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Unlike microbes and mammals, cistrome dynamics in plants remains unclear. Here, using GOLDEN2-LIKE (GLK) transcription factor as an example, the authors find that most GLK binding sites are species-specific and the binding divergence is caused by cis-variations through inter-species transformation experiment.

Neurotoxic methylmercury (MeHg) in rice poses health risks. This study explores the roles of various cropland microbial communities in MeHg formation on a large scale and identifies that Geobacteraceae are the key predictors of MeHg bioaccumulation in paddy soil systems, which holds the potential for mitigating global mercury exposure.

The gut microbiota may play a role in cardiovascular diseases. Here, the authors perform a metagenome-wide association study on stools from individuals with atherosclerotic cardiovascular disease and healthy controls, identifying microbial strains and functions associated with the disease.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

An improved watermelon reference genome and whole-genome resequencing of 414 cultivated and wild accessions provide insights into fruit quality traits and dessert watermelon evolution.

Data from two large longitudinal cohorts in China, in which the participants were clustered into five groups based on their metabolic characteristics, show that a signature of microbiome age modulates the risk of cardiovascular disease in metabolically unhealthy individuals.

Federated learning, a method for training artificial intelligence algorithms that protects data privacy, was used to predict future oxygen requirements of symptomatic patients with COVID-19 using data from 20 different institutes across the globe.

The nuclear dot protein 52 (NDP52) is an autophagy receptor known to trigger autophagy following bacterial infection. Here, Cui et al. show that NDP52 also triggers an anti-viral response following hepatitis B virus (HBV) infection. NDP52 forms a tripartite complex with Rab9 and envelope proteins of HBV and targets the virus to Rab9-dependent lysosomal degradation pathway.

Computational deconvolution with single-cell RNA sequencing data as a reference is pivotal for interpreting spatial transcriptomics data. Here, authors present Redeconve, which improves the resolution by more than 100-fold with higher accuracy and speed.

Core genome multilocus sequence typing (cgMLST) is used to classify bacterial strains for epidemiological applications. Here, the authors describe a distributed cgMLST scheme that does not require a central database of allelic sequences, and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria.

While Bell inequalities have been violated several times—mostly in photonic systems—their violations within particle physics experiments are less explored. Here, the BESIII Collaboration showcases Bell-violating nonlocal correlations between entangled hyperon pairs.

Dual-comb spectroscopy with time–frequency dissemination and high-power frequency combs enables sensing CO₂ and H₂O over a 113 km turbulent open-air path, with a sensing precision as high as 2 parts per million of CO₂.

Improving signal to noise ratio of Raman spectra is vital for the application. Here, authors show a noise learning method that learns the noise feature of a spectrometer. This improves the signal to noise ratio and makes deep learning to be instrument dependent instead of sample dependent.

By constructing a graph-based grapevine pangenome reference (Grapepan v.1.0) and incorporating structural variations and phenotypic maps, the study investigates the genetic basis of agronomic traits, empowering grapevine genomic breeding.

HOPX is a transcription factor epigenetically silenced in several cancers. Here the authors, by analysing methylation profiles, identify HOPX as a suppressor of metastasis in nasopharyngeal carcinoma: mechanistically HOPX inhibitsSNAILtranscription through deacetylation-mediated silencing.

Manipulation of Hh and other genes involved in neural development of the chordate amphioxus reveals conservation and differences in neural patterning mechanisms between vertebrates and amphioxus.

Host defense against helminth infection is mediated by mucosal type 2 immunity. Using gain- and loss-of-function mouse models, and mouse intestinal organoids, Xiong et al. show that SIRT6 modulates tuft and goblet cell expansion in intestinal epithelium by activating STAT6 to maintain type 2 mucosal immunity in response to helminth infection.

Lytic polysaccharide monooxygenases contribute to microbial degradation of chitin, but how the resulting oxidized chitooligosaccharides are utilized by microbes is unclear. Here, the authors describe a complete pathway for oxidative chitin utilization in marine bacteria.

A fusion and glue platform was developed to determine the cryo-EM structures of GPCRs in diverse states ranging from β2-adrenergic receptors to adhesion receptors.

Soil-borne wheat yellow mosaic virus (WYMV) poses a serious threat to global wheat production. Here, the authors report that the nuclear inclusion protease-a produced by WYMV interacts with a small peptide catalyzed by TaRD21A protease activity to mediate WYMV resistance through activating MAPK signaling pathway.

By incorporating chiral molecules into conventional superconductor lattices such as TaS₂ to form a hybrid superlattice, non-centrosymmetry could be introduced and can be shown to help lead to unconventional superconductivity.

Epigenetic modifications are crucial for plant development. Here, the authors find an epigenetically mediated double negative cascade for pollen formation and anther dehiscence, offering new insights into epigenetic regulation of anther development.

The mediators of bone-fat axis remain largely unknown. Here, the authors show SHN3 gene-deficiency in bone can protect mouse models from weight gain driven by diet-induced obesity through secreting a bone-derived cytokine, C-fragment of SLIT2, which could stimulate adipocyte browning.

Surface-enhanced Raman scattering is a powerful spectroscopy technique that can be used to study substances down to the level of single molecules. But the practical applications have been limited by the need for metal substrates with roughened surfaces or in the form of nanoparticles. Here a new approach — shell-insulated nanoparticle-enhanced Raman spectroscopy — is described, and its versatility demonstrated with numerous test substances.

In Arabidopsis, the UV receptor UVR8 is functionally connected to DNA methylase DRM2. Through this interaction, UV light prevents DRM2 association with chromatin, suppressing DNA methylation and the associated transcriptional changes.

Precise adaptation of motor timing is vital in sensorimotor coordination. Here, the authors show that mice can rapidly adjust conditioned eyelid closure between delay and trace eyeblink conditioning, and that this adaptation is dependent on the modulation of medial prefrontal cortex activity.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

Integrative analyses of transcriptome and whole-genome sequencing data for 1,188 tumours across 27 types of cancer are used to provide a comprehensive catalogue of RNA-level alterations in cancer.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

Whole-genome sequencing data for 2,778 cancer samples from 2,658 unique donors across 38 cancer types is used to reconstruct the evolutionary history of cancer, revealing that driver mutations can precede diagnosis by several years to decades.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Prostate cancer (PrCa) involves a large heritable genetic component. Here, the authors perform multivariate fine-mapping of known PrCa GWAS loci, identifying variants enriched for biological function, explaining more familial relative risk, and with potential application in clinical risk profiling.

By analysing the genome of over 9,000 pig-associated isolates, this study shows that modernized agricultural systems have favoured the acquisition of antimicrobial resistance genes, population expansion and global transmission of pig-enriched Salmonella over the past century.

In the COMPASSION-04 trial, first-line treatment with a bispecific antibody targeting CTLA-4 and PD-1 and chemotherapy in patients with locally advanced or metastatic gastric or gastroesophageal junction adenocarcinoma resulted in clinical responses with a manageable safety profile.

Investigating the inner structure of baryons is important to further our understanding of the strong interaction. Here, the BESIII Collaboration extracts the absolute value of the ratio of the electric to magnetic form factors and its relative phase for e + e − → J/ψ → ΛΣ decays, enhancing the signal thanks to the vacuum polarisation effect at the J/ψ peak.

A self-powered electrical stimulation system that harvests wind and raindrop energy has the capacity to stimulate crop growth via the all-weather triboelectric nanogenerator. A small-scale experiment shows that the system can increase ~26.3% of the germination speed and ~17.9% of yield for peas.

Nonribosomal lipopeptides contain an acyl chain important for bioactivity, but its incorporation into the peptidyl backbone, mediated by the starter condensation (Cs) domain of nonribosomal peptide synthases, is not fully understood. Here, the authors show that acyl chains of different lengths can be obtained by engineering Cs domains and identify residues that determine the selectivity for acyl chains.

The efficacy of cancer radio-immunotherapy is limited by the immunosuppressive tumor microenvironment. Here the authors report fusogenic liposomes loaded with Auranofin, a gold containing drug approved for rheumatoid arthritis, multivariate-gated aptamer assemblies and PD-L1 aptamers, as an adjuvant for melanoma-targeted radio-immunotherapy.

Using a cross-species integrative approach, this study identifies Brd9 as a critical osteogenic regulator that modulates Sp7 expression through cooperation with Wnt/β-catenin signaling.

Analysis of whole-genome sequencing data across 2,658 tumors spanning 38 cancer types shows that chromothripsis is pervasive, with a frequency of more than 50% in several cancer types, contributing to oncogene amplification, gene inactivation and cancer genome evolution.