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The R package barcodetrackR facilitates the analysis and visualization of clonal tracking data, and it includes a graphical user interface to allow researchers without programming experience to utilize various quantitative tools.

Cytosine base editors use an uracil-containing intermediate to introduce C•G to T•A and C•G to G•C point mutations. Here, the authors couple gene knockdown with reporters of these two cytosine base editing outcomes to identify the cellular DNA repair factors that process this intermediate.

Using mosaic variant barcode analysis, clonal dynamics of specific cell types are deconvolved in the human forebrain.

There is a genetic component to the risk of severe COVID-19, but the genetic effects are difficult to separate from social constructs that covary with genetic ancestry. To address this, the authors identify determinants of COVID-19 severity using admixture mapping, viral phylodynamics, and host immune and metagenomic sequencing.

Factors controlling the transfer of microbes from the ocean to the atmosphere are unclear. Here, Michaud et al. study this process in an enclosed ocean-atmosphere facility, and show that the degree of aerosolization of bacteria and viruses is taxon-specific.

As phase 1 of the Earth Microbiome Project, analysis of 16S ribosomal RNA sequences from more than 27,000 environmental samples delivers a global picture of the basic structure and drivers of microbial distribution.

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.

Due to their intense moisture transport, atmospheric rivers are associated with hydrological hazards such as extreme rainfall and flooding. This Review discusses how atmospheric-river characteristics and impacts may change with warming, synthesizing physical theory, observations and modelling.

Biotechnology offers a sustainable route to manufacturing, but closing the loop towards safeguarding biodiversity remains challenging. Here, we explore how partnerships with Indigenous Peoples and Local Communities (IP&LC) can promote an ethical and circular bioeconomy.

A novel approach to analyse high-depth Hi-C data provides a comprehensive chromatin interaction map at approximately 5–10 kb resolution in human fibroblasts; this reveals that TNF-α-responsive enhancers are already in contact with target promoters before signalling and that this chromatin looping is a strong predictor of gene induction.

Ecosystem services provided by dung beetles are an underappreciated component of terrestrial ecosystems. Here, the authors report a standardized distributed experiment which shows that dung removal rate, a key ecosystem process in pastures, is greater under high beetle functional diversity regardless of grazing intensity.

Genetic disposition can impact response to virus infection. Here, the authors used a reinfection approach with antigenically distinct SARS-CoV-2 variants Omicron and Beta and show that differences in the immune response correlate with disease outcome in mouse models with different genetic background upon reinfection.

SARS-CoV-2-specific antibodies and memory B cells are significantly reduced, but CD4⁺ and CD8⁺ T cells are robustly activated, in patients with multiple sclerosis on anti-CD20 monotherapy versus healthy controls after BNT162b2 or mRNA-1273 mRNA vaccination.

Lineage specification and development require a hierarchy of transcription factors. Murre and colleagues have compiled a genome-wide set of cis-acting targets centered on E2A, EBF1 and Foxo1 that govern early B cell development.

A global dataset of the satellite-tracked movements of pelagic sharks and fishing fleets show that sharks—and, in particular, commercially important species—have limited spatial refuge from fishing effort.

Programmable double-strand DNA breaks (DSBs) can be harnessed for precision genome editing through manipulation of the homology-directed repair (HDR) pathway. Here the authors report the development of the double tap - double tap implements secondary gRNAs which target Cas9 to common indel sequences and provides a second chance at HDR.

Lineage development is accompanied by specification of gene expression. Murre and colleagues show that during B cell development, many genes relocate in the nucleus, driven by chromatin-looping interactions with transcription factors.

Inter-organelle signaling coordinates adaptive responses via currently unknown mechanisms. Here, Tapia et al. show that KDEL signaling repositions lysosomes in a complex process termed ‘traffic-induced degradation response for secretion’ (TIDeRS) that connects multiple pathways and Golgi secretion.

Proangiogenic signalling pathways are activated in chronic inflammation, but although antiangiogenic treatments are routinely incorporated into cancer therapy, surprisingly few clinical trials have investigated this approach in patients with chronic inflammatory diseases. However, this situation could soon change — a wide range of small-molecule inhibitors with improved specificity, and techniques to target such inhibitors to specific cell types, are currently undergoing clinical and preclinical development.

To describe the biochemical composition of an organism multiple data sets must be combined and this information can then be used forin silico analysis. By combining metabolism and transcription data, Lerman et al. discovered new regulons and improved the gene annotation for the simple organism Thermotoga maritima.

This Registered Report presents evidence from 87 countries and regions showing that brief emotion-regulation interventions consistently reduced negative emotions and increased positive emotions during the COVID-19 pandemic.

Hsiehchen and colleagues assess the association between tumor mutational burden and survival in a real-world cohort of patients with microsatellite-stable cancers.

This Review explores the genetic basis of diversification and adaptation in non-human primates, including their responses to ecological and environmental changes.

Protein-energy wasting (PEW), manifested by low serum levels of albumin and weight loss, is common in patients with chronic kidney disease (CKD) and is a strong predictor of mortality. The authors of this Review discuss the evidence indicating that dietary interventions and nutritional support can mitigate PEW and improve outcomes in patients with CKD. They also describe how in-center meals and oral supplements during dialysis may improve survival and quality of life in this group of patients.

Large-scale mapping of chromatin state and transcription factor binding have uncovered many broad chromatin domains along linear genomic DNA, but it is unclear how these functional domains are organized in three-dimensional nuclear space. A new study now shows that many domains exist as loops connected by CCTC-binding factor (CTCF), providing new insights into the higher-order structure of chromatin organization in the nucleus.

The status of the harlequin toads has not improved since 2004 despite species rediscoveries accompanied by increasing conservation efforts, and habitat destruction and degradation continue to threaten them today, according to an analysis of population status records over the period 2004–2022.

Population study of whole genomes of wild uakary monkeys (Cacajao genus) exposes how the dynamic and highly heterogeneous Amazon basin may have shaped complex connectivity patterns and driven fast population differentiation on these.

In an inter-laboratory study, the authors compare the accuracy and performance of three optical density calibration protocols (colloidal silica, serial dilution of silica microspheres, and colony-forming unit (CFU) assay). They demonstrate that serial dilution of silica microspheres is the best of these tested protocols, allowing precise and robust calibration that is easily assessed for quality control and can also evaluate the effective linear range of an instrument.