Browse Articles

Author Correction: Prediction of the transient coolant jet released from the nose cone at supersonic flow via machine learning

Solanum pan-genetics reveals paralogues as contingencies in crop engineering

Abstract Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops1,2. A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops (that is, those locally cultivated within a circumscribed area)3–5 to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops6,7. Here, by establishing a pan-genome of the crop-rich genus Solanum 8 and integrating functional genomics and pan-genetics, we show that gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression and function. By augmenting our pan-genome with African eggplant cultivars9 and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size. The loss of a redundant paralogue of the classical fruit size regulator CLAVATA3 (CLV3)10,11 was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy, followed by a large cultivar-specific deletion, created a single fused CLV3 allele that modulates fruit organ number alongside an enzymatic gene controlling the same trait. Our findings demonstrate that paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species.

Cathepsin D inhibits AGEs-induced phenotypic transformation in vascular smooth muscle cells

Systematic bone tool production at 1.5 million years ago

A two-sample Mendelian randomization study of type 1 diabetes and the risk of 22 site-specific cancers

Abstract Previous observational studies have suggested a potential link between Type 1 Diabetes (T1D) and site-specific cancer risk. However, the nature of this association remains uncertain due to confounding factors, reverse causation, and biases inherent in observational research. To address this gap, we conducted a two-sample Mendelian randomization (MR) study to assess the causal relationship between T1D and 22 site-specific cancers. Using summary statistics from large-scale genome-wide association studies of European ancestry, comprising data on T1D (N = 520,580) and the 22 site-specific cancers, we selected single nucleotide polymorphisms strongly associated with T1D as instruments for our analysis. Causal relationships were primarily evaluated through inverse-variance weighting-based analyses, supplemented by three additional methods: MR-Egger, weighted median, and mode-based estimate. Sensitivity analyses were performed, excluding genetic variants with potential pleiotropic effects. The finding demonstrated a causal association between T1D and increased risks of lung cancer (OR = 1.018, 95% CI 1.004–1.033, p = 0.011), colorectal cancer (OR = 1.022, 95% CI 1.003–1.041, p = 0.019), and prostate cancer (OR = 1.018, 95% CI 1.005–1.030, p = 0.006). Conversely, T1D was associated with decreased risks of breast cancer (OR = 0.989, 95% CI 0.981–0.998, p = 0.016), lymphoma (OR = 0.999, 95% CI 0.974–0.999, p = 0.003), malignant melanoma (OR = 0.999, 95% CI 0.989–0.999, p = 0.001), and non-melanoma skin cancer (OR = 0.999, 95% CI 0.899–0.999, p = 0.003). Our MR study provides an evidence of causal association between T1D and altered risks of various site-specific cancers. Further research is recommended to validate this finding in diverse populations to enhance the generalizability of findings across different ethnic groups.

Phosphate-enabled mechanochemical PFAS destruction for fluoride reuse

Abstract Perfluoroalkyl and polyfluoroalkyl substances (PFASs) are persistent, bioaccumulative and anthropogenic pollutants that have attracted the attention of the public and private sectors because of their adverse impact on human health1. Although various technologies have been deployed to degrade PFASs with a focus on non-polymeric functionalized compounds (perfluorooctanoic acid and perfluorooctanesulfonic acid)2–4, a general PFAS destruction method coupled with fluorine recovery for upcycling is highly desirable. Here we disclose a protocol that converts multiple classes of PFAS, including the fluoroplastics polytetrafluoroethylene and polyvinylidene fluoride, into high-value fluorochemicals. To achieve this, PFASs were reacted with potassium phosphate salts under solvent-free mechanochemical conditions, a mineralization process enabling fluorine recovery as KF and K2PO3F for fluorination chemistry. The phosphate salts can be recovered for reuse, implying no detrimental impact on the phosphorus cycle. Therefore, PFASs are not only destructible but can now contribute to a sustainable circular fluorine economy.

Influential nodes identification for complex networks based on multi-feature fusion

Protein sequence modelling with Bayesian flow networks

Optimizing structural integrity of a pressure vessel via finite element analysis and machine learning based XGBoost approaches

Solidification of Earth’s mantle led inevitably to a basal magma ocean

Abstract One of the main interpretations of deep-rooted geophysical structures in the mantle1 is that they stem from the top-down solidification of the primitive basal magma ocean of Earth above the core2–6. However, it remains debated whether solids first formed at the bottom of the mantle, solidifying upward, or above the melts, solidifying downward. Here we show that gravitational segregation of dense, iron-rich melts from lighter, iron-poor solids drives mantle evolution, regardless of where melting curves and geotherms intersect. This process results in the accumulation of iron-oxide-rich melts above the core, forming a basal magma ocean. We numerically model mantle solidification using a new multiphase fluid dynamics approach that integrates melting phase relations and geochemical models. This enables estimating the compositional signature and spatial distribution of primordial geochemical reservoirs, which may be directly linked to the isotopic anomalies measured in Archean rocks7–11. We find that a substantial amount of solids is produced at the surface of the planet, not at depth, injecting geochemical signatures of shallow silicate fractionation in the deep mantle. This work could serve as a foundation for re-examining the intricate interplay between mantle dynamics, petrology and geochemistry during the first thousand million years of the evolution of rocky planets.

Plasmid-driven strategies for clone success in Escherichia coli

Jorunnamycin A induces apoptosis in pancreatic ductal adenocarcinoma cells, spheroids, and patient-derived organoids by modulating KRAS-mediated survival pathways

Author Correction: The dynamics of plasmon-induced hot carrier creation in colloidal gold

Impact of carbon nanodot uptake on complex impedance charge transport and energy storage mechanism in aloe vera leaves

Pathogenic mutation impairs functional dynamics of Hsp60 in mono- and oligomeric states

Addressing cross-population domain shift in chest X-ray classification through supervised adversarial domain adaptation

Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences

Abstract Pathogen genomics can provide insights into underlying infectious disease transmission patterns1,2, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential3–5. In particular, genetically proximal viruses should be highly informative about transmission events as genetic proximity indicates epidemiological linkage. Here we use pairs of identical sequences to characterize fine-scale transmission patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age and residence location information between March 2021 and December 2022. This corresponds to 59,660 sequences with another identical sequence in the dataset. We find that the location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postcodes with male prisons, consistent with transmission between prison facilities. We find that transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. Overall, this study improves our ability to use large pathogen genome datasets to understand the determinants of infectious disease spread.

Crypt density and recruited enhancers underlie intestinal tumour initiation

GWAS meta-analysis using a graph-based pan-genome enhanced gene mining efficiency for agronomic traits in rice

Increased risk of cardiomyopathy in individuals with methamphetamine related disorders in Taiwan

Abstract To explore whether Methamphetamine-related disorders (MRDs) will cause the risk of cardiomyopathy in the future. This study used Taiwan’s Longitudinal Generation Tracking Database (LGTD) to conduct a 1:4 paired analysis of sex, age, and inclusion year. 17,071 patients with MRDs and 153 patients with cardiomyopathy were selected; 68,264 patients without MRDs and 274 patients with cardiomyopathy were also selected. This study used SPSS 22 statistical software to conduct Cox regression analysis. Patients with MRDs had a 3.421-folds higher risk of cardiomyopathy than patients without MRDs. Men have a 0.735-fold lower risk of developing cardiomyopathy than women. In terms of age group, aged 50–64 and ≧ 65 have a 1.145- and 1.332-folds higher risk of cardiomyopathy, respectively, compared to those aged 20–49. For each one-point increase in Charlson Comorbidity Index (CCI), the risk of cardiomyopathy rises by 58.3%. Specifically, for three types of Methamphetamines (Methamphetamine and other psychostimulant dependence, Methamphetamine or related acting sympathomimetic abuse, Methamphetamine psychosis), the HR for cardiomyopathy in patients with MRDs was 3.864 (p < 0.001), 2.916 (p < 0.001), and 2.295 (p = 0.016) times higher, respectively, compared to patients without MRDs. The Kaplan-Meier log-rank test was used to calculate the cumulative risk of MRDs, showing a significant difference in the cumulative cardiomyopathy incidence between the MRDs and non-MRDs groups (long-rank test, p < 0.001). MRDs will increase the risk of cardiomyopathy. Women are more susceptible to cardiomyopathy than men, and the risk escalates for individuals aged 50–64 and those 65 years or older, compared to the 20–49-year age group. Additionally, an increase in the CCI correlates with a heightened risk of cardiomyopathy. There are important differences between these groups in terms of duration, frequency, and severity of use, with longer exposure and more frequent use increasing the risk of dependence and psychosis, but individual susceptibility, dose, and use patterns also play key roles.