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An in-depth analysis of tissue biopsies from patients with multiple myeloma and CAR T cell therapy-associated immune-related adverse events (CirAEs) after treatment with commercial BCMA-targeted CAR T cell therapy shows that CD4⁺ CAR T cells mediate off-tumor toxicities and that high CD4:CD8 ratio at apheresis, robust early CAR T cell expansion, ICANS and ciltacabtagene autoleuce treatment are independently associated with the development of CirAEs.

CaBLAM is a bioluminescent genetically encoded calcium indicator that delivers high-contrast signals as shown in cell culture, in the in vivo mouse brain and in zebrafish larvae.

Adult human tissues from diverse sites around the body are used to reconstruct cellular phylogenies from early development, using somatic mutations as an internal barcode.

Researchers from Hawaii and an international consortium have produced a draft genome assembly for 'SunUp', the first commercial virus-resistant transgenic fruit tree. Comparison of this plant genome to those of Arabidopsis and others sheds light on evolution of characteristics such as biosynthesis, starch deposition, control of photosynthesis and pathways for creating volatile compounds.

A Bayesian state-dependent evolutionary phylodynamic model (SDevo) quantifies the difference in division rates between cells at the periphery and interior of a tumour. In simulations and using clinical hepatocellular carcinoma data, the authors use SDevo to interrogate spatial patterns in tumour growth.

This work presents a unified MS/MS spectral library of drugs and metabolites integrated with standardized pharmacologic metadata, enabling scalable, individualized profiling of drug exposure and metabolism directly from untargeted metabolomics data.

In a randomized, placebo-controlled trial, an inhaled phage cocktail was well tolerated in adults with cystic fibrosis and chronic Pseudomonas aeruginosa infection, with evidence of lung delivery and signs of bacterial reduction.

Alcanivorax borkumensis is a marine, oil-degrading bacterium. Here, the authors describe the synthesis of a cellular biosurfactant. Loss of the biosurfactant affects attachment of mutant cells to the oil–water interface, highlighting its importance for biofilm formation on oil droplets.

XBB.1.5 of SARS-CoV-2 is a descendant of XBB.1 and has mutations in spike and ORF8, making it more infectious to humans. Here, the authors examined in detail the differences in virological properties of the two variants.

The enteric nervous system integrates microbial cues to regulate gut function. Using an optogenetic gut culture model, authors show lineage- and frequency-specific neuronal control of immune responses and barrier integrity, shaped by gut microbes.

Several cases of replicated radiations (in which sets of similar forms evolve repeatedly within different regions) have been described in animals. Here the authors provide a well-documented example in plants, specifically the Oreinotinus lineage within the angiosperm clade Viburnum in its spread from Mexico to Argentina through disjunct cloud forest environments.

Ito et al. present CoVFit, an AI model that predicts variant fitness (transmissibility) from spike protein sequences alone. They further demonstrate its utility in forecasting viral evolution via single amino acid mutations.

Antibiotic resistance is a major public health concern, exacerbated by antibiotic over-prescription. Here we show, using game theory, that reduction of over-prescription can be achieved by discretizing the clinical information given to physician, e.g., by decision support systems.

Recent Omicron SARS-CoV-2 subvariants independently acquire 5 key Spike mutations. Here, the authors evaluate the evolutionary importance of the 5 mutations and characterize the virological properties of variant BQ.1.1 harboring all 5 mutations.

Understanding global forces impacting forests is increasingly vital. This study finds that human factors follow climate as the most important factors affecting forest structure globally and are the dominant factor regionally, even in many protected areas and so-called intact forest landscapes.

A meta-analysis of associations between human genetic variation and gut microbial structural variations shows that ABO genotype differentially affects the presence of Faecalibacterium prausnitzii strains containing GalNAc utilization pathway in the gut.

A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common resistance mechanisms and shows no toxicity towards human cells.

Fruit acidity is an important factor affecting fleshy fruit taste. Here, the authors identify the PHgene that regulates fruit acidity in a number of species and report a mutation that is responsible for the diversification and evolution of the sweet melon.

Joint injury and disease are leading causes of disability, with mammalian joints exhibiting poor regenerative capacity. Here the authors showed that after loss of a whole joint, adult zebrafish regenerate de novo articular cartilage, ligament, and synovium into a complex joint organ.

In this genomic epidemiology study from Ghana, the authors sequence ~1,000 SARS-CoV-2 whole genomes from March 2020 to September 2021. They describe changes in the predominant circulating lineages over time and infer how variants of concern were likely introduced into the country.

The nonlinear behavior of the East Asian summer monsoon (EASM) remains largely unknown. Here, an ensemble reconstruction of EASM rainfall since the Last Glacial Maximum is presented and five tipping points in this monsoon system are identified.

NKG2D is a central activating receptor know to recognise stress ligangs upregulated during cancer or infection. Here, Charpak-Amikam et al show that NKG2D also recognises fungal pathogens and plays a critical role in mounting an appropriate immune response to them.

There are many available ways to rank species for conservation prioritization. Here the authors identify species of mammals and birds that are both spatially restricted and functionally distinct, finding that such species are currently insufficiently protected and disproportionately sensitive to current and future threats.

XBB is the first recombinant, globally dominant variant of SARS-CoV-2. Here, the authors examine the variant’s origins and virological properties, showing it is the first example of SARS-CoV-2 improving its fitness through recombination.

Neural mechanisms underlying the canonical computations underlying economic choice are not fully understood. Here authors show that gaze is highly relevant in decision processes, both at the behavioral level and at the neural level for value encoding gating and reactivation, for choice evaluation and reevaluation.

Analysis of 100 consecutive personalized bacteriophage therapy cases supports the use of personalized and sometimes pre-adapted, bacteriophage preparations, often in combination with antibiotics.

A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.

In this work, researchers engineer HIV-1 immunogens using molecular dynamics simulations to enhance vaccine designs that select for specific antibody mutations. Their approach improved the selection of mutations crucial for broadly neutralizing antibody responses, offering a promising strategy for HIV vaccine development.

In this Perspective, the authors highlight agroforestry as a natural climate solution, discussing definitional refinements, controls on mitigation potential and remote sensing innovations. They assess the status of agroforestry in the context of climate ambitions, identifying key areas and opportunities.

The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.

The bacterium Helicobacter pylori, often found in the human stomach, can be classified into distinct subpopulations associated with the geographic origin of the host. Here, the authors provide insights into H. pylori population structure by collecting over 1,000 clinical strains from 50 countries and generating and analyzing high-quality bacterial genome sequences.

Network expansion of trait-associated genes for 1,002 human phenotypes identifies pleiotropic gene modules and biological processes associated with multiple traits, and potential opportunities for drug repurposing and development.

A genome-wide association study of 207 taxa and 205 pathways representing gut microbial composition and function from 7,738 individuals of the Dutch Microbiome Project identifies genetic associations at the LCT and ABO loci.

Keypoint-MoSeq is an unsupervised behavior segmentation algorithm that extracts behavioral modules from keypoint tracking data acquired with diverse algorithms, as demonstrated in mice, rats and fruit flies. The extracted modules faithfully reflect human-annotated behaviors even though they are obtained in an unsupervised fashion.

In two mouse models of intestinal cancer, mutant p53 has an oncogenic effect in the distal gut but a tumour-suppressive effect in the proximal gut, and these opposing properties are determined by the gut microbiome.

The heterogenous nature of rheumatoid arthritis renders the prediction of responsiveness to biological treatments difficult. Here the authors analyze bulk RNA-seq data from the STRAP trial (n = 208) to build a machine-learning model for predicting responses to etanercept, tocilizumab and rituximab with AUCs around 0.75 to potentially assist in therapy planning.

We demonstrate that the transmembrane protease TMPRSS2 is a receptor for coronavirus HKU1; it triggers HKU1-mediated cell–cell fusion and viral entry by binding to both HKU1A and HKU1B spikes.

A specific type of glycosylation—sialylation—is more common on immunoglobulin E from individuals with a peanut allergys than from non-atopic people, suggesting that it has a role in regulating anaphylaxis.

A review of observation-based evidence suggests that four interconnected Earth system tipping elements have moved towards their critical thresholds, highlighting the need for better monitoring and increased mitigation efforts.

A substudy nested within a double-blind cluster-randomized controlled trial in Bangladesh shows that drinking chlorinated water had relatively minor impacts on children’s gut microbiome development in this setting.

HLA peptidomic analysis identifies recurrent intracellular bacteria-derived peptides presented on HLA-I and HLA-II molecules in melanoma tumours, revealing how bacteria can modulate immune functions and responses to cancer therapies.

Single-nucleus RNA sequencing of human visceral and subcutaneous adipose tissues is used to identify adipocyte subpopulations and explore their developmental trajectories and interactions.

Plasmodium knowlesi infects macaques and can cause malaria in humans. Here, Dankwa et al. show that the absence of a sialic-acid component on the surface of macaque red blood cells (RBCs) limits infection of human RBCs with P. knowlesi, but the parasite can adapt to invade human RBCs by using alternative pathways.

Biomarker analysis of the phase 4 R4RA trial identifies pretreatment synovial biopsy features selectively associated with response to rituximab or tocilizumab, and leads to the development of models that might predict treatment benefit in patients with rheumatoid arthritis