Biology subjects

Huang, S.

Publications and source records attributed to Huang, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Autophagy-driven Presynaptic Reorganization as a Molecular Signature of Brain Resilience.

Neural circuits must remain functionally stable while responding flexibly to changing demands, stressors, and aging-related decline. While this balance is thought to be maintained through plasticity programs that integrate molecular, metabolic, and activity-dependent signals to reconfigure synapses structurally and functionally, direct mechanistic models of how such adaptations are orchestrated remain scarce. Here, we show that targeted impairment of autophagy in the Drosophila mushroom body (MB), a key sleep-regulatory and integrative center in the fly brain, triggers a brain-wide remodeling at presynaptic active zones (AZ). Quantitative proteomics revealed a specific upregulation of AZ scaffold proteins (including BRP, RIM, and Unc13A), accompanied by reduced levels of calcium channel subunits and increased Shaker-type potassium channels. These changes occurred largely independent of transcription and highlight a coordinated, excitability-tuning response centered on the AZ. Behaviorally, MB-specific autophagy impairment increased sleep and modestly extended lifespan. These adaptations resembled a previously described resilience program termed PreScale, which promotes restorative sleep homeostasis in response to sleep deprivation and early, still reversible brain aging. Conversely, overexpression of Atg5 in the MB delayed the onset of PreScale. Notably, autophagic disruption confined to MB neurons also caused widespread, non-cell autonomous accumulation of Ref(2)P and ATG8a-positive aggregates across the brain, revealing systemic propagation of proteostatic stress. Together, our findings identify MB autophagy as a key regulator of synaptic architecture and sleep-associated resilience. Such early acting programs may actively preserve circuit function and behavioral output by regulating synaptic plasticity, and define a genetically tractable model for how local stress signals can orchestrate brain-wide adaptation via post-transcriptional synaptic reprogramming.

neuroscience↗

bioRxiv2025

Homozygous kinase-dead Csf1r mutation in outbred mice reveals essential and redundant functions of tissue resident macrophages

The proliferation, differentiation and survival of cells of the macrophage lineage depends on signals from the macrophage colony-stimulating factor receptor (CSF1R). On a C57BL/6J background homozygous kinase-dead Csf1r mutation (Csf1rE631K/E631K - E631Km/m) causes perinatal lethality. Here we demonstrate that E631Km/m mice on a mixed genetic background (C57 x BALB/c F2) are osteopetrotic and growth retarded but viable as adults with no other gross developmental deficits. They lack osteoclasts, microglia and most peripheral tissue resident macrophages and exhibit perturbed hematopoiesis. Although CD169+ tissue resident macrophages in bone marrow are considered an essential component of the hematopoietic niche, CD169 is undetectable in E631Km/m marrow and F4/80+ macrophages are depleted. These changes are associated with expansion of mature and immature granulocytes and reduced B cells, whereas monocytes and stem and progenitor populations are unaffected as a proportion of total cells. Erythropoiesis in bone marrow is maintained in E631Km/m mice, associated with a residual population of CSF1R-independent CD169-ve/F4/80+ macrophages. Nevertheless, splenic extramedullary hematopoiesis in E631Km/m mice indicates a degree of bone marrow insufficiency. Red pulp macrophages are retained but CD169+ marginal metallophil macrophages are absent and CD209b+ (SIGNR1) macrophages are present but disorganized. Circulating white blood cell count is unchanged in E631Km/m mice, but the proportion of neutrophils is greatly increased whilst B cells and monocytes are reduced. This novel model reveals the essential roles of CSF1R-dependent macrophages in hematopoiesis and demonstrates that many developmental and homeostatic functions attributed to murine resident tissue macrophages are redundant and/or specific to inbred mouse strains.

immunology↗

bioRxiv2025

A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction

Chronic lung injury generates metaplasia which occasionally, but ominously, progresses to squamous dysplasia and squamous lung cancer. To identify mechanisms through which disrupted tissue homeostasis contributes to malignant initiation and progression, we used in vivo and in vitro heterotypic recombinant models of human bronchial epithelial cells (hBECs) and fibroblasts. We demonstrate that injury-associated TGF-{beta} signaling creates a fibroblast state dependent upon HSP47 upregulation. These fibroblasts accumulated collagen, thus elevating tissue stiffness and activating mechanosignaling that sustained YAP-dependent embryonic-like, pro-malignant activities in adjacent hBECs. This Stress/Tension-Instructive Fibroblast (STIF) state, exhibited by stressed fibroblasts in premalignant and malignant lesions across multiple cancer types, was sufficient to reprogram disease-free hBECs to metaplasia and to drive hBECs with compromised tumor suppressor function to dysplasia, yet could be inhibited and reversed. STIFs suffice to activate epithelial phenotypes reminiscent of oncogene-mediated cell transformation and induce (pre)malignancy via increased force transmission, providing novel targets for prevention. Statement of significanceTissue injury creates a regenerative pro-tumorigenic Stress/Tension-Instructive Fibroblast (STIF) state which is sufficient to activate a YAP-dependent, pre-malignant program to induce or unmask pre-cancerous phenotypes in epithelial cells through mechanotransduction. Inhibition of STIF activity or mechanosignaling prevents metaplasia and progression to dysplasia. HighlightsO_LITissue injury creates a pro-tumorigenic Stress/Tension-Instructive Fibroblast (STIF) state in multiple organs that precedes and persists through cancer C_LIO_LISTIF signaling alone, working through fibroblasts and not epithelial cells, is sufficient to activate embryonic-like plasticity and induce epithelial pre-cancerous metaplastic lesions C_LIO_LISTIFs program (pre)malignant phenotypes in adjacent epithelial cells through mechanosignaling by activating YAP prior to tumor formation C_LIO_LIInhibiting STIFs or mechanosignaling prevents/reverts metaplasia and prevents progression to dysplasia C_LI

cancer biology↗

bioRxiv2025

Blocking Osteoprotegerin Reprograms Cancer Associated Fibroblast to Promotes Immune Infiltration into the Tumor Microenvironment

AbstractThe stromal compartment of many solid tumors plays a critical role in shaping an immunosuppressive microenvironment that limits the effectiveness of immune-based therapies1. Among stromal constituents, cancer-associated fibroblasts (CAFs) have emerged as key regulators of antitumor immunity2-5. Here, we identify a distinct subset of CAFs in both murine and human stroma-rich cancers that secrete osteoprotegerin (OPG)-- a soluble decoy receptor that neutralizes receptor activator of nuclear factor kappa-B ligand (RANKL) and TNF-related apoptosis-inducing ligand (TRAIL), both of which are involved in T cell function. In vitro, OPG directly impairs CD8 T cell-mediated killing of target cells. In murine models of pancreatic and breast cancer, antibody-mediated blockade of OPG promotes robust immune infiltration into the tumor microenvironment, leading to significant tumor regression. Stromal profiling revealed that OPG blockade induces a shift in CAF cells--reducing immunosuppressive OPG fibroblasts while expanding interferon-responsive fibroblasts, thus recalibrating the tumor stroma toward a pro-immunogenic landscape. These findings uncover a previously unrecognized mechanism of stromal immune suppression and highlight OPG as a stromal immune checkpoint controlling CD8 T cell infiltration. Targeting OPG may offer a novel therapeutic strategy to convert immunologically "cold" tumors into T cell-infiltrated, tumor microenvironment.

cancer biology↗

bioRxiv2025

From Development to Regeneration: Insights into Flight Muscle Adaptations from Bat Muscle Cell Lines

Skeletal muscle regeneration depends on muscle stem cells, which give rise to myoblasts that drive muscle growth, repair, and maintenance. In bats--the only mammals capable of powered flight--these processes must also sustain contractile performance under extreme mechanical and metabolic stress. However, the cellular and molecular mechanisms underlying bat muscle physiology remain largely unknown. To enable mechanistic investigation of these traits (Graphical Abstract), we established the first myoblast cell lines from the pectoralis muscle of Pteronotus mesoamericanus, a highly maneuverable aerial insectivore. Using both spontaneous immortalization and exogenous hTERT/CDK4 overexpression, we generated two stable cell lines that retain proliferative capacity and differentiate into contractile myotubes. These cells exhibit frequent spontaneous contractions, suggesting robust functional integrity at the neuromuscular junction. In parallel, we performed transcriptomic and metabolic profiling of native pectoralis tissue to define molecular programs supporting muscle specialization. Gene expression analyses revealed enriched pathways for muscle metabolism, development, and regeneration, highlighting the supporting roles in tissue maintenance and repair. Consistent with this profile, the flight muscle is triglyceride-rich, which serves as an important fuel source for energetically demanding processes, including muscle contraction and cellular recovery. Integration of transcriptomic and metabolic data identified three key metabolic modules--glucose utilization, lipid handling, and nutrient signaling--that likely coordinate ATP production and support metabolic flexibility. Together, these complementary tools and datasets provide the first in vitro platform for investigating bat muscle research, enabling direct exploration of muscle regeneration, metabolic resilience, and evolutionary physiology. Graphical AbstractEstablishment of bat muscle cell cultures from the Mesoamerican mustached bat (P. mesoamericnus) provides an in vitro platform to investigate muscle regeneration and flight muscle biology. The pectoralis major muscle was isolated to generate primary myoblast cultures, which were expanded and immortalized using hTERT/CDK4. The resulting myoblast lines retain proliferative and differentiation capacity. RNA sequencing of native pectoralis muscle tissue revealed molecular signatures of myogenic regulation, stress resilience, and tissue remodeling, supporting the relevance of these in vitro models for studying muscle maintenance and regenerative mechanisms. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/662643v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@490f49org.highwire.dtl.DTLVardef@8ab615org.highwire.dtl.DTLVardef@b840e1org.highwire.dtl.DTLVardef@ab92eb_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

An active Unc13A is Reboundless in sleep homeostasis

One of the major characteristics of sleep is homeostatic sleep rebound following sleep loss. While the molecular mechanisms of baseline sleep regulation have been intensively studied, a specific molecular understanding of sleep rebound remains elusive. Here, we show that a constitutively active form of the Munc13-family presynaptic release factor Unc13A, which lacks the inhibitory Ca2+/calmodulin interaction domain (Unc13AWRWR), dominantly suppressed sleep rebound upon acute sleep deprivation, leading to a nearly complete elimination of recovery sleep ("reboundless"). In contrast, baseline sleep remained largely normal. Through a genetic modifier screen, we found that this dominant "reboundless" phenotype of Unc13AWRWR was rescued by a partial loss of Snap, a cofactor of NSF required for disassembly and recycling of post-fusion cis-SNARE complex. Given that Unc13A promotes fusion-competent trans-SNARE complex formation, these findings suggest that sleep rebound may depend on a delicate balance between SNARE complex assembly and recycling. Additionally, we found that expression of a human disease-associated active Unc13A (Unc13APL) variant attenuated baseline and rebound sleep. Since both Unc13AWRWR and Unc13APL were shown to promote presynaptic release probability (Pr), we speculate that Unc13A suppresses recovery sleep likely by increasing Pr and subsequently enhancing synaptic transmission, probably through elevated trans-SNARE formation and efficient cis-SNARE recycling. Taken together, our data demonstrate a fundamental role of Unc13A and SNARE dynamics in sleep homeostasis.

neuroscience↗

bioRxiv2025

Morphology-Aware Profiling of Highly Multiplexed Tissue Images using Variational Autoencoders

Spatial proteomics (highly multiplexed tissue imaging) provides unprecedented insight into the types, states, and spatial organization of cells within preserved tissue environments. To enable single-cell analysis, high-plex images are typically segmented using algorithms that assign marker signals to individual cells. However, conventional segmentation is often imprecise and susceptible to signal spillover between adjacent cells, interfering with accurate cell type identification. Segmentation-based methods also fail to capture the morphological detail that histopathologists rely on for disease diagnosis and staging. Here, we present a method that combines unsupervised, pixel-level machine learning using autoencoders with traditional segmentation to generate single-cell data that captures information on protein abundance, morphology, and local neighborhood in a manner analogous to human experts while overcoming signal spillover. We demonstrate the generality of this approach by applying it to CyCIF, Lunaphore COMET, and CODEX data, and show that it can learn histological features across multiple spatial scales.

pathology↗

bioRxiv2025

Electric fields trigger ceramide-dependent budding of exosome vesicles into multivesicular endosomes and boost the generation of exosomes

Exosomes hold immense therapeutic and diagnostic potential, yet their clinical translation remains constrained by low yields. Physiological electric fields (EFs), naturally occurring during wound healing and embryo development, have unexplored roles in exosome biogenesis. Here, we demonstrate that physiological-strength EFs (Direct Current, 50-200 mV/mm) dramatically enhance cellular exosome secretion, achieving a nearly 100-fold increase in a strength-dependent manner. Mechanistically, EFs augmented intraluminal vesicle formation within multivesicular bodies. We proposed a novel EF-driven membrane electroassembly and vesiculogenesis hypothesis and tested it using giant plasma membrane vesicles. We reconstructed EF-induced membrane remodeling and observed EFs driving inward budding of nanoscale exosome-like vesicles. Notably, alternating current EFs (50-400 Hz) exhibited significantly diminished efficacy compared to direct current EFs, highlighting membrane electropolarization-dependent modulation. Pharmacological inhibition of the lipid raft and ceramide almost abolishes EF-induced exosome secretion. Inhibition of the PI3K partially attenuated EF-triggered exosome release. Our findings not only unveil EFs as a potent physiological regulator of exosome secretion but also establish a novel, high-yield production strategy leveraging bioelectric cues. Significant statementWe reported that the bodys natural bioelectricity, the faint electric currents in healing wounds and embryo development, can trigger cells to release 100 times more "natural nanoscale vesicle couriers" called exosomes. This pure physical method is far more efficient than current available technologies, paving the way for breakthroughs in cancer early detection, stem cell therapies, and precision medicine. We found that gentle electric fields can "blow" the cell membrane to release exosomes like "soap bubbles". This explains how bioelectricity controls cell communication during development and wound healing. In short, harnessing the bodys hidden "electric language" unlocks a fast and natural way to mass-produce exosomes.

cell biology↗

bioRxiv2025

Comparative Systematic Analysis of Gray Matter BiophysicalModels on a Public Dataset

Biophysical models of diffusion tailored to characterize gray matter (GM) microstructure are gaining traction in the neuroimaging community. NEXI, SMEX, SANDI, and SANDIX represent recent efforts to incorporate different microstructural features,such as soma contributions and inter-compartment exchange, into the diffusion MRI (dMRI) signal. In this work, we present a comparative evaluation of these four gray matter models on a single, publicly available in vivo human dataset, the Connectome Diffusion Microstructure Dataset (CDMD), acquired with two diffusion times. Using the open-source Gray Matter Swiss Knife toolbox, we estimate cortical microstructure metrics in 26 healthy subjects and evaluate goodness of fit, anatomical patterns and consistency with previous studies. CDMD data yielded GM parameter estimates consistent with values reported in previous studies. This retrospective cross-model analysis establishes the feasibility of estimating exchange models from only two diffusion times and highlights trade-offs in biological specificity, model complexity, and fitting robustness, critical considerations when choosing a model for future clinical and research applications.

neuroscience↗

bioRxiv2025

Alterations of the composition and spatial organization of the microenvironment following non-dysplastic Barrett's esophagus through progression to cancer

Barretts esophagus (BE), a metaplastic condition that is the only known precursor for esophageal adenocarcinoma (EAC), is relatively common, but progression to cancer is infrequent. BE is inflamed but the contribution of the immune system to the carcinogenic process is unknown. To this end, we contrasted non-dysplastic metaplasia of BE patients, captured when they did not progress (non-progressors), did subsequently, but had not yet progressed (pre-progressors) or had already progressed to EAC (progressors). Using spatial multiplexed 56-protein analysis, serial laser capture microdissection (LCM) RNAseq and shallow whole genome sequencing, we identified prooncogenic immune neighbourhoods and dysregulated immune cell populations predictive of subsequent progression to EAC. Indeed, spatial analysis revealed that M1 macrophages, regulatory natural killer (NK) cells, neutrophils and altered ratios of intraepithelial CD4+ and CD8+ lymphocytes typify tumor microenvironmental (TME) changes associated with cancer initiation. Spatially derived cell-to-cell interactions revealed progression-specific immune cell interaction signatures predominantly involving M1 macrophages NK cells and plasma cells. Furthermore, LCM RNAseq analysis identified gene expression hot signatures enriched in pre-progression and progression samples. Notably, we also observed a correlation between immune cells and copy number alterations in progressor metaplasia. By exposing coordinated changes in the immune cell landscape in patients at high risk of developing EAC, this multi-omic dataset provides novel diagnostic and therapeutic opportunities

cancer biology↗

bioRxiv2025

Oblique Thick Light-Sheet Microscopy with Spatiotemporal 3D Localization for RNA Imaging in Intact 50 μm-Thick Sections

Neuron typing in intact brain sections demands 3D imaging reconciling thickness compatibility with large-area coverage--a persistent challenge for RNA imaging methods limited by either restricted fields-of-view (<1 mm2) or thin-section constraints (<20 m). Here we introduce oblique thick light-sheet microscopy integrated with spatiotemporal 3D localization, enabling multiplexed RNA imaging across 50 m-thick tissue sections and centimeter-scale regions. The 45{degrees} illumination geometry achieves optical-interference-free imaging in >100 m-thick tissues during single-plane scans, while a spatiotemporal localization algorithm recovers submicron resolution by pinpointing fluorescence in situ hybridization (FISH) spots within volumetric excitation. This strategy reveals layer-spanning neuronal distributions and region-specific expression gradients unattainable with conventional RNA imaging approaches. By resolving the historical trade-off between imaging depth and spatial coverage, our platform advances whole-brain transcriptomics, enabling 3D neuron typing capability critical for deciphering brain-wide cellular architectures.

biophysics↗

bioRxiv2025

Under salt stress quinoa stomatal guard cells control transpiration in an ABA-primed manner

O_LIStomatal guard cells, located at the interface between the leaf and the atmosphere, play a key role in transpiration control and photosynthetic CO2 uptake. Halophytes like Chenopodium quinoa tolerate high soil salinity, but the mechanisms governing guard cell responses to salinity stress in relation to the associated epidermal bladder cells (EBCs) remain unknown. C_LIO_LIIn this study, responses of C. quinoa guard cells under salinity stress and external ABA application were analyzed using RNA profiling and voltage-clamp-based electrophysiology. C_LIO_LIUnder salt stress, guard cell RNA profiles reported the activation of ABA synthesis and signaling pathways. However, unlike EBCs, guard cells became transcriptionally insensitive to ABA. Voltage-clamp recordings revealed that under high Na+ concentrations, guard cells activity of K+ uptake channels remained unaffected, while they were impaired in ABA-induced activation of anion channels. As a consequence of a unique guard cell ABA response in salt-adapted plants, stomatal transpiration was reduced and CO2 sensitivity enhanced. C_LIO_LIWe propose that under salt stress, C. quinoa guard cells rewire their hormone signaling to switch from an ABA-sensitive to an ABA-insensitive mode. This adaptation may reflect the halophytes ability to perceive salinity as a non-stressful condition, allowing efficient water usage and sustained growth in saline environments. C_LI

plant biology↗

bioRxiv2025

Divergent photosynthesis and leaf respiration responses of four common subtropical tree species to modest warming

Subtropical forests are vital to global carbon pools, and their responses to increasing warming may significantly influence carbon sequestration. However, how subtropical tree species adjust the photosynthesis and respiration process in response to climatic warming through phenotypic plasticity is still unclear which is critical for predicting future forest carbon dynamics. In this study we investigate the effects of controlled warming experiment (1.5 {+/-} 0.5) on growth and leaf economic traits especially photosynthesis and respiration in four common subtropical tree species. Our findings reveal that modest warming enhanced photosynthesis, stomatal conductance, and night respiration, leaf anatomical traits as well as growth in Schima superba, Ormosia pinnata, and Pinus massoniana, of those species under warming. In contrast, Castanopsis hystrix demonstrated reduced performance in all measured traits because it may lack adaptive traits critical for warming resilience, indicating a divergent response to the same environmental condition. Our findings highlight the species-specific variation in how subtropical trees adjust traits associated with trees capacity to acclimate to increased temperatures. Specifically, Ormosia pinnata, Pinus massoniana, and Schima superba may exhibit beneficial responses to warming, whereas Castanopsis hystrix may experience negative effects in future climatic conditions which alters future carbon storage and tree diversity. Thus, our study offers new insights for further research on common trees under warming to improve predictions of forest dynamics under climate change, aiding conservation efforts to address environmental pressures.

ecology↗

bioRxiv2025

The hypoxic response extends lifespan through a bioaminergic and peptidergic neural circuit.

A coordinated response to stress is crucial for promoting the short- and long-term health of an organism. The perception of stress, frequently through the nervous system, can lead to physiological changes that are fundamental to maintaining homeostasis. Activating the response to low oxygen, or hypoxia, extends healthspan and lifespan in C. elegans. However, despite some positive impacts, negative effects of the hypoxic response in specific tissues prevent translation of their benefits in mammals. Thus, it is imperative to identify which components of this response promote longevity. Here, we interrogate the cell-nonautonomous signaling pathway downstream of genetic activation of the hypoxic response. We find that HIF-1-mediated signaling in ADF serotonergic neurons is both necessary and sufficient for lifespan extension. Signaling through the serotonin receptor SER-7 in the GABAergic RIS interneurons is necessary in this process. Our findings also highlight the involvement of additional neural signaling molecules, including the neurotransmitters tyramine and GABA, and the neuropeptide NLP-17, in mediating longevity effects. Finally, we demonstrate that oxygen- and carbon-dioxide-sensing neurons act downstream of HIF-1 in this circuit. Together, these insights develop a circuit for how genetic induction of the hypoxic response cell-nonautonomously modulates aging and suggests valuable targets for modulating aging in mammals.

physiology↗

bioRxiv2025

Metabolic modulation of intratumoral cholesterol with gut microbiota for the treatment of colorectal cancer

Excess cholesterol is positively correlated with colorectal cancer (CRC). Current therapeutic strategies for modulating cholesterol levels in CRC are limited and often come with complications. Here, we demonstrated that microbiome shunting of intestinal cholesterol to anticancer metabolites is a safe and applicable therapeutic approach for CRC. By screening major microbial metabolic products of cholesterol, we found that 4-cholesten-3-one (4-C-3) was selectively depleted in fecal samples and tumor tissues of patients with CRC. 4-C-3 exhibits strong antitumor effects on human CRC cell lines, patient-derived organoids, and patient-derived xenograft (PDX) models. Mechanistically, 4-C-3 suppresses CRC tumorigenesis by dually targeting the epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homologue (KRAS). 4-C-3 directly binds to EGFR, blocking its signal transduction by inhibiting the binding of EGFR ligands. Additionally, 4-C-3 inhibits oncogenic KRAS variants, such as KRASG12D, by suppressing nucleotide exchange activity and effector engagement. By targeting both EGFR and KRAS, 4-C-3 reduces primary resistance to anti-EGFR therapies caused by KRAS mutations in CRC. As a proof-of-concept study, we showed that delivery of 4-C-3 by Oscillibacter ruminantium, a 4-C-3- producing commensal bacterium that is reduced in CRC patients, or a nonpathogenic Escherichia coli strain engineered to specifically convert intestinal cholesterol into 4-C-3, removed intratumoral cholesterol and led to rapid tumor regression in multiple models of CRC. These results suggest that microbial therapies for restoring intestinal cholesterol homeostasis represent a new therapeutic avenue for CRC.

cancer biology↗

bioRxiv2025

On the edge of extinction: Delayed plant genetic response to forest edge dynamics

Understanding genetic responses to forest dynamics is essential for predicting the long-term viability of understory plant populations and for developing effective conservation strategies. This study investigates genetic extinction debt and colonization credit in Circaea lutetiana, a clonal forest understory species, across its European range. Using pooled genotype-by-sequencing data from 40 forest edge and core populations, we examined to what extent population size, latitude and historical changes in forest configuration predict genetic diversity. Our findings reveal that the historical forest configuration profoundly shapes present-day genetic diversity. Long-established forest edge populations exhibit significantly reduced allelic richness (-9%) compared to core populations, indicating the partial pay-off of a genetic extinction debt. In contrast, populations from recently established forest edges maintain comparable allelic richness to core populations, suggesting delayed population genetic responses to land use changes. Finally, populations established in areas that were afforested during the past 250 years exhibit lower genetic diversity than historical forest core populations, indicating a delay in genetic recovery and thus a potential genetic colonization credit. Our results highlight that C. lutetiana populations are not at equilibrium with the current forest configuration, underscoring the role of lagged genetic responses across very long time scales. Connectivity and population size further moderate genetic diversity, with smaller, isolated populations particularly vulnerable to genetic erosion. Given the limited research on delayed evolution in forest understory species, our results improve the understanding of extinction risk dynamics and underscore the need for history-informed restoration efforts.

ecology↗

bioRxiv2025

Deciphering of single-cell chromatin accessibility and transcriptome reveals the discrepancy for ex vivo human erythropoiesis

BackgroundErythroid cells can be generated from hematopoietic stem and progenitor cells (HSPC) derived from various sources; however, few studies decode ex vivo human erythropoiesis for the discrepancies at single-cell multi-omics resolution and uncover the underlying restraints for erythrocyte regeneration. ResultsWe deciphered ex vivo human erythropoiesis at two differentiation states from three sources at single-cell chromatin accessibility and transcriptomes level. We identified detrimental myeloid differentiation tendencies during early differentiation. These tendencies were linked to low glutamine activity in cord blood- and iPSC-derived erythropoiesis. The erythroid progenitor differentiation is restricted by cell cycle and hypoxia signaling deficiencies, which are pronounced in the iPSC-derived erythropoiesis. We delineated the erythroid differentiation trajectory of various ex vivo erythropoiesis systems, and revealed a distinct roadmap from HSC to orthochromatic erythroblast with unprecedented resolution. The integrative analysis of single-cell chromatin accessibility and transcriptome across developmental stages uncovered a dynamic coordination, and highlighted the pivotal role of chromatin accessibility and associated enhancers in regulating ex vivo erythropoiesis. Cell-cell communications in the ex vivo erythropoiesis system were not as well established as those in the BM, suggesting that modulating cell-cell communication signals in distinct ex vivo erythropoiesis system may facilitate erythrocyte regeneration. ConclusionsThis study comprehensively characterized the discrepancies and constraints in ex vivo human erythropoiesis at single-cell multi-omics resolution, offering novel strategies to overcome these constraints. These insights are critical for advancing functional erythrocyte generation and have significant implications for clinical applications.

developmental biology↗

bioRxiv2025

SISE, free LabView-based software for ion flux measurements

Plant growth and development strongly depend on the uptake of soil minerals and their distribution within plants. Various electrophysiological techniques have been developed to study these ion transport processes, from the single molecule-to whole plant level. An important non-invasive method is provided by Scanning Ion-Selective Electrodes (SISE), which are used to detect ion fluxes. These SISE-measurements depend on software that coordinates the perpetually electrode movement between two positions, as well as data collection and analysis. We developed two LabView-based programs; the SISE-monitor and SISE-analyser that enable ion flux recordings and their analysis, respectively. These applications are freely available, both as windows-executable files that enable routine measurements, as well as the LabView source code that allows deep insights into the routines used for measurement and further development of the programs to include new functions.

biophysics↗