Search

vConTACT3 enables multirank, large-scale classification of eukaryotic and prokaryotic viruses.

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.

When doubly-degenerate band crossings known as Kramers nodal lines intersect the Fermi level, they form exotic three-dimensional Fermi surfaces composed of massless Dirac fermions. Here, the authors present evidence that the 3R polytypes of TaS₂ and NbS₂ are Kramers nodal line metals with open octdong and spindle-torus Fermi surfaces, respectively.

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.

Here, a combination of forward genetics and genome-wide association analyses has been used to show that variation at a single genetic locus in Arabidopsis thaliana underlies phenotypic variation in vegetative growth as well as resistance to infection. The strong enhancement of resistance mediated by one of the alleles at this locus explains the allele's persistence in natural populations throughout the world, even though it drastically reduces the production of new leaves.

The authors find that TDP-43 loss of function—the pathology defining the neurodegenerative conditions ALS and FTD—induces novel mRNA polyadenylation events, which have different effects, including an increase in RNA stability, leading to higher protein levels.

Metal–ligand cooperative catalysis involves both the metal and the ligand moieties present in a complex interacting with substrates. Cooperative catalysis is central to the mechanisms of hydrogenases, lactate racemase and alcohol dehydrogenase. This Perspective describes these enzymes, as well as the small-molecule mimics inspired by these elaborate natural catalysts.

A new version of nanorate DNA sequencing, with an error rate lower than five errors per billion base pairs and compatible with whole-exome and targeted capture, enables epidemiological-scale studies of somatic mutation and selection and the generation of high-resolution selection maps across coding and non-coding sites for many 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.

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.

A key component of quantum error correction is the decoding algorithm, which needs to be accurate but also with a computational overhead that doesn’t lead to backlogs and allows fast logical clock rates. Here, the authors show an FPGA-driven decoder featuring a coarse-grained parallel architecture and on-the-fly error model updates, allowing both high accuracy and real-time operation.

The LGN is a critical stage between the retina and visual cortex, but the properties of human LGN neurons are not fully understood. Here the authors report that they closely resemble those in monkeys and that closure of one eye increases the activity of putative inhibitory neurons connected to that eye.

H5N1 avian influenza viruses caused an outbreak in dairy cattle. We show that the potential for avian viruses to replicate in cow cells varies across H5N1 evolution, suggesting that the risk of spillover into mammals differs between variants.

Here the authors provide an explanation for 95% of examined predicted loss of function variants found in disease-associated haploinsufficient genes in the Genome Aggregation Database (gnomAD), underscoring the power of the presented analysis to minimize false assignments of disease risk.

Behavioural and psychosocial interventions can effectively reduce the risk of cardiovascular disease. In this Perspective, Burg et al. identify the elements and actions needed for a broad implementation of these interventions in standard cardiovascular care.

Typical quantum error correcting codes assign fixed roles to the underlying physical qubits. Now the performance benefits of alternative, dynamic error correction schemes have been demonstrated on a superconducting quantum processor.

Streptococcus equi subsp. zooepidemicus imports glucose via the bacterial mannose phosphotransferase system (PTS_man), which inhibits stringent response, supports growth in cerebrospinal fluid and promotes brain damage during meningitis.

A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.

Genomic analyses applied to 14 childhood- and adult-onset psychiatric disorders identifies five underlying genomic factors that explain the majority of the genetic variance of the individual disorders.

An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

Neural circuits in adult mouse visual cortex are stabilized by astrocytes, which secrete CCN1, resulting in reduced plasticity and increased maturation of multiple cell types.

Here, as part of the Sherlock-Lung study, the authors profile the microbiomes of 940 lung cancers in never smokers finding no significant associations with demographic and clinical features, suggesting lung bacteria are unlikely to have a sizable role in lung cancer.

High-depth sequencing of non-cancerous tissue from patients with metastatic cancer reveals single-base mutational signatures of alcohol, smoking and cancer treatments, and reveals how exogenous factors, including cancer therapies, affect somatic cell evolution.

Covalent KRAS inhibitors show initial responses but resistance limits durability. Here drug-induced hapten peptides are identified and characterized, enabling production of high affinity, cross-HLA T cell engagers that stabilize low density hapten peptide MHCs to drive tumor-specific killing.

Trends in global H₂ sources and sinks are analysed from 1990 to 2020, and a comprehensive budget for the decade 2010–2020 is presented.

The authors demonstrate dual-probe multi-messenger imaging of high-energy-density plasmas based on laser-wakefield-accelerated electrons. This enables spatiotemporally resolved simultaneous probing of plasma hydrodynamics and electromagnetic field evolution with both x-ray and electron beams.

This study shows that non-invasive ultrasound to the human nucleus accumbens can modulate deep brain activity and enhance reward-guided learning, offering a potential alternative to invasive neuromodulation therapies.

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.

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.

Femtosecond photoexcitation drives a coherent twist–untwist motion of the moiré superlattice in 2° and 57° twisted WSe₂/MoSe₂ heterobilayers.

Druckman et al. document gaps in trust in scientists in the USA. People from groups less represented among scientists (for example, women and those with lower economic status) are less trusting. Increasing the representation of these groups within science increases trust.

How to effectively communicate climate change to the public has long been studied and debated. Through a registered report megastudy, researchers tested the ten most-cited climate change messaging strategies published, finding that many had significant, but small, effects on climate change attitudes.

The authors present a scalable mass spectral search tool that identifies both known molecules and structural variants by estimating match significance. The method revealed biosynthetic pathways in Streptomyces, expanding the scope of metabolite discovery.

Here, the authors examine the mechanisms behind cheatgrass’s successful invasion of North American ecosystems. Their genetic analyses and common garden experiments demonstrate that multiple introductions and migrations facilitated cheatgrass local adaptation.

Electrochemical acid-base production has attractive applications in mineral recovery and CO₂ removal, but current membrane-based designs are plagued by resistive losses. The authors report a membrane-less system generating useful acid and base solutions at high rates with less energy.

Electrical tuning of the recombination zone in circularly polarized (CP) OLEDs enables switching the CP generation mechanism between normal and anomalous CP electroluminescence. This is exploited to electrically control the handedness of emitted CP light from the same device with the same enantiomer material.

Roles of of viruses in ocean subsurface oxygen maxima are unclear. Here, the authors analyse Bermuda Atlantic Time Series data to show that viruses may drive SOM in stratified oceans by boosting nutrient recycling and phytoplankton productivity linking virus activity to oxygen buildup and a stronger microbial loop.

Poly-ADP-ribose polymerase 1 (PARP1) plays key roles in DNA repair, transcription, and replication. Here, the authors used a single-molecule approach to reveal how PARP1 identifies DNA single-strand breaks in nucleosomes and how PARP1 activity regulates its DNA and chromatin binding kinetics.

The role of structural variants (SVs) in Mycobacterium tuberculosis has been understudied. In this study, the authors leverage 859 high-quality, diverse, long-read assemblies to construct pangenome reference graphs (PRGs).

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.

Mismatch repair pathway is frequently dysregulated across cancer types, commonly represented by loss of MLH1 or MSH2 gene expression. Here the authors model MLH1 missense mutations from patients to study how cytoplasmic localization of MLH1, promotes resistance to endocrine therapy but predicts response to cell cycle inhibitors in breast cancer.

Electrochemical amine regeneration offers a renewable, low-temperature pathway for CO₂ capture. Here, the authors reveal how anions regulate interfacial copper redox kinetics that control electrochemical CO₂ release using in-situ spectroscopic and computational analyses.

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.

cfDNA fragmentomics is a potential clinically applicable method for identifying cancer. Here, the authors assess fragmentomics analysis methods and their application to commercial targeted sequencing panels.

Deaminases of the APOBEC3 family contribute to the mutagenesis of various cancers, including urothelial carcinoma (UC) of the bladder. Here, the authors use functional studies and transcriptomics to demonstrate that APOBEC3 promotes tumour progression and squamous trans-differentiation in UC through IL-1α and downstream activation of the AP-1 transcription factor.

Geminin regulates DNA replication by binding CDT1 and preventing MCM helicase loading. Using a reconstituted system and structural modelling, the authors find geminin inhibits via steric clash with MCM, not by blocking the CDT1–MCM interface. Combined with CDK activity, it fully halts licensing.

Emerging materials between molecules and materials demand new modeling approaches. Here, the authors present a localized active space approach that enables accurate and efficient band structure calculations to capture long-range charge and energy transfer in correlated materials.