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One of this week's email contributors takes to task those who would hold up the foraminifera as an example of a gap free fossil record.

The responses to Norman Macleod's previous e-mail contribution were such tahe this week we have given him the opportunity to respond.

Many protein–protein interactions depend on Short Linear Motifs (SLiMs). In this study, the authors use large-scale binding assays, deep mutational scanning, and structural analysis to map SLiMs recognised by human cyclins and uncover the rules that determine their specificity and affinity.

Wastewater treatment plants are important reservoirs of antibiotic resistance genes (ARGs). Here, the authors analyze ARGs in a global collection of samples from wastewater treatment plants across six continents, providing insights into biotic and abiotic mechanisms that appear to control ARG diversity and distribution.

Antarctica is increasingly popular as a site for tourism and scientific research. The growth of marine traffic and the presence of major research stations have increased the anthropogenic deposition of heavy metals into this fragile ecosystem.

CRISPR activation of 1,836 human transcription factors recapitulates fibroblast transcriptional states observed in vivo and identifies regulators that can revert inflammatory states.

The number of individuals in a given space influences animal interactions and network dynamics. Here the authors identify general rules underlying density dependence in animal networks and reveal some fundamental differences between spatial and social dynamics.

Beck et al. conducted single-cell and spatial profiling of embryonal tumors with multilayered rosettes, finding that malignant cellular hierarchies are driven by developmental programs and specific members of the chromosome 19 microRNA cluster.

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.

Soil priming could release large amounts of soil C into the atmosphere. Here the authors show that experimental warming boosts soil priming and CO₂ emissions in grasslands potentially due to microbial changes. Model accuracy could be improved by incorporating these mechanisms.

A risk score developed using biological, psychological and social factor data from the UK Biobank can predict different pain conditions, the risk of chronic pain spreading across body sites and the prognosis of chronic pain up to 9 years later.

The authors examine the effect of long-term experimental warming on the complexity and stability of molecular ecological networks in grassland soil microbial communities. They find warming increases network complexity, which is strongly correlated with network stability.

Dengue is a major public health concern in the Americas, and the Caribbean can be a source for reintroduction and spread. Here, the authors use travel surveillance data and genomic epidemiology to reconstruct Dengue epidemic dynamics in the Caribbean from 2009-2022.

Hu et al. discovered that the truncated form of human epidermal growth factor receptor 2 (HER2), called p95HER2, drives tumor progression and resistance to the antibody–drug conjugate trastuzumab deruxtecan in HER2⁺ breast cancer. Blocking p95HER2 restores antitumor immunity.

Fillingim et al. show that biological and psychosocial factors jointly predict conditions associated with chronic pain.

The authors investigate the response of Archaea to experimental warming in a tallgrass prairie ecosystem. Warming was linked to reduced diversity and convergent succession, with further links to changed ecosystem function. Stochastic processes dominated community changes but decreased over time.

Gene expression is precisely modulated with CRISPR interference and mismatched guide RNAs.

The authors performed phylogenetically controlled behavioural assays and analysed brain transcriptomes across five avian families, identifying convergent patterns of gene expression associated with aggression and nesting behaviour in obligate cavity-nesting birds.

The dynamic intertides, located between marine and terrestrial ecosystems, serve as a favorable habitat for exploring virus-host relationships. Here, the authors recover 20,102 viral OTUs from twelve intertidal zones along the Chinese coasts, with further analyses expanding our understanding of intertidal viromes within an ecological framework.

HORNET, a method that uses unsupervised machine learning and deep neural networks to analyse atomic force microscopy data enables structural determination of RNA molecules in multiple conformations.

The molecular mechanisms underlying resistance to therapy in Chronic lymphocytic leukemia (CLL) remain to be explored. Here, the authors perform multi-omics analysis in a mouse model of ibrutinib resistance and suggest proteasome inhibition for overcoming it.

The role of paddy rice agriculture in the spatial and temporal dynamics of atmospheric methane concentration remains unclear. Here, Zhang et al. show that regions with dense rice paddies have high satellite-based column averaged CH₄ concentrations (XCH₄), and that seasonal dynamics of XCH₄ mirror those of paddy rice growth.

Crowdsourcing analysis improves computational prediction of cytotoxic responses in humans.

Learning and remembering new information is a major challenge for students of all levels. Here, the authors show that “neural alignment” across brains is associated with learning success of STEM concepts in a real-life college course and predicts learning outcomes.

Species with low genetic diversity have limited capacity to adapt to environmental change. This study finds that the skin microbiome and non-genetic (epigenetic) modifications of the DNA represent additional sources of variation that could help low diversity fish survive environmental challenges.

Mitochondrial ribosomal proteins have been identified as longevity regulators in C. elegans and mammalian systems, their role in longevity is linked to mitonuclear protein imbalance and the mitochondrial unfolded protein response.

Sun et al. report human lifespan changes in the brain’s functional connectome in 33,250 individuals, which highlights critical growth milestones and distinct maturation patterns and offers a normative reference for development, aging and diseases.

COVID-19 can be associated with neurological complications. Here the authors show that markers of brain injury, but not immune markers, are elevated in the blood of patients with COVID-19 both early and months after SARS-CoV-2 infection, particularly in those with brain dysfunction or neurological diagnoses.

Preservation of oral microbiome ancient DNA from Oceania is much better than human ancient DNA. The authors leverage this to demonstrate that oral microbial community composition in Oceania is not only distinct from the rest of the world, but it may also be associated with patterns of ancient human migration in the region.

Currently, there is limited knowledge about the spatial heterogeneity of glioma-driving molecular events. Here, the authors employ a multiomics approach to characterize the spatial transcriptomic heterogeneity of various types of gliomas and identify spatially distinct tumor subclones with genomic plasticity driven by mutations on extrachromosomal DNA.

Individual dopaminergic neurons encode future rewards over distinct temporal horizons.

Cognitive abilities change with age, but why some decline and some do not is not clear. Here, the authors use data from the Cam-CAN cohort to show that distributed, multi-component brain responsivity and default-mode deactivation supports and characterizes preserved cognition across the adult lifespan.

Environmental and biotic factors control ecological communities. Here, the authors study community ribosomal rRNA gene copy number in coastal sediment and ocean bacterial communities, and in microcosm nutrient addition experiments, to propose a conceptual framework of how nutrient supply and ecological interactions shape the community.

When modern humans colonized India is debated. Here, Clarkson and colleagues report an archaeological site in India that has been occupied for approximately 80,000 years and contains a stone tool assemblage attributed to Homo sapiens that matches artefacts from Africa, Arabia, and Australia.

Taxonomic compositions in bathtub faucet water microbiomes showed household individuality, with differences in the prevalences of non-tuberculous mycobacterial species. A similar antimicrobial resistome was detected.

A field investigation at a former nuclear waste disposal site shows how environmental stress modulates subsurface microbial community assembly.

A unified framework is presented that integrates observed spatial patterns of individual trees in forests with ecological processes into a novel coexistence theory.

Here, Bottery et al show that resistance to next generation antifungals is more likely to occur within azole resistant Aspergillus fumigatus due to the close linkage between a globally distributed azole resistance allele and a DNA repair variant which elevates mutation rates.