Biology subjects

Lim, C.

Publications and source records attributed to Lim, C..

At least 19 recordsLinked to original sources

bioRxiv2026

RAPPL-Seq Enables Rapid, High-Sensitivity Ribosome Profiling of Scarce Samples

Ribosome profiling is a powerful method for transcriptome-wide monitoring of translation activity in vivo, but its use is limited by lengthy protocols, reliance on specialized equipment and inefficient recovery of ribosome-protected fragments (RPFs). To overcome these challenges, we developed RAPPL-Seq, a magnetic bead-based affinity capture method that enables fast and efficient RPF isolation. RAPPL-Seq achieves high recovery efficiency, short processing time, and robust performance with limited input material. It is broadly applicable across multiple sample types, including cell lines, primary tissues, and human biospecimens. RAPPL-Seq can also be paired with translation inhibitors to characterize inhibitor- and tissue-specific mRNA translation. RAPPL-Seq efficiently captured translatomes of glioblastoma (GBM) and adjacent non-tumor brain tissues from patient biopsies. Together, these findings establish RAPPL-Seq as a straightforward, easily accessible, and highly sensitive approach that extends translatome studies to scarce experimental and clinical samples, opening new avenues for mechanistic insight and therapeutic discovery.

molecular biology↗

bioRxiv2026

Adversity severity shapes caregiving predictors and neural correlates of infant social behavior

Early-life adversity is associated with highly variable developmental outcomes, but identifying sources of this heterogeneity is difficult because variation in outcome is typically accompanied by variation in exposure. Animal models provide experimental leverage by standardizing features of the early environment while allowing variation in developmental experience and outcome to remain observable. Using a graded limited bedding and nesting model spanning normative rearing, moderate restriction, and severe scarcity, we asked what distinguishes social outcomes among animals exposed to the same resource restriction. Severe scarcity increased adverse maternal handling while leaving organized nurturing behaviors intact. Following the P8-P12 rearing manipulation, pups were tested outside the home cage in a P13 social approach assay. Severe scarcity reduced the proportion of pups that approached the dam, but outcomes varied substantially among scarcity litters. Greater typical maternal pup transport predicted greater approach, whereas a greater proportion of rough transport predicted poorer approach. Transport composition did not differ across rearing conditions, but its relationship with social behavior did. Amygdala intercalated-cell recruitment also covaried with social approach under severe scarcity despite limited condition-level differences in regional c-Fos. Plasma corticosterone differed across rearing conditions but did not covary detectably with the principal caregiving, behavioral, or neural measures. Maternal transport and intercalated-cell recruitment were not robustly associated, identifying separable experiential and neural correlates of behavioral variation. These findings show that standardizing an environmental constraint does not produce uniform developmental experience or outcome, and that caregiving experiences preserved across rearing conditions can distinguish social outcomes under severe scarcity.

neuroscience↗

bioRxiv2026

Electron microscopy reveals water networks inside hydrated cellulose fibers

Cellulose is a highly abundant linear glucose polymer that exists in amorphous and fibrillar forms1-3. Primarily produced by vascular plants but also microbes and tunicates, cellulose predominantly performs architectural functions by stabilizing cell walls, tissues, and multicellular communities4-9. Owing to its association with other cell surface materials, physiological higher-order structures of cellulose have been difficult to obtain. Here, we describe a never-dried tunicate cellulose fibril structure by cryogenic electron microscopy, which resolves a fiber of more than 360 cellulose strands. Our data reveals linear and severely twisted fiber segments that are interspersed with solvent channels. Solid-state NMR analyses and molecular dynamics simulations indicate the presence of structural water molecules that form a network connecting neighboring cellulose chains. Confocal and super-resolution MINFLUX fluorescence imaging using cellulose-specific probes as well as biochemical analyses demonstrate shared surface and material properties of plant and tunicate cellulose fibers. Combined, our data suggest that architectural water molecules may be common features of cellulose fibers and likely other polysaccharide assemblies in their hydrated physiological states.

molecular biology↗

bioRxiv2026

Arginine methyltransferase signalling is hyperactive in conditions of neuromuscular junction instability and muscle atrophy

Background: The neuromuscular junction (NMJ) is the site of communication between myofibers and a-motor neurons. Cellular and molecular mechanisms that determine, maintain, and remodel the neuromuscular synapse are poorly understood. Coactivator-associated arginine methyltransferase 1 (CARM1) post-translationally modifies target proteins by methylating arginine residues and has emerged as a key determinant of skeletal muscle biology. Methylarginine signalling is required for the maintenance and repair of the NMJ, but the direct role of CARM1 on the NMJ in health and disease remains unexplored, particularly in humans. Methods: We generated Carm1 skeletal muscle-specific knockout-out (mKO) mice to gain a basic understanding for the role of the enzyme in NMJ biology under homeostatic and denervated conditions. Additionally, we investigated CARM1 activity in severe mouse models of neuromuscular disorders (NMDs) including D2.mdx and Smn2B/- mice, which replicate Duchenne's muscular dystrophy (DMD) and spinal muscular atrophy (SMA), respectively, and exhibit chronic remodelling of the NMJ. Lastly, to evaluate if methylarginine signalling is implicated during NMJ instability in human skeletal muscle, we obtained samples from healthy volunteers before and after 14 days of single leg immobilization as well as from patients with myotonic dystrophy type 1. Results: Our results demonstrated that Carm1 mRNA expression and activity are elevated (P<0.05) in NMJ-enriched regions of healthy murine skeletal muscle. Carm1 muscle-specific deletion reduced NMJ compactness (-9.3%; P<0.05), increased fragmentation (+33%; P<0.05), and disrupted the expression of synapse-specific transcripts basally and following sciatic nerve transection. In skeletal muscle from pre-clinical models of NMDs, we observed a compensatory upregulation in CARM1-dependent arginine methylation as evident by +54% and +71 increases (P<0.05) in asymmetric dimethylarginine (ADMA)-marked CARM1 substrates in DMD and SMA mice, respectively. Similarly, muscle CARM1 was hyperactive with increased NMJ instability during neuromuscular disuse (+22%; P<0.05), and disease (+30%; P<0.05), in humans. In a cohort of muscular dystrophy patients and healthy volunteers, elevated CARM1 signalling was negatively correlated with clinical metrics of skeletal muscle health including grip strength (r = -0.583; P<0.05) as well as positively correlated with mRNA expression of NMJ machinery such as CHRNA1 (r = 0.578; P<0.05). Conclusion: In summary, we highlight that muscle-specific CARM1 is required for maintaining NMJ morphology and transcriptional regulation. Insults to NMJ stability during muscle disuse or in myopathic conditions were associated with enhanced CARM1-mediated methylarginine signalling in mice and humans. Collectively, our findings demonstrate CARM1 as a key mediator of NMJ biology and plasticity in health and disease.

physiology↗

bioRxiv2026

Cell-state-dependent responses to PLK1 inhibition reveal a non-canonical microtubule-endolysosomal vulnerability in quiescent leukemia stem cells

Relapse in cancer is frequently driven by therapy-resistant quiescent cancer stem cells. Conventional chemotherapy has been designed to target proliferating tumor cells and is generally presumed to be ineffective against non-cycling cancer stem cells. Using acute myeloid leukemia (AML) as a model, we challenge this prevailing view by showing that inhibition of the mitotic master regulator Polo-like kinase 1 (PLK1), a kinase extensively pursued for antiproliferative cancer therapy, unexpectedly eradicates quiescent leukemia stem cells (LSC) through a mechanism distinct from its canonical mitotic function. In proliferating AML cells, PLK1 inhibition (PLK1i) induced G2/M arrest and mitotic catastrophe. In contrast, quiescent LSC underwent apoptosis independent of mitotic arrest, revealing a cell-state-dependent mode of drug action. Mechanistically, PLK1i initiated a multi-step process through disruption of a previously unrecognized, stem cell-specific interaction between PLK1 and MAP1A, resulting in perturbed vesicle trafficking and endolysosomal homeostasis characterized by altered receptor internalization, vesicle accumulation and lysosomal dysfunction, ultimately culminating in apoptotic cell death. Combinatorial pharmacologic perturbation studies established microtubule regulation as a critical determinant of quiescent LSC survival, while ex vivo and in vivo assays demonstrated depletion of functionally-defined LSC following PLK1i. These findings identify a previously unrecognized role for PLK1 in intracellular trafficking and establish MAP1A-dependent control of vesicle homeostasis as a mechanistic determinant of cancer stem cell survival. More broadly, this study demonstrates that classical antimitotic compounds, including microtubule-targeting agents and PLK1 inhibitors, can eradicate both cycling leukemic blasts and quiescent LSC through distinct, cell state-dependent mechanisms, challenging proliferation-centric models of chemotherapy action.

cancer biology↗

bioRxiv2026

A molecular description of plant cellulose biosynthesis inhibition

Dictating cell growth and morphology, cellulose biosynthesis is intrinsic to plant cell biology. Accordingly, cellulose biosynthesis inhibitors (CBIs) are important herbicides, toxins, and experimental tools. We currently lack mechanistic understanding of CBI activity, preventing engineering of herbicide selectivity and disease immunity. Contrasting classical inhibitors, we unexpectedly identify the unusual Streptomyces phytotoxin thaxtomin A as the only in vitro-active CBI, with unprecedentedly broad-spectrum activity against various cellulose synthase enzymes. High-resolution cryo-electron microscopy reveals that thaxtomin A leverages exotic nitroaromatic chemistry to target a strictly conserved site in cellulose synthases polysaccharide secretion channel. Strikingly, in vitro biosynthesis and biophysical assays demonstrate thaxtomin As near-picomolar efficacy. Plant and algal systems reveal that its global arrest of cellulose biosynthesis produces an osmotically driven crisis in expanding cells. Finally, site-directed mutagenesis generates the first toxin-resistant cellulose synthase. Our results underscore celluloses critical function in plant lifeforms and inform efforts to inhibit related enzymes across kingdoms.

plant biology↗

bioRxiv2026

Long-term exposure to polyamines leads to bacteriophage resistance in Pseudomonas aeruginosa

Bacteria often evolve resistance to phage infection by altering the cell-surface structures required for viral adsorption. However, the role extracellular metabolites play in influencing phage susceptibility and the evolution of phage resistance remains unclear. Here, we evaluated whether sustained exposure to putrescine, a polyamine released during phage-mediated cell lysis, alters susceptibility of the pathogen Pseudomonas aeruginosa to the type IV pili-dependent phage DMS3vir. Using adaptive laboratory evolution over [~]66 generations, we evolved P. aeruginosa with or without putrescine and with or without DMS3vir. As expected, direct phage exposure rapidly led to complete phage resistance. Interestingly, populations exposed to putrescine also developed phage resistance by the end of the experiment, despite having never encountered the phage. Whole-population genome sequencing revealed parallel mutations in genes associated with type IV pili and the global transcriptional regulator mexT. Using transposon insertion mutants in the type IV ATPases pilT and pilB, we confirmed that disruption of these genes leads to DMS3vir phage resistance. We also used a type IV pilus biogenesis factor fimV transposon mutant, which showed a putrescine-dependent reduction in phage susceptibility. These findings show that sustained exposure to a host-derived metabolite can drive the evolution of phage resistance through modification of key phage-adsorption sites and regulatory genes. Our work identifies elevated polyamine exposure as a selective pressure that promotes type IV pili-mediated phage resistance, even in the absence of phage exposure. IMPORTANCEPseudomonas aeruginosa is a major cause of hospital-acquired infections and a key priority for phage-based therapies. Previous work has shown that the polyamine putrescine is released into the extracellular environment during cell lysis. These signals can then transiently reduce susceptibility to bacteriophage infection and alert neighboring cells to danger. Our research demonstrates that long-term exposure to putrescine can drive heritable phage resistance without prior exposure to phage. We show that resistance is linked to mutations in genes involved in type IV pili assembly. This work further demonstrates the critical role that polyamines can play in promoting phage resistance in bacterial communities.

microbiology↗

bioRxiv2026

Nanoparticle-delivered resiquimod induces brain tumor regression in medulloblastoma and diffuse midline glioma models by interrupting paracrine growth support and activating myeloid immune signaling and phagocytosis

In pediatric brain tumors medulloblastoma (MB) and diffuse midline glioma (DMG), tumor-associated myeloid cells (TAMs) support malignant progression by secreting paracrine growth factors and suppressing local immune function. We studied the potential for reversing this cancer-supportive phenotype by stimulating TAM pathogen receptors using ResiPOx, a brain-permeant, polyoxazoline nanoparticle formulation of the TLR7/8 agonist resiquimod. ResiPOx showed blood-brain barrier penetration and anti-tumor efficacy, extending progression-free survival (PFS) in mice with MB and DMG. Integrated cellular and molecular analysis including scRNA-seq showed that ResiPOx expanded TAM populations and reprogrammed TAMs toward anti-tumoral states, blocking paracrine IGF1 signaling and inducing local cytokine signaling and phagocytosis of tumor cells. In rhesus macaques, systemic ResiPOx was well tolerated and induced brain transcriptional patterns that resembled ResiPOx responses in DMG and MB mouse models, indicating effects in non-human primates that highlight translational potential. Our data show that ResiPOx reshapes the brain tumor microenvironment to inhibit tumor growth. As a systemically administered, brain penetrant immunomodulator, ResiPOx is able to reach multifocal and unresectable brain tumors, including MB and DMG.

cancer biology↗

bioRxiv2026

Dynamic proteomic profiling reveals protein-specific regulation of synthesis rates underpinning the divergent adaptation of human muscle to endurance and resistance training

Endurance (END) or resistance exercise (RE) training results in adaptations that give rise to distinct skeletal muscle phenotypes. Hallmarks of RE include increases in muscle fibre and muscle cross-sectional area and strength, whereas END increases mitochondrial content. Such distinct phenotypes arise from differential metabolic and mechanical signal transduction, transcriptional, and protein translation pathways, culminating in exercise mode-specific adaptations in the muscle proteome. However, little empirical data exist on the protein-specific dynamic responses underlying training-mode-specific adaptations in humans. Using a model of unilateral exercise combined with stable isotope labelling with deuterium oxide, we measured changes in synthesis and abundance from baseline and during early (week 1) and later (week 10) periods of adaptation to END and RE training in young healthy adults (n = 14; 8 female, 6 male; 20 {+/-} 1 y, 70 {+/-} 10 kg). We quantified changes in the abundance (n = 1146 proteins) and synthesis (n = 247 proteins) profiles of skeletal muscle across a 5-day pre-training baseline period and during early and later adaptation to RE and END. Abundance profiling revealed mode-specific proteome remodelling, whereby RE increased ribosomal and contractile protein networks, whereas END increased mitochondrial inner membrane proteins after 10 weeks of training. The protein-specific synthesis rates of 119 proteins showed training-induced differences (P < 0.1 and log2 fold change > 1), including subsets of structural proteins that responded differently to RE and END training modes. Notably, distinct Z-disc proteins, such as XIRP1 (RE-specific) and LDB3 (END-specific), exhibited mode-specific regulation despite sharing a similar subcellular localisation. We report, for the first time, that divergent phenotypic adaptations to RE and END extend beyond changes in bulk fraction-specific synthesis rates and are regulated by training-mode-specific adaptations in distinct protein subsets within similar subcellular protein locations.

physiology↗

bioRxiv2026

Synthetic circRNAs employ IRES activity for translation in cells and in cell-free translation systems

Gene regulation through translation is critical for spatiotemporal protein expression. Internal ribosomal entry sites (IRESes) mediate mRNA-specific translation by recruiting ribosomes to 5' untranslated regions. Circular RNAs (circRNAs), naturally occurring and stable RNAs, are increasingly used as synthetic tools for sustained therapeutic protein translation by IRES-driven initiation. However, the functionality of different IRESes in synthetic circRNAs remains sparsely characterized. We systematically examine circRNA reporter translation by viral and cellular IRESes in human cells and in diverse in vitro translation systems. Improved circRNA purification by urea-PAGE and RNase R-treatment removes contaminants that induce RNA sensing. Viral CVB3 and HCV, as well as cellular Hoxa9, Chrdl1, Cofilin and c-Myc IRESes, effectively drive circRNA translation. We also establish circRNA translation in a recently developed human cell-free extract that recapitulates IRES-dependent regulation, and allows for precise engineering of HCV IRES-mediated translation. These findings inform IRES selection for synthetic circRNA translation relevant for circRNA-based medicine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/715045v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1a60d08org.highwire.dtl.DTLVardef@a1a7d6org.highwire.dtl.DTLVardef@112042aorg.highwire.dtl.DTLVardef@1cf6c34_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Regulatory element modules as universal features for single-cell chromatin analysis

Single-cell chromatin accessibility data provide important insights into the activity of DNA regulatory elements in health and disease. However, the analysis of these data is made challenging by the lack of a common set of features for use in downstream analysis. This results in individual studies quantifying dataset-specific peak regions that cannot be directly compared to other studies. To address this challenge, we developed a comprehensive set of DNA regulatory element modules (REMO) for the human genome. Here we show how REMO can be applied to single-cell chromatin data to better separate cell states in a low-dimensional space compared to peak matrix quantification, greatly improve the scalability of dimension reduction steps, and enable automated annotation of cell types. This is accompanied by new memory-efficient and scalable software for the quantification of single-cell chromatin accessibility data. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/692786v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@17b5da0org.highwire.dtl.DTLVardef@3fbe64org.highwire.dtl.DTLVardef@ecc378org.highwire.dtl.DTLVardef@15363a_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Dedifferentiation-Driven Oncogenic Stemness Promotes Tumor-Sustaining Adaptability in the Intestinal Epithelium

Intestinal tumorigenesis can occur via two distinct routes: bottom-up tumorigenesis occurs from mutations sustained in the Lgr5 stem cells, whereas top-down tumorigenesis is driven by dedifferentiation of epithelial cells near the intestinal lumen. While sporadic human colon adenomas exhibit features of top-down tumorigenesis, their biological determinants remain elusive. Here, using a Smad4 loss-of-function and {beta}-catenin gain-of-function (Smad4LOF:{beta}-cateninGOF) mouse model, we demonstrate that dedifferentiation-derived oncogenic stem cells sustain tumorigenesis more effectively than endogenous mutant stem cells harboring the mutation. The dedifferentiating villi epithelial cells showed early expression of CD44 and Lgr5, supporting oncogenic stemness. Aberrant Notch signaling in the villi epithelium was also detected at the onset of dedifferentiation, suggesting its contribution to dedifferentiation. Single-cell RNA sequencing revealed a distinct population of dedifferentiation-derived stem cells enriched for proliferative, metabolic, and mouse embryonic stem cell-like gene signatures, consistent with enhanced plasticity and tumorigenic potential. These mutant cells exhibited growth factor independence, indicating a capacity for niche-independent proliferation and metabolic adaptation to sustain tumor growth. These findings identify dedifferentiation-driven stemness, aberrant Notch activation, and metabolic plasticity as cooperative mechanisms that promote top-down intestinal tumorigenesis. This study provides insight into how oncogenic dedifferentiation contributes to tumor heterogeneity and persistence and has implications for therapeutic resistance in colorectal cancer.

cancer biology↗

bioRxiv2025

Social stress worsens colitis through beta-adrenergic-driven oxidative stress in intestinal mucosal compartments

AbstractPsychological stress is a known risk factor for inflammatory bowel disease (IBD), but the mechanisms linking stress to worsened disease remain unclear. Because distinct stress paradigms activate different neuroimmune circuits, it is critical to investigate model-specific effects. We examined how social stress primes the gut for heightened inflammation and whether this is mediated by specific neuroendocrine pathways, including 2-/{beta}-adrenergic (sympathetic) or glucocorticoid/ corticotropin-releasing hormone receptor (CRHR1) (HPA axis) signaling. Mice were exposed to social disruption (SDR) stress and pre- treated with pharmacological antagonists targeting 2-adrenergic receptors (idazoxan), {beta}-adrenergic receptor ({beta}-AR) (propranolol), glucocorticoid receptor (mifepristone), or CRHR1 (antalarmin). Intestinal epithelial cell (IEC) gene expression and microbiota composition were assessed following SDR. To determine disease impact, SDR was combined with either Citrobacter rodentium infection or dextran sulfate sodium (DSS)-induced colitis, with interventions including the {beta}-AR inhibitor propranolol and the NADPH oxidase inhibitor apocynin. SDR significantly upregulated expression of Dual oxidase 2 (Duox2), Dual oxidase maturation factor 2 (Duoxa2), and inducible nitric oxide synthase 2 (Nos2) in IECs (2- to 8- fold, p < 0.0001), effects reversed by {beta}-AR blockade but not 2-adrenergic, CRH, or glucocorticoid inhibition. SDR also induced microbial dysbiosis, characterized by reduced alpha-diversity and compositional shifts, which was rescued by propranolol. Stress exacerbated disease severity in both infectious (C. rodentium) and chemically induced (DSS) colitis, amplifying colonic expression of Duox2, Nos2, and Ccl2, especially. Apocynin mitigated stress-induced ROS/RNS production and body weight loss even prior to colitis onset, reduced colonic gene expression of key oxidative enzymes, and alleviated both chemically and infectious colitis severity. These findings provide strong evidence that social stress sensitizes the gut to inflammation through {beta}-adrenergic and NADPH oxidase-driven oxidative stress, highlighting potential therapeutic targets for mitigating stress-exacerbated IBD. HighlightsSocial disruption (SDR) and restraint stress (RST) activate distinct neuroendocrine pathways, with SDR driving epithelial ROS/RNS pathways via {beta}-adrenergic signaling. {beta}-adrenergic blockade prevents SDR-induced epithelial priming, microbial dysbiosis, and colitis exacerbation. NADPH oxidase inhibition with apocynin mitigates stress-induced oxidative stress and disease severity across different colitis models. Findings identify {beta}-adrenergic and redox pathways as therapeutic targets for stress-exacerbated IBD.

immunology↗

bioRxiv2025

Inferring Spatially Varying Bending Stiffness of Biopolymers with Deep-Learning Approach

The bendability of biopolymers, including DNA, actin filaments, and microtubules, is crucial to diverse biological processes, such as cell motility and cytoskeletal organization. While conventional polymer models like the worm-like chain model assume uniform bending stiffness along the contour, biopolymers in reality often attain spatially varying bending stiffness as a result of complex cellular interactions. For instance, the bending stiffness of actin filaments and microtubules varies in response to associated binding proteins or chemical modifications. Despite its biological implications, measuring the position-dependent persistence length along polymer contours remains challenging. Here, we present a deep-learning-based method that quantitatively predicts spatially varying bending stiffness of biopolymers. Our framework segments a polymer chain into short over-lapping fragments, predicts local persistence lengths using a deep-learning model, and reconstructs full profiles. Using simulated data, we demonstrate that our approach achieves high accuracy and robustness even under data-scarce conditions. Applied to various biological systems, our method reveals a spatially varying stiffness from tip to base in filopodia as well as spatially heterogeneous stiffness in microtubules. Additionally, we investigate the internal mechanism of our deep-learning model and show that the model utilizes multiple physics-related features for persistence length estimation while adaptively adjusting its attention based on polymer stiffness.

biophysics↗

bioRxiv2025

Global Skeletal Muscle Metabolomics Reveals Mechanisms Behind Higher Response to Resistance Training in Older Adults

To understand the mechaisnm behind high respond (HighR) compared to low respond (LowR) to resistnace training (RT) and whey protein supplementation (20g/day), we analysied vastus laterails muscle biopsies from a total of 50 participants. Utilising the MRI muscle cross-sectional area (CSA) data, we defined responders as those who had hypertrophy exceeding the 1.7% method error. Quadriceps CSA in the lower responder (LowR) (n=25, mean age 69{+/-}5 years) and HighR (n=25, mean age 67{+/-}4 years) increased from 53.6 {+/-} 12.1 cm2 to 55.4 {+/-} 12.8 cm2 after 10 weeks of RET (3.3 {+/-} 1.7%, P < 0.001) and increased the absolute CSA in the higher responders (HighR) from 53.7 {+/-} 12.5 cm2 to 59.2 {+/-} 13.6 cm2 (10.3 {+/-} 2.0%, P < 0.001). Muscle biopsies were taken from the vastus lateralis before and after RT. We performed untargeted liquid chromatography-mass spectrometry metabolomics to investigate changes in muscle metabolic regulation. The partial least squares discriminant analysis (PLS-DA) yielded the best results using the polar extracts, achieving a 75% average correct classification rate for predicting HighR and LowR. There was no signifncat differences in metabolomic profile at the basline. Our findings revealed several metabolic pathways, including branched-chain amino acid catabolism, tryptophan metabolism (indole and kynurenine pathways), the TCA cycle, gut-derived metabolites, carnitine shuttle metabolism as prominent pathways disrupted in LowR. We provide new insights and has the potential to identify and enhance interventions targeting muscle metabolism, ultimately improving muscle mass and strength to reduce the risk of sarcopenia and frailty in older age.

systems biology↗

bioRxiv2025

Mouse Single-Cell Long-Read Splicing Atlas by Ouro-Seq

Alternative splicing creates cellular and phenotypic diversity; thus, characterizing splicing patterns across diverse cell types is essential for a comprehensive understanding of these cell types. However, existing full-length single-cell RNA-sequencing methods suffer from multiple technical limitations, such as the pervasive presence of reverse transcription artifacts across genes. Here, we introduce Ouro-Seq, a novel single-cell long-read sequencing framework with a versatile artifact removal mechanism for characterizing full-length mRNA species expressed by individual cells. We also developed a computational pipeline that identifies genuine full-length cDNAs and normalizes full-length mRNA size distributions for integration. Using Ouro-Seq, we constructed the Mouse Single-Cell Long-Read Splicing Atlas by collecting full-length transcriptomes of 103,304 nuclei or cells from 12 major organs and tissues of adult mice. Our atlas comprehensively characterizes alternative splicing, alternative promoter usage, and alternative polyadenylation events across cell types, revealing previously unappreciated functional heterogeneity among individual cells. Different cell types exhibit largely distinct expression patterns of various isoforms, corresponding to their specific morphologies and biological functions. Our splicing atlas and generalized long-read frameworks will empower researchers to fully interpret biological variation across full-length transcriptomes of single cells.

genomics↗

bioRxiv2025

Sensorimotor adaptation reveals systematic biases in 3D perception.

The existence of biases in visual perception and their impact on visually guided actions has long been a fundamental yet unresolved question. Evidence revealing perceptual or visuomotor biases has typically been disregarded because such biases in spatial judgments can often be attributed to experimental measurement confounds. To resolve this controversy, we leveraged the visuomotor systems adaptation mechanism -- triggered only by a discrepancy between visual estimates and sensory feedback -- to directly indicate whether systematic errors in perceptual and visuomotor spatial judgments exist. To resolve this controversy, we leveraged the adaptive mechanisms of the visuomotor system to directly reveal whether systematic biases or errors in perceptual and visuomotor spatial judgments exist. In a within-subject study (N=24), participants grasped a virtual 3D object with varying numbers of depth cues (single vs. multiple) while receiving haptic feedback. The resulting visuomotor adaptations and aftereffects demonstrated that the planned grip size, determined by the visually perceived depth of the object, was consistently overestimated. This overestimation intensified when multiple cues were present, despite no actual change in physical depth. These findings conclusively confirm the presence of inherent biases in visual estimates for both perception and action, and highlight the potential use of visuomotor adaptation as a novel tool for understanding perceptual biases.

neuroscience↗

bioRxiv2024

AMH regulates ovary size by counteracting ovarian follicle cluster effects.

Serum anti-Mullerian hormone (AMH) is the primary clinical indicator of mature oocyte counts in the ovaries, but its biological role remains poorly understood. Mammalian ovaries have a finite lifetime of oocytes that are slowly depleted as the dormant follicles housing the oocytes initiate maturation. Less than 0.1% of these follicles will reach maturity and ovulate an oocyte. Recent studies suggest that AMH is a key regulator that removes most of these follicles at early stages of follicle maturation. Most AMH is secreted as an inactive precursor protein, and we show that the required activating-enzymes are largely present outside the follicle. We then measured AMH concentrations in ovarian stroma with microdialysis showing that activity is confined to a short range from the site of secretion. To examine short-range interactions between follicles, we reconstructed the ovarian follicle positions from sheep ovaries in 3D space. This showed that most early follicles develop in proximity to more advanced follicles. Active immunisation of sheep against AMH to inhibit signalling, greatly expanded early follicle numbers, but almost entirely in proximity to large follicles. Large follicle proximity appears to greatly enhance early follicle survival, and AMH appears to attenuate this effect to prevent follicle overgrowth beyond sustainable limits.

physiology↗