Nature Communications - 2 April 2014

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Weekly Content Alert 02 April 2014  Featured image: Caro et al. find that the biting fly avoidance is the most likely reason why zebras have stripes. Latest content: Articles Journal homepage Recommend to library Web feed     Latest Articles View all Articles     Microlens arrays in the complex visual system of Cretaceous echinoderms Przemyslaw Gorzelak, Mariusz A. Salamon, Rafal Lach, Michal Loba and Bruno Ferré Some echinoderms have photosensory organs composed of microlenses, yet the evolutionary origin of these microlenses is unclear. Here, Gorzelak et al. describe evidence of microlenses in Late Cretaceous brittle stars and starfish, suggesting that such visual systems were already present at this time. 01 April 2014 | doi: 10.1038/ncomms4576 Biological Sciences  Evolution  Palaeontology  Direct visualization of HIV-enhancing endogenous amyloid fibrils in human semen Shariq M. Usmani, Onofrio Zirafi, Janis A. Müller, Nathallie L. Sandi-Monroy, Jay K. Yadav, Christoph Meier, Tanja Weil, Nadia R. Roan, Warner C. Greene, Paul Walther, K. Peter R. Nilsson, Per Hammarström, Ronald Wetzel, Christopher D. Pilcher, Friedrich Gagsteiger, Marcus Fändrich, Frank Kirchhoff and Jan Münch Semen-derived peptides can form amyloid fibrils that boost HIV infection in vitro, but the existence of such fibrils in semen remained to be demonstrated. Here, the authors show that human semen contains amyloid fibrils, which can bind HIV particles and increase their infectiveness. 01 April 2014 | doi: 10.1038/ncomms4508 Biological Sciences  Medical research  Microbiology  Virology  Caloric restriction reduces age-related and all-cause mortality in rhesus monkeys OPEN Ricki J. Colman, T. Mark Beasley, Joseph W. Kemnitz, Sterling C. Johnson, Richard Weindruch and Rozalyn M. Anderson Caloric restriction extends the lifespan of various organisms but whether it works in monkeys is controversial. Here, Colman et al. report that caloric restriction reduces all-cause mortality of rhesus macaques, and perform a weight comparison that aims to reconcile their findings with contradictory results from a similar study. 01 April 2014 | doi: 10.1038/ncomms4557 Biological Sciences  Medical research  Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans OPEN Ekaterina E. Khrameeva, Katarzyna Bozek, Liu He, Zheng Yan, Xi Jiang, Yuning Wei, Kun Tang, Mikhail S. Gelfand, Kay Prufer, Janet Kelso, Svante Paabo, Patrick Giavalisco, Michael Lachmann and Philipp Khaitovich Modern human genomes contain Neanderthal sequences, but it is unclear whether these were selected. Here, Khrameeva et al. show that Neanderthal sequences associated with lipid catabolism are three times more frequent in Europe, suggesting that these sequences might have been beneficial to Europeans. 01 April 2014 | doi: 10.1038/ncomms4584 Biological Sciences  Evolution  Genetics  The function of zebra stripes Tim Caro, Amanda Izzo, Robert C. Reiner, Hannah Walker and Theodore Stankowich The function of zebra stripes remains unclear as none of the options have been validated ecologically. Here, the authors, matching striping patterns to environmental variables, test the main hypotheses against each other and find that biting fly avoidance best explains the presence of stripes in equids. 01 April 2014 | doi: 10.1038/ncomms4535 Biological Sciences  Ecology  Evolution  Morphological and functional remodelling of the neuromuscular junction by skeletal muscle PGC-1α Anne-Sophie Arnold, Jonathan Gill, Martine Christe, Rocío Ruiz, Shawn McGuirk, Julie St-Pierre, Lucía Tabares and Christoph Handschin The peroxisome proliferator activated receptor γ co-activator 1α (PGC-1α) is implicated in regulating the morphology and function of the neuromuscular junction. Here, Arnold et al. show that PGC-1α promotes the remodeling of pre- and postsynaptic neuromuscular junction sites, even in the absence of physical activity. 01 April 2014 | doi: 10.1038/ncomms4569 Biological Sciences  Neuroscience  The Vibrio cholerae type VI secretion system employs diverse effector modules for intraspecific competition OPEN Daniel Unterweger, Sarah T. Miyata, Verena Bachmann, Teresa M. Brooks, Travis Mullins, Benjamin Kostiuk, Daniele Provenzano and Stefan Pukatzki Some strains of the pathogen Vibrio cholerae can kill each other by injecting effector proteins that are toxic in the absence of cognate 'immunity' proteins. Here, the authors show that strains with high pathogenic potential possess matching effector-immunity sets and can coexist. 01 April 2014 | doi: 10.1038/ncomms4549 Biological Sciences  Evolution  Microbiology  PCAF-dependent epigenetic changes promote axonal regeneration in the central nervous system Radhika Puttagunta, Andrea Tedeschi, Marilia Grando Sória, Arnau Hervera, Ricco Lindner, Khizr I. Rathore, Perrine Gaub, Yashashree Joshi, Tuan Nguyen, Antonio Schmandke, Claudia J. Laskowski, Anne-Laurence Boutillier, Frank Bradke and Simone Di Giovanni Epigenetic codes translate external stimuli into targeted and long-lasting gene regulation. In this study, the authors show that regenerative retrograde signalling activates the epigenetic modifying enzyme PCAF, inducing gene expression and promoting axon regeneration in a mouse spinal cord injury model. 01 April 2014 | doi: 10.1038/ncomms4527 Biological Sciences  Genetics  Neuroscience  Glassiness and exotic entropy scaling induced by quantum fluctuations in a disorder-free frustrated magnet OPEN I. Klich, S.-H. Lee and K. Iida Spin liquids and spin ices arise when spins arranged on a lattice have several states that are close in energy, a phenomenon referred to as frustration. Here, Klich et al. show that quantum fluctuations can induce a spin liquid to freeze into a glassy state. 01 April 2014 | doi: 10.1038/ncomms4497 Physical Sciences  Condensed matter  Theoretical physics  Acidosis overrides oxygen deprivation to maintain mitochondrial function and cell survival OPEN Mireille Khacho, Michelle Tarabay, David Patten, Pamela Khacho, Jason G. MacLaurin, Jennifer Guadagno, Richard Bergeron, Sean P. Cregan, Mary-Ellen Harper, David S. Park and Ruth S. Slack In hypoxic conditions, cells depend on anaerobic respiration, which results in extracellular acidosis. Khacho et al. find that acidosis serves a protective function, enhancing mitochondrial respiratory capacity and sustaining ATP synthesis despite limited oxygen availability, by both promoting mitochondrial fusion and inhibiting fission. 01 April 2014 | doi: 10.1038/ncomms4550 Biological Sciences  Cell biology  Corals record long-term Leeuwin current variability including Ningaloo Niño/Niña since 1795 OPEN J. Zinke, A. Rountrey, M. Feng, S.-P. Xie, D. Dissard, K. Rankenburg, J.M. Lough and M.T. McCulloch El Niño Southern Oscillation has a strong impact on current strength and ocean temperatures off the western Australian coast, but long-term variability is poorly understood. Zinke et al. show a strong link between La Niña and El Niño events and decadal Leeuwin current variability in coral records since 1795. 01 April 2014 | doi: 10.1038/ncomms4607 Earth Sciences  Climate science  Oceanography  Metallodendrimers in three oxidation states with electronically interacting metals and stabilization of size-selected gold nanoparticles Yanlan Wang, Lionel Salmon, Jaime Ruiz and Didier Astruc Metallodendrimers containing redox-robust centres are functional molecules with many potential applications. Here, the authors fabricate iron containing metallodendrimers in a range of oxidation states and investigate their interactions with, and stabilization of, gold nanoparticles. 01 April 2014 | doi: 10.1038/ncomms4489 Chemical Sciences  Inorganic chemistry  Materials science  Organic chemistry  Whisker barrel cortex delta oscillations and gamma power in the awake mouse are linked to respiration OPEN J. Ito, S. Roy, Y. Liu, Y. Cao, M. Fletcher, L. Lu, J.D. Boughter, S. Grün and D.H. Heck Oscillatory neuronal activity in the mammalian neocortex is implicated in cognitive processes but its generation is poorly understood. In this study, the authors show that delta band oscillatory activity in mice phase-locks with respiratory activity and that this is mediated by activity in the olfactory bulb. 01 April 2014 | doi: 10.1038/ncomms4572 Biological Sciences  Neuroscience  Evading the strength–ductility trade-off dilemma in steel through gradient hierarchical nanotwins OPEN Yujie Wei, Yongqiang Li, Lianchun Zhu, Yao Liu, Xianqi Lei, Gang Wang, Yanxin Wu, Zhenli Mi, Jiabin Liu, Hongtao Wang and Huajian Gao It is a long-standing goal in metallurgy to enhance the strength of materials without sacrificing ductility. Here, the authors demonstrate that applying pre-torsion to a twinning-induced plasticity steel generates a hierarchical nanotwin structure, improving strength whilst retaining ductility. 01 April 2014 | doi: 10.1038/ncomms4580 Physical Sciences  Materials science  Timing of inorganic phosphate release modulates the catalytic activity of ATP-driven rotary motor protein OPEN Rikiya Watanabe and Hiroyuki Noji The F1-ATPase is a motor protein which exhibits rotary motion as a result of catalytic hydrolysis of ATP. Here, the authors investigate how the sequence of this reaction influences molecular rotation, showing that premature product release can result in protein inactivation. 01 April 2014 | doi: 10.1038/ncomms4486 Biological Sciences  Biophysics  Estimating the effective density of engineered nanomaterials for in vitro dosimetry Glen DeLoid, Joel M. Cohen, Tom Darrah, Raymond Derk, Liying Rojanasakul, Georgios Pyrgiotakis, Wendel Wohlleben and Philip Demokritou The assessment of nanomaterial toxicity can be hampered by difficulties in determining cell dosage. Here, the authors present a simple method for determination of nanomaterial agglomerate density in liquid media, enabling accurate calculation of dose delivered to cells in an in vitro system. 28 March 2014 | doi: 10.1038/ncomms4514 Biological Sciences  Cell biology  Nanotechnology  Fossil pollen records indicate that Patagonian desertification was not solely a consequence of Andean uplift L. Palazzesi, V.D. Barreda, J.I. Cuitiño, M.V. Guler, M.C. Tellería and R. Ventura Santos It is postulated that the Patagonian steppe evolved purely as a consequence of Andean uplift 15 million years ago, yet direct evidence is lacking. Palazzesi et al. present a bioclimatic analysis of pollen assemblages and show that Patagonian desertification began much more recently than previously thought. 28 March 2014 | doi: 10.1038/ncomms4558 Earth Sciences  Climate science  Molecular insights into the membrane-associated phosphatidylinositol 4-kinase IIα OPEN Qiangjun Zhou, Jiangmei Li, Hang Yu, Yujia Zhai, Zhen Gao, Yanxin Liu, Xiaoyun Pang, Lunfeng Zhang, Klaus Schulten, Fei Sun and Chang Chen Type II PI4-kinase dysfunction is associated with diseases including cancer and Alzheimer's disease; however, the development of specific modulators has been hampered by a lack of structural information. Zhou et al. present the crystal structure of PI4KIIα in its ADP-bound form, providing insight into its regulation. 28 March 2014 | doi: 10.1038/ncomms4552 Biological Sciences  Biochemistry  Epigenetic plasticity of Cd8a locus during CD8+ T-cell development and effector differentiation and reprogramming OPEN Kim L. Harland, E. Bridie Day, Simon H. Apte, Brendan E. Russ, Peter C. Doherty, Stephen J. Turner and Anne Kelso CD8 expression levels on peripheral CD8+ T cells are regulated during development and effector differentiation. Here, the authors show that methylation patterns at the Cd8a locus, whose product is essential for surface CD8 expression, can change during T-cell development, activation, cytokine polarization and reprogramming. 28 March 2014 | doi: 10.1038/ncomms4547 Biological Sciences  Cell biology  Immunology  Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana Sabrina Kleessen, Roosa Laitinen, Corina M. Fusari, Carla Antonio, Ronan Sulpice, Alisdair R. Fernie, Mark Stitt and Zoran Nikoloski Resources are finite for living organisms; therefore, compromises are required when partitioning resources to different tasks. Here, the authors use the Pareto concept to show how a trade-off is achieved in terms of the performance and metabolic efficiency in a panel of 97 Arabidopsis thaliana accessions. 28 March 2014 | doi: 10.1038/ncomms4537 Biological Sciences  Ecology  Plant sciences  Ediacaran matground ecology persisted into the earliest Cambrian Luis A. Buatois, Guy M. Narbonne, M. Gabriela Mángano, Noelia B. Carmona and Paul Myrow A transition from microbial-dominated Ediacara biota into modern ecosystems marks the beginning of the Cambrian. Here, Buatois et al. describe Ediacaran microbial mats in an early Cambrian formation in Canada suggesting that Ediacara biota persisted in the early Cambrian and abruptly disappeared later on. 28 March 2014 | doi: 10.1038/ncomms4544 Biological Sciences  Ecology  Evolution  Palaeontology  Multimodal label-free detection and discrimination for small molecules using a nanoporous resonator Jinsung Park, Doyeon Bang, Kuewhan Jang, Eunkyoung Kim, Seungjoo Haam and Sungsoo Na When molecules bind to a cantilever, their resonant frequency shifts, providing a sensitive molecular detection scheme. Park et al. coat the surfaces of such resonators with nanoporous gold, enabling them to discriminate between molecules via surface-enhanced Raman spectroscopy. 28 March 2014 | doi: 10.1038/ncomms4456 Chemical Sciences  Analytical chemistry  Applied physics  Nanotechnology  Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids Lynnette Fernandez-Cuesta, Martin Peifer, Xin Lu, Ruping Sun, Luka Ozretic, Danila Seidel, Thomas Zander, Frauke Leenders, Julie George, Christian Müller, Ilona Dahmen, Berit Pinther, Graziella Bosco, Kathryn Konrad, Janine Altmüller, Peter Nürnberg, Viktor Achter, Ulrich Lang, Peter M. Schneider, Magdalena Bogus et al. Pulmonary carcinoids account for about 2% of pulmonary neoplasms. Here, the authors carry out gene copy number analysis, genome/exome, and transcriptome sequencing of pulmonary carcinoids and identify frequent mutations in chromatin-remodelling genes that can drive tumorigenesis in these tumours. 27 March 2014 | doi: 10.1038/ncomms4518 Biological Sciences  Cancer  Genetics  Tunable plasmons in atomically thin gold nanodisks A. Manjavacas and F.J. García de Abajo Rapid optical modulation is vital to many optoelectronic applications, like communications or imaging technologies. Here, the authors study the optical modulation of atomically thin gold nanodisks and find they have similar absorption cross-sections to spherical particles of the same width. 27 March 2014 | doi: 10.1038/ncomms4548 Physical Sciences  Optical physics  Theoretical physics  Elastic anisotropy of experimental analogues of perovskite and post-perovskite help to interpret D'' diversity OPEN Akira Yoneda, Hiroshi Fukui, Fang Xu, Akihiko Nakatsuka, Akira Yoshiasa, Yusuke Seto, Kenya Ono, Satoshi Tsutsui, Hiroshi Uchiyama and Alfred Q. R. Baron Seismological observations of the D'' layer near the core–mantle boundary are difficult to interpret and the minerals present are unstable at ambient conditions. Yoneda et al. present experiments using analogues, suggesting the observations are due to preferred crystal orientations. 27 March 2014 | doi: 10.1038/ncomms4453 Earth Sciences  Geology and geophysics  SLC7A14 linked to autosomal recessive retinitis pigmentosa OPEN Zi-Bing Jin, Xiu-Feng Huang, Ji-Neng Lv, Lue Xiang, Dong-Qing Li, Jiangfei Chen, Changjiang Huang, Jinyu Wu, Fan Lu and Jia Qu Retinitis pigmentosa is the leading cause of inherited blindness worldwide. Here, the authors use exome sequencing to identify mutations in SLC7A14 that may be linked to the disease, and provide functional support for the role of this gene in retinal development and visual function in mice and zebrafish. 27 March 2014 | doi: 10.1038/ncomms4517 Biological Sciences  Genetics  Molecular biology  Hepatic IRE1α regulates fasting-induced metabolic adaptive programs through the XBP1s–PPARα axis signalling Mengle Shao, Bo Shan, Yang Liu, Yiping Deng, Cheng Yan, Ying Wu, Ting Mao, Yifu Qiu, Yubo Zhou, Shan Jiang, Weiping Jia, Jingya Li, Jia Li, Liangyou Rui, Liu Yang and Yong Liu The IRE1α-XBP1 signalling pathway is part of the ER stress response but has also been linked to glucose and lipid metabolism. Here the authors show that IRE1α in the liver acts as a nutrient-sensor, regulating the metabolic adaptation to fasting and a ketogenic diet by inducing PPARα expression. 27 March 2014 | doi: 10.1038/ncomms4528 Biological Sciences  Medical research  Surface reconstruction and chemical evolution of stoichiometric layered cathode materials for lithium-ion batteries Feng Lin, Isaac M. Markus, Dennis Nordlund, Tsu-Chien Weng, Mark D. Asta, Huolin L. Xin and Marca M. Doeff Surfaces of electrodes evolve with charging and discharging cycles, leading to deterioration of battery performance. Here Lin et al. report structural reconstruction and chemical evolution at the surface of a stoichiometric layered cathode material with spectroscopy and microscopy techniques. 27 March 2014 | doi: 10.1038/ncomms4529 Chemical Sciences  Applied physics  Materials science  Physical chemistry  Spontaneous tumour regression in keratoacanthomas is driven by Wnt/retinoic acid signalling cross-talk Giovanni Zito, Ichiko Saotome, Zongzhi Liu, Enrico G. Ferro, Thomas Y. Sun, Don X. Nguyen, Kaya Bilguvar, Christine J. Ko and Valentina Greco Keratoacanthomas are skin tumours that spontaneously regress but the mechanisms leading to regression are unknown. Here, using a mouse chemical carcinogenesis model, the authors show that tumour regression is driven by activation of retinoic acid signalling that induces Wnt inhibition and tumour differentiation. 26 March 2014 | doi: 10.1038/ncomms4543 Biological Sciences  Cancer  Cell biology  Symmetry-protected topological phases from decorated domain walls Xie Chen, Yuan-Ming Lu and Ashvin Vishwanath The class of quantum phases with symmetry-protected topological properties can be generalized in the concept of symmetry-protected topological phases. Here, Chen and colleagues present an intuitive way of constructing a large class of those phases in different dimensions. 26 March 2014 | doi: 10.1038/ncomms4507 Physical Sciences  Condensed matter  A solution to the collective action problem in between-group conflict with within-group inequality OPEN Sergey Gavrilets and Laura Fortunato In many group-living organisms high-rank individuals act as bullies usurping a greater share of resources. Here, Gavrilets and Fortunato show that in between-group conflicts such individuals will expend more effort towards the group's success and pay higher costs than their groupmates. 26 March 2014 | doi: 10.1038/ncomms4526 Biological Sciences  Evolution  An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production OPEN Thomas L. Ruegg, Eun-Mi Kim, Blake A. Simmons, Jay D. Keasling, Steven W. Singer, Taek Soon Lee and Michael P. Thelen Ionic liquids (ILs) are important solvents in the microbial production of biofuels, but can inhibit microbial growth. Here, the authors transfer newly discovered IL-resistance genes from rain forest soil bacteria to E. coli and report growth and biofuel production at IL levels that are otherwise toxic to native strains. 26 March 2014 | doi: 10.1038/ncomms4490 Biological Sciences  Bioengineering  Biotechnology  Controllable fatigue cracking mechanisms of copper bicrystals with a coherent twin boundary L.L. Li, Z.J. Zhang, P Zhang, Z.G. Wang and Z.F. Zhang Understanding the relationship between coherent twin boundaries and fatigue cracking is challenging. Here, the authors engineer the orientation of a twin boundary in a copper bicrystal, finding that fatigue crack nucleation varies with boundary orientation relative to the load axis. 26 March 2014 | doi: 10.1038/ncomms4536 Physical Sciences  Materials science  Lymph node-independent liver metastasis in a model of metastatic colorectal cancer Ida B. Enquist, Zinaida Good, Adrian M. Jubb, Germaine Fuh, Xi Wang, Melissa R. Junttila, Erica L. Jackson and Kevin G. Leong It remains unclear whether colorectal cancer metastases in the liver arise from intermediate metastases in the lymph nodes or directly from the primary tumour. Enquist et al. demonstrate lymph node-independent metastasis using a mouse model in which tumours are transplanted directly onto the luminal surface of the colon. 26 March 2014 | doi: 10.1038/ncomms4530 Biological Sciences  Cancer    Nature Communiactions JOBS of the week Postdoctoral Scientist University of South Alabama Research Associate x 2 (Fixed Term) University of Cambridge Research Assistant University of Bristol Research Fellow London School of Hygiene & Tropical Medicine PhD Student Position in Malaria Research Heidelberg University Hospital Research Fellow x4 University of Aberdeen Postdoctoral Fellow Centre for Integrative Biology (CIBio) - University of Trento Postdoctoral Associate University of Florida Research Associate University of Glasgow Postdoctoral Researcher Cancer Research UK London Research Institute (LRI) More Science jobs from Nature Communiactions EVENT Tumor Models Boston 22.07.14 Boston, USA More science events from     Advertisement The Structural Genomics Consortium (SGC), Natureconferences, and the Sao Paulo Research Foundation are pleased to present: Chemical Probe-based Open Science: Uncovering New Human and Plant Biology April 28-29, 2014 Faculdade de Ciencias Medicas, State University of Campinas (UNICAMP), Brazil Click here for more information or to register for this conference today!     Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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