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Along with the rapid merge and development of biotechnology and nanotechnology, various DNA nanostructure scaffolds have been designed, characterized and exploited for a range of applications. Particularly, we have seen the evolution of surface-confined DNA probes with rational design from one-dimensional to two-dimensional and then to three-dimensional, which greatly improve our ability to control the density, orientation and passivation of the surface. In this review, we aim to summarize recent progress on the improvement of probe–target recognition properties by introducing DNA nanostructure scaffolds. A range of new strategies have proven to provide significantly enhanced spatial positioning range and accessibility of the probes on surface over previously reported linear structures. We will also describe applications of DNA nanostructure scaffold-based biosensors.

Cr³⁺-sensitized lanthanide-doped nanoparticles afford high-brightness luminescence in the near-infrared region for applications in in vivo non-invasive bioimaging.

Understanding deregulation of biological pathways in cancer can provide insight into disease etiology and potential therapies. Here, as part of the PanCancer Analysis of Whole Genomes (PCAWG) consortium, the authors present pathway and network analysis of 2583 whole cancer genomes from 27 tumour types.

There’s an emerging body of evidence to show how biological sex impacts cancer incidence, treatment and underlying biology. Here, using a large pan-cancer dataset, the authors further highlight how sex differences shape the cancer genome.

Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

In somatic cells the mechanisms maintaining the chromosome ends are normally inactivated; however, cancer cells can re-activate these pathways to support continuous growth. Here, the authors characterize the telomeric landscapes across tumour types and identify genomic alterations associated with different telomere maintenance mechanisms.

Whole-genome sequencing data from more than 2,500 cancers of 38 tumour types reveal 16 signatures that can be used to classify somatic structural variants, highlighting the diversity of genomic rearrangements in cancer.

Viral pathogen load in cancer genomes is estimated through analysis of sequencing data from 2,656 tumors across 35 cancer types using multiple pathogen-detection pipelines, identifying viruses in 382 genomic and 68 transcriptome datasets.

Analysis of cancer genome sequencing data has enabled the discovery of driver mutations. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium the authors present DriverPower, a software package that identifies coding and non-coding driver mutations within cancer whole genomes via consideration of mutational burden and functional impact evidence.

A pan-cancer genomic analysis reports the effects of structural variations on chromatin domains (TADs). Most TAD disruptions do not result in appreciable changes in expression of nearby genes.

An analysis of 2,954 genomes from 38 cancer subtypes identified 19,166 retrotransposition events in 35% of samples. Aberrant LINE-1 retrotranspositions can lead to the deletion of tumor-suppressor genes as well as the amplification of oncogenes.

Some cancer patients first present with metastases where the location of the primary is unidentified; these are difficult to treat. In this study, using machine learning, the authors develop a method to determine the tissue of origin of a cancer based on whole sequencing data.

Many tumours exhibit hypoxia (low oxygen) and hypoxic tumours often respond poorly to therapy. Here, the authors quantify hypoxia in 1188 tumours from 27 cancer types, showing elevated hypoxia links to increased mutational load, directing evolutionary trajectories.

Multi-omics datasets pose major challenges to data interpretation and hypothesis generation owing to their high-dimensional molecular profiles. Here, the authors develop ActivePathways method, which uses data fusion techniques for integrative pathway analysis of multi-omics data and candidate gene discovery.

The characterization of 4,645 whole-genome and 19,184 exome sequences, covering most types of cancer, identifies 81 single-base substitution, doublet-base substitution and small-insertion-and-deletion mutational signatures, providing a systematic overview of the mutational processes that contribute to cancer development.

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.

Cancers evolve as they progress under differing selective pressures. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, the authors present the method TrackSig the estimates evolutionary trajectories of somatic mutational processes from single bulk tumour data.

Ribonucleoprotein aggresomes exclude ribonucleases and protect mRNA to promote rapid translation reactivation and cellular recovery after stress alleviation in Escherichia coli.

In this study, Yang et al. compile a global dataset to uncover the degree to which plants coordinate root and seed traits. They report a global positive correlation between root diameter and seed size, driven by dual roles of arbuscular mycorrhiza in phosphorus uptake and pathogen defence.

The balance between apoptosis and autophagy is critical for normal development, proper tissue function, and disease pathogenesis. Here, the authors show previously unannotated BIRC6 domains, including a ubiquitin-like domain, and how it utilizes its ubiquitylation function to regulate both apoptosis and autophagy.

Pulmonary veno-occlusive disease (PVOD) is a fatal disease characterised by remodelling of pulmonary veins and haemosiderin accumulation in macrophages. Here the authors examine the lack of GCN2 in PVOD as this has been observed in human disease and deficiency of GCN2 in mouse and rat PVOD models alters transcriptome profiles and increases macrophage ferroptosis.

The pathogenesis of hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC) remains to be understood. Here the authors identify that USP26 deubiquitinase drives the progression of HBV-associated HCC via regulating the protein stability of Sirtuin 1.

Cervical cancer remains a significant public health problem in many regions. Here, the authors perform a proteogenomic analysis of cervical cancer in Chinese patients; they reveal proteomic subgroups associated with clinical and biological features, and a potential biomarker of response to radiotherapy.

By constructing a graph-based grapevine pangenome reference (Grapepan v.1.0) and incorporating structural variations and phenotypic maps, the study investigates the genetic basis of agronomic traits, empowering grapevine genomic breeding.

Protein-rich diets are known to enhance fecundity but often reduce lifespan across various species. Here, the authors demonstrate that fruit flies undergo a sex-specific post-mating dietary shift that balances fecundity with overall fitness, regulated by leucokinin-labeled neural circuits.

Lanthanide downshifting nanoparticles with tunable emissions in the NIR-IIb sub-window (1,500–1,700 nm) region are ideal for deep-tissue imaging. Biofunctionalized core–shell, cubic-phase thulium-based nanoprobes show the non-invasive imaging of murine cerebral vasculature and the tracking of single immune cells and their extravasation in an inflammatory microenvironment.

Erbium quantum emitters operating in the telecom C band are promising for spin-photon interfaces but achieving both optical and spin coherence has been challenging. Gupta et al. report two types of erbium dopants in epitaxial Y₂O₃ thin films occupying distinct lattice sites and exhibiting long spin and optical coherence times

Cui et al. report analogue photoelectronic reservoir computing with IGZO synaptic transistors as the reservoir and TaOX-based memristor array as the output layer. A receptive field inspired encoding scheme is implemented to simplify the feature extraction for dynamic vision processing.

Metabolic dysfunction is an important characteristic of vascular smooth muscle cells (VSMCs) phenotypic transition in aortic dissection. Here, the authors show lncRNA H19 could encode a peptide, GMRSP. GMRSP regulates the glycolysis by counteracting hnRNP A2B1-mediated pyruvate kinase M pre-mRNA alternative splicing and control the phenotypic transition of VSMCs.

Persistent luminescence is a promising bioimaging technique that is not affected by background autofluorescence, but its in vivo application is challenged by the fact that the materials currently available are activated by high-energy light, with emission in the ultraviolet and visible spectral windows. In this paper the authors engineer X-ray activated, lanthanide-based nanoparticles with a tunable emission in the biologically relevant NIR-II spectral region, which allows high-contrast, multimodal in vivo deep-tissue organ imaging.

There is a lack of guiding parameters to design metallic materials such as high-entropy alloys with strength-ductility synergy. Here, the authors propose such an effective parameter κ, the ratio of short-ranged interactions between closed-pack planes, experimentally validated by six alloys.

Electrolyte design is key for high-energy lithium metal batteries, but structure–performance links are hard to predict. A framework using the normalized cation/anion–solvent affinity enables quantitative prediction of microstructure, transport and interphase, driving exceptional performance.

The genome sequences of 175 Ebola virus from five districts in Sierra Leone, collected during September–November 2014, show that the rate of virus evolution seems to be similar to that observed during previous outbreaks and that the genetic diversity of the virus has increased substantially, with the emergence of several novel lineages.

In a recent clinical trial for oral administration of cipargamin in individuals with malaria, there was an emergence of recrudescent parasites with a G358S mutation in PfATP4. In this work, the authors investigate the effect of this mutation on the function of the ATPase, on parasite growth and susceptibility to antimalarial drugs.

This paper determines the oxygen fugacity of the Chang’e-6 basalts from the South Pole–Aitken (SPA) basin on the farside of the Moon. The results show that the mantle beneath the farside SPA basin is more reduced than that beneath the nearside, as determined by the Apollo and Chang’e-5 basalts.

The acidophilic fungus Acrodontium crateriforme is present in traps of the carnivorous plant Drosera spatulata and promotes prey digestion.

The authors propose a set of guidelines for far-UVC optical design, under which the multi-stimulated far-UVC luminescence at 222 nm in Pr³⁺ -doped SrF₂ is realized, offering unique opportunities for solar-blind imaging and structural health monitoring in complex environments.

The heterogeneity of HSPCs in response to IR stress remains poorly characterized. Here, the authors provide insights into the molecular intricacies of IR-induced BM injury and reveal the roles of BMP4-BMPR2 signaling in radiation resistance of HSCs.

Inflammatory conditions often affect colorectal cancer patients, and their effect on their ongoing treatment is a pressing medical question. Here authors show that inflammation interferes with local anti-tumour immune response and inhibits response to immune checkpoint blockade therapy via immunosuppressive neutrophil leukocytes.

In this study, authors identified neutralizing antibodies by isolating B cells from SARS-CoV-2 Delta infected patients and detect altered structural features, likely introduced by somatic hypermutation, that are involved in epitope binding and increase neutralization breadth against virus variants.

Analysis of big Argo data reveals that model representation of global ocean circulation near 1000-m depth is substantially compromised by inaccuracies. Only 3.8% of the mid-depth ocean circulation can be considered accurately modelled.

Cholinergic neurons in the diagonal band of Broca degenerate early in Alzheimer’s disease. Here the authors show that in healthy mice, these cholinergic inputs innervate newborn neurons in the hippocampus, and that loss of this innervation in an Alzheimer’s disease model leads to impairments in spatial memory.