPR37. Finally, PDX rapidly modulates nociceptor neuron responses by suppressing C-fiber-induced muscle reflex in vivo and calcium responses in DRG neurons ex vivo and reducing TRPA1/TRPV1-induced acute pain and neurogenic inflammation in vivo. Our findings highlight multiple benefits of PDX to manage postoperative pain and promote perioperative recovery.

neuroscience↗

bioRxiv2025

Slow synaptic plasticity from the hippocampus underlies gradual mapping and fragmentation of novel spaces by grid cells

Animals construct internal "cognitive maps" of the world during navigation in spatial and non-spatial domains, with grid cells in the medial entorhinal cortex (MEC) playing a key role. This requires associating internal position estimates with external cues to reduce spatial uncertainty over time. However, how grid cell representations evolve in novel spaces to support map formation is unclear. To address this question, we longitudinally imaged calcium dynamics of grid cells over 10 days as mice learn operant tasks in novel virtual linear tracks. We observe that spatial tuning of grid cells is present immediately in novel tracks but evolves as a significant fraction of spatial fields shift backward on a run-by-run basis, within and across days. Backward shifts are more prevalent and persistent in successful learners. The fields gradually stabilize across days, anchored by landmarks, suggesting slow plasticity. The backward shifts partially reset daily, reflecting a slower consolidation timescale. While individual fields of a cell shift differentially, co-active fields of co-modular grid cells shift together, indicating their coupled dynamics on the same two-dimensional torus. Spatial learning leads to systematic changes and stabilization of their population phase trajectory, including lateral shift, rotation, and phase resets at landmarks, forming a landmark-fragmented representation for the environment. Next, we build an entorhinal-hippocampal model that provides a mechanistic explanation of the diverse phenomena - grid field shifts, increasing fidelity, and fragmentation of the spatial map - and predicts slow Hebbian plasticity in the hippocampus-to-entorhinal pathway. Supporting this, electrophysiology demonstrates that learning-performance-correlated weakening of local inhibition facilitates potentiation of indirect hippocampal inputs to superficial MEC. Together, our study provides multifaceted evidence of slow hippocampus-to-MEC plasticity, elucidating the formation of stable and fragmented cognitive maps that combine internal and cue-driven positional estimates in rich environments during learning. This mechanism may extend to broader memory processes involving this circuit.

neuroscience↗

bioRxiv2025

Copper Stress Trigger Organelles Communication and Chromatin Condensation Leading to Cell Death in Solanum lycopersicum

Copper (Cu) is a vital micronutrient for plants but becomes highly toxic when present in excess, disrupting redox balance and damaging cellular structures. While the physiological and mitochondrial responses to Cu toxicity are well-documented, the nuclear-level consequences, particularly chromatin remodeling and gene regulatory changes, remain poorly understood. In this study, we used the root apex of Solanum lycopersicum as a model system to explore how increasing copper concentrations affect organelle integrity, stress signaling, and nuclear architecture. Using confocal and super-resolution imaging with organelle-specific markers and immunostaining, we observed that mitochondria was the earliest affected to Cu stress, exhibiting fragmentation, membrane depolarization, and cytochrome c release led to reactive oxygen species (ROS) accumulation, activation of AMPK, suppression of mTOR signaling, and nuclear translocation of NRF2. Critically, we found that copper exposure induced profound nuclear alterations, including shrinkage, lobulation, peripheral chromatin tethering, and global condensation events tightly correlated with stress signaling. H3K4me3 immunostaining revealed a shift from active euchromatin to condensed, transcriptionally silent states, leading to membrane rupture and cell death in root tip cells. Our findings show that the nucleus actively integrates organelle-derived stress signals, with chromatin remodeling as a key marker of copper toxicity. This highlights potential for chromatin-based diagnostics and stress-resilient crop breeding. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/665307v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@15a3595org.highwire.dtl.DTLVardef@1740149org.highwire.dtl.DTLVardef@1007f24org.highwire.dtl.DTLVardef@19b1a20_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

Direct Visualization of Anesthesia-induced Subcellular Dysfunction in Non-Neuronal Tissues of C. elegans

Volatile anaesthetics such as isoflurane, halothane, and sevoflurane are extensively utilized for their reversible induction of unconsciousness, exhibiting well-defined impacts on neural networks. However, their influence on non-neuronal and developing tissues is inadequately comprehended, generating concerns for vulnerable categories, including children and individuals receiving extended anesthesia. To rectify this deficiency, we examined the subcellular impacts of anaesthetics utilizing HEK 293T and HepG2 cell lines, alongside with Caenorhabditis elegans as a comprehensive organismal model. In vitro treatment to lidocaine and isoflurane resulted in mitochondrial depolarization, lysosomal aggregation, and buildup of reactive oxygen species (ROS). In vivo, 8% isoflurane induced mitochondrial fragmentation, loss of branching, and disruption of tubular lysosomes, indicating compromised energy metabolism and autophagic stress. We detected selective transcriptional inhibition of neuron- and immune-related promoters, although RNA Pol I remained active, indicating energy-conservation strategies. Systemic oxidative stress was validated by TIR-1::GFP aggregation and lipofuscin accumulation. Our research is one of the initial investigations that defines anaesthesia-induced subcellular dysfunction beyond the nervous system, providing novel insights for safer anaesthetic protocols and informing long-term health evaluations, especially in individuals who are developing or chronically exposed. Significance statementWhile volatile anaesthetics are widely used for inducing unconsciousness, their effects beyond neurons remain poorly understood. This study reveals that clinically used anaesthetics such as isoflurane and lidocaine cause profound subcellular dysfunction in non-neuronal systems, including mitochondrial depolarization, lysosomal disruption, transcriptional repression, and systemic oxidative stress. Using both human cell lines and Caenorhabditis elegans, we uncover conserved patterns of organellar damage and stress responses. These findings have critical implications for pediatric, intensive care, and long-term anaesthesia cases, urging the need to reassess anaesthetic safety profiles and develop biomarkers for systemic toxicity. Our work opens new avenues for designing cell-type-specific protective strategies under anaesthetic exposure.

pharmacology and toxicology↗

bioRxiv2025

A Hierarchical Cascade of Organellar Silencing and their Regeneration under Anaesthetic Stress in Plants

Anaesthetics are pharmacological drugs that temporarily inhibit neural activity by acting on voltage-gated sodium channels and GABA receptors. Although their neurological mechanisms are well-defined, their wider cellular effects, especially in non-neuronal systems, are inadequately understood d. This study utilized Solanum lycopersicum plants root apex cells as a transparent model to examine anaesthetic-induced subcellular alterations via live-cell fluorescence imaging, immunostaining, and super-resolution microscopy. Our findings, first of its kind, demonstrate the initial comprehensive model of sequential causal structure and hierarchical cascade of organelle collapse of different but important organelles such as mitochondria, lysosome, vesicles trafficking and nuclear architectures under anaesthesia in plants. The nucleus is identified as the most important controller of recovery potential and cellular fate. In a time dependent experiment, we found that plant cells exposed to lidocaine for up to four hours could still recover mitochondrial potential, lysosomal function, and nuclear integrity when anaesthesia is removed. However, beyond four hours, the damage, especially to the nucleus, was irreversible, and cells proceeded to programmed cell death. Our data further demonstrate that organelle functions can recover after brief exposure to anaesthetic stress. However, prolonged exposure prevents recovery, resulting in the irreversible degradation of the nucleus leading to complete cell death. The results present novel targets for preventative therapies, such as mitochondrial antioxidants, lysosomal stabilizers, and nuclear structural protectants that could mitigate anaesthetic-induced damage.

plant biology↗

bioRxiv2025

Hyperglycemic state and fluid shear stress affect metastatic breast cancer cell migration via focal adhesion kinase

We tested how the diabetes-related hyperglycemic condition affects the migration of highly metastatic triple-negative breast cancer (TNBC) cells, MDA-MB-231, under a physiological fluid shear environment. MDA-MB-231 cells displayed a significantly enhanced migratory behavior under a high glucose condition (25 mM) specifically when exposed to flow at 15 dyne/cm2 shear stress. In contrast, the effect of fluid shear was marginal under low glucose (5 mM). Normal epithelial MCF-10A cells, on the other hand, showed increased migration by fluid shear under both low and high glucose conditions. The fluid shear-triggered MDA-MB-231 cell migration under high glucose was significantly abrogated by a focal adhesion kinase (FAK) inhibitor, supporting the mediatory role of FAK in MDA-MB-231 TNBC cell sensing of the high glucose-fluid shear environment during migration. The role of FAK was further demonstrated by the effects of FAK inhibitor on MDA-MB-231 cell migration in scratch wound healing and Boyden chamber migration assays. Our studies provide evidence that high glucose and fluid shear could jointly trigger MDA-MB-231 TNBC cell migration that requires FAK activity. These may provide improved mechanistic insights into how concurrent diabetes may impact the pro-metastatic behavior of breast cancer and suggest the impact of exploring FAK as a relevant therapeutic target.

bioengineering↗

bioRxiv2025

A theory and recipe to construct general and biologically plausible integrating continuous attractor neural networks

Across the brain, circuits with continuous attractor dynamics underpin the representation and storage in memory of continuous variables for motor control, navigation, and mental computations. The represented variables have various dimensions and topologies (lines, rings, euclidean planes), and the circuits exhibit continua of fixed points to store these variables, and the ability to use input velocity signals to update and maintain the representation of unobserved variables, effectively integrating the incoming velocity signal. Integration constitutes a general computational strategy that enables variable state estimation when direct observation of the variable is not possible, suggesting that it may play a critical role in other cognitive processes. While some neural network models for integration exist, a comprehensive theory for constructing neural circuits with a given topology and integration capabilities is lacking. Here, we present a theoretically-driven design framework, Manifold Attractor Direct Engineering (MADE), to automatically, analytically, and explicitly construct biologically plausible continuous attractor neural networks with diverse user-specified topologies. We show how these attractor networks can be endowed with accurate integration functionality through biologically realistic circuit mechanisms. MADE networks closely resemble biological circuits where the attractor mechanisms have been characterized. Additionally, MADE offers innovative and minimal circuit models for uncharacterized topologies, enabling a systematic approach to developing and testing mathematical theories related to cognition and computation in the brain.

neuroscience↗

bioRxiv2025

Insights into gallbladder cancer pathogenesis from a living organoid gallbladder cholangiocyte biorepository

Gallbladder cancer (GBC) while rare worldwide has a high prevalence in India. Pathogenesis is unclear and outcomes poor. Gallbladder cholangiocyte organoids (GCOs) or gallbladder carcinoma organoids (GBCOs) were developed and serially propagated from surgically resected gallbladder tissues with benign or malignant diseases, respectively. Patient derived organoids (PDOs) were derived from 15 normal; 58 inflamed; 12 xanthogranulomatous cholecystitis (XGC); 5 pre-invasive neoplasm and 13 invasive malignant gallbladder pathologies. Protocol optimisation achieved 58% (69/119) success in organoid generation and expansion. Organoids maintained tight junction integrity; P-gp pump and enzymatic activity; preserved tissue-specific gene and protein marker expression; histological features and genetic variations. Cryopreserved organoids from 62 patients with primary tissue and high-quality DNA, RNA and protein derivatives have been banked. In gene expression analyses of tissue, XGC samples clustered with malignant subtypes, separate from benign pathologies. Derived XGC organoids showed a similar clustering. Enriched hallmark pathways in XGC support neoplastic change through chronic inflammation. PDOs generated from different gallbladder pathologies are a promising model to investigate the pathogenesis of GBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/651639v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@465f3dorg.highwire.dtl.DTLVardef@16c5f0org.highwire.dtl.DTLVardef@11d4807org.highwire.dtl.DTLVardef@163d072_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Genomic Architecture of the Resistance to Phytophthora Cactorum 2 (RPc2) Locus in Strawberry (Fragaria x ananassa)

Phytophthora crown rot (PhCR), caused by Phytophthora cactorum, is a soilborne disease with broad impacts to cultivated strawberries in the United States and worldwide. While a resistance locus, RPc2, has been identified in octoploid strawberries, the underlying genomic architecture and mechanism remain unclear. Here, we fine-mapped the RPc2 region to 546 kb, containing 92 genes, and constructed a chromosome-scale haplotype-phased genome of resistant breeding selection FL 16.33-8. Comparative genome analyses with high-quality octoploid reference genomes, Florida Brilliance (FaFB1) and Royal Royce (FaRR1), identified two candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1). Gene functions were validated using an Agrobacterium-mediated transient expression assay. Furthermore, by leveraging the population structure of the RPc2 locus among genetically diverse breeding populations, we unveiled the complexity of genetic architecture and recent selective sweeps associated with RPc2. Notably, the predominant resistant haplotype (RPc2-H3) is prevalent in most commercial strawberry varieties in the US. The findings from this study are facilitating the advancement of genome-assisted breeding strategies for resistance to PhCR in strawberries. SummaryO_LIPhytophthora crown rot (PhCR), caused by the soilborne pathogen Phytophthora cactorum, is a disease with broad impacts to cultivated strawberries worldwide. The Resistance to Phytophthora Cactorum 2 (RPc2) locus is widespread in important cultivars and is a target of selection in breeding programs. Despite its importance, the genomic architecture and mechanisms of RPc2 remain poorly characterized. C_LIO_LIWe performed fine-mapping and delimited the genomic region to a 546 kb segment containing 92 genes. We developed a chromosome-scale haplotype-phased genome from an elite resistant line, FL16.33-8, and made comparisons to reference genomes of Florida Brilliance (FaFB1) and Royal Royce (FaRR1) to uncover gene sequence and structural variants in resistant accessions. C_LIO_LIThrough comparative genomics and transcriptome profiling, we identified three candidate genes, Wall Associated Kinase 1 (WAK1) and Cyclic Nucleotide Gated Channel 1 (CNGC1) and CNGC2. The functions of these genes were validated using a simplified Agrobacterium-mediated transformation method for transient gene expression in strawberry crowns and roots. C_LIO_LIAn examination of the population structure of the RPc2 locus among genetically diverse accessions (N=1029) revealed that the predominant H3 resistant haplotype is widespread in breeding accessions in the US, supporting the findings of a previous study on recent selective sweeps associated with RPc2. Results from this study are advancing genome-assisted breeding strategies for enhancing resistance to PhCR in strawberry. C_LI

plant biology↗

bioRxiv2024

Carbon nanodots as a red emissive fluorescent probe for the super-resolution microscopy of DNA dynamics during paclitaxel treatment

Paclitaxel is a commonly used frontline chemotherapeutic drug for cancer treatment. It is known to be functional by arresting the microtubule disassembly during mitosis. Recently, a non-mitotic pathway has been evolving and thus contemplating the mitotic mechanism. Here, using super-resolution microscopy (SRM), we directly visualized the nuclear dynamics and unveiled the mechanism of paclitaxel treatment. A new class of non-toxic, biocompatible and highly fluorescent carbon nanodots (CNDs) were used as a fluorescent probe that were highly capable to directly stain the nuclear DNA, capture the SRM imaging of chromosome and the chromatin structures. Apart from SRM imaging of chromosomes during all stages of normal mitotic cell division, CNDs successfully visualized the formation of lagging, mis-segregated and bridging chromosomes which leads to the multi-micronucleus formation upon paclitaxel treatment. A detailed chromatin remodelling analysis suggested that heterochromatin played an important role in the formation of condensed multi-micronucleus, ultimately leading to cell death. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/620846v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1d5bb12org.highwire.dtl.DTLVardef@ecd313org.highwire.dtl.DTLVardef@15bb3corg.highwire.dtl.DTLVardef@b79273_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗