Wednesday, April 26, 2017

Nature Communications - 26 April 2017

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26 April 2017 
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April 2017 marks the 25th Anniversary of Nature Genetics! To celebrate, the editors have selected some past papers which are free to read for a limited time. 

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September 17-19, 2017 | Seattle, WA, USA

Presented by: Adaptive Biotechnologies | Nature Immunology | Nature Medicine | Nature Biotechnology


AGRICULTURAL GENOMICS 2017 - Functional Genomics toward Green Crops for Sustainable Agriculture 

Hosting Organizations: National Key Laboratory of Crop Genetic Improvement | Huazhong Agricultural University | Nature Genetics | Nature Plants | Nature Communications

October 25-27, 2017
Conference Hall, National Key Laboratory of Crop Genetic Improvement | Wuhan, China
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  Latest Editorial View all Editorials  
Fake news threatens a climate literate world OPEN
As the challenges and environmental consequences of climate change manifest, the need for a society of science-literate citizens is becoming increasingly apparent. Achieving this, however, is no easy task, particularly given the proliferation of fake news and the seeds of confusion it can sow
20 April 2017 | doi: 10.1038/ncomms15460
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An extra-uterine system to physiologically support the extreme premature lamb OPEN
Emily A. Partridge, Marcus G. Davey, Matthew A. Hornick, Patrick E. McGovern, Ali Y. Mejaddam, Jesse D. Vrecenak, Carmen Mesas-Burgos, Aliza Olive, Robert C. Caskey, Theodore R. Weiland, Jiancheng Han, Alexander J. Schupper, James T. Connelly, Kevin C. Dysart, Jack Rychik, Holly L. Hedrick, William H. Peranteau and Alan W. Flake
The ability to support the development of a premature fetus in the form of an extracorporeal system has had limited success. Here, the authors show that an extra-uterine device that mimics the intra-uterine environment can provide physiologic support for the extreme premature lamb fetus for four weeks.
25 April 2017 | doi: 10.1038/ncomms15112

Refined genetic maps reveal sexual dimorphism in human meiotic recombination at multiple scales OPEN
Claude Bhérer, Christopher L. Campbell and Adam Auton
It is known that males have lower recombination rates than females over much of the genome but little is known about differences at a fine scale. Here the authors combine data from over 100,000 meioses and show that the majority of differences can be explained by variation in hotspot magnitude.
25 April 2017 | doi: 10.1038/ncomms14994

KDM3 epigenetically controls tumorigenic potentials of human colorectal cancer stem cells through Wnt/β-catenin signalling OPEN
Jiong Li, Bo Yu, Peng Deng, Yingduan Cheng, Yongxin Yu, Kareena Kevork, Sivakumar Ramadoss, Xiangming Ding, Xinmin Li and Cun-Yu Wang
Epigenetic factors can regulate functional properties of human colorectal cancer stem cells. Here, the authors show that histone demethylases of the KDM3 family activate Wnt signalling in colorectal cancer stem cells by erasing H3K9me2 marks on Wnt target genes and recruiting MLL1 to promote H3K4 methylation.
25 April 2017 | doi: 10.1038/ncomms15146

A reversible dendrite-free high-areal-capacity lithium metal electrode OPEN
Hui Wang, Masaki Matsui, Hiroko Kuwata, Hidetoshi Sonoki, Yasuaki Matsuda, Xuefu Shang, Yasuo Takeda, Osamu Yamamoto and Nobuyuki Imanishi
Despite recent technological advances, it remains challenging to realize reversible high-areal-capacity lithium metal anodes. Here, the authors demonstrate such an anode by tailoring the top solid electrolyte interphase layer.
25 April 2017 | doi: 10.1038/ncomms15106

Gold nanoclusters-assisted delivery of NGF siRNA for effective treatment of pancreatic cancer OPEN
Yifeng Lei, Lixue Tang, Yangzhouyun Xie, Yunlei Xianyu, Lingmin Zhang, Peng Wang, Yoh Hamada, Kai Jiang, Wenfu Zheng and Xingyu Jiang
Nerve growth factor (NGF) contributes to the sustained growth and metastasis of pancreatic cancer cells. Here, the authors develop a gold nanocluster-coupled siRNA against NGF that efficiently silences the NGF gene and inhibits tumour growth of pancreatic cancer in mice.
25 April 2017 | doi: 10.1038/ncomms15130

Ruthenium-cobalt nanoalloys encapsulated in nitrogen-doped graphene as active electrocatalysts for producing hydrogen in alkaline media OPEN
Jianwei Su, Yang Yang, Guoliang Xia, Jitang Chen, Peng Jiang and Qianwang Chen
Ruthenium is the cheapest platinum-group metal, yet active hydrogen evolution catalysts with low amounts of ruthenium have yet to be designed. Here, the authors report the preparation of a ruthenium–cobalt nanoalloy and demonstrate its potential as an effective hydrogen evolution catalyst in basic media.
25 April 2017 | doi: 10.1038/ncomms14969

Visible light guided manipulation of liquid wettability on photoresponsive surfaces OPEN
Gibum Kwon, Divya Panchanathan, Seyed Reza Mahmoudi, Mohammed A. Gondal, Gareth H. McKinley and Kripa K. Varanasi
Controlling surface wettability using visible light is highly attractive for a range of liquid separation technologies. Here, Varanasi, McKinley and colleagues fabricate dye-sensitized photocatalytic TiO2 surfaces on which liquid droplet motion can be externally manipulated by visible light illumination.
25 April 2017 | doi: 10.1038/ncomms14968

Two-dimensional Mo1.33C MXene with divacancy ordering prepared from parent 3D laminate with in-plane chemical ordering OPEN
Quanzheng Tao, Martin Dahlqvist, Jun Lu, Sankalp Kota, Rahele Meshkian, Joseph Halim, Justinas Palisaitis, Lars Hultman, Michel W. Barsoum, Per O.Å. Persson and Johanna Rosen
Vacancies in 2D materials can influence their properties, however controlling their formation remains a challenge. Here the authors show that selective etching of a 3D laminate with in-plane chemical ordering results in formation of MXenes with ordered divacancies, as well as elevated conductance and supercapacitance.
25 April 2017 | doi: 10.1038/ncomms14949

Active matter logic for autonomous microfluidics OPEN
Francis G. Woodhouse and Jörn Dunkel
Active fluids consist of self-driven particles that can drive spontaneous flow without the intervention of external forces. Here Woodhouse et al. show how to design logic circuits using this phenomenon in active fluid networks, which could be further exploited for autonomous microfluidic computing.
25 April 2017 | doi: 10.1038/ncomms15169

Synthesis of extended polycyclic aromatic hydrocarbons by oxidative tandem spirocyclization and 1,2-aryl migration OPEN
Xuan Zhang, Zhanqiang Xu, Weili Si, Kazuaki Oniwa, Ming Bao, Yoshinori Yamamoto and Tienan Jin
Simple synthetic routes to polyaromatic hydrocarbons are important due to their applications in organic electronics. Here the authors report a straightforward synthesis of a diverse range of polyaromatic hydrocarbons, via a one-pot oxidative cyclisation and subsequent 1,2-aryl migration.
25 April 2017 | doi: 10.1038/ncomms15073

Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells OPEN
Feng Pan, Thomas S. Wingo, Zhigang Zhao, Rui Gao, Hideki Makishima, Guangbo Qu, Li Lin, Miao Yu, Janice R. Ortega, Jiapeng Wang, Aziz Nazha, Li Chen, Bing Yao, Can Liu, Shi Chen, Ophelia Weeks, Hongyu Ni, Brittany Lynn Phillips, Suming Huang, Jianlong Wang et al.
TET2 catalyses DNA demethylation and is mutated in various blood cancers; in particular Tet2 null mice develop haematological neoplasms. Here the authors show that this effect could be due to the increased frequency of mutation associated with TET2 loss in haematopoietic stem/progenitor cells.
25 April 2017 | doi: 10.1038/ncomms15102

Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis OPEN
Amy T. Y. Yeung, Christine Hale, Amy H. Lee, Erin E. Gill, Wendy Bushell, David Parry-Smith, David Goulding, Derek Pickard, Theodoros Roumeliotis, Jyoti Choudhary, Nick Thomson, William C. Skarnes, Gordon Dougan and Robert E. W. Hancock
In vitro models to study the role of host genetics in the response to chlamydial infection are limited. Here, Yeung et al. show that macrophages derived from human induced pluripotent stem cells (which can be genetically manipulated) support chlamydial infection and can be used for this purpose.
25 April 2017 | doi: 10.1038/ncomms15013

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density OPEN
Nicholas M. Pearce, Tobias Krojer, Anthony R. Bradley, Patrick Collins, Radosław P. Nowak, Romain Talon, Brian D. Marsden, Sebastian Kelm, Jiye Shi, Charlotte M. Deane and Frank von Delft
Building a ligand into a weak region of an electron density map of a protein is a subjective process. Here, the authors present a new method to obtain a clear electron density for a bound ligand based on multi-crystal experiments and 3D background correction.
24 April 2017 | doi: 10.1038/ncomms15123

Time-reversal symmetry breaking hidden order in Sr2(Ir,Rh)O4 OPEN
Jaehong Jeong, Yvan Sidis, Alex Louat, Véronique Brouet and Philippe Bourges
Exploring ordered states in similarly structured oxides aids the understanding of structure-property correlations. Here the authors discover an unconventional magnetic order in Sr2(Ir,Rh)O4, which is analogous to a loop-current phase in cuprate superconductors with the same lattice structure.
24 April 2017 | doi: 10.1038/ncomms15119

Disrupted neuronal maturation in Angelman syndrome-derived induced pluripotent stem cells OPEN
James J. Fink, Tiwanna M. Robinson, Noelle D. Germain, Carissa L. Sirois, Kaitlyn A. Bolduc, Amanda J. Ward, Frank Rigo, Stormy J. Chamberlain and Eric S. Levine
Angelman syndrome (AS) is characterized by developmental delay and intellectual disability, but the underlying pathophysiology is not well understood. Here the authors use induced pluripotent stem cell-derived neurons from AS patients and find impaired maturation of resting membrane potential and action potential firing, and defects in synaptic activity associated with the disease.
24 April 2017 | doi: 10.1038/ncomms15038

Energy scaling of targeted optimal control of complex networks OPEN
Isaac Klickstein, Afroza Shirin and Francesco Sorrentino
The energy required to control a dynamical complex network can be prohibitively large when there are only a few control inputs. Here the authors demonstrate that if only a subset of the network is targeted the energy requirements decrease exponentially.
24 April 2017 | doi: 10.1038/ncomms15145

DNA single-strand break-induced DNA damage response causes heart failure OPEN
Tomoaki Higo, Atsuhiko T. Naito, Tomokazu Sumida, Masato Shibamoto, Katsuki Okada, Seitaro Nomura, Akito Nakagawa, Toshihiro Yamaguchi, Taku Sakai, Akihito Hashimoto, Yuki Kuramoto, Masamichi Ito, Shungo Hikoso, Hiroshi Akazawa, Jong-Kook Lee, Ichiro Shiojima, Peter J. McKinnon, Yasushi Sakata and Issei Komuro
DNA damage response (DDR) is activated in cardiomyocytes of the failing heart, but the type of DNA damage leading to DDR is unclear. Higo et al. show that in mice heart failure is caused in part by unrepaired DNA single-strand breaks in cardiomyocytes, which activate persistent DDR and trigger an NF-κB-dependent cardiac inflammation.
24 April 2017 | doi: 10.1038/ncomms15104

LPP is a Src substrate required for invadopodia formation and efficient breast cancer lung metastasis OPEN
Elaine Ngan, Konstantin Stoletov, Harvey W. Smith, Jessica Common, William J. Muller, John D. Lewis and Peter M. Siegel
Lipoma preferred partner (LPP) mediates TGFβ-induced breast cancer cell migration and invasion. Here the authors show that LPP is a Src-family kinase substrate that regulates the formation of protrusions of the plasma membrane -called invadopodia- required for breast cancer metastasis.
24 April 2017 | doi: 10.1038/ncomms15059

Neuronal IFN-beta–induced PI3K/Akt-FoxA1 signalling is essential for generation of FoxA1+Treg cells OPEN
Yawei Liu, Andrea Marin, Patrick Ejlerskov, Louise Munk Rasmussen, Marco Prinz and Shohreh Issazadeh-Navikas
Neurons can convert pathogenic T cells to anti-inflammatory FoxA1+ regulatory T cells (Tregs), which can ameliorate EAE, but the molecular mechanism is only partially understood. Liu et al. show that autocrine interferon β signalling induces PDL1 expression in neurons, which is essential for neurons to reprogramme pathogenic T cells to FoxA1+ Tregs.
24 April 2017 | doi: 10.1038/ncomms14709

Volumetric chemical imaging by stimulated Raman projection microscopy and tomography OPEN
Xueli Chen, Chi Zhang, Peng Lin, Kai-Chih Huang, Jimin Liang, Jie Tian and Ji-Xin Cheng
Recent advances have enabled high-speed three-dimensional optical imaging through the use of fluorescent markers. Here, Chen et al. integrate stimulated Raman imaging into those methods, enabling the label-free and chemically specific volumetric imaging of complex samples.
24 April 2017 | doi: 10.1038/ncomms15117

Band structure engineered layered metals for low-loss plasmonics OPEN
Morten N. Gjerding, Mohnish Pandey and Kristian S. Thygesen
Here the authors show that Ohmic losses are reduced in certain layered metals, such as the transition metal dichalcogenide, due to a small density of states for scattering in the near-IR originating from the electronic band structure, thus leading to improved performance for low-loss plasmonic applications.
24 April 2017 | doi: 10.1038/ncomms15133

Structure and function of the divalent anion/Na+ symporter from Vibrio cholerae and a humanized variant OPEN
Rongxin Nie, Steven Stark, Jindrich Symersky, Ronald S. Kaplan and Min Lu
Divalent anion/Na+ symporter (DASS) transporters move intermediates of the Krebs cycle across the cell membrane. Here the authors present the substrate-bound structures of VcINDY, a DASS from Vibrio cholerae, which provide insights into the underlying transport mechanism.
24 April 2017 | doi: 10.1038/ncomms15009

A metallic molybdenum dioxide with high stability for surface enhanced Raman spectroscopy OPEN
Qiqi Zhang, Xinshi Li, Qiang Ma, Qing Zhang, Hua Bai, Wencai Yi, Jingyao Liu, Jing Han and Guangcheng Xi
Semiconducting materials are potential SERS substrates as alternatives to noble metals, but often suffer from poor stabilities and sensitivities. Here, the authors use molybdenum dioxide as a SERS material, showing high enhancement factors and stability to oxidation even at high temperatures.
24 April 2017 | doi: 10.1038/ncomms14903

Platinum-nickel alloy excavated nano-multipods with hexagonal close-packed structure and superior activity towards hydrogen evolution reaction OPEN
Zhenming Cao, Qiaoli Chen, Jiawei Zhang, Huiqi Li, Yaqi Jiang, Shouyu Shen, Gang Fu, Bang-an Lu, Zhaoxiong Xie and Lansun Zheng
While crystal phase modification may endow materials with altered functionality, the fabrication of allomorphic noble metal nanomaterials is challenging. Here, the authors synthesize an unusual hexagonal close-packed platinum-nickel alloy and demonstrate its enhanced hydrogen evolution catalytic activity.
24 April 2017 | doi: 10.1038/ncomms15131

Photostriction of strontium ruthenate OPEN
Tzu-Chiao Wei, Hsin-Ping Wang, Heng-Jui Liu, Dung-Sheng Tsai, Jr-Jian Ke, Chung-Lun Wu, Yu-Peng Yin, Qian Zhan, Gong-Ru Lin, Ying-Hao Chu and Jr-Hau He
Light-induced deformation known as photostriction could be used for green energy devices but in most materials the effect is too small to be of practical use. Here, Wei et al. study the photostriction of strontium ruthenate and find photon-induced strain efficiencies of more than one percent.
24 April 2017 | doi: 10.1038/ncomms15108

Clonal evolution in myelodysplastic syndromes OPEN
Pedro da Silva-Coelho, Leonie I. Kroeze, Kenichi Yoshida, Theresia N. Koorenhof-Scheele, Ruth Knops, Louis T. van de Locht, Aniek O. de Graaf, Marion Massop, Sarah Sandmann, Martin Dugas, Marian J. Stevens-Kroef, Jaroslav Cermak, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Theo de Witte, Nicole M. A. Blijlevens, Petra Muus, Gerwin Huls et al.
Myelodysplastic syndromes are a broad group of haematopoietic malignancies that often progress to acute myeloid leukaemia. Here, the authors show that linear and branched evolution occurs within myelodysplastic syndrome and these patterns can be impacted by treatment.
21 April 2017 | doi: 10.1038/ncomms15099

Electrochemical generation of sulfur vacancies in the basal plane of MoS2 for hydrogen evolution OPEN
Charlie Tsai, Hong Li, Sangwook Park, Joonsuk Park, Hyun Soo Han, Jens K. Nørskov, Xiaolin Zheng and Frank Abild-Pedersen
In order to fully utilize sulfur vacancies in MoS2 catalysts for industrial applications, a facile and general route for making sulfur vacancies in MoS2 is needed. Here, the authors introduce a scalable route towards generating sulfur vacancies on the MoS2 basal plane using electrochemical desulfurization.
21 April 2017 | doi: 10.1038/ncomms15113

Direct comparison of distinct naive pluripotent states in human embryonic stem cells OPEN
S. Warrier, M. Van der Jeught, G. Duggal, L. Tilleman, E. Sutherland, J. Taelman, M. Popovic, S. Lierman, S. Chuva De Sousa Lopes, A. Van Soom, L. Peelman, F. Van Nieuwerburgh, D. I. M. De Coninck, B. Menten, P. Mestdagh, J. Van de Sompele, D. Deforce, P. De Sutter and B. Heindryckx
Human embryonic stem cells (hESCs) in culture display a state of primed pluripotency, but recent protocols have been developed that enable hESCs to adopt a naive-like pluripotent state. Here the authors perform a side-by-side comparison of methods used to culture naive hESCs and confirm the role of PI3K/AKT/mTORC signalling in facilitating the induction of naive pluripotency.
21 April 2017 | doi: 10.1038/ncomms15055

PIF1 family DNA helicases suppress R-loop mediated genome instability at tRNA genes OPEN
Phong Lan Thao Tran, Thomas J. Pohl, Chi-Fu Chen, Angela Chan, Sebastian Pott and Virginia A. Zakian
The budding yeast genome encodes two Pif1 family helicases, Pif1 and Rrm3, previously shown to have distinct functions in the maintenance of telomeres and other aspects of genome stability. Here the authors identify a role for Pif1 (and Rrm3) in promoting DNA replication and suppressing R-loop mediated DNA damage at tRNA genes.
21 April 2017 | doi: 10.1038/ncomms15025

Single-photon test of hyper-complex quantum theories using a metamaterial OPEN
Lorenzo M. Procopio, Lee A. Rozema, Zi Jing Wong, Deny R. Hamel, Kevin O’Brien, Xiang Zhang, Borivoje Dakić and Philip Walther
Hyper-complex quantum theories are generalizations of quantum mechanics where amplitudes are generalized complex numbers. Here the authors study phase commutation in a photonic experiment, reporting consistency with standard quantum mechanics and placing precise bounds on hyper-complex theories.
21 April 2017 | doi: 10.1038/ncomms15044

A mouse tissue transcription factor atlas OPEN
Quan Zhou, Mingwei Liu, Xia Xia, Tongqing Gong, Jinwen Feng, Wanlin Liu, Yang Liu, Bei Zhen, Yi Wang, Chen Ding and Jun Qin
While we have abundant data for transcription factor (TF) binding sites and TF expression at the mRNA level, our knowledge of TFs at the protein level and their DNA-binding activities is sparser. Here, the authors address this by using the catTFRE approach to profile active TFs in 24 adult and 8 fetal mouse tissues, and presenting the TF networks in major mouse organs.
21 April 2017 | doi: 10.1038/ncomms15089

Bone-in-culture array as a platform to model early-stage bone metastases and discover anti-metastasis therapies OPEN
Hai Wang, Lin Tian, Amit Goldstein, Jun Liu, Hin-Ching Lo, Kuanwei Sheng, Thomas Welte, Stephen T.C. Wong, Zbigniew Gugala, Fabio Stossi, Chenghang Zong, Zonghai Li, Michael A. Mancini and Xiang H.-F. Zhang
The bone microenvironment may alter therapeutic responses of disseminated breast cancer cells. Here the authors establish an ex vivo bone metastasis model, termed BICA, to delineate the effects of bone microenvironment and to rapidly discover anti-metastasis drugs.
21 April 2017 | doi: 10.1038/ncomms15045

Global distribution of particle phase state in atmospheric secondary organic aerosols OPEN
Manabu Shiraiwa, Ying Li, Alexandra P. Tsimpidi, Vlassis A. Karydis, Thomas Berkemeier, Spyros N. Pandis, Jos Lelieveld, Thomas Koop and Ulrich Pöschl
Secondary organic aerosols (SOA) are important for climate and aerosol quality, but the phase state is unclear. Here, the authors show that SOA is liquid in tropical and polar air, semi-solid in the mid-latitudes, solid over dry lands and in a glassy solid phase state in the middle and upper troposphere.
21 April 2017 | doi: 10.1038/ncomms15002

Exploratory adaptation in large random networks OPEN
Hallel I. Schreier, Yoav Soen and Naama Brenner
Recent works suggest that cellular networks may respond to novel challenges on the time-scale of cellular lifetimes through large-scale perturbation of gene expression and convergence to a new state. Here, the authors demonstrate the theoretical feasibility of exploratory adaptation in cellular networks by showing that convergence to new states depends on known features of these networks.
21 April 2017 | doi: 10.1038/ncomms14826

Life cycle assessment needs predictive spatial modelling for biodiversity and ecosystem services OPEN
Rebecca Chaplin-Kramer, Sarah Sim, Perrine Hamel, Benjamin Bryant, Ryan Noe, Carina Mueller, Giles Rigarlsford, Michal Kulak, Virginia Kowal, Richard Sharp, Julie Clavreul, Edward Price, Stephen Polasky, Mary Ruckelshaus and Gretchen Daily
Life cycle assessments are used by corporations to determine the sustainability of raw source materials. Here, Chaplin-Kramer et al. develop an improved life cycle assessment approach incorporating spatial variation in land-use change, and apply this framework to a bioplastic case study.
21 April 2017 | doi: 10.1038/ncomms15065

Fine structure of the topological defect cores studied for disclinations in lyotropic chromonic liquid crystals OPEN
Shuang Zhou, Sergij V. Shiyanovskii, Heung-Shik Park and Oleg D. Lavrentovich
Topological defects play important roles in determining material properties, whilst their core regions remain unexplored due to strongly distorted structures. Zhou et al. take advantage of extended core regions in a chromonic liquid crystal and show both a radial and azimuthal dependent director and scalar order parameter.
21 April 2017 | doi: 10.1038/ncomms14974

The glutamate/cystine xCT antiporter antagonizes glutamine metabolism and reduces nutrient flexibility OPEN
Chun-Shik Shin, Prashant Mishra, Jeramie D. Watrous, Valerio Carelli, Marilena D’Aurelio, Mohit Jain and David C. Chan
The factors that limit the nutrient flexibility of cells remain largely unknown. Here, the authors identify the glutamate/cysteine antiporter xCT in a genetic screen for glucose dependency and show it determines the ability of cells to survive under conditions of low glucose by limiting the utilization of glutamine.
21 April 2017 | doi: 10.1038/ncomms15074

The human amygdala parametrically encodes the intensity of specific facial emotions and their categorical ambiguity OPEN
Shuo Wang, Rongjun Yu, J. Michael Tyszka, Shanshan Zhen, Christopher Kovach, Sai Sun, Yi Huang, Rene Hurlemann, Ian B. Ross, Jeffrey M. Chung, Adam N. Mamelak, Ralph Adolphs and Ueli Rutishauser
The amygdala processes emotional facial expressions, but its exact contributions are unclear. Wang. et al. use behavioural analysis of amygdala lesion patients, fMRI, and single-neuron recordings to show that both emotional intensity and ambiguity signals are processed in the human amygdala.
21 April 2017 | doi: 10.1038/ncomms14821

Noumeavirus replication relies on a transient remote control of the host nucleus OPEN
Elisabeth Fabre, Sandra Jeudy, Sébastien Santini, Matthieu Legendre, Mathieu Trauchessec, Yohann Couté, Jean-Michel Claverie and Chantal Abergel
Large dsDNA viruses either replicate in or disrupt the nucleus to gain access to host RNA polymerases, or they rely on virus-encoded, packaged RNA polymerases. Here, the authors show that Noumeavirus replicates in the cytoplasm and relies on a transient recruitment of nuclear proteins to initiate replication.
21 April 2017 | doi: 10.1038/ncomms15087

Gating of TonB-dependent transporters by substrate-specific forced remodelling OPEN
Samuel J. Hickman, Rachael E. M. Cooper, Luca Bellucci, Emanuele Paci and David J. Brockwell
Bacterial outer membrane TonB-dependent transporters (TBDTs) mediate the influx of several nutrients. Here the authors use single-molecule force spectroscopy to show that the interaction between TonB and Escherichia coli TBDT BtuB is mechanically resistant to the pulling that gates the BtuB channel.
21 April 2017 | doi: 10.1038/ncomms14804

A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue OPEN
Flaminia Talos, Antonina Mitrofanova, Sarah K. Bergren, Andrea Califano and Michael M. Shen
The identification of master regulator genes that may be manipulated in vitro to regulate reprogramming has been difficult. Here, the authors use a computational systems approach to identify three genes (FoxA1, Nkx3.1 and the androgen receptor) that can reprogramme fibroblasts to prostate tissue.
21 April 2017 | doi: 10.1038/ncomms14662

T follicular helper and T follicular regulatory cells have different TCR specificity OPEN
Ana Raquel Maceiras, Silvia Cristina Paiva Almeida, Encarnita Mariotti-Ferrandiz, Wahiba Chaara, Fadi Jebbawi, Adrien Six, Shohei Hori, David Klatzmann, Jose Faro and Luis Graca
T follicular helper and regulatory cells are generated in the germinal centre; however, whether antigen specificity defines their differential functions is unclear. Here the authors show that T cells with distinct antigen specificity spectra are recruited to the germinal centre to establish these two populations.
21 April 2017 | doi: 10.1038/ncomms15067

Transiently antigen-primed B cells return to naive-like state in absence of T-cell help OPEN
Jackson S. Turner, Matangi Marthi, Zachary L. Benet and Irina Grigorova
B-cell encounter with antigen is thought to result in anergy, cell death, or a productive B-cell response. Here the authors show that transient antigen acquisition can enable B-cell recruitment into productive responses or a return to a naive-like state, depending on availability of T-cell help.
21 April 2017 | doi: 10.1038/ncomms15072

Bi1Te1 is a dual topological insulator OPEN
Markus Eschbach, Martin Lanius, Chengwang Niu, Ewa Młyńczak, Pika Gospodarič, Jens Kellner, Peter Schüffelgen, Mathias Gehlmann, Sven Döring, Elmar Neumann, Martina Luysberg, Gregor Mussler, Lukasz Plucinski, Markus Morgenstern, Detlev Grützmacher, Gustav Bihlmayer, Stefan Blügel and Claus M. Schneider
Coexistence of a topological insulator phase and a topological crystalline insulator phase helps to maintain topological properties under a controlled symmetry breaking perturbation. Here, Eschback et al. report a superlattice of Bi and Bi2Te3 to be such a dual topological insulator.
21 April 2017 | doi: 10.1038/ncomms14976

Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations OPEN
David Brown, Dominiek Smeets, Borbála Székely, Denis Larsimont, A. Marcell Szász, Pierre-Yves Adnet, Françoise Rothé, Ghizlane Rouas, Zsófia I. Nagy, Zsófia Faragó, Anna-Mária Tőkés, Magdolna Dank, Gyöngyvér Szentmártoni, Nóra Udvarhelyi, Gabriele Zoppoli, Lajos Pusztai, Martine Piccart, Janina Kulka, Diether Lambrechts, Christos Sotiriou et al.
Tumour heterogeneity is well-known; however, studies analysing the progression from primary to metastatic disease are still limited. Here, the authors used phylogenetic analyses and found that for some patients there are multiple seeding events from the primary tumour accompanied by cross-seeding between metastases.
20 April 2017 | doi: 10.1038/ncomms14944

Lamin B1 is required for mature neuron-specific gene expression during olfactory sensory neuron differentiation OPEN
Crystal M. Gigante, Michele Dibattista, Frederick N. Dong, Xiaobin Zheng, Sibiao Yue, Stephen G. Young, Johannes Reisert, Yixian Zheng and Haiqing Zhao
Emerging evidence suggests that lamins regulate gene expression during cellular differentiation. Gigante et al. show that lamin B1 is necessary for the upregulation of mature neuron-specific genes during olfactory neuron differentiation, and its deficiency leads to attenuated olfactory neuron response to odour in mice.
20 April 2017 | doi: 10.1038/ncomms15098

Role of chiral quantum Hall edge states in nuclear spin polarization OPEN
Kaifeng Yang, Katsumi Nagase, Yoshiro Hirayama, Tetsuya D. Mishima, Michael B. Santos and Hongwu Liu
Quantum Hall phases in two-dimensional systems have chiral edges, along which electrons propagate in one direction without backscattering. Here, the authors use nuclear magnetic resonance to demonstrate how chiral modes establish dynamical nuclear polarization in a quantum Hall ferromagnet.
20 April 2017 | doi: 10.1038/ncomms15084

Activation of the hypothalamic feeding centre upon visual prey detection OPEN
Akira Muto, Pradeep Lal, Deepak Ailani, Gembu Abe, Mari Itoh and Koichi Kawakami
Hypothalamus is important for regulating feeding behaviour. Here the authors report genetic identification of neurons in the pretecto-hypothalamic circuit, and their causal involvement in prey detection and prey capture, using a combination of functional imaging and ablation studies in freely swimming zebrafish larvae.
20 April 2017 | doi: 10.1038/ncomms15029

FRET biosensor uncovers cAMP nano-domains at β-adrenergic targets that dictate precise tuning of cardiac contractility OPEN
Nicoletta C. Surdo, Marco Berrera, Andreas Koschinski, Marcella Brescia, Matias R. Machado, Carolyn Carr, Peter Wright, Julia Gorelik, Stefano Morotti, Eleonora Grandi, Donald M. Bers, Sergio Pantano and Manuela Zaccolo
cAMP/PKA signalling plays important roles in physiology, but there are a lack of tools to spatially distinguish cAMP. Here the authors present a FRET-based cAMP biosensor they call CUTie that can directly compare cAMP signals at multiple subcellular sites and detect nanoscale heterogeneity in cAMP in cardiac myocytes.
20 April 2017 | doi: 10.1038/ncomms15031

Metabolic labelling of the carbohydrate core in bacterial peptidoglycan and its applications OPEN
Hai Liang, Kristen E. DeMeester, Ching-Wen Hou, Michelle A. Parent, Jeffrey L. Caplan and Catherine L. Grimes
N-acetyl-muramic acid (NAM) is a core component of the bacterial peptidoglycan (PG) cell wall, and is recognised by the innate immune system. Here the authors engineer Gram-negative and Gram-positive bacteria to incorporate a modified NAM into the backbone of PG, which can be labelled with click chemistry for imaging and tracking.
20 April 2017 | doi: 10.1038/ncomms15015

A genome-wide association study identifies six novel risk loci for primary biliary cholangitis OPEN
Fang Qiu, Ruqi Tang, Xianbo Zuo, Xingjuan Shi, Yiran Wei, Xiaodong Zheng, Yaping Dai, Yuhua Gong, Lan Wang, Ping Xu, Xiang Zhu, Jian Wu, Chongxu Han, Yueqiu Gao, Kui Zhang, Yuzhang Jiang, Jianbo Zhou, Youlin Shao, Zhigang Hu, Ye Tian et al.
Primary biliary cholangitis is an autoimmune liver disease. Here, the authors show that variants in interleukin genes which potentially deregulate their expression are associated with this condition, and suggest that the IL21 signalling pathway may have a role in disease aetiology.
20 April 2017 | doi: 10.1038/ncomms14828

Chytrid fungus infection in zebrafish demonstrates that the pathogen can parasitize non-amphibian vertebrate hosts OPEN
Nicole Liew, Maria J. Mazon Moya, Claudia J. Wierzbicki, Michael Hollinshead, Michael J. Dillon, Christopher R. Thornton, Amy Ellison, Jo Cable, Matthew C. Fisher and Serge Mostowy
New infections of the amphibian chytrid fungus could arise from other animal reservoirs in the environment. Here, Liew et al. demonstrate that zebrafish can be infected by chytrid similarly to amphibians, expanding our understanding of how this pathogen can parasitize its hosts.
20 April 2017 | doi: 10.1038/ncomms15048

Prior context in audition informs binding and shapes simple features OPEN
Claire Chambers, Sahar Akram, Vincent Adam, Claire Pelofi, Maneesh Sahani, Shihab Shamma and Daniel Pressnitzer
Perception can be swayed by prior context. Here the authors report an auditory illusion in which sounds with ambiguous pitch shifts are perceived as shifting upward or downward based on the preceding contextual sounds, explore the neural correlates, and propose a probabilistic model based on temporal binding.
20 April 2017 | doi: 10.1038/ncomms15027

Crystal structures of the NO sensor NsrR reveal how its iron-sulfur cluster modulates DNA binding OPEN
Anne Volbeda, Erin L. Dodd, Claudine Darnault, Jason C. Crack, Oriane Renoux, Matthew I. Hutchings, Nick E. Le Brun and Juan C. Fontecilla-Camps
NsrR is a bacterial transcriptional regulator that acts as a nitric oxide (NO) sensor. Here, the authors present the crystal structure of NsrR, which reveals an unusual Fe-S cluster coordination and explains how NO exposure leads to the degradation of the cluster.
20 April 2017 | doi: 10.1038/ncomms15052

Enhanced superconductivity accompanying a Lifshitz transition in electron-doped FeSe monolayer OPEN
X. Shi, Z-Q Han, X-L Peng, P. Richard, T. Qian, X-X Wu, M-W Qiu, S. C. Wang, J. P. Hu, Y-J Sun and H. Ding
The origin of superconductivity enhancement in FeSe monolayer grown on SrTiO3 compared to bulk FeSe is still a debated issue. Here, Shi et al. report a further 15 K jump of Tc accompanying a second Lifshitz transition triggered by electron doping in FeSe/SrTiO3 monolayer films.
19 April 2017 | doi: 10.1038/ncomms14988

Efficient electrical control of thin-film black phosphorus bandgap OPEN
Bingchen Deng, Vy Tran, Yujun Xie, Hao Jiang, Cheng Li, Qiushi Guo, Xiaomu Wang, He Tian, Steven J. Koester, Han Wang, Judy J. Cha, Qiangfei Xia, Li Yang and Fengnian Xia
Layered black phosphorous has gained significant attention in the 2D materials community, and dynamical control of its bandgap is key to enable novel applications. Here, the authors demonstrate continuous electrical bandgap tuning using moderate displacement fields.
19 April 2017 | doi: 10.1038/ncomms14474

Adrenergic-mediated loss of splenic marginal zone B cells contributes to infection susceptibility after stroke OPEN
Laura McCulloch, Craig J. Smith and Barry W. McColl
Risk of infection is high after stroke, but the causes are not clear. Here the authors implicate altered beta–adrenergic signalling after stroke that results in a reduction in IgM-mediated protection by marginal zone B cells.
19 April 2017 | doi: 10.1038/ncomms15051

Hierarchical assembly of centriole subdistal appendages via centrosome binding proteins CCDC120 and CCDC68 OPEN
Ning Huang, Yuqing Xia, Donghui Zhang, Song Wang, Yitian Bao, Runsheng He, Junlin Teng and Jianguo Chen
Centriole subdistal appendages (SDAs) anchor microtubules in interphase cells, but their composition and assembly mechanisms are unclear. Here the authors show that two new SDA components, CCDC120 and CCDC68, are required for hierarchical SDA assembly and centrosome microtubule anchoring.
19 April 2017 | doi: 10.1038/ncomms15057

Electron transport and visible light absorption in a plasmonic photocatalyst based on strontium niobate OPEN
D. Y. Wan, Y. L. Zhao, Y. Cai, T. C. Asmara, Z. Huang, J. Q. Chen, J. Hong, S. M. Yin, C. T. Nelson, M. R. Motapothula, B. X. Yan, D. Xiang, X. Chi, H. Zheng, W. Chen, R. Xu,   Ariando, A. Rusydi, A. M. Minor, M. B. H. Breese et al.
Metallic oxide SrNbO3 has been identified as an efficient hydrogen evolution photocatalyst. Here, Venkatesan and co-workers show that its visible light absorption stems from plasmon resonance, thanks to its large carrier density (despite a large 4.1 eV bandgap), as opposed to from an interband transition.
19 April 2017 | doi: 10.1038/ncomms15070

Thermogenic adipocytes promote HDL turnover and reverse cholesterol transport OPEN
Alexander Bartelt, Clara John, Nicola Schaltenberg, Jimmy F. P. Berbée, Anna Worthmann, M. Lisa Cherradi, Christian Schlein, Julia Piepenburg, Mariëtte R. Boon, Franz Rinninger, Markus Heine, Klaus Toedter, Andreas Niemeier, Stefan K. Nilsson, Markus Fischer, Sander L. Wijers, Wouter van Marken Lichtenbelt, Ludger Scheja, Patrick C. N. Rensen and Joerg Heeren et al.
Activation of brown adipose tissue (BAT) reduces the development of atherosclerosis in animal models. Here the authors show that BAT activation also increases reverse cholesterol transport and turnover of high-density lipoprotein, which likely contributes to the anti-atherosclerotic effect of BAT activation.
19 April 2017 | doi: 10.1038/ncomms15010
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  Latest Corrigenda  
Corrigendum: Pharmacological inhibition of adipose triglyceride lipase corrects high-fat diet-induced insulin resistance and hepatosteatosis in mice OPEN
Martina Schweiger, Matthias Romauch, Renate Schreiber, Gernot F Grabner, Sabrina Hütter, Petra Kotzbeck, Pia Benedikt, Thomas O Eichmann, Sohsuke Yamada, Oskar Knittelfelder, Clemens Diwoky, Carina Doler, Nicole Mayer, Werner De Cecco, Rolf Breinbauer, Robert Zimmermann and Rudolf Zechner
25 April 2017 | doi: 10.1038/ncomms15490

Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts OPEN
Kuan-lin Huang, Shunqiang Li, Philipp Mertins, Song Cao, Harsha P. Gunawardena, Kelly V. Ruggles, D. R. Mani, Karl R. Clauser, Maki Tanioka, Jerry Usary, Shyam M. Kavuri, Ling Xie, Christopher Yoon, Jana W. Qiao, John Wrobel, Matthew A. Wyczalkowski, Petra Erdmann-Gilmore, Jacqueline E. Snider, Jeremy Hoog, Purba Singh et al.
25 April 2017 | doi: 10.1038/ncomms15479

Corrigendum: MHC-dependent inhibition of uterine NK cells impedes fetal growth and decidual vascular remodeling OPEN
Jens Kieckbusch, Louise M. Gaynor, Ashley Moffett and Francesco Colucci
20 April 2017 | doi: 10.1038/ncomms15444
Biological Sciences  Immunology 

Corrigendum: Coherent creation and destruction of orbital wavepackets in Si:P with electrical and optical read-out OPEN
K. L. Litvinenko, E. T. Bowyer, P. T. Greenland, N. Stavrias, Juerong Li, R. Gwilliam, B. J. Villis, G. Matmon, M. L. Y. Pang, B. Redlich, A. F. G. van der Meer, C. R. Pidgeon, G. Aeppli and B. N. Murdin
20 April 2017 | doi: 10.1038/ncomms15445
Physical Sciences  Atomic and molecular physics  Nanotechnology  Optical physics 
  Latest Errata  
Erratum: CD40-signalling abrogates induction of RORγt+ Treg cells by intestinal CD103+ DCs and causes fatal colitis OPEN
Christian Barthels, Ana Ogrinc, Verena Steyer, Stefanie Meier, Ferdinand Simon, Maria Wimmer, Andreas Blutke, Tobias Straub, Ursula Zimber-Strobl, Esther Lutgens, Peggy Marconi, Caspar Ohnmacht, Debora Garzetti, Bärbel Stecher and Thomas Brocker
24 April 2017 | doi: 10.1038/ncomms15439

Erratum: Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise OPEN
Maria Theresia Pöschko, Victor V. Rodin, Judith Schlagnitweit, Norbert Müller and Hervé Desvaux
19 April 2017 | doi: 10.1038/ncomms15379

Focus on Disease models: reproducibility and translation 

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