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Analysis of whole-genome sequencing data from hematopoietic stem and progenitor cells taken from patients with myeloma shows how treatment shapes clonal architecture and sheds light on the evolution of treatment-related myeloid neoplasms.

The authors estimate genomic vulnerability for closely related species of rainbowfish. They find that narrow endemic species that have hybridized with a warm-adapted generalist show reduced vulnerability to climate change and that hybridization may facilitate evolutionary rescue for such species.

This study reports the mouse islet atlas, a curated resource integrating scRNA-seq data of over 300,000 cells from nine datasets, covering pancreas development, homeostasis and disease states.

This study estimates the green cooling distribution and the population most exposed to heat in 14 major European areas. It found that lower-income residents, immigrants and unemployed residents are more vulnerable compared with upper-income residents, nationals and homeowners.

Ritter et al. present a spatial transcriptomics and deep learning-based approach named NePSTA (neuropathology spatial transcriptomic analysis) and leverage it to improve neuropathological diagnostics and enhance central nervous system tumor subtype classification.

A predictive model of soil microbiome composition is tested against community surveys from across the United States, showing an increase in predictability with spatial scale when using both functional and taxonomic groups.

The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of genome architecture and spatial genome regulation emerged early in animal evolution.

Here, Schuldt et al. collate data from two long-term grassland and forest biodiversity experiments to ask how plant diversity facets affect the diversity of higher trophic levels. The results show that positive effects of plant diversity on consumer diversity are mediated by plant structural and functional diversity, and vary across ecosystems and trophic levels.

Analysis of ground-sourced and satellite-derived models reveals a global forest carbon potential of 226 Gt outside agricultural and urban lands, with a difference of only 12% across these modelling approaches.

This study presents a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences. From over 2 million mtDNA sequences, they find a negative quadratic latitudinal gradient in genetic diversity evenness, peaking in the subtropics and correlating with hot, stable environments.

The role of developmental pathways in medulloblastoma tumours (MB) with sonic hedgehog (SHH) activation remains to be explored. Here, the authors perform multi-omic analysis and characterise the key transcriptomic and metabolic patterns of highly differentiated cells in SHH MBs.

Analysis of whole-genome sequences of 25,465 individuals of European ancestry shows that rare variants contribute substantially to the heritability of height and body mass index.

Spatial visualization of metabolites in tissues via mass spectrometry imaging can be prone to user perception bias. Here, the authors report the computational framework moleculaR that introduces probabilistic data-dependent molecular mapping of nonrandom spatial patterns of metabolite signals.

Wood density is an important plant trait. Data from 1.1 million forest inventory plots and 10,703 tree species show a latitudinal gradient in wood density, with temperature and soil moisture explaining variation at the global scale and disturbance also having a role at the local level.

Comparing data on genetic monitoring efforts across Europe with the distributions of areas at species’ climatic niche margins, the authors show that monitoring efforts should be expanded to populations at trailing niche margins to include genetic variation that may prove important for adaptation to ongoing climate warming.

Abdellaoui et al. synthesize genomic evidence on the link between socio-economic status and heredity. They show how social stratification may create selection pressures, meaning that individuals are clustered in distinct environments. This may have consequences for genetic architectures and social inequality.

The authors evolved antibiotic-resistant Helicobacter pylori in the absence of antibiotics and presence of DNA from antibiotic-sensitive strains. Horizontal gene transfer mediated the molecular reverse evolution of the antibiotic-resistance gene to the antibiotic-sensitive allele, and the authors used theoretical modelling to determine the evolutionary conditions that promote reverse evolution.

A nested orbit-to-ground approach for microbial landscape patterns at different scales, tested in the high Andes, provides a machine learning-based search tool for detecting biosignatures on terrestrial planets.

Ischemic stroke, caused by sudden oxygen and substrate deprivation of the CNS, is a leading cause of disability and death. Here, the authors characterize in a rodent model the molecular signature of glial cells in response to ischemic stroke at single cell resolution.

Bleckwehl et al. present a spatial transcriptomic map of atherosclerotic plaques across disease stages, revealing cellular recruitment and migration patterns and intercellular communication dynamics as a valuable resource for future research.

Forest structure depends both on extrinsic factors such as climate and on intrinsic properties such as community composition and diversity. Here, the authors use a dataset of stand structural complexity based on LiDAR measurements to build a global map of structural complexity for primary forests, and find that precipitation variables best explain global patterns of forest structural complexity.

Springtails are omnipresent soil arthropods, vital for ecosystems. In the first global assessment of springtails, this study shows a 20-fold biomass difference between the tundra and the tropics, with distinct temperature-related patterns for diversity and metabolism that suggest climate change may restructure the functioning of soil biodiversity.

Identifying spatially variable genes (SVGs) is essential for linking molecular cell functions with tissue phenotypes. Here, authors introduce a non-parametric model that detects SVGs from two or three-dimensional spatial transcriptomics data by comparing gene expression patterns at granularities.

Here the authors show that a Newcastle disease virus based COVID-19 vaccine expressing a stabilized spike protein induces protective immunity in small animal models and reduces replication of variants of concerns. This vaccine candidate can be produced by influenza virus vaccine manufactures around the world.

Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.

Plasmodium vivax generally accounts for a low proportion of malaria cases in Africa, but population-level data on the distribution of infections is limited. Here, the authors use data from the Democratic Republic of the Congo and show that the prevalence is low (~3%) and diffusely spread.

Using a multi-OMICS approach, Haas et al identify 54 human genes and 16 host-targeting chemical compounds that regulate influenza A virus infection in lung epithelial cells, including AHNAK and COBP1 which are also essential for SARS-CoV-2 infection.

Spatial transcriptomics (ST) enables gene expression characterisation within tissue sections, but comparing across sections and technologies remains challenging. Here, authors develop STalign to spatially align ST data and demonstrate applications including aligning to common coordinate frameworks.

Loss-of-function variants in thyroid hormone transporter MCT8 cause a neurodevelopmental and metabolic disorder. Here the authors identify genotype-phenotype relationships, advance insights in MCT8 (dys)function and create a pathogenicity-severity variant classifier.

A genome-wide association study including over 76,000 individuals with schizophrenia and over 243,000 control individuals identifies common variant associations at 287 genomic loci, and further fine-mapping analyses highlight the importance of genes involved in synaptic processes.

The advantage of living in cities compared with rural areas with respect to height and BMI in children and adolescents has generally become smaller globally from 1990 to 2020, except in sub-Saharan Africa.

A detailed whole-body model of the fruit fly, developed using a physics-based simulation and deep reinforcement learning, accurately replicates real fly behaviour.

Subramanian et al. use the EcoTyper machine-learning framework to characterize the tumor, immune and stromal cell states and ecosystems that comprise sarcomas.

Omics data’s diversity and high-dimensionality challenge integration across technologies and with imaging. Here, authors introduce mapping method xIV-LDDMM that estimates geometric and feature transformations to integrate tissue-scale atlases with molecular and cellular-scale data.

Here the authors show that lowering IGF-1R levels in endothelial cells improves insulin sensitivity, boosts energy use, and supports beneficial changes in adipose tissue, offering insights into potential treatments for obesity-related metabolic disorders.

Differential responses of plant and animal functional diversity to climatic variation could affect trait matching in mutualistic interactions. Here, Albrecht et al. show that network structure varies across an elevational gradient owing to bottom-up and top-down effects of functional diversity.

Plasmacytoid dendritic cells monitor the bone marrow for apoptotic megakaryocytes (MKs) and deliver IFNα to the MK niche, triggering local on-demand proliferation and maturation of MK progenitors.