Biology subjects

Liu, J.

Publications and source records attributed to Liu, J..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Low-intensity focused ultrasound pulsation along the anterior-posterior thalamic axis differentially modulates the latency of reporting conscious visual experience

Background: Transcranial low-intensity focused ultrasound (LIFU) neuromodulation can alter human task performance depending on target and acoustic configurations. However, single behavioral endpoints cannot locate effects within multistep tasks, and predefined target labels ignore acoustic variations. Objective: To determine whether thalamic LIFU affects visual categorization or subsequent subjective report latency and whether the effects vary with target, acoustic parameter, and beam location. Methods: Sixty healthy adults were randomized to 70% or 5% duty cycle (DC70 or DC5) and received sonication on four left thalamic targets with matched pulse repetition frequency (10 Hz) and temporal-average intensity (0.72 W/cm2). Behavioral models tested target-by-DC interactions in categorization (RT1) and subjective report (RT2) latencies. Spatial analyses correlated focal spot coordinates and voxel-wise intensity from 179 acoustic simulations to baseline-adjusted RT2. Results: The target-by-DC interaction was detected for RT2 but not RT1. At the ventroposterior thalamic target, adjusted RT2 was 55.9 ms longer under DC70 than DC5. More anterior focal spots shortened RT2 under DC70 but increased RT2 under DC5. Correlation between intensity and adjusted RT2 significantly differed between DC70 and DC5 in 18.8% of thalamic voxels. These voxels formed an anterior mediodorsal-motor set and a posterior pulvinar-dominant set. Conclusions: The latency of reporting conscious visual experience, but not categorization latency, was affected by thalamic LIFU. This effect varied jointly with anterior-posterior target engagement and acoustic configuration. Analyzing sequential reaction times separately and treating field variation as an anatomical variable revealed associations not fully captured by a single endpoint or predefined target labels.

neuroscience↗

bioRxiv2026

Heparan sulfate selectively inhibits the collagenase activity of matrix metalloproteinase 13

Matrix metalloproteinase 13 (MMP13) is a zinc-dependent protease that plays key roles in extracellular matrix remodeling. Like several other MMPs, MMP13 has been shown to interact with heparan sulfate (HS), a highly sulfated glycosaminoglycan found at the cell surface and in the extracellular matrix, but the significance of the interaction remains unknown. Here we report that while zymogen and mature forms of MMP13 both bind HS with high affinity, their interactions with HS display markedly different characteristics in terms of preferred HS structure and binding kinetics. By structure-guided mutagenesis, we identified a large HS-binding site of MMP13 consists of 10 residues in the hemopexin domain, 3 residues in the catalytic domain, and 2 residues in the linker region. While these basic residues participate in binding to both zymogen and mature forms of MMP13, the relative contribution of many residues differs substantially between the two forms, which likely contributes to their distinct HS-binding characteristics. Binding of HS to mature MMP13 resulted in selective inhibition of the collagenase activity of MMP13 in a length- and sulfation-dependent manner, but the binding had no effect on degradation of non-collagen substrates. Mechanistically, the inhibitory effect of HS likely results from reduced interdomain flexibility after binding of HS, and/or HS-induced dimerization of MMP13. In sum, our study establishes HS as a multifaceted regulator of MMP13 activity, and discovers that the HS-binding site of MMP13 is a novel exosite that can be targeted to inhibits its collagenase activity.

biochemistry↗

bioRxiv2026

Pto evolved from malectin-like RLKs phosphorylates AvrPtoB to promote Prf-mediated immunity in Solanum pimpinellifolium

Bacterial speck, caused by Pseudomonas syringae pv. tomato (Pst), is a devastating disease of tomato that severely limits global tomato productivity. Understanding the molecular mechanisms underlying Pst and tomato is essential for developing disease resistant varieties. Here, we demonstrate that Pto, the first disease-resistance gene conferring recognition of a specific pathogen, phosphorylates Pst type III effector AvrPtoB at serine 335 site. This post-translational modification triggers the dissociation of the Prf immune complex, enhancing immune signaling and reducing bacterial pathogenicity. Furthermore, evolutionary analyses indicate that Pto-associated proteins originated from malectin-like receptor kinases (MLRs) through loss of the extracellular domain. Crucially, we identified two key amino acid substitutions, Arg158 and Glu258 in Pto, which replace the ancestral lysine residues in MLRs (SpHREK1-1, SpHERK1-2 and SpHERK1-3). These substitutions stabilize Pto by preventing degradation mediated by AvrPtoB's E3 ubiquitin ligase activity. Our findings reveal a novel mechanism, by which Pto phosphorylates a bacterial effector to trigger enhanced immunity and elucidate the key evolutionary adaptations that have shaped Pto into a stable resistance protein.

plant biology↗

bioRxiv2026

Pre-existing antibiotic tolerance facilitates plasmid-mediated carbapenem resistance evolution in clinical Klebsiella pneumoniae

Antibiotic tolerance enables bacteria to survive bactericidal antibiotic exposure and has been linked to resistance evolution in laboratory systems and individual infections, but its role in plasmid-mediated resistance evolution in clinical populations remains unclear. Here, we analyzed a longitudinal collection of more than 800 clinical Klebsiella pneumoniae isolates spanning 1997-2020. Among 779 minimum inhibitory concentration (MIC)-defined ertapenem-susceptible isolates, 137 (17.6%) displayed hidden ertapenem tolerance, defined by enhanced survival after 6 h at 30 times the isolate-specific ertapenem MIC, mostly without extended lag time or reduced growth rate. Tolerance was detected before local ertapenem introduction and was enriched among ertapenem-resistant isolates, supporting a population-level association between pre-existing tolerance and the emergence of carbapenem resistance. Genomic and plasmid-curing analyses separated plasmid-mediated carbapenem resistance from plasmid-independent antibiotic tolerance. Moreover, tolerant recipient backgrounds enhanced resistance plasmid acquisition, preserved viable recipients following antibiotic exposure and accelerated ceftazidime-avibactam resistance evolution. A phylogeny-guided variant-enrichment analysis further identified the uhpABC regulatory operon as a candidate tolerance-associated locus, and coordinated expression of the complete operon increased ertapenem survival. Together, these findings identify clinical antibiotic tolerance as a pre-existing, MIC-hidden phenotype that can facilitate plasmid-mediated carbapenem resistance evolution in K. pneumoniae.

microbiology↗

bioRxiv2026

Trehalose exerts cryoprotective effects on piglet testicular tissue

The cryopreservation of testicular tissue is crucial for maintaining male fertility; However, its efficacy is often compromised by oxidative stress and mitochondrial dysfunction. Trehalose, a natural cryoprotectant, demonstrates significant potential, yet its specific mechanisms, particularly in mitochondrial regulation, remain insufficiently characterized. This study aimed to investigate the cryoprotective effects of trehalose on testicular tissue from 18-21-day-old piglets, with a focus on mitochondrial metabolism. Samples were cryopreserved via a slow-freezing protocol in a modified standard solution containing 200 mmol/L trehalose. The protective effect was evaluated by measuring testosterone synthesis, blood testis barrier (BTB) and spermatogenesis. Additionally, protective outcomes were assessed by measuring cell viability, tissue morphology, reactive oxygen species (ROS) levels, apoptosis rates, and testosterone secretion following freeze-thaw cycles. Transcriptomic sequencing and bioinformatics analyses were conducted to elucidate the underlying molecular mechanism. Cryopreservation led to reduced testosterone synthesis and secretion, decreased levels of BTB-binding proteins, and impaired spermatogenesis. Results indicated that 200 mmol/L trehalose significantly improved cell survival, decreased apoptosis and ROS levels, and enhanced testosterone secretion. 200 mmol/L trehalose partially increased the expression of StAR and CYP11A1 genes associated with testosterone synthesis while it protected the tight junction proteins Claudin-11, ZO-1 and the gap junction protein Cx43. Consequently, it exerted a reproductive protective effect by increasing the expression of key spermatogenic regulators DDX25, HMGB2, acrosomal protein DYP19L2, and sperm tail proteins AKAP4 and CFAP44. Transcriptomic profiling demonstrated that trehalose predominantly restored the transcriptional expression of genes involved in the mitochondrial electron transport chain and oxidative phosphorylation pathways, including ND2, COX2, ATP8, ATP6, ND5, ND6 and CYTB. These findings indicate that trehalose primarily protects piglet testicular tissue during cryopreservation by enhancing mitochondrial function, thereby providing a molecular basis for optimizing cryopreservation protocols.

cell biology↗

bioRxiv2026

Whole-genome duplication drives biosynthetic gene cluster fragmentation and regulatory rewiring of monoterpene indole alkaloid metabolism in Strychnos

Whole-genome duplications (WGDs) reshape plant genomes by generating redundancy, after which lineage-specific architectures emerge through fractionation, gene loss and rearrangement. How specialized metabolic pathways remain functionally integrated after such large-scale restructuring remains poorly understood. This problem is especially relevant for biosynthetic gene clusters (BGCs), which physically organize specialized-metabolism genes yet can be disrupted by post-duplication rearrangement. Here, we present the first chromosome-level genomes for Loganiaceae, including near telomere-to-telomere assemblies of Strychnos ignatii and S. pubescens, together with a draft genome of the extinct species S. ridleyi. Following a lineage-specific WGD, the two extant Strychnos species evolved contrasting genome-evolutionary trajectories and metabolite profiles: S. ignatii shows expansion of monoterpenoid- and monoterpene indole alkaloid (MIA)-associated gene families and strychnine-type MIA dominance, whereas S. pubescens exhibits elevated transposable element activity associated with DNA-binding with one finger (DOF)-linked regulatory rewiring and broader sesquiterpenoid- and triterpenoid-rich chemistry. Crucially, both species retain active strychnine biosynthesis despite fragmentation of a deeply conserved alkaloid BGC in MIA-producing Gentianales, revealing how pathway function can persist after disruption of ancestral BGC architecture. Comparative metabolomic and transcriptomic pathway analyses indicate norfluorocurarine oxidase (NO) as a major divergence point associated with strychnine accumulation. Promoter analyses, yeast one-hybrid assays, and electrophoretic mobility shift assays support a model in which S. ignatii retains the canonical jasmonate-responsive MYB, MYC2/bHLH, and AP2/ERF cis-regulatory module at NO, whereas the orthologous S. pubescens promoter shows reduced capacity to recruit these activators and instead exhibits a DOF-associated architecture. Together, our results show that WGD can decouple physical cluster architecture from pathway function, allowing specialized metabolic pathways to remain active while divergent chemical phenotypes evolve through lineage-specific combinations of coding-space expansion and transposable-element-associated cis-regulatory rewiring.

evolutionary biology↗

bioRxiv2026

Visual deprivation in adulthood engages presynaptic plasticity of thalamocortical synapses

Synaptic plasticity between neurons in first order thalamus and layer 4 cortex is greatest during an early postnatal critical period and was thought to decrease irreversibly with age. However, here we show that robust and reversible plasticity can be induced in adult mice at synapses between dLGN axons and visual cortex layer 4 neurons by prolonged dark exposure (DE) and light reintroduction (LRx). Unexpectedly, the experience-dependent change in synaptic strength was mediated by a change in presynaptic structure, organization and function. DE/LRx declusters/clusters synaptic vesicles and reorganizes presynaptic molecular geometry. Furthermore, DE/LRx decreases/increases visually-evoked and spontaneous calcium signaling and neurotransmitter release probability in dLGN axonal boutons. The presynaptic plasticity mechanism described here has a high threshold for engagement which would allow maintenance of synapse stability across a wide activity range, and reactivation of thalamocortical plasticity in extraordinary conditions.

neuroscience↗

bioRxiv2026

The human papillomavirus L2 protein in the capsid is an ensemble of related structures poised to exit the virus particle

The human papillomavirus (HPV) capsid contains 360 molecules of the L1 protein, which assembles into pentamers that form the capsid shell, and up to 72 molecules of the L2 protein. The C-terminus of the L2 protein must emerge from the capsid, insert into the endosome membrane, and protrude into the cytoplasm to bind to cellular proteins that mediate trafficking of the virus to the nucleus during virus entry. Computational analysis predicts that much of L2 is disordered, but the stoichiometry, structure and location of L2 in the capsid remain elusive. Here, we use cryo-EM single particle analysis of HPV16 pseudovirus capsids with and without the L2 protein combined with AlphaFold3 predictions and molecular dynamics simulations to develop a structural model of L2 within the capsid. Our results revealed that a single molecule of L2 associates with the inner surface of most L1 pentamers. The relatively rigid structure of the pentamer forces the long intrinsically disordered segments of L2 to adopt numerous related, compact, stable conformations in the capsid, whereas the structured elements of L2 remain folded but adopt varied positions in space largely beneath the pentamer. A finger-like projection of L2 extends into the central pore of the pentamer, but many different segments of the disordered domains of L2 can form fingers. In some models the C-terminus of L2 extends through the pore to the exterior surface of the capsid positioned to insert into the endosomal membrane. Consistent with these models, analysis of purified pseudoviruses showed that the C-terminus of multiple L2 molecules is exposed on the surface of each capsid. These findings provide a structural basis for understanding how L2 is organized in the capsid poised to initiate its action during virus entry.

microbiology↗

bioRxiv2026

The HES1-SOD1 Antagonism Shapes Senescence Heterogeneity and Impacts Metastatic Relapse of Circulating Tumor Cells

Circulating tumor cells (CTCs) encounter multiple challenges within the blood microenvironment, including oxidative stress, flow shear forces, and immune surveillance, often leading to anoikis. Recently, a transitional state of CTC senescence has been identified, contributing to metastatic inefficiency. However, the molecular mechanisms linking senescent CTCs to disease relapse remain to be defined. By integrating a genetic model of cortactin knockdown-induced CTC senescence with single-cell multi-omic analyses, we revealed two distinct senescent CTC subpopulations marked by HES1 expression levels. These HES1low and HES1high subpopulations exhibited differential evolutionary trajectory dynamics and unique molecular and metabolic signatures, which were significantly correlated with adverse clinical outcome across several patient cohorts. HES1low senescent CTCs displayed enhanced mitochondrial fitness, oxidative phosphorylation, and ROS-detoxifying capabilities, resulting in more efficient tumor regrowth with a pro-inflammatory and thrombotic phenotype when compared to the HES1high group. Mechanistically, HES1 directly bound to the Sod1 promoter and repressed its expression, leading to redox imbalance and mitochondrial dysfunction that were linked to weakened tumor regrowth capacity. Both senescent CTC subpopulations were broadly resistant to cytotoxic and targeted therapies, yet they showed elevated dependency on anti-apoptosis programs that make them susceptible to dual blockade by SOD1 inhibitor and the anti-senolytic drug ABT737 in vivo. Finally, in a prospective cohort of on-treatment melanoma patients, HES1 senescent CTCs were highly enriched in patients with progressive disease. Thus, the HES1-SOD1 antagonism shapes CTC senescence heterogeneity and contributes to differential tumor relapse, which can be therapeutically explored for eliminating residual metastatic disease.

cancer biology↗

bioRxiv2026

Cell line resources for the study of neurofibromin: functions, phenotypes, and drug discovery/development

Our labs have been studying neurofibromin function and phenotype for over a decade with the intent of generating targeted therapeutics for Neurofibromatosis type 1 (NF1). In the process, we have generated numerous human cell lines containing variants within the NF1 gene. Herein, we present data characterizing these cell lines and make them publicly available for use by researchers both within and outside the NF1 community. We describe lines that contain both well-characterized patient-specific variants either at their endogenous locus or as exogenous cDNAs, as well as variants of uncertain significance (VUS), engineered as heterozygous, homozygous, and compound heterozygous variants. Methods to generate each line and subsequent validation steps are detailed including targeted sequencing, Western blot analysis for neurofibromin expression and ERK activation. The utility of each line is dependent on the variant of interest, the parental cell line, and the mechanism of action relevant to possible therapeutic targeting.

genetics↗

bioRxiv2026

MAFB is essential for the maintenance of adult human α-cell identity and glucagon secretion

Dysregulated hormone secretion and erosion of endocrine cell identity are features of type 1 and type 2 diabetes, but the transcriptional programs maintaining adult human islet identity and function remain poorly defined. The large MAF transcription factor MAFB is expressed in human - and {beta}-cells, marks their most functionally mature subpopulations, and is downregulated in diabetes, but its role in adult human islets has not been tested directly. Using shRNA-mediated MAFB knockdown (KD) in whole and CD26+ -cell-enriched human pseudoislets, we found that whole pseudoislet MAFB KD impaired glucagon synthesis and secretion while only modestly reducing insulin content and cAMP-potentiated insulin release. Single-cell profiling detected no {beta}-cell transcriptional response beyond MAFB KD itself, consistent with buffering by the related {beta}-cell-enriched MAFA transcription factor. In contrast, -cell-restricted MAFB KD unmasked a cell-autonomous requirement for MAFB in stimulus-secretion coupling. MAFB deficiency also destabilized -cell identity, downregulating canonical -cell and neuroendocrine secretory genes while ectopically inducing mesenchymal and extracellular matrix remodeling programs. In addition, MAFB-dependent downregulation of electron transport chain genes was confined to a large -cell subcluster, manifesting as impaired islet-wide mitochondrial respiration within the broader -cell population. Together, these findings identify MAFB as an essential adult human -cell maintenance factor that links diabetes-associated downregulation to impaired glucagon secretion, -cell identity erosion, and mitochondrial dysfunction. RESEARCH IN CONTEXTO_LIWhat is already known about this subject? O_LIMAFB is expressed in adult human - and {beta}-cells, marks their most functionally mature subpopulations, and is downregulated in type 1 and type 2 diabetes C_LIO_LIIn human stem cell models, MAFB is essential for generating insulin-producing {beta}-like cells, whereas glucagon-producing -like cells are reduced but still formed C_LIO_LINeither model addresses adult human islets: rodent MafB becomes -cell restricted after birth, and stem cell models capture differentiation, not maintenance C_LI C_LIO_LIWhat is the key question? O_LIIs MAFB required to maintain identity and secretory function in adult human islet cells? C_LI C_LIO_LIWhat are the new findings? O_LIMAFB knockdown in primary human pseudoislets impaired glucagon synthesis and secretion but minimally affected {beta}-cells, consistent with buffering by MAFA C_LIO_LIKnockdown in CD26+ -cell-enriched pseudoislets revealed a cell-autonomous requirement for MAFB in stimulus-secretion coupling, and destabilized -cell identity by inducing mesenchymal and extracellular matrix programs C_LIO_LIMAFB loss downregulated electron transport chain genes in the largest -cell subcluster and reduced mitochondrial respiration C_LI C_LIO_LIHow might this impact on clinical practice in the foreseeable future? O_LIPreserving MAFB activity in adult human -cells may represent a strategy to limit -cell dysfunction in diabetes C_LI C_LI

physiology↗

bioRxiv2026

A cross-modal generative model for incomplete and degradedprostate MRI with multicentre clinical validation

Missing or degraded sequences can limit prostate multiparametric MRI. We developed MSCNet, a sequence-conditioned cross-modal generative framework for reconstructing unavailable contrasts and restoring degraded acquisitions. Across ten completion tasks, task-specific MSCNet achieved mean structural similarity of 0.818 versus 0.798 for the strongest task-matched comparators; matched-capacity analyses showed larger differences in lesion fidelity and boundary preservation. In a blinded 1,000-case reader study, overall image quality met the prespecified non-inferiority criterion for DWI, ADC and T2W completion, but not T1W. In a separate 200-case diagnostic assessment, AUCs for clinically significant cancer were 0.860 with acquired images, 0.841 with MSCNet and 0.797 with baseline-generated images. A locked 186-case three-hospital cohort supported multicentre transportability. These retrospective results support quality-controlled cross-modal reconstruction as an adjunct to acquired prostate MRI.

bioengineering↗

bioRxiv2026

The Y chromosome gene KDM5D restrains CD8+ T cell antitumor immunity through TCR and cholesterol-exhaustion programs

Sex differences in immunity shape cancer risk, autoimmunity, and responses to immunotherapy, yet the sex-chromosome genes that regulate antitumor T cell function remain incompletely defined. Here, we identify the Y chromosome-encoded KDM5D histone demethylase as a male-specific suppressor of CD8+ T cell antitumor immunity. In murine colorectal cancer (CRC) models, male CD8+ T cells displayed reduced cytokine production, proliferation, cytotoxicity, TCR{beta} abundance, and proximal TCR signaling relative to female CD8+ T cells. CRISPR-RNP-mediated KDM5D depletion in male CD8+ T cells enhanced effector function, increased TCR{beta} expression, augmented TCR signaling, and improved tumor control after adoptive transfer. Transcriptomic and functional analyses further linked KDM5D to cholesterol biosynthesis and exhaustion-associated programs, with KDM5D depletion reducing SREBP2/XBP1-associated cholesterol and exhaustion signatures. Correspondingly, human CRC single-cell analyses supported the clinical relevance of this axis, showing enrichment of exhausted and cholesterol-associated CD8+ T cell states in male tumors. Pharmacologic inhibition of cholesterol biosynthesis with lovastatin partially attenuated select exhaustion-associated markers in male CD8+ T cells and delayed tumor growth in vivo. Together, these findings define KDM5D as a sex chromosome-encoded regulator of male CD8+ T cell dysfunction and point to cholesterol-exhaustion programs as a potential therapeutic vulnerability in male CRC.

cancer biology↗

bioRxiv2026

Reversible m6Am methylation of snRNA by FTO controls morphine reward and tolerance without altering analgesia

Mu opioids, such as morphine, are effective analgesics, but their reward and tolerance drive opioid use disorder. A major goal is to achieve analgesia without these harmful effects. Here we show that morphine reward and tolerance require the RNA demethylase FTO. Genetic depletion and pharmacologic inhibition of FTO each reduced morphine reward, measured by conditioned-place preference, and reduced antinociceptive tolerance to morphine and fentanyl, without altering analgesia. Although FTO is known to erase m6A on mRNA, we found no effect of FTO depletion on m6A sites, but markedly increased levels of m6Am on snRNA. The effects of FTO depletion were suppressed in mice that cannot make m6Am, supporting the role of m6Am in morphine reward and tolerance. We show that FTO depletion regulates a gene expression network linked to morphine signaling. FTO inhibitors may therefore provide useful adjuvants to mu opioids in pain management and treatment of opioid use disorder.

neuroscience↗

bioRxiv2026

A Practice on Antibody Hydrophobic Interaction Chromatography Retention Time Prediction using Pre-Trained Large Language Model Fine-Tuning

Hydrophobicity is a critical property associated with the risk of non-specific binding, and it is commonly assessed using hydrophobic interaction chromatography retention time. Several computational approaches have been developed to predict antibody developability based on pre-trained language models. Such models can be fine-tuned with limited labeled antibody sequences and, in principle, do not require structural information, which is often challenging to obtain. Nevertheless, few studies have achieved strong performance in hydrophobicity prediction without incorporating structural features. Here, we present a case study of fine-tuning the pre-trained model IgBert to predict antibody hydrophobicity. Using Herceptin as a reference, we performed hydrophobic interaction chromatography retention time experiments and generated Herceptin-adjusted datasets. The fine-tuned model achieved a best R2 of 0.916, underscoring the critical role of rigorous data quality control. We also synthesized and validated 20 commercially available antibody sequences, and the results showed that the predicted hydrophobic properties were correctly reflected. Our findings provide practical guidance and highlight considerations for future applications of fine-tuned pre-trained language models in antibody hydrophobicity prediction.

bioinformatics↗

bioRxiv2026

Synthetic Longitudinal Tabular Data Generation via Copula

Synthetic data generation is increasingly used to enable data sharing and secondary analysis while protecting participant privacy, particularly for longitudinal tabular health data, where repeated measures per subject create within-subject dependence that most synthetic data methods are not designed to preserve. Existing generative methods, particularly generative adversarial network (GAN)-based approaches, can model complex distributions, but their estimated dependence structures are often difficult to interpret and their performance may be unstable or prone to overfitting in modestly sized datasets. Here we show that eCDF-copula, a statistically rooted approach using the empirical cumulative distribution function (eCDF) and copula modeling, preserves within- and between-visit dependence structure. To handle pervasive missing data, we propose a two-stage strategy combining multiple imputation with copula-based synthesis, enabling a variance decomposition that quantifies replication variability across methods. We benchmarked the proposed approach against four established methods on two longitudinal clinical datasets spanning markedly different sample sizes (n = 120 vs. n = 3, 612). eCDF-copula achieved resemblance and utility exceeding those of state-of-the-art synthetic data methods, while maintaining comparable privacy.

bioinformatics↗

bioRxiv2026

Physical laws predict methane hotspots in global mountain waters

Accurate accounting of aquatic methane emissions is critical for climate change mitigation, yet current global budgets overlook a key driver: the elevation-regulated atmospheric pressure. Here, we present the first large-scale investigation of methane ebullition across 164 shallow waters spanning elevations from sea level to 4886 meters. We demonstrate that ebullition rate increases with elevation-over four times higher at >3000 m a.s.l. than at sea level-due to two synergistic, pressure-dependent physical mechanisms: a degas effect (enhanced bubble formation) and a trigger effect (facilitated bubble ascent). Independent theoretical prediction of the combined effects shows near-perfect agreement with the empirical elevation trend, quantitatively confirming that these physical mechanisms are the primary drivers of enhanced ebullition at high elevations. Our findings reveal that mountain aquatic ecosystems represent unaccounted methane hotspots that have been systematically underestimated in global inventories.We therefore call for urgent integration of these ecosystems into IPCC assessments and targeted mountain mitigation and sustainable management strategies.

ecology↗

bioRxiv2026

LTBP isoforms differentially encode TGF-β spatial localization and activation

TGF-{beta} signals through a conserved pathway yet produces diverse outcomes, pointing to regulatory mechanisms upstream of receptor engagement. A family of four latent TGF-{beta} binding proteins (LTBPs) tether pro-TGF-{beta}s and control their localization and activation, but how distinct LTBPs contribute to this regulation is unclear. Here we combine cryo-electron microscopy with functional assays to dissect LTBP-pro-TGF-{beta} interactions. We resolve the LTBP-1/pro-TGF-{beta}1 and LTBP-3/pro-TGF-{beta}3 complex structures, revealing a conserved yet plastic hydrophobic binding interface, and systematically map key residues across all four LTBP and three pro-TGF-{beta} subtypes that determine binding specificity and affinity. Unexpectedly, LTBP-2, previously thought incapable of TGF-{beta} binding, engages pro-TGF-{beta}1 through a covalent linkage via its 16th EGF-like domain, providing a mechanistic link between LTBP-2 function and TGF-{beta} signaling. Beyond tethering, LTBP-3 shifts pro-TGF-{beta}3 from spontaneous activation toward integrin dependence, establishing LTPBs as dynamic modulators that dictate not only where but also how TGF-{beta} is unleashed. Collectively, these findings establish that LTBPs are not redundant ECM scaffolds but a family of functionally distinct regulators that differentially encode TGF-{beta} spatial localization and activation, with implications for isoform-selective therapeutic strategies.

biochemistry↗