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Influenza A H1N1/2009 virus emerged from swine and rapidly replaced the seasonal H1N1 virus. Here, the authors show that natural selection acting on H1N1/2009 after introduction into humans was driven by adaptation to the new host but later selection has been driven by immunological escape.

SPNS2 exports S1P and FTY720-P to control immune cell migration. Here, the authors use cryo-EM, immunofluorescence, in vitro binding and in vivo S1P export, and MD simulations to uncover the mechanisms of SPNS2’s transport and inhibition.

The changing climate threatens water quality in lakes, particularly oxygen levels. Here the authors present evidence for northern lakes of rapidly reducing oxygen levels, mainly driven by longer stratification in the warm season, with implications for lake ecosystems.

Glyphosate is the world’s most widely-used herbicide. Here, Belbin et al. show that plant responses to glyphosate, and therefore herbicide activity, depend on plant circadian rhythms suggesting that considering the time-of-day of application could lead to more efficient agrochemical use.

Ancestral avian influenza A viruses are used to identify adaptive changes in viral polymerase and nucleoproteins that enable efficient replication and transmission in pigs.

Malaria parasites invade erythrocytes to proliferate, but visualizing this rapid process is challenging. Here the authors use live imaging and genome-editing of P. knowlesi to dissect invasion and establish the roles of two vital parasite proteins.

SOX2 is required for the maintenance of glioblastoma stem cells (GSCs). Here the authors identify that the RING family E3 ubiquitin ligase TRIM26 promotes SOX2 stability in a non-canonical ligase-independent manner and thus, increases the tumorigenicity of GSCs.

Centrosome separation, promoted by the kinesin Eg5, is antagonized by the guanine nucleotide exchange factor Tiam1 through an unknown mechanism. Here Whalley et al. show that Tiam1 is phosphorylated by cyclin-dependent kinase 1 in prophase, leading to downstream activation of p21-activated kinases (PAKs).

Decisions on where to source nickel for use in low-carbon technologies must consider the biomass losses caused by mining. This study found that, in many cases, these unaccounted emissions were significant relative to other Scope 1 and Scope 2 emissions from nickel extraction and processing.

Systematic analysis from the Global Burden of Disease study reported that, despite global improvements from 1990 to 2021, dietary iron deficiency-associated disease burden remains high in women, children and residents in low socio-demographic index countries.

Using 1,854 routinely collected clinical samples from early in pregnancy, with validation in an external cohort, low-coverage cfDNA sequence data identified distinctive features among those who developed preeclampsia.

Global in situ observations show greenhouse gas emissions from wetlands are lowest when the water table is near the surface, and therefore rewetting wetlands could substantially reduce future emissions.

TRIM23 is identified as an essential regulator of virus-induced autophagy that mediates restriction to several RNA and DNA viruses. K27-mediated ubiquitylation activates TRIM23 GTPase activity, triggering its relocalization and selective autophagy.

Shen et al. report a method for multiplexing isogenic iPSCs for single-cell RNA-seq. With it, they created an atlas of in vitro differentiation and identified TMEM88 as a regulator of cardiovascular development, impacting blood pressure in adult mice.

Amazonian Dark Earth is soil that has had mysteriously high fertility since ancient times, despite the fact that surrounding soils have very low nutrients. Here the authors’ use of isotope reconstructions indicate that these soils predate human settlement and could have alluvial and burning origins.

The genomic and immune landscape of pre-invasive lung adenocarcinoma is poorly understood. Here, the authors perform exome and transcriptome sequencing on precursor legions and invasive lung adenocarcinomas, identifying recurrently mutated genes in pre/minimally invasive cases, and arm level alteration events linked to immune infiltration.

Spillover of the highly pathogenic avian influenza H5N1 virus to dairy cattle and the findings of a clinical, pathological and epidemiological investigation in nine affected farms are reported.

Sorting nexin 27 (SNX27) regulates endosomal sorting of glutamate receptors. Loo et al.show that SNX27 is localized to recycling endosomes within dendritic spines where it interacts with glutamate receptors, allowing them to be shuttled to the postsynaptic membrane.

Influenza is an infectious respiratory disease that, in humans, is caused by influenza A and influenza B viruses. This Primer discusses the biological features of influenza viruses, their effects on human and animal health and the mitigation strategies to reduce the burden of this disease.

Post-translational modifications are critical for regulating the DNA damage response. Here, the authors identify a methylation-deubiquitination crosstalk between methyltransferase PRMT1 and deubiquitinase USP11, showing that the enzymes regulate each other’s functions in DNA repair.

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.

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.

Evolutionary analysis of swine-origin H1N1 influenza A virus provides evidence that it was derived from several viruses circulating in swine and that it possesses genes from avian, swine and human origin. Furthermore, transmission to humans may have occurred several months before recognition of the current outbreak.

Taking into account all known factors, the planet warmed 0.2 °C more last year than climate scientists expected. More and better data are urgently needed.

Helsen et al. use experimental evolution and chromosome engineering to probe the link between karyotype changes and the cell division machinery. They conclude that spindle organization dictates the available trajectories for karyotype evolution.

The SMC5/6 complex is critical for genome stability. Here, the authors identify mutations in SLF2 and SMC5 as cause of Atelís Syndrome characterized by microcephaly, short stature, anemia, segmented chromosomes and mosaic variegated hyperploidy.

G protein-coupled receptors (GPCRs) are involved in many physiological processes and are targets of intense drug discovery research. Here, the authors describe llama-derived nanobodies that allosterically modulate rhodopsin, a prototypical GPCR.

Degeneration of the retinal pigment epithelium is a hallmark of geographic atrophy, a type of age-related macular degeneration. Kerur et al. show that this degeneration results from a multistep pathway in which mitochondrial dysfunction in RPE cells, triggered by accumulation of Alu RNA, leads to activation of the noncanonical inflammasome via a cGAS–STING–IRF3 signaling axis.

Transient senescence induced by DNA damage responses provide a neuroprotective mechanism against iron dysregulation seen during intracerebral haemorrhage, offering mechanistic insights and potential therapeutic avenues.

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.

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.

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 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.

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.

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.

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.

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.