Biological sciences articles within Nature Communications

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  • Article
    | Open Access

    The transcriptional co-factors Yap and TAZ are regulated by Hippo signalling and mechanical forces via their nucleocytoplasmic shuttling. Here the authors identify a RhoA-regulated C-terminal nuclear localization signal and a TEAD-regulated N-terminal nuclear export signal of TAZ in an epithelial cell line.

    • Michael Kofler
    • , Pam Speight
    •  & András Kapus

  • Article
    | Open Access

    Gene pairs that are coexpressed across various environmental conditions in multiple species suggest functional similarity. Here the authors analyze patterns of gene expression co-evolution across diverse eukaryotes, and identify hundreds of protein complexes and pathways whose gene expression levels have co-evolved since their ancient divergence.

    • Trevor Martin
    •  & Hunter B. Fraser

  • Article
    | Open Access

    The detailed folding mechanisms of membrane proteins in their natural bilayer-like environments remains poorly understood due to the lack of tools for measuring stabilities and kinetics. Here, by simulating the folding of GlpG in a bilayer, the authors provide support for the helical-hairpin hypothesis and prompt a re-evaluation of a long-standing paradigm, the two-stage hypothesis.

    • Wei Lu
    • , Nicholas P. Schafer
    •  & Peter G. Wolynes

  • Article
    | Open Access

    Associations between corals and symbiotic microorganisms could be driven by the environment or shared evolutionary history. Here, the authors examine relationships between coral phylogenies and associated microbiomes, finding evidence of phylosymbiosis in microbes from coral skeleton and tissue, but not mucus.

    • F. Joseph Pollock
    • , Ryan McMinds
    •  & Jesse R. Zaneveld

  • Article
    | Open Access

    Artificial gene circuits represent intellectual property that under some circumstances may need to be obfuscated to prevent discovery by third parties. Here the authors use encryption by overlapping recombinase sites and steganography by the introduction of superfluous components, to obscure circuit topology.

    • Oliver Purcell
    • , Jerry Wang
    •  & Timothy K. Lu

  • Article
    | Open Access

    In vitro culture has detrimental effects on transcriptomes and epigenetic programming of zygotes. Here the authors use microfluidic technology to co-culture bovine oviduct epithelial cells with zygotes and show that the transcriptomes and global methylation patterns of these zygotes are more similar to in vivo zygotes than to conventionally cultured zygotes.

    • Marcia A. M. M. Ferraz
    • , Hoon Suk Rho
    •  & Bart M. Gadella

  • Article
    | Open Access

    The molecular mechanisms that underlie associations in GWAS, incl. chronic kidney disease (CKD), are largely unknown. Here, the authors perform an integrative analysis of genetic, transcriptomic and epigenomic data from human kidney to pinpoint plausible molecular pathways of CKD genetic associations.

    • Xiaoguang Xu
    • , James M. Eales
    •  & Maciej Tomaszewski

  • Article
    | Open Access

    The use of enzymes as drugs requires that they persist within target tissues over therapeutically relevant time frames. Here the authors use a galectin-3 fusion to anchor enzymes at injection sites for up to 14 days.

    • Shaheen A. Farhadi
    • , Evelyn Bracho-Sanchez
    •  & Gregory A. Hudalla

  • Article
    | Open Access

    Drug resistance is one of the major causes of cancer-related deaths. Here, the authors using single cell RNA-seq of oral squamous cell carcinoma patient samples pre- and post-cisplatin treatment show that phenotypically homogenous cell populations display cell state plasticity, with poised chromatin marks at mesenchymal genes in epithelial cells, and that the loss of stem factor Sox2 but gain of Sox9 expression (with de novo gain of H3K27ac sites) is associated with drug-induced adaptation.

    • Ankur Sharma
    • , Elaine Yiqun Cao
    •  & Ramanuj DasGupta

  • Article
    | Open Access

    The Androgen Receptor (AR) is the main driver of prostate cancer and functions in conjunction with chromatin modifications. Here, the authors comprehensively profile 100 primary prostate carcinomas by sequencing RNA transcripts in combination with ChIP-sequencing for AR and the active histone marks H3K27ac, H3K4me3 and repressive mark H3K27me3.

    • Suzan Stelloo
    • , Ekaterina Nevedomskaya
    •  & Wilbert Zwart

  • Article
    | Open Access

    The mammalian stomach is a complex organ with diverse roles in health and disease. Here, the authors integrate proteomics and transcriptomics to analyze the mouse stomach at 15 time points during development, providing molecular level insights into system-wide developmental changes.

    • Xianju Li
    • , Chunchao Zhang
    •  & Jun Qin

  • Article
    | Open Access

    Sulfolobus islandicus is a model organism within the TACK superphylum of the Archaea. Here, the authors perform a genome-wide analysis of essential genes in this organism, show that the proteinaceous S-layer is not essential, and explore potential stages of evolution of the essential gene repertoire in Archaea.

    • Changyi Zhang
    • , Alex P. R. Phillips
    •  & Rachel J. Whitaker

  • Article
    | Open Access

    Despite major drug discovery efforts, the therapeutic options for glioblastoma (GBM) remain inadequate. Here they analyze patient-derived xenograft model of GBM to quantitatively map distribution and cellular response to the EGFR inhibitor erlotinib, and report heterogeneous erlotinib delivery to intracranial tumors to be inadequate to inhibit EGFR signaling.

    • Elizabeth C. Randall
    • , Kristina B. Emdal
    •  & Nathalie Y. R. Agar

  • Article
    | Open Access

    Aerobic ethanol production, a phenomenon referred as Crabtree effect, allows yeast to outcompete other microorganisms in sugar rich environments. Here, the authors show that overexpression of a Gal4-like transcription factor can transform Komagataella phaffii from Crabtree effect negative to positive.

    • Özge Ata
    • , Corinna Rebnegger
    •  & Diethard Mattanovich

  • Article
    | Open Access

    Standard approaches for heritability and set testing in statistical genetics rely on parametric models that might not hold in reality and give inflated p-values. Here, the authors develop a fast method for permutation-based testing of marker sets and of heritability that does not suffer from model misspecification.

    • Regev Schweiger
    • , Eyal Fisher
    •  & Eran Halperin

  • Article
    | Open Access

    Human induced pluripotent stem cell derived cardiomyocytes are a powerful model for cardiogenesis and disease in vitro. Here the authors comprehensively map cardiac differentiation using multiple modalities, including single-cell RNA seq and CyTOF, in cells with a gain  or loss of function in key cardiac transcription factors.

    • Jared M. Churko
    • , Priyanka Garg
    •  & Joseph C. Wu

  • Article
    | Open Access

    Phytochromes are photoreceptors that are present in plants, bacteria and fungi. Here the authors present crystal structures of the phytochrome Agp2 from Agrobacterium fabrum in the parent Pfr state as well as a functional Meta-F intermediate and discuss mechanistic implications for photoconversion.

    • Andrea Schmidt
    • , Luisa Sauthof
    •  & Patrick Scheerer

  • Article
    | Open Access

    Vitamin B12 is an essential nutrient with limited natural sources. Here the authors transfer 28 pathway synthesis genes from several bacteria including R. capsulatus to E. coli and, using metabolic engineering and optimised fermentation conditions, achieve high yields.

    • Huan Fang
    • , Dong Li
    •  & Dawei Zhang

  • Article
    | Open Access

    Research on plant root-associated microbial communities may help develop more efficient or sustainable crop production methods. Here the authors analyse the citrus rhizosphere microbiome, using both amplicon and deep shotgun metagenomic sequencing of samples collected across six continents.

    • Jin Xu
    • , Yunzeng Zhang
    •  & Nian Wang

  • Article
    | Open Access

    Mineralized plaque, or dental calculus, is a valuable reservoir of the ancient oral microbiome. Here, the authors use quantitative metaproteomics to analyze the dental calculus of 21 individuals from a medieval cemetery, identifying human and microbial proteins that shed light on their oral health status.

    • Rosa R. Jersie-Christensen
    • , Liam T. Lanigan
    •  & Jesper V. Olsen

  • Article
    | Open Access

    Mutations in genes encoding subunits of the BAF complex can cause Coffin–Siris and Nicolaides–Baraitser syndromes. Here the authors identify overlapping DNA methylation signatures in individuals with subtypes of these two syndromes that suggest a functional link and can be used to diagnose subjects with unclear clinical presentations.

    • Erfan Aref-Eshghi
    • , Eric G. Bend
    •  & Bekim Sadikovic

  • Article
    | Open Access

    Invasive cells respond to contact guidance cues during migration. Here, using micro- and nanopatterning with different ligands and varying stiffness, the authors find that cells can make cellular protrusions through both contractility-dependent and contractility-independent means.

    • Erdem D. Tabdanov
    • , Vikram V. Puram
    •  & Paolo P. Provenzano

  • Article
    | Open Access

    While autapses are synapses made by a neuron onto itself, its functional significance in pyramidal cells are not clear. Here, the authors show that in the mammalian neocortex, autapses of pyramidal cells can enhance burst firing and coincidence detection from other inputs.

    • Luping Yin
    • , Rui Zheng
    •  & Yousheng Shu

  • Article
    | Open Access

    Rewarding events are prioritized in memory, but to support adaptive decision-making memory should also be prioritized for the events leading up to a reward. Here, the authors show that reward retroactively prioritizes memory for proximal, neutral events that precede the reward.

    • Erin Kendall Braun
    • , G. Elliott Wimmer
    •  & Daphna Shohamy

  • Article
    | Open Access

    Common radical fluorination reagents, such as Selectofluor®, are penalized by the need for metal catalysts and possible oxidation side reactions. Here, the authors reported the synthesis and application of N-fluoro-N-arylsulfonamides (NFASs) as third generation of radical fluorinating reagents to overcome those limitations.

    • Daniel Meyer
    • , Harish Jangra
    •  & Philippe Renaud

  • Article
    | Open Access

    Early childhood educational intervention has positive outcomes in adulthood, including higher education attainment, economic status, and overall health. This study shows that adults who underwent such intervention have greater enforcement of equality norm during social decision-making, potentially motivated by future planning.

    • Yi Luo
    • , Sébastien Hétu
    •  & Craig Ramey

  • Article
    | Open Access

    The effects of epigenetic regulators on different tumor cell populations can affect their potential as anticancer targets. In this study, the authors demonstrate that the histone methyltransferase G9a is a suppressor of lung tumor-propagating cells and tumor progression, acting through chromatin modification with MMP10 as one of its targets for metastasis regulation.

    • S. P. Rowbotham
    • , F. Li
    •  & C. F. Kim

  • Review Article
    | Open Access

    Facilitation is a well-known ecological interaction among free-living species, but symbionts residing in or on a host can also positively affect other symbiont species. Here, the authors review examples of facilitation among symbionts, revealing how facilitation theory can improve understanding of these interactions.

    • Flore Zélé
    • , Sara Magalhães
    •  & Alison B. Duncan

  • Article
    | Open Access

    Brain microglial cells can be replenished by blood-derived monocytes, but many aspects of this repopulation remain unclear. Here the authors show that the brain microglial niche can be replaced both by proliferating, residential microglia as well as differentiated Ly6Chi monocytes, with the latter having overlapping but distinct characteristics.

    • Harald Lund
    • , Melanie Pieber
    •  & Robert A. Harris

  • Article
    | Open Access

    The transcription factor RORγt is essential for the differentiation of TH17 cells, thymocyte development and lymphoid organogenesis. Here the authors show that the function of RORγt is regulated by PIAS4-mediated sumoylation that stabilize the interaction with SRC1 and KAT2A, to enhance the transcriptional activity of RORγt.

    • Zhiheng He
    • , Jing Zhang
    •  & Zuoming Sun

  • Article
    | Open Access

    RIG-I and MDA5, are cytosolic restriction factors and receptors for RNA viruses. Here the authors show during KSHV lytic infection that substrates for recognition by RIG-I and MDA5 are misprocessed RNAs derived from noncoding host RNA molecules, suggesting antiviral immunity can be engaged by sensing of misprocessed cellular RNAs.

    • Yang Zhao
    • , Xiang Ye
    •  & John Karijolich

  • Article
    | Open Access

    The recognition of the mRNA codon by the tRNA anticodon is crucial for protein synthesis. Here the authors introduce non-standard nucleotides in bacterial and eukaryotic mRNA to reveal the minimal hydrogen bond requirement of codon-anticodon interaction for efficient and accurate translation.

    • Thomas Philipp Hoernes
    • , Klaus Faserl
    •  & Matthias David Erlacher

  • Article
    | Open Access

    The metabolic regulator protein family, mTOR, regulate natural killer (NK) cell development and function, but the underlying mechanism is unclear. Here, the authors show that Raptor/mTORC1 and Rictor/mTORC2 form a feedback crosstalk network to variegate cytokine and cellular signaling and modulate NK maturation and effector functions.

    • Fangjie Wang
    • , Meng Meng
    •  & Youcai Deng

  • Article
    | Open Access

    The construction of complex RNA-delivered genetic circuits in mammalian cells is challenging, though offers advantages over DNA circuits in clinical use. Here the authors construct a set of logic gates that respond to multiple miRNAs and demonstrate an apoptosis-regulatory AND gate.

    • Satoshi Matsuura
    • , Hiroki Ono
    •  & Hirohide Saito

  • Article
    | Open Access

    Natural killer cells may respond better on second antigen encounters, but how this memory is induced or maintained in vivo is not clear. Here the authors show that memory NK cells expressing interleukin-7 (IL-7) receptor are induced in the lymph nodes but later recruited to liver for long term, IL-7 dependent survival and memory maintenance.

    • Xianwei Wang
    • , Hui Peng
    •  & Zhigang Tian

  • Article
    | Open Access

    Assembly of large, repeat-rich eukaryotic genomes remains challenging. Here, the authors use BioNano Genomics DLS optical mapping and single-molecule nanopore sequencing to generate a chromosome-scale assembly of a new Sorghum bicolor accession and identify variation compared to the publicly available S. bicolor genome.

    • Stéphane Deschamps
    • , Yun Zhang
    •  & Haining Lin

  • Article
    | Open Access

    Wnt signaling is known to regulate the formation of the blood-brain barrier. Here Hübner et al. dissect the underlying mechanisms using high resolution live imaging in zebrafish, and find that Wnt regulates anastomosis of angiogenic sprouts in the brain by counteracting sphingosine-1-phosphate receptor signaling.

    • Kathleen Hübner
    • , Pauline Cabochette
    •  & Wiebke Herzog

  • Article
    | Open Access

    Cardiac progenitor cells (CPCs) form cardiomyocytes, pericytes, smooth muscle and endothelial cells during embryonic development. Here, the authors characterize mouse CPCs marked by Nkx2.5 and Isl1 from E7.5 to E9.5 by single cell RNA-seq and ATAC-seq, showing fate transitions involve distinct open chromatin state.

    • Guangshuai Jia
    • , Jens Preussner
    •  & Thomas Braun

  • Article
    | Open Access

    While young muscle faithfully regenerates damaged myofibers, aged muscle is impaired. Here the authors show the “anti-aging” protein α-Klotho is upregulated in young muscle after damage via promoter demethylation and this regulation is lost in aging, resulting in mitochondrial damage and an impaired healing response.

    • A. Sahu
    • , H. Mamiya
    •  & F. Ambrosio

  • Article
    | Open Access

    Salmonella employ a range of strategies to counter host defences during infection. Here, Aulicino et al. use single-cell RNA-sequencing to examine the effects of invasive and non-invasive strains of Salmonella, revealing discrete and divergent immune evasion strategies in infected and bystander dendritic cells.

    • Anna Aulicino
    • , Kevin C. Rue-Albrecht
    •  & Alison Simmons

  • Article
    | Open Access

    It is unclear how removal of axon debris and initiation of axon regeneration following nerve injury is co-regulated. In this study, the authors show that the extracellular domain (ECD) of the engulfment receptor, CED-1, functions as an adhesion molecule to promote axonal regeneration after injury, independent of its function in phagocytosis

    • Hui Chiu
    • , Yan Zou
    •  & Chieh Chang

  • Article
    | Open Access

    Mechanical and metabolic cues contribute to regulate cell and tissue homeostasis but how they are integrated is not known. Here the authors show that the amino acid transporter and integrin coreceptor CD98hc regulates mechanical signaling downstream of integrins indirectly through regulating sphingolipid availability.

    • Etienne Boulter
    • , Soline Estrach
    •  & Chloé C. Féral

  • Article
    | Open Access

    Pyrenestes finches have a bill size polymorphism thought to be maintained by disruptive selection. Here, the authors identify a single candidate region, including insulin-like growth factor 1, differentiating small and large bill size morphs and a wider region differentiating the mega-billed morph.

    • Bridgett M. vonHoldt
    • , Rebecca Y. Kartzinel
    •  & Thomas B. Smith

  • Article
    | Open Access

    Soluble fumarate reductases are essential for eukaryotic cell survival under anaerobic conditions but their mechanism is not fully understood. Here, the authors present structural and enzymatic analyses of yeast fumarate reductase Osm1, elucidating the molecular basis of maintaining redox balance during anaerobiosis.

    • Sunghwan Kim
    • , Chang Min Kim
    •  & Hyun Ho Park

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