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The structure of a Stig cyclase, HpiC1, reveals how it catalyzes Cope rearrangement and 6-exo-trig cyclization, including how it controls the position of electrophilic aromatic substation that distinguishes hapalindole from fischerindole alkaloids.

Phaeocystales are ecologically significant nanoplankton whose evolutionary history and functional diversity remain incompletely characterized. Here, the authors integrate genomic and transcriptomic data to reveal their lineage diversification, metabolic plasticity, and adaptation to polar and temperate regimes.

The authors conduct a national inventory on individual tree carbon stocks in Rwanda using aerial imagery and deep learning. Most mapped trees are located in farmlands; new methods allow partitioning to any landscape categories, effective planning and optimization of carbon sequestration and the economic benefits of trees.

Sulphate-reducing microorganisms have key roles in the biogeochemical cycling of sulphur, carbon, nitrogen and metals, as well as great biotechnological potential. Here, Zhou and colleagues describe recent applications of 'omics' tools to study the stress responses of these organisms, particularlyDesulfovibriospp., at the cell, population, community and ecosystem levels.

Mass spectrometry-based lipidomics and metabolomics generate large, complex datasets requiring effective analysis. Here, authors review key statistical and visualization methods alongside widely used R and Python tools, and provide a GitBook with step-by-step code for accessible, reproducible data analysis.

Newman et al. find that higher education is consistently associated with better health indicators, while higher income correlates with greater well-being, based on a large-scale Ecological Momentary Assessment study.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

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.

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

A global shortage of suitable donor kidneys is the primary challenge in kidney transplantation. In this Review, the authors describe different methods of donor kidney preservation, discussing the strengths and limitations of each method and noting how advances in donor organ perfusion could improve organ utilization and patient outcomes.

The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 cancer whole genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.

In people with severe brain injuries, stimulation restored consciousness by engaging a deep brain circuit for wakefulness—revealing a target that may also guide treatment in stroke and epilepsy.

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.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

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.

Dietary n-6 PUFAs enhance adipose tissue expandability through the PPARγ–LPCAT3 membrane remodelling axis.

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.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

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.

Analysis of 20 chemical and morphological plant traits at diverse sites across 6 continents shows that the transition from semi-arid to arid zones is associated with an unexpected 88% increase in trait diversity.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.

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.

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.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

This study demonstrates that growth arrest under stress in Arabidopsis protects meristem cells from DNA damage, challenging the idea that it is merely due to energy trade-offs and highlighting its role as an active defense strategy.

Staphylococcus aureus adapts to diverse host environments during infection. Here, the authors use transposon sequencing to reveal niche-specific genes and identify 27 core genes required for S. aureus fitness across intracellular, blood, and organ niches.

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.

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.

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.

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.

Despite being a hallmark of cancer, the identification of targetable vulnerabilities of aneuploid cancer cells remains limited. Here, the authors develop RPE1-hTERT cell lines with varying degrees of aneuploidy to investigate the consequences of chromosomal imbalance, identifying CRAF as an aneuploid-selective therapeutically targetable vulnerability.

The complex nature of food supply chains makes it a crucial exercise to estimate the impacts of disruptions caused by climate disasters. By applying an integrated modelling framework to Australia and considering heatwaves, cyclones and other climate events, this study presents novel ways of quantifying regional and sectoral spillover effects—including job and income losses, food and nutrient availability, and diet quality.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

Obesity leads to pathological expansion of white adipose tissue driving vascular dysfunction. Here, the authors utilize single-cell RNA sequencing to elucidate endothelial heterogeneity and demarcate key differences in obesity-associated vascular alterations in subcutaneous and visceral white adipose tissue.

Konturek-Ciesla et al show that low intensity conditioning with antibody mediated haematopoietic stem cell (HSC) depletion coupled to HSC transplantation boosts blood cell and immune cell generation in aging mice, slowing disease. This approach may help treat age-related blood disorders in humans.

Invertebrate and microbe communities support reef ecosystems and coral health. Here, the authors characterize these communities from degraded and healthy reefs, showing that transplanting these healthy communities improved coral health at degraded reefs.

Little is known about how detritivorous invertebrates cope with high levels of defensive plant polyphenols. Here, Liebekeet al. identify a new class of surface-active metabolites in earthworms exposed to high-polyphenol diets, and show that they play a protective role against precipitation of proteins.

Small-bodied faunivory has been proposed as the ancestral condition of most major synapsid clades, but here using a time-calibrated metatree of 1,888 fossil synapsids, the authors show that while faunivory is commonly ancestral, small body size in radiation forerunners is a relatively late innovation, arising in the Late Triassic.