Biology subjects

Kumar, A.

Publications and source records attributed to Kumar, A..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Protocol for green synthesis of excellent fluorescent mango leaves-derived carbon for advanced theragnostic in biological applications

Carbon quantum dots (CQDs) are zero-dimensional fluorescence nanoparticles that are less than 10 nm in size. They have unique properties like tunable surface functionality, biocompatibility, fluorescence, and low toxicity. This study outlines a detailed protocol for synthesizing CQDs from mango leaf powder using a reflux method at 160 C and 400 rpm for a duration of two hours. The synthesized CQDs were comprehensively characterized using the following techniques, including UV-visible spectroscopy, fluorescent spectrophotometry, atomic force microscopy, dynamic light scattering and zeta potential measurement, Fourier transform infrared spectroscopy, and scanning electron microscopy. In vitro analysis was conducted through an MTT assay, revealing that the CQDs exhibit reduced toxicity in RPE1 cells compared to the control group. Additionally, a concentration-dependent cellular uptake assay was performed to further evaluate the biological performance of the CQDs. The findings suggest the potential of CQDs as safe and effective nanomaterials for various biological applications, including drug delivery and bioimaging.

bioengineering↗

bioRxiv2025

Discovery of Small Molecules and a Druggable Groove That Regulate DNA Binding and Release of the AP1 Transcription Factor DeltaFOSB

{Delta}FOSB, a member of the AP1 family of transcription factors, mediates long-term neuroadaptations underlying drug addiction, seizure-related cognitive decline, dyskinesias, and several other chronic conditions. AP1 transcription factors are notoriously difficult to modulate pharmacologically due to the absence of well-defined binding pockets. Here, we identify a novel site on {Delta}FOSB, located outside the DNA-binding cleft, that accommodates small molecules. We show that sulfonic acid-containing compounds bind to this site via an induced-fit mechanism, reorienting side chains critical for DNA binding, and that they may hinder the {Delta}FOSB bZIP -helix from binding to the major groove of DNA. In vivo, direct administration of one such compound, JPC0661, into the brain reduces {Delta}FOSB occupancy at genomic AP1 consensus sites by approximately 60% as determined by CUT&RUN-sequencing. These findings suggest that DNA binding and release by AP1 transcription factors can be controlled via small molecules that dock into a novel site that falls outside of the DNA-binding cleft. Minimal sequence conservation across 29 bZIP domain-containing transcription factors in this druggable groove suggests that it can be exploited to develop AP1-subunit-selective compounds. Our studies thus reveal a novel strategy to design small-molecule inhibitors of {Delta}FOSB and other members of the bZIP transcription factor family.

neuroscience↗

bioRxiv2025

Efficient in vivo pharmacological inhibition of deltaFOSB, an AP1 transcription factor, in brain

{Delta}FOSB, an unusually stable member of the AP1 family of transcription factors, mediates long-term maladaptations that play a key role in the pathogenesis of drug addiction, cognitive decline, dyskinesias, and several other chronic neurological and psychiatric conditions. We have recently identified that 2-phenoxybenzenesulfonic acid-containing compounds disrupt the binding of {Delta}FOSB to DNA in vitro in cell-based assays, and one such compound, JPC0661, disrupts {Delta}FOSB binding to genomic DNA in vivo in mouse brain with partial efficiency. JPC0661 binds to a groove outside of the DNA-binding cleft of the {Delta}FOSB/JUND bZIP heterodimer in the co-crystal structure. Here, we generated a panel of analogs of JPC0661 with the goal of establishing structure-activity relationships and improving its in vivo efficacy by replacing the amino-pyrazolone cap moiety with various substituents. We show that one such analog, YL0441, disrupts the binding of {Delta}FOSB to DNA in vitro and in vivo, and suppresses {Delta}FOSB-function in cell-based assays. Importantly, infusion of YL0441 into the hippocampus of APP mice (a mouse model for Alzheimers disease) leads to virtually complete loss of {Delta}FOSB bound to genomic DNA by CUT&RUN sequencing. Our findings corroborate that DNA binding/release of AP1 transcription factors can be controlled via small molecules, even by analogs of a compound that binds to a groove outside of the DNA-binding cleft, and that our lead can be optimized via medicinal chemistry to yield a highly efficacious inhibitor of {Delta}FOSB function in vivo. These findings define a strategy to design small-molecule inhibitors for other AP1- and AP1-related transcription factors. IN BRIEFWe demonstrate the creation of a highly effective inhibitor, YL0441, of {Delta}FOSB, an AP1 transcription factor, which decreases the number of {Delta}FOSB-bound sites to genomic DNA by [~]94% upon in vivo infusion to the hippocampus of APP mice, a mouse model for Alzheimers disease. This work generates a highly novel probe compound to assess the therapeutic value of {Delta}FOSB in vivo, a transcription factor with a critical role in mediating long-term changes in gene expression in several neuropsychiatric disorders in addition to Alzheimers disease, including drug addiction, seizure-related cognitive decline, and dyskinesias.

neuroscience↗

bioRxiv2025

Identification and functional characterization of LDB3 gene variants in DCM patients from Indian Population

The LIM domain-binding protein 3 (LDB3), also known as Z-band alternatively spliced protein (ZASP), is a key component of the Z-disc, essential for maintaining sarcomeric integrity and transmitting contractile force in cardiomyocytes. Genetic variants in LDB3 have been implicated in cardiomyopathies, including dilated cardiomyopathy (DCM). In this study, we have screened 100 idiopathic DCM cases along with controls by Sanger sequencing and identified nine non-synonymous (p.S184I, p.D193N, p.K204R, p.R229C, p.P295T, p.Q402P, p.F465I, p.F496L, p.P606S), seven synonymous (p.T91=, p.A152=, p.D168=, p.S182=, p.A279=, p.S347=, p.A358=), and seven intronic (c.322-50G>C, c.548+53A>C, c.718+47G>C, c.718+81G>A, c.755+11G>A, c.755+86G>A, c.*30C>G) variants, among which six (p.S184I, p.D193N, p.P295T, p.F465I, p.F496L, p.P606S) missense variants were novel. In-vitro studies demonstrated that p.K204R increased LDB3 expression whereas p.S184I, p.F465I, p.F496L, p.P606S reduced LDB3 expression. Immunostainning revealed cytoplasmic aggregation of the p.K204R-LDB3 protein. The variant p.R229C also over-expressed the mutant protein. In case of variant, p.P295T, Z-disc was severely disrupted indicating impaired Z-disc integrity. Furthermore, synonymous variants showed altered mRNA folding, stability, and codon usage bias, potentially affecting translation efficiency. In-silico analyses predicted p.F465I, p.F496L, p.P606S, and p.S184I variants to be deleterious, significantly altering protein structure. Structural modeling using AlphaFold2 showed high RMSD values, suggesting conformational destabilization. Collectively, these findings highlight LDB3 as a hypermutable candidate gene for DCM in our cohort that may contribute to DCM pathogenesis by perturbing protein structure, expression, and cellular localization, underscoring the critical role of LDB3 in cardiac muscle function and disease.

genetics↗

bioRxiv2025

Delay selection by spike-timing-dependent plasticity shapes efficient networks for signal transmission

Information processing in the brain relies on efficient communication between different brain regions. Brain oscillations can control signal transmission in brain networks by modulating the timing and excitability of sender and receiver areas. For effective transmission, signals should arrive at target areas when their excitability is maximized. For reciprocally connected neural populations, this mechanism works if the transmission delay matches the period of their evoked oscillation. However, the mechanisms underlying such development of the connections with matched delays remain elusive. While transmission delays in brain networks change during development, the process by which delays are tuned for efficient transmission is unknown. Here, we demonstrate that the well-known Hebbian learning rule can provide a mechanism for selecting connections with delays that match the period of network oscillations. We consider a reciprocally connected bi-layer network of excitatory and inhibitory neurons that generate network-level oscillations spontaneously or in response to external stimuli. When exposed to spiketiming-dependent plasticity (STDP), the network self-organizes to potentiate connections with delays matching the oscillation period, while depressing those with non-matching delays. Our findings shed light on how transmission delays may evolve during learning and development to optimize the organization of brain networks for efficient signal transmission.

neuroscience↗

bioRxiv2025

Genome-wide Screening Identifies Unique Host-Directed Drugs and Pro-viral Signalling Pathways for SARS-CoV-2

SARS-CoV-2 is a positive-sense RNA virus and was responsible for the devastating COVID-19 pandemic. Although the current disease burden is less severe, there are limited treatment options, significant gaps in knowledge, and a looming threat of the emergence of variants and future pandemics. To address these challenges, we performed genome-wide CRISPR knockout screens in a novel human lung cell line NCI-H23ACE2, as well as in HEK293TACE2 cells, with SARS-CoV-2 Wuhan virus, with the aim of identifying host-dependency factors that could predict effective antivirals. We identified four host-directed drugs, donepezil, dH-ergocristine, trametinib and sorafenib, that could potentially be repurposed to treat coronavirus infections. Three of the drugs inhibited SARS-CoV-2, HCoV-229E, and HCoV-OC43, suggesting they could be used as pan-coronavirus antivirals. We also confirmed that SARS-CoV-2 relies on the NRAS/Raf/MEK/ERK signaling pathway for its replication. Our study highlights the robustness and efficiency of a bilateral approach of gene silencing and antiviral screening to identify host-dependency factors and effective antivirals.

microbiology↗

bioRxiv2025

Preclinical evaluation of Targeted IL-1β Knockdown via CD44-Immunoliposomes: A Nano-therapy against the Inflammatory Microenvironment

Chronic inflammation, characterized by the infiltration of macrophages and the heightened release of pro-inflammatory cytokines, is the underlying cause of the pathogenesis of many critical diseases. Therapeutic interventions for controlling inflammation via gene knockdown of inflammatory mediators have emerged as a promising approach for regulating uncontrolled inflammation. This study explores the potential of siIL-1{beta}-anti-CD44-Liposomes (SIL) as a potent anti-inflammatory therapy against pro-inflammatory RAW264.7 macrophages via gene specific knockdown of IL-1{beta} mRNA through RNAi, and the subsequent down-regulation of the pro-inflammatory cytokine loop. The designed SIL exhibited a uniform size of 131.1 {+/-} 0.5 nm with a quasi-spherical morphology and sustained release of siIL-1{beta} within 24 hours. The reduction in pro-inflammatory cytokines like IL-1{beta}, TNF-, and IL-6 and inflammatory enzymes iNOS and COX-2; and the simultaneous increase in the anti-inflammatory cytokine IL-4, is indicative of the formulations therapeutic efficacy in reducing inflammation at a cellular level. The effects of SIL on the Macrophage-T cell crosstalk also uncovers the liposomes efficacy in reducing cytokine-mediated T cell effector functions. The nuanced effects of siIL-1{beta}-anti-CD44-Liposomes on in-vivo model of chronic inflammation underscore their potential for precise therapeutic interventions in inflammatory conditions, with multifaceted anti-inflammatory effects on tissue levels and cytokine levels. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/683015v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@f4d0f9org.highwire.dtl.DTLVardef@c3c24aorg.highwire.dtl.DTLVardef@8c115org.highwire.dtl.DTLVardef@bc863d_HPS_FORMAT_FIGEXP M_FIG Schematic representation of the study: CD44 receptors are elevated in LPS activated macrophages, which can be targeted by using anti-CD44 Liposomes, for RNA therapy. IL-1 knockdown via siRNA leads to lower inflammatory nature of macrophages, compromising its the antigen presentation and T-cell activation. This lowers the cytokine storm in inflammatory milieu and lower tissue damage can be achieved. Created with BioRender.com. C_FIG

pharmacology and toxicology↗

bioRxiv2025

Urinary Exosomal miRNA Profiling Reveals Sensitive Non-Invasive Diagnosis of Bladder Cancer

UnstructuredmiRNAs represent a transformative advancement in both research and clinical management of urinary bladder cancer (UBC), emerging as clinically significant molecular targets with the potential to revolutionize existing diagnostic standards. This study exploited the robust stability of miRNAs and profiled urinary miRNAs in UBC patients and controls through miRNA sequencing, revealing an expanded and altered miRNA repertoire in cancer samples. Validation in an independent cohort revealed fold changes for miR-6724-5p, miR-1273h-5p, miR-7704, miR-200-5p, and miR-10400-5p ranged from [~]46 to [~]2,777 (p < 0.01). Stage-specific analyses highlighted dynamic miRNA expression linked to tumor progression. Diagnostic evaluation identified an optimal three-miRNA panel comprising miR-6724-5p, miR-10400-5p, and miR-7704, achieving diagnostic accuracies (AUC > 70%) and high sensitivity (>90%). These data demonstrate the potential of urinary mature miRNAs as robust biomarkers for non-invasive detection and monitoring of UBC in early stages, supporting their translation into clinical diagnostic assays pending larger prospective studies. StructuredO_ST_ABSBackgroundC_ST_ABSUrinary microRNAs (miRNAs) are promising candidates due to their molecular stability and disease-specific expression. miRNAs represent a transformative advancement in both research and clinical management of urinary bladder cancer (UBC), emerging as actionable molecular targets with the potential to revolutionize existing diagnostic standards. MethodsSmall RNA sequencing was performed on urine samples from UBC patients and healthy controls to profile miRNA expression. Mature miRNAs were prioritized by exclusion of precursor forms using computational filtering. Validation by quantitative RT-PCR was conducted on an independent, age-matched cohort (n = 45). Diagnostic potential of candidate miRNAs was assessed by receiver operating characteristic (ROC) curves and area under the curve (AUC) analyses. ResultsSequencing identified 865 known and 11 novel miRNAs, with UBC samples showing greater miRNA diversity (708 known miRNAs) compared to controls (540). Ten miRNAs were significantly dysregulated in UBC (p < 0.05). Validation revealed fold changes for miR-6724-5p, miR-1273h-5p, miR-7704, miR-200-5p, and miR-10400-5p ranged from [~]46 to [~]2,777 (p < 0.01). Stage-specific analyses highlighted dynamic miRNA expression linked to tumor progression. A three-miRNA panel (miR-6724-5p, miR-10400-5p, miR-7704) demonstrated superior diagnostic performance (AUC > 70%, sensitivity > 90%). ConclusionMature urinary miRNAs exhibit reproducible, stage-specific dysregulation in UBC and a combinatorial panel offers sensitive, specific non-invasive detection. These findings warrant further multicenter validation for clinical application.

cancer biology↗

bioRxiv2025

Filling knowledge gaps on vulnerable electric ray Narcine timlei (Elasmobranchii: Torpediniformes: Narcinidae) through ecological and biological studies

Narcine timlei (Bloch & Schneider, 1801), commonly known as the brown numbfish, recently moved from Data Deficient to Vulnerable in IUCN Red List. However, the biological information on the species is still lacking. In the present study, we provide an integrative assessment of populational dynamics on N. timlei. Morphological and molecular analyses ascertain the species identity as N. timlei. A total of 331 individuals were examined, comprising 156 males and 175 females, including 13 gravid, bringing an overall sex ratio of 1:1.21. We observed the highest specimens during the post-monsoon season (33.5%), and minimum during summer (18%). Length-weight relationships indicated negative allometric growth (b=2.78). Most specimens fall under the 17-20 cm size class, and a few exceeded 23 cm. Pregnant females carried 2 to 9 embryos. A total of 69 embryos from 13 females were obtained. Embryo length and weight were 5.18 {+/-} 0.22 cm and 2.02 {+/-} 0.36 g, respectively. No correlation was observed between maternal length and fecundity (R2 = 0.0036). Male to female embryo ratio was skewed to 1:1.3. The average length of electric organs in adults was 4.30 {+/-} 0.47 cm. Mean electrocyte count for adults was 117.55 {+/-} 14.48, while in embryos it was 123.36 {+/-} 15.9, indicating early developmental establishment of electrocyte structure in N. timlei. We strongly recommend long term species-specific monitoring and management measures to ensure conservation of this ecologically significant but often overlooked batoid.

zoology↗

bioRxiv2025

ISGylation Mechanism Uncovers Conformational Specificity for HECT-family E3 ligase

Interferon-stimulated gene 15 (ISG15), composed of N-terminal and C-terminal ubiquitin-like domains (NTD/CTD), plays a critical role in antiviral immunity. Although the ubiquitination mechanism is well established, the mechanisms governing ISG15 transfer, particularly from E2 to E3 and subsequent lysine conjugation, remain unknown. Here, we reveal that UbcH8(E2)[~]ISG15 exhibits striking specificity for HECT-family E3 ligases (particularly HERC5) but is inactive with RING or RBR E3. In contrast, UbcH8[~]Ub preferentially engages RBR E3, indicating a switched E2-E3 specificity depending on the conjugated ubiquitin-like modifier. Structural and biochemical studies uncover how a unique closed conformation of UbcH8[~]ISG15 enables trans-thiolation mediated by selective HECT-family E3 ligases. We further demonstrate that HERC5s C-lobe specifically recognizes donor ISG15 for lysine conjugation, explaining its exclusive ISGylation activity and lack of ubiquitination function. These findings delineate the molecular basis of ISG15 conjugation and reveal how its pathway has evolved distinct mechanisms from ubiquitination, offering new avenues for therapeutic intervention in infection and immunity.

biophysics↗

bioRxiv2025

Oxidative stress-induced proteolytic activation of polyphenol oxidase triggers an oxidized flavonoids-mediated stress signaling in Camellia sinensis

Environmental perturbations often increase reactive oxygen species (ROS) production, inducing oxidative damage to various biomolecules. The cellular system utilizes ROS or ROS-generated metabolites to instigate signaling pathways, resulting in acclimation, growth inhibition, or programmed cell death (PCD) for sustaining stress. Various stress-generated or stress-activated signaling components and downstream pathways are identified in model plants; however, they are largely unexplored in non-model plants. Here, we report a stress-induced proteolytic activation of an evolutionarily conserved chloroplast-localized enzyme, polyphenol oxidase (PPO), that oxidizes catechins into theaflavins (TFs) and initiates a stress signaling under drought in Camellia sinensis (Tea). Germplasm-based analysis revealed a heightened proteolytic activation of PPO and consequent TFs accumulation in drought-susceptible genotypes. Transcriptome analysis revealed that PPO activation and TFs accumulation were linked to the activation of UPR(unfolded protein response)-like response, which was reinforced by virus-induced silencing and overexpression of PPO, and direct feeding of TFs in tea plants. Pharmacological treatments revealed that TFs interact with HSP90, activating a canonical IRE-bZIP60-dependent ER stress pathway resulting in PCD. Similar proteolytic activation of PPO and subsequent instigation of stress signaling in other plant species (tomato and wheat) demonstrated that PPO acts as an evolutionarily conserved stress sensor, instigating an inter-organelle communication in plants. Significance statementPPO, an evolutionarily conserved and chloroplast/plastid localized enzyme, senses stress and undergoes proteolytic activation to generate oxidized flavonoids/quinones that function as signaling molecules in Tea and likely in other plants. The oxidized flavonoids modulate protein folding machinery and augment folding stress, especially in the ER, inducing canonical IRE1-bZI60-dependent PCD. The finding shows that specific secondary metabolites likely have roles in instigating intra- and intercellular communication to sustain the adversities of stress in different plant species.

plant biology↗

bioRxiv2025

NEST-Scoring, a Novel miRNA Target Gene Profile Network Analysis of Placenta-Derived Extracellular Vesicles in a Transgenic Rat Model of Preeclampsia

Preeclampsia is a multisystem hypertensive disorder of pregnancy and a leading cause of maternal morbidity and mortality. Despite its increasing incidence and the debilitating nature of its cerebrovascular complications, the underlying mechanisms remain incompletely understood. The goals of this study were to 1) determine whether middle cerebral artery (MCA) hemodynamics are altered in late gestation (LG) or two months postpartum in transgenic rats with preeclampsia compared to normal pregnant Sprague-Dawley (SD) rats, and 2) evaluate the microRNA (miRNA) profiles of circulating placental-derived extracellular vesicles (EVPD) using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway framework using NEST-Scoring [Node, Edge, System, Topology], a novel target gene profile network analysis. Our data showed elevated blood pressure in transgenic preeclampsia rats at both LG and two months post-partum (PP-2M) compared to normal pregnant SD rats in the setting of hypertension. The heart rate was also significantly higher in preeclampsia rats at LG. No differences were observed in left MCA (LMCA) velocities between strains or time points. However, LMCA resistance and pulsatility indexes were lower at PP-2M in transgenic preeclampsia rats compared to SD rats. Exposure to preeclampsia differentially altered the miRNA profiles of circulating EVPD in transgenic preeclampsia rats at both LG and PP-2M. The identified miRNA targets were associated with key vascular and cellular regulatory pathways, suggesting a mechanistic link between placental dysfunction and postpartum vascular alterations in this preeclampsia model. Overall, this study suggests that the TGA-PE rat model could be a valuable platform to study the mechanistic link between preeclampsia and cerebrovascular disease.

bioinformatics↗

bioRxiv2025

Fiber-type vulnerability and proteostasis reprogramming in skeletal muscle during pancreatic cancer cachexia

Cachexia is a debilitating syndrome marked by progressive skeletal muscle wasting, commonly affecting cancer patients, particularly those with pancreatic cancer. Despite its clinical significance, the molecular mechanisms underlying cancer cachexia remain poorly understood. In this study, we utilized single-nucleus RNA sequencing (snRNA-seq) and bulk RNA-seq, complemented by biochemical and histological analyses, to investigate molecular alterations in the skeletal muscle of the KPC mouse model of pancreatic cancer cachexia. Our findings demonstrate that KPC tumor growth induces myofiber-specific changes in the expression of genes involved in proteolytic pathways, mitochondrial biogenesis, and angiogenesis. Notably, tumor progression enhances the activity of specific transcription factors that regulate the mTORC1 signaling pathway, along with genes involved in translational initiation and ribosome biogenesis. Skeletal muscle-specific, inducible inhibition of mTORC1 activity further exacerbates muscle loss in tumor-bearing mice, highlighting its protective role in maintaining muscle mass. Additionally, we uncovered novel intercellular signaling networks within the skeletal muscle microenvironment during pancreatic cancer-induced cachexia. Together, these results reveal previously unrecognized molecular mechanisms that regulate skeletal muscle homeostasis and identify potential therapeutic targets for the treatment of pancreatic cancer-associated cachexia.

cell biology↗

bioRxiv2025

Identification of donor landraces for early vegetative stage salinity tolerance in wheat by employing multivariate selection indices

Soil salinity (EC of [≥]4 dS m-1) is a major abiotic stress leading to decreased crop production due to osmotic, ionic, and cellular ionic imbalance balance. The current study aims to identify salinity-tolerant wheat landraces by investigating morpho-physiological traits. Three hundred fifty wheat landraces and check lines were evaluated for salt stress (15 dS m-1) tolerance in a hydroponic set-up. The clustering analysis categorized 350 genotypes into four control and 15 dS m-1 conditions clusters. Across the multi-trait genotype-ideotype distance index (MGIDI), Smith Hazel Index (SHI), and Stress Susceptibility Index (SSI), seven genotypes were consistently identified as tolerant among the top 150. In comparison, 12 genotypes were consistently classified as least tolerant. These identified tolerant landraces serves as important resources and novel salt tolerance donors for wheat. The tolerant*sensitive, tolerant* tolerant check, crosses can be used for generating RIL populations to delineate genetic basis of salt tolerance of newly identified lines.

physiology↗

bioRxiv2025

Contextual Cues and Transition Statistics Drive Expression of Competing Motor Memories

Learning multiple motor skills without interference and expressing the correct one in a changing environment is a fundamental challenge. Contextual cues are known to help separate these memories, but how they interact during retrieval is not well understood. We investigated how the stability, recency, and transitional statistics of learning environments influence this process. Across six visuomotor adaptation experiments, participants learned opposing rotations (Tasks A and B) tagged with distinct contextual cues under different schedules (blocked or interleaved) and were tested in stable or dynamic environments. We found that while contextual cues can successfully separate memories, expression is systematically biased by learned transition statistics: towards more stable memories after imbalanced training, and towards more recent memories when stabilities are matched. Critically, when the stable statistics of training mismatched the volatile statistics of testing, cue-based retrieval collapsed, and behavior was dominated by these stability or recency biases. Conversely, learning in a high-entropy, interleaved environment enabled precise, cue-appropriate expression regardless of the testing schedule. These results demonstrate that memory retrieval is not cue-driven but arises from an arbitration process between cues and transition priors. Our findings reveal that memory retrieval involves weighting sensory information against latent priors derived from the history of context transitions. This work provides a unifying theoretical framework for understanding adaptive memory expression, positing that the brain leverages the learned statistical structure of the environment to infer which memory to recall, thereby balancing cue-driven selection with the stability and predictability of past experience. This principle offers a unifying explanation for interference, spontaneous recovery, and the benefits of variable practice, providing a more holistic model of adaptive motor behavior. Statement of SignificanceHow does a tennis player instantly switch between a forehand and a backhand? Our work reveals a fundamental principle of how the brain organizes and retrieves memories. We demonstrate that recalling a skill is not just about recognizing a contextual cue, but about an internal process of integrating that cue with the learned statistics of the environment, such as the stability and recency of past experiences. This finding provides a unifying framework for phenomena like interference and spontaneous recovery. It has significant implications for designing more effective training in sports and rehabilitation, where structuring practice around environmental statistics can optimize learning and promote flexible skill application.

neuroscience↗

bioRxiv2025

Inhibition of the neurodevelopmental disorder-associated 16p11.2 gene QPRT leads to altered cell type distribution in human stem cell-derived cerebral organoids

The 16p11.2 gene QPRT, encoding a key enzyme of the kynurenine pathway, has been linked to neurodevelopmental disorders including autism spectrum disorder (ASD). To investigate its role in early human brain development, we inhibited QPRT in stem cell-derived cerebral organoids. QPRT inhibition resulted in reduced organoid size, driven by premature neural differentiation resulting in depleted progenitor populations. Single-cell transcriptomics revealed an excitation/inhibition imbalance, with reduced excitatory and increased inhibitory neuron populations. We observed metabolic stress signatures, including pseudo-hypoxia, oxidative stress, and mitochondrial dysfunction, likely linked to NAD+ depletion and QUIN accumulation following QPRT inhibition. Notably, downregulation of LHX2 and PRDX1 may underlie impaired neural patterning and excitotoxic vulnerability. In addition, we report astrocytic and radial glia dysfunctions, indicating broad effects across multiple cell types. Disease gene enrichment analyses showed significant overlap with ASD-associated genes, especially during early differentiation. These findings suggest the loss or reduction of QPRT to shift neural development and neuronal homeostasis towards an imbalance in excitatory and inhibitory neuronal populations, a mechanism previously associated with neurodevelopmental disorders.

cell biology↗

bioRxiv2025

Cortical Representation of Pitch Perception in Mice

Pitch perception arises from temporal and spectral cues in sound. We hypothesized that mice rely on temporal cues because they have wide auditory filters, resembling humans with hearing loss or cochlear implants. Using computational modeling, behavioral assays, and widefield calcium imaging, we found that the structure of periodotopy in auditory cortex predicts how well mice recognize temporal pitch cues, establishing mice as a robust model for temporal pitch perception.

neuroscience↗

bioRxiv2025

Alanine catabolism of Paneth cells maintains intestinal stem cell function during dietary restriction

Background and aimsPaneth cell niche promotes the function of intestinal stem cells (ISCs) during reduced food intake, but how ISC activity can be boosted when availability of resources is simultaneously reduced remains unknown. MethodsMice were subjected to dietary restriction (DR) and ad libitum (AL) dietary regime. FACS-sorted DR and AL Paneth cells and Lgr5+ stem cells were co-cultured, and organoid formation supportive capacity of Paneth cells was assessed. The role of Gpt2 - a Paneth cell specific mitochondrial alanine transaminase, was investigated by targeting pharmacologically and genetically in the intestinal organoids. By using U-13C labelled Alanine, an intercellular metabolic exchange assay was developed - and a conversion and transport of lactate from Paneth cells to stem cells, was followed by metabolomics. The in vivo role of Gpt2 was investigated in a conditional knock out mouse model. ResultsWe discovered that an increase in ISC function upon dietary restriction (DR) or DR mimicking condition, is dependent on Gpt2 in Paneth cells. Metabolic tracing of alanine directly showed DR boosts Paneth cell alanine catabolism, increasing lactate production via gluconeogenesis. Alanine derived lactate is shuttled from Paneth cells to neighboring stem cells, promoting TCA cycle and enhancing the ISC function during DR. Correspondingly, pharmacologic inhibition in vitro and genetic targeting of Gpt2 in vivo abolished the DR induced capacity of Paneth cells to support ISC function. ConclusionsOur results unravel dynamic intercellular metabolic cooperation in tissue adaptation, where Paneth cells upregulated Gpt2 catabolize increased amount of alanine to generate lactate as a transferable energy source, and to augment stem cell functions under DR.

cell biology↗