Biological sciences articles within Nature Communications

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  • Article
    | Open Access

    There is debate about the structural organization of the yeast centromeric nucleosome and the role of the nonhistone protein Scm3 in its assembly. Dechassaet al.find that yeast centromeric nucleosomes organize DNA in a left-handed superhelix, and show that Scm3 is a specific nucleosome assembly factor.

    • Mekonnen Lemma Dechassa
    • , Katharina Wyns
    •  & Karolin Luger

  • Article
    | Open Access

    ADAR enzymes edit double-stranded RNA, converting adenosines to inosines, and are essential for neuronal function. Eggingtonet al. quantify edit sites in RNA using a Sanger sequencing protocol and use the resulting data to develop algorithms to predict RNA edit sites.

    • Julie M. Eggington
    • , Tom Greene
    •  & Brenda L. Bass

  • Article
    | Open Access

    Global darkness from an asteroid impact 65.5 million years ago led to massive extinction of oceanic phytoplankton, but coastal groups survived. Ribeiroet al.revive coastal dinoflagellates after a century of dormancy, suggesting phytoplankton survived the extinction and helped restore photosynthesis in the ocean.

    • Sofia Ribeiro
    • , Terje Berge
    •  & Marianne Ellegaard

  • Article
    | Open Access

    The molecular mechanisms that regulate TH17 cell diversity are poorly understood. Ouyang et al. show that the transcription factor interferon regulatory factor-8 is required for TH17-cell differentiation and that its absence increases the severity of an experimental model of colitis.

    • Xinshou Ouyang
    • , Ruihua Zhang
    •  & Huabao Xiong

  • Article
    | Open Access

    IKK kinases activate nuclear factor-κB, and the activated form of this transcription factor is found in endothelial cells in diseased tissue. In this study, mice lacking IKKβ in the endothelium are generated, and it is shown that defects in endothelial cell function are both IKK kinase activity dependent and independent.

    • Noboru Ashida
    • , Sucharita SenBanerjee
    •  & Anthony Rosenzweig

  • Article
    | Open Access

    Two-dimensional fluid interfaces are ubiquitous, but studying their surface dynamic properties is difficult because of coupling between the film and bulk fluid. Choiet al.combine active microrheology with fluorescence microscopy to image fluid interfaces under applied stress.

    • S.Q. Choi
    • , S. Steltenkamp
    •  & T.M. Squires

  • Article |

    Calorie restriction has been associated with increased life span and delayed decline of memory in animals, suggesting a role in neuronal plasticity. In this study, food restriction is demonstrated to enhance plasticity in the central nervous system and trigger the recovery from ocular deprivation in adulthood.

    • Maria Spolidoro
    • , Laura Baroncelli
    •  & Lamberto Maffei

  • Article
    | Open Access

    The Q-cycle is thought to be an essential energetic component of the photosynthetic electron-transfer chain. Here, Chlamydomonas mutants with an inactive Q-cycle but normal levels ofb6fcomplexes are shown to display photosynthetic growth, demonstrating the dispensability of the Q-cycle in the oxygenic photosynthetic chain.

    • Alizée Malnoë
    • , Francis-André Wollman
    •  & Fabrice Rappaport

  • Article
    | Open Access

    Saccharomycesyeasts can produce ethanol from sugars in the presence of oxygen. In this study, the authors demonstrate thatDekkera bruxellensis, a distantly related yeast, can also produce and consume ethanol due to the loss of a cis-regulatory element from the promoters of genes crucial for respiration.

    • Elżbieta Rozpędowska
    • , Linda Hellborg
    •  & Jure Piškur

  • Article
    | Open Access

    Duchenne muscular dystrophy is caused by a loss of thedystrophin gene, and control of dystrophin mRNA splicing could aid treatment of the disease. Nishida et al. show that a small molecule promotes skipping of exon 31 and increases production of a functional dystrophin protein in a patient.

    • Atsushi Nishida
    • , Naoyuki Kataoka
    •  & Masafumi Matsuo

  • Article |

    The detailed interactions of membrane proteins with their lipid environment are poorly understood. Sonntaget al. use low-resolution X-ray crystallographic data and molecular dynamics simulations to study the manner in which the sarcoendoplasmic reticulum Ca2+–ATPase adapts to different membrane environments.

    • Yonathan Sonntag
    • , Maria Musgaard
    •  & Lea Thøgersen

  • Article |

    PTEN is a phosphatase that regulates the phosphatidylinositol-3 kinase signalling pathway and is inactivated in many tumour types. Heet al.show that a mannosidase, α-mannosidase 2C1, can inactivate PTEN in prostate cancer cells, and that PTEN-positive human prostate tumours overexpress α-mannosidase 2C1.

    • Lizhi He
    • , Catherine Fan
    •  & Damu Tang

  • Article |

    Pair-wise electrophysiology is difficult inCaenorhabditis elegansbecause the recordings are relatively short-lived. In this study, the authors investigate the synaptic currents associated with escape responses by immobilizing worms on a micropatterned agar substrate and stimulating neurons using channelrhodopsin-2.

    • Theodore H. Lindsay
    • , Tod R. Thiele
    •  & Shawn R. Lockery

  • Article |

    Little is known about the effects of molecular crowding and confinement on biomolecule function. Castronovoet al. investigate the reactions of restriction enzymes with DNA confined in bushy matrices and find that the enzymes enter at the side of the matrix before diffusing two-dimensionally.

    • Matteo Castronovo
    • , Agnese Lucesoli
    •  & Giacinto Scoles

  • Article |

    N-methyl-D-aspartate receptors mediate excitatory synaptic transmission, and those containing GluN2D subunits have an unusually long deactivation time. Vance et al. show that the conformational variability of the ligand-binding domain and the structure of the activating ligand influence deactivation time.

    • Katie M. Vance
    • , Noriko Simorowski
    •  & Hiro Furukawa

  • Article
    | Open Access

    The study of prion diseases has been hampered as there is no method to distinguish newly formed abnormal prion protein conformers. Here, the authors describe a method to study newly formed abnormal prion protein and demonstrate that it is produced within 1 minute of cell exposure to prions.

    • R. Goold
    • , S. Rabbanian
    •  & S.J. Tabrizi

  • Article
    | Open Access

    In vitrostudies have suggested that the ubiquitin ligase, Nedd4-2, regulates several proteins, including the epithelial sodium channel. Here by examining Nedd4-2-deficient mice, the authors demonstrate that Nedd4-2 is essential for epithelial sodium channel regulation, fetal and postnatal lung function and animal survival.

    • Natasha A. Boase
    • , Grigori Y. Rychkov
    •  & Sharad Kumar

  • Article
    | Open Access

    Exosomes released from cells can transfer RNA to recipient cells. In this study, the authors demonstrate that microRNAs in exosomes from T cells can be transferred to antigen-presenting cells during immune synapsis, and that this can alter gene expression, suggesting a new form of cellular communication.

    • María Mittelbrunn
    • , Cristina Gutiérrez-Vázquez
    •  & Francisco Sánchez-Madrid

  • Article
    | Open Access

    Cyanide-releasing defence systems in plants and animals are important to the evolution of plant–herbivore interactions. The authors identify the enzymes responsible for biosynthesis of cyanogenic glucosides by Six-spot Burnet moth caterpillars, which have evolved independently from the known plant pathway.

    • Niels Bjerg Jensen
    • , Mika Zagrobelny
    •  & Søren Bak

  • Article |

    The spinal V2a interneurons control left–right limb alternation during mouse locomotion, but only at high frequencies. In this study, the authors show that only half of these neurons are active during locomotion, and that they receive increasing synaptic drive to increase their activity as locomotion accelerates.

    • Guisheng Zhong
    • , Kamal Sharma
    •  & Ronald M. Harris-Warrick

  • Article
    | Open Access

    In the developing eye, the lens and retina are derived from different embryonic tissues, and how these two structures develop next to each other is of interest. In this study, the authors show that transforming growth factor-β secreted by neural crest cells is critical for the positioning of the lens next to the retina.

    • Timothy Grocott
    • , Samuel Johnson
    •  & Andrea Streit

  • Article
    | Open Access

    Eukaryotic cell plasma membranes possess a mechanism to repair tears caused by stimuli such as mechanical stress. The authors demonstrate that annexin-A5, when assembled into two-dimensional arrays in the presence of calcium, is required for membrane repair.

    • Anthony Bouter
    • , Céline Gounou
    •  & Alain R. Brisson

  • Article
    | Open Access

    Regulatory T cells are characterized by the expression of Foxp3, however, how the expression of this protein is controlled is unclear. Here, the authors show that the nuclear orphan receptor, Nr4a2, is a transcriptional activator of Foxp3, and suggest that it is required for the function of regulatory T cells.

    • Takashi Sekiya
    • , Ikkou Kashiwagi
    •  & Akihiko Yoshimura

  • Article
    | Open Access

    Plasmids are present in many bacteria and are often transferred between different species causing horizontal gene transfer. By comparing the sequences of 25 plasmid DNA backbones, the authors show that homologous recombination is prevalent in plasmids and that the plasmids have adapted to persist in different host bacteria.

    • Peter Norberg
    • , Maria Bergström
    •  & Malte Hermansson

  • Article
    | Open Access

    The global prevalence of the Duffy blood group variants is important due to the resistance that the Duffy-negative phenotype generally confers uponPlasmodium vivax infection. Hay et al.generate global frequency maps of the common Duffy alleles to show transmission patterns of the malaria parasite.

    • Rosalind E. Howes
    • , Anand P. Patil
    •  & Simon I. Hay

  • Article
    | Open Access

    Many animals can do simple quantity discrimination, but they often perform poorly when food is used. Here, the authors show that monkeys are good at food quantity discrimination when they are not allowed to eat it, suggesting that the mental representation of the stimuli is more important than the physical quality.

    • Vanessa Schmitt
    •  & Julia Fischer

  • Article
    | Open Access

    It has been proposed that stem cells use nonrandom chromosome segregation to avoid the accumulation of replication-induced mutations. Here, the authors examine intestinal epithelial stem cell division and show, using label exclusion and retention assays, that the cells segregate their chromosomes randomly.

    • Marion Escobar
    • , Pierre Nicolas
    •  & Catherine Legraverend

  • Article
    | Open Access

    Deubiquitinating enzymes are involved in multiple cellular processes, including cell viability. The authors reveal a role for the deubiquitinating enzyme, USP17, in the migration of cells in response to chemokines and show that USP17 is required for the relocalization of GTPases involved in cell motility.

    • Michelle de la Vega
    • , Alyson A. Kelvin
    •  & James A. Johnston

  • Article
    | Open Access

    The presence of earthworms is known to enhance the quality and moisture of soil in cool and wet climates. Evanset al. show that termites and ants can improve soil quality in warmer and drier climates—their presence results in elevated water infiltration and nitrogen content, leading to increased wheat yields.

    • Theodore A. Evans
    • , Tracy Z. Dawes
    •  & Nathan Lo

  • Article |

    The formation of hydrophilic protein–protein interactions cannot be explained by charge–charge interactions. Here, molecular simulations reveal that water forms an adhesive hydrogen-bonded network between proteins, stabilizing intermediate states before the bound complex forms.

    • Mazen Ahmad
    • , Wei Gu
    •  & Volkhard Helms

  • Article |

    Phosphorylation of the microtubule-associated protein tau is associated with disease, but other post-translational modifications of tau are not well studied. Here, Cohenet al. study the acetylation of tau and suggest that this form of the protein may be associated with tauopathies.

    • Todd J. Cohen
    • , Jing L. Guo
    •  & Virginia M. Y. Lee

  • Article |

    Single-molecule force spectroscopy is used to study single molecule interactions, but probing short-lived events is difficult. Here, a nanomechanical interface is developed, which allows the study of microsecond timescale interactions.

    • Mingdong Dong
    •  & Ozgur Sahin

  • Article
    | Open Access

    Lipid phosphodiesters affect the conformation of certain potassium channels, but the details of the lipid-channel interactions are unclear. Here, the KvAP channel is found to switch from an active to a resting state when the channels are transferred from a phospholipid membrane to a bilayer lacking phosphodiesters.

    • Hui Zheng
    • , Weiran Liu
    •  & Qiu-Xing Jiang

  • Article
    | Open Access

    Asymmetric partitioning of centrosomes has been reported inDrosophilaneuroblasts, but whether this type of division has implications for stem cell self-renewal is unclear. In this study, the authors show that the asymmetric division of the centrosomes correlates with the asymmetric fate of the cells and that the daughter centrosome is retained by the neuroblast.

    • Jens Januschke
    • , Salud Llamazares
    •  & Cayetano Gonzalez

  • Article
    | Open Access

    Inflammation can result in the formation of tumours, but the immune system is also involved in the elimination of cancer cells. Here, the authors show that inflammation driven by tumour-specific CD4+T cells results in tumour regression and identify a list of cytokines associated with cancer prevention.

    • Ole Audun Werner Haabeth
    • , Kristina Berg Lorvik
    •  & Alexandre Corthay

  • Article |

    Pronucleus DNA becomes demethylated during zygotic development. Here, the authors demonstrate that the reduction in 5-methylcytosine levels is accompanied by an increase in the presence of 5-hydroxymethylcytosine, and suggest that this has a role in developmental reprogramming.

    • Mark Wossidlo
    • , Toshinobu Nakamura
    •  & Jörn Walter

  • Article |

    Matrilocal and patrilocal populations are predicted to have greater genetic diversity in mitochondrial DNA and the Y-chromosome, respectively. Here, no difference in the diversity of the Y-chromosome was found in two such groups, suggesting that local diversity was caused by male gene flow in expanding populations.

    • Ellen Dröfn Gunnarsdóttir
    • , Madhusudan R. Nandineni
    •  & Mark Stoneking

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