Biology subjects

Xu, Y.

Publications and source records attributed to Xu, Y..

At least 163 records · Page 9Linked to original sources

bioRxiv2026

Hepatic Ketogenesis Attenuates Cardiac Hypertrophy via Metabolic Reprogramming

BackgroundHeart failure with preserved ejection fraction (HfpEF) is increasingly recognized as a multisystem disorder linked to the cardiovascular-kidney-metabolic (CKM) syndrome. While the falling heart undergoes metabolic reprogramming, the interorgan crosstalk regulating myocardial substrate preference in HFpEF remains elusive. We aimed to clarify the role of systemic and local ketogenesis in the pathogenesis of cardiac hypertrophy and HFpEF. MethodsA mouse model of HFpEF was employed using a high-fat diet combined with NG-Nitro-L-arginine methyl ester hydrochloride (L-NAME). Cardiac hypertrophy and systemic metabolic profiling including ketogenesis were evaluated. To dissect the role of site-specific ketogenesis, we generated inducible cardiomyocyte-specific (Hmgcs2{Delta}iCM) and hepatocyte-specific (Hmgcs2{Delta}Hep) knockout mice of HMG-CoA synthase 2 (Hmgcs2), deficient in the rate-limiting enzyme for ketogenesis. Cardiomyocyte -specific nuclei were isolated for transcriptomic (RNA-seq) and in vitro assays in H9C2 cells were used to elucidate molecular mechanisms. ResultsThe HFpEF model successfully exhibited diastolic dysfunction, impaired exercise capacity and cardiac hypertrophy with elevated circulating ketone body concentration. Myocardial metabolomics and snRNA-seq identified a profound metabolic shift characterized by the accumulation of long-chain fatty acids and Krebs cycle intermediates, coupled with the transcriptional downregulation of insulin signaling and fatty acid degradation pathways. Although circulating ketone body level was upregulated, Hmgcs2{Delta}iCM mice showed no exacerbation of the HFpEF phenotype. In contrast, Hmgcs2{Delta}Hep mice exhibited significantly aggravated cardiac hypertrophy (HW/TL; Hmgcs2flox: 7.41 {+/-} 0.87: Hmgcs2{Delta}Hep: 8.29 {+/-} 0.73; p = 0.0154). Mechanistically, hepatic ketogenesis was required to maintain circulating beta-hydroxybutyrate (BHB) levels, which directly modulated cardiomyocyte metabolism. BHB acted as a metabolic signal to dampen fatty acid overload and facilitate glucose utilization. ConclusionsOur study identifies a critical "liver-heart axis" where hepatic ketogenesis serves as an essential regulator of myocardial metabolic resilience. Impaired hepatic ketogenesis creates a metabolic mismatch that drives pathological cardiac remodeling. These findings highlight the liver as a therapeutic target within the CKM syndrome framework, suggesting that restoring the hepato-cardiac metabolic bridge may ameliorate HFpEF progression. What is New?O_LIThis study identifies a novel liver-adipose-heart axis that governs myocardial metabolic resilience during the development of heart failure with preserved ejection fraction (HFpEF). C_LIO_LIWe demonstrate that while both the liver and heart upregulate ketogenesis under metabolic stress, only hepatic ketogenesis--and not cardiac-intrinsic ketogenesis--is essential for mitigating pathological cardiac remodeling. C_LIO_LIMechanistically, liver-derived {beta} -hydroxybutyrate acts as a critical C_LIO_LIendocrine signal that dampens fatty acid oxidation and facilitates myocardial glucose utilization. C_LI What Are the Clinical Implications?O_LIOur findings highlight the liver as a central therapeutic target within the cardiovascular-kidney-metabolic (CKM) syndrome framework, where hepatic metabolic failure directly drives cardiac dysfunction. C_LIO_LIRestoring the hepato-cardiac metabolic bridge, through either hepatic-targeted therapies or ketone body supplementation, represents a promising strategy to enhance myocardial metabolic flexibility and ameliorate HfpEF in patients with multi-organ metabolic disorders. C_LI

biochemistry↗

bioRxiv2026

Semantic-Guided Spatial Representation Learning for Spatial Domain Identification

MotivationSpatial domain identification is a fundamental task in spatial transcriptomics analysis, aiming to partition tissue sections into coherent regions that reflect underlying biological organization. Most existing methods rely on gene expression similarity and spatial proximity, which can be insufficient when expression measurements are sparse, noisy, or weakly discriminative. In such settings, representation learning faces ambiguity in determining how spatial neighborhood information and expression-based similarity should be jointly utilized. ResultsWe present GreS, a spatial domain identification framework that incorporates gene-level semantic priors into spatial representation learning. GreS models spatial adjacency and expression-driven similarity using two complementary neighborhood graphs and leverages aggregated gene semantic information to guide how these views are weighted at the spot level. Rather than redefining neighborhood relationships, semantic priors act as contextual signals that modulate the relative contribution of spatial and expression-based cues during domain inference. We evaluate GreS on diverse spatial transcriptomics datasets, including layered brain tissue, embryonic development, and heterogeneous tumor microenvironments. Across these settings, GreS consistently identifies spatial domains that are structurally coherent and biologically interpretable, outperforming existing methods in quantitative accuracy and qualitative spatial organization. Our ablation analyses further demonstrate that performance gains arise from biologically meaningful and properly aligned semantic information, rather than from increased model complexity or auxiliary features. Availability and Implementationhttps://github.com/ai4nucleome/GreS Contactyanlinzhang@hkust-gz.edu.cn Supplementary InformationA Supplementary file is submitted together with this manuscript.

bioinformatics↗

bioRxiv2026

Visualizing Interchromosomal Interactions at Sub-Megabase Resolution Using Network Clustering Coefficients

Specific interchromosomal interactions involve communication between non-homologous chromosomes, enabling coordinated genomic activities such as gene regulation. However, because these communications are often embedded within a nonspecific and noisy background of contact interactions, it is essential to annotate these interaction patterns at the resolution of genomic positions. Such annotation facilitates clean visualization and comparison with linear genomic features to reveal underlying biological functions. We developed and validated a set of network-based metrics as cross-chromosomal interaction descriptors that bridge complex 3D genome structures and 1D functional genomics. By utilizing graph-theoretic representations, these network-based features succinctly summarize complex inter-chromosomal relationships. We constructed a graph representation of contact interactions derived from Hi-C data and implemented three annotations that capture the distinct "many-body" nature of the interactions. Among these, we demonstrate that {Delta}C4 (a cis-contact-mediated 4-cycle interaction metric) is superior to both {Delta}C3 (a cis-contact-mediated 3-cycle metric) and C4E (a direct 4-cycle metric of trans contacts) at filtering noise and providing the most straightforward interpretation. Applying these metrics to chromosomes 17, 19, and 22 of the GM12878 cell line, we found clear evidence that different chromosomes rely on a shared set of interaction hot spots to communicate. Overall, this network-based framework reveals distinct chromosomal regulation patches and provides insight into how chromosomes associate with each other and organize relative to the nuclear envelope.

genomics↗

bioRxiv2026

Library transgenesis in zebrafish through delayed site-specific mosaic integration for in vivo pooled screening of transgenes

Functional screening through systematic deletion, editing or addition of libraries of genes is a powerful approach for discovering gene functions and developing improved molecular tools. However, due to the need for high throughput, such campaigns are typically conducted in vitro, leading to many discoveries, especially tools and therapeutics, which fail to translate in vivo. Tissue context, cellular physiology, and systemic regulation shape both tool performance and gene function in ways that simplified culture systems cannot predict. Pooled in vivo screening methods have the potential to enable screening within living animals while preserving the physiological context, but current approaches using viral vectors face three critical limitations: multi-transgene insertions per cell confound genotype-phenotype association, viral packaging constrains transgene size, and cell-type tropism restricts and biases targeting. Here, we introduce a zebrafish library transgenesis method that overcomes these limitations through delayed site-specific mosaic integration. We exploit a temporal delay between library microinjection with PhiC31 mRNA, and library integration, to allows the library to spread episomally throughout the developing embryo before integration begins. This produces mosaic animals where each cell independently integrates one randomly-selected library member, enforced by a single genomic AttP landing site. We demonstrate delivery of multi-kilobase transgenes with high library coverage of 1,378-1,989 unique integrants per animal, and single-transgene-per-cell in [~]99% of brain cells. This method provides a platform for direct in vivo screening of large transgene libraries with single-transgene precision, with potential applications in both biological discovery and tool development.

bioengineering↗

bioRxiv2026

Surf2Spot: A Surface-Informed Geometry-Aware Model for Predicting Binder and Nanobody Design Hotspots

Protein-protein interactions (PPIs) and nanobody-antigen interactions (NAIs) play essential roles in cellular function, yet accurate hotspot prediction remains challenging. We present Surf2Spot, a deep learning framework that integrates sequence embeddings, structural features, and protein surface properties to predict interaction hotspots. By jointly modeling structural and physicochemical determinants, Surf2Spot achieves superior performance on curated PPI and NAI datasets, improving F1-scores by 45.9-46.9% and AUPRC by 43.2% over existing methods. Case studies on NbPDS1 and VdPDA1 demonstrate that Surf2Spot accurately recovers experimentally validated hotspots clustered within functional domains. When incorporated into binder design pipelines (RFdiffusion and BindCraft), Surf2Spot-guided designs yielded a 4-fold increase in successful design throughput and enhanced binding affinities compared to baseline strategies. These results establish Surf2Spot as a powerful tool for hotspot discovery and rational protein engineering.

bioinformatics↗

bioRxiv2026

The C. elegans nervous system reads the internal state of the hydrogen peroxide-detoxification machinery to trigger escape from this common reactive chemical

Hydrogen peroxide (H2O2) is the most common reactive chemical threat faced by organisms. Here, we map the neural circuit that drives chemotactic escape from environmental H2O2 in the nematode C. elegans. Twenty-four neuron classes with sensory endings at the mouth and nose of the animal detect H2O2. Their response dynamics encode stimulus intensity and exposure history, and their partial redundancy makes avoidance resilient to the loss of individual inputs. Sensing begins when H2O2 oxidizes the peroxidatic and resolving cysteines of the cytosolic peroxiredoxin PRDX-2, which relays this oxidative signal to cysteines on the LITE-1 and GUR-3 ion channels, triggering calcium influx in sensory neurons that drive escape. Most of these neurons release glutamate to drive H2O2-dependent excitation of AIA interneurons, whereas others signal through non-glutamatergic routes, providing multiple routes for signal transmission. Thus, the C. elegans nervous system acts as a hydrogen peroxide sentinel that monitors H2O2-induced changes in the intracellular H2O2-detoxification machinery and relays them to interneurons driving organism-wide escape. This raises the possibility that circuit defects in aging and neurodegenerative disease arise from altered peroxiredoxin-mediated H2O2 signaling rather than primarily from direct macromolecular damage.

neuroscience↗

bioRxiv2026

Precursor-Dependent Routing of Aromatic Amino Acids Determines Lignin Structure in Grasses by Sensitivity-Enhanced Solid-State NMR

Lignin biosynthesis in grasses exhibits unique metabolic flexibility, yet the precursor-specific routing of carbon into lignin polymers remains poorly resolved in planta. Here, we combine 13C-isotope labeling with solid-state NMR under sensitivity-enhancement by dynamic nuclear polarization (DNP), to directly track phenylalanine- and tyrosine-derived carbon incorporation into the lignin polymer in Brachypodium distachyon. Precursor-specific 13C labeling reveals that phenylalanine is the dominant contributor to canonical guaiacyl and syringyl lignins, whereas tyrosine preferentially enriches hydroxyphenyl lignin and hydroxycinnamates, including ferulates characteristic of grass cell walls. Two-dimensional 13C-13C correlation NMR resolves distinct lignin moieties arising from each precursor. Disruption of p-coumarate 3-hydroxylase (C3H) selectively impairs phenylalanine-derived lignification, while tyrosine-derived lignin remains comparatively unchanged, maintaining polymer assembly through alternative metabolic routes. These findings show precursor-dependent control of lignin composition and reveal tyrosine-mediated lignification as a compensatory pathway in grasses. This work also establishes precursor-resolved solid-state NMR and DNP as a powerful framework for dissecting lignin biosynthesis and metabolic plasticity in plant cell walls. SIGNIFICANCE STATEMENTLignin is a complex plant polymer that strengthens cell walls but also limits the efficiency of biomass processing for agriculture and bioenergy. Grasses possess a unique lignin biosynthetic flexibility that is not well understood. By combining stable isotope labeling with solid-state NMR spectroscopy, we directly traced how the aromatic amino acids, phenylalanine and tyrosine, contribute differently to lignin formation in intact grass cell walls. We show that phenylalanine primarily builds conventional lignin structures, whereas tyrosine supplies alternative phenolic components and maintains lignin synthesis even when a key biosynthetic enzyme is disrupted. This metabolic flexibility helps explain the unique structural aspects of grass cell walls and identifies precursor-level control as a promising strategy for engineering lignin composition to improve biomass utilization.

plant biology↗

bioRxiv2026

Construction and Immunogenicity Detection of Canine Parvovirus-like Particles Fusion with Canine Febrile Antigen Epitopes

This study aimed to design and evaluate the immunogenicity of a dual-valent virus-like particles (VLP) vaccine that can simultaneously target Canine distemper virus (CDV) and Ca nine parvovirus virus (CPV).By bioinformatic analysis, conserved antigen epitopes of the three major functional proteins of CDV were screened and inserted into CPV-VP2 proteins by two different methods to construct recombinant expression plasmids CDPV1 versus CDPV2.Thr ee-dimensional structure, hydrophobicity and stability predictions of the two recombinant proteins showed that their hydrophobicity were 0.233 and 0.251, and their structural stability scores were 0.77 and 0.78, respectively.Recombinant plasmids were co-transformed with molecular chaperone pTf16 to be expressed in E. coli BL21(DE3), respectively, and the optimal expression conditions were determined after optimization: 0.25 mmol/L IPTG, 2 g/L L-arabinose in duction, and culture at 25{degrees}C for 16 h.Purified recombinant proteins can self-assemble in vitro to form VLPs about 23.5 nm in diameter with a hemagglutination titer of 1:29.The mouse immune test showed that the hemagglutination inhibition titer peaked on the 7th day after the third immunization, and the neutralizing Antibody level could reach up to 1:28.The CPV VLP s constructed in this institute carrying CDV antigen epitopes were able to successfully assemble in vitro and were well immunogenic, providing experimental basis for the development of a canine polyvalent vaccine.

immunology↗

bioRxiv2026

THIK-1 channel mediates microglial glucose sensing and modulates AgRP neurons

Microglia play essential roles in maintaining energy homeostasis, and their dysfunction contributes to metabolic disease. Although high-fat diet (HFD) exposure induces microglial activation, the underlying mechanisms remain poorly defined. Here, we identified a previously unrecognized role for THIK-1 channel in mediating glucose sensing of microglia in arcuate nucleus of the hypothalamus (ARH), during HFD-induced obesity. Pharmacological inhibition of THIK-1 channel with tetrapentylammonium (TPA) suppresses feeding and attenuates body-weight gain in diet induced obese mice. Mechanistically, inhibition of agouti-related peptide (AgRP) neurons is indispensable for TPA-induced hypophagia. Moreover, THIK-1 inhibition promotes microglial phagocytosis of perineuronal nets (PNNs), leading to reduced AgRP neuronal activity and feeding suppression. Together, these findings establish THIK-1 as a critical glucose sensor in hypothalamic microglia and uncover a microglia-dependent pathway through which overnutrition modulates AgRP neuronal activity via PNN remodeling to regulate energy balance, highlighting THIK-1 as a potential therapeutic target for treatment of diet-induced obesity.

neuroscience↗

bioRxiv2026

A Bear-Specific Coding Exon in TMEM41B Is Associated with Cold Adaptation

AbstractBears exhibit an unusual form of hibernation in which core body temperature remains relatively high despite profound suppression of whole-body metabolism. How such a warm yet hypometabolic state is achieved remains poorly understood. Here, through integrative analysis of 238 RNA-seq datasets spanning seven species, we identify transmembrane protein 41B (TMEM41B) as an evolutionarily conserved factor associated with thermogenic capacity. Loss of Tmem41b in mice and Drosophila results in severe cold intolerance, whereas its overexpression enhances thermogenic performance, supporting a conserved role in heat production. Comparative genomic analyses reveal a bear-specific 51-amino acid N-terminal extension in TMEM41B, arising from a 5' untranslated region mutation that converts a premature stop codon into coding sequence. Interactome profiling indicates that this bear-specific isoform differs from the canonical TMEM41B in its protein interaction landscape, including reduced association with components of mitochondria-associated endoplasmic reticulum membranes such as voltage-dependent anion-selective channel protein 1 (VDAC1). Consistent with this altered interaction profile, the extended isoform is associated with reduced mitochondrial oxidative activity. Functional analyses further suggest that the 51- amino acid extension modulates multiple cellular programs, including suppression of oxidative phosphorylation and myogenic differentiation alongside activation of osteogenic pathways, collectively biasing cells toward a hypometabolic state. Notably, expression of the polar bear TMEM41B isoform in mice induces a torpor-like phenotype under fasting conditions. Together, these findings identify TMEM41B as a conserved regulator of thermogenic capacity and suggest that evolutionary modification of its N terminus may contribute to metabolic suppression and energy conservation during bear hibernation.

evolutionary biology↗

bioRxiv2026

Python metabolomics uncovers a conserved postprandial metabolite and gut-brain feeding pathway

Most mammals consume small and frequent meals. By contrast, pythons are ambush predators that exhibit extreme feeding and fasting patterns and provide a unique model for uncovering molecular mediators of the postprandial response1-3. Using untargeted metabolomics, here we show that circulating levels of the metabolite para-tyramine-O-sulfate (pTOS) are increased >1,000-fold in pythons after a single meal. In pythons, pTOS production occurs in a microbiome-dependent manner via sequential decarboxylation and sulfation of dietary tyrosine. In both pythons and mice, pTOS administration activates a neural population in the ventromedial hypothalamus (VMH). In mice, these VMH neurons are required for the anorexigenic effects of pTOS. Chronic administration of pTOS to diet-induced obese male mice suppresses food intake and body weight. pTOS is also present in human blood, where its levels are increased after a meal. Together, these data uncover a conserved postprandial anorexigenic metabolite that links nutrient intake to energy balance.

physiology↗

bioRxiv2026

Convergence of Cortical and Thalamic Origins of Free Behavior Modulation of Mouse Primary Visual Cortex

The quality of sensory information flow in the brain may be affected by uninstructed free animal behavior. However, the specific circuit pathways that merge sensory and free behavior remain obscure. In mouse primary visual cortex (V1), we combine two-photon calcium imaging of cortical neurons and thalamo-cortical LGN (lateral geniculate nucleus) boutons with simultaneous measurements of facial movements. When controlling for spurious time-structured nonsense correlations, we observed representations of both eye movements and non-ocular facial movement features in both LGN bouton and V1 cortical neuron activity during grating input stimulation. Further, the correlation between V1 neurons and facial movement is larger for grating stimulation compared to blank stimulation, likely due to the integration of LGN inputs and modulation of V1 from higher brain centers during grating stimulation. Together, our results suggest a convergence of uninstructed non-visual signals from a persistent top-down pathway and a stimulus-gated bottom-up pathway in primary visual cortex.

neuroscience↗

bioRxiv2026

Probiotic phage steering of disease suppressive rhizosphere microbiome

Current phage therapy approaches predominantly focus on targeting pathogenic bacteria, overlooking the vast potential of phages that interact with beneficial, plant growth-promoting (probiotic) bacteria. Here we tested if a single phage targeting a probiotic Stenotrophomonas maltophilia bacterium can steer the rhizosphere microbiome disease suppressiveness against Ralstonia solanacearum phytopathogen. We find that S. maltophilia quickly evolves resistance to its phage via mutations in ssb and TonB genes and by upregulating anti-phage defense systems. Crucially, evolution of phage resistance reprograms the bacterial transcriptome and metabolome, leading to unexpectedly enhanced antimicrobial activity against the R. solanacearum. Furthermore, exposing S. maltophilia to phage in the tomato rhizosphere increases the microbiota-wide disease suppressiveness by stabilizing bacterial diversity and facilitating pathogen suppression by other resident species. Our findings suggest that probiotic-specific phages could be used as ecological and evolutionary engineers to steer the rhizosphere microbiome disease suppressiveness through activation of antagonistic bacterial interactions.

evolutionary biology↗

bioRxiv2025

The inactivation of DHHC7 in mouse liver promotes diet-induced obesity through a hepatic Prg4-GPR146 axis

The liver secretes hepatokines that coordinate whole-body metabolism. Posttranslational lipidation of signaling proteins by DHHC palmitoyltransferases controls membrane targeting and signaling, yet the role of hepatic palmitoylation in systemic metabolic regulation is largely unexplored. Using an inducible, liver-specific DHHC7 knockout (D7LKO) mouse, we report that loss of DHHC7 in hepatocytes potentiates adenylyl cyclase-PKA-CREB signaling through reducing palmitoylation of inhibitory G protein subunit (Gi), leading to transcriptional elevation and secretion of proteoglycan 4 (Prg4). Elevated circulating Prg4 acts on adipocytes by binding GPR146 via Prg4s N-terminal SMB domain, suppressing adipocyte PKA substrate phosphorylation and hormone-sensitive lipase (HSL) Ser563 phosphorylation, thereby impairing lipolysis. Under high-fat diet (HFD) feeding, D7LKO mice and mice with adenoviral hepatic Prg4 overexpression develop pronounced obesity characterized by increasing brown, subcutaneous, and visceral fat mass and adipocyte hypertrophy; strikingly, these animals show little impairment in glucose tolerance or circulating triglycerides but display elevated plasma cholesterol. Conditioned medium containing Prg4 recapitulates suppression of adipocyte HSL phosphorylation in vitro, and SMB-deleted Prg4 fails to bind GPR146 or inhibit HSL phosphorylation. Our findings define a liver palmitoylation- hepatokine axis that controls adipose lipolysis and predisposes to diet-induced fat accumulation, establishing Prg4-GPR146 as a mechanistic link between hepatic signaling and adipose energy mobilization.

physiology↗

bioRxiv2025

Chromatin profiling for everyone: FFPE-CUTAC for the theory and practice of modern molecular biology

In 2025, together with the Fred Hutch Summer Undergraduate Research and Summer High School Internship programs, we developed and implemented a laboratory genomics research experience to introduce students to modern molecular biology techniques and bioinformatics. The course centered around using a new method we had developed in 2023 that uses readily available fixed tissue sections on glass slides. Students performed a series of steps to tagment genomic locations of RNA Polymerase II and then used PCR to enrich libraries for next-generation sequencing in a core facility. Students then visualized their data in genomic browser tracks and assessed the results. At the end of the summer, students prepared and presented their work and experiences in seminar format to their cohorts. Overall, the technical simplicity of on-slide chromatin profiling introduced the students to laboratory practice and current techniques in genomics, bioinformatics, and medical sciences.

scientific communication and education↗

bioRxiv2025

Ensemble-DeepSets: an interpretable deep learning framework for single-cell resolution profiling of immunological aging

Immunosenescence increases susceptibility to infection and reduces vaccine responsiveness, yet bulk transcriptomic clocks obscure the cellular heterogeneity underlying this process. Here, we present IDEAL-Age, an interpretable deep learning framework that operates directly on single-cell PBMC transcriptomes. Benchmarking against 31 methods across independent cohorts demonstrates superior predictive performance. The frameworks interpretability uncovers linear and non-linear transcriptomic dynamics that reveal phase-specific physiological transitions, and identifies pro-youthful or pro-aging cellular contributions. Application to systemic lupus erythematosus (SLE) reveals accelerated immunological aging driven by interferon-associated monocyte shifts. IDEAL-Age establishes a high-resolution computational framework for deciphering systemic immune aging.

bioinformatics↗

bioRxiv2025

Engineered translation release factor 1 suppresses disease-causing nonsense mutations and enables multi-site nonstandard amino acids incorporation

Nonsense mutations convert sense codons into premature termination codons (PTC), resulting in early termination of translation of mRNAs, underlie [~]11% of human genetic diseases. Restoring translation of genes carrying nonsense mutations remains a major therapeutic challenge. Here we present OPENER (Overexpression of Protein-engineered eRF1 for Nonsense Elision and Readthrough), a strategy to efficiently suppress nonsense mutations based on engineered variants of the eukaryotic translation termination factor eRF1. Through saturation mutagenesis of the human eRF1 N-domain, we identified variants, notably eRF1S77E, that promote efficient readthrough of all three PTCs (UAG, UGA, UAA) and rescue 12 pathogenic PTCs reporters in multiple disease contexts. Systemic delivery of OPENER-S77E via AAV8 in a Duchenne muscular dystrophy mouse model (DmdQ995X) restored dystrophin expression, improved muscle function, and ameliorated pathology without detected toxicity. Furthermore, when combined with orthogonal engineered aminoacyl-tRNA synthetase/tRNA pairs, OPENER-S77E enabled efficient, multi-site incorporation of nonstandard amino acids (BocK and AzF) into a single protein in mammalian cells, achieving efficiency of 27.77% and 19.83%, respectively. The incorporation efficiency of BocK was further enhanced to 32.80% in conditional eRF1-knockout cells. OPENER thus provides a platform for treating nonsense-mediated diseases and expands the synthetic biology toolkit for precise protein engineering.

synthetic biology↗

bioRxiv2025

Vulnerability and adaptations to climate change in EU protected areas: a Natura 2000 managers' perspective

The Natura 2000 (N2K) network is a key conservation instrument in the European Union, but its effectiveness is challenged by climate change. We surveyed 382 N2K managers to investigate their perceptions of climate change and related site adaptation strategies. Warming and precipitation shifts were frequently perceived as threats, with vulnerability of N2K sites highest in the Mediterranean and lowest in the Boreal region. Our results suggest that the official N2K site information stored in the Standard Data Forms greatly under-report managers assessment of vulnerability. Around half of the surveyed managers implemented adaptation strategies, which, when characterised following a Resist-Accept-Direct framework, aimed not only at resisting, but also at directing and accepting the effects of climate change. Managers also highlighted the need for scientific knowledge on local vulnerability and increased funding to improve the implementation of adaptation strategies inside protected areas.

ecology↗