Wednesday, March 15, 2017

Nature Communications - 15 March 2017

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This year's Frontiers in Biology Insight features Reviews on how genomics is helping to uncover the peopling of the world, the interplay between morphogens and morphogenesis in determining organismal shape, the factors that influence the immune response to cancer, advances in single-cell genomics, and the effects of base modifications in messenger RNA.
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Real-time divergent evolution in plants driven by pollinators OPEN
Daniel D. L. Gervasi and Florian P Schiestl
Pollinators are thought to be a driver of plant diversification, but their effects are difficult to disentangle from those of other biotic and abiotic factors. Here, the authors let plants evolve under different pollination regimes and show rapid and divergent evolution of plant height, floral traits and mating system.
14 March 2017 | doi: 10.1038/ncomms14691

Nrl knockdown by AAV-delivered CRISPR/Cas9 prevents retinal degeneration in mice OPEN
Wenhan Yu, Suddhasil Mookherjee, Vijender Chaitankar, Suja Hiriyanna, Jung-Woong Kim, Matthew Brooks, Yasaman Ataeijannati, Xun Sun, Lijin Dong, Tiansen Li, Anand Swaroop and Zhijian Wu
Retinitis pigmentosa is mainly caused by mutations that initially affect survival of rod photoreceptors, leading to secondary loss of cones. Here the authors use gene editing to prevent rod degeneration, leading to survival of cones and improved vision in mice.
14 March 2017 | doi: 10.1038/ncomms14716

Vulnerability of Louisiana’s coastal wetlands to present-day rates of relative sea-level rise OPEN
Krista L. Jankowski, Torbjörn E Törnqvist and Anjali M Fernandes
Coastal Louisiana wetlands face some of the world’s highest rates of relative sea-level rise and loss. Here, the authors show that there is a strong regional component to coastal Louisiana wetland vulnerability to relative sea-level rise as well as contributing to the understanding of subsidence in the region.
14 March 2017 | doi: 10.1038/ncomms14792

Suppressive IL-17A+Foxp3+ and ex-Th17 IL-17AnegFoxp3+ Treg cells are a source of tumour-associated Treg cells OPEN
Stephanie Downs-Canner, Sara Berkey, Greg M. Delgoffe, Robert P. Edwards, Tyler Curiel, Kunle Odunsi, David L. Bartlett and Nataša Obermajer
Th17 cells can transdifferentiate into regulatory T (Treg) cells. Here the authors characterize tumour-driven Th17-to-Treg cell transdifferentiation and identify potential cancer therapy targets.
14 March 2017 | doi: 10.1038/ncomms14649

Palladium-catalysed synthesis of triaryl(heteroaryl)methanes OPEN
Shuguang Zhang, Byeong-Seon Kim, Chen Wu, Jianyou Mao and Patrick J. Walsh
Molecules with 4 aryl groups attached to a central carbon atom have proven challenging to synthesize despite their attractiveness for a variety of applications. Here the authors report a Pd-catalysed arylation of di- and triarylmethanes, giving a high-yielding route to an array of tetraarylmethanes.
14 March 2017 | doi: 10.1038/ncomms14641

Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9 OPEN
Peiwu Qin, Mahmut Parlak, Cem Kuscu, Jigar Bandaria, Mustafa Mir, Karol Szlachta, Ritambhara Singh, Xavier Darzacq, Ahmet Yildiz and Mazhar Adli
CRISPR-Cas9 has been used to image repetitive loci in live cells to explore genome organization. Here the authors demonstrate the imaging of low-repeat regions with a single-guide RNA and the imaging of a non-repetitive region, allowing the tracking of transcriptionally active and inactive regions.
14 March 2017 | doi: 10.1038/ncomms14725

Single-cell tracking of flavivirus RNA uncovers species-specific interactions with the immune system dictating disease outcome OPEN
Florian Douam, Gabriela Hrebikova, Yentli E. Soto Albrecht, Julie Sellau, Yael Sharon, Qiang Ding and Alexander Ploss
Analysis of virus replication on a single-cell level is often hampered by a lack of specific or sensitive enough reagents. Here, Douam et al. use RNA-flow technique to track (+) and (−) strand RNA of yellow fever virus in hematopoietic cells in mouse models and identify virus-host interactions that affect disease outcome.
14 March 2017 | doi: 10.1038/ncomms14781

An immortalized adult human erythroid line facilitates sustainable and scalable generation of functional red cells OPEN
Kongtana Trakarnsanga, Rebecca E. Griffiths, Marieangela C. Wilson, Allison Blair, Timothy J. Satchwell, Marjolein Meinders, Nicola Cogan, Sabine Kupzig, Ryo Kurita, Yukio Nakamura, Ashley M. Toye, David J. Anstee and Jan Frayne
The generation of a sustainable supply of erythroid progenitors is essential for the reliable production of an in vitro derived red blood cell clinical product. Here the authors immortalize early human erythroblasts to generate the first cell line capable of differentiation into functional adult reticulocytes.
14 March 2017 | doi: 10.1038/ncomms14750

A general derivation and quantification of the third law of thermodynamics OPEN
Lluís Masanes and Jonathan Oppenheim
The third law of thermodynamics, first formulated in 1912, states that any process cannot reach absolute zero temperature in finite time. Here, the authors derive the third law in the quantum regime as a bound on the resources necessary to cool a system to any temperature.
14 March 2017 | doi: 10.1038/ncomms14538

Inhibition of hepatic lipogenesis enhances liver tumorigenesis by increasing antioxidant defence and promoting cell survival OPEN
Marin E. Nelson, Sujoy Lahiri, Jenny D. Y. Chow, Frances L. Byrne, Stefan R. Hargett, David S. Breen, Ellen M. Olzomer, Lindsay E. Wu, Gregory J. Cooney, Nigel Turner, David E. James, Jill K. Slack-Davis, Carolin Lackner, Stephen H. Caldwell and Kyle L. Hoehn
The lipogenic pathway is often upregulated in liver tumours and regarded as a therapeutic target. Here, the authors show instead that blocking lipogenesis via knockout of acetyl-CoA carboxylase genes results in increased susceptibility to liver tumorigenesis associated with an increased antioxidant defence.
14 March 2017 | doi: 10.1038/ncomms14689

Rare earth separations by selective borate crystallization OPEN
Xuemiao Yin, Yaxing Wang, Xiaojing Bai, Yumin Wang, Lanhua Chen, Chengliang Xiao, Juan Diwu, Shiyu Du, Zhifang Chai, Thomas E. Albrecht-Schmitt and Shuao Wang
Trivalent lanthanides possess similar chemical properties, making their separation from one another challenging. Here, Wang and colleagues demonstrate that their subtle chemical differences can be greatly amplified during borate crystallization, leading to a low cost and highly efficient separation strategy.
14 March 2017 | doi: 10.1038/ncomms14438

Photothermally triggered actuation of hybrid materials as a new platform for in vitro cell manipulation OPEN
Amy Sutton, Tanya Shirman, Jaakko V. I. Timonen, Grant T England, Philseok Kim, Mathias Kolle, Thomas Ferrante, Lauren D Zarzar, Elizabeth Strong and Joanna Aizenberg
Mechanical forces within the cell’s environment play a crucial role in their growth, differentiation and behaviour. Here, the authors develop a photothermal responsive cell culture substrate for the assessment of how cell growth can be affected by manipulating the strain profile of the substrate.
13 March 2017 | doi: 10.1038/ncomms14700

Temporal controls on silicic acid utilisation along the West Antarctic Peninsula OPEN
George E. A. Swann, Jennifer Pike, Melanie J. Leng, Hilary J. Sloane and Andrea M. Snelling
Sea-ice plays a key role in regulating nutrient dynamics and primary productivity along the Antarctica Peninsula margin. Here, the authors show that over the last 13 kyr nutrient dynamics have also been regulated by glacial discharge, highlighting the potential for future changes as glaciers continue to melt.
13 March 2017 | doi: 10.1038/ncomms14645

Identification of common non-coding variants at 1p22 that are functional for non-syndromic orofacial clefting OPEN
Huan Liu, Elizabeth J. Leslie, Jenna C. Carlson, Terri H. Beaty, Mary L. Marazita, Andrew C. Lidral and Robert A. Cornell
Many genetic variants have been associated with complex congenital disorders, but their function is not always clear. Here, the authors develop a pipeline to functionally characterize such variants, and show potential roles for three SNPs in non-syndromic cleft lip and palate.
13 March 2017 | doi: 10.1038/ncomms14759

Barcode extension for analysis and reconstruction of structures OPEN
Cameron Myhrvold, Michael Baym, Nikita Hanikel, Luvena L Ong, Jonathan S Gootenberg and Peng Yin
Techniques for structural characterization and quantification of DNA origami are still poorly developed, despite advances in other aspects of DNA nanotechnology. Here, the authors combine barcoding and next generation sequencing to simultaneously image and quantify self-assembled DNA nanostructures.
13 March 2017 | doi: 10.1038/ncomms14698

Controllable conversion of quasi-freestanding polymer chains to graphene nanoribbons OPEN
Chuanxu Ma, Zhongcan Xiao, Honghai Zhang, Liangbo Liang, Jingsong Huang, Wenchang Lu, Bobby G. Sumpter, Kunlun Hong, J. Bernholc and An-Ping Li
A key step in the on-surface synthesis of graphene nanoribbons is thermal annealing of polymer precursors on a metal substrate. Here, Ma et al. decouple the cyclodehydrogenation reaction from the catalytic metal substrate and grow graphene nanoribbons by injecting charges at molecular sites.
13 March 2017 | doi: 10.1038/ncomms14815

Self-amplified Amazon forest loss due to vegetation-atmosphere feedbacks OPEN
Delphine Clara Zemp, Carl-Friedrich Schleussner, Henrique M. J. Barbosa, Marina Hirota, Vincent Montade, Gilvan Sampaio, Arie Staal, Lan Wang-Erlandsson and Anja Rammig
Relatively little is understood about seasonal effect of climate change on the Amazon rainforest. Here, the authors show that Amazon forest loss in response to dry-season intensification during the last glacial period was likely self-amplified by regional vegetation-rainfall feedbacks.
13 March 2017 | doi: 10.1038/ncomms14681

Double-stranded RNA virus outer shell assembly by bona fide domain-swapping OPEN
Zhaoyang Sun, Kamel El Omari, Xiaoyu Sun, Serban L. Ilca, Abhay Kotecha, David I. Stuart, Minna M. Poranen and Juha T. Huiskonen
Double-shelled bacteriophage φ6 is a well-studied model system used to understand assembly of dsRNA viruses. Here the authors report a near-atomic resolution cryo-EM structure of φ6 and propose a model for the structural transitions occurring in the outer shell during genome packaging.
13 March 2017 | doi: 10.1038/ncomms14814

Pre-plaque conformational changes in Alzheimer’s disease-linked Aβ and APP OPEN
O. Klementieva, K. Willén, I. Martinsson, B. Israelsson, A. Engdahl, J. Cladera, P. Uvdal and G. K. Gouras
Studying the physiological confirmation of amyloid β (Aβ) and amyloid precursor protein (APP) often uses techniques that could disrupt their conformation. Here, the authors use non-destructive microscopy approaches to study the confirmation of Aβ and APP in mouse models of Alzheimer’s disease.
13 March 2017 | doi: 10.1038/ncomms14726

Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria OPEN
Masahiro Kanno, Austin L. Carroll and Shota Atsumi
Cyanobacteria are promising biofactories to reduce atmospheric CO2 and convert it into chemicals. Here the authors engineer Synechococcus elongatus carbon metabolism to increase 2,3-butanediol production from glucose and CO2 under light and dark conditions.
13 March 2017 | doi: 10.1038/ncomms14724

Sfrp5 identifies murine cardiac progenitors for all myocardial structures except for the right ventricle OPEN
Masayuki Fujii, Akane Sakaguchi, Ryo Kamata, Masataka Nagao, Yutaka Kikuchi, Silvia M. Evans, Masao Yoshizumi, Akihiko Shimono, Yumiko Saga and Hiroki Kokubo
It is unclear which progenitors define different regions of the heart. Here, the authors find Secreted frizzled-related protein 5 is expressed in murine progenitor cells for the outflow tract, first heart field, and sinus venosus, but not the right ventricle, and Wnt inhibition prevents progenitor proliferation.
13 March 2017 | doi: 10.1038/ncomms14664

E3 ligase FBXW7 is critical for RIG-I stabilization during antiviral responses OPEN
Yinjing Song, Lihua Lai, Zhenlu Chong, Jia He, Yuanyuan Zhang, Yue Xue, Yiwei Xie, Songchang Chen, Ping Dong, Luoquan Chen, Zhimin Chen, Feng Dai, Xiaopeng Wan, Peng Xiao, Xuetao Cao, Yang Liu and Qingqing Wang
The innate immune response to many RNA viruses depends on recognition of viral RNA by RIG-I. Here the authors show that, upon virus infection, FBXW7 interacts with RIG-I and inhibits ubiquitin-mediated degradation of RIG-I, resulting in increased interferon signalling in vitro and in vivo.
13 March 2017 | doi: 10.1038/ncomms14654

Dynamic transcriptomes identify biogenic amines and insect-like hormonal regulation for mediating reproduction in Schistosoma japonicum OPEN
Jipeng Wang, Ying Yu, Haimo Shen, Tao Qing, Yuanting Zheng, Qing Li, Xiaojin Mo, Shuqi Wang, Nana Li, Riyi Chai, Bin Xu, Mu Liu, Paul J Brindley, Donald P McManus, Zheng Feng, Leming Shi and Wei Hu
For reproduction, the human parasite Schistosoma japonicum relies on a complex and incompletely understood interplay between female and male schistosomes. Here the authors sequence the transcriptome of female and male schistosomes across eight time points during sexual development.
13 March 2017 | doi: 10.1038/ncomms14693

Quantum correlation enhanced super-resolution localization microscopy enabled by a fibre bundle camera OPEN
Yonatan Israel, Ron Tenne, Dan Oron and Yaron Silberberg
Classical physics enabled subdiffraction-limited imaging has rarely been extended to the quantum regime. Here, Israel et al. develop a super-resolution localization microscopy based on non-classical photon statistics, enabling optical tracking of multiple quantum emitters.
13 March 2017 | doi: 10.1038/ncomms14786

Brigatinib combined with anti-EGFR antibody overcomes osimertinib resistance in EGFR-mutated non-small-cell lung cancer OPEN
Ken Uchibori, Naohiko Inase, Mitsugu Araki, Mayumi Kamada, Shigeo Sato, Yasushi Okuno, Naoya Fujita and Ryohei Katayama
Resistance to EGFR-tyrosine kinase inhibitors in non-small-cell lung cancer is mediated by the C797S/T790M/activating mutation. Here, the authors identify brigatinib as a potential drug that in combination with anti-EGFR can overcome resistance in mutated cells.
13 March 2017 | doi: 10.1038/ncomms14768

Structure and assembly of scalable porous protein cages OPEN
Eita Sasaki, Daniel Böhringer, Michiel van de Waterbeemd, Marc Leibundgut, Reinhard Zschoche, Albert J. R. Heck, Nenad Ban and Donald Hilvert
Self-assembling proteins that form capsid-like structures act as molecular containers for diverse cargoes. Here, the authors solve the cryo-EM structures of lumazine synthase shells, and show that supercharged mutants form expanded assemblies, indicating that electrostatics can be exploited to engineer cage architecture.
10 March 2017 | doi: 10.1038/ncomms14663

Engineering fungal de novo fatty acid synthesis for short chain fatty acid production OPEN
Jan Gajewski, Renata Pavlovic, Manuel Fischer, Eckhard Boles and Martin Grininger
The production of short chain fatty acids by microorganisms has numerous industrial and biofuel applications. Here the authors reprogramme S. cerevisiae fatty acid synthase with five mutations to produce C6- and C8-fatty acids and identify thioesterases responsible for hydrolysis of short chain acyl-CoA hydrolysis.
10 March 2017 | doi: 10.1038/ncomms14650

EGFR/ARF6 regulation of Hh signalling stimulates oncogenic Ras tumour overgrowth OPEN
Chiswili Chabu, Da-Ming Li and Tian Xu
EGFR signalling is required for oncogenic Ras driven tumorigenesis. In this study, using a Drosophila tumour model the authors demonstrate that depletion of Arf6, a Ras-related GTP-binding protein activated by EGFR, supresses oncogenic Ras driven overgrowth via modulation of Hedgehog signalling.
10 March 2017 | doi: 10.1038/ncomms14688

Observation of stable Néel skyrmions in cobalt/palladium multilayers with Lorentz transmission electron microscopy OPEN
Shawn D. Pollard, Joseph A. Garlow, Jiawei Yu, Zhen Wang, Yimei Zhu and Hyunsoo Yang
Néel skyrmions are spin textures with a magnetization that rotates from in- to out-of-plane with distance from its centre. Here, the authors show that Lorentz transmission electron microscopy can be used to directly image Néel skyrmions with high resolution in thick exchange-coupled magnetic multilayers.
10 March 2017 | doi: 10.1038/ncomms14761

Structural basis of homo- and heterotrimerization of collagen I OPEN
Urvashi Sharma, Loïc Carrique, Sandrine Vadon-Le Goff, Natacha Mariano, Rainier-Numa Georges, Frederic Delolme, Peppi Koivunen, Johanna Myllyharju, Catherine Moali, Nushin Aghajari and David J. S. Hulmes
Heterotrimers of collagen I (two α1 chains, one α2 chain) are crucial for the normal function of multiple tissues and organs. Here the authors show the molecular basis of both homotrimerization (three α1 chains) and heterotrimerization of collagen I through specific intermolecular interactions.
10 March 2017 | doi: 10.1038/ncomms14671

Lnc-mg is a long non-coding RNA that promotes myogenesis OPEN
Mu Zhu, Jiafan Liu, Jia Xiao, Li Yang, Mingxiang Cai, Hongyu Shen, Xiaojia Chen, Yi Ma, Sumin Hu, Zuolin Wang, An Hong, Yingxian Li, Yao Sun and Xiaogang Wang
Long non-coding mRNAs play important roles in muscle development and regeneration. Here the authors identify a long non-coding mRNA that promotes myogenesis by sequestering miR-125b, leading to increased expression of insulin-like growth factor 2.
10 March 2017 | doi: 10.1038/ncomms14718

Stage-specific functions of Semaphorin7A during adult hippocampal neurogenesis rely on distinct receptors OPEN
Bart C. Jongbloets, Suzanne Lemstra, Roberta Schellino, Mark H. Broekhoven, Jyoti Parkash, Anita J. C. G. M. Hellemons, Tianyi Mao, Paolo Giacobini, Henriette van Praag, Silvia De Marchis, Geert M. J. Ramakers and R. Jeroen Pasterkamp
The functions of semaphorins in the adult brain are poorly understood. Here the authors show that Sema7A carries out stage-specific functions in the adult hippocampus via differential receptor usage; in progenitor cells, Sema7A inhibits proliferation via acting on PlexinC1, whereas in adult-born neurons, it promotes dendrite growth through β1-integrins.
10 March 2017 | doi: 10.1038/ncomms14666

Allosteric modulation of peroxisomal membrane protein recognition by farnesylation of the peroxisomal import receptor PEX19 OPEN
Leonidas Emmanouilidis, Ulrike Schütz, Konstantinos Tripsianes, Tobias Madl, Juliane Radke, Robert Rucktäschel, Matthias Wilmanns, Wolfgang Schliebs, Ralf Erdmann and Michael Sattler
PEX19 is a chaperone and import receptor for peroxisomal membrane proteins (PMPs). Here the authors present the structure of the farnesylated C-terminal domain of PEX19, and its interaction with PMPs reveals how the farnesyl moiety allosterically reshapes the PMP binding surface and modulates PEX19 function.
10 March 2017 | doi: 10.1038/ncomms14635

Quantum coherence selective 2D Raman–2D electronic spectroscopy OPEN
Austin P. Spencer, William O. Hutson and Elad Harel
Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally is challenging. Here the authors develop a method called GAMERS that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity.
10 March 2017 | doi: 10.1038/ncomms14732

Templated bilayer self-assembly of fully conjugated π-expanded macrocyclic oligothiophenes complexed with fullerenes OPEN
José D. Cojal González, Masahiko Iyoda and Jürgen P. Rabe
Controlling the self-assembly of oligothiophene complexes that are used in multi-functional thin films can be challenging. Here the authors show a hierarchy of non-covalent interactions for robust self-assembly that orders Saturn-like complexes of fullerenes with oligothiophene macrocycles.
10 March 2017 | doi: 10.1038/ncomms14717

Adipocytes promote malignant growth of breast tumours with monocarboxylate transporter 2 expression via β-hydroxybutyrate OPEN
Chun-Kai Huang, Po-Hao Chang, Wen-Hung Kuo, Chi-Long Chen, Yung-Ming Jeng, King-Jen Chang, Jin-Yuh Shew, Chun-Mei Hu and Wen-Hwa Lee
Invasion of the adipose tissue correlates with poor prognosis in breast cancer. Here, the authors show that mammary gland adipocytes promote malignancy via β-hydroxybutyrate, which acts on cancer cells through the monocarboxylate transporter MCT2 resulting in tumour-promoting epigenetic modifications.
10 March 2017 | doi: 10.1038/ncomms14706

Laser-mediated rupture of chlamydial inclusions triggers pathogen egress and host cell necrosis OPEN
Markus C. Kerr, Guillermo A. Gomez, Charles Ferguson, Maria C. Tanzer, James M. Murphy, Alpha S. Yap, Robert G. Parton, Wilhelmina M. Huston and Rohan D Teasdale
Chlamydiae replicate in host cells within specialised vacuoles (inclusions), which are eventually ruptured to liberate the bacteria, leading to cell lysis. Here, Kerr et al. use a laser ablation technique and videomicroscopy to show that inclusion rupture triggers a necrotic pathway in the host cell.
10 March 2017 | doi: 10.1038/ncomms14729

In vivo gastrointestinal drug-release monitoring through second near-infrared window fluorescent bioimaging with orally delivered microcarriers OPEN
Rui Wang, Lei Zhou, Wenxing Wang, Xiaomin Li and Fan Zhang
The sustained release of drugs within the gastrointestinal tract as well as their detection following administration is a challenge. Here, the authors develop a microcarrier that supported sustained drug release in the gastrointestinal tract in vivo and could be monitored with real-time imaging.
10 March 2017 | doi: 10.1038/ncomms14702

A molecule-like PtAu24(SC6H13)18 nanocluster as an electrocatalyst for hydrogen production OPEN
Kyuju Kwak, Woojun Choi, Qing Tang, Minseok Kim, Yongjin Lee, De-en Jiang and Dongil Lee
Volcano plots for electrocatalytic hydrogen production show the best catalysts as those ensuring the hydrogen binding step is thermodynamically neutral. Here, the authors report fabrication of a highly active thermoneutral electrocatalyst via doping of a single platinum atom into a gold nanocluster.
10 March 2017 | doi: 10.1038/ncomms14723

Theory of optimal balance predicts and explains the amplitude and decay time of synaptic inhibition OPEN
Jaekyung K. Kim and Christopher D. Fiorillo
Inhibition and excitation are counterbalanced at synapses, but the conditions that constitute optimal balance are not known. Here the authors show through modelling that the properties of synaptic inhibition are fine-tuned to maintain an optimal balance in which peak excitation reaches precisely to spike threshold.
10 March 2017 | doi: 10.1038/ncomms14566

The Shc1 adaptor simultaneously balances Stat1 and Stat3 activity to promote breast cancer immune suppression OPEN
Ryuhjin Ahn, Valérie Sabourin, Alicia M. Bolt, Steven Hébert, Stephanie Totten, Nicolas De Jay, Maria Carolina Festa, Yoon Kow Young, Young Kyuen Im, Tony Pawson, Antonis E. Koromilas, William J. Muller, Koren K. Mann, Claudia L. Kleinman and Josie Ursini-Siegel
Tyrosine kinase signalling in cancer cells promotes immune evasion. Here, the authors show that tyrosine kinases engage scaffold protein Shc1 to promote immunosuppression in breast cancer by simultaneously activating STAT3 immunosuppressive signals and impairing STAT1-driven anti-tumour immune responses.
09 March 2017 | doi: 10.1038/ncomms14638

Oriented graphene nanoribbons embedded in hexagonal boron nitride trenches OPEN
Lingxiu Chen, Li He, Hui Shan Wang, Haomin Wang, Shujie Tang, Chunxiao Cong, Hong Xie, Lei Li, Hui Xia, Tianxin Li, Tianru Wu, Daoli Zhang, Lianwen Deng, Ting Yu, Xiaoming Xie and Mianheng Jiang
Graphene nanoribbons are promising candidates for 2D material electrical interconnects; however, the top-down fabrication of nanoribbons has remained a challenge. Here, Chen et al. have used a hexagonal boron nitride template to grow narrow, integrated graphene nanoribbons with small bandgaps.
09 March 2017 | doi: 10.1038/ncomms14703

RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans OPEN
Heehwa G. Son, Mihwa Seo, Seokjin Ham, Wooseon Hwang, Dongyeop Lee, Seon Woo A. An, Murat Artan, Keunhee Seo, Rachel Kaletsky, Rachel N. Arey, Youngjae Ryu, Chang Man Ha, Yoon Ki Kim, Coleen T. Murphy, Tae-Young Roh, Hong Gil Nam and Seung-Jae V. Lee
The decline of DNA and protein quality control contributes to organismal ageing. Here, Son et al. report that nonsense-mediated mRNA decay, a RNA quality control mechanism, is enhanced in long-lived daf-2 mutant worms and contributes to their longevity by regulating expression of the yars-2/tyrosyl tRNA synthetase.
09 March 2017 | doi: 10.1038/ncomms14749

TRIB2 confers resistance to anti-cancer therapy by activating the serine/threonine protein kinase AKT OPEN
Richard Hill, Patricia A. Madureira, Bibiana Ferreira, Inês Baptista, Susana Machado, Laura Colaço, Marta dos Santos, Ningshu Liu, Ana Dopazo, Selma Ugurel, Angyal Adrienn, Endre Kiss-Toth, Murat Isbilen, Ali O. Gure and Wolfgang Link
The emergence of drug resistance is a major obstacle in the treatment of cancer patients. Here, the authors show that TRIB2 expression increases resistance to PI3K inhibition by promoting AKT activation and the subsequent FOXO inactivation and disruption of p53 function.
09 March 2017 | doi: 10.1038/ncomms14687

Optimal adaptive control for quantum metrology with time-dependent Hamiltonians OPEN
Shengshi Pang and Andrew N. Jordan
Quantum metrology investigates the improvement given to precision measurements by exploiting quantum mechanics, but it has been mostly limited to systems with static Hamiltonians. Here the authors study it in the general case of time-varying Hamiltonians, showing that optimizing the quantum Fisher information via quantum control provides an advantage.
09 March 2017 | doi: 10.1038/ncomms14695

An electrically actuated molecular toggle switch OPEN
Lukas Gerhard, Kevin Edelmann, Jan Homberg, Michal Valášek, Safa G. Bahoosh, Maya Lukas, Fabian Pauly, Marcel Mayor and Wulf Wulfhekel
Robust molecular junctions demand highly reproducible switching between two or more well-defined conductance states upon control. Here, Gerhard et al. show the utility of elastic deformation of tripodal spirobifluorene derivatives in the junction of a scanning tunnelling microscope to achieve this goal.
09 March 2017 | doi: 10.1038/ncomms14672

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
CD103+ dendritic cells induce iTreg cells to maintain immune balance in the gut, but how CD40-signalling regulates this process is unclear. Here the authors show that mice with constitutive CD11c-specific CD40-signalling have altered CD103+ dendritic cell migration, reduced iTreg cell induction, and fatal colitis.
09 March 2017 | doi: 10.1038/ncomms14715

Deconvolution of Buparlisib’s mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention OPEN
Thomas Bohnacker, Andrea E. Prota, Florent Beaufils, John E. Burke, Anna Melone, Alison J. Inglis, Denise Rageot, Alexander M. Sele, Vladimir Cmiljanovic, Natasa Cmiljanovic, Katja Bargsten, Amol Aher, Anna Akhmanova, J. Fernando Díaz, Doriano Fabbro, Marketa Zvelebil, Roger L. Williams, Michel O. Steinmetz and Matthias P. Wymann
Buparlisib/BKM120 is in phase 3 clinical trials as a phosphoinositide 3-kinase (PI3K) inhibitor. Here, Bohnacker et al. combine chemical biology and structural biology approaches to segregate BKM120’s biological actions, and suggest that it causes mitotic arrest predominantly by binding microtubules and disrupting their dynamics.
09 March 2017 | doi: 10.1038/ncomms14683

Intervalley scattering by acoustic phonons in two-dimensional MoS2 revealed by double-resonance Raman spectroscopy OPEN
Bruno R. Carvalho, Yuanxi Wang, Sandro Mignuzzi, Debdulal Roy, Mauricio Terrones, Cristiano Fantini, Vincent H. Crespi, Leandro M. Malard and Marcos A. Pimenta
Double-resonance Raman scattering is a sensitive spectroscopic probe of the interplay between electrons and phonons in a crystal. Here, the authors unveil the signature of double-resonance intervalley scattering by acoustic phonons in two-dimensional MoS2, underpinning the physics of valley depolarization.
09 March 2017 | doi: 10.1038/ncomms14670

Structure-guided mutagenesis reveals a hierarchical mechanism of Parkin activation OPEN
Matthew Y. Tang, Marta Vranas, Andrea I. Krahn, Shayal Pundlik, Jean- François Trempe and Edward A. Fon
Parkin and PINK1 are involved in damaged mitochondria clearance; however the sequence of events of Parkin activation is not clear. Here, the authors show that binding to phospho-ubiquitin on mitochondria enables Parkin phosphorylation, which allows Repressor Element of Parkin removal, E3 ligase activation and mitophagy.
09 March 2017 | doi: 10.1038/ncomms14697

Triamidoamine thorium-arsenic complexes with parent arsenide, arsinidiide and arsenido structural motifs OPEN
Elizabeth P. Wildman, Gábor Balázs, Ashley J. Wooles, Manfred Scheer and Stephen T. Liddle
Advances in actinide chemistry have led to the isolation of a range of uranium–ligand multiple bonds, but analogous thorium complexes are rare. Here, the authors prepare thorium–arsenic complexes that are stabilized by bulky triamidoamine ligands and exhibit ThAsH2, ThAs(H)K, ThAs(H)Th and ThAsTh linkages.
09 March 2017 | doi: 10.1038/ncomms14769

MicroRNA-92a is a circadian modulator of neuronal excitability in Drosophila OPEN
Xiao Chen and Michael Rosbash
Accumulating evidence suggests that microRNAs play a role in circadian regulation. Here the authors show that in the Drosophila brain, mir-92a suppresses the excitability of PDF neurons—key circadian pacemaker cells in Drosophila—via inhibiting the translation of its target sirt2.
09 March 2017 | doi: 10.1038/ncomms14707

Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery OPEN
Kyung-Koo Lee, Kwanghee Park, Hochan Lee, Yohan Noh, Dorota Kossowska, Kyungwon Kwak and Minhaeng Cho
The lithium solvation structure in the electrolyte solution for lithium-ion batteries has not been fully understood. Here, the authors show ultrafast fluxional exchange of carbonate solvent molecules in and out of lithium-ion solvation sheath utilizing coherent two-dimensional infrared spectroscopy.
08 March 2017 | doi: 10.1038/ncomms14658

Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness OPEN
Stefanie Heilmann-Heimbach, Christine Herold, Lara M. Hochfeld, Axel M. Hillmer, Dale R. Nyholt, Julian Hecker, Asif Javed, Elaine G. Y. Chew, Sonali Pechlivanis, Dmitriy Drichel, Xiu Ting Heng, Ricardo C. -H. del Rosario, Heide L. Fier, Ralf Paus, Rico Rueedi, Tessel E. Galesloot, Susanne Moebus, Thomas Anhalt, Shyam Prabhakar, Rui Li et al.
Male-pattern baldness is a common condition in which hair is progressively lost from the scalp. Here, the authors find 23 new genetic variants associated with this condition and suggest that it is not an isolated trait but may share an underlying biological basis with various diseases.
08 March 2017 | doi: 10.1038/ncomms14694

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae OPEN
Marie Trussart, Eva Yus, Sira Martinez, Davide Baù, Yuhei O. Tahara, Thomas Pengo, Michael Widjaja, Simon Kretschmer, Jim Swoger, Steven Djordjevic, Lynne Turnbull, Cynthia Whitchurch, Makoto Miyata, Marc A. Marti-Renom, Maria Lluch-Senar and Luís Serrano
The three-dimensional architecture of genome-reduced bacteria is poorly understood. Here the authors combine Hi-C with super-resolution microscopy in Mycoplasma pneumoniae and provide evidence of how supercoiling and local organization influences gene regulation.
08 March 2017 | doi: 10.1038/ncomms14665

Stabilizing short-lived Schiff base derivatives of 5-aminouracils that activate mucosal-associated invariant T cells OPEN
Jeffrey Y. W. Mak, Weijun Xu, Robert C. Reid, Alexandra J. Corbett, Bronwyn S. Meehan, Huimeng Wang, Zhenjun Chen, Jamie Rossjohn, James McCluskey, Ligong Liu and David P. Fairlie
MAIT cells are activated by MR1 restricted antigens derived from riboflavin biosynthesis. Here the authors characterize MAIT cell antigenicity and synthesize a water stable antigen that activates human MAIT cells in vitro and mouse MAIT cells in vivo.
08 March 2017 | doi: 10.1038/ncomms14599

Reconstituting development of pancreatic intraepithelial neoplasia from primary human pancreas duct cells OPEN
Jonghyeob Lee, Emily R. Snyder, Yinghua Liu, Xueying Gu, Jing Wang, Brittany M. Flowers, Yoo Jung Kim, Sangbin Park, Gregory L. Szot, Ralph H. Hruban, Teri A. Longacre and Seung K. Kim
Models of human pancreatic intraepithelial neoplasia (PanIN) development do not exist. Here, the authors induce oncogenic KRAS and mutations in CDKN2A, SMAD4 and TP53 in primary human pancreatic cells to generate a PanIN model that recapitulates molecular and pathologic features of native PanINs.
08 March 2017 | doi: 10.1038/ncomms14686

ATF3 acts as a rheostat to control JNK signalling during intestinal regeneration OPEN
Jun Zhou, Bruce A. Edgar and Michael Boutros
Stress response JNK signalling is important for cell death-induced regeneration. Here the authors show in adult Drosophila enterocytes that ATF3 regulates the expression of Raw, a JNK antagonist, to control intestinal regeneration and barrier function in response to infection.
08 March 2017 | doi: 10.1038/ncomms14289

Highly selective and active CO2 reduction electrocatalysts based on cobalt phthalocyanine/carbon nanotube hybrid structures OPEN
Xing Zhang, Zishan Wu, Xiao Zhang, Liewu Li, Yanyan Li, Haomin Xu, Xiaoxiao Li, Xiaolu Yu, Zisheng Zhang, Yongye Liang and Hailiang Wang
Electrochemical reduction of carbon dioxide is a sustainable way of producing carbon-neutral fuels. Here, the authors take a combined nanoscale and molecular approach to develop a highly active and selective cobalt phthalocyanine/carbon nanotube hybrid electrocatalyst for carbon dioxide reduction to carbon monoxide.
08 March 2017 | doi: 10.1038/ncomms14675

PARP1 promotes gene expression at the post-transcriptiona level by modulating the RNA-binding protein HuR OPEN
Yueshuang Ke, Yanlong Han, Xiaolan Guo, Jitao Wen, Ke Wang, Xue Jiang, Xue Tian, Xueqing Ba, Istvan Boldogh and Xianlu Zeng
PARP1, in addition to its role in DNA repair, has a role in regulating gene transcription via PARylation of target proteins. Here the authors show that HuR is targeted after lipopolysaccharide exposure to regulate the inflammatory gene expression at post-transcriptional level.
08 March 2017 | doi: 10.1038/ncomms14632

Designing exotic many-body states of atomic spin and motion in photonic crystals OPEN
Marco T. Manzoni, Ludwig Mathey and Darrick E. Chang
Cold atoms coupled to photonic crystals constitute a platform for exploring many-body physics. Here the authors study the effect of coupling between the atomic internal degrees of freedom and motion, showing that such systems can realize extreme spin-orbital coupling and uncover a rich phase diagram.
08 March 2017 | doi: 10.1038/ncomms14696

A phenol-enriched cuticle is ancestral to lignin evolution in land plants OPEN
Hugues Renault, Annette Alber, Nelly A. Horst, Alexandra Basilio Lopes, Eric A. Fich, Lucie Kriegshauser, Gertrud Wiedemann, Pascaline Ullmann, Laurence Herrgott, Mathieu Erhardt, Emmanuelle Pineau, Jürgen Ehlting, Martine Schmitt, Jocelyn K. C. Rose, Ralf Reski and Danièle Werck-Reichhart
The phenolic polymer lignin is thought to have contributed to adaptation of early land plants to terrestrial environments. Here Renault et al. show that moss, which does not produce lignin, contains an ancestral phenolic metabolism pathway that produces a phenol-enriched cuticle and prevents desiccation.
08 March 2017 | doi: 10.1038/ncomms14713

MAX inactivation is an early event in GIST development that regulates p16 and cell proliferation OPEN
Inga-Marie Schaefer, Yuexiang Wang, Cher-wei Liang, Nacef Bahri, Anna Quattrone, Leona Doyle, Adrian Mariño-Enríquez, Alexandra Lauria, Meijun Zhu, Maria Debiec-Rychter, Susanne Grunewald, Jaclyn F. Hechtman, Armelle Dufresne, Cristina R. Antonescu, Carol Beadling, Ewa T. Sicinska, Matt van de Rijn, George D. Demetri, Marc Ladanyi, Christopher L. Corless et al.
In gastrointestinal stromal tumours early mutations in known genes are frequently followed by chromosome 14q deletion. Here the authors find mutations resulting in loss of MAX protein expression conserved between primary tumours and metastases in the same patients, suggesting that MAX mutation is an early event.
08 March 2017 | doi: 10.1038/ncomms14674

Effects of an invasive predator cascade to plants via mutualism disruption OPEN
Haldre S. Rogers, Eric R. Buhle, Janneke HilleRisLambers, Evan C. Fricke, Ross H. Miller and Joshua J. Tewksbury
Invasive brown treesnakes decimated the forest bird community on the island of Guam. Now, Rogers and colleagues document the indirect effects of the snake on trees, linking snake-initiated bird loss to reduced seed dispersal and plant recruitment on Guam compared to nearby uninvaded islands.
08 March 2017 | doi: 10.1038/ncomms14557

DNA methyltransferase DNMT3a contributes to neuropathic pain by repressing Kcna2 in primary afferent neurons OPEN
Jian-Yuan Zhao, Lingli Liang, Xiyao Gu, Zhisong Li, Shaogen Wu, Linlin Sun, Fidelis E. Atianjoh, Jian Feng, Kai Mo, Shushan Jia, Brianna Marie Lutz, Alex Bekker, Eric J. Nestler and Yuan-Xiang Tao
Transcriptional changes occur in the dorsal root ganglion in response to nerve injury and may contribute to neuropathic pain. Here the authors show that the DNA methyltransferase DNMT3a is upregulated in rodents following nerve injury, and may contribute to pain-like behaviour by decreasing expression of the voltage-gated potassium channel Kv1.2.
08 March 2017 | doi: 10.1038/ncomms14712
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