Wednesday, April 23, 2014

Nature Communications - 23 April 2014

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23 April 2014 
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Miyasaka et al. visualise specific neuronal subpopulations that connect the olfactory bulb with higher olfactory centers in the zebrafish brain.
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Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors
Yiyang Gong, Mark J. Wagner, Jin Zhong Li and Mark J. Schnitzer
Genetically encoded optical voltage sensors measure the electrical activity of various tissues with limited effectiveness, due to the sensors' suboptimal performance metrics. Gong et al. create a sensor with increased brightness, fast kinetics and improved dynamic ranges when compared with previous sensors.
22 April 2014 | doi: 10.1038/ncomms4674
Biological Sciences  Neuroscience 

Ravens notice dominance reversals among conspecifics within and outside their social group OPEN
Jorg J. M. Massen, Andrius Pašukonis, Judith Schmidt and Thomas Bugnyar
Social intelligence requires the understanding of third-party relations, which is known to occur in humans and primates. Here, Massen et al. show that ravens respond differently to sound recordings of dominance interactions between other ravens, suggesting that ravens also understand third-party relations.
22 April 2014 | doi: 10.1038/ncomms4679
Biological Sciences  Neuroscience  Zoology 

On the fate of pumice rafts formed during the 2012 Havre submarine eruption OPEN
Martin Jutzeler, Robert Marsh, Rebecca J. Carey, James D. L. White, Peter J. Talling and Leif Karlstrom
Pumice rafts result from volcanic eruptions into and onto water, and can be extensive and potentially hazardous, but tracking their dispersal is difficult. Jutzeler et al. combine satellite imagery and an ocean model to accurately forecast pumice raft dispersal routes.
22 April 2014 | doi: 10.1038/ncomms4660
Earth Sciences  Geology and geophysics  Oceanography 

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates OPEN
Camille Berthelot, Frédéric Brunet, Domitille Chalopin, Amélie Juanchich, Maria Bernard, Benjamin Noël, Pascal Bento, Corinne Da Silva, Karine Labadie, Adriana Alberti, Jean-Marc Aury, Alexandra Louis, Patrice Dehais, Philippe Bardou, Jérôme Montfort, Christophe Klopp, Cédric Cabau, Christine Gaspin, Gary H. Thorgaard, Mekki Boussaha et al.
Although whole-genome duplications (WGDs) are rare events, they have an important role in shaping vertebrate evolution. Here, the authors sequence the rainbow trout genome and show that rediploidization after WGD occurs in a slow and stepwise manner.
22 April 2014 | doi: 10.1038/ncomms4657
Biological Sciences  Evolution  Genetics 

Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development
Jimena Giudice, Zheng Xia, Eric T. Wang, Marissa A. Scavuzzo, Amanda J. Ward, Auinash Kalsotra, Wei Wang, Xander H. T. Wehrens, Christopher B. Burge, Wei Li and Thomas A. Cooper
Alternative splicing is a process during gene expression that increases the diversity of proteins encoded by a single gene. Here, the authors perform RNA-sequencing on cardiac cells from mice and show that extensive changes in gene expression and alternative splicing occur during the first month after birth.
22 April 2014 | doi: 10.1038/ncomms4603
Biological Sciences  Medical research  Molecular biology 

Marine ice regulates the future stability of a large Antarctic ice shelf OPEN
Bernd Kulessa, Daniela Jansen, Adrian J. Luckman, Edward C. King and Peter R. Sammonds
Signs of instability in the Antarctic Larsen C ice shelf have raised concerns that it might soon collapse like its northern neighbour Larsen B. Kulessa et al. combine an ice-shelf model with satellite and geophysical data to show that despite dynamic similarities, Larsen C is presently stabilized by marine ice.
22 April 2014 | doi: 10.1038/ncomms4707
Earth Sciences  Geology and geophysics 

Quantifying quality in DNA self-assembly OPEN
Klaus F. Wagenbauer, Christian H. Wachauf and Hendrik Dietz
Sequence-programmable self-assembly of DNA enables the formation of a variety of complex structures; however, determining the quality of these multi-chain structures is challenging. Here the authors address this problem by using a fluorescent probe to measure the amount of unpaired bases in the DNA assemblies.
22 April 2014 | doi: 10.1038/ncomms4691
Physical Sciences  Bioengineering  Biophysics 

Nanotechnology 

Defect-induced plating of lithium metal within porous graphene networks
Rahul Mukherjee, Abhay V. Thomas, Dibakar Datta, Eklavya Singh, Junwen Li, Osman Eksik, Vivek B. Shenoy and Nikhil Koratkar
The use of metallic lithium electrodes in batteries would lead to dendritic growth problems. Here, Mukherjee et al. use porous graphene electrodes to entrap lithium metal at defect sites, achieving much improved specific capacities over extended cycling.
22 April 2014 | doi: 10.1038/ncomms4710
Physical Sciences  Materials science  Nanotechnology 

Co-option of a photoperiodic growth-phase transition system during land plant evolution
Akane Kubota, Shogo Kita, Kimitsune Ishizaki, Ryuichi Nishihama, Katsuyuki T. Yamato and Takayuki Kohchi
Flowering is triggered by changes in day length, which are detected by a network of genes including GI and FKF1. Kubota et al. show that GI and FKF1 homologues control transition from vegetative- to reproductive growth in the liverwort, revealing a more ancient than expected evolutionary origin for flowering control.
22 April 2014 | doi: 10.1038/ncomms4668
Biological Sciences  Evolution  Plant sciences 

Experimental demonstration of a graph state quantum error-correction code
B. A. Bell, D. A. Herrera-Martí, M. S. Tame, D. Markham, W. J. Wadsworth and J. G. Rarity
Noise and decoherence are serious problems for scalable quantum computing schemes. Using an all-optical approach, Bell et al. explore the use of four-qubit graph states for encoding quantum information, and show that they can reliably detect and correct errors against loss.
22 April 2014 | doi: 10.1038/ncomms4658
Physical Sciences  Optical physics 

APC/C is an essential regulator of centrosome clustering
Konstantinos Drosopoulos, Chan Tang, William C. H. Chao and Spiros Linardopoulos
Cells with multiple centrosomes, as are often observed in cancer, can still divide successfully because the centrosomes cluster to form a single spindle pole body. Drosopoulos et al. show that degradation of the kinesin Eg5 by APC/C-CDH1 is required for centrosome clustering.
22 April 2014 | doi: 10.1038/ncomms4686
Biological Sciences  Cell biology 

Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation
Stefan Köster, Katharina van Pee, Martina Hudel, Martin Leustik, Daniel Rhinow, Werner Kühlbrandt, Trinad Chakraborty and Özkan Yildiz
The cytolysin, listeriolysin O (LLO), is expressed by Listeria and forms pores in the phagosomal membrane in response to decreased pH. Here, Yildiz et al. solve the crystal structure of LLO, identify residues that serve as the pH sensor, and determine the mechanism of pore formation in host membranes.
22 April 2014 | doi: 10.1038/ncomms4690
Biological Sciences  Biochemistry  Biophysics 

Microbiology 

Enhancing adult nerve regeneration through the knockdown of retinoblastoma protein
Kimberly J. Christie, Anand Krishnan, Jose A. Martinez, Kaylynn Purdy, Bhagat Singh, Shane Eaton and Douglas Zochodne
Retinoblastoma protein (Rb) is a key inhibitor of cell cycle progression and its deletion is implicated in cancer. Here, the authors show that Rb is also involved in regulating nerve regeneration, since silencing Rb promotes neurite outgrowth and recovery of sensorimotor responses after nerve injury.
22 April 2014 | doi: 10.1038/ncomms4670
Biological Sciences  Neuroscience 

Orbital resolution of molecules covalently attached to a clean semiconductor surface
Jing Hui He, Wei Mao, Guo Qin Xu and Eng Soon Tok
It is difficult to spatially resolve molecular orbitals of molecules on highly reactive semiconductor surfaces. Here, Xu et al. use scanning tunnelling microscopy to study pyridazine molecules on a clean germanium surface, and hybridized molecular orbitals are directly imaged.
22 April 2014 | doi: 10.1038/ncomms4721
Chemical Sciences  Materials science  Nanotechnology 

Physical chemistry 

Ultrafast vapourization dynamics of laser-activated polymeric microcapsules
Guillaume Lajoinie, Erik Gelderblom, Ceciel Chlon, Marcel Böhmer, Wiendelt Steenbergen, Nico de Jong, Srirang Manohar and Michel Versluis
Laser-induced vapourization has great potential in many applications, but the underlying physical mechanisms are not clear. Here, Lajoinie et al. study oil-filled polymer microcapsules using coupled optical and acoustic detection, and report new insights into the laser-activated processes.
22 April 2014 | doi: 10.1038/ncomms4671
Physical Sciences  Fluids and plasma physics 

Nanotechnology  Optical physics 

Silicon carbide-derived carbon nanocomposite as a substitute for mercury in the catalytic hydrochlorination of acetylene
Xingyun Li, Xiulian Pan, Liang Yu, Pengju Ren, Xing Wu, Litao Sun, Feng Jiao and Xinhe Bao
Acetylene hydrochlorination is an industrially important reaction but is, in many instances, still catalyzed by mercury chloride. Here, the authors report a nanocomposite of pyrrolic nitrogen-doped carbon capable of activating acetylene, which also exhibits promising performance in vinyl chloride formation.
22 April 2014 | doi: 10.1038/ncomms4688
Chemical Sciences  Catalysis  Materials science 

Social heuristics shape intuitive cooperation
David G. Rand, Alexander Peysakhovich, Gordon T. Kraft-Todd, George E. Newman, Owen Wurzbacher, Martin A. Nowak and Joshua D. Greene
Whether or not intuition favours cooperative decision making has been controversial. Rand et al. carry out a meta-analysis of 15 studies involving volunteers playing economic games, and confirm a role for intuition in cooperation, which varies according to the volunteers' previous experience with similar games.
22 April 2014 | doi: 10.1038/ncomms4677
Biological Sciences  Evolution  Neuroscience 

Cellular protection using Flt3 and PI3Kα inhibitors demonstrates multiple mechanisms of oxidative glutamate toxicity
Yunyi Kang, Stefano Tiziani, Goonho Park, Marcus Kaul and Giovanni Paternostro
Cellular oxidative stress is implicated in neurodegeneration. Here, Kang et al. show that the receptor tyrosine kinase Flt3 and the signalling molecule PI3Kα play key roles in glutamate-mediated oxidative stress in neuronal cells, which can be prevented by Flt3- or PI3Kα-specific inhibitors.
17 April 2014 | doi: 10.1038/ncomms4672
Biological Sciences  Cell biology  Neuroscience 

IKKα restoration via EZH2 suppression induces nasopharyngeal carcinoma differentiation
Min Yan, Yan Zhang, Bin He, Jin Xiang, Zi-feng Wang, Fei-meng Zheng, Jie Xu, Ming-yuan Chen, Yu-liang Zhu, Hai-jun Wen, Xiang-bo Wan, Cai-feng Yue, Na Yang, Wei Zhang, Jia-liang Zhang, Jing Wang, Yang Wang, Lian-hong Li, Yi-xin Zeng, Eric W.-F. Lam et al.
Nasopharyngeal carcinomas often present as undifferentiated tumours. Here, Yan et al. show that reduced expression of IKK via promoter methylation results in the undifferentiated phenotype of the tumours and that treatment with retinoic acid can reverse these features.
17 April 2014 | doi: 10.1038/ncomms4661
Biological Sciences  Cancer 

Local adaptation limits lifetime reproductive success of dispersers in a wild salmon metapopulation
Daniel A. Peterson, Ray Hilborn and Lorenz Hauser
Population dynamics depends on the interaction of dispersal and local adaptation, yet empirical evidence showing the role of these processes is scarce. Here, Peterson et al. show that in a wild population of salmon, gene flow is limited by selection against immigrants rather than by barriers to dispersal.
17 April 2014 | doi: 10.1038/ncomms4696
Biological Sciences  Ecology  Evolution 

Unc5C and DCC act downstream of Ctip2 and Satb2 and contribute to corpus callosum formation OPEN
Swathi Srivatsa, Srinivas Parthasarathy, Olga Britanova, Ingo Bormuth, Amber-Lee Donahoo, Susan L. Ackerman, Linda J. Richards and Victor Tarabykin
The neocortex is responsible for higher level cognitive functions and long-range neural connections are critical for mediating these functions. Here, Srivatsa et al. show that axon guidance molecules downstream of transcription factors Stab2 and Ctip2 play a role in the establishment of cortical connections during mouse brain development.
17 April 2014 | doi: 10.1038/ncomms4708
Biological Sciences  Developmental biology  Neuroscience 

Polymeric molecular sieve membranes via in situ cross-linking of non-porous polymer membrane templates
Zhen-An Qiao, Song-Hai Chai, Kimberly Nelson, Zhonghe Bi, Jihua Chen, Shannon M. Mahurin, Xiang Zhu and Sheng Dai
Porous materials are ideal candidates for molecular sieving applications, but it is often difficult to process them into membranes with high permeability and selectivity. Qiao et al. develop an approach of controlling porosity of organic polymers by in situ cross-linking in non-porous polymer membranes.
16 April 2014 | doi: 10.1038/ncomms4705
Chemical Sciences  Materials science  Nanotechnology 

Carrier multiplication in graphene under Landau quantization
Florian Wendler, Andreas Knorr and Ermin Malic
The absence of a bandgap and competing phonon-induced electron-hole recombination makes extraction of charge carriers difficult in graphene. Here, the authors show theoretically that a tunable bandgap can be introduced in graphene via Landau quantization, allowing for significant carrier multiplication.
16 April 2014 | doi: 10.1038/ncomms4703
Physical Sciences  Condensed matter  Materials science 

Paired oxygen isotope records reveal modern North American atmospheric dynamics during the Holocene
Zhongfang Liu, Kei Yoshimura, Gabriel J. Bowen, Nikolaus H. Buenning, Camille Risi, Jeffrey M. Welker and Fasong Yuan
The Pacific North American teleconnection strongly influences modern climate in North America, yet long-term variability remains unknown. Liu et al. reconstruct precipitation histories from palaeoisotope proxy records and identify modern atmospheric patterns during the Holocene.
16 April 2014 | doi: 10.1038/ncomms4701
Earth Sciences  Climate science 

Shared developmental programme strongly constrains beak shape diversity in songbirds
Joerg A. Fritz, Joseph Brancale, Masayoshi Tokita, Kevin J. Burns, M. Brent Hawkins, Arhat Abzhanov and Michael P. Brenner
The extent and mechanisms by which developmental process may constraint natural variation are poorly understood. Here, Fritz et al. show that beak shape in songbirds is strongly constrained by developmental mechanics shared by several bird species.
16 April 2014 | doi: 10.1038/ncomms4700
Biological Sciences  Developmental biology  Ecology 

Evolution 

Supersymmetric mode converters
Matthias Heinrich, Mohammad-Ali Miri, Simon Stützer, Ramy El-Ganainy, Stefan Nolte, Alexander Szameit and Demetrios N. Christodoulides
In its optical manifestation, supersymmetry can potentially establish close relationships between seemingly different dielectric structures. Here, the authors use the perfect global phase matching afforded by supersymmetry for mode conversion and mode division multiplexing in highly multimoded systems.
16 April 2014 | doi: 10.1038/ncomms4698
Physical Sciences  Optical physics 

Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling OPEN
Maria Mooshammer, Wolfgang Wanek, Ieda Hämmerle, Lucia Fuchslueger, Florian Hofhansl, Anna Knoltsch, Jörg Schnecker, Mounir Takriti, Margarete Watzka, Birgit Wild, Katharina M. Keiblinger, Sophie Zechmeister-Boltenstern and Andreas Richter
Nitrogen availability in soils is predominantly controlled by microorganisms, yet our understanding of their organic nitrogen use is limited. Mooshammer et al. show that microbial nitrogen use efficiency is dependent on resource stoichiometry and substrate type.
16 April 2014 | doi: 10.1038/ncomms4694
Earth Sciences  Biogeochemistry 

Length-dependent thermal conductivity in suspended single-layer graphene
Xiangfan Xu, Luiz F. C. Pereira, Yu Wang, Jing Wu, Kaiwen Zhang, Xiangming Zhao, Sukang Bae, Cong Tinh Bui, Rongguo Xie, John T. L. Thong, Byung Hee Hong, Kian Ping Loh, Davide Donadio, Baowen Li and Barbaros Özyilmaz
Graphene is known to display unique functional properties due to its two-dimensional structure. Here, the authors measure the thermal conductivity of suspended graphene as a function of sample length, finding that thermal conductivity is higher in longer samples as a result of two-dimensional phonons.
16 April 2014 | doi: 10.1038/ncomms4689
Physical Sciences  Condensed matter  Materials science 

Unexpected interplay of bonding height and energy level alignment at heteromolecular hybrid interfaces
Benjamin Stadtmüller, Daniel Lüftner, Martin Willenbockel, Eva M. Reinisch, Tomoki Sueyoshi, Georg Koller, Serguei Soubatch, Michael G. Ramsey, Peter Puschnig, F. Stefan Tautz and Christian Kumpf
Typically for surface adsorption there is a direct relationship between interaction strength and geometric distance—a stronger interaction leads to a shorter distance between interacting objects. Here the authors show a case where a stronger interaction leads to a larger distance, and explain this apparent paradox.
16 April 2014 | doi: 10.1038/ncomms4685
Chemical Sciences  Condensed matter  Nanotechnology 

Physical chemistry 

Self-assembled ultrathin nanotubes on diamond (100) surface
Shaohua Lu, Yanchao Wang, Hanyu Liu, Mao-sheng Miao and Yanming Ma
Theoretical determination of surface structures can be problematic when the configuration space is complex. Here Lu et al. develop an automated surface structure-searching method, and when applied on studying surface reconstruction of a diamond surface, self-assembled carbon nanotubes are found.
16 April 2014 | doi: 10.1038/ncomms4666
Physical Sciences  Materials science 

Chemical control of electrical contact to sp2 carbon atoms OPEN
Thomas Frederiksen, Giuseppe Foti, Fabrice Scheurer, Virginie Speisser and Guillaume Schull
Understanding metal-molecule contacts is crucial for molecular electronic devices. Here, the authors use a C60-terminated scanning tunnelling tip to probe how the chemical nature of the contacting atom on the substrate electrode determines the transport properties.
16 April 2014 | doi: 10.1038/ncomms4659
Physical Sciences  Atomic and molecular physics 

Nanotechnology 

Forensic genomics as a novel tool for identifying the causes of mass mortality events
Pierre De Wit, Laura Rogers-Bennett, Raphael M. Kudela and Stephen R. Palumbi
Mass mortality events of fish and invertebrates are increasingly frequent in coastal zones, yet it is often difficult to identify their causes. Here, the authors provide evidence that a combined field and genomics approach could help identifying the specific cause of mass mortality events.
16 April 2014 | doi: 10.1038/ncomms4652
Biological Sciences  Ecology  Genetics 

Variation in Arabidopsis flowering time associated with cis-regulatory variation in CONSTANS OPEN
Ulises Rosas, Yu Mei, Qiguang Xie, Joshua A. Banta, Royce W. Zhou, Gabriela Seufferheld, Silvia Gerard, Lucy Chou, Naeha Bhambhra, Jennifer Deane Parks, Jonathan M. Flowers, C. Robertson McClung, Yoshie Hanzawa and Michael D. Purugganan
The transcription factor CONSTANS regulates the timing of flowering in Arabidopsis. Rosas et al. report that genetic variation in the cis-regulatory regions of this gene contributes to natural phenotypic variation in flowering time.
16 April 2014 | doi: 10.1038/ncomms4651
Biological Sciences  Genetics  Plant sciences 

Determining the polarization state of an extreme ultraviolet free-electron laser beam using atomic circular dichroism
T. Mazza, M. Ilchen, A. J. Rafipoor, C. Callegari, P. Finetti, O. Plekan, K. C. Prince, R. Richter, M. B. Danailov, A. Demidovich, G. De Ninno, C. Grazioli, R. Ivanov, N. Mahne, L. Raimondi, C. Svetina, L. Avaldi, P. Bolognesi, M. Coreno, P. O'Keeffe et al.
Intense extreme UV and X-ray coherent sources are set to revolutionize numerous research areas, yet characterization of their polarization remains elusive. Here, Mazza et al. measure the polarization state of circularly polarized extreme UV light from a free-electron laser using circular dichroism.
16 April 2014 | doi: 10.1038/ncomms4648
Physical Sciences  Optical physics 

Visualization of exciton transport in ordered and disordered molecular solids
Gleb M. Akselrod, Parag B. Deotare, Nicholas J. Thompson, Jiye Lee, William A. Tisdale, Marc A. Baldo, Vinod M. Menon and Vladimir Bulović
Excitons are bound electron-hole pairs that mediate light absorption and emission in organic devices. Here, the authors use spatial, spectral and time-resolved imaging to visualize exciton transport in tetracene crystals and thin films, showing the role of disorder on the diffusion of excitons.
16 April 2014 | doi: 10.1038/ncomms4646
Physical Sciences  Applied physics  Materials science 

MHC-I expression renders catecholaminergic neurons susceptible to T-cell-mediated degeneration
Carolina Cebrián, Fabio A. Zucca, Pierluigi Mauri, Julius A. Steinbeck, Lorenz Studer, Clemens R. Scherzer, Ellen Kanter, Sadna Budhu, Jonathan Mandelbaum, Jean P. Vonsattel, Luigi Zecca, John D. Loike and David Sulzer
MHC-I is expressed in neurons where it is implicated in synaptic plasticity and neuron regeneration. Here, Cebrián et al. report an increase in MHC-I expression in brain neurons from Parkinson's disease patients, which is triggered by microglial activation and circulating dopamine.
16 April 2014 | doi: 10.1038/ncomms4633
Biological Sciences  Immunology  Neuroscience 

Organic magnetoelectroluminescence for room temperature transduction between magnetic and optical information
Ferran Macià, Fujian Wang, Nicholas J. Harmon, Andrew D. Kent, Markus Wohlgenannt and Michael E. Flatté
The small spin-orbit interaction makes transduction between the magnetic and optical information challenging in organic materials. Here, the authors show that the room temperature electroluminescence of an organic material can be controlled by the fringe fields of a nearby magnet.
16 April 2014 | doi: 10.1038/ncomms4609
Physical Sciences  Applied physics  Materials science 

Nanotechnology 

One-dimensional self-confinement promotes polymorph selection in large-area organic semiconductor thin films
Gaurav Giri, Ruipeng Li, Detlef-M. Smilgies, Er Qiang Li, Ying Diao, Kristina M. Lenn, Melanie Chiu, Debora W. Lin, Ranulfo Allen, Julia Reinspach, Stefan C. B. Mannsfeld, Sigurdur T. Thoroddsen, Paulette Clancy, Zhenan Bao and Aram Amassian
Solution-shearing process has been recently developed as a large-area coating method of producing crystallographic organic thin films, but how this process works is still unknown. Giri et al. monitor it in real time and find the degree of polymorphism can be tailored by varying solution conditions.
16 April 2014 | doi: 10.1038/ncomms4573
Chemical Sciences  Materials science  Nanotechnology 
 
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