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Defining the spatial organization of tissues and organs like the brain from large datasets is a major challenge. Here, authors introduce CellTransformer, an AI tool that defines spatial domains in the mouse brain based on spatial transcriptomics, a technology that measures which genes are active in different parts of tissue.

Available wheat genomes are annotated by projecting Chinese Spring gene models across the new assemblies. Here, the authors generate de novo gene annotations for the 9 wheat genomes, identify core and dispensable transcriptome, and reveal conservation and divergence of gene expression balance across homoeologous subgenomes.

The International Brain Laboratory presents a brain-wide electrophysiological map obtained from pooling data from 12 laboratories that performed the same standardized perceptual decision-making task in mice.

A fresh approach to protein design that incorporates excited intermediate states enables precise control over the lifetime of protein interactions, with potential applications in cell-signalling modulation and in biosensors and synthetic circuits.

The authors integrate single-cell transcriptomic data with prior gene graphs to produce a biologically meaningful cell state manifold that can predict driver genes for genetic perturbations and differentiation events across diverse cell types.

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.

The Connectome Annotation Versioning Engine (CAVE) is a platform for proofreading, annotating and analyzing datasets reaching the petascale. Currently, CAVE is used for electron microscopy datasets, but it can potentially be used for other large-scale datasets.

A single-cell sequencing study using more than 30,000 tumour genomes from human ovarian cancers shows that whole-genome doubling is an ongoing mutational process that drives tumour evolution and disrupts immunity.

The NeuroXiv platform enables AI-powered open mining of a database of reconstructions of more than 175,000 mouse neurons, registered to the Common Coordinate Framework. The platform supports queries about connectivity, projection patterns and other morphological features.

Using volumetric electron microscopy, the authors map and analyze the structure of cortical inhibition with synaptic resolution across a column of visual cortex.

Zhao et al. present RAPiDock, an all-atom diffusion model that predicts peptide–protein binding patterns across 92 amino acid types, enabling high-throughput virtual screening for advancing therapeutic peptide design.

A high-bandwidth neuromotor interface offers performant out-of-the-box generalization across people.

By analysing the smartphone data of 2,112,288 participants, in particular observing and comparing the activity of the same individual in two different environments, we find that increases in the walkability of environments result in increases in daily physical activity, providing evidence of the importance of the built environment on physical health.

A large language model designed for health monitoring provides personalized sleep and fitness predictions, insights and advice.

There are a number of programs available for digital reconstruction of neural morphology. Here the authors present a standardized specification of the SWC file format, and introduce xyz2swc, a tool that converts reconstruction formats described in the literature into the SWC standard.

Dense calcium imaging combined with co-registered high-resolution electron microscopy reconstruction of the brain of the same mouse provide a functional connectomics map of tens of thousands of neurons of a region of the primary cortex and higher visual areas.

As part of the BICCN consortium, the authors used a single-cell transcriptomic imaging method to produce a highly defined atlas of cell types across the mouse primary motor cortex.

 A transcriptomic cell-type atlas of the whole adult mouse brain with ~5,300 clusters built from single-cell and spatial transcriptomic datasets with more than eight million cells reveals remarkable cell type diversity across the brain and unique cell type characteristics of different brain regions. 

In this study, the authors assess the global response to the toxic aldehyde glyoxal (GO) in Pseudomonas aeruginosa, suggesting that GO controls quorum sensing during infection through a mechanism involving a novel protein, ArqI.

The understanding of defects in bromide-based perovskites remains elusive. Electric biasing and introducing bromide in the precursor solution during crystal growth is shown to significantly reduce defects in formamidinium lead bromide.

Satellite data show declining global forest recovery from tree mortality since the 1990s, driven by warming and water scarcity. Canopy water recovers slower than greenness, stressing the need for a multifaceted approach to assessing recovery.

Reconstruction of neuronal morphology imaged by brightfield microscopy remains a challenge. Here, authors show gene expression correlates of laminar innervation on transcriptomically defined cortical populations by developing a method for automation.

A large proportion of methane emissions from natural gas production sites are released by a fraction of high-emitting sources. Here, using Monte Carlo simulations, the authors reveal that super-emitters occur due to abnormal process conditions, explaining component and site-based inventory discrepancies.

Chen et al. show that in mice, extracellular matrix remodeling drives early migration of the anterior signaling center, establishing the body axis sooner than expected—a mechanism potentially conserved in humans.

Warmer and more arid conditions are triggering forest die-off and mortality events worldwide, but how are the droughts’ characteristics leading to tree death? This study shows that tree-killing droughts are longer and more intense in dry versus wet biomes, while mortality-inducing droughts are higher in intensity in angiosperm-dominated forests.

Bull et al. developed a mathematical model for how bacteria colonise urinary catheters. The model reveals that different strategies may be needed to reduce catheter associated infection for long-term vs short-term catherised patients

Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by certain bacteria and fungi that establish symbiotic relationships with plants. Here, the authors show that LCOs are produced also by many other, non-symbiotic fungi, and regulate fungal growth and development.

3D brain atlases enable spatial data integration across studies. Here, the authors present the Developmental Mouse Brain Common Coordinate Framework, a 3D multimodal atlas from embryonic to adult ages for cell type mapping through brain development.

A consensus cell type atlas for the fly brain provides both an intellectual framework and open-source toolchains for brain-scale comparative connectomics.

When enzymes require rescue strategies to complete progression through their reaction, but natural safety nets fail, disease states can ensue.

Invasive Spartina grasses accumulate high levels of intracellular dimethylsulfoniopropionate (DMSP). Here, the authors report the isolation and characterization of the genes involved in DMSP biosynthesis and show that administration of DMSP by root uptake or overexpression of the DMSP biosynthesis genes results in salinity and drought tolerance in Arabidopsis.

In mouse, an axonal connectivity map showing the wiring patterns across the entire brain has been created using an EGFP-expressing adeno-associated virus tracing technique, providing the first such whole-brain map for a vertebrate species.

Small-scale farmers in Southeast Asia are increasingly turning to monocultures of oil palm and rubber to maximize income. Clough and colleagues demonstrate that this land-use change in Indonesia comes at a cost to a wide array of ecosystem functions and biodiversity.

FlyWire is an online community and a platform for proofreading electron microscopy-based connectome data of the Drosophila brain.

The frequency of severe droughts is increasing in many regions around the world as a result of climate change. An analysis of tree growth and mortality data from forests worldwide suggests that large trees fare worse under drought than small trees.

A pangenome of the Cannabis genus including 193 genomes demonstrates high variability in most of the genome but low diversity in cannabinoid synthesis genes and provides a resource for future genetic studies and crop optimization.

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.

Skilled reaching movements are critical for survival. Here, the authors show in mice that the parafascicular (Pf) and ventroanterior/ventrolaber (VAL) nuclei of the thalamus govern distinct circuits related to reaching direction and speed, respectively.

DeepInterpolation is a self-supervised deep learning-based denoising approach for calcium imaging, electrophysiology and fMRI data. The approach increases the signal-to-noise ratio and allows extraction of more information from the processed data than from the raw data.

Smooth topological photonic interfaces lead to less localized boundary modes which improves their guiding characteristics in both spin- and valley Hall metasurfaces. The modes become insensitive to the lattice details, showcasing improved bandgap crossing and longer propagation distances.

A large, open dataset containing parallel recordings from six visual cortical and two thalamic areas of the mouse brain is presented, from which the relative timing of activity in response to visual stimuli and behaviour is used to construct a hierarchy scheme that corresponds to anatomical connectivity data.

The human Fallopian tube (FT) is implicated as a site of origin for pelvic serous cancers. Here the authors conduct multi-omics analysis on over 100 FTs. The results challenge the assumption that BRCA1/2 mutation carriers exhibit significant molecular alterations in normal FTs before loss of heterozygosity (LOH) occurs, and suggest that tumorigenesis in BRCA1/2 carriers requires LOH or secondary genetic events rather than haploinsufficiency alone.

Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of the carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation and gain further insights into asterid genome evolution, including characterization of two new polyploidization events.