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Fishing has had a profound impact on global reef shark populations, and the absence or presence of sharks is strongly correlated with national socio-economic conditions and reef governance.

Over 170 susceptibility loci have been identified by genome-wide association studies in breast cancer. Here, the authors interrogated the role of risk-associated variants from non-breast tissue, and using expression quantitative trait loci, identify potential target genes of known breast cancer susceptibility variants, as well as 11 regions not previously known to be associated with breast cancer risk.

With a shRNA targeted screen, Ferrer, Cho, Boon et al. identify a role for Gstt1 in enhancing epithelial–mesenchymal transition and disseminated tumour cell features in a subset of slow-cycling cells, thereby facilitating metastatic progression.

Li et al. identify a human TCF1-expressing stem-like T cell population that is associated with immune-mediated pathogenesis in ulcerative colitis.

Here the authors show that a homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters the accessibility of variant-distal methylation sites in EPRS1 mRNA, revealing a new RNA-dependent mechanism by which genetic variants can influence gene expression and disease.

In this immunological ancillary study of the PREVAC trial, the authors show that approved Ebola virus vaccines induce memory T-cell responses that persist during the five year follow-up after initial vaccination.

The Omicron variant evades vaccine-induced neutralization but also fails to form syncytia, shows reduced replication in human lung cells and preferentially uses a TMPRSS2-independent cell entry pathway, which may contribute to enhanced replication in cells of the upper airway. Altered fusion and cell entry characteristics are linked to distinct regions of the Omicron spike protein.

Time-series observations from the JWST of the transiting exoplanet WASP-39b show gaseous water in the planet’s atmosphere and place an upper limit on the abundance of methane.

Federated ML (FL) provides an alternative to train accurate and generalizable ML models, by only sharing numerical model updates. Here, the authors present the largest FL study to-date to generate an automatic tumor boundary detector for glioblastoma.

A NutNet experiment in 57 grasslands across six continents shows that when herbivores are excluded from grasslands with a long coevolutionary history of grazing plant diversity is reduced, while in grasslands without a long grazing history the evolutionary history of the plant species regulates the response of plant diversity.

Artificial Intelligence can support diagnostic workflows in oncology, but they are vulnerable to adversarial attacks. Here, the authors show that convolutional neural networks are highly susceptible to white- and black-box adversarial attacks in clinically relevant classification tasks.

Determining the safe operating space for sustainable food production depends on the interactions of multiple processes within the Earth system. Expert knowledge provides critical insight into how these processes interact that improves Earth system modelling and our understanding of the limits of global food production.

In a prospective international cohort of 1,127 patients with non-small-cell lung cancer and ctDNA-guided therapy, ctDNA detection was associated with shorter survival, independently of clinicopathologic features and metabolic tumor volume.

Polyketides are assembled by modular polyketide synthases and undergo chemical tailoring reactions. A dehydratase domain variant catalyzes two sequential elimination reactions from thioester intermediates to produce conjugated diene modifications.

Results from the precision oncology ARROW trial identify the RET receptor tyrosine kinase as a tissue-agnostic target and the drug pralsetinib’s potential as a well-tolerated treatment option with rapid, robust and durable anti-tumor activity in patients with diverse RET fusion–positive solid tumors.

A dataset of 3D images from more than 200,000 human induced pluripotent stem cells is used to develop a framework to analyse cell shape and the location and organization of major intracellular structures.

Using 46 years of individually monitored data for European red deer, the authors show that older individuals become less socially connected, with correlated changes to their spatial behaviour.

A dataset of 16 plant traits sampled from 2,461 individual trees from 74 tropical forest sites around the world is used to show a strong link between climate and plant functional diversity and redundancy, with drier tropical forests likely being less able to respond to declines in water availability.

Genome-wide association meta-analyses identify 26 risk loci for epilepsy, including 19 loci specific to genetic generalized epilepsy. Prioritized candidate genes implicate synaptic processes and overlap with targets of antiseizure medications.

Using viral sequence data, individuals with persistent SARS-CoV-2 infections were identified, and had higher odds of self-reporting long COVID, in a large community surveillance study.

A newly developed RIPK3 inhibitor blocks necroptosis of lung cells, reduces lung inflammation and prevents mortality in a mouse model of influenza A virus infection.

The transcription factor FOXO1 has a key role in human T cell memory, and manipulating FOXO1 expression could provide a way to enhance CAR T cell therapies by increasing CAR T cell persistence and antitumour activity.

In this study, Smith and colleagues employ analogue experiments to show the controlling parameters on sediment bedforms in pyroclastic density current deposits. The findings are applied and validated on natural deposits.

Highly accurate antibody tests for SARS-CoV-2 are needed for surveillance in low-prevalence populations. Here, the authors find seroprevalence of less than 1% in two San Francisco Bay Area populations at the beginning of April, and that seroreactivity is generally predictive of in vitro neutralising activity.

Expression of three Yamanaka transcription factors in mouse retinal ganglion cells restores youthful DNA methylation patterns, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice, suggesting that mammalian tissues retain a record of youthful epigenetic information that can be accessed to improve tissue function.

The mini-mScope is a miniature microscope that can image neural activity at the mesoscale in most of the dorsal cortex of freely behaving mice.

Zhang et al. identify and characterize supermeres as extracellular nanoparticles that exhibit unique biological and functional properties with potential prognostic and therapeutic value across distinct diseases.

Physiological matching of blood flow to the demand for oxygen by the heart is required for sustained cardiac health, yet the underlying mechanisms are obscure. Here, the authors report a key role for acute modifications to the redox state of intracellular pyridine nucleotides in coronary smooth muscle and their impact on voltage-gated K + channels in metabolic vasodilation

In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.

How Earth’s atmosphere became oxygenated remains enigmatic. Here the authors use mathematical and phylogenetic analyses to find that Earth’s oxygenation is induced by the interactions of microbial oxidative metabolites with sediment minerals.

Most Amazon tree species are rare but a small proportion are common across the region. The authors show that different species are hyperdominant in different size classes and that hyperdominance is more phylogenetically restricted for larger canopy trees than for smaller understory ones.

SARS-CoV-2 nucleocapsid (N) protein is responsible for viral genome packaging. Here the authors employ single-molecule spectroscopy with all-atom simulations to provide the molecular details of N protein and show that it undergoes phase separation with RNA.

Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures, with enormous societal and economic costs. Here, the authors demonstrate the feasibility of a test-trace-quarantine strategy using an agent-based model and detailed data on the Seattle region.

The cellular heterogeneity in brain obscures the identification of robust cellular regulatory networks. Here the authors integrate genome-wide chromosome conformation data from sorted neurons and glia, with transcriptomic and enhancer profiles, to characterize cell-type-specific gene regulatory landscapes in the human brain, and provide insights into cell-type-specific gene regulatory networks in brain disorders.

The systemic immune features that distinguish COVID-19 from common infections remain incompletely elucidated. Here McClain et al. compare RNA sequencing in peripheral blood between subjects with SARS-CoV-2 and other respiratory infections and demonstrate dysregulated immune responses in COVID-19 with both heterogeneous and conserved components.

The pituitary gland plays important roles in the regulation of key physiological functions. Here the authors provide a multiomics atlas including transcriptome, chromatin accessibility, and methylation status of over 70,000 single nuclei (sn) from mouse pituitaries.

After compiling literature data on mammal parasites across urban and non-urban areas, the authors show that mammals in urban areas have more parasites overall without disproportionately more zoonotic ones, as is commonly thought.

Monoclonalization, the isolation and expansion of a single cell derived from a cultured population, is an essential step in large-scale human cell culture and experiments. A new deep learning-based workflow called Monoqlo automatically detects colony presence and identifies clonality from cellular imaging, enabling single-cell selection protocols to be scalable while minimizing technical variability.

micov computes coverage breadth across genomes and samples. Its application in metagenomics highlights strain heterogeneity, uncovers associations linking genetic elements to phenotypic traits, and aids taxonomic filtering in low-biomass settings.

The relationships that control seed production in trees are key to understand evolutionary pressures that have shaped forests. A global synthesis of fecundity data reveals that while seed production is not constrained by a strict size-number trade-off, it is influenced by taxonomy and nutrient allocation.

Single-cell whole-genome sequencing shows that 'foreground' cell-to-cell structural variation and alterations in copy number are associated with genomic diversity and evolution in triple-negative breast and high-grade serous ovarian cancers.