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Root-knot nematodes locate host plants by sensing microbial volatiles shaped by plant defence metabolites, revealing a surprising ecological link between plant chemistry, soil microbes and parasite behaviour in the rhizosphere.

A high-resolution transcriptomic and epigenomic cell-type atlas of the developing mouse visual cortex from embryonic to postnatal development is presented, providing a real-time dynamic molecular map associated with individual cell types and specific developmental events.

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.

iGluSnFR4f and iGluSnFR4s are the latest generation of genetically encoded glutamate sensors. They are advantageous for detecting rapid dynamics and large population activity, respectively, as demonstrated in a variety of applications in the mouse brain.

Humanity’s Last Exam, a multi-modal benchmark at the frontier of human knowledge, is designed to be an expert-level closed-ended academic benchmark with broad subject coverage.

Global Burden of Disease estimates show that between 1990 and 2023, the prevalence and burden of drug use disorders, inclusive of amphetamine, cannabis, cocaine and opioid use, have been increasing in high-income countries, particularly in the USA.

Long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons, which diversify extensively after birth in the cortex and striatum, but show limited postnatal changes in the septum, preoptic area and pallidum.

Specific pain-sensing nociceptors and chemosensory tuft cells form a circuit to promote type 2 immune responses in the intestine.

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.

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.

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.

Seagrass genomes of the deep-water Zostera pacifica and shallow-water Z. marina from the Eastern Pacific Ocean provide evidence for low-light adaptation exemplified in the wild hybrid Z. marina × pacifica subjected to low-light stress in aquaria.

 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. 

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.

There are limited vaccines available for Ebola virus and none for broad protection from filoviruses. Here, the authors rationally design vaccines using nanoparticles and stabilized Ebola virus and other filovirus glycoproteins, characterize antibody epitopes and profile lymph node and antibody responses in mice.

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.

A generative artificial intelligence-powered method enables de novo design of highly active enzymes based on information about the geometry of residues in the active site, without requiring protein backbone or sequence information.

RFdiffusion2, an extension of the RFdiffusion framework, builds de novo enzyme active sites using atom-level functional group constraints.

This study explores the genetic structure of hepatitis C virus outbreaks in rural U.S communities affected by the opioid crisis. Analysis of intra-host viral populations from 692 participants reveals hidden transmission networks.

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.

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.

Atomic-resolution microscopy and AI reveal how metallic nanowires grow inside carbon nanotubes through atom-by-atom wetting, advancing understanding of how next-generation materials can be synthesized from the atomic scale up.

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 hippocampus can replay long spatial sequences without ripples. When present, ripples cluster in spatially restricted zones as a function of replayed location that remap with barrier changes, implying a tagging role in consolidation.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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.