Search

Understanding HIV evolution during early infection is important for prevention strategies. Here, leveraging deep sequencing during acute infection, the authors show a higher-than-expected frequency of multiple transmitted viruses, highlighting fluctuating viral lineages, which may inform future vaccine development.

Neonatal sepsis caused by Escherichia coli is associated with reduced transfer of pathogen-specific maternal antibodies and, in a mouse model, can be prevented by maternal preconceptual colonization with probiotic E. coli.

The ancient X and Y chromosomes of cannabis and hop display interesting patterns of molecular evolution and harbor key floral genes. Here the authors show that the X chromosome, not the Y, determines sex, and identify an X-linked ethylene biosynthesis gene as a candidate for sex-determination.

PTCHD1-AS, which encodes a long non-coding RNA, is associated with the aetiology of autism spectrum disorder in humans through striatal molecular and circuit-level dysregulation.

How RNA isoforms and chemical marks evolve across species remains poorly understood. This study uses direct RNA long-read sequencing across mammals to show that conserved isoforms account for most expression, while isoform-specific conserved m6A and coordinated splicing reveal conserved regulatory mechanisms.

Massively parallel reporter assays promise rapid in vivo characterization of enhancer AAVs. Here, through systematic testing, authors uncover pervasive technical and biological noise, including chimeric AAV species, that exposes fundamental limitations in pooled enhancer screening.

Women diagnosed with attention deficit hyperactivity disorder (ADHD) in childhood have a significantly higher risk of developing physical and mental health conditions (multimorbidity) in early adulthood. ADHD and socioeconomic deprivation independently increase this risk, and in combination have a synergistic effect.

Using xenograft inflammation–recovery models and single-cell multiomics, a haematopoietic stem cell population after inflammatory stress is identified.

Jayaram et al. assessed the performance of the combination of circulating tumor DNA and serum prostate-specific antigen for dynamic monitoring of metastatic prostate cancer at first-line treatment in this prospective observational clinical trial.

A comparison of sequencing of complex mock communities performed at multiple depths and analysed using different methods establishes minimum standards that can ensure the accuracy of metagenomic analysis for a particular objective.

A phylogenetic analysis examined the origins of the first mpox outbreak in Sierra Leone and found evidence of an emerging lineage (G.1) that has likely descended from the Nigerian epidemic and emerged in Sierra Leone months before first detection.

In a first-in-human trial combining the transplantation of CD33-negative CRISPR-edited hematopoietic cells with the CD33-targeted antibody–drug conjugate gemtuzumab ozogamicin, all transplanted patients achieved primary engraftment, and the treatment was well tolerated.

Restricting or permitting H3K27me3 spreading concentrates or dilutes canonical PRC1 (cPRC1), respectively, which affects three-dimensional chromatin interactions. Disruption of cPRC1 compromises repression of Polycomb target genes and induces differentiation and tumor regression in H3K27M-mutant glioma.

Genome-wide analysis coupled with long-read sequencing identifies a repeat expansion in GOLGA8A associated with high risk for atypical frontotemporal lobar degeneration with ubiquitin-positive inclusions.

Targeted sequencing of neurodegenerative disease genes and transcriptome-wide sequencing in postmortem brain and spinal cord samples from individuals with amyotrophic lateral sclerosis or frontotemporal dementia identify somatic mutations as likely drivers of disease pathology.

Supported by both experimental and human data, this study reveals that poor sleep weakens immune responses to influenza vaccination and increases infection risk, highlighting sleep as a modifiable determinant for vaccination effectiveness.

The 1918 flu pandemic killed 50 million people — and it could happen again.

It’s just a game — isn’t it?

Decreased brain volumes and increased NfL levels can be observed earlier than disease diagnosis in short-tandem-repeat-associated neurological diseases.

Decima learns to predict cell-type-specific gene expression based on DNA sequences, contributing to the analysis of gene regulation and design of context-specific regulatory elements.

Segmented Filamentous Bacteria (SFB) in mice are important gut commensals in both health and disease. Here, Kiran et al. characterize a novel human SFB species that is widespread in Africa and show that humans worldwide harbor multiple SFB species and at least six SFB lineages.

Pooled production of recombinant AAV vectors leads to frequent genetic recombination.

The authors resolve 63 structurally diverse haplotype structures for the 22q11.2 deletion syndrome region. Deletion risk differs depending on structure; individuals of African ancestry are enriched for inverted repeats that predispose to inversion.

N-Nitrosamine cancer risk may be vastly underestimated due to adult-focused safety testing. Here, the authors reveal that younger mice are profoundly susceptible to NDMA-induced genotoxicity and tumorigenesis, and demonstrate that this risk is suppressed by DNA repair.

DNA-sequencing data from primary tumours and paired metastases from participants in the TRACERx lung study and PEACE autopsy programme are used to analyse the metastatic diversity of advanced non-small cell lung cancer and the seeding patterns that underpin it.

Lu et al. report that PCBP1 safeguards AARS2 alternative splicing in the heart, and that loss of PCBP1 disrupts AARS2 splicing, leading to infantile mitochondrial cardiomyopathy. Loss of cardiac PCBP1 or AARS2 impairs oxidative phosphorylation and activates mitonuclear signaling and the unfolded protein response pathway.

A large-scale proteomics analysis of the dark proteome by the TransCODE Consortium reveals many translated non-canonical open reading frames to encode microproteins and peptideins.

A pangenome reference for the phenotypically diverse crop sorghum aims to help accelerate future efforts to breed crops that are better adapted to changing environments.

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.

The authors present SVclone, a computational method for inferring the cancer cell fraction of structural variants from whole-genome sequencing data.

Structural variants are an underexplored source of genetic diversity. Here, the authors use phased pangenome graphs to improve detection of these variants in dairy cattle and link these variants to traits of economic importance.

This study challenges the paradigm that resistance mutations precede fitness compensatory adaptations, showing that pre-existing alterations in mycobacterial oxidative stress responses can prime rapid evolution of resistance without fitness costs.

Endosomal sequestration of lipid-based nanoparticles is a barrier to delivery of nucleic acids. Here the authors test an array of cholesterol variants and perform in-depth investigation of nanoparticle shape, internal structure and intracellular trafficking.

DNA variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve genotyping accuracy, however this increases computational complexity. Here the authors develop an approximate haplotagging method that simplifies the process and enables state-of-the-art variant calling performance with multiple sequencing platforms.

Transparent conducting electrodes are a key performance and sustainability bottleneck in high-efficiency perovskite–silicon tandem solar cells. This Review examines how optical, electrical and interfacial losses in transparent conducting electrodes arise in tandem cells and outlines strategies to enable scalable, low-indium electrodes for next-generation devices.

Kozlova et al. report a functional role for NDRG1 in regulating R-loops and DNA repair, thereby linking cancer-associated fibroblast-derived extracellular matrix to chemotherapy responses in pancreatic cancer.

Escherichia coli is widespread in healthy breastfed infants, yet its ecological role is unclear. Here, the authors provide insights into the mechanisms supporting its persistence and co-existence with dominant Bifidobacterium, including potential cross-feeding of human milk oligosaccharides.

Genetic analyses in more than 15,000 individuals from across the Americas, including individuals with autism and family members, define the genetic landscape of autism in Latin American populations and identify significant overlap with other ancestries.

With the generation of large pan-cancer whole-exome and whole-genome sequencing projects, a question remains about how comparable these datasets are. Here, using The Cancer Genome Atlas samples analysed as part of the Pan-Cancer Analysis of Whole Genomes project, the authors explore the concordance of mutations called by whole exome sequencing and whole genome sequencing techniques.

Structural features of DNA double-strand break (DSB) ends play key roles in determining DNA repair pathway usage and outcomes. Here, the authors identify ERCC6L2, a poorly characterized ATPase, as playing a minimal role in blunt end DSB repair but crucial for repair of staggered end DSBs.

In this study, long-read RNA sequencing achieves accurate single-nucleotide polymorphism calling, haplotype phasing and allele-specific expression analysis.

The assignment of genetic variants to the two copies of the genome present in cells (phasing) is crucial for predicting the consequences, interaction and inheritance of variants, but is limited by the length of sequencing reads and stretches of homozygosity in the genome. Here the authors develop a method that utilizes DNA methylation signals from Oxford Nanopore Technologies sequencing data to improve phasing.

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.