Wednesday, June 27, 2018

Nature Communications - 27 June 2018

Nature Communications

Do you have a career question? 

The Naturejobs podcast features one-on-one Q&As, panel discussions and other exclusive content to help scientists with their careers. Hosted on the Naturejobs blog, the podcast is also available on iTunes and Soundcloud. 

Listen today!
Weekly Content Alert
Nature Communications is fully open access. Read more.
27 June 2018 
Latest content:
Author Correction
Flexible Electronics - Visions of a Flexible Future

This second nature conference on the theme of flexible electronics will set its sights firmly on the future, by exploring how such developments will impact on society by helping to tackle challenges in areas such as health, energy, ubiquitous electronics and the "Internet of Things".

October 12-14, 2018 | Xi'an, China
Journal homepage
Recommend to library
Web feed

Nature Spotlight on Hong Kong: Building science innovation 

Hong Kong is maximising major scientific innovation and commercial benefits through its proximity to the research and development hubs in mainland China. Yet barriers to collaboration remain. 

Access the full supplement for more >> 

Advertisement webcasts

Nature Research Custom Media presents a webcast on: Practical Considerations for T Cell Receptor (TCR) Therapies Targeting Solid Tumors

Date: Tuesday, July 17, 2018

Join the webcast to learn about the advantages of automated cell cloning and methods for rapid cloning and validation of functional TCRs.

This webcast has been produced on behalf of the sponsor who retains sole responsibility for content 

Register for FREE 

Sponsored by: Berkeley Lights Inc 
  Nature Communications - fully open access

All new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For more information visit the website.

Visit our open access funding page or contact to learn more about APC funding.
  Latest Comment    
Dissecting the mammary gland one cell at a time OPEN
Simona Cristea & Kornelia Polyak
26 June 2018 | doi: 10.1038/s41467-018-04905-2
Computational biology and bioinformatics  Stem cells 
  Latest Articles View all Articles  

mTORC1 accelerates retinal development via the immunoproteasome OPEN
Ji-Heon Choi, Hong Seok Jo, Soyeon Lim, Hyoung-Tai Kim, Kang Woo Lee, Kyeong Hwan Moon, Taejeong Ha, Sang Soo Kwak, Yeha Kim, Eun Jung Lee, Cheol O. Joe & Jin Woo Kim

One of the determinants of the neuronal subtype produced from retinal progenitor cells is their proliferative potential. Here the authors show that mTORC1 promotes progenitor cell cycle progression and hence accelerated development in mouse retina through induction of the immunoproteasome which enhances the degradation of cyclins.

27 June 2018 | doi: 10.1038/s41467-018-04774-9
Developmental neurogenesis  Mitosis 

Reducing histone acetylation rescues cognitive deficits in a mouse model of Fragile X syndrome OPEN
Yue Li, Michael E. Stockton, Brian E. Eisinger, Yinghua Zhao, Jessica L. Miller, Ismat Bhuiyan, Yu Gao, Zhiping Wu, Junmin Peng & Xinyu Zhao

Loss of fragile X mental retardation protein (FMRP) leads to fragile X syndrome, associated with cognitive dysfunction. Here the authors show that mice lacking FMRP show reduced hippocampal neurogenesis and cognitive deficits, which can be rescued by reducing histone acetylation.

27 June 2018 | doi: 10.1038/s41467-018-04869-3
Adult neurogenesis  Autism spectrum disorders  Neural stem cells 

Identification of genes associated with cortical malformation using a transposon-mediated somatic mutagenesis screen in mice OPEN
I-Ling Lu, Chien Chen, Chien-Yi Tung, Hsin-Hung Chen, Jia-Ping Pan, Chia-Hsiang Chang, Jia-Shing Cheng, Yi-An Chen, Chun-Hung Wang, Chia-Wei Huang, Yi-Ning Kang, Hsin-Yun Chang, Lei-Li Li, Kai-Ping Chang, Yang-Hsin Shih, Chi-Hung Lin, Shang-Yeong Kwan & Jin-Wu Tsai

Cortical malformations have a variety of causes. Here the authors use transposon mutagenesis to insert mutations into neural stem cells in the developing mouse cortex to screen for new candidate genes for cortical malformation, and validate some targets in human brain tissue.

27 June 2018 | doi: 10.1038/s41467-018-04880-8
Developmental disorders  Neuronal development 

Sustained SREBP-1-dependent lipogenesis as a key mediator of resistance to BRAF-targeted therapy OPEN
Ali Talebi, Jonas Dehairs, Florian Rambow, Aljosja Rogiers, David Nittner, Rita Derua, Frank Vanderhoydonc, Joao A. G. Duarte, Francesca Bosisio, Kathleen Van den Eynde, Kris Nys, Mónica Vara Pérez, Patrizia Agostinis, Etienne Waelkens, Joost Van den Oord, Sarah-Maria Fendt, Jean-Christophe Marine & Johannes V. Swinnen

Melanoma patients harbouring BRAFV600E mutation generally develop resistance to targeted therapy. In this study, the authors demonstrate that SREBP-1-mediated induction of lipid biosynthesis contributes to therapy resistance in BRAF mutant melanoma.

27 June 2018 | doi: 10.1038/s41467-018-04664-0
Cancer metabolism  Cancer therapeutic resistance  Melanoma  Phospholipids 

Southern Hemisphere westerlies as a driver of the early deglacial atmospheric CO2 rise OPEN
L. Menviel, P. Spence, J. Yu, M. A. Chamberlain, R. J. Matear, K. J. Meissner & M. H. England

Despite decades of research, the sequence of events leading to the deglacial atmospheric CO2 rise remains unclear. Menviel et al. show that Southern Ocean convection driven by intensified Southern Hemisphere westerlies during Heinrich stadial 1 can explain the abrupt pCO2 rise and changes in atmosphere and ocean carbon isotopes.

27 June 2018 | doi: 10.1038/s41467-018-04876-4
Carbon cycle  Physical oceanography 

The mitochondrial DNA polymerase gamma degrades linear DNA fragments precluding the formation of deletions OPEN
Nadee Nissanka, Sandra R. Bacman, Melanie J. Plastini & Carlos T. Moraes

Mitochondrial DNA fragments are rapidly degraded when double strand breaks occur. Here the authors reveal that the exonuclease activity of polymerase gamma is important for efficient degradation of these fragments and to avoid formation of large deletions.

27 June 2018 | doi: 10.1038/s41467-018-04895-1
Genomic instability  Mitochondria 

A dopaminergic switch for fear to safety transitions OPEN
Ray Luo, Akira Uematsu, Adam Weitemier, Luca Aquili, Jenny Koivumaa, Thomas J. McHugh & Joshua P. Johansen

Fear memories are overcome only when it is ascertained that fearful responses are not appropriate. Here the authors demonstrate that activity in dopamine neurons is necessary to extinguish fear responses and two distinct dopamine neuron projections exert opposing effects on extinction learning.

27 June 2018 | doi: 10.1038/s41467-018-04784-7
Amygdala  Motivation  Prefrontal cortex 

C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains OPEN
Ragini Bhargava, Manbir Sandhu, Sanychen Muk, Gabriella Lee, Nagarajan Vaidehi & Jeremy M. Stark

Many factors are involved in end joining (EJ) repair of double strand breaks. Here the authors present a method to identify a chromosomal break repair event that requires classical non homologues end joining (C-NHEJ) using Cas9-based end joining tools, and define a role of CNHEJ factor XLF in repair.

27 June 2018 | doi: 10.1038/s41467-018-04867-5
Double-strand DNA breaks  Non-homologous-end joining 

Uncovering hidden brain state dynamics that regulate performance and decision-making during cognition OPEN
Jalil Taghia, Weidong Cai, Srikanth Ryali, John Kochalka, Jonathan Nicholas, Tianwen Chen & Vinod Menon

Brain activity is driven, in part, by external stimuli and demands, but internal brain states also change over time. Here, the authors use a novel Bayesian algorithm to track dynamic transitions between hidden neural states in human brain activity and to relate brain dynamics with behavior.

27 June 2018 | doi: 10.1038/s41467-018-04723-6
Attention  Cognitive control  Dynamical systems  Network models 

Dissociable neural mechanisms track evidence accumulation for selection of attention versus action OPEN
Amitai Shenhav, Mark A. Straccia, Sebastian Musslick, Jonathan D. Cohen & Matthew M. Botvinick

Decision-making involves parallel information processing regarding what stimulus dimension to pay attention to and what action to take. Here, the authors show that vmPFC tracks the value of the attended attribute while dACC tracks the degree to which it is attended.

27 June 2018 | doi: 10.1038/s41467-018-04841-1
Attention  Cognitive control  Decision  Human behaviour  Reward 

Controllable water surface to underwater transition through electrowetting in a hybrid terrestrial-aquatic microrobot OPEN
Yufeng Chen, Neel Doshi, Benjamin Goldberg, Hongqiang Wang & Robert J. Wood

Some animals have multimodal locomotive capabilities to survive in different environments. Inspired by nature, Chen et al. build a centimeter-scaled robot that is capable of walking on water, underwater, on land, and transiting among all three, whose ‘feet’ break water by modifying surface tension.

27 June 2018 | doi: 10.1038/s41467-018-04855-9
Biomechanics  Fluidics  Mechanical engineering 

From the betweenness centrality in street networks to structural invariants in random planar graphs OPEN
Alec Kirkley, Hugo Barbosa, Marc Barthelemy & Gourab Ghoshal

The betweenness centrality is a metric commonly used in network analysis. Here the authors show that the distribution of this metric in urban street networks is invariant in the case of 97 cities. This invariance could affect network flows, dynamics and congestion management in cities.

27 June 2018 | doi: 10.1038/s41467-018-04978-z
Applied mathematics  Complex networks 

Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods OPEN
Michiel van de Waterbeemd, Sem Tamara, Kyle L. Fort, Eugen Damoc, Vojtech Franc, Philipp Bieri, Martin Itten, Alexander Makarov, Nenad Ban & Albert J. R. Heck

The authors demonstrate a 3-tier mass spectrometry approach, including bottom-up and top-down proteomics, as well as native mass spectrometry to provide a detailed description of proteoforms, protein processing and post-translational modifications present within ribosomes from bacteria, plant, and human.

27 June 2018 | doi: 10.1038/s41467-018-04853-x
Proteomics  Ribosomal proteins 

Large-scale genetic analysis reveals mammalian mtDNA heteroplasmy dynamics and variance increase through lifetimes and generations OPEN
Joerg P. Burgstaller, Thomas Kolbe, Vitezslav Havlicek, Stephanie Hembach, Joanna Poulton, Jaroslav Piálek, Ralf Steinborn, Thomas Rülicke, Gottfried Brem, Nick S. Jones & Iain G. Johnston

Mitochondrial populations in cells may consist of heteroplasmic mixtures of mtDNA types, and their evolution through development, aging and generations is central to genetic diseases. Here the authors dissect these population dynamics using a large mouse-based data set to characterise the dynamics of heteroplasmy mean and variance throughout life and across generations.

27 June 2018 | doi: 10.1038/s41467-018-04797-2
Applied mathematics  Mitochondria  Mitochondrial genome  Stochastic modelling 

KMT2D/MLL2 inactivation is associated with recurrence in adult-type granulosa cell tumors of the ovary OPEN
R. Tyler Hillman, Joseph Celestino, Christopher Terranova, Hannah C. Beird, Curtis Gumbs, Latasha Little, Tri Nguyen, Rebecca Thornton, Samantha Tippen, Jianhua Zhang, Karen H. Lu, David M. Gershenson, Kunal Rai, Russell R. Broaddus & P. Andrew Futreal

Adult-type granulosa cell tumors of the ovary (aGCTs) are rare and recurrence is difficult to treat. Here, the authors observe in aGCT a novel recurrent somatic truncating mutation of KMT2D, more frequent in recurrent aGCT, and also non-genetic loss of KMT2D expression.

27 June 2018 | doi: 10.1038/s41467-018-04950-x
Medical genomics  Ovarian cancer 

Nuclear Smad6 promotes gliomagenesis by negatively regulating PIAS3-mediated STAT3 inhibition OPEN
Jiantong Jiao, Rui Zhang, Zheng Li, Ying Yin, Xiangming Fang, Xiaopeng Ding, Ying Cai, Shudong Yang, Huijun Mu, Da Zong, Yuexin Chen, Yansong Zhang, Jian Zou, Junfei Shao & Zhaohui Huang

In glioma STAT3 signaling contributes to gliomagenesis. Here, the authors show that Smad6 expression correlates with poor survival and is overexpressed in glioma cells, and regulates STAT3 activity via negatively regulating PIAS3.

27 June 2018 | doi: 10.1038/s41467-018-04936-9
Cancer prevention  CNS cancer 

Thermally-induced reversible structural isomerization in colloidal semiconductor CdS magic-size clusters OPEN
Baowei Zhang, Tingting Zhu, Mingyang Ou, Nelson Rowell, Hongsong Fan, Jiantao Han, Lei Tan, Martin T. Dove, Yang Ren, Xiaobing Zuo, Shuo Han, Jianrong Zeng & Kui Yu

Few structural isomers of colloids, with identical masses but different structures, have been identified. Here, the authors observe an interesting example of structural isomerism in a pair of semiconductor magic-size clusters, which reversibly transform between one another with first-order unimolecular reaction kinetics.

27 June 2018 | doi: 10.1038/s41467-018-04842-0
Inorganic chemistry  Quantum dots 

Extremely strong polarization of an active asteroid (3200) Phaethon OPEN
Takashi Ito, Masateru Ishiguro, Tomoko Arai, Masataka Imai, Tomohiko Sekiguchi, Yoonsoo P. Bach, Yuna G. Kwon, Masanori Kobayashi, Ryo Ishimaru, Hiroyuki Naito, Makoto Watanabe & Kiyoshi Kuramoto

(3200) Phaethon is a near-Earth asteroid discovered in 1983 that has large inclination and eccentricity. Here, the authors perform polarimetric observation of Phaethon over a wide range of solar phase angle and report that the asteroid exhibits a very strong linear polarization.

27 June 2018 | doi: 10.1038/s41467-018-04727-2
Asteroids, comets and Kuiper belt 

Direct visualization of current-induced spin accumulation in topological insulators OPEN
Yang Liu, Jean Besbas, Yi Wang, Pan He, Mengji Chen, Dapeng Zhu, Yang Wu, Jong Min Lee, Lan Wang, Jisoo Moon, Nikesh Koirala, Seongshik Oh & Hyunsoo Yang

Charge-to-spin conversion is a key theme of spintronics and its realization in topological materials is highly desired. Here, Liu et al. report spatial imaging of current-induced spin accumulation at the edges of Bi2Se3 and BiSbTeSe2 topological insulators.

27 June 2018 | doi: 10.1038/s41467-018-04939-6
Electronic devices  Spintronics  Topological insulators 

Discovery of ZrCoBi based half Heuslers with high thermoelectric conversion efficiency OPEN
Hangtian Zhu, Ran He, Jun Mao, Qing Zhu, Chunhua Li, Jifeng Sun, Wuyang Ren, Yumei Wang, Zihang Liu, Zhongjia Tang, Andrei Sotnikov, Zhiming Wang, David Broido, David J. Singh, Gang Chen, Kornelius Nielsch & Zhifeng Ren

Identifying new compounds with intrinsically high conversion efficiency is the key to demonstrating next-generation thermoelectric modules. Here, Zhu et al. report the discovery of p-type ZrCoBi-based half Heuslers with thermoelectric conversion efficiency of 9% and large high-temperature stability.

27 June 2018 | doi: 10.1038/s41467-018-04958-3
Synthesis and processing  Thermoelectrics 

A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion OPEN
Sam J. B. Mallinson, Melodie M. Machovina, Rodrigo L. Silveira, Marc Garcia-Borràs, Nathan Gallup, Christopher W. Johnson, Mark D. Allen, Munir S. Skaf, Michael F. Crowley, Ellen L. Neidle, Kendall N. Houk, Gregg T. Beckham, Jennifer L. DuBois & John E. McGeehan

Catabolizing lignin-derived aromatic compounds requires an aryl-O-demethylation step. Here the authors present the structures of GcoA and GcoB, a cytochrome P450-reductase pair that catalyzes aryl-O-demethylations and show that GcoA displays broad substrate specificity, which is of interest for biotechnology applications.

27 June 2018 | doi: 10.1038/s41467-018-04878-2
Biophysical chemistry  Enzyme mechanisms  Enzymes  Multienzyme complexes  X-ray crystallography 

Operando X-ray photoelectron spectroscopy of solid electrolyte interphase formation and evolution in Li2S-P2S5 solid-state electrolytes OPEN
Kevin N. Wood, K. Xerxes Steirer, Simon E. Hafner, Chunmei Ban, Shriram Santhanagopalan, Se-Hee Lee & Glenn Teeter

Solid-state electrolytes may improve the performance of batteries; however, many are unstable towards metallic lithium, and little is known about the chemical evolution of the interfaces that form during cycling. Here, the authors use an operando method to map the formation and evolution of a solid-electrolyte interphase during cycling.

27 June 2018 | doi: 10.1038/s41467-018-04762-z
Batteries  Chemical physics  Electrochemistry  Energy storage 

Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria OPEN
Chen Dong, Jason Fontana, Anika Patel, James M. Carothers & Jesse G. Zalatan

The absence of effective gene activators in bacteria limits regulated expression programs. Here the authors design synthetic bacterial CRISPR-Cas transcriptional activators that can be used to construct multi-gene programs of activation and repression.

27 June 2018 | doi: 10.1038/s41467-018-04901-6
CRISPR-Cas systems  Metabolic engineering  Synthetic biology 

An effect of serotonergic stimulation on learning rates for rewards apparent after long intertrial intervals OPEN
Kiyohito Iigaya, Madalena S. Fonseca, Masayoshi Murakami, Zachary F. Mainen & Peter Dayan

Serotonin (5-HT) plays many important roles in reward, punishment, patience and beyond, and optogenetic stimulation of 5-HT neurons has not crisply parsed them. The authors report a novel analysis of a reward-based decision-making experiment, and show that 5-HT stimulation increases the learning rate, but only on a select subset of choices.

26 June 2018 | doi: 10.1038/s41467-018-04840-2
Cognitive neuroscience  Learning algorithms  Learning and memory  Machine learning  Reward 

Revealing the immune perturbation of black phosphorus nanomaterials to macrophages by understanding the protein corona OPEN
Jianbin Mo, Qingyun Xie, Wei Wei & Jing Zhao

The formation of a protein corona around nanomaterials is known to have significant effects upon materials in biological applications. Here, the authors report on a study into understanding the protein corona formed on black phosphorus and the implications for interactions with macrophages.

26 June 2018 | doi: 10.1038/s41467-018-04873-7
Chemical biology  Immunology  Materials science 

Reciprocity of social influence OPEN
Ali Mahmoodi, Bahador Bahrami & Carsten Mehring

Humans give and receive social influence—e.g. advice—in many situations, but it is not known whether social influence is a reciprocal process, like trade. Here, the authors show that people are more likely to follow a partner's advice if that partner has previously complied with their advice.

26 June 2018 | doi: 10.1038/s41467-018-04925-y
Human behaviour  Neuroscience  Psychology  Social behaviour 

miR-23b and miR-218 silencing increase Muscleblind-like expression and alleviate myotonic dystrophy phenotypes in mammalian models OPEN
Estefania Cerro-Herreros, Maria Sabater-Arcis, Juan M. Fernandez-Costa, Nerea Moreno, Manuel Perez-Alonso, Beatriz Llamusi & Ruben Artero

Depletion of the splicing factors MBNL 1 and 2 causes myotonic dystrophy. Here, the authors show that miR-23b and miR-218 target MBNL proteins, and that antagonists to these miRNAs rescue mis-splicing events in myoblasts and boost MBNL expression and rescue pathology in mouse models.

26 June 2018 | doi: 10.1038/s41467-018-04892-4
Antagomir and RNA sponge  Neuromuscular disease  RNAi 

Estimating spatiotemporally varying malaria reproduction numbers in a near elimination setting OPEN
Isobel Routledge, José Eduardo Romero Chevéz, Zulma M. Cucunubá, Manuel Gomez Rodriguez, Caterina Guinovart, Kyle B. Gustafson, Kammerle Schneider, Patrick G.T. Walker, Azra C. Ghani & Samir Bhatt

Twenty one countries have been identified for malaria elimination by 2020 and their progress needs to be constantly evaluated. Here, the authors present a method that estimates individual reproduction numbers and their variation through time and space and use it to monitor elimination success in El Salvador between 2010 and 2016.

26 June 2018 | doi: 10.1038/s41467-018-04577-y
Computational biology and bioinformatics  Infectious-disease epidemiology  Infectious diseases  Malaria 

Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1 OPEN
Hamed Kooshapur, Nila Roy Choudhury, Bernd Simon, Max Mühlbauer, Alexander Jussupow, Noemi Fernandez, Alisha N. Jones, Andre Dallmann, Frank Gabel, Carlo Camilloni, Gracjan Michlewski, Javier F. Caceres & Michael Sattler

hnRNP A1 is an auxiliary factor that promotes the Microprocessor-mediated processing of pri-mir-18a, of the oncomiR-1 cluster. Here the authors employ an integrative structural biology approach and provide insights into the molecular mechanism of how hnRNP A1 facilitates pri-mir-18a biogenesis.

26 June 2018 | doi: 10.1038/s41467-018-04871-9
Proteins  RNA  SAXS  Solution-state NMR  Structural biology 

An antifungal polyketide associated with horizontally acquired genes supports symbiont-mediated defense in Lagria villosa beetles OPEN
Laura V. Flórez, Kirstin Scherlach, Ian J. Miller, Andre Rodrigues, Jason C. Kwan, Christian Hertweck & Martin Kaltenpoth

Burkholderia bacteria protect the offspring of Lagria beetles against pathogens. Here, Flórez et al. identify an antifungal polyketide that is likely encoded by a horizontally acquired gene cluster on the genome of a dominant, uncultured Burkholderia symbiont of Lagria villosa.

26 June 2018 | doi: 10.1038/s41467-018-04955-6
Chemical biology  Chemical ecology  Ecology  Evolutionary ecology  Natural products 

Paracrine effect of regulatory T cells promotes cardiomyocyte proliferation during pregnancy and after myocardial infarction OPEN
Serena Zacchigna, Valentina Martinelli, Silvia Moimas, Andrea Colliva, Marco Anzini, Andrea Nordio, Alessia Costa, Michael Rehman, Simone Vodret, Cristina Pierro, Giulia Colussi, Lorena Zentilin, Maria Ines Gutierrez, Ellen Dirkx, Carlin Long, Gianfranco Sinagra, David Klatzmann & Mauro Giacca

Regulatory T cells (Tregs) expand during pregnancy to promote tolerance towards the fetus. Here the authors show that Tregs induce proliferation of fetal and maternal cardiomyocytes during pregnancy and enhance myocardial repair via proliferation-promoting paracrine actions.

26 June 2018 | doi: 10.1038/s41467-018-04908-z
Cardiac regeneration  Cell division  T cells 

In utero nanoparticle delivery for site-specific genome editing OPEN
Adele S. Ricciardi, Raman Bahal, James S. Farrelly, Elias Quijano, Anthony H. Bianchi, Valerie L. Luks, Rachael Putman, Francesc López-Giráldez, Süleyman Coşkun, Eric Song, Yanfeng Liu, Wei-Che Hsieh, Danith H. Ly, David H. Stitelman, Peter M. Glazer & W. Mark Saltzman

The correction of genetic defects in utero could allow for improved outcomes of gene therapy. Here, the authors demonstrate safe delivery of nanoparticles to fetal mouse tissues, and show that nanoparticles containing peptide nucleic acids to edit the beta-globin gene are effective in a mouse model of beta-thalassemia.

26 June 2018 | doi: 10.1038/s41467-018-04894-2
Genetic engineering  Nanoparticles  Peptide nucleic acid oligo  Targeted gene repair 

Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance OPEN
Tianmin Wang, Changge Guan, Jiahui Guo, Bing Liu, Yinan Wu, Zhen Xie, Chong Zhang & Xin-Hui Xing

Systemic investigation of the bacterial genome is essential for both basic microbiology and bioengineering. Here the authors demonstrate CRISPRi pooled screening as a high-throughput tool for identifying gene and phenotype associations in bacteria.

26 June 2018 | doi: 10.1038/s41467-018-04899-x
Bacterial genetics  CRISPR-Cas systems  Functional genomics  High-throughput screening 

Towards femtosecond on-chip electronics based on plasmonic hot electron nano-emitters OPEN
Christoph Karnetzky, Philipp Zimmermann, Christopher Trummer, Carolina Duque Sierra, Martin Wörle, Reinhard Kienberger & Alexander Holleitner

For future ultrafast opto-electronic circuits, optical signals must be interfaced with coherent electronic signals. The authors develop asymmetric plasmonic nanojunctions that convert fs light pulses to THz electronic transients that can propagate on-chip for up to a mm, enabling such an interface.

25 June 2018 | doi: 10.1038/s41467-018-04666-y
Nanophotonics and plasmonics  Optoelectronic devices and components  Ultrafast photonics 

Sensory overamplification in layer 5 auditory corticofugal projection neurons following cochlear nerve synaptic damage OPEN
Meenakshi M. Asokan, Ross S. Williamson, Kenneth E. Hancock & Daniel B. Polley

Deep layer auditory cortex neurons project to a number of limbic and subcortical auditory structures. Here, the authors show how these corticofugal projections adjust response gain following noise-induced cochlear damage.

25 June 2018 | doi: 10.1038/s41467-018-04852-y
Cortex  Sensory processing 

Spontaneous buckling of contractile poroelastic actomyosin sheets OPEN
Y. Ideses, V. Erukhimovitch, R. Brand, D. Jourdain, J. Salmeron Hernandez, U. R. Gabinet, S. A. Safran, K. Kruse & A. Bernheim-Groswasser

Active matter composed of filaments and molecular motors can contract. Here, the authors report the spontaneous out-of-plane buckling of reconstituted contracting poroelastic actomyosin sheets in the absence of external cues.

25 June 2018 | doi: 10.1038/s41467-018-04829-x
Biological physics  Biomaterials  Self-assembly 

Translational control of depression-like behavior via phosphorylation of eukaryotic translation initiation factor 4E OPEN

Translation of mRNA contributes to neuronal function and complex behaviours, and inflammation is thought to contribute to depression. Here the authors show that mice lacking phosphorylation sites in eIF4E (eukaryotic initiation factor 4E) display anxiety- and depression-like behaviour and decreased IkBα expression; furthermore TNFα delivery to the medial prefrontal cortex induces depression-like behaviour and deficits in serotonergic transmission.

25 June 2018 | doi: 10.1038/s41467-018-04883-5
Depression  Neuroimmunology 

Mutually exclusive acetylation and ubiquitylation of the splicing factor SRSF5 control tumor growth OPEN
Yuhan Chen, Qingyang Huang, Wen Liu, Qiong Zhu, Chun-Ping Cui, Liang Xu, Xing Guo, Ping Wang, Jingwen Liu, Guanglong Dong, Wenyi Wei, Cui Hua Liu, Zhichun Feng, Fuchu He & Lingqiang Zhang

Changes in glucose metabolism can lead to tumor development, but the involvement of splicing factors is unclear. Here, the authors screened for SR proteins and identified SRSF5 stability is enhanced in response to glucose elevation to promote alternative splicing of CCAR1 which facilitates tumor growth.

25 June 2018 | doi: 10.1038/s41467-018-04815-3
Acetylation  RNA splicing  Ubiquitylation 

Antifungal tolerance is a subpopulation effect distinct from resistance and is associated with persistent candidemia OPEN
Alexander Rosenberg, Iuliana V. Ene, Maayan Bibi, Shiri Zakin, Ella Shtifman Segal, Naomi Ziv, Alon M. Dahan, Arnaldo Lopes Colombo, Richard J. Bennett & Judith Berman

The authors show that antifungal tolerance, defined as the fraction of growth of a fungal pathogen above the minimal inhibitory concentration, is due to the slow growth of subpopulations of cells that overcome drug stress, and that high tolerance is often associated with persistent infections.

25 June 2018 | doi: 10.1038/s41467-018-04926-x
Antifungal agents  Cellular microbiology  Fungal biology  Pathogens  Preclinical research 

Site-specific characterization of endogenous SUMOylation across species and organs OPEN
Ivo A. Hendriks, David Lyon, Dan Su, Niels H. Skotte, Jeremy A. Daniel, Lars J. Jensen & Michael L. Nielsen

Proteomics is a powerful method to study protein SUMOylation, but system-wide insights into endogenous SUMO2/3 modification events are still sparse. Here, the authors develop a more sensitive SUMO proteomics approach, providing detailed maps of endogenous SUMO2/3 sites in human cells and mouse tissues.

25 June 2018 | doi: 10.1038/s41467-018-04957-4
Mass spectrometry  Proteomics  Sumoylation 

Early Neolithic executions indicated by clustered cranial trauma in the mass grave of Halberstadt OPEN
Christian Meyer, Corina Knipper, Nicole Nicklisch, Angelina Münster, Olaf Kürbis, Veit Dresely, Harald Meller & Kurt W. Alt

Prehistoric warfare and massacres of Linearbandkeramik (LBK) communities are evidenced by mass graves from the Early Neolithic of Central Europe. Here, Meyer et al. describe a newly discovered mass grave from Germany revealing the execution of a predominantly adult male group of non-local individuals.

25 June 2018 | doi: 10.1038/s41467-018-04773-w
Archaeology  Biological anthropology 

Materials informatics for self-assembly of functionalized organic precursors on metal surfaces OPEN
Daniel M. Packwood & Taro Hitosugi

Bottom-up fabrication via on-surface molecular self-assembly is a useful way to make nanomaterials, but finding appropriate precursor molecules for a given structure remains a challenge. Here the authors present an informatics technique linking self-assembled structures with precursor properties, helping identify molecules for target nanomaterials.

25 June 2018 | doi: 10.1038/s41467-018-04940-z
Computational methods  Molecular self-assembly  Statistics 

Direct observation of exciton–exciton interactions OPEN
Jakub Dostál, Franziska Fennel, Federico Koch, Stefanie Herbst, Frank Würthner & Tobias Brixner

Some photo-physical processes in multichromophore systems might get triggered only if two excitations are present. Here, the authors introduce exciton–exciton-interaction 2D spectroscopy, which is a non-linear optical method that can selectively track the time evolution of such effects.

25 June 2018 | doi: 10.1038/s41467-018-04884-4
Energy transfer  Self-assembly  Optical spectroscopy 

Arousal dependent modulation of thalamo-cortical functional interaction OPEN
Iain Stitt, Zhe Charles Zhou, Susanne Radtke-Schuller & Flavio Fröhlich

Thalamo-cortical circuit dynamics are tuned according to behavioral demands, yet the neural mechanisms are not well understood. Here the authors report arousal level-dependent switch in the functional interactions between the thalamus and cortex in ferrets both in spontaneous activity as well as during visual processing.

25 June 2018 | doi: 10.1038/s41467-018-04785-6
Neuroscience  Visual system 

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA OPEN
Atanu Maiti, Wazo Myint, Tapan Kanai, Krista Delviks-Frankenberry, Christina Sierra Rodriguez, Vinay K. Pathak, Celia A. Schiffer & Hiroshi Matsuo

APOBEC3G (A3G) is a single-stranded DNA (ssDNA) cytidine deaminase that restricts HIV-1. Here the authors provide molecular insights into A3G substrate recognition by determining the 1.86 Å resolution crystal structure of its catalytic domain bound to ssDNA.

25 June 2018 | doi: 10.1038/s41467-018-04872-8
Enzyme mechanisms  HIV infections  X-ray crystallography 

Glycolytic metabolism is essential for CCR7 oligomerization and dendritic cell migration OPEN
Hannah Guak, Sara Al Habyan, Eric H. Ma, Haya Aldossary, Maia Al-Masri, So Yoon Won, Thomas Ying, Elizabeth D. Fixman, Russell G. Jones, Luke M. McCaffrey & Connie. M. Krawczyk

The activation of dendritic cells (DC) is associated with a metabolic switch from oxidative to glycolytic metabolism. Here, the authors show that both strong and weak stimuli cause an immediate increase in glycolysis, but only strong stimuli induce long-term glycolytic reprogramming.

25 June 2018 | doi: 10.1038/s41467-018-04804-6
Cell migration  Dendritic cells  Metabolomics 

Simultaneous and stoichiometric purification of hundreds of oligonucleotides OPEN
Alessandro Pinto, Sherry X. Chen & David Yu Zhang

Chemically synthesized DNA oligonucleotides (oligos) require purification to remove truncated species. Here, the authors developed a high-throughput method for oligo purification that also normalises the concentrations of the oligos in the final samples.

25 June 2018 | doi: 10.1038/s41467-018-04870-w
Bioanalytical chemistry  Isolation, separation and purification 

Structural bases of TRP channel TRPV6 allosteric modulation by 2-APB OPEN
Appu K. Singh, Kei Saotome, Luke L. McGoldrick & Alexander I. Sobolevsky

The transient receptor potential channel TRPV6 mediates calcium uptake in epithelia and its expression is increased in several cancer types. Here, authors present structures of TRPV6 bound to 2-APB, a TRPV6 inhibitor, and show that 2-APB induces TRPV6 channel closure by modulating protein–lipid interactions.

25 June 2018 | doi: 10.1038/s41467-018-04828-y
Cryoelectron microscopy  Nanocrystallography  Permeation and transport 

Topological light-trapping on a dislocation OPEN
Fei-Fei Li, Hai-Xiao Wang, Zhan Xiong, Qun Lou, Ping Chen, Rui-Xin Wu, Yin Poo, Jian-Hua Jiang & Sajeev John

Although topological confinement of waves to the edges is common, lower-dimensional wave confinement is scarce. Here, Li et al. demonstrate that concurrent wavevector and real-space topology can lead to a topologically protected zero-dimensional cavity mode in a two-dimensional photonic crystal.

25 June 2018 | doi: 10.1038/s41467-018-04861-x
Metamaterials  Photonic crystals  Sub-wavelength optics 

Accelerating the discovery of insensitive high-energy-density materials by a materials genome approach OPEN
Yi Wang, Yuji Liu, Siwei Song, Zhijian Yang, Xiujuan Qi, Kangcai Wang, Yu Liu, Qinghua Zhang & Yong Tian

The synthesis of explosive materials that are stable, highly dense, and have low sensitivity to external stimuli is a challenge. Here, the authors use a genomic approach to accelerate the discovery of insensitive high explosive molecules with good detonation and low sensitivity properties.

22 June 2018 | doi: 10.1038/s41467-018-04897-z
Computational chemistry  Materials chemistry  Organic chemistry 

Systematic design of superaerophobic nanotube-array electrode comprised of transition-metal sulfides for overall water splitting OPEN
Haoyi Li, Shuangming Chen, Ying Zhang, Qinghua Zhang, Xiaofan Jia, Qi Zhang, Lin Gu, Xiaoming Sun, Li Song & Xun Wang

Water splitting by nanostructured, abundant catalysts provides a renewable means to make carbon neutral fuels, but the ideal material morphology and composition remain uncertain. Here, the authors prepare superaerophobic, multi-metallic sulfide nanotube arrays as bifunctional water splitting catalysts.

22 June 2018 | doi: 10.1038/s41467-018-04888-0
Electrocatalysis  Materials chemistry  Synthesis and processing 

Evidence of an active volcanic heat source beneath the Pine Island Glacier OPEN
Brice Loose, Alberto C. Naveira Garabato, Peter Schlosser, William J. Jenkins, David Vaughan & Karen J. Heywood

The West Antarctic Ice Sheet sits atop an extensional rift system with volcano-like features, yet we do not know if any of these volcanoes are active, because identifying subglacial volcanism remains a challenge. Here, the authors find evidence in helium isotopes that a large volcanic heat source is emanating from beneath the fast-melting Pine Island Ice Glacier.

22 June 2018 | doi: 10.1038/s41467-018-04421-3
Cryospheric science  Marine chemistry  Natural hazards  Volcanology 

Coupling of electrochemically triggered thermal and mechanical effects to aggravate failure in a layered cathode OPEN
Pengfei Yan, Jianming Zheng, Tianwu Chen, Langli Luo, Yuyuan Jiang, Kuan Wang, Manling Sui, Ji-Guang Zhang, Sulin Zhang & Chongmin Wang

Electrochemical processes induce thermo-mechanical effects that mediate battery performance. Here the authors directly visualize cracking dynamics in a thermally perturbed, delithiated LiNi0.6Mn0.2Co0.2O2 cathode to demonstrate coupling between thermal, mechanical and electrochemical factors.

22 June 2018 | doi: 10.1038/s41467-018-04862-w

Uterine glands coordinate on-time embryo implantation and impact endometrial decidualization for pregnancy success OPEN
Andrew M. Kelleher, Jessica Milano-Foster, Susanta K. Behura & Thomas E. Spencer

The transcription factor FOXA2 is specifically expressed in uterine glands. Here, using two conditional FOXA2 knockout mouse models, the authors show that glandular epithelia of the endometrium are required for timely embryo implantation and subsequent endometrial decidualization during successful pregnancy establishment.

22 June 2018 | doi: 10.1038/s41467-018-04848-8
Embryogenesis  Reproductive biology 

A microfluidics platform for combinatorial drug screening on cancer biopsies OPEN
Federica Eduati, Ramesh Utharala, Dharanija Madhavan, Ulf Peter Neumann, Thomas Longerich, Thorsten Cramer, Julio Saez-Rodriguez & Christoph A. Merten

Cancer patients exhibit specific sensitivities toward drug combinations that cannot be easily predicted. Here the authors setup a microfluidic platform that allows testing of multiple drug combinations correctly predicting sensitivity in vivo and they use it on patients biopsies to define effective drugs.

22 June 2018 | doi: 10.1038/s41467-018-04919-w
Assay systems  Cancer therapy 

A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity OPEN
Jeremy J. Gam, Jonathan Babb & Ron Weiss

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression but many quantitative aspects of miRNA biology remain to be elucidated. Based on a library of miRNA sensors, the authors quantify miRNA regulation at single cell level and develop a model to predict miRNA target interactions.

22 June 2018 | doi: 10.1038/s41467-018-04575-0
Computational models  miRNAs  Reporter genes  Synthetic biology 

Reconfigurable photonic generation of broadband chirped waveforms using a single CW laser and low-frequency electronics OPEN
Hugues Guillet de Chatellus, Luis Romero Cortés, Côme Schnébelin, Maurizio Burla & José Azaña

Producing versatile radio-frequency chirped waveforms often requires complicated techniques. The authors use a fiber-optic frequency-shifting loop to create a low-complexity photonic chirp generator with high bandwidth and fully flexible properties for application in radar, spectroscopy, and imaging.

22 June 2018 | doi: 10.1038/s41467-018-04822-4
Microwave photonics  Other photonics 

Secondary lymphoid organ fibroblastic reticular cells mediate trans-infection of HIV-1 via CD44-hyaluronan interactions OPEN
Tomoyuki Murakami, Jiwon Kim, Yi Li, Glenn Edward Green, Ariella Shikanov & Akira Ono

Fibroblastic reticular cells (FRCs) are important regulators of T cell survival, proliferation, and migration in secondary lymphoid organs, but their role in HIV infection isn’t studied. Here, Murakami et al. show that FRCs enhance HIV spread via CD44- and hyaluronan-mediated trans-infection.

22 June 2018 | doi: 10.1038/s41467-018-04846-w
HIV infections  Mechanisms of disease  Viral transmission  Virus–host interactions 

Stem cell factor is selectively secreted by arterial endothelial cells in bone marrow OPEN
Chunliang Xu, Xin Gao, Qiaozhi Wei, Fumio Nakahara, Samuel E. Zimmerman, Jessica Mar & Paul S. Frenette

Endothelial cells (EC) are known to contribute to haematopoietic stem cell (HSC) maintenance in the bone marrow (BM). Here the authors demonstrate that arterial ECs can be distinguished from sinusoidal ECs by podoplanin and Sca-1 expression, and that specifically arterial, but not sinusoidal ECs maintain HSCs by secreting SCF.

22 June 2018 | doi: 10.1038/s41467-018-04726-3
Haematopoietic stem cells  Stem-cell niche  Stem-cell research 

LINC complex-Lis1 interplay controls MT1-MMP matrix digest-on-demand response for confined tumor cell migration OPEN
Elvira Infante, Alessia Castagnino, Robin Ferrari, Pedro Monteiro, Sonia Agüera-González, Perrine Paul-Gilloteaux, Mélanie J. Domingues, Paolo Maiuri, Matthew Raab, Catherine M. Shanahan, Alexandre Baffet, Matthieu Piel, Edgar R. Gomes & Philippe Chavrier

The ability of cancer cells to migrate through small, constricted areas is limited by nuclear stiffness. Here the authors show that in turn nuclear stiffness stimulates the delivery of enzymes important for the degradation of the extracellular matrix and the formation of invadopodia in association with fibers thus opposing nuclear movement.

22 June 2018 | doi: 10.1038/s41467-018-04865-7
Cancer  Invadopodia 

Distinct submembrane localisation compartmentalises cardiac NPR1 and NPR2 signalling to cGMP OPEN
Hariharan Subramanian, Alexander Froese, Peter Jönsson, Hannes Schmidt, Julia Gorelik & Viacheslav O. Nikolaev

Natriuretic peptides (NPs) are important hormones that regulate cardiovascular physiology by increasing cGMP levels in cardiomyocytes. Here the authors use scanning ion conductance microscopy and a cGMP FRET sensor to identify a differential localisation pattern for the natriuretic peptide receptors within the heart.

22 June 2018 | doi: 10.1038/s41467-018-04891-5
Cellular imaging  Nanoscale biophysics 

Calmodulin shuttling mediates cytonuclear signaling to trigger experience-dependent transcription and memory OPEN
Samuel M. Cohen, Benjamin Suutari, Xingzhi He, Yang Wang, Sandrine Sanchez, Natasha N. Tirko, Nataniel J. Mandelberg, Caitlin Mullins, Guangjun Zhou, Shuqi Wang, Ilona Kats, Alejandro Salah, Richard W. Tsien & Huan Ma

Activity-dependent gene expression is thought to involve translocation of Ca2+/calmodulin (CaM) to the nucleus. Here, the authors examine a translocation-deficient mutant of γCaMKII, a Ca2+/CaM shuttle protein, to show that translocation of Ca2+/CaM is required for memory and synaptic plasticity.

22 June 2018 | doi: 10.1038/s41467-018-04705-8
Cellular neuroscience  Molecular neuroscience 

The photosystem I assembly apparatus consisting of Ycf3–Y3IP1 and Ycf4 modules OPEN
Sreedhar Nellaepalli, Shin-Ichiro Ozawa, Hiroshi Kuroda & Yuichiro Takahashi

Photosystem I is a large multiprotein complex embedded in the chloroplast thylakoid membrane. Here the authors provide evidence for a modular assembly process, whereby Ycf3 facilitates assembly of the reaction center, while Ycf4 incorporates peripheral core and light harvesting complex subunits to the reaction center.

22 June 2018 | doi: 10.1038/s41467-018-04823-3
Photosystem I 

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions OPEN
Arif Harmanci & Mark Gerstein

Functional genomics data from many studies are widely shared publicly for their value in biomedical and disease research. Here, the authors show sensitive information leakage is possible by analyzing functional genomics signal profiles, and develop an anonymization procedure for privacy protection.

22 June 2018 | doi: 10.1038/s41467-018-04875-5
Computational biology and bioinformatics  Data mining  Epigenetics 

Precision therapeutic targeting of human cancer cell motility OPEN
Li Xu, Ryan Gordon, Rebecca Farmer, Abhinandan Pattanayak, Andrew Binkowski, Xiaoke Huang, Michael Avram, Sankar Krishna, Eric Voll, Janet Pavese, Juan Chavez, James Bruce, Andrew Mazar, Antoinette Nibbs, Wayne Anderson, Lin Li, Borko Jovanovic, Sean Pruell, Matias Valsecchi, Giulio Francia et al.

In this study, the authors identify and validate a halogen-substituted isoflavanone able to inhibit prostate cancer cell motility, invasion and metastasis in vitro and in vivo. They demonstrate its ability to selectively inhibit activation of client proteins that stimulate cell motility.

22 June 2018 | doi: 10.1038/s41467-018-04465-5
Chemical tools  Targeted therapies 

Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data OPEN
Kieran R Campbell & Christopher Yau

Cross-sectional omic data often have non-homogeneous genetic, phenotypic, or environmental backgrounds. Here, the authors develop a statistical framework to infer pseudotime trajectories in the presence of such factors as well as their interactions in both single-cell and bulk gene expression analysis

22 June 2018 | doi: 10.1038/s41467-018-04696-6
Computational biology and bioinformatics  Machine learning 

TLR9 activation via microglial glucocorticoid receptors contributes to degeneration of midbrain dopamine neurons OPEN
Layal Maatouk, Anne-Claire Compagnion, Maria-Angeles Carrillo-de Sauvage, Alexis-Pierre Bemelmans, Sabrina Leclere-Turbant, Vincent Cirotteau, Mira Tohme, Allen Beke, Michaël Trichet, Virginie Bazin, Bobby N. Trawick, Richard M. Ransohoff, François Tronche, Bénédicte Manoury & Sheela Vyas

Inflammation is a component of Parkinson’s disease. Here the authors show that activation of Toll-like receptor 9 controlled by microglial glucocorticoid receptor signaling, contributes to dopamine neuron loss in a model of Parkinson’s disease.

22 June 2018 | doi: 10.1038/s41467-018-04569-y
Neuroimmunology  Parkinson's disease 

Rational Zika vaccine design via the modulation of antigen membrane anchors in chimpanzee adenoviral vectors OPEN
César López-Camacho, Peter Abbink, Rafael A. Larocca, Wanwisa Dejnirattisai, Michael Boyd, Alex Badamchi-Zadeh, Zoë R. Wallace, Jennifer Doig, Ricardo Sanchez Velazquez, Roberto Dias Lins Neto, Danilo F. Coelho, Young Chan Kim, Claire L. Donald, Ania Owsianka, Giuditta De Lorenzo, Alain Kohl, Sarah C. Gilbert, Lucy Dorrell, Juthathip Mongkolsapaya, Arvind H. Patel et al.

Zika virus (ZIKV) is an emerging global health issue, but currently no licensed vaccine achieves lasting protective immunity. Here the authors show that a ZIKV vaccine containing the envelop protein without the transmembrane domain and the precursor membrane protein can provide effective protection in mouse models.

22 June 2018 | doi: 10.1038/s41467-018-04859-5
Molecular medicine  Vaccines  Viral infection 

Pulmonary pericytes regulate lung morphogenesis OPEN
Katsuhiro Kato, Rodrigo Diéguez-Hurtado, Do Young Park, Seon Pyo Hong, Sakiko Kato-Azuma, Susanne Adams, Martin Stehling, Britta Trappmann, Jeffrey L. Wrana, Gou Young Koh & Ralf H. Adams

Pericytes surround endothelial tubules and help maintain the integrity of blood vessels. Here the authors show that pericytes regulate lung morphogenesis via paracrine signalling controlled by components of the Hippo pathway.

22 June 2018 | doi: 10.1038/s41467-018-04913-2
Cell signalling  Morphogenesis 

Formal enantioconvergent substitution of alkyl halides via catalytic asymmetric photoredox radical coupling OPEN
Jiangtao Li, Manman Kong, Baokun Qiao, Richmond Lee, Xiaowei Zhao & Zhiyong Jiang

Enantioselective substitution reactions of racemic alkyl halides are inherently limited by the specificity of their stereochemical course (SN1 or SN2). Here, the authors report a radical coupling strategy for the enantioselective aminoalkylation of α-bromoketones for modular, highly enantioselective Csp3−Csp3 bond formation.

22 June 2018 | doi: 10.1038/s41467-018-04885-3
Asymmetric catalysis  Synthetic chemistry methodology  Organocatalysis  Photocatalysis 

A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes OPEN
Alexander Ohmann, Chen-Yu Li, Christopher Maffeo, Kareem Al Nahas, Kevin N. Baumann, Kerstin Göpfrich, Jejoong Yoo, Ulrich F. Keyser & Aleksei Aksimentiev

Mimicking enzyme function and improving upon it is a challenge facing nanotechnology. Here the authors design a DNA nanostructure that catalyzes the transport of lipids between bilayers at a rate three orders of magnitude higher than biological enzymes.

21 June 2018 | doi: 10.1038/s41467-018-04821-5
Computational biophysics  DNA nanostructures  Membrane biophysics  Nanobiotechnology 

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL OPEN
Shuiming Qian, Xinchen Lv, Ray N. Scheid, Li Lu, Zhenlin Yang, Wei Chen, Rui Liu, Melissa D. Boersma, John M. Denu, Xuehua Zhong & Jiamu Du

Histone mark reader proteins bind to particular histone modifications and regulate chromatin state. Here, Qian et al. show that the SHORT LIFE reader has a unique ability to recognize both activating and repressive histone marks and that these interactions enable SHORT LIFE to repress flowering in plants.

21 June 2018 | doi: 10.1038/s41467-018-04836-y
Epigenetics  Plant molecular biology  X-ray crystallography 

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes OPEN
Yukihide Momozawa, Julia Dmitrieva, Emilie Théâtre, Valérie Deffontaine, Souad Rahmouni, Benoît Charloteaux, François Crins, Elisa Docampo, Mahmoud Elansary, Ann-Stephan Gori, Christelle Lecut, Rob Mariman, Myriam Mni, Cécile Oury, Ilya Altukhov, Dmitry Alexeev, Yuri Aulchenko, Leila Amininejad, Gerd Bouma, Frank Hoentjen et al.

Most of the more than 200 known genetic risk loci for inflammatory bowel disease (IBD) reside in regulatory regions. Here, the authors provide eQTL datasets for six circulating immune cell types and ileal, colonic and rectal biopsies to map regulatory modules and identify potential causative genes for IBD.

21 June 2018 | doi: 10.1038/s41467-018-04365-8
Genetics research  Genome-wide association studies  Immunogenetics  Inflammatory bowel disease 

Conformational switching of the pseudokinase domain promotes human MLKL tetramerization and cell death by necroptosis OPEN
Emma J. Petrie, Jarrod J. Sandow, Annette V. Jacobsen, Brian J. Smith, Michael D. W. Griffin, Isabelle S. Lucet, Weiwen Dai, Samuel N. Young, Maria C. Tanzer, Ahmad Wardak, Lung-Yu Liang, Angus D. Cowan, Joanne M. Hildebrand, Wilhelmus J. A. Kersten, Guillaume Lessene, John Silke, Peter E. Czabotar, Andrew I. Webb & James M. Murphy

RIPK3-mediated phosphorylation of the mixed lineage kinase domain-like (MLKL) pseudokinase is thought to be the trigger for MLKL activation during necroptotic signaling. Here the authors provide evidence that the transition of human MLKL from a monomeric state to a tetramer is essential for necroptosis signalling.

21 June 2018 | doi: 10.1038/s41467-018-04714-7
Kinases  Mass spectrometry  Necroptosis  SAXS 

High-veracity functional imaging in scanning probe microscopy via Graph-Bootstrapping OPEN
Xin Li, Liam Collins, Keisuke Miyazawa, Takeshi Fukuma, Stephen Jesse & Sergei V. Kalinin

Scanning probe microscopy methods can generate high-dimensional data sets that correspond to a low-dimensional sample. Here, Li et al. develop a graphical bootstrapping method to quantitatively visualize large-scale high-dimensional datasets.

21 June 2018 | doi: 10.1038/s41467-018-04887-1
Imaging techniques  Structural properties 

Mitotic polarization of transcription factors during asymmetric division establishes fate of forming cancer cells OPEN
Yongqing Liu, Laura Siles, Xiaoqin Lu, Kevin C. Dean, Miriam Cuatrecasas, Antonio Postigo & Douglas C. Dean

Transition from premalignant lesion to cancer cell highlights tumor initiation. Here, the authors use a model of K-Ras-initiated lung cancer to document two successive asymmetric divisions, each driven by mitotic polarization of key transcription factors, which lead to generation of initial cancer cells.

21 June 2018 | doi: 10.1038/s41467-018-04663-1
Cancer  Lung cancer  Non-small-cell lung cancer 

Predictive modeling of battery degradation and greenhouse gas emissions from U.S. state-level electric vehicle operation OPEN
Fan Yang, Yuanyuan Xie, Yelin Deng & Chris Yuan

The effects of battery degradation on the energy consumption and greenhouse gas emissions from electric vehicles are unknown. Here the authors show that the lifetime of a typical battery is between 5.2 and 13.3 years across the U.S., with an 11.5–16.2% increase in energy consumption and CO2 emissions.

21 June 2018 | doi: 10.1038/s41467-018-04826-0
Energy and behaviour  Projection and prediction 

Lateralized hippocampal oscillations underlie distinct aspects of human spatial memory and navigation OPEN

Theta oscillations are implicated in memory formation. Here, the authors show that low-theta oscillations in the hippocampus are differentially modulated between each hemisphere, with oscillations in the left increasing when successfully learning object–location pairs and in the right during spatial navigation.

21 June 2018 | doi: 10.1038/s41467-018-04847-9
Cognitive neuroscience  Hippocampus  Spatial memory 
Nature Communications
JOBS of the week
Postdoctoral Fellow
University of Colorado Anschutz Medical Campus
Research Associate
University College London (UCL)
Higher Scientific Officer
Institute of Cancer Research (ICR)
Research Assistant (Post-Doc)
Institute of Vascular Signalling, Center for Molecular Medicine at the Faculty of Medicine, Goethe University
Research Assistant (Post-Doc)
Institute of Vascular Signalling, Center for Molecular Medicine at the Faculty of Medicine, Goethe University
Postdoctoral Scientist Postdoctoral Scientist
Boehringer Ingelheim
Research Fellow
Birmingham University
Staff Associate
Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University
Postdoctoral Positions
Johns Hopkins University School of Medicine Department of Hetatology
Postdoctoral Fellow 0
Houston Methodist Research Institute, Department of Nanomedicine
More Science jobs from
Nature Communications
Young Researchers in BioSiences
Cluj-Napoca, Romania
More science events from
  Latest Author Correction    
Author Correction: Hexokinase-2 depletion inhibits glycolysis and induces oxidative phosphorylation in hepatocellular carcinoma and sensitizes to metformin OPEN
Dannielle DeWaal, Veronique Nogueira, Alexander R. Terry, Krushna C. Patra, Sang-Min Jeon, Grace Guzman, Jennifer Au, Christopher P. Long, Maciek R. Antoniewicz & Nissim Hay
26 June 2018 | doi: 10.1038/s41467-018-04182-z
Cancer metabolism  Hepatocellular carcinoma  Molecular biology 

Calls for nominations: 
2018 John Maddox Prize for Standing up for Science

Recognising the work of individuals who promote science in the face of hostility.

Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. With Nature Briefing, we'll keep you updated on the latest research, so you can focus on yours.

Click here to sign up.
nature events
Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here.

Find the latest scientific conferences, courses, meetings and symposia on For event advertising opportunities across the Nature Publishing Group portfolio please contact
 More Nature Events
You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your account
(You will need to log in to be recognised as a registrant)

For further technical assistance, please contact our registration department

For other enquiries, please contact our customer feedback department

Springer Nature | One New York Plaza, Suite 4500 | New York | NY 10004-1562 | USA

Springer Nature's worldwide offices:
London - Paris - Munich - New Delhi - Tokyo - Melbourne
San Diego - San Francisco - Washington - New York - Boston

Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS.

© 2018 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
Springer Nature

No comments: