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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.

Interannual variation in tree intrinsic water use efficiency is largely controlled by water availability. Here, the authors find that this constraint has strengthened over the past six decades, particularly for gymnosperms, primarily due to rising atmospheric CO₂ and increasing climatic dryness.

Stereogenic sp³-hybridized carbon centres are the principal building blocks of chiral organic molecules. Usually, these centres are configurationally fixed. Now, low-energy pericyclic rearrangements have been used to create rigid cage molecules with fluxional sp³-stereochemistry, influencing chiral information transfer. The sp³-carbon stereochemistry of the cages is inverted through strain-assisted Cope rearrangements.

Phylogenetic statistical analyses, biophysical models and information from the fossil record show that an evolutionary signal of natural selection acted to increase the flight efficiency of pterosaurs over millions of years.

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.

This study quantifies heat exposure and its impact on construction worker productivity in Taiwan. It finds that heat stress in the labor-intensive construction sector carries a substantial economic burden.

In this prospective longitudinal study of alcohol consumption and patterns in heavy drinking young adults, significant reductions in alcohol use quantity, frequency and problems were observed from pre- to post-pandemic onset.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

In this study, the authors analyse 2,409 nasopharyngeal swabs from 300 infants in Botswana to investigate the impacts of respiratory virus infection on the colonisation dynamics of bacterial respiratory pathobionts.

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.

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.

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.

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

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.

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.

Analysis of species distribution models in a pan-African database comprising chronometrically dated archaeological sites over the past 120,000 years shows major expansion in the human niche from 70 ka, driven by adaptation to diverse habitats.

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.

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 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.

Plasmid copy number heterogeneity can be used as a tool to build synthetic microbial populations that adapt to changing environments due to specific plasmid-encoded fitness effects.

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.

Phylogenetic analysis of halophilic archaea, including two previously undescribed clades, reveals four independent evolutionary adaptations to hypersaline environments, caused by duplications and horizontal gene transfers.

Environmental variation has been hypothesized to favour the evolution of large brains capable of adjusting behaviour to changing circumstances. Here, Sayolet al. find that across more than 1200 bird species, species with relatively large brains are indeed associated with more variable habitats.

The analysis of pairs of identical SARS-CoV-2 genome sequences enables characterization of transmission patterns between geographies and age groups.

Combining a large-scale dataset of 23 ungulate species (in which newborns follow contrasting tactics of predator avoidance) with continuous-time stochastic movement models, the authors reveal that there are multiple dimensions of maternal movement behaviour and space use.

Little is known about how climate change impacts glacier-fed streams (GFSs) microbiomes. Here, using a modelling framework based on global GFS metagenomic, climatic and environmental data the authors predict future increases in GFS bacterial biomass and diversity, but potential loss of clades adapted to extreme conditions.

Live birth and an annual life cycle potentially enable access to new ecological niches and subsequent species diversification. Here, Helmstetter et al.build the phylogeny for fish in the order Cyprinodontiformes and find that, though live birth and annualism have each evolved multiple times, only live birth is associated with increased diversification.

Big data collected through apps can facilitate large-scale study of diet and lifestyles. Information from the ZOE COVID Study indicates the variety and extent of impacts that the COVID-19 pandemic has had on the diets and lifestyles of adults in the United States and the United Kingdom.

Using measurements from 139 global lakes, the authors demonstrate how long-term thermal habitat change in lakes is exacerbated by species’ seasonal and depth-related constraints. They further reveal higher change in tropical lakes, and those with high biodiversity and endemism.

The Qinghai-Tibet Plateau is as cold as the Arctic, but presents unique hypoxia and high ultraviolet conditions. Here the authors find that gene flow from Arctic gyrfalcons aids plateau saker falcons’ cold adaptation, and independent non-coding genomic changes underlie hypoxic and ultraviolet responses.

A software tool, EPIC, is developed to determine protein complex membership using chromatographic fractionation–mass spectrometry data, and is applied to map the global Caenorhabditis elegans interactome.

AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.

Normothermic machine perfusion of the liver improved early graft function, demonstrated by reduced peak serum aspartate transaminase levels and early allograft dysfunction rates, and improved organ utilization and preservation times, although no differences were seen in graft or patient survival.

This study examines the impact of herbivorous insects on biogeochemical cycling within forests. From a global network of 74 plots within 40 mature, undisturbed broadleaved forests, they show that background levels of insect herbivory are sufficiently large to alter both ecosystem element cycling and influence terrestrial carbon cycling.

This study analyzed data on 793 cities to see how the COVID-19 pandemic affected their climate commitment and actions. It found that although climate actions persist, funding has fallen and less than half of the cities implemented green recovery initiatives.