Search

A genomic barcoding scheme called two-layer DNA seqFISH+ enables the simultaneous mapping of more than 100,000 loci and has been used to identify cell-type-specific subnuclear compartments in the mouse brain.

This study presents a computational approach that effectively uses time-resolved multi-trait data from a high-throughput phenotyping platform for the genomic prediction of morphometric, geometric and colourimetric traits of Arabidopsis and maize lines.

NatD is an acetyltransferase responsible for N-α-terminal acetylation of the histone H4 and H2A and has been linked to cell growth. Here the authors show that NatD-mediated acetylation of histone H4 serine 1 competes with the phosphorylation by CK2α at the same residue thus leading to the upregulation of Slug and tumor progression.

An artificial intelligence model defines a data-driven set of total parenteral nutrition compositions to assist clinicians in personalized treatment of neonates in intensive care and is able to adapt recommendations to patient status, with validation from large external cohorts and a blinded reader study.

This research explores the linguistic traces of evidence-based reasoning and intuitive decision-making in congressional speeches from 1879 to 2022. The analysis suggests that evidence-based language has continued to decline since the mid-1970s, together with a decline in legislative productivity.

The genetic basis of C-reactive protein levels remains underexplored in diverse populations. Here, the authors show 113 loci associated with CRP across ancestries, highlighting 55 novel genes and ancestry-specific signals with functional and disease relevance.

There is currently no approved influenza vaccine for newborns, so development of such a vaccine is warranted. Here the authors show, using a African green monkey newborn model, that an adjuvanted nanoparticle vaccine containing the stem region of influenza hemagglutinin can induce robust IgG responses, with the functionality of the antibodies linked to viral clearance.

Brief ciprofloxacin exposure in humans drives antibiotic resistance evolution in gut bacteria through selective sweeps, particularly involving DNA gyrase mutations, which persist long after exposure and demonstrate the human gutʼs capacity to promote resistance evolution.

How does the brain balance specialization and integration? Using high-resolution MRI and a post-mortem atlas, this study reveals how local and global cortical organization are linked, shaping functional diversity across brain areas.

The authors show that brain inflammation in COVID-19 correlates with viral load, systemic inflammation and virus-sensing pattern recognition receptors. Microglial dysfunction occurs at sites of vascular inflammation with myelin injury and synapse loss.

Dendritic cells (DCs) induce infection-protective immune memory, which has yet to be exploited for cancer therapy. Here we show that type 1 DC vaccines quantitatively and qualitatively favors anti-tumor T cell memory that prevents cancer relapse.

Arrayed and pooled high-throughput screening is crucial for drug discovery and CRISPR functional genomics. Here, the authors present dFLASH; a dual FLuorescent transcription factor Activity Sensor for Histone-integrated live-cell reporting for high performance screening applications across numerous pathways and screening contexts.

LINE-1 activity was quantified in a large, pan-cancer dataset, finding locus-specific heterogeneity and new associations using a computational pipeline. A mathematical mediation model of p53 and L1 interactions was inferred. Somatic retrotransposition was seen in Li-Fraumeni Syndrome with heritable TP53 mutations.

Mechanisms underlying treatment failure of antileishmanial therapy are unclear. Here the authors provide transcriptome data of innate immune cells from cutaneous leishmaniasis patients undergoing treatment and find that a heightened type-I interferon response is associated with treatment failure.

Sun et al. report human lifespan changes in the brain’s functional connectome in 33,250 individuals, which highlights critical growth milestones and distinct maturation patterns and offers a normative reference for development, aging and diseases.

The authors conduct a national inventory on individual tree carbon stocks in Rwanda using aerial imagery and deep learning. Most mapped trees are located in farmlands; new methods allow partitioning to any landscape categories, effective planning and optimization of carbon sequestration and the economic benefits of trees.

This systematic review and meta-analysis aimed to estimate the relationship between death anxiety and distress or symptoms of mental disorders. The findings suggest consistently positive associations between death anxiety and distress outcomes.

This work integrates duplex sequencing with cost-effective Ultima sequencing to enhance the accuracy of whole-genome circulating cell-free DNA profiling.

COMET, an artificial intelligence method that improves the analysis of small medical studies using large clinical databases, has been created. COMET can help develop better artificial intelligence tools and identify key biomarkers across many diseases, potentially changing medical research.

The identification of cellular targets for natural products that potently inhibit the growth of cancer cell lines implicates oxysterol-binding proteins in the growth of cancer cells. These natural products, termed ORPphilins, also affect sphingomyelin biosynthesis.

A method called UltraSelex for identifying RNA aptamers has been developed. UltraSelex is noniterative and can combine biochemical partitioning, high-throughput sequencing and computational signal-to-background rank modeling of hits in approximately 1 day.

A benchmarking competition improves tools that predict how regulatory regions control gene expression.

The ability to physically partition the human brain at a spatial resolution comparable to neuroimaging methods enabled the development of a brain-wide atlas of mitochondrial content, specialization and enzymatic oxidation and phosphorylation activities.

In a broad cross-tissue analysis, the authors show that a receptor called EDA2R steadily increases with age in both humans and animal models, and becomes even more active in conditions like obesity and diabetes, intensifying inflammation-like processes in muscle cells.

ADP-heptose binds to ALPK1, triggering transcriptional reprogramming and NF-κB activation, endowing pre-leukaemic cells with a competitive advantage due to excessive clonal proliferation.

MASLD is a growing global health concern. Here, the authors define a senescent hepatocyte gene signature (SHGS), demonstrate its clinical relevance, and identify senolytic therapies that selectively eliminate SHGS+ hepatocytes to improve MASLD and systemic health.

Perturbed B cell responses have been associated with Crohn’s disease. Here, the authors sequence the B cell receptor repertoire in patients with Crohn’s disease and identify shared B cell clones, thus implicating the presence of common Crohn’s disease-associated antigens driving a pathogenic B cell response.

The biological mechanisms of rehabilitation after stroke are not fully understood. Here authors identify parvalbumin interneurons as a key mediator of rehabilitation-induced stroke recovery and a drug targeting these neurons as a potential therapy.

Genetic mechanisms of blood pressure regulation remain poorly defined. Here, the authors perform a kidney multi-omics study to identify 399 kidney effector genes, 11 miRNAs and 97 proteins for blood pressure and hypertension.

A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions, with generalizability to unseen cell types.

Transcriptomic and proteomic analyses of cells and matrix along the fibrotic trajectory in mouse lung identified PI16 as an anti-fibrotic factor with potential for therapeutic application in humans.

Anxiety-like behaviour in mice, as a result of psychological stress, is shown to be mediated by GDF15 release in response to adipose tissue lipolysis.

Bernier, Hefendehl et al. describe a stromal progenitor cell population consisting of pericytes, venular smooth muscle cells and perivascular fibroblasts in the adult brain that modify their function and coordinate blood vessel repair following stroke.

Catena et al. report that melanoma-secreted midkine impairs differentiation and function of dendritic cells, limiting antitumor immunity and response to immune checkpoint blockade.

The ratio between the levels of two synaptic proteins in cerebrospinal fluid predicts future cognitive resilience versus decline among presymptomatic individuals and individuals with early Alzheimer’s disease harboring amyloid and tau pathology.

A workflow using conserved amino acid domains identifies viruses in sequence data at single-cell resolution.

AI-guided epigenetic classification is integral for accurate brain tumour diagnosis. Here, the authors introduce an interpretable framework to explain the AI process, revealing biological insights and potential therapeutic targets.

This study assessed COVID-19 social science preprints’ replicability using structured groups. Both beginners and more-experienced participants used a elicitation protocol to make better-than-chance predictions about the reliability of research claims under high uncertainty.

Meyer and Schumacher use simulations to show that accumulation of stochastic variation is sufficient to build clocks that can measure both chronological and biological age, sensitive to changes induced by smoking, calorie restriction, parabiosis and reprogramming.

The freshwater planarian S. mediterranea is an important model organism for regeneration research but its use in aging research is little explored and S. mediterranea is commonly referred to as immortal. Here Dai et al. report age-associated physiological and molecular changes in the sexual lineage of S. mediterranea, and global reversal of such changes after regeneration.

Over time, paralogous genes accumulate changes in their sequences that do not affect their function, which is called cryptic variation. Using paralogous myosins, this study shows how cryptic variation modulates the functional effect of mutations and biases duplicates to distinct evolutionary fates.

Analysis of copy number alterations in 1,451 patient-derived xenografts (PDXs) and matched patient tumor samples shows strong conservation from patient tumors through late-passage PDXs and a lack of systematic copy number evolution driven by the mouse host.

Deconvolution methods infer levels of immune infiltration from bulk expression of tumour samples. Here, authors assess 6 published and 22 community-contributed methods via a DREAM Challenge using in vitro and in silico transcriptional profiles of admixed cancer and healthy immune cells.

Analysis of pre- and post-chemotherapy samples collected from 22 patients with high-risk neuroblastoma using single-nucleus RNA and ATAC sequencing and spatial omics characterizes therapy-related changes in cell composition and the tumor microenvironment.

In this study, the authors show that low levels of VDAC2 and Bak in hepatocyte mitochondria make them resistant to cell death induced by truncated Bid (tBid), while increased VDAC2 and Bak in liver cancer cells allow specific targeting by combinations of tBid activators and Mcl-1 inhibitors.

The analysis of pairs of identical SARS-CoV-2 genome sequences enables characterization of transmission patterns between geographies and age groups.

In a phase 1/2 trial in patients with advanced non-small-cell lung cancer (NSCLC), followed by a phase 2 trial in an EGFR-mutant selected population, treatment with the TROP2-targeting antibody–drug conjugate sacituzumab tirumotecan led to encouraging clinical response rates, especially in patients with EGFR-mutant NSCLC, which was supported by mechanistic data.

In this study the authors consider the structural variants (SVs) present within cancer cases of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. They report hundreds of genes, including known cancer-associated genes for which the nearby presence of a SV breakpoint is associated with altered expression.