Nature Communications - 16 April 2014

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Weekly Content Alert 16 April 2014  Featured image: Miyasaka et al. visualise specific neuronal subpopulations that connect the olfactory bulb with higher olfactory centers in the zebrafish brain. Latest content: Articles Corrigendum Journal homepage Recommend to library Web feed   Advertisement They're recruiting scientists just like you! The Naturejobs Career Expo is coming to Boston, Massachusetts on May 20, 2014. Take advantage of this free opportunity to meet employers, attend workshops and further develop your career. Don't wait-register today!        Latest Articles View all Articles     Experimental orthotopic transplantation of a tissue-engineered oesophagus in rats Sebastian Sjöqvist, Philipp Jungebluth, Mei Ling Lim, Johannes C. Haag, Ylva Gustafsson, Greg Lemon, Silvia Baiguera, Miguel Angel Burguillos, Costantino Del Gaudio, Antonio Beltrán Rodríguez, Alexander Sotnichenko, Karolina Kublickiene, Henrik Ullman, Heike Kielstein, Peter Damberg, Alessandra Bianco, Rainer Heuchel, Ying Zhao, Domenico Ribatti, Cristián Ibarra et al. Patients with oesophageal diseases may require surgical removal and replacement of the oesophagus. Here the authors seed mesenchymal stromal cells on a decellularized rat oesophagus and show that this bioengineered tissue construct restores swallowing function after transplantation into rats. 15 April 2014 | doi: 10.1038/ncomms4562 Biological Sciences  Medical research  Gut microbiome of the Hadza hunter-gatherers OPEN Stephanie L. Schnorr, Marco Candela, Simone Rampelli, Manuela Centanni, Clarissa Consolandi, Giulia Basaglia, Silvia Turroni, Elena Biagi, Clelia Peano, Marco Severgnini, Jessica Fiori, Roberto Gotti, Gianluca De Bellis, Donata Luiselli, Patrizia Brigidi, Audax Mabulla, Frank Marlowe, Amanda G. Henry and Alyssa N. Crittenden Gut microbes influence our health and may contribute to human adaptation to different lifestyles. Here, the authors describe the gut microbiome of a community of hunter-gatherers and identify unique features that could be linked to a foraging lifestyle. 15 April 2014 | doi: 10.1038/ncomms4654 Biological Sciences  Evolution  Microbiology  Contact of cis-Golgi with ER exit sites executes cargo capture and delivery from the ER OPEN Kazuo Kurokawa, Michiyo Okamoto and Akihiko Nakano Protein traffic from the endoplasmic reticulum (ER) to the Golgi is mediated by COPII-coated vesicles that bud from ER exit sites and fuse with the cis-Golgi. Kurokawa et al. show that in budding yeast, the cis-Golgi reaches out to ER exit sites in a 'hug-and-kiss' mechanism to facilitate cargo transfer. 14 April 2014 | doi: 10.1038/ncomms4653 Biological Sciences  Cell biology  Mechanisms of charge transfer and redistribution in LaAlO3/SrTiO3 revealed by high-energy optical conductivity T.C. Asmara, A. Annadi, I. Santoso, P.K. Gogoi, A. Kotlov, H.M. Omer, M. Motapothula, M.B.H. Breese, M. Rübhausen, T. Venkatesan, Ariando and A. Rusydi The origin of the two-dimensional electron gas at complex oxide interfaces is often explained by the polar catastrophe model, which involves a charge transfer mechanism. Using optical conductivity analysis, the authors assign and quantify the charge transfer, corroborating the polar catastrophe scenario. 14 April 2014 | doi: 10.1038/ncomms4663 Physical Sciences  Condensed matter  Nanotechnology  Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication OPEN Andrea Piunti, Alessandra Rossi, Aurora Cerutti, Mareike Albert, Sriganesh Jammula, Andrea Scelfo, Laura Cedrone, Giulia Fragola, Linda Olsson, Haruhiko Koseki, Giuseppe Testa, Stefano Casola, Kristian Helin, Fabrizio d'Adda di Fagagna and Diego Pasini Polycomb (PcG) proteins are known to promote cell proliferation by silencing expression of the tumour suppressor Ink4A-Arf. Piunti et al. show that PcG proteins also regulate tumour progression independently of this role, revealing a requirement for PRC1 and PRC2 in replication fork progression. 14 April 2014 | doi: 10.1038/ncomms4649 Biological Sciences  Cell biology  Molecular biology  Timescales for detecting a significant acceleration in sea level rise OPEN Ivan D. Haigh, Thomas Wahl, Eelco J. Rohling, René M. Price, Charitha B. Pattiaratchi, Francisco M. Calafat and Sönke Dangendorf Global sea levels are rising as a result of climate change, but at what rate, and whether this rate is increasing is open to debate. Haigh et al. show that the earliest detection of significant increase in the rate of sea level rise can only be achieved once interannual and multidecadal variability is removed. 14 April 2014 | doi: 10.1038/ncomms4635 Earth Sciences  Climate science  Oceanography  Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1 Takashi Baba, Hiroyuki Otake, Tetsuya Sato, Kanako Miyabayashi, Yurina Shishido, Chia-Yih Wang, Yuichi Shima, Hiroshi Kimura, Mikako Yagi, Yasuhiro Ishihara, Shinjiro Hino, Hidesato Ogawa, Mitsuyoshi Nakao, Takeshi Yamazaki, Dongchon Kang, Yasuyuki Ohkawa, Mikita Suyama, Bon-Chu Chung and Ken-Ichirou Morohashi The transcription factor NR5A1 has so far mainly been known for regulating the biosynthesis of steroids. Here the authors discover that NR5A1 also has a role in energy metabolism, demonstrating that NR5A1 regulates several key enzymes involved in the breakdown of glucose. 14 April 2014 | doi: 10.1038/ncomms4634 Biological Sciences  Cell biology  Medical research  Joint estimation of phase and phase diffusion for quantum metrology Mihai D. Vidrighin, Gaia Donati, Marco G. Genoni, Xian-Min Jin, W. Steven Kolthammer, M.S. Kim, Animesh Datta, Marco Barbieri and Ian A. Walmsley Phase estimation is an important element of quantum metrology, but the influence of noise cannot always be well characterized. Vidrighin et al. analyse and experimentally demonstrate methods providing simultaneous estimation of a phase shift and the amplitude of phase diffusion at the quantum limit. 14 April 2014 | doi: 10.1038/ncomms4532 Physical Sciences  Optical physics  Tyrosine-mediated two-dimensional peptide assembly and its role as a bio-inspired catalytic scaffold Hyung-Seok Jang, Jung-Ho Lee, Yong-Sun Park, Young-O Kim, Jimin Park, Tae-Youl Yang, Kyoungsuk Jin, Jaehun Lee, Sunghak Park, Jae Myoung You, Ki-Woong Jeong, Areum Shin, In-Seon Oh, Min-Kyung Kwon, Yong-Il Kim, Hoon-Hwe Cho, Heung Nam Han, Yangmee Kim, Yoon Ho Chang, Seung R. Paik et al. It is well known that the interplay between molecular ordering and interface geometry can determine the morphology of two-dimensional systems. Here, the authors report facet formation in water droplets, driven by peptide assembly, and investigate the structural and sequence motifs that affect this behaviour. 11 April 2014 | doi: 10.1038/ncomms4665 Chemical Sciences  Biochemistry  Biotechnology  Nanotechnology  Trapping of drops by wetting defects OPEN Dieter 't Mannetje, Somnath Ghosh, Rudy Lagraauw, Simon Otten, Arjen Pit, Christian Berendsen, Jos Zeegers, Dirk van den Ende and Frieder Mugele Precise control of moving droplets on surface defects is essential for microfluidic applications. Here the authors formalize a generic rule to describe droplet trapping using two dimensionless parameters and show how electrically tunable defects guide sliding drops in microfluidic channels. 11 April 2014 | doi: 10.1038/ncomms4559 Physical Sciences  Fluids and plasma physics  Nanotechnology  Vibrational nano-spectroscopic imaging correlating structure with intermolecular coupling and dynamics Benjamin Pollard, Eric A. Muller, Karsten Hinrichs and Markus B. Raschke Quantifying intermolecular coupling and local morphology is important to understand soft matter systems. Pollard et al. show how multispectral vibrational near-field optical microscopy can be used to image molecular-scale morphology and intermolecular interactions with nanometre spatial resolution. 11 April 2014 | doi: 10.1038/ncomms4587 Physical Sciences  Materials science  Optical physics  Physical chemistry  Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen OPEN Kifayathullah Liakath-Ali, Valerie E. Vancollie, Emma Heath, Damian P. Smedley, Jeanne Estabel, David Sunter, Tia DiTommaso, Jacqueline K. White, Ramiro Ramirez-Solis, Ian Smyth, Karen P. Steel and Fiona M. Watt Large-scale efforts are put into the generation of knockout mutant mice for many individual genes. Here, the authors systematically screen skin from 538 mutant mice and identify 50 mutants with epidermal phenotypes, of which 9 are also associated with human skin defects. 11 April 2014 | doi: 10.1038/ncomms4540 Biological Sciences  Developmental biology  Genetics  Protein accumulation in the endoplasmic reticulum as a non-equilibrium phase transition OPEN Zoe Budrikis, Giulio Costantini, Caterina A. M. La Porta and Stefano Zapperi Misfolded protein accumulation is a hallmark of many neurodegenerative diseases. Here Budrikis et al. model protein aggregation in the endoplasmic reticulum and show that it is the result of a non-equilibrium phase transition caused by tipping the balance from the rates of protein production to degradation. 11 April 2014 | doi: 10.1038/ncomms4620 Biological Sciences  Biochemistry  Bioinformatics  Neuroscience  Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism OPEN Roser Corominas, Xinping Yang, Guan Ning Lin, Shuli Kang, Yun Shen, Lila Ghamsari, Martin Broly, Maria Rodriguez, Stanley Tam, Shelly A. Trigg, Changyu Fan, Song Yi, Murat Tasan, Irma Lemmens, Xingyan Kuang, Nan Zhao, Dheeraj Malhotra, Jacob J. Michaelson, Vladimir Vacic, Michael A. Calderwood et al. Autism spectrum disorder (ASD) is a complex genetic trait that encompasses a range of neurodevelopmental disorders. Here, the authors clone brain-expressed alternatively-spliced isoforms of ASD risk factors and construct a network of protein interactions that provides further insight into the disease aetiology. 11 April 2014 | doi: 10.1038/ncomms4650 Biological Sciences  Genetics  Neuroscience  Lin28a regulates neuronal differentiation and controls miR-9 production OPEN Jakub S. Nowak, Nila Roy Choudhury, Flavia de Lima Alves, Juri Rappsilber and Gracjan Michlewski microRNAs regulate gene expression and control cell fate and differentiation processes. In this work, Nowak et al. reveal that brain-specific miR-9 is under post-transcriptional control and that the pre-miR-9 binding protein Lin28a decreases the levels of mature miR-9 during retinoic acid-mediated neuronal differentiation. 11 April 2014 | doi: 10.1038/ncomms4687 Biological Sciences  Cell biology  Neuroscience  Spectroscopic detection and state preparation of a single praseodymium ion in a crystal T. Utikal, E. Eichhammer, L. Petersen, A. Renn, S. Götzinger and V. Sandoghdar So far, high-resolution spectroscopy of single ions has been limited to electromagnetic traps in vacuum. Utikal et al. show that the combination of cryogenic laser spectroscopy and optical microscopy allows individual addressing, preparation and readout of praseodymium ions in Y2SiO5 crystals. 11 April 2014 | doi: 10.1038/ncomms4627 Physical Sciences  Atomic and molecular physics  Nanotechnology  Bottom-up synthesis of high surface area mesoporous crystalline silicon and evaluation of its hydrogen evolution performance Fang Dai, Jiantao Zai, Ran Yi, Mikhail L. Gordin, Hiesang Sohn, Shuru Chen and Donghai Wang Porous silicon is a technologically important material; however, many top-down etching fabrication processes result in significant material wastage. Here, the authors report a bottom-up self-templating fabrication route and assess the hydrogen evolution performance of the resulting material. 10 April 2014 | doi: 10.1038/ncomms4605 Chemical Sciences  Materials science  Inducing a direct-to-pseudodirect bandgap transition in wurtzite GaAs nanowires with uniaxial stress G. Signorello, E. Lörtscher, P.A. Khomyakov, S. Karg, D.L. Dheeraj, B. Gotsmann, H. Weman and H. Riel The band structure can strongly influence the light emission efficiency of semiconductors. Here, Signorello and colleagues demonstrate that a small uniaxial stress can change the band structure sufficiently to switch the luminescence of wurtzite GaAs nanowires on and off. 10 April 2014 | doi: 10.1038/ncomms4655 Physical Sciences  Nanotechnology  Optical physics  Optofluidic sorting of material chirality by chiral light Georgiy Tkachenko and Etienne Brasselet Sorting of material chirality is demanded in many industries, and conventional strategies are limited to the usage of chiral shape of the entity to be sorted. Tkachenko and Brasselet present a passive optical sorting method to achieve the same goal, which relies on the chirality–light interaction. 10 April 2014 | doi: 10.1038/ncomms4577 Physical Sciences  Applied physics  Fluids and plasma physics  Optical physics  Nucleic acid sensing by T cells initiates Th2 cell differentiation Takayuki Imanishi, Chitose Ishihara, Mohamed El Sherif Gadelhaq Badr, Akiko Hashimoto-Tane, Yayoi Kimura, Taro Kawai, Osamu Takeuchi, Ken J. Ishii, Shun'ichiro Taniguchi, Tetsuo Noda, Hisashi Hirano, Frank Brombacher, Glen N. Barber, Shizuo Akira and Takashi Saito Nucleic acids modulate T cell responses; however, the physiological significance of this property remains unclear. Here, the authors show that self-DNA complexes with antimicrobial peptides or histones, which mediates T cell costimulation to induce Th2 cell differentiation. 10 April 2014 | doi: 10.1038/ncomms4566 Biological Sciences  Immunology  A mutation in the enzyme monoamine oxidase explains part of the Astyanax cavefish behavioural syndrome Yannick Elipot, Hélène Hinaux, Jacques Callebert, Jean-Marie Launay, Maryline Blin and Sylvie Rétaux Astyanax mexicanus exists as either river-dwelling or cave-adapted subtypes. Elipot et al. identify a mutation in the cavefish monoamine oxidase gene, which leads to differential serotonin degradation in the brain and which may be associated with differences in behaviour between the subtypes. 10 April 2014 | doi: 10.1038/ncomms4647 Biological Sciences  Evolution  Neuroscience  MicroRNA-302b augments host defense to bacteria by regulating inflammatory responses via feedback to TLR/IRAK4 circuits Xikun Zhou, Xuefeng Li, Yan Ye, Kelei Zhao, Yan Zhuang, Yi Li, Yuquan Wei and Min Wu Bacterial infection stimulates a powerful inflammatory response that must be regulated to prevent tissue damage. Zhou et al. identify microRNA-302b as a feedback suppressor of inflammatory signalling that alleviates lung injury following Pseudomonas infection by targeting the NF-κB activator IRAK4. 10 April 2014 | doi: 10.1038/ncomms4619 Biological Sciences  Immunology  Microbiology  Crossover from random three-dimensional avalanches to correlated nano shear bands in metallic glasses Jon-Olaf Krisponeit, Sebastian Pitikaris, Karina E. Avila, Stefan Küchemann, Antje Krüger and Konrad Samwer Understanding the activation of the units that control plastic deformation in metallic glasses is important. Here, the authors use dynamic mechanical analysis to analyse the statistics of the activation of these units, observing a crossover from three-dimensional random activity to two-dimensional shear banding. 10 April 2014 | doi: 10.1038/ncomms4616 Physical Sciences  Materials science  Correlated optical and isotopic nanoscopy OPEN Sinem K. Saka, Angela Vogts, Katharina Kröhnert, François Hillion, Silvio O. Rizzoli and Johannes T. Wessels Secondary ion mass spectrometry is effective for imaging cellular turnover, but it cannot identify subcellular structures such as organelles. Here the authors show a method for correlating this technique with high-resolution fluorescence microscopy, enabling the measurement of turnover in cellular compartments. 10 April 2014 | doi: 10.1038/ncomms4664 Biological Sciences  Cell biology  Immunology  Optical physics  Generation of colonic IgA-secreting cells in the caecal patch Kazunori Masahata, Eiji Umemoto, Hisako Kayama, Manato Kotani, Shota Nakamura, Takashi Kurakawa, Junichi Kikuta, Kazuyoshi Gotoh, Daisuke Motooka, Shintaro Sato, Tomonori Higuchi, Yoshihiro Baba, Tomohiro Kurosaki, Makoto Kinoshita, Yosuke Shimada, Taishi Kimura, Ryu Okumura, Akira Takeda, Masaru Tajima, Osamu Yoshie et al. Gut-associated Peyer's patches are lymphoid tissues that generate IgA-secreting cells, however less is known about related caecal patches. Here, Masahata et al. show that caecal patches produce IgA-positive B cells that migrate to the intestines to maintain faecal microbiota homeostasis. 10 April 2014 | doi: 10.1038/ncomms4704 Biological Sciences  Immunology  Receptor mimicry by antibody F045–092 facilitates universal binding to the H3 subtype of influenza virus Peter S. Lee, Nobuko Ohshima, Robyn L. Stanfield, Wenli Yu, Yoshitaka Iba, Yoshinobu Okuno, Yoshikazu Kurosawa and Ian A. Wilson Influenza A H3 viruses circulate in humans and bind host cells using the haemagglutinin (HA) glycoprotein. Here, Lee et al. perform a structural analysis of antibody F045–092 with broadly neutralizing activity against the H3 subtype and reveal its interaction with the HA receptor binding site. 10 April 2014 | doi: 10.1038/ncomms4614 Biological Sciences  Immunology  Virology  Universal dispersion of surface plasmons in flat nanostructures OPEN Franz-Philipp Schmidt, Harald Ditlbacher, Ulrich Hohenester, Andreas Hohenau, Ferdinand Hofer and Joachim R. Krenn The dimensionality of nanostructures is important in determining their properties. Using electron spectroscopy, Schmidt et al. systematically study the plasmonic modes in silver nanodisks as they vary their dimensionality, and find that they can be scaled to the film and edge modes of extended silver films. 10 April 2014 | doi: 10.1038/ncomms4604 Physical Sciences  Nanotechnology  Optical physics  Phonon localization drives polar nanoregions in a relaxor ferroelectric M.E. Manley, J.W. Lynn, D.L. Abernathy, E.D. Specht, O. Delaire, A.R. Bishop, R. Sahul and J.D. Budai Relaxor ferroelectrics are of interest for applications such as actuators and sensors because of their very large electromechanical responses. Here the authors show that phonon localization drives the generation of the polar nanoregions that explain this electromechanical behaviour. 10 April 2014 | doi: 10.1038/ncomms4683 Physical Sciences  Condensed matter  Materials science  Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides OPEN Diana Paola Granados, Dev Sriranganadane, Tariq Daouda, Antoine Zieger, Céline M. Laumont, Olivier Caron-Lizotte, Geneviève Boucher, Marie-Pierre Hardy, Patrick Gendron, Caroline Côté, Sébastien Lemieux, Pierre Thibault and Claude Perreault Mass spectrometry (MS) has furthered our understanding of MHC class I-associated peptides (MIPs), but the technique is inadequate for studying MIP-associated polymorphisms. Here, the authors combine high-throughput MS with exome and transcriptome sequencing to identify polymorphic MIPs from two female siblings. 09 April 2014 | doi: 10.1038/ncomms4600 Biological Sciences  Genetics  Immunology  Processed pseudogenes acquired somatically during cancer development OPEN Susanna L. Cooke, Adam Shlien, John Marshall, Christodoulos P. Pipinikas, Inigo Martincorena, Jose M.C. Tubio, Yilong Li, Andrew Menzies, Laura Mudie, Manasa Ramakrishna, Lucy Yates, Helen Davies, Niccolo Bolli, Graham R. Bignell, Patrick S. Tarpey, Sam Behjati, Serena Nik-Zainal, Elli Papaemmanuil, Vitor H. Teixeira, Keiran Raine et al. Germline pseudogenes have an important role in human evolution. Here, the authors analyse sequencing data from 660 cancer samples and find evidence for the formation of somatically acquired pseudogenes, a new class of mutation, which may contribute to cancer development. 09 April 2014 | doi: 10.1038/ncomms4644 Biological Sciences  Cancer  Genetics  Olfactory projectome in the zebrafish forebrain revealed by genetic single-neuron labelling Nobuhiko Miyasaka, Ignacio Arganda-Carreras, Noriko Wakisaka, Miwa Masuda, Uygar Sümbül, H. Sebastian Seung and Yoshihiro Yoshihara Genetic approaches can be used to visualize neurons at single-cell resolution. Miyasaka et al. utilize genetic single neuron tracing to investigate zebrafish olfactory circuitry, characterizing neuronal projection patterns that are part of the secondary olfactory pathway. 09 April 2014 | doi: 10.1038/ncomms4639 Biological Sciences  Neuroscience  The phosphatase JKAP/DUSP22 inhibits T-cell receptor signalling and autoimmunity by inactivating Lck Ju-Pi Li, Chia-Yu Yang, Huai-Chia Chuang, Joung-Liang Lan, Der-Yuan Chen, Yi-Ming Chen, Xiaohong Wang, Alice J. Chen, John W. Belmont and Tse-Hua Tan JNK pathway-associated phosphatase (JKAP) is a dual-specificity phosphatase known to regulate substrates in several signalling cascades. Here, Li et al. demonstrate that JKAP has a key role in negative regulation of proximal T-cell receptor signalling and suppression of T-cell-mediated autoimmunity. 09 April 2014 | doi: 10.1038/ncomms4618 Biological Sciences  Immunology    Nature Communications JOBS of the week Postdoctoral Research Assistant Queen Mary University of London Clinical Research Fellow University of Edinburgh PhD student German Cancer Research Center (DKFZ) Research Associate Cambridge Institute for Medical Research (CIMR) Bioinformatician University of Glasgow Postdoctoral Fellow University of Idaho PhD Student Fritz Haber Institute of the Max Planck Society Research assistant Brown University Research Technican University of Sussex More Science jobs from Nature Communications EVENT Mind & Brain Prize 2014 19.11.14 Torino, Italy More science events from       Latest Corrigendum     Corrigendum: Visualizing autophosphorylation in histidine kinases Patricia Casino, Laura Miguel-Romero and Alberto Marina 14 April 2014 | doi: 10.1038/ncomms4645 Biological Sciences  Biochemistry  Molecular biology      Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast: The power of imaging flow cytometry in immunology. 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