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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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300 records · Page 7Linked to original sources

bioRxiv2026

m1A58 acts as a conformational checkpoint coupling human initiator tRNA maturation to translation initiation

tRNAs are characterized by extensive chemical modifications that influence tRNA fate. N1-methyladenosine at position 58 (m1A58) is a widespread core tRNA modification linked to physiological and pathological processes. However, how m1A58 coordinate tRNA folding and processing to ensure translational efficiency in mammalian cells remains largely unknown. Using acute dTAG-mediated degradation and CRISPR-Cas9 knockout, we identified initiator methionine tRNA (tRNAiMet) as selectively vulnerable to m1A58 loss, lacking the isodecoder buffering observed for most other tRNA isoacceptors. NMR analysis of the tRNAiMet showed that m1A58 stabilizes D/T-loop interactions, consistent with a maturation-competent conformation. In vitro processing assays further demonstrated that m1A58 promotes RNase P-mediated 5'-leader removal and RNase Z-mediated 3'-trailer cleavage, while La/SSB protects accumulated precursors. Disrupting this checkpoint impaired the assembly of the eIF2-containing 43S pre-initiation complex and global protein synthesis, which was substantially rescued by adding m1A58-modified tRNAiMet. Acute TRMT6 degradation elicited temporally coordinated gene-expression responses involving proteostasis, transport and signaling. Together, these findings establish m1A58 as a conformational checkpoint coupling human initiator-tRNA maturation to translation initiation and stress responses.

molecular biology↗

bioRxiv2026

GABAB Receptors Gate Sex-Specific Synaptic Plasticity in the Nucleus Accumbens

Excitatory synaptic plasticity within the nucleus accumbens (NAc) drives motivated behaviors, and dysregulation is implicated in several psychiatric disorders marked by impaired reward processing. The NAc integrates glutamatergic input, which conveys information about reward, context, and behavioral goals, with local GABAergic signaling that regulates excitatory transmission and medium spiny neuron (MSNs) output. However, little is known regarding GABA-dependent modulation of activity-dependent excitatory synaptic plasticity. Here, we investigated GABAB receptor (GABABR) regulation of plasticity at hippocampus (Hipp)-NAc synapses, at which plasticity is a key mediator of reward-related behaviors. Using whole-cell electrophysiological recordings in mouse brain slices, we found that pharmacological inhibition of GABABRs converts long-term potentiation (LTP) into long-term depression (LTD) selectively in females, identifying a sex-specific role for GABABRs in modulating long-term plasticity of Hipp-MSN synapses. This LTD required mGluR5 activation and estrogen receptor alpha (ER) in both D1- and D2-expressing MSN subtypes, while only D1-MSNs suggested that LTD was expressed presynaptically through a CB1 receptor-dependent mechanism. Notably, GABABR inhibition did not alter basal synaptic transmission, indicating a specific role for these receptors in gating plasticity beyond regulation of basal excitatory drive. Together, these findings identify a novel, sex-specific mechanism by which GABABRs control the direction of synaptic plasticity.

neuroscience↗

bioRxiv2026

EXTRARNAS: A Framework for Extracting RNA Structures with Multiple Tools

Accurate annotation of RNA base-pairing interactions is essential for structural analysis, benchmarking, and data-driven RNA structure prediction. Several tools can extract RNA interactions from three-dimensional coordinates, but their outputs are heterogeneous and may disagree, particularly for non-canonical base pairs. We present EXTRARNAS, a Java-based framework for automated, reproducible, and user-friendly large-scale extraction of RNA structural annotations with multiple tools. EXTRARNAS processes batches of RNA structures specified by PDB identifier and chain, or provided as local PDB files, executes annotation tools through a Docker-based environment, and parses tool-specific outputs using ANTLR4-based grammars. For each structure-tool pair, the framework generates standard BPSEQ files for canonical cis Watson-Crick interactions and introduces BPSEQE, a standardized text format for representing the extended secondary structure, preserving canonical, non-canonical, and multiple interactions per nucleotide. The current prototype supports RNAView, MC-Annotate, and RNAPolis Annotator. We demonstrate EXTRARNAS on eight RNA structures containing triple-helix motifs, comparing extracted canonical pairs against curated BPSEQ references and evaluating the recovery of manually validated Hoogsteen interactions. The results show consistent differences among tools, especially for non-canonical interactions, highlighting the need for standardized representations such as BPSEQE to support reproducible comparison and future consensus-based annotation.

bioinformatics↗

bioRxiv2026

CyChat: a conversational Cytoscape app for no-code, reproducible network analysis

Network-based analyses of molecular interactions are useful for interpreting high-throughput omics data and identifying therapeutic targets. Cytoscape is the standard platform for these tasks, but users face a trade-off between accessible graphical workflows that are difficult to document and reproducible automation in Python or R that requires programming expertise. General-purpose coding assistants can generate Cytoscape Automation scripts, but remain external to Cytoscape. We present CyChat, a Cytoscape Desktop app that integrates a chat interface and a large language model (LLM) agent into the application. CyChat translates natural language into executable Cytoscape Automation workflows, runs generated Python code, and exports chat sessions with executed code as standalone Jupyter notebooks. To reduce setup barriers, CyChat includes an embedded Python runtime and supports both cloud-based and locally hosted LLMs. CyChat was evaluated across ten Cytoscape workflows using seven LLM providers, each represented by one LLM. The strongest configuration achieves a pass rate above 99%. In a qualitative evaluation based on a published network visualization, CyChat completes the task in 1.5-5 minutes, compared with 15-20 minutes for manual GUI workflows by computational biologists. CyChat is available through the Cytoscape App Store at https://apps.cytoscape.org/apps/cychat.

bioinformatics↗

bioRxiv2026

Bacterial Peptidoglycan Extends Lifespan by Activating Lysosomal Activity through V-ATPase Binding

Lysosomal dysfunction is a hallmark of aging, yet whether microbial components actively regulate this organelle to influence longevity remains unknown. Here, we identify bacterial peptidoglycan (PGN), a major cell wall component degraded by host lysozyme, as an evolutionarily conserved activator of lysosomal function that extends lifespan in both C. elegans and mice. We show that aging leads to an intestinal decline in lysozyme expression, which impairs bacterial cell-wall digestion and results in systemic PGN deficiency. Late-life PGN supplementation (starting at 18 months of age) significantly prolongs mouse lifespan and improves healthspan. Mechanistically, PGN localizes to lysosomes and directly binds V-ATPase subunits, enhancing ATP hydrolysis activity and promoting lysosomal acidification. This effect is abolished by V-ATPase inhibition (bafilomycin A1) or genetic disruption of lysosomal components (cup-5 and vha-12 mutants), confirming that functional V-ATPase is strictly required for lysosomal function and the longevity benefit. Importantly, PGN restores lysosomal acidification in aged cells, alleviates cellular senescence markers, and improves multiple hallmarks of aging including locomotion and muscle integrity. Collectively, these findings reveal an evolutionarily conserved mechanism whereby hosts exploit bacterial cell wall components to maintain cellular homeostasis, establishing a gut microbiome-lysosome-longevity axis with implications for microbiome-based anti-aging interventions.

physiology↗

bioRxiv2026

Structure-Constrained Intrinsic Timescales Across Tasks

Intrinsic neural timescale (INT) quantifies the persistence of spontaneous neural dynamics and offers a principled metric for characterizing brain-wide temporal organization. Although a hierarchy of INTs has been established during rest, how task engagement reconfigures this organization and how it is constrained by the structural connectome (SC) remain poorly understood. Here, we systematically mapped whole-brain INT using high-resolution fMRI data from the Human Connectome Project during rest and seven tasks spanning working memory, gambling, motor, language, social, relational, and emotion domains. Task engagement induced robust, regionally heterogeneous changes in INT while largely preserving the brain-wide temporal hierarchy across cognitive states. SC-INT coupling remained strong but consistently decreased during tasks, indicating that anatomical architecture continues to constrain INT, although its influence is attenuated under task demands. To investigate these findings mechanistically, we employed a multiscale, whole-brain neuronal-network model, which revealed that INT increase and peak within a broad critical-like regime. Strong SC-INT coupling, as observed empirically, emerged in the subcritical regime, weakened progressively with increasing network excitability, and reversed in the supercritical regime. These results demonstrate that task engagement reconfigures INTs while maintaining their hierarchical organization, suggesting that both resting and task states operate largely within a common subcritical dynamical regime.

neuroscience↗

bioRxiv2026

Neural spiketrains and population vectors entangle neural representations

Neural recordings are usually analyzed by comparing neural spiketrains or comparing time bins (population vectors). If multiple variables drive the neural activity these comparisons will be affected by all of them. Our aim is to disentangle these different latent variables or covariates that drive neural activity and reveal their structure and geometry. The central idea of the paper is that a matrix is disentangled when its rows and columns are local on each other, a condition we call bidirectional locality. In such a matrix, rows and columns encode the same geometry and they respond to only one localized part of it. This suggests finding bidirectional local matrices in a given data matrix, from which we can recover the geometry of the covariates driving it in a straightforward way. We present two ways of doing just this. The first method, coherent projections, works by finding non-negative projections of the neural data matrix (neurons by time bins) that are bidirectionally local. The second method, clumps, works by finding dense submatrices of the neural data matrix, that each identify a local region of one covariate. We apply these methods to two neural datasets, showing that they can separate grid cell modules and reveal a movement-driven low-dimensional structure in the motor cortex.

neuroscience↗

bioRxiv2026

Whole-body Super-resolution Functional and Molecular Imaging with Panoramic Photoacoustic-Ultrasound Tomography

Photoacoustic (PA) and ultrasound (US) imaging provide complementary molecular, functional, and anatomical contrasts. Here, we present a panoramic PA-US imaging platform that integrates multispectral PA computed tomography (PACT) along with reflection-mode and transmission-mode US imaging through a single shared full-ring ultrasound array. We employ an ultrafast planewave transmission scheme in reflection-mode US for power Doppler (PWD) imaging and ultrasound localization microscopy (ULM). Additionally, we use the transmission-mode US to reconstruct a spatially resolved speed of sound (SoS) map that corrects both PA and US reconstruction. Such correction sharpens the resolution of PACT, suppresses the artifacts of PWD, and improves microbubble localization of ULM. Elevational scanning further enables whole-body volumetric imaging with co-registered PA and US contrasts. The integrated system maps photoswitchable DrBphP1-expressing tumors alongside their blood perfusion and oxygenation environment. Applying the platform to monitor unilateral renal ischemia-reperfusion injury, we report that microvascular perfusion and renal oxygenation recover at different rates. Collectively, we demonstrate that the integrated PA-US imaging platform provides a unified framework for multiparametric study of anatomy, perfusion, microvascular flow, oxygenation, and molecular activities.

bioengineering↗

bioRxiv2026

RSV competes with the host for translational machinery without a host shutoff strategy

RNA viruses often enhance ribosome recruitment to their own mRNAs through non-canonical sequence elements or by degrading host mRNA. Respiratory syncytial virus (RSV) produces mRNAs with host-like features, including 5'-cap and poly(A) tail. Therefore, the virus lacks an obvious mechanism to preferentially protect its own mRNAs or recruit ribosomes. Furthermore, it remains unknown how RSV interacts with antiviral defense pathways that would reduce cap-dependent translation. Using spike-in normalized sequencing of total and ribosome-associated RNA, we found that RSV does not appear to evoke any host shutoff mechanisms to limit the expression of host genes. These findings show that RSV manages to make use of available ribosomes by competing effectively with host mRNAs and any translational shutoff mechanism would be detrimental. Consistent with this, we found that following activation of antiviral host pathways that reduce cap-dependent translation, translation of RSV mRNAs is decreased to the same extent as host mRNAs. Furthermore, we found that RSV infection does not trigger the dsRNA-activated kinase PKR (which initiates the ISR) and OAS (activates endonuclease RNase L) pathways. These data support a model in which RSV achieves viral protein production, not though inhibiting the host, but by successfully competing with host mRNAs and avoiding activation of antiviral pathways.

molecular biology↗

bioRxiv2026

Arabidopsis Acyl-CoA Binding Protein 4, ACBP4, functions in developmentally programmed endoreduplication

Powdery mildew fungi induce localized endoreduplication, a variant of the cell cycle in which DNA is replicated but cells do not divide, in leaf mesophyll cells underlying the fungal feeding structure. Induced endoreduplication occurs concurrent with powdery mildew (PM) spore production and is associated with enhanced metabolic capacity and flux to lipids. The final ploidy of these cells is highly correlated with fungal spores produced and is the consequence of both basal (developmental) ploidy and PM-induced endoreduplication programs. Herein, we find the Arabidopsis lipid trafficking and regulatory protein ACYL-COA BINDING PROTEIN 4 (ACBP4) enhances PM spore production on Arabidopsis leaves. ACBP4 does not limit plant defense but instead supports basal mesophyll cell ploidy, with decreased final ploidy in cells underlying the fungal feeding structure in acbp4 mutants compared to wild-type (WT). Leaf epidermal cell size is decreased and stomatal density is increased in acbp4, consistent with a role for ACBP4 in developmentally programmed endoreduplication. Moreover, hypocotyl elongation in the dark, which is driven by programmed developmental endoreduplication, shows reduced hypocotyl length, cell length and ploidy in acbp4 versus WT. Together, our findings establish a novel means by which a plant ACBP promotes cell metabolism and development, with potential applications to agricultural productivity and quality.

plant biology↗

bioRxiv2026

Evolutionary origins of protein novelty across an entire yeast subphylum

Novel protein-coding sequences fuel molecular and cellular evolutionary innovations and frequently contribute to species-defining characteristics. They can originate either de novo from previously noncoding sequences or through extreme divergence of already coding ones. How frequently each mechanism occurs and how they shape the structural and functional potential of the resulting proteins remains unclear. Here, we conducted a broad computational investigation of genetic and protein novelty throughout the entire subphylum of Saccharomycotina yeasts. We detected more than 5,000 robust de novo genes across 332 species and compared them to more than 6,000 novel genes resulting from extreme sequence divergence, revealing two quantitatively similar but qualitatively distinct modes of evolution of novelty. A remarkable 40% of de novo proteins are predicted to localize to mitochondria compared to only 20% of divergent, with the latter also being substantially longer and more disordered. A detailed analysis of conservatively predicted tertiary structures of novel proteins shows that ''invention'' of new folds occurs more frequently through de novo emergence. We also illustrate cases of evolutionary ''re-invention'' of existing protein folds from noncoding sequences. Our work deepens our understanding of the origins and importance of novel proteins, opening new directions for further structural and functional characterization.

genomics↗

bioRxiv2026

Gene duplication of SNAPC1 generates transcription factors for snRNAs and sex-specific piRNAs

Piwi-interacting RNAs (piRNAs) are small non-coding RNAs essential for transposon silencing and germline integrity across metazoans. In many species, piRNA expression is sexually dimorphic, yet the molecular mechanisms underlying this sex specificity remain poorly understood. In Caenorhabditis elegans, sexually dimorphic piRNA expression is regulated at the transcriptional level. We previously identified SNPC-1.3, a paralog of the small nuclear RNA (snRNA) activating protein complex (SNAPc/SNPC) subunit SNAPC1, as a male-specific piRNA transcription factor. However, the factors governing female piRNA expression remained elusive. Here, we identify SNPC-1.2, a second SNPC-1 paralog, as a female-specific piRNA transcription factor. SNPC-1.2 interacts with the core piRNA transcriptional machinery, binds female piRNA loci, is required for female piRNA expression, and promotes hermaphrodite fertility. In contrast, a third paralog, SNPC-1.1, retains the ancestral SNAPc function in snRNA transcription and is dispensable for piRNA biogenesis. Together, these findings reveal how gene duplication and functional specialization within the snpc-1 gene family generate specificity factors that direct the core SNAP complex to distinct genomic targets, providing a molecular mechanism for sexually dimorphic piRNA expression while maintaining canonical snRNA transcription.

molecular biology↗

bioRxiv2026

Initial tumor composition shapes resistance evolution and treatment outcomes in non-small cell lung cancer

Drug resistance is a leading cause of treatment failure in non-small cell lung cancer (NSCLC), yet how resistance evolves during treatment and whether its fitness consequences depend on tumor composition remains poorly understood. Using a game-theoretic mathematical model fitted to longitudinal in-vitro data from alectinib-sensitive and alectinib-resistant H3122 NSCLC cells grown under different treatment and microenvironmental conditions, we found that the fitness effect of evolving resistance depended critically on the initial proportion of resistant cells in the tumor. When resistant cells were initially rare, resistance evolved faster and increasing resistance was associated with a growth advantage. When resistant cells were initially frequent, increasing resistance was associated with a fitness cost. In both cases, increasing resistance eroded treatment efficacy. In the gain-of-resistance regime, stabilization therapy could maintain a stable tumor equilibrium only if resistant cells were excluded. Maximum tolerated dosing was not always optimal for maximizing time to progression; intermediate doses performed better when they kept the initial tumor growth rate close to zero. These results suggest that evolutionary therapy for NSCLC should account not only for the abundance of resistant cells, but also for how resistance is evolving and what fitness consequences it currently carries in individual patients.

cancer biology↗

bioRxiv2026

Excessive cholesterol accumulation in microglia increases neuronal synaptic vulnerability to amyloid-beta

Cholesterol efflux is an important determinant of cellular lipid homeostasis. However, how microglial excessive cholesterol accumulation affects neuronal synaptic integrity remains poorly understood, particularly in the context of Alzheimer's disease. Here, we utilized a conditional knockout mouse model targeting the cholesterol transporters ABCA1 and ABCG1 in microglia. The microglia-specific ABCA1/ABCG1 deficiency triggered marked cholesterol accumulation, microglial hypertrophy, downregulation of the homeostatic marker P2ry12, and upregulation of the reactivity-associated marker CD11b, indicating shift toward a reactive phenotype. This phenotype was accompanied by increased reactive oxygen species, consistent with enhanced oxidative stress in ABCA1/ABCG1-deficient microglia compared with control. Using organotypic hippocampal slice cultures, we investigated the downstream neuronal outcomes of microglial ABCA1/ABCG1 deficiency. Under basal conditions, microglial ABCA1/ABCG1 knockdown did not significantly alter dendritic spine density in CA1 pyramidal neurons. However, upon exposure to amyloid-beta (A{beta}) stress, microglial ABCA1/ABCG1 deficiency markedly exacerbated dendritic spine loss in CA1 pyramidal neurons. Taken together, our findings highlight an important role for ABCA1/ABCG1-dependent cholesterol efflux in maintaining microglial homeostasis and limiting neuronal synaptic vulnerability to A{beta}-associated stress. These results support further investigation of microglial cholesterol transport as a potential target for preserving synaptic resilience in Alzheimer's disease.

neuroscience↗

bioRxiv2026

Redundant information across functionally coupled cortical networks supports rapid perceptual decisions in the ferret

Coordinated activity across cortical areas transforms sensory inputs into perceptual decisions, yet how task-relevant information is distributed across sites and linked to functional interactions and behavior remains unclear. Conventional functional connectivity measures reveal statistical dependencies between neural signals but cannot distinguish information encoded uniquely at individual sites, shared redundantly across sites, or available only from their joint activity. Here, we used Partial Information Decomposition (PID) to characterize stimulus information during fast and slow correct decisions. We analyzed local field potentials (LFPs) extracted from mesoscale electrocorticographic recordings from auditory, visual, and parietal cortices in ferrets performing a visual and audiovisual spatial-detection task. Time- and frequency-resolved analyses of local field potential power and phase showed that stimulus-side information was strongest in the theta and alpha bands and greater during fast than slow responses. PID applied to pairs of recording sites revealed that fast responses were associated with earlier and stronger unique information and a greater relative contribution of redundancy, whereas synergistic contributions were smaller. During fast responses, redundancy was selectively associated with stronger LFP power-envelope coupling. These findings indicate that faster perceptual decisions involve a frequency-specific reorganization of cortical information, characterized by early local encoding and enhanced redundant information across functionally interacting sites.

neuroscience↗

bioRxiv2026

Function-driven geometry directs human pilosebaceous unit development

Single-cell technologies have generated cell censuses of tissues, however, how tissue geometry reflects functional needs remains poorly characterized. The human pilosebaceous unit offers a tractable model, a prenatally-formed complex mini-organ combining hair and sebum production with a stem cell reservoir. Using histomorphology, spatial transcriptomics, and single-cell multiomics on the same human prenatal scalp skin samples (8-19 post-conception weeks), integrated and analyzed using machine learning approaches, we built a spatiotemporal map of pilosebaceous unit development. We demonstrate that epithelial-mesenchymal interactions coordinate cellular fate and organogenesis, using an in vitro hair-bearing skin organoid model to validate this tissue-patterning. In addition, we show sebaceous gland developmental programmes are overcome during tumor formation. Our large-scale multi-modal analysis provides a unique framework for understanding form and function of tissues with applications in tissue engineering and pathology.

developmental biology↗

bioRxiv2026

Lipogenic gene expression and substrate sensitivity in the bovine mammary gland shape milk fat composition

Milk fat is produced by mammary epithelial cells (MEC) through a conserved mechanism shared among all fat-producing cells across biological kingdoms. Although highly conserved, different tissues and organisms produce distinctive fat compositions. Notably, ruminant milk fat is characterized by enrichment in short and medium chain fatty acids. We hypothesized that this unique profile is driven by MEC-specific metabolic characteristics related to their response to lipogenic substrates. To study this, we compared bovine MEC and udder-derived fibroblasts in terms of their lipogenic capacity and fatty acid composition when exposed to lipogenic building blocks. When exposed to acetate, MEC showed coordinated upregulation of acyl-CoA short-chain synthetase 1 (ACSS1) and diacylglycerol transferase (DGAT), while expression of acyl-CoA synthetase long-chain 1 (ACSL1) decreased. Medium chain fatty acids were also elevated in acetate-treated MEC and not in fibroblasts. The role of ACSS1 in the production of medium chain fatty acids in MEC was confirmed by knockdown experiments. Metabolomics analysis showed that in MEC acetate treatment triggered a broad metabolic response, primarily amino acids catabolism, energy and polar lipid metabolism. Collectively, these findings demonstrate effective utilization of acetate for de novo fatty acid synthesis in MEC with preferred tendency to produce medium chain fatty acids.

cell biology↗

bioRxiv2026

Design and Validation of New Primers for Specific and Sensitive Real-time PCR Detection and Quantification of Seven Botulinum Encoding Genes (Serotype A-G) of Clostridium botulinum

Botulinum neurotoxins (BoNTs) comprise a highly diverse group of seven serotypes (from A-G) and over 40 subtypes worldwide. Previous primer- and probe-based nucleic acid amplification tests (NAATs) for detection of BoNT encoding genes are challenged by high levels of nucleotide polymorphism both across and within subtypes. In this study, multiple BoNT gene sequences were aligned to identify highly conserved regions for the design of new primers that enable the detection of all seven serotypes under the same conditions. Specific primer sets were designed and validated using in silico, conventional and real-time PCR with constructed plasmids carrying the target fragments and spiked food matrices. The established procedure achieved highly specific and sensitive detection of BoNT serotypes A-G with sensitivity of 10 copies/reaction and a total turnaround time of approximately 1.5 hours. The procedure also eliminated the carryover PCR product by using uracil-N-glycosylase in combination with dUTP in the assay reaction mix. This study provides an alternative NAAT with higher coverage and compliments the traditional mouse bioassays in enhancing global botulism surveillance capabilities.

molecular biology↗