Biology subjects

Lin, L.

Publications and source records attributed to Lin, L..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Inherent Biomechanical Properties of the Lung: In vivo-Ex vivo Comparisons in Mice

Mammalian lungs operate within a thoracic "cage" composed of parietal pleura, rib cage, skeletal muscle, and diaphragm, yet clinical ventilator metrics largely reflect the combined mechanics of lung and surrounding structures and the thoracic cage. We hypothesized that thoracic boundary conditions selectively alter measured lung biomechanics. We performed paired pulmonary function testing (FlexiVent) in C57BL6 mice of both sexes spanning development through adulthood, measuring quasi-static pressure-volume behavior and dynamic forced-oscillation parameters in vivo (supine, mechanically ventilated) and again ex vivo in the same lungs. In a subset, we additionally compared in vivo and ex vivo {micro}CT-derived lung volumes, including a pressure-fixed ex vivo protocol using snap freezing at controlled inflation pressure. Quasi-static pressure-volume curves were similar between conditions, with near-identity at higher pressures and only modest divergence at low pressures, consistent with thoracic structures primarily modulating recruitment/de-recruitment rather than intrinsic elastic recoil. Maximal volume at 30 cmH2O showed strong in vivo-ex vivo correlation and minimal bias, and static compliance and PV-loop hysteresis exhibited small biases relative to reported disease-model effect sizes. In contrast, dynamic mechanics demonstrated a clear in vivo elevation of tissue damping (G) with only modest change in tissue elastance (H) and little change in Newtonian resistance (Rn), producing a meaningful increase in hysteresivity ( = G/H). This dissociation implicates frequency-dependent mechanical heterogeneity (e.g., time-constant mismatch/pendelluft) imposed or amplified by nonuniform thoracic loading. Ex vivo {micro}CT enabled reliable whole-lung segmentation and correlated with ex vivo PFT volumes at matched pressures, whereas in vivo volumetry showed weaker agreement. These results indicate that thoracic structures contribute modest restriction but disproportionately increase dynamic dissipation and heterogeneity, suggesting that ex vivo functional testing and oscillometry-like metrics may better detect biomechanical changes inherent to lung parenchyma.

physiology↗

bioRxiv2026

Microstructural and Biomechanical Determinants of Biological Aging

The pulmonary artery undergoes measurable structural and mechanical deterioration with age, but whether these changes can be integrated into a quantitative normative aging prediction model has not been demonstrated. Using two-photon imaging and paired vascular mechanical measurements from C57BL6 mice spanning 6 to 24 months, we developed a multimodal support vector regression (SVR) model integrating collagen fiber orientation, straightness, and hemodynamic mechanical parameters to predict normative age. Fiber orientation was encoded via the von Mises probability density function referenced to the circumferential and axial vessel wall axes providing a principled circular-variable encoding of both mean direction and concentration. The microstructure-only model achieved leave-one-out (LOO) R{superscript 2} = 0.596, Mean Absolute Error (MAE) = 3.43 months. Adding vascular mechanical parameters (PWV) raised a combined LOO R{superscript 2} to 0.834 (MAE = 2.26 months), a 40.1% improvement. Because pulmonary vascular and parenchymal aging are mechanistically coupled, lung mechanics were included as a complementary readout to assess whether airway mechanics contribute independent predictive signal beyond vascular microstructure alone. A sex dimorphism was observed, where females drove the majority of the collagen-based predictive signal (female-only R{superscript 2} = 0.960 vs. male-only R{superscript 2} = 0.658). These results establish a multimodal framework for vascular biological age quantification that integrates structural and mechanical aging signatures.

bioengineering↗

bioRxiv2026

Biological Aging of the Cardiopulmonary System

Age-related stiffening of large arteries is a predictor of cardiovascular morbidity and mortality, yet how pulmonary vascular stiffening integrates with right ventricular (RV) and lung functional decline--and how best to quantify "biological" cardiopulmonary aging--remains unclear. Here we map cardiopulmonary aging across the adult murine lifespan by integrating RV, proximal pulmonary artery (PA), and lung biomechanics with single-cell transcriptomics. Using ex vivo biaxial testing of the proximal PA, in vivo echocardiography, and lung mechanics, we find that cardiopulmonary aging is phase-dependent: PA circumferential stiffening and reduced distensibility progress largely linearly with age; whereas, RV remodeling and lung mechanical changes exhibit non-linear trajectories. This is consistent with early intrinsic functional decline of cells and organs followed by later, extrinsic load-dependent structural adaptation. To quantify organ-level biological aging, we apply principal component analysis to PA, RV, and lung feature sets to derive physiology-based aging scores that summarize coordinated variance within and across organs. Anchoring differential gene expression in PA single-cell RNA-seq to these continuous biological aging scores rather than chronological age reveals extensive, cell-type-specific remodeling programs (13,636 genes) that are sparse or non-informative when modeled by chronologic age. Biological aging associates across endothelia, smooth muscle cells, fibroblasts, and perivascular macrophages with increased oxidative phosphorylation signatures alongside suppression of adaptive/regulatory pathways, including impaired endothelial mechanotransduction, reduced smooth muscle Wnt signaling, altered extracellular matrix remodeling programs, and erosion of macrophage innate immune and TGF{beta}/NF-{kappa}B signaling nodes. These findings support a model in which pulmonary arterial stiffening is not merely a marker but an active contributor to cardiopulmonary aging via a biomechanical-metabolic-inflammatory uncoupling that diminishes vasoactive and mechano-adaptive reserve and promotes a positive feedback loop. Together, our work establishes physiology-derived biological aging as a powerful framework for interpreting vascular single-cell aging trajectories and identifies mechanistic pathways to target pulmonary vascular stiffening and preserve cardiopulmonary function with age.

physiology↗

bioRxiv2026

Asymmetric introgression and thermal advantage jointly drive climate-mediated lineage turnover in a mixed-ploidy reed

Species distribution forecasts commonly overlook intraspecific genetic variation, missing a potentially important mechanism of ecosystem change: climate-driven range shifts among lineages within a species native range. Here we integrate population genomic analysis of 495 individuals, multi-site common garden experiments, and species distribution modeling based on 837 occurrence records for three major genetic lineages of the foundation grass Phragmites australis in China. The octoploid FEAU lineage (haplotype P) exhibits superior heat tolerance (critical temperature Tcrit and T50) and produces significantly greater total biomass in three of four common gardens compared to the cold-adapted CN lineage (tetraploid, haplotypes O/M), which occupies a climatic niche with lower annual mean temperature (Bio1) and mean temperature of the wettest quarter (Bio8). Genomic analyses further reveal bidirectional but asymmetric introgression, with admixed individuals showing a systematic bias toward FEAU ancestry. Under the high-emission scenario (SSP5-8.5) by 2070, projected highly suitable habitat for the FEAU lineage expands by 18.6%, while the CN lineage shows a smaller relative increase. By contrast, the subtropical SW lineage (haplotypes U/I) exhibits limited and stable suitable habitat. These results demonstrate that climate change interacts with intraspecific variation among polyploidy-associated lineages, manifested through differences in thermal tolerance, biomass production, and asymmetric gene flow, to drive potential lineage replacement within a native range, a process already suggested by field observations of FEAU expansion in a plateau lake. Our findings argue for integrating evolutionary history and genetic identity into ecological forecasting to better anticipate ecosystem responses under ongoing climate warming.

ecology↗

bioRxiv2026

A Bioprinted Head and Neck Cancer Organoid-Based Platform for Evaluating Multimodal Therapies

Treatment of advanced head and neck squamous cell carcinoma (HNSCC) often involves radiotherapy combined with chemotherapy, targeted therapy, or immunotherapy. However, due to its anatomical and molecular heterogeneity, identifying the most effective treatment for each patient remains a major clinical challenge. To address this need, we developed a high-throughput organoid-based drug screening platform that uses patient-derived organoids to assess candidate treatment regimens. We validated the platform by establishing bioprinted 3D organoids of human HNSCC cell lines and exposing them to X-ray radiation in combination with various small-molecule drugs and biologics. We quantified viability using ATP release assays and assessed extracellular matrix (ECM) invasion with a machine learning-based brightfield image analysis pipeline. Proof-of-concept experiments with HPV-negative HNSCC lines (HN30 and HN31, established from primary and metastatic disease from the same patient) and HPV-positive HNSCC cells (SCC154) revealed different therapy agents that can radiosensitize each cell line. Image analysis showed that copanlisib, afatinib, and ibrutinib could limit ECM invasion of HN31, while the AKT inhibitor ipatasertib promotes invasion of HN30 cells, consistent with previous studies. Application of the platform to patient-derived HPV+ oropharyngeal tumor organoids showed that they shared sensitivity to several agents while also exhibiting differences against certain therapies. Cetuximab, sorafenib, and nedisertib significantly radiosensitized organoids from two clinical samples. This work demonstrates the feasibility of performing sensitivity screening by integrating bioprinting, conventional viability assays, and advanced image analysis techniques. This platform has the potential to enable a personalized therapeutic pipeline for patients with advanced HNSCC, optimizing responses to radiotherapy and targeted agents to improve clinical outcomes while avoiding modulators that may promote tumor invasion.

cancer biology↗

bioRxiv2026

Genetic canalization of nutrient resorption: evidence from a widespread grass under effective salt stress

Nutrient resorption is a key plant strategy for nutrient conservation, yet whether it responds plastically to non-nutrient stressors such as salinity remains unresolved. Using a common garden experiment with 110 genotypes of the cosmopolitan grass Phragmites australis, we first established that the imposed salinity treatment induced strong multi-level stress responses: above-ground biomass declined by >60%, sodium accumulated 3- to 5-fold across all leaf stages, and 484 metabolites showed significant differential accumulation, including canonical markers of osmotic and oxidative stress. Against this backdrop of confirmed stress, we found that nutrient resorption efficiency (NuRE) remained largely unaffected by salinity. Instead, NuRE was strongly correlated with phylogeographic lineage, ecotype, and latitude of origin, demonstrating evolutionary canalization rather than short-term acclimation. Element-specific regulatory patterns were also evident: while phosphorus resorption followed concentration-dependent control regardless of stress, nitrogen control was disrupted under salinity, and potassium resorption showed no such dependence. Our findings reveal that intraspecific variation in nutrient resorption is predominantly shaped by historical adaptation and geographic context, not by plasticity to salinity. This genetic canalization of a key functional trait implies that predictions of nutrient cycling under global change must account for the phylogeographic composition of plant populations.

ecology↗

bioRxiv2026

Glutamate transporter xCT is important for cGAS-dependent interferon responses to DNA and to HSV-1

Metabolic reprogramming is a key component of antiviral immunity, yet how metabolite transport regulates innate immune signaling remains incompletely understood. Here, we show that infection with herpes simplex virus 1 (HSV-1) and stimulation with cytosolic DNA induce the cellular export of glutamate via the xCT (SLC7A11) transporter and that inhibition of xCT reduces cellular resistance to viral replication. Mechanistically, xCT inhibition impaired cGAS-STING signaling by reducing DNA-induced cGAMP production, thereby diminishing type I interferon (IFN/{beta}) responses and downstream induction of interferon-stimulated genes. Interestingly, modulating intracellular glutamate levels through inhibition of other glutamate pathways, e.g., glutaminolysis or glutamate import, also affected cellular IFN responses, suggesting that glutamate is a central control knob for DNA sensing. Finally, we demonstrate that HSV-1 suppresses xCT expression via a mechanism dependent on the immediate early viral protein ICP27, thereby promoting viral replication by limiting cGAS-dependent IFN induction. Together, these findings identify xCT-dependent glutamate transport as a critical metabolic regulator of cGAS-STING-mediated antiviral immunity.

immunology↗

bioRxiv2026

CellChem: Cellular transcriptional responses reshape molecular representation space for efficient and multi-scale drug discovery

Despite decades of progress in computational drug discovery, deep learning-based molecular representation models remain largely structure-centric, assuming that chemical similarity approximates functional similarity. However, drug effects in cells are shaped not only by chemical similarity but also by molecular interactions in the cellular context. To capture this complexity, we introduce CellChem, a cellular-chemical representation-learning framework that learns cell-guided molecular representations of small-molecule actions within cells. By incorporating large-scale cellular transcriptional profiles during pretraining, CellChem reshapes molecular representation space from structure-centric to a balanced integration of structure and function. The learned CellChem molecular representations exhibit biologically meaningful geometric organization, such that distances between molecules encode not only structural similarity but also similarity in the cellular responses they elicit, independent of downstream tasks. Using downstream derivative models such as cell-guided compound-protein interaction prediction and drug-induced transcriptional response profile generation, CellChem supports highly efficient, multi-scale drug discovery, achieving significantly better performance than traditional models.

molecular biology↗

bioRxiv2026

Autoluminescence characteristics of 25 Phalaenopsis orchids following transient transformation with eFBP2

Engineering autoluminescent plants, especially horticultural crops, has recently emerged as a promising research area, with one current approach involving the transgenic introduction of fungal bioluminescence pathway genes. Although autoluminescent plants such as tobacco and petunia have been created, it remains unclear whether all horticultural plants have the potential to be autoluminescent after genetic modification, especially those having flowers with dark colors and thick cuticles. To understand whether, and what if any, floral traits affect autoluminescence potential, we assess the autoluminescence characteristics of 25 representative Phalaenopsis cultivars after transient transformation of fungal bioluminescence pathway genes, alongside several key morphological and biochemical traits. Our results demonstrate that autoluminescence characteristics are correlated with floral color lightness, organ textures and epidermal cell types. In contrast, the content of the substrates of luciferin--caffeic acid and tyrosine, and the infiltration ease of inoculation solution into floral organs after injection, have limited effects on autoluminescence characteristics. Autoluminescence intensity can be reasonably predicted using five floral traits investigated, as 80.4% of variation can be explained by these traits. Our study not only identifies specific Phalaenopsis cultivars with high potential for developing autoluminescent lines but also provides a selection framework applicable to other horticultural crops.

plant biology↗

bioRxiv2026

The mechanism of Hsa_circ_0000629 in bronchial asthma through sponge adsorption of miR-212-5p/NLRP3

To explore the mechanism of Hsa_circ_0000629 adsorbing miR-212-5p/ nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3) through sponge in bronchial asthma. Twenty BALB/C mice were randomly divided into a normal control group and an asthma group. Pathological changes in lung tissue were observed via HE staining. Human bronchial epithelial cells (16HBE) were transfected with Hsa_circ_0000629 overexpression group (Hsa_circ_0000629-over), Hsa_circ_0000629 siRNA (Hsa_circ_0000629-si), mimic NC, miR-212-5p mimic, inhibitor NC, miR-212-5p inhibitor, and LPS+Hsa_circ_0000629 si. LPS-induced asthmatic cell models (LPS group) and untransfected 16HBE cells (NC group) served as controls. qRT-PCR was used to measure Hsa_circ_0000629, miR-212-5p and NLRP3 expression. ELISA assessed interleukin 18 (IL-18), interleukin 1{beta} (IL-1{beta}), interleukin 6 (IL-6) and tumor necrosis factor - (TNF-) levels. Cell proliferation and the apoptosis were evaluated by EDU assay and flow cytometry, respectively. Western blot analyzed Cleaved-caspase 1, 3 and 9 proteins expression. Dual-luciferase assay verified the binding sites of Hsa_circ_0000629 to miR-212-5p and NLRP3 to miR-212-5p. HE staining revealed inflammatory cell infiltration, bronchial wall thickening, smooth muscle hyperplasia, and alveolar destruction in asthmatic mice. Compared with the controls, Hsa_circ_0000629 and NLRP3 expression were significantly increased, while miR-212-5p expression was decreased in asthmatic lung tissues. In 16HBE cells, Hsa_circ_0000629-over and LPS groups showed elevated Hsa_circ_0000629 and NLRP3 expression but reduced miR-212-5p levels. Silencing Hsa_circ_0000629 in LPS-treated cells (LPS+Hsa_circ_0000629-si) reversed these effects. Overexpression of miR-212-5p counteracted Hsa_circ_0000629-induced NLRP3 upregulation, while miR-212-5p inhibition enhanced NLRP3 expression. LPS exposure increased TNF-, IL-18, IL-6, and IL-1{beta} levels, reduced cell proliferation, and promoted apoptosis. These changes were attenuated by Hsa_circ_0000629 silencing or miR-212-5p overexpression. Western blot confirmed that Hsa_circ_0000629 overexpression upregulated Cleaved-Caspase 1, 3, and 9, whereas miR-212-5p mimic or Hsa_circ_0000629-si reversed this trend. Dual-luciferase assays demonstrated targeted interactions among Hsa_circ_0000629, miR-212-5p, and NLRP3. Interference with Hsa_circ_0000629 expression can alleviate LPS induced apoptosis in 16HBE cells and inhibit the expression of inflammatory factors by targeting the miR-212-5p/NLRP pathway, which may be a new target for the treatment of asthma.

immunology↗

bioRxiv2026

c-MYC is an aggregation-prone, amyloidogenic protein

The transcription factor c-MYC is a central regulator of diverse biological processes and an oncogenic driver. Paradoxically, c-MYC also exhibits intrinsic tumor-suppressive activity through apoptosis, a phenomenon known as the "c-MYC paradox". Here, we identify c-MYC as an intrinsically amyloidogenic protein. Under proteotoxic stress, c-MYC becomes detergent-insoluble aggregates. Notably, even in the absence of stress, c-MYC assembles into soluble amyloid-like oligomers in human cancer tissues and Alzheimers disease brains. In vitro, recombinant c-MYC proteins spontaneously form amyloid oligomers and protofibrils. In contrast, its obligate dimerization partner MAX is non-amyloidogenic and suppresses c-MYC amyloidogenesis. Mapping studies identify two short linear sequences within intrinsically disordered regions that confer amyloidogenicity. Importantly, the amyloid state of c-MYC induces apoptosis largely independently of transcription. Thus, these findings reveal a previously unrecognized amyloidogenic property of c-MYC, which contributes to its tumor-suppressing activity. Conceptually, c-MYC amyloidogenesis may serve as a built-in failsafe mechanism to restrain its oncogenic potential.

cell biology↗

bioRxiv2026

The Stochastic Pacemaker: Cumulative Behavioral Noise Drives Morphological Plasticity in Pea Aphids

Phenotypic variation within a single genotype under the same environment (intragenetic variation), the biologically meaningful part of Verror, is frequently treated as a statistical nuisance rather than a biological reality, yet it represents an evolutionary driver of fitness that remains poorly integrated into evolutionary theory. The mechanism that translates such stochasticity into deterministic developmental phenotypic outcomes is not well understood. Here, we test a cumulative stochasticity model using wing polyphenism of the pea aphid (Acyrthosiphon pisum), where asexual mothers produce winged instead of wingless offspring in response to tactile cues. The model predicts that stochastic variation in maternal locomotor behavior alters the rate of tactile cue accumulation and thereby influences the probability of producing winged offspring. We demonstrate that maternal locomotor activity acts as a "stochastic pacemaker", where an individuals movement determines the rate at which it actively constructs its environment and accumulates environmental cues. Our results reveal that genotypes differ significantly in both mobility and the temporal pattern of wing induction, with behavioral variation explaining approximately 20% of the total phenotypic variance across genotypes. Crucially, we show that maternal mobility increases progressively during crowding, accompanied by significant temporal heteroscedasticity. This expanding variance and increase in mean suggest that initial, trivial stochasticity is magnified into systematic behavioral divergence through the integration of environmental signals. By demonstrating that total accumulated locomotor activity predicts offspring phenotype, we provide a mechanistic bridge between transient behavioral noise and stable morphological shifts. More broadly, our work reveals that Verror is a dynamic product of behavioral history, suggesting a fundamental role for individual-level niche construction in generating macro-phenotypic diversity.

evolutionary biology↗

bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

MATR3 is essential for oocyte growth and maturation quality through a dual molecular mechanism

The molecular mechanisms governing mRNA accumulation during oocyte growth, essential for developmental competence, remain poorly understood. This study investigates the role of Matrin-3 (MATR3), a highly expressed RNA-binding protein in growing oocytes (GOs), using oocyte-specific knockout mouse models and human oocyte maturation arrest (OMA) samples. The results showed that MATR3 was more abundant in GOs than fully-grown oocytes (FGOs), highly expressed in the nucleus of non-surrounded nucleolus (NSN) oocytes, and exited the nucleus during the NSN-to-surrounded nucleolus (SN) transition. In OMA patients, MATR3 nuclear localization was missed, with smaller oocytes than FGOs. Further, Matr3 deletion in mouse GOs caused restricted oocyte growth, global transcription disorders, follicle development failure, blocked GO-granulosa cell communication (via reduced Gdf9 and Radixin expression), and infertility. Mechanistically, MATR3 regulated transcription by recruiting H3K9me2-demethylating lysine-specific demethylase 3B or binding target gene promoters, like Radixin. These findings reveal a critical role of MATR3 in orchestrating transcription and paracrine signaling during oogenesis and suggest its potential as a diagnostic and therapeutic target for OMA.

physiology↗

bioRxiv2026

The genome of an aneuploid cultivar facilitates elucidating the genetic bases of trait polymorphisms in Phalaenopsis orchids

As an important ornamental crop, Phalaenopsis orchids exhibit extraordinary trait diversity with unclear genetic bases. Here, we present a haplotype-resolved, chromosome-level genome for an aneuploid cultivar Santiago. We reveal pervasive variation in the number and sequence among homoeologous genes. When serving as a reference, this genome facilitates the genetic understanding of trait variation in a hybrid population that is highly representative in trait polymorphisms. Specifically, nucleotide polymorphisms in a potential long-distance enhancer and the consequential expression variation of PsAGL6-2, presence/absence of PsMYB12 and b-type homoeologous gene of PsMYB2 determine lip morphology variation, presence/absence of venation-associated stripes and background pink color, respectively. Diverse functions of PsMYBx1 in repressing anthocyanin accumulation across different cultivars further enhances the color patterning diversity in Phalaenopsis. Our study provides a practical framework for using a highly heterogeneous, haplotype-resolved genome to decode phenotypic diversity and has the potential to promote marker-assisted breeding in Phalaenopsis.

genomics↗

bioRxiv2026

eScreen: a deep learning framework for functionally decoding the regulatory genome at single-nucleotide resolution

The human genome is densely populated with cis-regulatory elements (CREs), yet deciphering their functional regulatory syntax and combinational logic remains a fundamental challenge. Here, we integrate 379 genome-scale CRISPR screen experiments, encompassing 21 million perturbations across 23 cell types, to construct a compendium of 41,239 high-confidence functional CREs from 530,527 candidates. Leveraging this resource, we develop eScreen, a deep learning model built on the StripedHyena2 architecture to functionally decode the regulatory genome at single-nucleotide resolution. eScreen achieves three primary functions: (1) predicts genome-wide cell-type-specific CRE functional activity with high accuracy, outperforming existing models; (2) provides mechanistic interpretation of regulatory syntax at single-nucleotide resolution; (3) dissects the functional organization of enhancer clusters through in silico perturbation analysis. We perform multiple independent CRISPR knockout, CRISPR interference (CRISPRi), and base editing screens to validate these functions of eScreen both at scale and on individual cases. Furthermore, we provide an interactive web server (https://escreen.huanglabxmu.com/) for the community to access the integrated CRISPR screen resources and eScreen functions. Collectively, our work establishes a highly precise and convenient tool to decode the causal effects of the regulatory genome.

genomics↗

bioRxiv2026

Calcium directs actin assembly via allosteric activation of formin INF2

Calcium signals spatiotemporally orchestrate cytoskeletal dynamics, typically through Rho GTPase-mediated signaling cascades, yet the direct molecular transducers that convert local calcium transients into spatially controlled actin assembly have remained elusive. Here, we uncover a structure-based mechanism by which calcium-bound calmodulin (Ca2+-CaM) directly activates formin INF2 to drive actin assembly. We demonstrate that Ca2+-CaM binds to the diaphanous inhibitory domain (DID) of INF2 with nanomolar affinity, inducing allosteric conformational changes that sterically disrupt INF2 autoinhibition. The unexpected bipartite Ca2+-CaM binding interface on INF2 enables ultrasensitive decoding of local calcium microdomains, such as ER-mitochondrial contacts, where activated INF2 promotes actin polymerization to facilitate mitochondrial fission. We further show that the Charcot-Marie-Tooth disease-associated INF2 R91G mutation enhances Ca2+-CaM binding via optimized interfacial dynamics, suggesting a gain-of-function disease mechanism. Our work establishes the Ca2+-CaM-INF2 axis as a direct molecular transducer linking spatial calcium signals to actin-dependent organelle dynamics, defining a Rho-GTPase-independent paradigm for calcium-cytoskeleton communication, with broad implications for INF2-linked pathologies.

biochemistry↗

bioRxiv2026

CCycDB: an integrative knowledgebase to fingerprint microbially mediated carbon cycling processes

Microorganisms play essential roles in mediating biogeochemical cycling of carbon across Earths ecosystems. Understanding the processes and underlying mechanisms for microbially mediated carbon cycling is therefore critical for advancing global ecology and climate change research. To comprehensively depict these complex biogeochemical processes, we developed CCycDB, a knowledge-based functional gene database, to accurately fingerprint microbially-mediated carbon cycling pathways and gene families, particularly from shotgun metagenomes. The CCycDB database comprises 4,676 gene families classified into six major functional categories, further structured into 45 level-1 and 188 level-2 sub-categories, encompassing a total of 10,991,724 high-quality reference sequences. Validation using both synthetic and real-world datasets demonstrated that CCycDB outperforms existing orthology databases in terms of accuracy, coverage and specificity. By directly targeting carbon-cycling functional gene families, CCycDB provided promising routines to reconstruct both functional gene and taxonomic profiles associated with microbially mediated carbon cycling. Application of CCycDB to shotgun metagenomes from diverse and complex ecosystems revealed pronounced habitat-specific differences in carbon cycling processes and their associated microbial taxa. Collectively, CCycDB provides a powerful and reliable tool for profiling carbon cycling processes from both functional and taxonomic perspectives in complex ecosystems. CCycDB is accessible at https://ccycdb.github.io/. Impact StatementThe microbially mediated carbon cycling processes are the most complex biogeochemical processes in the Earths biosphere, playing profound regulatory roles on global climate changes. A key bottleneck in linking microbial communities to global change is the lack of integrated tools for comprehensive carbon cycle profiling. Here, we present CCycDB, a tool that serves a dual purpose--first being a reference database that obtains functional gene and taxonomic profiles and functioning as a customized routine for efficiently aligning sequences and querying associated functional information. CCycDB enables researchers to accurately link microbial community dynamics to carbon cycling and transforming pathways, thereby advancing integrated global change studies with microbes and ecological research via complex metagenomic datasets.

microbiology↗