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The drivers of coexistence between species with different growth rates are of interest in both ecology and applied microbial science. The authors show, via modelling, that species interactions moderated by consumption or degradation of chemicals can allow coexistence.

Transcription termination or pausing during DNA replication in bacteria and humans results in DNA damage with exposed 3′ single-stranded DNA ends and mutations.

AI decision support system non-homogenously influences clinical decisions in dynamic treatment regimen, as it depends on several factors including prior knowledge, preference, disease type, treatment modality, and AI’s learned behavior and inherent biases.

Genotype and exome sequencing of 150,000 participants and whole-genome sequencing of 9,950 selected individuals recruited into the Mexico City Prospective Study constitute a valuable, publicly available resource of non-European sequencing data.

Transcriptomic analysis may provide information about the differentiation state and cell of origin of a cancer. Here, the authors assess mRNA signals in 1300 childhood and adult renal tumors and report a fetal origin of childhood tumors and no dedifferentiation of adult tumors.

Knock-in mice conditionally or constitutively expressing Cas12 variants enable a wide range of ex vivo and in vivo applications requiring multiplexed genome engineering.

In this age of abundant remote-sensing data, global datasets are increasingly relied upon to analyse the planet at unprecedented scale and resolution. We offer three considerations on uncertainties and potential misapplications of global datasets, to ensure results appropriate for decision making.

Understanding the molecular effects of disease variants in relevant tissues is essential to understanding and treating disease. Here, the authors discover expression and protein quantitative trait loci in cartilage and synovium from 115 osteoarthritis patients to pinpoint genes of action and potential drug treatments.

A meta-analysis of genome-wide association studies across different populations highlights new risk loci and provides a genetic risk score that can stratify prostate cancer risk across ancestries.

A study reports the development of an algorithm, BISCUT, that detects genomic loci under selective pressure by relying on the distribution of breakpoints across chromosome arms, and uses it to explore how aneuploidies affect tumorigenesis.

In Vibrio cholerae, a type IVa pilus (T4aP) binds to exogenous DNA, and threads this DNA through the outer membrane secretin, PilQ. Here authors present the cryoEM structure of PilQ from native V. cholerae cells and design a series of mutants to reversibly regulate VcPilQ gate dynamics.

A diverse, multidisciplinary panel of 386 experts in COVID-19 response from 112 countries provides health and social policy actions to address inadequacies in the pandemic response and help to bring this public health threat to an end.

Genetic and epidemiological investigations have yet to reveal what drives the large difference in ASD prevalence between the sexes. Here authors examine chromosome aneuploidy in a large ASD case-control cohort and report sex chromosome haploinsufficiency is a strong ASD risk factor, while the extra Y effect increases ASD risk significantly more than the extra X effect.

Carotid intima-media thickness (cIMT) and plaque are associated with subclinical atherosclerosis and coronary heart disease (CHD). Here, the authors identify and prioritize genetic loci for cIMT and plaque by GWAS and colocalization approaches and further demonstrate genetic correlation with CHD and stroke.

Aberrant changes in DNA methylation have been implicated in various neurodevelopmental disorders but remain under studied in developmental and epileptic encephalopathies. Here, the authors demonstrate the diagnostic utility of genome-wide DNA methylation analyses toward identifying molecular etiologies in developmental and epileptic encephalopathies.

The GLASS Consortium studies the evolutionary trajectories of 222 patients with a diffuse glioma to aid in our understanding of tumour progression and treatment failure

Improving inference in large-scale genetic data linked to electronic medical record data requires the development of novel computationally efficient regression methods. Here, the authors develop a Bayesian approach for association analyses to improve SNP-heritability estimation, discovery, fine-mapping and genomic prediction.

Colitis is one of the most common immune-related adverse events in patients with cancer treated with immune checkpoint inhibitors. Here the authors show that a polygenic risk score for ulcerative colitis can predict immune checkpoint inhibitor-mediated colitis in patients with cancer.

The accuracy of nanopore DNA sequencing is substantially improved by application of a variable-voltage sequencing mode.

Analysis of snRNA genes in individuals with rare disorders identifies de novo and recurrent variants in RNU5B-1 and RNU5A-1, in addition to previously unreported cases with pathogenic or likely pathogenic variants in RNU4-2.

Here authors show that machine learning derives the degree of background retinal pigmentation with more nuance than self-described ethnicity. Retinal pigment scores are associated with genes linked to melanin and may improve algorithmic fairness.

Although varicose veins are a common condition, the genetic basis is not well understood. Here, the authors find genetic variants associated with varicose veins and show that a higher polygenic risk score for varicose veins correlates with a greater likelihood of patients undergoing surgical treatment.

Modelling studies suggest that large-scale win–win solutions are available, but practitioners confronted with real-world complexity are sceptical. This study shows that increasing the number of objectives, the number of stakeholders or the number of constraints decreases the availability of win–win outcomes.

A population epigenomic analysis of wild Arabidopsis thaliana accessions is presented, obtained by sequencing their whole genomes, methylomes and transcriptomes; thousands of DNA methylation variants are identified, some of which are associated with methylation quantitative trait loci.

The majority of scoliosis is considered idiopathic with onset in adolescence (AIS) and has a genetic contribution. Here, the authors perform an exome wide association study of data from 457 severe AIS cases and 987 controls, and find a missense variant in SLC39A8 is associated with AIS.

This study shows that conserving approximately half of global land area through protection or sustainable management could provide 90% of ten of nature’s contributions to people and could meet representation targets for 26,709 species of mammals, birds, amphibians, and reptiles. This finding supports recent commitments to conserve at least 30% of global lands and waters by 2030.

Longitudinal multi-omics reveals shifts to the human microbiome across multiple body sites and the associated immune responses during short-term spaceflight.

Few genome-wide association studies have explored the genetic architecture of age-of-onset for traits and diseases. Here, the authors develop a Bayesian approach to improve prediction in timing-related phenotypes and perform age-of-onset analyses across complex traits in the UK Biobank.

Comparisons within the human pangenome establish that homologous regions on short arms of heterologous human acrocentric chromosomes actively recombine, leading to the high rate of Robertsonian translocation breakpoints in these regions.

Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

Tissue agnostic treatments can be used to target known cancer mutations, independent of cancer type. Here, the authors identified tissue-agnostic biomarkers in 21.5% of patients in a cohort of 295,316 tumor samples, and observed variable clinical benefit of tissue-agnostic treatments across cancer types.

Alterations in the tumour suppressor genes STK11 and/or KEAP1 can identify patients with advanced non-small-cell lung cancer who are likely to benefit from combinations of PD-(L)1 and CTLA4 immune checkpoint inhibitors added to chemotherapy.

Whole-genome sequencing is used to analyse the landscape of somatic mutation in intestinal crypts from 16 mammalian species, revealing that rates of somatic mutation inversely scale with the lifespan of the animal across species.

Neuroendocrine carcinomas (NECs) arise from different anatomic sites, but have similar histological and clinical features. Here, the authors show that the epigenetic landscape of a range of NECs converges towards a common epigenetic state, while distinct subtypes occur within neuroendocrine prostate cancer contributing to intratumor heterogeneity in clinical samples.

The transition from normal esophageal tissue to squamous carcinoma is characterized by an altered SOX2 cistrome. This transcriptional reprogramming activates endogenous retroviruses and double-stranded RNA expression, creating a dependency on the RNA editing enzyme ADAR1.

CUT and HOX are conserved DNA binding elements prevalent in human transcription factors. Here, the authors use an integrative approach to study the mechanism of CUT-HOX cross-talk towards DNA binding by the prostate cancer target ONECUT2.

ONIX is a data acquisition system for recording freely behaving mice. It can accommodate a variety of recording technologies, while maintaining minimal impact on animal behavior.

Recognising cross-ecosystem linkages between terrestrial and aquatic ecosystems is vital for sustainable management and conservation of freshwater biota. Here, the authors show that land use activities are strongly linked to the reliance of benthic and pelagic consumers on terrestrial energy sources in boreal lake food webs.

Noel et al. show aberrant updating of expectations in three distinct mouse models of autism spectrum disorder. Brain-wide neurophysiology data suggest this stems from excess units encoding deviations from prior mean and a lack of sensory prediction errors in frontal areas.

Primary prostate tumours are known to be genetically heterogeneous and clonal selection has the potential to drive metastasis. Here Hong et al. show that the acquisition of TP53 mutations is linked to clonal expansion and metastatic progression to lethality.

Endoplasmic reticulum and inflammatory stress are associated with diabetes. Maestas et al. use single-cell sequencing to profile primary human islets under stress and identified tissue and cell-type responses.

Analysis of over 6000 single-site variants of SARS-CoV-2 Papain-Like protease uncovers critical mutations involved in enzymatic function and highlight the potential for drug-escape.

The history of human populations in the islands of the central and western Mediterranean is poorly understood. Here, the authors generate ancient-DNA data from the Balearic Islands, Sicily and Sardinia, and estimate the level and timing of steppe pastoralist, Iranian and North African ancestries in these populations.

Major histocompatibility complex (MHC) loss of heterozygosity, allele-specific mutation and measurement of expression and repression (MHC Hammer) detects disruption to human leukocyte antigens due to mutations, loss of heterogeneity, altered gene expression or alternative splicing. Applied to lung and breast cancer datasets, the tool shows that these aberrations are common across cancer and can have clinical implications.

A retrospective analysis using PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing finds an association between adeno-associated virus type 2 and paediatric hepatitis of unknown cause.

Stephanie London and colleagues from the CHARGE Consortium report genome-wide association studies for pulmonary function.