Search

Tissue phenotypes arise from molecular states of individual cells and their spatial organisation, so spatial omics assays can help reveal how they emerge. Here, the authors apply graph neural networks to classify tissue phenotypes from spatial omics patterns, and use this approach to understand patterns in cancers and their microenvironments.

Analysis of mitochondrial genomes (mtDNA) by using whole-genome sequencing data from 2,658 cancer samples across 38 cancer types identifies hypermutated mtDNA cases, frequent somatic nuclear transfer of mtDNA and high variability of mtDNA copy number in many cancers.

Results for the final phase of the 1000 Genomes Project are presented including whole-genome sequencing, targeted exome sequencing, and genotyping on high-density SNP arrays for 2,504 individuals across 26 populations, providing a global reference data set to support biomedical genetics.

Virus-host competition drives evolution of diverse antiviral defences in bacteria and antidefense systems in their viruses (phages). Here, Silas et al. use a functional screen of phage accessory genes to show how bacterial cell-surface sugars can be major determinants of phage host-range, and how some phage proteins injected into bacterial cells inhibit host immunity.

Here, using samples from ~1,100 individuals, the authors define the nasal microbiome linked to Staphylococcus aureus colonization, identifying seven communities- either S. aureus-dominated or dominated by other bacteria.

Mesothelioma is a highly lethal cancer that remains challenging to diagnose. Here, the authors curate a histomorphological atlas of resected mesothelioma and map it using self-supervised AI endorsed by human pathological assessment, revealing patterns that generate highly interpretable predictions.

Chapman, Klaourakis and colleagues reveal that a lymphatic vasculature with poor clearance capacity in perinatal, regeneration-competent mouse hearts is required to retain pro-reparative macrophages and allow cardiac regeneration.

By leveraging the power of pretrained DNA foundation models, SegmentNT achieves performant genome annotation through segmenting different genic and regulatory elements.

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.

Chronic infection with SARS-CoV-2 leads to the emergence of viral variants that show reduced susceptibility to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma.

Sera from vaccinated individuals and some monoclonal antibodies show a modest reduction in neutralizing activity against the B.1.1.7 variant of SARS-CoV-2; but the E484K substitution leads to a considerable loss of neutralizing activity.

Tracking methane emissions from cows just got a little easier, David Adam reports.

David Adam plugs into a rechargeable battery fit for the twenty-first century.

An analysis of the impact of logging intensity on biodiversity in tropical forests in Sabah, Malaysia, identifies a threshold of tree biomass removal below which logged forests still have conservation value.

A new test for diseases like BSE could be round the corner. David Adam reports. .

Together with a companion paper, molecular details of immune responses in a pig-to-human xenotransplantation are identified through dense longitudinal multi-omics profiling of the xenograft and the host recipient, across the 61-day procedure.

nELISA miniaturizes the sandwich immunoassay and transforms it into a massively scalable platform for quantitative proteomics.

Ramadoss et al. show that bone-marrow-derived macrophages contribute to heart repair following myocardial infarction by secreting GPNMB, which binds to the orphan receptor GPR39 to improve myocyte contractility and reduce fibroblast activation.

Recent controversies over scientific fraud and other disputed findings have raised questions over the way in which journals select papers for publication. Is there a problem? And what more could be done to weed out dubious results? David Adam and Jonathan Knight investigate.

An initial draft of the human pangenome is presented and made publicly available by the Human Pangenome Reference Consortium; the draft contains 94 de novo haplotype assemblies from 47 ancestrally diverse individuals.

Loss-of-function mutations in EP300/KAT3B and CBP/KAT3A have been implicated in the pathogenesis of cancer. Here, the authors reveal that the EP300 protein has a role in mediating replication fork protection at sites of replication stalling and show that EP300-mutated cells recapitulate features of BRCA-deficient cancers.

Gene regulation in oocytes relies heavily on poly(A) tail-length changes. Here, the authors develop PAL-AI, a neural network model that predicts tail-length changes, identifies regulatory motifs, and links disruptive genetic variants to negative selection in humans, implicating tail-length control in female fertility.

Analyses of genome and exome sequencing data identify rare coding and structural variants associated with atrial fibrillation and highlight genetic links between atrial fibrillation and cardiomyopathies.

JWST observations of the ultra hot Jupiter WASP 121 b reveal helium escaping for most of its orbit, forming two giant tails moving in opposite directions. The results show how stellar radiation modifies planetary atmospheres.

FlexConsensus is a multi-autoencoder-based algorithm for merging different conformational landscapes from cryogenic electron microscopy heterogeneity analysis into a common latent space for the identification of similarities and differences among various methods. This helps in the validation of estimated conformational landscape and provides tools to streamline the heterogeneity workflow.

Microglia can alter their properties to adopt a wide spectrum of cellular phenotypes. Here, the authors show that remodeling of microglial mitochondria accompanies microglial responses to challenges and aging, and provide evidence that these organelles play a role in regulating basal microglial morphology, gene expression, and inflammatory profile.

The CMS Collaboration reports the measurement of the spin, parity, and charge conjugation properties of all-charm tetraquarks, exotic fleeting particles formed in proton–proton collisions at the Large Hadron Collider.

The use of deep learning in medical image segmentation is limited by the low availability of annotated images. Here, the authors develop GenSeg, a generative deep learning framework that can generate high-quality paired segmentation masks and medical images that can improve the performance of segmentation models under ultra low-data regimes across multiple scenarios.

Human–artificial intelligence (AI) dialogues can meaningfully impact voters’ attitudes towards presidential candidates and policy, demonstrating the potential of conversational AI to influence political decision-making.

Typical quantum error correcting codes assign fixed roles to the underlying physical qubits. Now the performance benefits of alternative, dynamic error correction schemes have been demonstrated on a superconducting quantum processor.

BPTF is known to regulate chromatin accessibility and self-renewal in mammary epithelial stem cells. Here, the authors discover that BPTF inhibition delays tumor formation, re-activates ERα expression, increases sensitivity to tamoxifen treatment, and inhibits metastatic development.

A national prospective study of patients requiring hospitalization for COVID-19 demonstrates global cognitive deficits at 1 year, associated with elevated brain injury markers and reduced gray matter volume.

Ring deconvolution microscopy leverages symmetry to provide fast and straightforward spatially varying deblurring and offers improved speed and image quality compared to standard approaches across diverse microscopy modalities.

Nimbus, a deep learning model, uses a large multiplexed imaging dataset to predict the likelihood of marker positivity in single cells.

Meta-analysis of genome-wide association studies on Alzheimer’s disease and related dementias identifies new loci and enables generation of a new genetic risk score associated with the risk of future Alzheimer’s disease and dementia.

David Adam reports on the most exciting development in canal travel since the thermos flask.

Laser light can make polymers move like muscle, David Adam discovers.

This report from the 1000 Genomes Project describes the genomes of 1,092 individuals from 14 human populations, providing a resource for common and low-frequency variant analysis in individuals from diverse populations; hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites, can be found in each individual.

COVID-19 can be associated with neurological complications. Here the authors show that markers of brain injury, but not immune markers, are elevated in the blood of patients with COVID-19 both early and months after SARS-CoV-2 infection, particularly in those with brain dysfunction or neurological diagnoses.

The cool sub-Neptune LP 791-18 c, with an equilibrium temperature of 355 K, was found to host a hazy atmosphere, distinct from any other temperate sub-Neptune studied so far. The discovery demonstrates the intrinsic diversity of these worlds.

Gene regulatory network architecture and complex dosage effects from paralogue diversification converge to shape phenotypic space, producing the potential for both strongly buffered phenotypes and sudden bursts of phenotypic change.

Jules Hoffmann shared the 2011 Nobel prize in Physiology or Medicine for discoveries in the activation of innate immunity against bacteria and fungi in fruit flies. Now based at the Institute of Molecular and Cellular Biology at Strasbourg University in France, Hoffmann talks to ádám and Dávid Tárnoki about how to use the immune system to kill cancer cells.

Whole-genome sequencing and phenotype data sharing are introduced in a national health system to streamline diagnosis and to discover coding and non-coding variants that cause rare diseases.

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.

Large genome-wide meta-analysis of clinically diagnosed late-onset Alzheimer’s disease (LOAD) from 94,437 individuals identifies new LOAD risk loci and implicates Aβ formation, tau protein binding, immune response and lipid metabolism.

A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.