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DNA polymerases are molecular machines that copy genetic material using a template. Here, authors characterize the ability of diverse polymerases to synthesize DNA without a template and show that environmental conditions can alter sequence composition, enabling guided kilobasescale DNA synthesis.

Here, Santamaria de Souza et al. explore the context-dependent fitness effects of glpT-deficiency in Salmonella enterica, showing mutants thrive in the gut lumen but are counter-selected by macrophages, highlighting antagonistic pleiotropy and niche-dependent adaptation.

Aeneas, a generative neural network trained on ancient texts, helps historians contextualize inscriptions and perform epigraphic tasks, offering an improved starting point for historical research.

The emplacement of the Karoo LIP occurred synchronously with the Toarcian crisis, which is characterized by negative carbon isotope excursions. Here the authors use carbon cycle modelling to show that thermogenic carbon released during LIP emplacement represents a plausible source for the negative excursions.

Researchers summarize key insights from the world’s first comprehensive investigation into how a pandemic started.

Here, the authors provide molecular insight into the remarkable ability of Tardigrades to withstand high levels of radiation by demonstrating that their Dsup protein interacts with multiple surfaces of the nucleosome to protect the genome from oxidative DNA damage.

Aspirin-related drugs suggest a way towards more effective stem-cell transplants.

Ithaca—a deep neural network for textual restoration, geographical attribution and dating of ancient Greek inscriptions—collaboratively aids historians’ study of damaged texts.

Understanding how machine learning models form internal representations remains a fundamental challenge. Here, the authors explore the geometric property of convexity in latent spaces as a lens to better understand and evaluate representations formed by machine learning algorithms.

The mantle upwelling beneath the Afar rift may be influenced by tectonic processes in the overriding lithospheric plates that shape the distribution of both the compositional heterogeneities and abundance of melt, according to a geochemical and statistical study of volcanic samples.

With edge computing on custom hardware, real-time inference with deep neural networks can reach the nanosecond timescale. An important application in this regime is event processing at particle collision detectors like those at the Large Hadron Collider (LHC). To ensure high performance as well as reduced resource consumption, a method is developed, and made available as an extension of the Keras library, to automatically design optimal quantization of the different layers in a deep neural network.

There seem to be several overlapping processes that induce resistance to antibiotics for bacteria and chemotherapy for tumour cells. This Perspective discusses how our understanding of bacterial resistance to antibiotics might inform our understanding of the resistance of tumours to therapy.

The adrenal medulla secretes hormones required for the fight-or-flight response, and its specialized cells need to be maintained throughout life. This study uses mouse models to pinpoint the stem cells of this organ and demonstrates how these ensure the turnover of specialized cells.

Improved effectors for CRISPRi/CRISPRa are developed following high-throughput screening of transcriptional domains.

Activation of caged fluorophores has mostly relied on the absorption of either a single ultraviolet photon or two NIR photons. Here, the authors show that two green photons (515 nm) can substitute for a single photon ( ~ 260 nm) to activate rhodamine-based dyes, thus enabling STED imaging in thick samples.

In social insects, the relative roles of individual immunity and social immunity in fighting pathogens remain unclear. Here the authors show that an ant’s individual immune pathways provide specialized protection against bacterial but not fungal infections, while social immunity protects against pathogenic fungi but not bacteria.

Exopolysaccharides (EPS) are perceived by legumes and regulate symbiosis with rhizobia. Here the authors describe the structure of the Lotus EPS receptor, EPR3 and show that it has atypical βαββ and βαβ folds that represent a structural signature for a unique class of EPS receptors in the plant kingdom.

This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease.

Businesses must understand and act to reduce their environmental footprint. Springer Nature has been working to address the impacts of its publishing operations since 2017, lowering office-based carbon emissions and improving sustainable practices.

An analysis of longitudinal cohort data across diverse populations suggests that the incidence of wasting between birth and 24 months is higher than previously thought, and highlights the role of seasonal factors that affect child growth.

The study presents a modular DNA origami-based single-molecule nanosensor that separates sensing from the signal output. It achieves high fluorescence resonance energy transfer contrast and enables tuning of the response window for improved sensor specificity, multiplexing and logic sensing.

A light-oxygen-voltage photoreceptor was found to bind short RNA stem loops in a light-dependent manner, which can be harnessed to regulate gene expression in bacteria and mammalian cells.

The details of how the protein folding and degradation systems collaborate to combat potentially toxic non-native proteins are unknown. Here the authors perform systematic studies of missense and nonsense variants of the cytosolic aspartoacylase, ASPA, where loss-of-function variants are linked to Canavan disease.

Analysis of data from 33 longitudinal cohorts from low- and middle-income countries indicates that conditions during pre-conception, pregnancy and the first few months of life are crucial in determining the risk of growth faltering in young children.

Stable isotopes are a useful tool for distinguishing two sources in a mixture, but frequently systems have more than two components. Here, the authors propose a new approach to allow conclusive partitioning between three sources, still using only two stable isotopes, looking at soil CO₂emissions.

Nerve cells that detect gentle touch in mice are a hit with cats too.

Understanding the factors underlying colonization of donor microbes in recipients of fecal microbiota transplantation is a necessary first step to aid development of directed approaches that aim to couple colonization to clinical outcomes.

A survey of species-level genes from 13,174 publicly available metagenomes shows that most species-level genes are specific to a single habitat, encode a small number of protein families and are under low positive (adaptive) pressure.

Earth’s surface temperature is stabilized by the drawdown of CO₂ owing to weathering of continental arcs, whose length is shown to be a primary control on global weathering fluxes, according to a probabilistic analysis of interdependencies.

To link aboveground fire ecology with belowground microbial trait ecology, the authors conduct laboratory experiments followed by analysis of field data from northern Canada. Fast-growing species initially dominate but decline between 1 and 5 yr post-fire, while neither fire survival nor adaptation to a post-fire environment are strong determinants of success.

A pooled analysis of longitudinal studies in low- and middle-income countries identifies the typical age of onset of linear growth faltering and investigates recurrent faltering in early life.

The Large Hadron Collider produces 40 million collision events per second, most of which need to be discarded by a real-time filtering system. Unsupervised deep learning algorithms are developed and deployed on custom electronics to search for rare events indicating new physics, rather than for specific events led by theory.

The human proteome represents a crucial link between complex disease and genetic/environmental factors. Here, the authors investigate 257 cardiometabolic-relevant protein biomarkers in whole genome sequencing data from 1328 individuals, revealing the genetic architecture underlying biomarker variation.

Resistance to first line treatment is a major hurdle in cancer treatment, that can be overcome with drug combinations. Here, the authors provide a large drug combination screen across cancer cell lines to benchmark crowdsourced methods and to computationally predict drug synergies.

That genetic mutations contribute to cancer is undisputed. What now emerges is that a cancer cell's microenvironment has a much stronger hand in the course a cancer takes than previously thought.

Analysis of transits of an ultra-hot giant exoplanet reports the precise abundance constraints of 14 major refractory elements, showing distinct deviations from proto-solar, along with a sharp transition temperature at which those elements are depleted.

Rheumatoid arthritis patients respond differently to anti-TNF treatment. Using community-based challenge, the authors show that currently available data does not reveal meaningful genetic predictors of response to anti-TNF therapy, thus confirming clinical observations.

By integrating geological observations, statistical analysis, geodynamic simulations and landscape-evolution models, a physical model is proposed to link the coevolution of craton margins and interiors with continental rifting.

Most kimberlites erupting in the past billion years on Earth did so about 30 million years after continental breakup, with dynamical and analytical models suggesting a control from rifting-related mantle delamination.

A change in the style of rifting in the North Atlantic led to carbon fluxes from subcrustal melting that helped trigger the Palaeocene–Eocene Thermal Maximum, according to geochemical analyses of volcanic sequences as well as melting and tectonic modelling.

Antibodies are a primary tool to assess histone post-translational modifications. However, different antibodies and batches might vary in their ability to recognize those modifications, depending on the kind of assay used. Now a systematic analysis of different antibodies and an open database containing the validation results are presented.

Neural processing speed slows with age, but the relationship between this slowing and brain atrophy is unknown. Here, authors show that age-related functional brain differences in auditory and visual processing are partly due to structural differences in the distinct brain regions underlying these processes.

A computational approach to generate reference-free protein families from the sequence space in metagenomes reveals an enormously diverse functional space.

Respiratory syncytial virus (RSV) is a common infection in children and older adults but little is known about within-host viral population diversity. Here, the authors perform deep sequencing and find that RSV subgroup B exhibited more diversity than subgroup A, with implications for development of therapeutics and vaccines.

Clinical studies have suggested that the therapeutic potential of polyclonal convalescent plasma is highest in the first days of symptoms. Here, the authors present results from a pooled analysis of two clinical trials in COVID-19 outpatients that did not provide conclusive evidence in favor of convalescent plasma.

Epigenetic changes associated with post-natal differentiation have been characterized. Here the authors generate epigenomic and transcriptional profiles from primary human breast cells, providing insights into the transcriptional and epigenetic events that define post-natal cell differentiation in vivo.