Nature Communications - 06 July 2016

Weekly Content Alert Nature Communications is now fully open access. Read more. 06 July 2016  Featured image: Aghajanian et al. show that a holoreceptor composed of receptors ErbB2 and Nrp1 binds Sema3d and guides coronary vessel patterning. Latest content: Review Articles Erratum Journal homepage Recommend to library Web feed   Advertisement Celebrating 10,000 articles published On the 20th April 2016, Nature Communications celebrated publishing its 10,000 article. To celebrate this milestone our editors have selected a sample of articles from each subject area published in the last five years. Access the highlights here and sign up for free article e-alerts to stay up-to-date on all the latest content as it is published.   Advertisement npj Regenerative Medicine is an online only, open access, peer-reviewed journal dedicated to publishing high-quality research on ways to help the human body repair, replace and regenerate damaged tissues and organs. The first articles have now been published.  Read the inaugural content       Nature Communications - now fully open access All new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For more information visit the website. Visit our open access funding page or contact openaccess@nature.com to learn more about APC funding.       Latest Review View all Reviews     How to make a sex chromosome OPEN Alison E. Wright, Rebecca Dean, Fabian Zimmer and Judith E. Mank Sex chromosome evolution begins when recombination between a homologous pair of chromosomes is halted. Here, Wright et al. review our current understanding of the causes and mechanisms of recombination suppression between incipient sex chromosomes and suggest future directions for the field. 04 July 2016 | doi: 10.1038/ncomms12087 Biological Sciences  Evolution  Genetics        Latest Articles View all Articles     End-Cretaceous extinction in Antarctica linked to both Deccan volcanism and meteorite impact via climate change OPEN Sierra V. Petersen, Andrea Dutton and Kyger C. Lohmann The cause of the end-Cretaceous mass extinction is still debated due to difficulties separating the influences of two closely-timed potential causal events (massive volcanism and meteorite impact). Here, the authors link the extinction to both kill mechanisms through a new paleotemperature record. 05 July 2016 | doi: 10.1038/ncomms12079 Earth Sciences  Climate science  Palaeontology  Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses OPEN Katannya Kapeli, Gabriel A. Pratt, Anthony Q. Vu, Kasey R. Hutt, Fernando J. Martinez, Balaji Sundararaman, Ranjan Batra, Peter Freese, Nicole J. Lambert, Stephanie C. Huelga, Seung J. Chun, Tiffany Y. Liang, Jeremy Chang, John P. Donohue, Lily Shiue, Jiayu Zhang, Haining Zhu, Franca Cambi, Edward Kasarskis, Shawn Hoon et al. Abnormal functions of RNA-binding proteins TAF15, FUS and TDP43 are associated with amyotrophic lateral sclerosis. Here, Kapeli et al. characterize the RNA targets of TAF15 and identify points of convergence and divergence between the targets of TAF15, FUS and TDP43 in several neuronal systems. 05 July 2016 | doi: 10.1038/ncomms12143 Biological Sciences  Neuroscience  Engineering biosynthesis of the anticancer alkaloid noscapine in yeast OPEN Yanran Li and Christina D. Smolke Noscapine is a potential anticancer drug that is traditionally isolated from the opium poppy Papaver somniferum. Here, Li and Smolke reconstitute the noscapine gene cluster in Saccharomyces cerevisiae, to achieve the microbial production of noscapine and related pathway intermediates, and provide new insights into the biosynthesis of noscapine. 05 July 2016 | doi: 10.1038/ncomms12137 Biological Sciences  Biotechnology  Molecular biology  Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila OPEN Vasiliy O. Sysoev, Bernd Fischer, Christian K. Frese, Ishaan Gupta, Jeroen Krijgsveld, Matthias W. Hentze, Alfredo Castello and Anne Ephrussi Early development is controlled by maternally deposited mRNAs and the RNA-binding proteins (RBPs) that regulate them. Here the authors describe the identification of a large number of RBPs bound to polyadenylated RNAs in Drosophila embryos before and after the maternal-to-zygotic transition, revealing changes in RBPs activity during development. 05 July 2016 | doi: 10.1038/ncomms12128 Biological Sciences  Biochemistry  Developmental biology  Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment OPEN Louie Wurch, Richard J. Giannone, Bernard S. Belisle, Carolyn Swift, Sagar Utturkar, Robert L. Hettich, Anna-Louise Reysenbach and Mircea Podar Many microbial lineages have not yet been cultured, which hampers our understanding of their physiology. Here, Wurch et al. use single-cell genomics to infer cultivation conditions for the isolation of a tiny ectosymbiotic nanoarchaeon and its crenarchaeota host from a geothermal spring. 05 July 2016 | doi: 10.1038/ncomms12115 Biological Sciences  Ecology  Microbiology  Systems biology  Bacterial partition complexes segregate within the volume of the nucleoid OPEN Antoine Le Gall, Diego I. Cattoni, Baptiste Guilhas, Céline Mathieu-Demazière, Laura Oudjedi, Jean-Bernard Fiche, Jérôme Rech, Sara Abrahamsson, Heath Murray, Jean-Yves Bouet and Marcelo Nollmann In most bacteria and archaea, a broadly conserved mitotic-like apparatus assures the inheritance of duplicated genetic material before cell division. Here, the authors use super-resolution microscopies to dissect the activities required for proper DNA segregation through the nucleoid interior. 05 July 2016 | doi: 10.1038/ncomms12107 Biological Sciences  Cell biology  Microbiology  Molecular biology  A neomorphic cancer cell-specific role of MAGE-A4 in trans-lesion synthesis OPEN Yanzhe Gao, Elizabeth Mutter-Rottmayer, Alicia M. Greenwalt, Dennis Goldfarb, Feng Yan, Yang Yang, Raquel C. Martinez-Chacin, Kenneth H. Pearce, Satoshi Tateishi, Michael B. Major and Cyrus Vaziri RAD18 is an important protein in trans-lesion synthesis, an error-prone damage-tolerant mode of DNA replication. Here the authors show that MAGE-A4 stabilizes RAD18 and allows cancer cells to maintain on-going DNA synthesis in the face of genotoxic injury. 05 July 2016 | doi: 10.1038/ncomms12105 Biological Sciences  Cancer  Molecular biology  Temperature mediates continental-scale diversity of microbes in forest soils OPEN Jizhong Zhou, Ye Deng, Lina Shen, Chongqing Wen, Qingyun Yan, Daliang Ning, Yujia Qin, Kai Xue, Liyou Wu, Zhili He, James W. Voordeckers, Joy D. Van Nostrand, Vanessa Buzzard, Sean T. Michaletz, Brian J. Enquist, Michael D. Weiser, Michael Kaspari, Robert Waide, Yunfeng Yang and James H. Brown Climate warming has a wide range of effects on biodiversity. Here, Zhou et al. show that although variation in environmental temperature is a primary driver of soil microbial biodiversity, microbes show much lower rates of turnover across temperature gradients than other major taxa. 05 July 2016 | doi: 10.1038/ncomms12083 Biological Sciences  Ecology  Patients with genetically heterogeneous synchronous colorectal cancer carry rare damaging germline mutations in immune-related genes OPEN Matteo Cereda, Gennaro Gambardella, Lorena Benedetti, Fabio Iannelli, Dominic Patel, Gianluca Basso, Rosalinda F. Guerra, Thanos P. Mourikis, Ignazio Puccio, Shruti Sinha, Luigi Laghi, Jo Spencer, Manuel Rodriguez-Justo and Francesca D. Ciccarelli Some individuals present with multiple synchronous colorectal tumours, but the genetic understanding of this is unclear. Here, the authors use a sequencing strategy to show that the synchronous tumours are genetically independent and the patients harbour rare germline damaging mutations in genes associated with the immune system. 05 July 2016 | doi: 10.1038/ncomms12072 Biological Sciences  Cancer  Genetics  Selective catalytic two-step process for ethylene glycol from carbon monoxide OPEN Kaiwu Dong, Saravanakumar Elangovan, Rui Sang, Anke Spannenberg, Ralf Jackstell, Kathrin Junge, Yuehui Li and Matthias Beller Conversion of one-carbon feedstocks to more complex structures is vital for the production of bulk chemicals. Here, the authors report a highly selective method for the conversion of carbon monoxide to ethylene glycol by means of an oxamide intermediate. 05 July 2016 | doi: 10.1038/ncomms12075 Chemical Sciences  Catalysis  Inorganic chemistry  Organic chemistry  Mechanistic insights into chemical and photochemical transformations of bismuth vanadate photoanodes OPEN Francesca M. Toma, Jason K. Cooper, Viktoria Kunzelmann, Matthew T. McDowell, Jie Yu, David M. Larson, Nicholas J. Borys, Christine Abelyan, Jeffrey W. Beeman, Kin Man Yu, Jinhui Yang, Le Chen, Matthew R. Shaner, Joshua Spurgeon, Frances A. Houle, Kristin A. Persson and Ian D. Sharp Metal oxide semiconductors are promising materials for solar energy capture but can suffer from stability problems. Here, the authors present a methodology for evaluating corrosion mechanisms and apply it to BiVO4, revealing chemical instabilities that are not predicted from thermodynamic considerations alone. 05 July 2016 | doi: 10.1038/ncomms12012 Chemical Sciences  Catalysis  Materials science  Physical chemistry  Single-pixel three-dimensional imaging with time-based depth resolution OPEN Ming-Jie Sun, Matthew P. Edgar, Graham M. Gibson, Baoqing Sun, Neal Radwell, Robert Lamb and Miles J. Padgett A three-dimensional imaging system which distributes the optical illumination over the full field-of-view is sought after. Here, the authors demonstrate the capability of reconstructing 128 × 128 pixel resolution three-dimensional scenes to an accuracy of 3 mm as well as real-time video with a frame-rate up to 12 Hz. 05 July 2016 | doi: 10.1038/ncomms12010 Physical Sciences  Applied physics  Optical physics  A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity OPEN Carsten Boesler, Norbert Rigo, Maria M. Anokhina, Marcel J. Tauchert, Dmitry E. Agafonov, Berthold Kastner, Henning Urlaub, Ralf Ficner, Cindy L. Will and Reinhard Lührmann The assembly of the splicesome involves several distinct stages that require the sequential action of DExD/H-box RNA helicases. Here, the authors uncover a new intermediate, the pre-B complex, that accumulates in the presence of an inactive form of the DEAD-box protein Prp28. 05 July 2016 | doi: 10.1038/ncomms11997 Biological Sciences  Biochemistry  Molecular biology  COPS5 amplification and overexpression confers tamoxifen-resistance in ERα-positive breast cancer by degradation of NCoR OPEN Renquan Lu, Xiaobo Hu, Junmei Zhou, Jiajun Sun, Alan Z. Zhu, Xiaofeng Xu, Hui Zheng, Xiang Gao, Xian Wang, Hongchuan Jin, Ping Zhu and Lin Guo The corepressor NCoR is required for tamoxifen-mediated ERα-dependent transcriptional repression. Here, the authors show that COPS5 confers tamoxifen-resistance through the degradation of NCOR, the recruitment of the co-activator PCAF to ERα binding sites and the subsequent ERα transcriptional activity. 04 July 2016 | doi: 10.1038/ncomms12044 Biological Sciences  Cancer  Cell biology  The neuritic plaque facilitates pathological conversion of tau in an Alzheimer’s disease mouse model OPEN Tong Li, Kerstin E. Braunstein, Juhong Zhang, Ashley Lau, Leslie Sibener, Christopher Deeble and Philip C. Wong Alzheimer’s disease (AD) is pathologically characterized by the accumulation of neuritic plaques and neurofibrillary tangles but it is not known whether the neuritic plaque is necessary to drive the conversion of wild-type tau. Here the authors developed a mouse model in which wild-type tau is converted into pathological tau in a neuritic plaque-dependent manner. 04 July 2016 | doi: 10.1038/ncomms12082 Biological Sciences  Medical research  Neuroscience  Light-melt adhesive based on dynamic carbon frameworks in a columnar liquid-crystal phase OPEN Shohei Saito, Shunpei Nobusue, Eri Tsuzaka, Chunxue Yuan, Chigusa Mori, Mitsuo Hara, Takahiro Seki, Cristopher Camacho, Stephan Irle and Shigehiro Yamaguchi Liquid crystals are used in many applications, such as removable adhesives, but this requires both good bonding strength, and its rapid disappearance under an external stimulus. Here, Saito and others report a dynamic liquid crystal material that loses is bonding strength under photo irradiation. 04 July 2016 | doi: 10.1038/ncomms12094 Chemical Sciences  Materials science  Physical chemistry  The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis OPEN Uri Ben-David, Gavin Ha, Prasidda Khadka, Xin Jin, Bang Wong, Lude Franke and Todd R. Golub Genetically engineered mouse models of cancer are useful in identifying oncogenes and tumour suppressors. Here, the authors use gene expression profiles to generate a catalogue of copy number aberrations in 45 mouse models, and compare mouse and human tumours to identify additional drivers of tumorigenesis. 04 July 2016 | doi: 10.1038/ncomms12160 Biological Sciences  Cancer  Genetics  High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level OPEN Hui Gong, Dongli Xu, Jing Yuan, Xiangning Li, Congdi Guo, Jie Peng, Yuxin Li, Lindsay A. Schwarz, Anan Li, Bihe Hu, Benyi Xiong, Qingtao Sun, Yalun Zhang, Jiepeng Liu, Qiuyuan Zhong, Tonghui Xu, Shaoqun Zeng and Qingming Luo High-throughput imaging methods for brain-wide connectome mapping with precise location reference have been lacking. Here authors report a method that allows simultaneous acquisition of fluorescently labelled neurons and cytoarchitectural landmarks in the same mouse brain at the single-cell resolution. 04 July 2016 | doi: 10.1038/ncomms12142 Biological Sciences  Cell biology  Neuroscience  Metal-induced rapid transformation of diamond into single and multilayer graphene on wafer scale OPEN Diana Berman, Sanket A. Deshmukh, Badri Narayanan, Subramanian K. R. S. Sankaranarayanan, Zhong Yan, Alexander A. Balandin, Alexander Zinovev, Daniel Rosenmann and Anirudha V. Sumant Direct growth of large-area graphene on dielectric substrates is a promising route to wafer scale integration. Here the authors use a rapid thermal annealing process to grow graphene layers on four-inch diameter polycrystalline diamond, eliminating the need for transfer. 04 July 2016 | doi: 10.1038/ncomms12099 Physical Sciences  Applied physics  Materials science  Nanotechnology  Hypoxia causes transgenerational impairments in reproduction of fish OPEN Simon Yuan Wang, Karen Lau, Keng-Po Lai, Jiang-Wen Zhang, Anna Chung-Kwan Tse, Jing-Woei Li, Yin Tong, Ting-Fung Chan, Chris Kong-Chu Wong, Jill Man-Ying Chiu, Doris Wai-Ting Au, Alice Sze-Tsai Wong, Richard Yuen-Chong Kong and Rudolf Shiu-Sun Wu Hypoxia has diverse effects on aquatic life. Wang et al. show that reproductive defects resulting from hypoxia are epigenetically heritable in Japanese rice fish, and that this intergenerational inheritance is accompanied by differential methylation and gene expression in sperm. 04 July 2016 | doi: 10.1038/ncomms12114 Biological Sciences  Ecology  Genetics  A chaotic self-oscillating sunlight-driven polymer actuator OPEN Kamlesh Kumar, Christopher Knie, David Bléger, Mark A. Peletier, Heiner Friedrich, Stefan Hecht, Dirk J. Broer, Michael G. Debije and Albertus P. H. J. Schenning It is highly desirable, yet challenging to build actuators in a dry environment that can undergo autonomous oscillation. Here, Kumar et al. achieve this goal in a soft actuator based on the use of a nematic liquid crystal film doped by ortho-fluoroazobenzene that is responsive to sunlight. 04 July 2016 | doi: 10.1038/ncomms11975 Chemical Sciences  Materials science  Structure and activation of pro-activin A OPEN Xuelu Wang, Gerhard Fischer and Marko Hyvönen Activins are members of the TGF-β family of growth factors that are processed from precursors into the mature proteins. Here, the authors use structural biology and biochemistry to examine the protein domain organisation and gain insights into the activation of pro-activin A. 04 July 2016 | doi: 10.1038/ncomms12052 Biological Sciences  Biochemistry  Biotic interchange between the Indian subcontinent and mainland Asia through time OPEN Sebastian Klaus, Robert J. Morley, Martin Plath, Ya-Ping Zhang and Jia-Tang Li The Paleogene continental collision between the Indian subcontinent and Asia initiated biotic interchange over a timescale of millions of years. Klaus et al. develop a phylogeographic method to estimate the dynamics of biotic interchange over these timescales, revealing periods of acceleration, stagnation and decline. 04 July 2016 | doi: 10.1038/ncomms12132 Biological Sciences  Ecology  Palaeontology  Neutrophils mediate Salmonella Typhimurium clearance through the GBP4 inflammasome-dependent production of prostaglandins OPEN Sylwia D. Tyrkalska, Sergio Candel, Diego Angosto, Victoria Gómez-Abellán, Fátima Martín-Sánchez, Diana García-Moreno, Rubén Zapata-Pérez, Álvaro Sánchez-Ferrer, María P. Sepulcre, Pablo Pelegrín and Victoriano Mulero The role of guanylate-binding proteins (GBPs) in innate immunity is increasingly recognized. Here the authors show that GBP4 activates inflammasome in zebrafish neutrophils, and that this process is critical for the clearance of Salmonella infection via prostaglandin D2. 01 July 2016 | doi: 10.1038/ncomms12077 Biological Sciences  Immunology  Gas–solid interfacial modification of oxygen activity in layered oxide cathodes for lithium-ion batteries OPEN Bao Qiu, Minghao Zhang, Lijun Wu, Jun Wang, Yonggao Xia, Danna Qian, Haodong Liu, Sunny Hy, Yan Chen, Ke An, Yimei Zhu, Zhaoping Liu and Ying Shirley Meng Oxygen activity can play a vital role in determining charge transport properties of materials. Here, the authors demonstrate a method to create oxygen vacancies on layered oxides via a gas-solid interface reaction, leading to materials with enhanced energy and power densities for Li-ion batteries. 01 July 2016 | doi: 10.1038/ncomms12108 Chemical Sciences  Materials science  Physical chemistry  Still and rotating myosin clusters determine cytokinetic ring constriction OPEN Viktoria Wollrab, Raghavan Thiagarajan, Anne Wald, Karsten Kruse and Daniel Riveline The cytokinetic ring consists of actin and myosin, but their organisation prior to and during constriction has not been observed. Here the authors observe that mammalian and yeast cells organise their rings differently, with mammalian cells forming a periodic pattern of myosin clusters and yeast rotating myosin clusters during constriction. 01 July 2016 | doi: 10.1038/ncomms11860 Biological Sciences  Cell biology  Genome-wide association study identifies multiple susceptibility loci for multiple myeloma OPEN Jonathan S. Mitchell, Ni Li, Niels Weinhold, Asta Försti, Mina Ali, Mark van Duin, Gudmar Thorleifsson, David C. Johnson, Bowang Chen, Britt-Marie Halvarsson, Daniel F. Gudbjartsson, Rowan Kuiper, Owen W. Stephens, Uta Bertsch, Peter Broderick, Chiara Campo, Hermann Einsele, Walter A. Gregory, Urban Gullberg, Marc Henrion et al. Previous genome-wide association studies have identified loci associated with the risk of multiple myeloma. Here, the authors present a meta-analysis of six genome wide association studies of the disease and identify eight new loci; functional studies identify genes as candidates for the basis of these associations. 01 July 2016 | doi: 10.1038/ncomms12050 Biological Sciences  Cancer  Genetics  Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity OPEN Duy P. Nguyen, Yuichiro Miyaoka, Luke A. Gilbert, Steven J. Mayerl, Brian H. Lee, Jonathan S. Weissman, Bruce R. Conklin and James A. Wells CRISPR-Cas9 has been widely used to manipulate genomes, however control over activity is necessary to explore transcriptional or epigenetic regulation. Here the authors use a split Cas9 fused to nuclear receptor ligand-binding domains to achieve tuneable Cas9 activity. 01 July 2016 | doi: 10.1038/ncomms12009 Biological Sciences  Biotechnology  Molecular biology  Highly selective plasma-activated copper catalysts for carbon dioxide reduction to ethylene OPEN Hemma Mistry, Ana Sofia Varela, Cecile S. Bonifacio, Ioannis Zegkinoglou, Ilya Sinev, Yong-Wook Choi, Kim Kisslinger, Eric A. Stach, Judith C. Yang, Peter Strasser and Beatriz Roldan Cuenya Carbon dioxide electroreduction is a promising route to hydrocarbon synthesis, but more efficient and selective catalysts are needed. Here the authors show that plasma-activated copper can catalyse the reduction of carbon dioxide to ethylene with high efficiency and reveal cationic copper as the active site. 30 June 2016 | doi: 10.1038/ncomms12123 Chemical Sciences  Catalysis  Materials science  Physical chemistry  Pironetin reacts covalently with cysteine-316 of α-tubulin to destabilize microtubule OPEN Jianhong Yang, Yuxi Wang, Taijing Wang, Jian Jiang, Catherine H. Botting, Huanting Liu, Qiang Chen, Jinliang Yang, James H. Naismith, Xiaofeng Zhu and Lijuan Chen Microtubule assembly and disassembly is the target of many anticancer therapies, with β-tubulin the most-frequent target. Here, the authors used biochemical and biophysical techniques to demonstrate pironetin binds to α-tubulin and thereby inhibits microtubule polymerization providing a basis for the rational design of novel anticancer drugs. 30 June 2016 | doi: 10.1038/ncomms12103 Biological Sciences  Biochemistry  Biophysics  Cancer  Impeding 99Tc(IV) mobility in novel waste forms OPEN Mal-Soon Lee, Wooyong Um, Guohui Wang, Albert A. Kruger, Wayne W. Lukens, Roger Rousseau and Vassiliki-Alexandra Glezakou Technetium-99 retention in spinel-containing glass is a promising strategy for radioactive waste management, but volatility is still an issue. Here, the authors show that doping magnetite with 1st row transition metals enhances technetium retention by altering the redox capacity of the Tc-containing spinel. 30 June 2016 | doi: 10.1038/ncomms12067 Chemical Sciences  Materials science  Physical chemistry  Deficient methylation and formylation of mt-tRNAMet wobble cytosine in a patient carrying mutations in NSUN3 OPEN Lindsey Van Haute, Sabine Dietmann, Laura Kremer, Shobbir Hussain, Sarah F. Pearce, Christopher A. Powell, Joanna Rorbach, Rebecca Lantaff, Sandra Blanco, Sascha Sauer, Urania Kotzaeridou, Georg F. Hoffmann, Yasin Memari, Anja Kolb-Kokocinski, Richard Durbin, Johannes A. Mayr, Michaela Frye, Holger Prokisch and Michal Minczuk The post-transcriptional 5-methylcytosine (m5C) modification occurs in a wide range of nuclear-encoded RNAs. Here the authors identify the mitochondrial tRNA-Met as a target for the m5C methyltransferase NSun3—found mutated in a mitochondrial disease patient—and link mitochondrial tRNA modifications with energy metabolism. 30 June 2016 | doi: 10.1038/ncomms12039 Biological Sciences  Biochemistry  Bioinformatics  Cell biology  LATS-YAP/TAZ controls lineage specification by regulating TGFβ signaling and Hnf4α expression during liver development OPEN Da-Hye Lee, Jae Oh Park, Tae-Shin Kim, Sang-Kyum Kim, Tack-hoon Kim, Min-chul Kim, Gun Soo Park, Jeong-Hwan Kim, Shinji Kuninaka, Eric N. Olson, Hideyuki Saya, Seon-Young Kim, Ho Lee and Dae-Sik Lim The Hippo pathway regulates the differentiation of stem and progenitor cells, but it is unclear how it acts in liver development. Here, the authors knockout Hippo pathway components Lats1 and 2 in the liver, causing suppression of hepatocyte differentiation but promoting biliary cell differentiation. 30 June 2016 | doi: 10.1038/ncomms11961 Biological Sciences  Cell biology  Developmental biology  Coronary vasculature patterning requires a novel endothelial ErbB2 holoreceptor OPEN Haig Aghajanian, Young Kuk Cho, Lauren J. Manderfield, Madison R. Herling, Mudit Gupta, Vivienne C. Ho, Li Li, Karl Degenhardt, Alla Aharonov, Eldad Tzahor and Jonathan A. Epstein Semaphorin ligands and cognate receptors are important in patterning the vasculature. Here, Aghajanian et al. report an unexpected role for ErbB2 in endothelial cells where it partners with Nrp1 to form a novel semaphoring holoreceptor required for embryonic vascular patterning. 30 June 2016 | doi: 10.1038/ncomms12038 Biological Sciences  Developmental biology  Long-read sequencing and de novo assembly of a Chinese genome OPEN Lingling Shi, Yunfei Guo, Chengliang Dong, John Huddleston, Hui Yang, Xiaolu Han, Aisi Fu, Quan Li, Na Li, Siyi Gong, Katherine E. Lintner, Qiong Ding, Zou Wang, Jiang Hu, Depeng Wang, Feng Wang, Lin Wang, Gholson J. Lyon, Yongtao Guan, Yufeng Shen et al. Short-read sequencing has inherent limitations in the characterisation of long repeat elements. Shi and Guo et al. combine single-molecule real-time sequencing and IrysChip to construct a Chinese reference genome that fills many gaps in the reference genome, and identify novel spliced genes. 30 June 2016 | doi: 10.1038/ncomms12065 Biological Sciences  Genetics  Prosaposin is a regulator of progranulin levels and oligomerization OPEN Alexandra M. Nicholson, NiCole A. Finch, Marcio Almeida, Ralph B. Perkerson, Marka van Blitterswijk, Aleksandra Wojtas, Basar Cenik, Sergio Rotondo, Venette Inskeep, Laura Almasy, Thomas Dyer, Juan Peralta, Goo Jun, Andrew R. Wood, Timothy M. Frayling, Christian Fuchsberger, Sharon Fowler, Tanya M. Teslovich, Alisa K. Manning, Satish Kumar et al. Increasing progranulin (PGRN) levels is a promising approach for treating frontotemporal dementia and other neurodegenerative diseases. Here Nicholson et al. show that the prosaposin (PSAP) locus is associated with plasma PGRN levels and demonstrate that PSAP can alter PGRN levels and its oligomerization. 30 June 2016 | doi: 10.1038/ncomms11992 Biological Sciences  Genetics  Neuroscience  Cortical idiosyncrasies predict the perception of object size OPEN Christina Moutsiana, Benjamin de Haas, Andriani Papageorgiou, Jelle A. van Dijk, Annika Balraj, John A. Greenwood and D. Samuel Schwarzkopf Perceiving the size of objects is subjective. Here the authors show that these subjective differences in size perception can be explained by the individual variance in spatial tuning of neuronal populations in the primary visual cortex. 30 June 2016 | doi: 10.1038/ncomms12110 Biological Sciences  Neuroscience  Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development OPEN Jinmiao Chen, Andreas Schlitzer, Svetoslav Chakarov, Florent Ginhoux and Michael Poidinger The tools for constructing cell lineages from single cell data are limited. Here, the authors present Mpath: an algorithm to derive multi-branching trajectories using neighbourhood-based cell state transitions, and use this to predict developmental trajectories in dendritic and muscle cells. 30 June 2016 | doi: 10.1038/ncomms11988 Biological Sciences  Bioinformatics  Cell biology  Developmental biology  Array of nanosheets render ultrafast and high-capacity Na-ion storage by tunable pseudocapacitance OPEN Dongliang Chao, Changrong Zhu, Peihua Yang, Xinhui Xia, Jilei Liu, Jin Wang, Xiaofeng Fan, Serguei V. Savilov, Jianyi Lin, Hong Jin Fan and Ze Xiang Shen Sodium ion batteries are a promising alternative to lithium ion technology, however their sluggish sodiation kinetics currently hinder performance. Here the authors fabricate ultrathin layered tin(II) sulfide nanostructures displaying a pseudocapacitance contribution for high capacity sodium ion anodes. 30 June 2016 | doi: 10.1038/ncomms12122 Chemical Sciences  Materials science  Nanotechnology  Physical chemistry  Acetate functions as an epigenetic metabolite to promote lipid synthesis under hypoxia OPEN Xue Gao, Shu-Hai Lin, Feng Ren, Jin-Tao Li, Jia-Jia Chen, Chuan-Bo Yao, Hong-Bin Yang, Shu-Xia Jiang, Guo-Quan Yan, Di Wang, Yi Wang, Ying Liu, Zongwei Cai, Ying-Ying Xu, Jing Chen, Wenqiang Yu, Peng-Yuan Yang and Qun-Ying Lei Cancer cells under stress use acetate to maintain the acetyl-CoA pool and fuel lipid biosynthesis. Here, the authors show that acetate also promotes de novo lipid synthesis by increasing histone acetylation at the promoters of lipogenic enzymes ACACA and FASN, thus inducing their expression. 30 June 2016 | doi: 10.1038/ncomms11960 Biological Sciences  Cancer  Cell biology  Molecular biology  Notch-independent RBPJ controls angiogenesis in the adult heart OPEN Ramón Díaz-Trelles, Maria Cecilia Scimia, Paul Bushway, Danh Tran, Anna Monosov, Edward Monosov, Kirk Peterson, Stacey Rentschler, Pedro Cabrales, Pilar Ruiz-Lozano and Mark Mercola Heart function after injury improves upon formation of new blood vessels. Here, the authors show that ablating a transcription factor RBPJ in the murine heart increases vascularization and maintains cardiac function after injury by increasing responsiveness to hypoxia, suggesting a new approach to treat heart injury. 30 June 2016 | doi: 10.1038/ncomms12088 Biological Sciences  Developmental biology  Medical research  Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues OPEN Stratis Tzoumas, Antonio Nunes, Ivan Olefir, Stefan Stangl, Panagiotis Symvoulidis, Sarah Glasl, Christine Bayer, Gabriele Multhoff and Vasilis Ntziachristos Spectral corruption impedes imaging of blood oxygen saturation. Here Tzoumas et al. describe light fluence in the spectral domain and introduce eigenspectra Multispectral Optoacoustic Tomography to account for wavelength-dependent light attenuation and estimate blood oxygen saturation within deep tissue. 30 June 2016 | doi: 10.1038/ncomms12121 Physical Sciences  Applied physics  Optical physics  The multicellularity genes of dictyostelid social amoebas OPEN Gernot Glöckner, Hajara M. Lawal, Marius Felder, Reema Singh, Gail Singer, Cornelis J. Weijer and Pauline Schaap Unicellular social amoebae aggregate to form a multicellular life stage, making them a model system for the evolution of multicellularity. Here, Glöckner et al. use a comparative genomic and transcriptomic approach to determine the origin of the genes essential for multicellularity in the social amoebae. 30 June 2016 | doi: 10.1038/ncomms12085 Biological Sciences  Evolution  Genetics  IL-13 from intraepithelial lymphocytes regulates tissue homeostasis and protects against carcinogenesis in the skin OPEN Tim Dalessandri, Greg Crawford, Mark Hayes, Rocio Castro Seoane and Jessica Strid Epidermal intraepithelial lymphocytes (IEL) produce IL-13, but the physiological role of this cytokine production is not clear. Here the authors show that IEL-production of IL-13 is a vital lymphoid stress surveillance mechanism driving crosstalk with epithelial cells to maintain tissue homeostasis and inhibit chemical carcinogenesis in mice. 30 June 2016 | doi: 10.1038/ncomms12080 Biological Sciences  Cancer  Immunology  Medical research  MCOLN1 is a ROS sensor in lysosomes that regulates autophagy OPEN Xiaoli Zhang, Xiping Cheng, Lu Yu, Junsheng Yang, Raul Calvo, Samarjit Patnaik, Xin Hu, Qiong Gao, Meimei Yang, Maria Lawas, Markus Delling, Juan Marugan, Marc Ferrer and Haoxing Xu Reactive oxygen species (ROS) damage cell components, necessitating their clearance through autophagy. Here, the authors show that ROS can induce autophagy by triggering TRPML1 to release Ca2+ from the lysosomal lumen, in turn activating the autophagy and lysosomal biogenesis regulator TFEB. 30 June 2016 | doi: 10.1038/ncomms12109 Biological Sciences  Cell biology  Molecular biology  MLP and CARP are linked to chronic PKCα signalling in dilated cardiomyopathy OPEN Stephan Lange, Katja Gehmlich, Alexander S. Lun, Jordan Blondelle, Charlotte Hooper, Nancy D. Dalton, Erika A. Alvarez, Xiaoyu Zhang, Marie-Louise Bang, Yama A. Abassi, Cristobal G. dos Remedios, Kirk L. Peterson, Ju Chen and Elisabeth Ehler Altered function of the muscle LIM protein (MLP) causes dilated cardiomyopathy in mice and humans. Lange et al. explain the molecular role of MLP in the heart by showing that it affects the signalling complex at the intercalated discs of failing hearts that consists of PKCα, PLCβ1 and CARP by inhibiting PKCα auto-phosphorylation and function. 29 June 2016 | doi: 10.1038/ncomms12120 Biological Sciences  Medical research  Finite particle size drives defect-mediated domain structures in strongly confined colloidal liquid crystals OPEN Ioana C. Gârlea, Pieter Mulder, José Alvarado, Oliver Dammone, Dirk G. A. L. Aarts, M. Pavlik Lettinga, Gijsje H. Koenderink and Bela M. Mulder Liquid crystals confined to micrometre-sized geometries can be well described by a continuum theory, where the size effect of constituent mesogens is negligible. Here, the authors show how the continuum theory breaks down in colloidal liquid crystal, leading to the formation of defect-mediated domains. 29 June 2016 | doi: 10.1038/ncomms12112 Physical Sciences  Condensed matter  Materials science  Rational design of ABC triblock terpolymer solution nanostructures with controlled patch morphology OPEN Tina I. Löbling, Oleg Borisov, Johannes S. Haataja, Olli Ikkala, André H. Gröschel and Axel H. E. Müller Self-assembly of diblock copolymers into useful nanostructures is well understood, unlike the solution self-assembly of triblock copolymers. Here, Müller and co-workers provide guidelines for the self-assembly of linear ABC triblock terpolymers into different multicompartment nanostructures. 29 June 2016 | doi: 10.1038/ncomms12097 Chemical Sciences  Materials science  Nanotechnology  Physical chemistry  Super stretchable hydrogel achieved by non-aggregated spherulites with diameters <5 nm OPEN Guoxing Sun, Zongjin Li, Rui Liang, Lu-Tao Weng and Lina Zhang Hydrogels containing nanoparticles have enhanced mechanical properties that can be limited if the size of the crosslinking nanoparticles is too large. Here, Zhang and others have produced non-aggregated spherulite nanoparticles with diameters of less than 5 nm and investigated their effect on hydrogels. 29 June 2016 | doi: 10.1038/ncomms12095 Chemical Sciences  Materials science  Nanotechnology  UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly OPEN Mirjam Hunziker, Jonas Barandun, Elisabeth Petfalski, Dongyan Tan, Clémentine Delan-Forino, Kelly R. Molloy, Kelly H. Kim, Hywel Dunn-Davies, Yi Shi, Malik Chaker-Margot, Brian T. Chait, Thomas Walz, David Tollervey and Sebastian Klinge Eukaryotic ribosome biogenesis involves a large number of maturations factors which are responsible for the stepwise assembly of the ribosomal subunits. Here the authors use an array of biochemical and structural biology methods to investigate the function of the UtpA and UtpB complexes as part of the small subunit processome. 29 June 2016 | doi: 10.1038/ncomms12090 Biological Sciences  Biochemistry  Biophysics  Superconcentrated electrolytes for a high-voltage lithium-ion battery OPEN Jianhui Wang, Yuki Yamada, Keitaro Sodeyama, Ching Hua Chiang, Yoshitaka Tateyama and Atsuo Yamada Electrode degradation due to metal-ion dissolution in conventional electrolyte hampers the performance of 5 V-class lithium ion batteries. Here, the authors employ a high concentration electrolyte to inhibit metal-ion dissolution and realize a stable high voltage LiNi0.5Mn1.5O4/graphite battery. 29 June 2016 | doi: 10.1038/ncomms12032 Chemical Sciences  Materials science  Physical chemistry  Magnetic assembly of transparent and conducting graphene-based functional composites OPEN Hortense Le Ferrand, Sreenath Bolisetty, Ahmet F. Demirörs, Rafael Libanori, André R. Studart and Raffaele Mezzenga Transparent and electrically conducting flexible films are in high demand but production can be both time-consuming and expensive. Here, the authors report a method for assembling modified graphene flakes in controlled distributions within polymeric matrices by use of magnetic fields. 29 June 2016 | doi: 10.1038/ncomms12078 Chemical Sciences  Applied physics  Materials science  Nanotechnology  SARI inhibits angiogenesis and tumour growth of human colon cancer through directly targeting ceruloplasmin OPEN Lei Dai, Xueliang Cui, Xin Zhang, Lin Cheng, Yi Liu, Yang Yang, Ping Fan, Qingnan Wang, Yi Lin, Junfeng Zhang, Chunlei Li, Ying Mao, Qin Wang, Xiaolan Su, Shuang Zhang, Yong Peng, Hanshuo Yang, Xun Hu, Jinliang Yang, Meijuan Huang et al. Ceruloplasmin has an important role in the stabilization and nuclear transport of HIF-1α, thus regulating VEGF expression. Here the authors show that the transcription factor SARI reduces colorectal cancer growth and angiogenesis in vivo by inducing the degradation of ceruloplasmin, thereby inhibiting the HIFα/VEGF axis. 29 June 2016 | doi: 10.1038/ncomms11996 Biological Sciences  Cancer  Cell biology  Marine reserves lag behind wilderness in the conservation of key functional roles OPEN Stéphanie D’agata, David Mouillot, Laurent Wantiez, Alan M. Friedlander, Michel Kulbicki and Laurent Vigliola The establishment of marine reserves in areas previously exploited by humans is recognised as an effective conservation tool. Through modelling effects of isolation from human influence, D'agata et al. show that marine reserves fall short of supporting key ecological values compared with wilderness areas. 29 June 2016 | doi: 10.1038/ncomms12000 Biological Sciences  Ecology  Surface engineering of hierarchical platinum-cobalt nanowires for efficient electrocatalysis OPEN Lingzheng Bu, Shaojun Guo, Xu Zhang, Xuan Shen, Dong Su, Gang Lu, Xing Zhu, Jianlin Yao, Jun Guo and Xiaoqing Huang Platinum-based nanowires are promising for fuel cell applications due to their high catalytic activity. Here the authors report on hierarchical platinum-cobalt nanowires with high-index facets showing specific/mass activities for oxygen reduction reaction 39.6/33.7 times higher than commercial Pt/C catalyst. 29 June 2016 | doi: 10.1038/ncomms11850 Chemical Sciences  Materials science  Physical chemistry  Droplet barcoding for massively parallel single-molecule deep sequencing OPEN Freeman Lan, John R. Haliburton, Aaron Yuan and Adam R. Abate The ability to accurately sequence long DNA molecules is important across biology. Here, Lan et al. report a droplet-based method that barcodes single DNA molecules, allowing the full-length molecules to be sequenced with multi-fold coverage using short-read next-generation sequencing. 29 June 2016 | doi: 10.1038/ncomms11784 Biological Sciences  Biotechnology  Molecular biology  The genetic regulatory signature of type 2 diabetes in human skeletal muscle OPEN Laura J. Scott, Michael R. Erdos, Jeroen R. Huyghe, Ryan P. Welch, Andrew T. Beck, Brooke N. Wolford, Peter S. Chines, John P. Didion, Narisu Narisu, Heather M. Stringham, D. Leland Taylor, Anne U. Jackson, Swarooparani Vadlamudi, Lori L. Bonnycastle, Leena Kinnunen, Jouko Saramies, Jouko Sundvall, Ricardo D'Oliveira Albanus, Anna Kiseleva, John Hensley et al. More than 90% of genetic variants associated with type 2 diabetes occur in non-coding regions. Scott et al. report genomes, epigenomes and transcriptomes of skeletal muscle from 271 participants with a range of glucose tolerances, revealing a genetic regulatory architecture enriched in muscle stretch/super enhancers. 29 June 2016 | doi: 10.1038/ncomms11764 Biological Sciences  Genetics  Medical research  The FNIP co-chaperones decelerate the Hsp90 chaperone cycle and enhance drug binding OPEN Mark R. Woodford, Diana M. Dunn, Adam R. Blanden, Dante Capriotti, David Loiselle, Chrisostomos Prodromou, Barry Panaretou, Philip F. Hughes, Aaron Smith, Wendi Ackerman, Timothy A. Haystead, Stewart N. Loh, Dimitra Bourboulia, Laura S. Schmidt, W. Marston Linehan, Gennady Bratslavsky and Mehdi Mollapour Hsp90 is required for the folding, stability and activity of several drivers of oncogenesis. Here the authors show that Folliculin-interacting proteins (FNIP) 1 and 2, whose expression correlates with the cellular response to Hsp90 inhibitors, are co-chaperones of Hsp90 that function by inhibiting its ATPase activity. 29 June 2016 | doi: 10.1038/ncomms12037 Biological Sciences  Biochemistry  Cancer    Nature Communications JOBS of the week Researcher (Full Time) Weill Cornell Medical School Postdoctoral Fellow Position Opening University of California Los Angeles Junior Group Leader Positions Institut Curie 3 PhD Positions University Medical Center Gottingen Postdoctoral scientist Hospital for Special Surgery Postdoctoral Researcher Maynooth University Research Associate University of Wisconsin - Madison Postdoctoral Positions University of Texas Research Scientist NHS The Royal Marsden NHS Foundation Trust Research Fellow The University of Warwick More Science jobs from Nature Communications EVENT Canceromatics III: Tumor Heterogeneity 13.11.16 Madrid, Spain More science events from       Latest Erratum     Erratum: Embryonic transcription is controlled by maternally defined chromatin state OPEN Saartje Hontelez, Ila van Kruijsbergen, Georgios Georgiou, Simon J. van Heeringen, Ozren Bogdanovic, Ryan Lister and Gert Jan C. Veenstra 05 July 2016 | doi: 10.1038/ncomms12208 Biological Sciences  Developmental biology  Molecular biology      Advertisement npj Science of Learning is a new open access, online-only journal that brings together the findings of neuroscientists, psychologists, and education researchers to understand how the brain learns. The first articles for npj Science of Learning have now been published. Visit the website now to explore all available content, and sign up to receive free article e-alerts.    Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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