Biology subjects

Li, Z.

Publications and source records attributed to Li, Z..

At least 433 records · Page 24Linked to original sources

bioRxiv2025

The XPF-like domain in SHOC1 required for homologous recombination and safeguarding autosome from meiotic silencing of unsynapsed chromatin

During meiosis, a group of evolutionarily conserved ZMM proteins plays essential roles in stabilizing the recombination intermediates and promoting crossover (CO) formation. In mice, SHOC1 forms a trimeric complex with the other two ZMM proteins, SPO16 and TEX11, to bind recombination intermediates after strand invasion. Although genetic variants of SHOC1 are clinically associated with meiotic arrest and male infertility, their precise molecular mechanisms and evolutionarily conserved functions in human gametogenesis remain enigmatic. Here, we delineated species-specific divergences between human and mouse SHOC1 complex, and identified a missense variant within the XPF-like domain in SHOC1 (c.A1769G:p.Q590R) that was associated with meiotic arrest and non-obstructive azoospermia (NOA). The disorder of the XPF-like domain in SHOC1 impaired DNA double-strand breaks repair by compromising its ability to bind branched DNA structures and the recruitment of M1AP, REDIC1, and ZMM factors to recombination intermediates, ultimately abolishing CO formation. Furthermore, the variant disrupted dynamic 3D chromatin structure in pachytene spermatocytes and induced defects in homologous chromosome synapsis. More importantly, the XPF-like domain in SHOC1 was revealed to prevent autosome intrusion into the sex body compartment, thereby safeguarding critical autosomal loci from meiotic silencing of unsynapsed chromatin (MSUC). Overall, our study demonstrated that the XPF-like domain in SHOC1 is required for homologous recombination and safeguarding autosome from MSUC in meiosis.

developmental biology↗

bioRxiv2025

Multimodal retinal imaging by visible light optical coherence tomography and phosphorescence lifetime ophthalmoscopy in the mouse eye

SignificanceOxygen metabolism is important to retinal disease development, but current imaging methods face challenges in resolution, throughput, and depth sectioning to spatially map microvascular oxygen. AimTo develop a multimodal system capable of simultaneous phosphorescence lifetime imaging scanning laser ophthalmoscopy (PLIM-SLO) and visible light optical coherence tomography (VIS-OCT) to capture capillary-level oxygen partial pressure (pO2) and structural volumes in rodents. ApproachC57BL/6 mice were imaged by VIS-OCT with high-definition (10 kHz raster) and Doppler (100 kHz circular) protocols. Phosphorescent probe Oxyphor 2P was retro-orbitally injected to enable intravascular PLIM-SLO imaging (200 {micro}s pixel dwell time), while a tunable lens was used to adjust the focal depth. The extracted phosphorescence lifetimes were used for pO2 calculation. Simultaneous imaging utilized a shared imaging path and synchronized data collection. ResultsVIS-OCT images revealed detailed anatomy and Doppler shifts, while PLIM-SLO provided capillary pO2 at multiple depths. A hemoglobin oxygen dissociation curve related retinal arterial pO2 to systemic oxygen saturation as inhaled oxygen was varied. Registered simultaneous images were captured and pO2 was empirically adjusted for the combined excitation. ConclusionsDetailed anatomical structures and capillary pO2 levels can be simultaneously imaged, providing a useful tool to study oxygen metabolism in rodent disease models.

bioengineering↗

bioRxiv2025

Ammonia-mediated Conformational Dynamics in SCAP for SREBP Activation

Cholesterol homeostasis is regulated by the sterol regulatory element-binding protein (SREBP) pathway, with the membrane-embedded SREBP-cleavage-activating protein (SCAP) and insulin-inducible gene protein (Insig)-1/2 acting as sterol sensors. Our previous studies unveiled a critical role of ammonia in activating the SREBP pathway. Here, we performed extensive molecular dynamics (MD) simulations to elucidate the structural mechanisms through which ammonia binding triggers SCAP/Insig dissociation and subsequently activate SREBP. The SCAP S4 helix exists in two distinct conformations: a partially unfolded S4 and an intact S4; the transition between these states may constitute a crucial aspect of SCAP activation. We first studied the binding of ammonia to SCAP in different S4 conformational states. We then explored how the binding of ammonia or 25-hydroxycholesterol (25-HC) affects the conformational transition of S4 using targeted MD simulations. Finally, we performed comparative analysis of the 25-HC-bound inactive SCAP and the ammonia-bound active SCAP. Collectively, our findings highlight the importance of S4 helix conformation in activating the SCAP protein. Our simulations suggest that ammonia and 25-HC act as an agonist and antagonist of SCAP activation, respectively. Specifically, ammonia binding facilitates the transition of S4 from the unfolded to the straight conformation, triggering subsequent conformational changes in the transmembrane domain of SCAP. These changes eventually promote the SCAP/Insig dissociation and alter the position of the MELADL motif at the membrane surface. Significant StatementCellular cholesterol homeostasis is tightly regulated by the SREBP pathway, which relies on the membrane proteins SCAP and Insig to sense sterol levels. While ammonia has recently been identified as a novel activator of this pathway, its structural mechanism of action remained unknown. Here, extensive molecular dynamics simulations reveal that ammonia binding promotes a critical conformational transition in the SCAP S4 helix, facilitating SCAP activation and its dissociation from Insig. Our findings show that ammonia and cholesterol act as opposing modulators--agonist and antagonist--of SCAP activity. This work uncovers a previously unrecognized structural switch in SCAP and provides new molecular insight into small-molecule regulation of cholesterol sensing.

molecular biology↗

bioRxiv2025

DynaRNA: Dynamic RNA Conformation Ensemble Generation with Diffusion Model

RNA plays a wide variety of roles in biological processes. In addition to serving as the coding messenger RNA (mRNA), the vast majority of RNAs function as non-coding RNAs (ncRNAs), where their dynamic structural ensemble is critical for mediating diverse biological functions. However, traditional experimental techniques and molecular dynamics (MD) simulations face significant challenges in characterizing the conformational dynamics of RNA, due to inherent methodological limitations and high computing power cost. We herein presented DynaRNA, a diffusion-based generative model for RNA conformation ensemble. DynaRNA employs denoising diffusion probabilistic model (DDPM) with equivariant graph neural network (EGNN) to directly model RNA 3D coordinates, enabling rapid exploration of RNA conformational space. DynaRNA enables end-to-end generation of RNA conformation ensemble reproducing experimental geometries without the need for Multiple Sequence Alignments (MSA) information. Our results demonstrate that DynaRNA effectively and accurately generate tetranucleotides ensemble with lower intercalation rate than molecular dynamics simulations. Besides, DynaRNA has the ability to capture rare excited states of HIV TAR(trans-activation response) element, and recapitulate de novo folding of tetraloops. DynaRNA serve as a versatile and efficient platform for modeling RNA structural dynamics, with broad implications potential in RNA structural biology, synthetic biology, and therapeutic development.

bioinformatics↗

bioRxiv2025

CSFeatures improves identification of cell type-specific differential features in single-cell and spatial omics data

Recent advancements in single-cell and spatial omics have enabled the analysis of gene expression patterns in cells and tissues with unprecedented precision. Genes that exhibit significant variation across different cell types or states are typically closely linked to cellular functional states and disease processes. However, current differential analysis methods often fail to adequately account for cell type specificity when identifying differentially expressed genes. CSFeatures effectively addresses this issue by comprehensively considering the expression level, the smoothness of expression distribution, and the proportion of gene expression in the target cell population as well as in each of the other cell populations. Through comprehensive experiments on eight single-cell RNA-seq datasets, it was demonstrated that CSFeatures can effectively identify cell type-specific genes that are highly expressed in the target cell population while being lowly expressed in all other populations. Moreover, it was validated that the underlying principle of CSFeatures can be generalized to other omics data, including single-cell ATAC-seq, spatial transcriptomics, and spatial ATAC-seq data. Furthermore, the differential features identified by CSFeatures are enriched in pathways, functional categories, and regulatory regions that are highly relevant to the specific functional states of the target cell population, providing insights into its gene regulation.

bioinformatics↗

bioRxiv2025

PLK1-mediated phosphorylation of PHGDH reprograms serine metabolism in advanced prostate cancer

Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to meet their increased biosynthetic and energetic demands. While cells possess the capacity for de novo serine biosynthesis, most transformed cancer cells heavily depend on exogenous serine uptake to sustain their growth, yet the regulatory mechanisms driving this metabolic dependency remain poorly understood. Here, we uncover a novel mechanism by which Polo-like kinase 1 (PLK1), often overexpressed in prostate cancer, orchestrates a metabolic shift in serine and lipid metabolism through the phosphorylation of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme of the serine synthesis pathway (SSP). We demonstrate that PLK1 phosphorylates PHGDH at three specific sites (S512, S513, S517), leading to a marked reduction in its protein level and enzymatic activity. This downregulation of SSP forces cancer cells to increase their reliance on exogenous serine uptake via the ASCT2 transporter, which, in turn, fuels the biosynthesis of lipids, including sphingolipids essential for tumor growth and survival. Targeting the SSP, serine uptake, or downstream lipid biosynthetic pathways may offer promising therapeutic avenues in PLK1-high advanced cancers.

cancer biology↗

bioRxiv2025

Testicular mRNA-LNP Delivery: A Novel Therapy for Genetic Spermatogenic Disorders

Uniform testicular maturation arrest is a severe form of male infertility characterized by the presence of germ cells that do not complete spermatogenic development. It is usually caused by meiotic arrest with genetic variants and difficult to treat via drugs or surgery. mRNA-lipid nanoparticle (LNP) delivery is a promising therapeutic option for maturation arrest with monogenic variants via protein replacement therapy. Herein, a spermatocytes-tropic LNP (Pool1-LNP3) was identified via a library of 30 ionizable lipids screening. And in vivo delivery of this novel LNP composition using rete testis microinjection was showed to be high spermatocytes targeting with high transfection efficiency. Thereafter, it was revealed that in vivo delivery of Pool1-LNP3 encapsulating Msh5 mRNA could promote crossover formation and restore spermatogenesis in Msh5D486Y/D486Y mouse models with DSB recombination defects. Notably, the offspring without genomic integration was born using intracytoplasmic sperm injection (ICSI) derived from rescue of Msh5D486Y/D486Ymouse and embryo transfer. Furthermore, no obvious inflammation and histologic damage in any tissue were detected after in vivo delivery of mRNA-LNP. In addition, it was demonstrated that Maps mRNA-LNP3 recovered spermatogenesis in Maps KO mouse with meiotic arrest. Altogether, these findings suggested that this spermatocytes-tropic mRNA-LNP delivery could become a viable and broad applicable strategy for treatment of spermatogenic disorders with genetic defects, providing a foundation for future clinical application.

molecular biology↗

bioRxiv2025

Deep-learning-enabled multi-omics analyses for prediction of future metastasis in cancer

Metastasis remains the leading cause of cancer-related mortality, yet predicting future metastasis is a major clinical challenge due to the lack of validated biomarkers and effective assessment methods. Here, we present EmitGCL, a deep-learning framework that accurately predicts future metastasis and its corresponding biomarkers. Based on a comprehensive benchmarking comparison, EmitGCL outperformed other computational tools across six cancer types from seven cohorts of patients with superior sensitivity and specificity. It captured occult metastatic cells in a patient with a lymph node-negative breast cancer, who was declared to have no evidence of disease by conventional imaging methods but was later confirmed to have a metastatic disease. Notably, EmitGCL identified HSP90AA1 and HSP90AB1 as predictable biomarkers for future breast cancer metastasis, which was validated across five independent cohorts of patients (n=420). Furthermore, we demonstrated YY1 transcription factor as a key driver of breast cancer metastasis which was validated through in-silico and CRISPR-based migration assays, suggesting that YY1 is a potential therapeutic target for deterring metastasis.

bioinformatics↗

bioRxiv2025

Adaptive Evolution of Gene Regulatory Networks in Mammalian Neocortical Neurons

Mammals have evolved a plethora of adaptations that have enabled them to thrive in diverse environments. Among the most significant is the emergence of a more complex brain, exemplified by the dramatic transformation of the dorsal cortex from a single layer of excitatory projection neurons (ExNs) in ancestors to a multilayered cerebral neocortex enriched with diverse intratelencephalic (IT) and extratelencephalic (ET) ExN subtypes. These ExNs established specialized projection systems, such as the corticospinal tract and corpus callosum, enhancing brain connectivity and functionality. However, the evolutionary mechanisms underlying these mammalian-specific adaptations remain elusive. By comparing the landscape of gene expression and cis-regulatory elements (CREs) in mouse ExN subtypes and by cross-species examination of mammalian and non-mammalian CREs, we identified mammalian-specific CREs and expression patterns. The mammalian-specific CREs include a subset bound by ZBTB18 that are associated with genes defining IT and ET subtypes and connectivity. Both ZBTB18 and these target genes have previously been implicated in intellectual disability and autism. Deletion of Zbtb18 in mouse ExNs dysregulated target gene expression, reduced molecular diversity, diminished corticospinal and callosal projections, and increased intrahemispheric cortico-cortical association projections to the prefrontal cortex, resembling features of non-mammalian dorsal pallium. Interestingly, ZBTB18 binding motifs are highly enriched in callosally projecting IT-biased CREs, where they show higher conservation specifically in mammals. This study uncovers critical components and mammalian-specific evolutionary adaptations within a regulatory node essential for neocortical ExN identity and connectivity, with implications for neurodevelopmental and neuropsychiatric disorders.

neuroscience↗

bioRxiv2025

A Reductive Uric Acid Degradation Pathway in Anaerobic Bacteria

Uric acid is a key intermediate in purine degradation across diverse organisms, while its accumulation in humans leads to inflammation and gout disease. Aerobic organisms degrade uric acid via a well-known "oxidative pathway" involving dearomatization of the purine core catalyzed by uric acid oxidases or dehydrogenases. The ability to degrade uric acid is also widespread in anaerobic bacteria, including gut bacteria, although the mechanisms are incompletely understood. Here, we report the biochemical characterization of a recently identified uric acid degradation gene cluster from Escherichia coli, and show that it encodes a "reductive pathway" for uric acid degradation. In this pathway, uric acid is first reduced to isoxanthine (2,8-dioxopurine) by a xanthine dehydrogenase homolog (XdhD), followed by dearomatization of the purine core catalyzed by a flavin-dependent reductase (YgfK). Stepwise cleavage of the pyrimidine and imidazole rings forms 2,3-diureidopropionate, and stepwise cleavage of the 2- and 3-ureido groups then forms 2,3-diaminopropionate, which is cleaved by a pyridoxal 5-phosphate-dependent lyase (YgeX) to pyruvate and ammonia. Detection of isoxanthine in clinical serum samples suggests it is a physiologically relevant circulating metabolite. A probiotic E coli Nissle strain was engineered for constitutive overexpression of the gene cluster, and oral administration in a uricase-knockout hyperuricemic mouse model significantly reduced the serum uric acid level and alleviated associated kidney injury, suggesting a potential route towards uricolytic probiotics.

biochemistry↗

bioRxiv2025

Direct interoceptive input to the insular cortex shapes learned feeding behavior

The insular cortex (insula) is an interoceptive hub, which senses internal states such as hunger, thirst, pain, and emotions. Previous studies suggest that the insula directly senses internal states, but the mechanisms remain elusive. We identified a population of leptin receptor-positive cells with a unique morphology in the insula (INSLepR). Based on leptins known role in signaling adiposity, we hypothesized that INSLepR neurons detect internal states to regulate food intake and body weight. Accordingly, we found that intra-insula leptin administration or optogenetic stimulation of INSLepR neurons impacts feeding behavior. Moreover, INSLepR neuron activity encodes feeding bouts in an internal-state dependent manner, and leptin alters insula neural dynamics in response to feeding, while also reshaping the transcriptome. Taken together, our data supports a model for direct interoceptive input to the insula, in which INSLepR cells integrate adiposity level signals to regulate feeding and body weight in a learned manner.

neuroscience↗

bioRxiv2025

When is microbial cross-feeding evolutionarily stable?

Cross-feeding, a phenomenon in which organisms share metabolites, is frequently observed in microbial communities across the natural world. One of the most common forms is waste-product cross-feeding, a unidirectional interaction in which the waste products of one microbe support the growth of another. Despite its ubiquity, it is not well-understood why waste-product cross-feeding persists when a single organism could in principle perform both the producer and consumer role. To address this question, we first analyze cross-feeding evolution in a minimal model of microbial metabolism. The model describes multi-step extraction of energy from a substrate in a simple but thermodynamically correct formulation. Surprisingly, we find that cross-feeding is never evolutionarily stable in this model. By analyzing models with more complex growth functions, we identify a novel mechanism for the evolutionary stability of waste-product cross-feeding, namely, generalized intracellular metabolite toxicity. Such toxicity arises because, in excess, the same intracellular metabolites that cells require for metabolism can be detrimental to growth (e.g., due to osmotic stress). We show that some but not all forms of such toxicity can lead to evolutionarily stable consortia of microbes that cross-feed waste products. This stability results from the potential of such consortia to divide the burden of toxic metabolites among a larger population, allowing them to perform their collective metabolism more efficiently than non-cross-feeders. More generally, we predict that growth penalties that scale nonlinearly with intracellular metabolite levels promote cross-feeding. We find that this mechanism for cross-feeding evolutionary stability implies nontrivial population dynamics, such as a discontinuity in population biomass at the onset of cross-feeding. Significance statementThe chemical reactions performed by microbes have large impacts on our world: from nitrification within the nitrogen cycle to the breakdown of fiber in animal digestive tracts. A striking commonality in many of these processes is that the chemical reactions are a collective effort, with the complete reaction subdivided between many microbes. This phenomenon is known as cross-feeding, and its origins are poorly understood. Understanding the eco-evolutionary forces promoting cross-feeding have the potential to not only enhance our understanding of natural ecosystems, but also improve our ability to engineer such distributed reactions in biotechnology. Here, we develop mathematical theory for the evolution of a common type of cross-feeding and provide predictions for what metabolic and environmental conditions promote this behavior.

microbiology↗

bioRxiv2025

Economic and Social Modulations of Innate Decision-Making in Mice Exposed to Visual Threats

When confronted by predators, animals make innate decisions with rapid reaction times--a trait shaped by natural selection to maximize survival. However, rapid reactions are effective only when grounded in accurate judgments and appropriate choices, which often require cognitive control. To address how such choices are shaped, we developed a behavioral paradigm to investigate how threat intensity, reward value, and social hierarchy shape decision-making in foraging mice exposed to overhead visual threats. Using a machine learning-based approach, we classified defensive responses into four distinct decision types. Mice showed rapid habituation to repeated looming threats, with substantial inter-individual variability in the rate of habituation. Across both early and late phases of habituation, threat intensity emerged as the primary determinant of decision-making, strongly biasing behavior toward escape. In contrast, the influence of reward value was context-dependent and became evident primarily in the late phase: under low-threat conditions, higher reward value suppressed defensive responses, consistent with value-based decision theory; whereas under high-threat conditions, higher reward value promoted escape, potentially reflecting heightened vigilance. Innate decision-making was further modulated by social hierarchy, with dominant mice showing greater vigilance and a stronger bias toward risk-averse behaviors, while subordinates were more reward-driven. To understand the underlying decision-making process, we developed a drift-diffusion leaky integrator model that successfully captures how threat intensity, reward value, and vigilance interact to shape defensive decisions. Together, these findings reveal how economic and social factors modulate innate decisions and provide a computational framework for understanding the interplay between instinctive reactions and cognitive control.

neuroscience↗

bioRxiv2025

Non-redundant roles of the HDAC3 corepressor complex subunits SMRT and NCOR in controlling inflammatory and metabolic macrophage pathways

Transcription factors and coregulators coordinate inflammatory and metabolic pathways in macrophages through epigenetic and transcriptional mechanisms. The HDAC3 corepressor complex plays fundamental roles in these mechanisms, with the homologous subunits SMRT and NCOR being critical for complex assembly and interactions with transcription factors and chromatin. However, the relative contribution of SMRT and NCOR in controlling complex-dependent macrophage pathways remains poorly understood. Here, we assessed their genome-wide roles in mouse macrophage RAW264.7 cells and in bone marrow-derived macrophages. Transcriptome analysis upon corepressor depletion identified six differentially expressed gene clusters. SMRT depletion primarily upregulated inflammation-related pathways, NCOR depletion primarily upregulated metabolism-related pathways. Epigenome analysis revealed that corepressor depletion differentially altered chromatin accessibility and H3K27 acetylation, consistent with transcriptome changes. Cistrome analysis revealed that both corepressors differentially influence each other at chromatin. SMRT uniquely controls the chromatin binding and nuclear localization of NCOR, GPS2 and HDAC3, thus acting as the chromatin anchor for the corepressor complex. Finally, corepressor depletion differentially modulated macrophage reprogramming in response to TLR4, IL4 and LXR signaling. Overall, our study reveals a hitherto underappreciated non-redundant role of SMRT and NCOR in coordinating chromatin accessibility, H3K27 acetylation, enhancer activity and transcription to differentially regulate inflammatory and metabolic macrophage pathways. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/653058v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1d9f2dforg.highwire.dtl.DTLVardef@1d81386org.highwire.dtl.DTLVardef@e9e536org.highwire.dtl.DTLVardef@1c74c15_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Parkinson's-Linked Synaptojanin 1 Loss in Dopamine Neurons Triggers Synaptic Degeneration and Striatal TH Interneuron Compensation

Presynaptic endocytic dysfunction is an early feature of Parkinson's disease (PD), but how dopamine circuits adapt to chronic synaptic failure remains unclear. In dopamine neuron-specific Synaptojanin 1 knockout mice, loss of this PD-linked endocytic protein causes terminal dystrophy and striatal dopamine deficiency, yet motor coordination is preserved. Chronic endocytic failure induces striatal dopamine-like neurons (DALNs) with circuit-dependent dopaminergic protein accumulation. DALNs do not arise through transcriptional reprogramming; instead, they acquire dopaminergic proteins from midbrain dopamine neurons through selective long-range transfer that favors soluble cargoes and can convey disease-associated proteins, including -synuclein and tau. Functionally, DALNs support local dopamine production, partially preserve motor performance and increase resistance to acute dopaminergic lesions. This adaptation is shared across PD-linked endocytic mutants and is developmentally constrained, but is not reproduced by acute denervation. Thus, synaptic endocytic stress triggers inter-neuronal protein transfer as an adaptive circuit mechanism supporting dopamine compensation and neuroprotection in early PD.

neuroscience↗

bioRxiv2025

MITF-Independent Melanocyte Progenitors are Highly Susceptible to GNAQ-induced Uveal Melanoma in Adult Zebrafish

Melanocytes reside in diverse microenvironments that influence their susceptibility to oncogenic transformation; however, investigation of rare melanoma subsets has been limited by the lack of suitable pre-clinical animal models. Here, we developed a primary, immune-competent zebrafish model to study uveal melanoma (UM) using choroidal melanocyte-targeted injection and electroporation of plasmids encoding human GNAQQ209L together with CRISPR/Cas9 cassettes for somatic tumor suppressor gene deletion. Single-cell transcriptional profiling of primary melanocytes and melanoma derived from the eye and skin revealed distinct transcriptional programs, with epithelial-to-mesenchymal transition pathways enriched in ocular tumors. In addition, choroidal fibroblasts from tumor-bearing eyes exhibited marked transcriptional changes, including increased fibronectin and collagen expression, consistent with stromal remodeling. Given prior associations between mitfa loss and accelerated GNAQQ209L tumor onset, the model was applied to determine whether melanocyte differentiation state contributes to the emergence of GNAQ-driven tumors. The increased susceptibility resulted from expansion of Mitfa-independent melanocyte progenitor populations in germline mitfa mutant zebrafish, rather than somatic mitfa loss in differentiated melanocytes, as conditional, melanocyte-specific mitfa deletion in adult zebrafish did not accelerate tumor growth. Furthermore, pax3a-positive melanocyte progenitor cells in mitfa-deficient zebrafish embryos and adult eyes and skin were highly susceptible to transformation induced by GNAQQ209L but not BRAFV600E. Analogous PAX3 positive populations were also identified in mouse and human single-cell transcriptomic datasets. Collectively, these findings establish a critical role for Mitfa-independent melanocyte progenitors in UM pathogenesis. Statement of SignificanceChoroid-targeted GNAQQ209L expression induces anatomically correct uveal melanoma in adult zebrafish, with germline mitfa deletion expanding mitfa-independent melanocyte progenitors with enhanced susceptibility that are transcriptionally distinct from the subpopulation transformed by BRAFV600E.

cancer biology↗

bioRxiv2025

White matter microstructure and macrostructure brain charts across the human lifespan

Normative reference charts are widely used in healthcare, especially for assessing the development of individuals by benchmarking anatomic and physiological features against population trajectories across the lifespan. Recent work has extended this concept to gray matter morphology in the brain, but no such reference framework currently exists for white matter (WM) even though WM constitutes the essential substrate for neuronal communication and large-scale network integration. Here, we present the first comprehensive WM brain charts, which describe how microstructural and macrostructural features of WM evolve across the lifespan, by leveraging over 35,120 diffusion MRI scans from 50 harmonized studies. Using generalized additive models for location, scale, and shape (GAMLSS), we estimate age- and sex-stratified trajectories for 72 individual white matter pathways, quantifying both tract-specific microstructural and morphometric features. We demonstrate that these WM brain charts enable four important applications: (1) defining normative trajectories of WM maturation and decline across distinct pathways, (2) identifying previously uncharacterized developmental milestones and spatial gradients of tract maturation, (3) detecting individualized deviations from normative patterns with clinical relevance across multiple neurological disorders, and (4) facilitating standardized, cross-study centile scoring of new datasets. By establishing a unified, interpretable reference framework for WM structure, these brain charts provide a foundational metric for research and clinical neuroscience. The accompanying open-access trajectories, centile scoring tools, and harmonization methods facilitate precise mapping of WM development, aging, and pathology across diverse populations. We release the brain charts and provide an out-of-sample alignment process as a Docker image: https://zenodo.org/records/17561821.

neuroscience↗

bioRxiv2025

Tracing Siderophore Precursors to Primary Metabolism for Ecological Applications

Microbial fitness depends on balancing between primary metabolism supporting basic survival, and secondary metabolism producing metabolites for environmental adaptation. These two systems are interconnected, with most secondary metabolites deriving from primary metabolic precursors. However, systematic frameworks for studying their relationships across diverse microbes remain limited. Using siderophores--iron-chelating secondary metabolites crucial for microbial competition--as a model, we developed a stepwise "siderophore-monomer-precursor-pathway analysis" framework to trace the biosynthetic connections from siderophore structures to primary metabolism. We applied this framework to an expanded SIDERITE database containing 1018 siderophore structures. To demonstrate practical applications, we identified specific precursors utilized by the beneficial rhizobacterium Bacillus amyloliquefaciens but not by the plant pathogen Ralstonia solanacearum. Supplementing these precursors under iron-limited conditions enhanced both siderophore production in B. amyloliquefaciens and its inhibitory activity against R. solanacearum. This work establishes a direct link between primary metabolism and siderophore-mediated microbial interactions, offering new strategies for pathogen suppression through targeted metabolic interventions.

biochemistry↗