Biological sciences articles within Nature Communications

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  • Article
    | Open Access

    Here the authors perform a gain-of-function screen and identify CDKN2C as a host factor for HBV replication, inducing cell cycle arrest and expression of HBV transcription enhancers. CDKN2C expression correlates with disease progression suggesting a potential role in HBV-induced liver disease.

    • Carla Eller
    • , Laura Heydmann
    •  & Thomas F. Baumert

  • Article
    | Open Access

    Brain disorders can create maladaptive attractions, such as in addiction or self-harming. Here the authors use multiple valence modes of the central amygdala to create such attractions, arbitrarily making rats into ‘sucrose addicts' or ‘cocaine addicts', or causing maladaptive attraction to shocks.

    • Shelley M. Warlow
    • , Erin E. Naffziger
    •  & Kent C. Berridge

  • Article
    | Open Access

    Identification of genes that determine and regulate cell identity remains challenging. Here, the authors use machine learning to identify cell identity genes and master regulator transcription factors based on gene expression profiles and histone modifications.

    • Bo Xia
    • , Dongyu Zhao
    •  & Kaifu Chen

  • Article
    | Open Access

    Sample index hopping results in various artefacts in multiplexed scRNA-seq experiments. Here, the authors introduce a statistical model to estimate sample index hopping rate in droplet-based scRNA-seq data and show that artifacts can be corrected by purging phantom molecules from the data.

    • Rick Farouni
    • , Haig Djambazian
    •  & Hamed S. Najafabadi

  • Article
    | Open Access

    Biology can profoundly influence the planet’s climate, but over Earth’s long history these effects are poorly constrained. Here the authors show that on early Earth, the evolution of microbes producing and consuming methane likely controlled warming and glacial events, and thus Earth’s habitability

    • Boris Sauterey
    • , Benjamin Charnay
    •  & Régis Ferrière

  • Article
    | Open Access

    Milk breastfeeding and prebiotic-supplemented formulas have varying effects on the infant gut microbiome. Here, in a randomized controlled clinical trial, the authors investigate the effects of a Lactobacillus paracasei-fermented formula on the immune defense mechanisms, microbiota and its metabolome in full term infants.

    • Paola Roggero
    • , Nadia Liotto
    •  & Maria Rescigno

  • Article
    | Open Access

    Environmental change and species diversity could jointly affect the stability of animal communities. Here the authors use citizen science data on bats, birds, and butterflies along urbanization and agricultural intensification gradients in France to show that both environmental change and diversity loss destabilise communities, but in different ways.

    • Théophile Olivier
    • , Elisa Thébault
    •  & Colin Fontaine

  • Article
    | Open Access

    In animal groups, the degree of alignment of individuals could have different benefits and costs for individuals depending on their reliance on private or social information. Here the authors show that in shoals of three-spined sticklebacks, some individuals reach resources faster when groups are disordered, a state which favours reliance on privately acquired information, while other individuals reach resources faster when groups are ordered, allowing them to exploit social information more effectively.

    • Hannah E. A. MacGregor
    • , James E. Herbert-Read
    •  & Christos C. Ioannou

  • Article
    | Open Access

    Nebulin-based nemaline myopathy is a heterogenous disease with unclear pathological mechanisms. Here, the authors generate a mouse model that mimics the most common genetic cause of the disease and demonstrate that muscle weakness in this model is associated with twisted actin filaments and altered tropomyosin and troponin behaviour.

    • Johan Lindqvist
    • , Weikang Ma
    •  & Henk Granzier

  • Article
    | Open Access

    Obesity and type 2 diabetes (T2D) are metabolic disorders characterized by insulin resistance in skeletal muscle. Here, the authors map skeletal muscle enhancer elements dynamically regulated after exposure to free fatty acid palmitate or inflammatory cytokine TNFα and identify target genes involved in metabolic dysfunction in skeletal muscle.

    • Kristine Williams
    • , Lars R. Ingerslev
    •  & Romain Barrès

  • Article
    | Open Access

    Here, the authors sample air and surfaces in hospital rooms of COVID-19 patients, detect SARS-CoV-2 RNA in air samples of two of three tested airborne infection isolation rooms, and find surface contamination in 66.7% of tested rooms during the first week of illness and 20% beyond the first week of illness.

    • Po Ying Chia
    • , Kristen Kelli Coleman
    •  & Daniela Moses

  • Article
    | Open Access

    Both geography and ecology can drive the origins of new species. Siqueira et al. show how geological changes in the structure of Miocene reefs and the concurrent evolution of new feeding strategies combine to explain why coral reefs contain such a diversity of fish species.

    • Alexandre C. Siqueira
    • , Renato A. Morais
    •  & Peter F. Cowman

  • Article
    | Open Access

    Local activity of the DNA methylation machinery remains poorly understood. Here, the authors present a theoretical and experimental framework to infer methylation and demethylation rates at genome scale in mouse embryonic stem cells, finding that maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies.

    • Paul Adrian Ginno
    • , Dimos Gaidatzis
    •  & Dirk Schübeler

  • Article
    | Open Access

    Mutations in the TRPV4 channel cause inherited neurodegeneration syndromes, but the molecular mechanisms are unknown. Here the authors reveal that TRPV4 activation causes dose-dependent, CaMKII-mediated neuronal dysfunction and axonal degeneration via disruption of mitochondrial axonal transport.

    • Brian M. Woolums
    • , Brett A. McCray
    •  & Thomas E. Lloyd

  • Article
    | Open Access

    ESCRT-III complexes assemble in vivo inside membrane structures with a negative Gaussian curvature, but how membrane shape influences ESCRT-III polymerization remains unclear. Here authors use structural and biophysical methods to show how human ESCRT-III polymers assemble on positively curved membranes and induce helical membrane tube formation.

    • Aurélie Bertin
    • , Nicola de Franceschi
    •  & Patricia Bassereau

  • Article
    | Open Access

    Self-sufficient cytochrome P450 monooxygenases, which contain all redox partners in a single polypeptide chain, are of interest for biotechnological applications. Here, the authors present the crystal structure of full-length Thermobispora bispora CYP116B46 and discuss the potential electron transfer pathway.

    • Lilan Zhang
    • , Zhenzhen Xie
    •  & Chun-Chi Chen

  • Article
    | Open Access

    ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here, the authors use cryo-ET, cryo-EM and mathematical modeling to reveal how the shape of the helical membrane tube arises from the assembly of two distinct bundles of helical filaments.

    • Joachim Moser von Filseck
    • , Luca Barberi
    •  & Aurélien Roux

  • Article
    | Open Access

    Sensory hypersensitivity is common in autism spectrum disorders. Using functional MRI, psychophysics, and computational modeling, Schallmo et al. show that differences in visual motion perception in ASD are accompanied by weaker neural suppression in visual cortex.

    • Michael-Paul Schallmo
    • , Tamar Kolodny
    •  & Scott O. Murray

  • Article
    | Open Access

    Defects in homologous recombination (HR) are found in some triple negative breast cancers, suggesting they may be sensitive to PARP inhibitors. In this phase II clinical trial of the PARP inhibitor rucaparib, changes in Ki67 levels did not correlate with markers of HR deficiency but HR deficiency was detected in 69% of tumours, indicating that PARP inhibitors may be a useful treatment.

    • Neha Chopra
    • , Holly Tovey
    •  & Nicholas C. Turner

  • Article
    | Open Access

    Adrenal aldosterone production is regulated by plasma angiotensin and potassium levels. Here the authors report that the neuropeptide substance P stimulates aldosterone production via neurokinin type 1 receptors (NK1R), and report a proof-of-concept placebo controlled clinical trial showing that a NK1R antagonist decreases aldosterone levels.

    • Julien Wils
    • , Céline Duparc
    •  & Hervé Lefebvre

  • Article
    | Open Access

    Multi-nucleotide variants (MNV) are genetic variants in close proximity of each other on the same haplotype whose functional impact is difficult to predict if they reside in the same codon. Here, Wang et al. use the gnomAD dataset to assemble a catalogue of MNVs and estimate their global mutation rate.

    • Qingbo Wang
    • , Emma Pierce-Hoffman
    •  & Daniel G. MacArthur

  • Article
    | Open Access

    Upstream open reading frames (uORFs), located in 5’ untranslated regions, are regulators of downstream protein translation. Here, Whiffin et al. use the genomes of 15,708 individuals in the Genome Aggregation Database (gnomAD) to systematically assess the deleteriousness of variants creating or disrupting uORFs.

    • Nicola Whiffin
    • , Konrad J. Karczewski
    •  & James S. Ware

  • Article
    | Open Access

    RNA G-quadruplexes (RG4s) have been functionally linked to cancer gene expression. Here, Herviou, Le Bras et al. have identified the protein machinery modulating RG4s and reveal the role and mechanism of hnRNP H/F and DHX36 in RG4-mediated translational regulation affecting cancer treatment in glioblastoma.

    • Pauline Herviou
    • , Morgane Le Bras
    •  & Stefania Millevoi

  • Article
    | Open Access

    Although the feeling of being stressed is ubiquitous and clinically significant, the underlying neural mechanisms are unclear. Using a novel predictive modeling approach, the authors show that functional hippocampal networks specifically and consistently predict the feeling of stress.

    • Elizabeth V. Goldfarb
    • , Monica D. Rosenberg
    •  & Rajita Sinha

  • Article
    | Open Access

    The relative contribution of fallopian tube (FT) or ovarian surface epithelium (OSE) to high-grade serous ovarian cancer (HG-SOC) development is unclear. Here, the authors establish organoid models from murine oviductal and OSE tissues that allow cancer modeling via CRISPR-Cas9 genome editing, and report a dual origin of murine HG-SOC.

    • Kadi Lõhmussaar
    • , Oded Kopper
    •  & Hans Clevers

  • Article
    | Open Access

    Glycosylation plays a key role in shielding of immunogenic epitopes on viral spike (S) proteins. Here Watanabe et al. report that glycans of coronavirus SARS and MERS S proteins are heterogeneously distributed and do not form an efficacious high-density global shield which would ensure efficient immune evasion.

    • Yasunori Watanabe
    • , Zachary T. Berndsen
    •  & Max Crispin

  • Article
    | Open Access

    DNA methylation is an epigenetic marker in all domains of life. Here, Jeudy et al., using single-molecule realtime sequencing, determine DNA methylation patterns in giant viruses and evolutionary analysis of virus encoded DNA methyltransferases suggests that they affect viral fitness.

    • Sandra Jeudy
    • , Sofia Rigou
    •  & Matthieu Legendre

  • Article
    | Open Access

    Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.

    • Lun Zhao
    • , Liang Xie
    •  & Xingwang Li

  • Article
    | Open Access

    Oocyte meiosis must achieve spindle bipolarization without predefined spatial cues. Yoshida et al. demonstrate that spindle bipolarization during meiosis I in mouse oocytes requires kinetochores to prevent chromosome segregation errors, a phenomenon that does not occur in error-prone human oocytes.

    • Shuhei Yoshida
    • , Sui Nishiyama
    •  & Tomoya S. Kitajima

  • Article
    | Open Access

    Mutualism is typically portrayed as a destabilizing process in community ecology. Here, via a random matrix model that considers species density, the author shows that mutualistic interactions can, in fact, enhance population density at equilibrium and increase community resilience to perturbation.

    • Lewi Stone

  • Article
    | Open Access

    Mammary epithelial cells are epigenetically modified during pregnancy, these changes can influence the pre-disposition to cancer. Here, the authors examine the epigenetic landscape of mammary epithelial cells pre and post pregnancy and identify changes to the epigenetic landscape, which can protect mice from Myc induced cancer.

    • Mary J. Feigman
    • , Matthew A. Moss
    •  & Camila O. dos Santos

  • Article
    | Open Access

    Gut microbiome has been linked to cavernous angioma (CA), a common vascular disease, but the role in humans remains unclear. Here, the authors combine 16S rRNA sequencing and shotgun metagenomics to profile the microbiome in a large cohort of human subjects with and without CA, and among subjects with different CA clinical features.

    • Sean P. Polster
    • , Anukriti Sharma
    •  & Issam A. Awad

  • Article
    | Open Access

    The DIS3L2 exonuclease degrades aberrant 7SL RNAs tagged by an oligouridine 3′-tail. Here the authors analyze DIS3L2 knockout mouse embryonic stem cells and suggest that DIS3L2-mediated quality control of 7SL RNA is important for ER-mediated translation and calcium ion homeostasis.

    • Mehdi Pirouz
    • , Chih-Hao Wang
    •  & Richard I. Gregory

  • Article
    | Open Access

    Over 100 million of opioid prescriptions are issued yearly in the USA alone, but the impact of opioid use on the immune system is barely characterized. Here the authors report antiviral immune response is blunted in several types of blood cells from opioid-dependent individuals, and when healthy donor cells are exposed to morphine in a dish.

    • Tanya T. Karagiannis
    • , John P. Cleary Jr
    •  & Christine S. Cheng

  • Article
    | Open Access

    Path integration abilities, important for spatial navigation, vary widely across individuals and deteriorate in old age. This work shows that path integration errors in general, as well as age-related path integration deficits, are mainly caused by accumulating noise in people’s velocity estimation.

    • Matthias Stangl
    • , Ingmar Kanitscheider
    •  & Thomas Wolbers

  • Article
    | Open Access

    Genomic studies of paleopteran insects, such as mayflies, are needed to reconstruct early insect evolution. Here, Almudi and colleagues present the genome of the mayfly Cloeon dipterum and use transcriptomics to characterize its adaptations to distinct habitats and the origin of insect wings.

    • Isabel Almudi
    • , Joel Vizueta
    •  & Fernando Casares

  • Article
    | Open Access

    F1Fo ATP synthase consists of two coupled rotary molecular motors: the soluble ATPase F1 and the transmembrane Fo. Here, the authors present cryo-EM structures of E. coli ATP synthase in four discrete rotational sub-states at 3.1-3.4 Å resolution and observe a rotary sub-step of the Fo motor cring that reveals the mechanism of elastic coupling between the two rotary motors, which is essential for effective ATP synthesis.

    • Meghna Sobti
    • , James L. Walshe
    •  & Alastair G. Stewart

  • Article
    | Open Access

    The ubiquitous oceanic bacteria harbour an external phosphate buffer for modulating phosphate (Pi) uptake. Here, using both oceanic SAR11, Prochlorococcus and Synechococcus strains as a model, the authors show that the Pi buffer accumulation in the periplasm is proton motive force-dependent and can be enhanced by light energy.

    • Nina A. Kamennaya
    • , Kalotina Geraki
    •  & Mikhail V. Zubkov

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