Biology subjects

Luo, H.

Publications and source records attributed to Luo, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Type 2 diabetes amplifies environmental Pb toxicity and intergenerational risk

Type 2 diabetes (T2D) and environmental lead (Pb) exposure intersect as prevalent global health challenges. Prior studies report elevated blood Pb in T2D, but the underlying mechanism and directionality remain unresolved. Here we show that T2D fundamentally alters Pb toxicokinetics, converting otherwise modest exposure into progressive organ injury and heritable risk. In a human cohort, elevated blood Pb in T2D specifically associated with impaired renal function rather than glycaemic control or adiposity. In db/db mice, diabetes increased oral Pb absorption through delayed gastrointestinal transit and epithelial barrier dysfunction, leading to enhanced systemic retention. With sustained exposure, renal Pb accumulation induced tubular stress that reduced effective clearance, creating a feed-forward loop in which diabetes promotes Pb retention and retained Pb accelerates kidney injury. Chronic Pb exposure exacerbated diabetic kidney injury without inducing hyperglycaemia, and short-course chelation attenuated renal stress markers. Beyond somatic toxicity, combined paternal T2D and Pb exposure programmed renal and neurobehavioral phenotypes across generations via sperm RNA. These findings redefine Pb from a passive environmental exposure to a context-dependent driver of disease, identify T2D as a vulnerability state that reshapes toxicant handling, and establish a mechanistic link between metabolic disease, environmental exposure and intergenerational risk. This work highlights the need for vulnerability-informed clinical management and environmental regulation in populations burdened by T2D.

genetics↗

bioRxiv2026

Tail Flaring as an Agonistic Signal in Hummingbirds

Bird tails in flight generate lift, reduce pressure drag, and stabilize pitch. Hummingbirds can sustain hovering in still air and generate lift in both the up- and downstroke due to their proportionally enormous primary flight muscles and derived wing skeleton. Given their mass-specific wing power, it is possible that tails are less essential to the aerodynamics of hummingbird flight than they are in other birds, freeing them for non-locomotor functions. Hummingbird tails are well known for their morphological elaboration as sexually selected ornaments, including sound generation. From informal observations of agonism, we hypothesized tail flaring may also be a visual signal used by males during fighting. To begin testing this, we measured the frequency and magnitude of tail flaring during fighting. We measured kinematics of tail flaring during male-male fighting of Calliope hummingbirds (Selasphorus calliope, n = 10) indoors. Consistent with our hypothesis, captive males exhibited greater angles of tail flare when engaged in a fight (34.6 {+/-} 45.5{degrees}, mean {+/-} sd) than when performing solitary landing (-14.2 {+/-} 9.12 {degrees}) and takeoff (-14.1 {+/-} 7.0 {degrees}) maneuvers. When birds won a fight, the angles of their tail spread were greater than when they lost (p = 0.01). Moreover, recordings of seven species of hummingbird in the field revealed 95% of inter- and intra- specific contests included tail flaring. We evaluate these results in the context of signaling during animal contests and propose future tests of whether tail flaring is an honest signal of individual quality and Resource Holding Potential. Summary StatementMale-male fighting is common in hummingbirds with competition over food and mates. During these competitions, tail flaring and waggle maneuvers are used as a signal of aggressive intent.

evolutionary biology↗

bioRxiv2025

Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms

RNA splicing shapes neuronal identity and disease risk, yet current maps lack the developmental resolution and depth to resolve this complexity. Here, we integrate deep long-read RNA sequencing and proteomics in iPSC-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half previously unknown) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Population genetics demonstrates that variants affecting novel exons and splice sites are under negative selection, underscoring the potential significance of these isoforms. During neuronal maturation, we observe that ASD risk genes undergo dynamic isoform switching, including microexon inclusion and intron retention, that remodel key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between splicing and polyadenylation. Finally, our atlas enables variant reinterpretation in ASD, highlighting the value of an isoform-centric view for interpreting pathogenic variation in neurodevelopment.

bioinformatics↗

bioRxiv2025

From genomic decay to functional advantage: Trait-based evidence for long-term host residency of a next-generation coral probiotic

A key bottleneck in microbiome engineering is ensuring the long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of the population MC10, identified by such signatures, has shown persistent colonization in corals in a companion study. Whether this persistence translates into a measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the coral model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both sympatric control strains. To understand the mechanistic basis of this probiotic efficacy, we characterized the functional profile of MC10 using an integrated multi-omics approach. The genome of MC10 is enriched in genes associated with host-interaction, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, which were phenotypically confirmed by detectable iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated motility-to-sessility proteomic reprogramming, downregulating flagellar motor components while upregulating flagellin and biofilm regulators. This response was distinct from its sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4s functional profile, particularly its sensitivity to oxidative stress, contrasts with the traits typically favored in conventional probiotic screens. Our results move beyond the descriptive identification of a coral probiotic by providing initial mechanistic insight into traits associated with long-term host association and improved thermal performance. These findings validate an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities, informing the rational design of durable probiotics.

microbiology↗

bioRxiv2025

Capturing Multi-Scale Dynamics of Aortic Valve Calcification With a Coupled Fluid Structure and Systems Biology Model

Calcific aortic valve disease (CAVD) arises from coupled interactions between blood flow, tissue mechanics, and cellular signaling. Hemodynamic forces influence endothelial and interstitial cell behavior, while the resulting tissue remodeling alters valve motion and flow patterns. Capturing this two-way feedback requires models that integrate fluid-structure mechanics with biochemical regulation, yet such multiscale coupling remains technically challenging. Previous computational models have focused on isolated aspects of the disease: fluid-structure interaction (FSI) simulations reproduce valve deformation and flow, and systems biology (SB) models describe molecular signaling that drives fibrosis and calcification. However, without coupling, these approaches cannot predict how mechanical dysfunction initiates biochemical remodeling or how biochemical changes feed back on mechanics. Here, we present a proof-of-principle, multi-physics computational framework that couples three-dimensional FSI simulations of aortic valve dynamics with a mechanistic SB model of calcification signaling. The FSI module resolves pulsatile blood flow and leaflet deformation, yielding local wall shear stresses and tissue strains throughout the cardiac cycle. These mechanical quantities are used as inputs to the SB module, which comprises key biochemical pathways governing inflammation, TGF-{beta}/SMAD signaling, and nitric-oxide (NO)-mediated inhibition within valvular cells. Simulations predict long-term calcification trajectories for valves of varying thickness, showing that fibrosis-induced stiffening lowers shear stress, reduces NO synthesis, and enhances TGF-{beta} activation, thereby accelerating calcification. While the current one-way coupling implementation is not intended yet for clinical applications, the framework is modular and extensible, allowing for future enhancements that will advance towards this goal. These include the incorporation of additional biological pathways in the SB model and implementation of a fully two-way coupling scheme between the FSI and SB models that will increase accuracy and predictive capability of the framework. By integrating physics-based hemodynamics with systems-level biochemistry, this study demonstrates the utility of a next-generation, multi-scale modeling platform for studying cardiovascular disease that unites blood flow dynamics and biochemical signaling.

systems biology↗

bioRxiv2025

Engineering an Anaerobic Microenvironment to Empower Hydrogenase-Catalyzed Hydrogen Therapy for Diabetic Wound Healing

The inherent oxygen sensitivity of hydrogenases has long restricted their applications to anaerobic systems. Here, we present a hybrid peptide-nanocluster hydrogel that establishes a self-sustaining anaerobic microenvironment to enable hydrogenase-catalyzed hydrogen therapy under aerobic conditions. This system integrates a custom-designed Fmoc-KYF peptide hydrogel with integrated silver nanoclusters (AgNCs), which host an engineered [NiFe]-hydrogenase (3S1C-Hyd-2). Mechanistic studies combining molecular dynamics simulations and spectroscopic analysis revealed that hydrophobic pockets within the peptide network trap oxygen molecules, while photoexcited AgNCs rapidly deplete invasive O2. Our design ensures stable hydrogen evolution, effectively overcoming the oxygen sensitivity that has long restricted hydrogenase applications in biomedical contexts. In vitro, the in-situ-generated hydrogen effectively scavenges reactive oxygen species, suppresses pro-inflammatory cytokine production. In a diabetic mouse model, this light-activated system markedly accelerates wound closure (87% by day 11), reduces oxidative stress, promotes macrophage polarization toward a reparative phenotype, enhances angiogenesis, and upregulates tissue repair pathways, as confirmed by transcriptomic profiling. Our work establishes a new bioengineering paradigm for constructing anaerobic microenvironments through synergistic material-enzyme-light interactions, offering a versatile platform for hydrogenase-enabled therapeutic interventions in oxidative stress-related diseases.

biochemistry↗

bioRxiv2025

De Novo Design of a Protein Binder to Probe Gas Channel and Enhance the Oxygen Tolerance of Hydrogenase

[NiFe]-hydrogenases exhibit outstanding catalytic performance for H2 production and oxidation but suffer from extreme O2 sensitivity, limiting their biotechnological potential. The identity and functional roles of gas channels that connect to the buried [NiFe] active site have remained unclear, impeding the rational engineering of O2-tolerant enzyme variants. In this study, we present an artificial intelligence-guided de novo protein binder design strategy, utilizing compact protein binders as selective molecular probes to map hydrophobic O2 diffusion pathways in Escherichia coli hydrogenase-2 (Hyd-2). By integrating RFdiffusion, ProteinMPNN, and AlphaFold, approximately 100,000 candidate binders were computationally screened, leading to the identification of two high-affinity binders, L1 and L2. Structural, biophysical, and electrochemical analyses reveal that L1 specifically occludes the primary O2 ingress channel, thereby enhancing the enzymes oxygen tolerance by more than threefold, whereas L2, which targets a putative secondary channel, exerts a negligible effect, demonstrating the nonfunctionality of this pathway. These results provide the first direct experimental evidence for a hierarchical organization of O2 diffusion channels in [NiFe]-hydrogenases and establish binder-mediated channel occlusion as a generalizable, mutation-free approach for probing gas transport mechanisms and selectivity in metalloenzymes.

biochemistry↗

bioRxiv2025

Modular mRNA lipid nanoparticle platform rescues diverse genetic male infertility

Genetic male infertility arises from diverse mutations that disrupt spermatogenesis, yet therapeutic strategies capable of restoring germ-cell function remain limited. Messenger RNA (mRNA) therapeutics offer a programmable and non-integrating approach, but their functional compatibility in structured and immune-privileged tissues remains unclear. Here we identify a temporal mismatch between mRNA delivery kinetics and the progression of spermatogenesis as a key barrier to functional rescue. We show that delivery efficiency does not predict outcome: formulations with high peak expression but short duration fail to support spermiogenesis, whereas sustained expression aligned with developmental timing enables recovery. Guided by this principle, we establish a testis-targeted mRNA delivery platform that restores spermatogenesis across multiple genetic models and generates functional sperm capable of supporting embryo development and multigenerational inheritance. The approach is modular, extends to human seminiferous tubules ex vivo, and is supported by comprehensive safety analyses. Together, these findings define a design constraint for RNA therapeutics in structured tissues: functional rescue requires temporal alignment between delivery kinetics and the therapeutic window defined by tissue-specific biological programs.

bioengineering↗

bioRxiv2025

Human brains construct individualized global rankings from identical few-shot local learning

Ranking--a ubiquitous relational structure--enables humans to organize complex information and overcome cognitive load, yet in real-world settings it is often inferred from sparse, few-shot learning of local pairwise relationships. How the human brain performs relational inference under such limited evidence remains unknown. We hypothesized that under few-shot learning, relational inference is shaped by inductive biases, such that individuals actively impose structured global relationships--often idiosyncratic--to constrain and unify limited local information. In a preregistered behavioral study combined with magnetoencephalography (MEG) recordings, we show that even after identical few-shot local pair learning, individuals construct stable and self-consistent, yet idiosyncratic, global rankings that diverge from the ground-truth order--a phenomenon not readily explained by classical computational models of transitive inference. MEG recordings further reveal that frontoparietal neural representations are reorganized to reflect each individuals subjective ranking rather than those of others. Together, these findings highlight the constructive and generative nature of human cognition: under sparse samples and limited computational resources, the human brain actively infers and imposes relational structure.

neuroscience↗

bioRxiv2025

Enterococcus faecalis delivers Obg GTPase via extracellular vesicles to instigate mTOR activity and promote HCC tumorigenesis

Hepatocellular carcinoma (HCC) is a malignant tumor that has been associated with dysbiosis of the gut microbiota. However, how the gut microbiota plays an oncogenic role in HCC remains largely unknown. Here, we show that Enterococcus faecalis (E. faecalis) is highly enriched in liver tumor tissues and is positively correlated with pathogenesis of HCC. E. faecalis promotes liver cancer cell proliferation, protein translation, cell migration and tumorigenesis. Mechanistically, we found that EF-derived extracellular vesicles (EF-EVs) deliver EF-Obg GTPase to activate host mTOR, thereby promoting liver cancer progression. Intriguingly, the EF-Obg protein exerts its influence on the mTOR pathway via a Ras-like G domain involved in GTP binding. EF-Obg exhibits a striking homology with the G1 site of the G domain of Rheb, a key positive regulator of mTOR. Obg gene is critical for E. faecalis to activate mTOR to promote hepatocarcinogenesis based on an engineered obg knockdown strain by CRISPR interference experiment. Clinically, abundant EF-Obg protein expression is correlated with enhanced activation of mTOR, leading to poor overall survival in HCC patients. Significantly, treatment of mTOR inhibitor Everolimus confers effectiveness in EF-colonized liver cancer orthotopic model, suggesting that Everolimus therapeutic approach can be effective for liver cancer patients with enriched E. faecalis. Taken together, we provide mechanistic and functional evidence to verify a direct causal relationship between tumor-resident E. faecalis enrichment and liver carcinogenesis, revealing that EF-Obg functions as a previously unidentified cross-kingdom activator of mTOR to promote liver tumorigenesis.

cell biology↗

bioRxiv2025

Programming Microbe-Computer Interaction for Customized Life-Nonlife and Cross-Life Communication

This extension of human-computer interaction (HCI) paradigm to the non-intelligent microbe-computer interaction (MCI) is attractive for building generalized life-nonlife communication. Main challenges lie in how to construct biohybrid interface within individual MCI unit and thereafter program cross-life communication based on these MCI units. Here, we propose the design and construction of opto-interfaced MCI unit composed of engineered microbes and computer terminals, for enabling quantifiable transduction between microbial signals and digital signals. These units were able to serve as biohybrid sensors, actuators and transceivers, supporting biomonitoring, bio-actuation and microbe-centric bidirectional operations. Based on these functional units, we established programmable cross-life communication architectures capable of unicast, multicast, and logic-gate-driven communication with temporal dynamic control. The architectures were validated in biomedical scenarios including tumor hypoxia biomarking, epidermal heavy metal detoxification, and colitis intervention, demonstrating robust performance in closed-loop diagnostic-therapeutic applications. Additionally, we integrated MCI with an unmanned surface vessel for environmental monitoring, highlighting its cross-domain potential. Collectively, we provide a scalable strategy for building customized life-nonlife and cross-life communication, which is expected as an important complement to internet of things (IoT).

synthetic biology↗

bioRxiv2025

Replicable, Transdiagnostic Behavioral and Neural Correlates of Sensory Over-responsivity

ObjectiveSensory over-responsivity (SOR), characterized by strong negative reactions to typically innocuous stimuli, is considered a symptom of autism spectrum disorder. However, SOR also affects 15-20% of children overall, including a majority of children with common psychiatric conditions. Despite its prevalence, the clinical specificity and neurobiological bases of SOR remain poorly understood. Our study aims to determine the specific clinical significance of SOR across diverse child samples and establish whether SOR is associated with replicable patterns of functional connectivity (FC). MethodWe analyzed data from 15,728 children (ages 6-17.9 years) across five datasets: three community samples, including the Adolescent Brain Cognitive Development [ABCD] and Healthy Brain Network [HBN] studies, and two autism-enriched samples. Bivariate and multivariate models examined associations between SOR and symptoms of anxiety, attention-deficit/hyperactivity disorder, depression, conduct disorder, and oppositional defiant disorder, as well as autistic traits. Analysis of resting-state functional MRI (fMRI) data from the ABCD study (n=4195) identified candidate brain-wide and circuit-specific FC correlates of mild SOR and tested replication of effects in an independent ABCD subsample (n=4190). Additional analyses tested extension to children with severe SOR in ABCD and replication in smaller samples [HBN (n=356), ABCD subset (n=356)]. ResultsMultivariate analyses revealed that SOR is associated with a remarkably consistent profile across samples: greater levels of both autistic traits and anxiety symptoms and, in community samples, lower levels of conduct disorder symptoms. Across samples, SOR is not reliably associated with symptoms of any other analyzed psychiatric conditions. Mild SOR is associated with brain-wide FC patterns and, specifically, reduced FC between cingulo-parietal network and bilateral caudate nucleus; these patterns show robust replication across independent ABCD subsamples and extension to severe SOR in ABCD but are not significant in smaller samples, indicating that large sample size is needed to reliably detect brain effects. ConclusionResults suggest that SOR may constitute a latent trait associated with both specific clinical risk and protection, and with replicable cortico-subcortical neural correlates. These findings advance our understanding of the neurobiology and clinical relevance of SOR. They may also inform clinical practice and future research aimed at understanding and supporting individuals with sensory challenges.

neuroscience↗

bioRxiv2025

Bone Marrow Adipokine Mediates Hematopoietic Regeneration and Stem Cell Fitness

Bone marrow (BM) hematopoietic stem cells (HSCs) are exquisitely sensitive to cues from the BM microenvironment (ME), which is critical for their engraftment and regeneration following myeloablative stress. Retinoic acid signaling, acting on both HSCs and niche cells, has emerged as a central regulator of this process. Among ME components, BM adipocytes (BMAs), which can comprise up to 45% of BM volume and expand dramatically during the pancytopenic phase after myeloablation, play a previously underappreciated role in hematopoietic recovery. Here, we identify retinoid X receptor (RXR) signaling in BMAs as a key regulator of the adipokine Resistin, which promotes HSC self-renewal and functional fitness by activating NF-{kappa}B signaling. Conditional loss of RXR in adiponectin-expressing cells suppressed Resistin production, resulting in reduced NF-{kappa}B activity in HSCs, impaired self-renewal, and defective multilineage hematopoietic regeneration. Functionally, in vivo Resistin neutralization impaired hematopoietic reconstitution, whereas supplementation with either monomeric or dimeric Resistin enhanced HSC self-renewal and long-term lympho-hematopoietic reconstitution in an NF-{kappa}B-dependent manner. Together, these findings establish BMA-derived Resistin as an RXR-dependent, critical extrinsic regulator of HSC self-renewal and regenerative hematopoiesis, underscoring its essential role in lympho-myeloid reconstitution after myeloablation. Disclosures: The authors declare no relevant conflicts of interest.

physiology↗

bioRxiv2025

The DDIT4L-TOM40-ATP5A pathway suppresses glioblastoma oncogenesis

The characteristics of glioblastoma (GBM), including resistance to cell death and aberrant energy metabolism, are associated with the function of mitochondria. To date, the inherent suppressors that couple mitochondrial function with cell death remain unclear. DNA damage-inducible transcript 4-like (DDIT4L) expression in human gliomas and its association with patient survival was determined by public databases, western-blot and immunostaining. The role of DDIT4L in regulating tumor growth was analyzed using lentivirus and PDX model. The mechanism of DDIT4L on GBM mitochondrial function was determined by different assays. Here, we show that DDIT4L is an endogenous inhibitor of GBM via suppressing mitochondrial function. DDIT4L was expressed at high levels in GBM and transported into mitochondria via single import channel TOM40 other than the import receptors TOM22, TOM20 or TOM70. Then, DDIT4L interacted with the subunit of ATP synthase, inhibited mitochondrial function and induced tumor cell apoptosis. Furthermore, the synthetic peptide DDIT4LV125-P132 suppressed GBM oncogenesis. Based on these results, DDIT4L suppresses GBM oncogenesis through both TOM40- and ATP5A-dependent mechanisms to curb mitochondrial dynamics and induce cell apoptosis, and the DDIT4LV125-P132 peptide is a potential therapy for GBM.

cancer biology↗

bioRxiv2025

The ORB2 RNA-binding protein represses translation of its target transcripts during the Drosophila maternal-to-zygotic transition via its functionally conserved Zinc binding 'ZZ' domain

Post-transcriptional regulation is particularly prominent during the maternal-to-zygotic transition (MZT), a developmental phase during which a large proportion of maternally provided mRNAs is repressed and cleared from metazoan embryos. RNA-binding proteins (RBPs) are key components of the post-transcriptional regulatory machinery. We show that the ORB2 RBP, the Drosophila ortholog of human Cytoplasmic Polyadenylation Element Binding Protein (hCPEB) 2-4 protein subfamily, binds to hundreds of maternally provided, rare-codon-enriched mRNAs in early embryos; that ORB2 targets are translationally repressed and unstable during the MZT; identify a U-rich motif enriched in ORB2 targets 3'UTRs; and show that this motif confers ORB2 binding and repression to a luciferase reporter mRNA in S2 tissue culture cells. When tethered to a luciferase reporter, ORB2 and hCPEB2 (but not ORB and hCPEB1) repress translation; the C-terminal Zinc-binding ( ZZ) domain of ORB2 is necessary and sufficient for repression. ORB2 interacts with a suite of post-transcriptional regulators in early embryos; a subset of these interactions is lost upon deletion of the ZZ domain, notably with the Cup repressive complex. ORB2-targets significantly overlap with those previously identified for the repressive RBP, Smaug (SMG). Analysis of the early embryos translatome in the presence or absence of the endogenous ZZ domain shows that mRNAs bound by ORB2 but not by SMG move onto polysomes upon ZZ domain deletion whereas co-bound transcripts do not, consistent with co-regulation of the latter set of transcripts by both RBPs. Our results assign a function to the ZZ domain and position ORB2 in the post-transcriptional network that regulates maternal transcripts during the Drosophila MZT. ARTICLE SUMMARYWe show that Drosophila ORB2, the ortholog of the human CPEB2 RNA-binding protein, negatively regulates its target mRNAs during the maternal-to-zygotic transition via its C-terminal Zinc-binding ( ZZ) domain.

genetics↗

bioRxiv2025

Evolutionary Genomics Guides Scalable Coral Probiotics for Climate Resilience

A universal bottleneck limiting probiotic efficacy in medicine, aquaculture, agriculture, and wildlife conservation is uncertain long-term colonization, necessitating repeated administration. We present an evolution-guided framework for probiotic identification based on genomic hallmarks of emerging host dependency, including widespread pseudogenization and insertion sequence proliferation driving genomic restructuring. Applied to coral reefs, we screened over 1,200 coral-associated bacterial isolates and identified Ruegeria MC10 as exhibiting these signatures. Its presence was associated with increased thermal tolerance of a model cnidarian. Following nursery application, MC10 persisted in reef corals for an 8-month monitoring period through a natural bleaching event, improving color retention and retaining algal photosynthesis performance. This work establishes a predictive, scalable pipeline for selecting persistent probiotics, directly addressing a central constraint on microbiome-based interventions across host systems.

microbiology↗

bioRxiv2025

PhysDock: A Physics-Guided All-Atom Diffusion Model for Protein-Ligand Complex Prediction

Accurate prediction of protein-ligand complexes remains a central challenge in structural biology. Traditional methods are computationally inefficient and prone to local minima, whereas deep learning approaches struggle to capture structural flexibility and physical plausibility. We introduce PhysDock, a physics-guided diffusion model that uniquely integrates (i) all-atom diffusion to model ligand flexibility and protein precision-flexibility (i.e., subtle conformational adjustments); (ii) physical priors as diffusion conditioning, alongside two-phase physics guidance during the denoising diffusion to ensure physical plausibility. PhysDock demonstrates state-of-the-art performance in redocking benchmarks and excels in the more challenging cross-docking assessments. For practical utility, PhysDock (i) resolves cannabinoid receptor selectivity across diverse molecules, achieving accuracy comparable to experiments; (ii) distinguishes most drug candidates from weak binders in virtual screening of NTRK3 kinase, while uncovering novel candidates with structural insights. PhysDock serves as a versatile tool for protein-ligand complex prediction, with substantial potential to accelerate structure-based drug discovery.

bioinformatics↗

bioRxiv2025

Proterozoic Tectonic Drivers Underpin Flavobacterial Diversification

Flavobacteria are keystone taxa in global carbon cycling, degrading complex glycans in marine and terrestrial ecosystems. In both environments, polysaccharides constitute a major fraction of organic matter but differ in origin: marine glycans primarily derive from micro- and macroalgae, while terrestrial counterparts originate from land plants. Flavobacteria deploy distinct suites of carbohydrate-active enzymes (CAZymes) tailored to these habitat-specific substrates, yet the evolutionary drivers of their diversification remain unresolved. Two competing hypotheses exist: one posits glycan specialization as the primary driver of divergence, while the other implicates extrinsic geological factors in shaping their evolution. By integrating mitochondrial- and plastid-based molecular clocks with eukaryotic fossil calibrations, we infer that flavobacteria emerged between 2.15 and 1.98 billion years ago (Gya), shortly after the Great Oxidation Event (GOE; 2.4-2.32 Gya). Subsequent diversification involved three independent marine-to-non-marine transitions during the Proterozoic Eon (1.98-1.70 Gya, 1.72-1.40 Gya, and 1.28-1.14 Gya), temporally aligned with the formation and the fragmentation of the Columbia supercontinent and preceded the evolution of the major glycan contributors in both marine and non-marine niches. This temporal mismatch disfavors the glycan specialization hypothesis, instead implicating tectonic-driven habitat shifts as the primary driver of lineage diversification. Non-marine flavobacteria exhibited higher turnover but lower net diversification rates than marine counterparts, reflecting the challenges of adapting to fragmented non-marine niches. Genome erosion and deleterious mutation accumulation further constrained reverse transitions, locking lineages into non-marine habitats. Our findings highlight Proterozoic tectonics, rather than substrate-specific CAZyme innovation, as the catalyst for flavobacterias evolutionary success across Earths carbon-rich biomes.

evolutionary biology↗