Biological sciences articles within Nature Communications

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  • Article
    | Open Access

    Interleukin-9 (IL-9) is important for allergy, autoimmunity and tumor immunity, but how its expression is regulated is unclear. Here the authors show the essential function of an enhancer, CNS-25 in mouse and CNS-18 in human, for IL-9 expression, with the deletion of this enhancer severely hampering IL-9 production in mice or human cells.

    • Byunghee Koh
    • , Amina Abdul Qayum
    •  & Mark H. Kaplan

  • Article
    | Open Access

    CD8 T cells can protect the liver from viral infection, but can also result in severe liver damage and organ failure. Here, the authors develop a mouse model reflecting fulminant CD8 T cell mediated viral hepatitis, which occurs in a perforin-dependent manner that is protected by the use of perforin inhibitors.

    • M. Welz
    • , S. Eickhoff
    •  & W. Kastenmüller

  • Article
    | Open Access

    Bacterial histidine kinases (HKs) play key roles in the response to stimuli and are regulated by reversible phosphorylation. Here, the authors show that the activity of a HK in the plant pathogen Xanthomonas campestris is modulated by irreversible, proteolytic modification in response to osmostress.

    • Chao-Ying Deng
    • , Huan Zhang
    •  & Wei Qian

  • Article
    | Open Access

    Constitutive deletion of Rcan1 has been previously shown to prevent Angiotensin II-induced aneurysm in mice. Here the authors show that tissue-specific inducible deletion of Rcan1 in vascular cell types predisposes to hypertension-mediated aortic rupture, intramural hematoma, and aneurysm, due to increased GSK-3b-mediated activation of ROCK and induction of a hypercontractile phenotype.

    • Silvia Villahoz
    • , Paula Sofía Yunes-Leites
    •  & Miguel R. Campanero

  • Article
    | Open Access

    Perceptual constancy requires neural representations selective for object identity, yet tolerant of identity-preserving transformations. Here, the authors show that sound identity is represented robustly in auditory cortex and that behavioral generalization requires precise timing of identity information.

    • Stephen M. Town
    • , Katherine C. Wood
    •  & Jennifer K. Bizley

  • Article
    | Open Access

    Transient receptor potential vanilloid channel 3 (TRPV3) responds to temperature and sensitizes upon repeated stimulation with either heat or agonists. Here authors present the cryo-EM structures of apo and sensitized human TRPV3 and describe the structural basis of sensitization.

    • Lejla Zubcevic
    • , Mark A. Herzik Jr.
    •  & Seok-Yong Lee

  • Article
    | Open Access

    Ubiquitination and ubiquitin-like modifications of proteins regulate multiple cellular processes but identifying substrates of specific E2 and E3 enzymes remains challenging. Here, the authors conjugate E2 enzymes with enrichable ubiquitin derivatives to identify substrates of specific E2/E3 pairs by mass spectrometry.

    • Gábor Bakos
    • , Lu Yu
    •  & Jörg Mansfeld

  • Article
    | Open Access

    Colorectal cancers (CRCs) often develop into untreatable metastatic disease of the liver. Here the authors report the modification of extracellular matrix proteins by citrullination in CRC metastases to the liver and propose that inhibition of citrullination could serve as therapeutic avenue in the treatment.

    • A. E. Yuzhalin
    • , A. N. Gordon-Weeks
    •  & R. J. Muschel

  • Article
    | Open Access

    Molecular details that underlie mechanical properties of spider silk are of great interest to material scientists. Here, the authors report a previously unknown three-state mechanism of folding and an expanded structure of a spider silk protein that may contribute to elasticity of spider silk.

    • Charlotte Rat
    • , Julia C. Heiby
    •  & Hannes Neuweiler

  • Article
    | Open Access

    Single-cell detection methods are limited by the trade-off between flow rate and measurement precision. Here the authors introduce active loading, an optically triggered microfluidic system to concentrate diluted cell samples, which reduces clogging and decreases processing time in single-cell assays.

    • Nicholas L. Calistri
    • , Robert J. Kimmerling
    •  & Scott R. Manalis

  • Article
    | Open Access

    Melanocytic nevus count is associated with melanoma risk. In this study, a meta-analysis of 11 nevus GWAS studies identifies novel SNPs in KITLG and 9q32, and bivariate analysis with melanoma GWAS meta-analysis reveals that most nevus genes affect melanoma risk, while melanoma risk loci do not alter the nevus count.

    • David L. Duffy
    • , Gu Zhu
    •  & Nicholas G. Martin

  • Article
    | Open Access

    Imaging tracking of the migration of cell-based drug delivery systems are needed for expanding their clinical application for glioma. Here they report inflammation activatable engineered neutrophils containing doxorubicin-loaded magnetic mesoporous silica nanoparticles to image and actively target brain tumors after resection.

    • Meiying Wu
    • , Haixian Zhang
    •  & Hairong Zheng

  • Article
    | Open Access

    The evolution and genetic nature of metastatic lesions is not completely characterized. Here the authors perform a comprehensive whole-genome study of colorectal metastases in comparison to matched primary tumors and define a multistage progression model and metastasis-specific changes that, in part, are therapeutically actionable.

    • Naveed Ishaque
    • , Mohammed L. Abba
    •  & Heike Allgayer

  • Article
    | Open Access

    Animal physiology, including reproduction, could respond to climate change in complex ways. Here, the authors use experiments with an insect model system to show that simulated heatwaves harm male reproductive potential by reducing sperm number and viability, an effect which persisted into the next generation

    • Kris Sales
    • , Ramakrishnan Vasudeva
    •  & Matthew J. G. Gage

  • Article
    | Open Access

    Publicly available single cell RNA-seq datasets represent valuable resources for comparative and meta-analysis. Here, the authors develop scQuery, a web server integrating over 500 different studies with over 300 unique cell types for comparative analysis of existing and new scRNA-seq data.

    • Amir Alavi
    • , Matthew Ruffalo
    •  & Ziv Bar-Joseph

  • Article
    | Open Access

    Gluten-free diets are increasingly common in the general population. Here, the authors report the results of a randomised cross-over trial involving middle-aged, healthy Danish adults, showing evidence that a low-gluten diet leads to gut microbiome changes, possibly due to variations in dietary fibres.

    • Lea B. S. Hansen
    • , Henrik M. Roager
    •  & Oluf Pedersen

  • Article
    | Open Access

    Excitatory glycine GluN1/GluN3A receptors are atypical NMDARs that have been difficult to study. Here the authors identify new properties of these receptors, including potentiation by the GluN1 antagonist CGP-78608 that allows detection of functional GluN1/GluN3A receptors in the juvenile brain.

    • Teddy Grand
    • , Sarah Abi Gerges
    •  & Pierre Paoletti

  • Article
    | Open Access

    The sense of ownership – of which objects belong to us and which to others - is an important part of our lives, but how the brain keeps track of ownership is poorly understood. Here, the authors show that specific brain areas are involved in ownership acquisition for the self, friends, and strangers.

    • Patricia L. Lockwood
    • , Marco K. Wittmann
    •  & Matthew F. S. Rushworth

  • Article
    | Open Access

    Chromothripsis and chromoanasynthesis lead to locally clustered rearrangements affecting one or a few chromosomes, but their impact on cancer development and progression is unclear. Here the authors analyse the role of DNA repair factors in brain tumors by whole-genome sequencing of tumors from mouse models of medulloblastoma or high grade gliomas.

    • Manasi Ratnaparkhe
    • , John K. L. Wong
    •  & Aurélie Ernst

  • Article
    | Open Access

    TssA is an important component of the bacterial type VI secretion system (T6SS). Here, Dix et al. integrate structural, phylogenetic and functional analysis of the TssA subunits, providing new insights into their role in T6SS assembly and function.

    • Samuel R. Dix
    • , Hayley J. Owen
    •  & Mark S. Thomas

  • Article
    | Open Access

    Uptake and release of glycerol from the small intestine and adipocytes is facilitated by a subclass of aquaporins (AQP), but how glycerol flow is regulated remains poorly understood. Here authors solve the crystal structure of AQP10 and show how lipolysis is coupled to AQP10 regulation in

    • Kamil Gotfryd
    • , Andreia Filipa Mósca
    •  & Pontus Gourdon

  • Article
    | Open Access

    Super-resolution microscopy using wavelengths in the near infrared (NIR) optical window is particularly appealing for live cell and tissue imaging, yet largely unexplored. Here the authors present NIR-STED nanoscopy of living mammalian cells using the new bacteriophytochrome-based fluorescent protein SNIFP.

    • Maria Kamper
    • , Haisen Ta
    •  & Stefan Jakobs

  • Article
    | Open Access

    Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.

    • Lukas F. Milles
    • , Eduard M. Unterauer
    •  & Hermann E. Gaub

  • Article
    | Open Access

    REX1 has been shown to regulate pluripotency of ESCs, genomic imprinting and preimplantation development in mice. Here the authors provide evidence that REX1 is the prime target of RNF12 E3 ubiquitin ligase and that Rex1 removal rescues the Rnf12 knockout phenotype in imprinted X chromosome inactivation in mice.

    • Cristina Gontan
    • , Hegias Mira-Bontenbal
    •  & Joost Gribnau

  • Article
    | Open Access

    Hepatitis E virus (HEV) infection can result in severe placental disease, but mechanisms underlying pathogenicity are poorly understood. Here, the authors develop an ex vivo model for HEV infection at the maternal-fetal interface and compare pathogenicity of different HEV genotypes.

    • Jordi Gouilly
    • , Qian Chen
    •  & Hicham El Costa

  • Article
    | Open Access

    Accurate and actionable biomarkers that integrate diverse molecular, functional and clinical information hold great promise in precision medicine. Here, the authors develop SIMMS, a method for pathway-based cross-disease biomarker discovery.

    • Syed Haider
    • , Cindy Q. Yao
    •  & Paul C. Boutros

  • Article
    | Open Access

    How interactions between binding partners form or break is hidden in the transition paths from the encounter to the formation of a stable complex. Here authors use single‐molecule spectroscopy to measure the transition path times for the association of two intrinsically disordered proteins that form a folded dimer upon binding and identify a metastable encounter complex.

    • Flurin Sturzenegger
    • , Franziska Zosel
    •  & Benjamin Schuler

  • Article
    | Open Access

    Regulatory T (Treg) cells may lose the expression of their master transcription factor, Foxp3, and be converted to pro-inflammatory cells. Here the authors show that this lineage plasticity may be mediated by the enhanced expression of another transcription regulator, Id2, which suppresses the transcription of Foxp3 to alter Treg lineage stability.

    • Sung-Min Hwang
    • , Garima Sharma
    •  & Sin-Hyeog Im

  • Article
    | Open Access

    MAIT cells are abundant in the lungs and confer protection against bacterial pathogens. Whilst activation of these cells has been described during viral infections, here van Wilgenburg and colleagues show that in a murine model MAIT cells contribute to the protective host immune response to influenza virus infection.

    • Bonnie van Wilgenburg
    • , Liyen Loh
    •  & Timothy S. C. Hinks

  • Article
    | Open Access

    Algorithms designed to find rare cells in single cell RNA-seq data sets cannot cope with data sets containing tens of thousands of cells. Here the authors present Finder of Rare Entities (FiRE), an algorithm that uses the Sketching technique to assign a rareness score to every expression profile in large RNA-seq data sets.

    • Aashi Jindal
    • , Prashant Gupta
    •  & Debarka Sengupta

  • Article
    | Open Access

    Intrinsically disordered proteins (IDPs) usually fold during binding to target proteins which involves the formation of a transient complex (TC). Here authors use single-molecule FRET to show that the lifetime of TC for IDP binding is very long due to the stabilization by non-native electrostatic interactions, which makes fast association possible.

    • Jae-Yeol Kim
    • , Fanjie Meng
    •  & Hoi Sung Chung

  • Article
    | Open Access

    Remarkable organ shape morphological diversity exists in fruits, vegetables and seeds. Here, the authors establish a link between OVATE Family Proteins and TONNEAU1 Recruiting Motif family proteins in the development pathway that governs fruit shape of tomato, melon, and cucumber as well as potato tuber shape.

    • Shan Wu
    • , Biyao Zhang
    •  & Esther van der Knaap

  • Article
    | Open Access

    Cell type deconvolution from bulk expression data rely on a reference expression matrix. Here, the authors introduce a basis matrix built using data from both healthy and diseased samples profiled on 42 platforms, reducing biases introduced by single-platform matrices built using healthy samples.

    • Francesco Vallania
    • , Andrew Tam
    •  & Purvesh Khatri

  • Article
    | Open Access

    Excess caloric intake leads to increased thermogenesis in brown adipose tissue, to limit weight gain. Here, the authors show that neuropeptide FF receptor-2 signalling promotes thermogenesis via control of NPY expression in the arcuate nucleus, and that it absence in mice leads to a failure of activation of diet-induced thermogenesis and the development of exacerbated obesity.

    • Lei Zhang
    • , Chi Kin Ip
    •  & Herbert Herzog

  • Article
    | Open Access

    Oestrogen receptors α (ERα) are expressed in a subset of mammary epithelial cells. Here, the authors identify cells with low-ERα protein levels and show that distinct cell populations have distinct requirements for the AF1 and AF2 domains of the ERα, and ERα acts in a biphasic manner dependent on developmental stage.

    • Stéphanie Cagnet
    • , Dalya Ataca
    •  & Cathrin Brisken

  • Article
    | Open Access

    In vivo existence of guanine-rich four-stranded RNA structures (G4-RNAs) has been a matter of debate. Here the authors developed a protocol, G4RP-seq, to capture and identify transcriptome-wide G4-RNA, providing insights into the formation of transient G4-RNA in live human cells.

    • Sunny Y. Yang
    • , Pauline Lejault
    •  & David Monchaud

  • Article
    | Open Access

    Polyfluorinated hexopyranoses display unique physical, chemical and biological properties, however their stereoselective synthesis is highly challenging. Here, the authors report a synthetic approach based on the chemical manipulation of inexpensive levoglucosan to obtain heavily fluorinated monosaccharides stereoselectively.

    • Vincent Denavit
    • , Danny Lainé
    •  & Denis Giguère

  • Article
    | Open Access

    Humans can perform complex motor movements at varying speeds. Here, the authors show that a recurrent neural network can be trained to exhibit temporal scaling obeying Weber’s law as well as validate a prediction of the model of improved precision of movements at faster speeds.

    • Nicholas F. Hardy
    • , Vishwa Goudar
    •  & Dean V. Buonomano

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