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Timothy D Searchinger, Stefan Wirsenius, Tim Beringer, Patrice Dumas
In this Letter, the PANGAEA repository was referred to incorrectly in the 'Code availability' and 'Data availability' sections of Methods: the link should be instead of . In addition, the sentence, "However, the more commonly used system 2 (75 kg ha-1  yr-1 ) generates roughly the same benefits as system 1…" should read, "However, the more commonly used system 2 (75 kg ha-1  yr-1 ) generates roughly the same benefits as sugarcane ethanol…" These errors have been corrected in the online versions of the Letter...
January 10, 2019: Nature
Michaela J Conley, Marion McElwee, Liyana Azmi, Mads Gabrielsen, Olwyn Byron, Ian G Goodfellow, David Bhella
To initiate infection, many viruses enter their host cells by triggering endocytosis following receptor engagement. However, the mechanisms by which non-enveloped viruses escape the endosome are poorly understood. Here we present near-atomic-resolution cryo-electron microscopy structures for feline calicivirus both undecorated and labelled with a soluble fragment of its cellular receptor, feline junctional adhesion molecule A. We show that VP2, a minor capsid protein encoded by all caliciviruses1,2 , forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement...
January 9, 2019: Nature
Mathieu Ringeard, Virginie Marchand, Etienne Decroly, Yuri Motorin, Yamina Bennasser
In mammals, 2'-O-methylation of RNA is a molecular signature by which the cellular innate immune system distinguishes endogenous from exogenous messenger RNA1-3 . However, the molecular functions of RNA 2'-O-methylation are not well understood. Here we have purified TAR RNA-binding protein (TRBP) and its interacting partners and identified a DICER-independent TRBP complex containing FTSJ3, a putative 2'-O-methyltransferase (2'O-MTase). In vitro and ex vivo experiments show that FTSJ3 is a 2'O-MTase that is recruited to HIV RNA through TRBP...
January 9, 2019: Nature
Kevin Monahan, Adan Horta, Stavros Lomvardas
The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells...
January 9, 2019: Nature
Alexandros Poulopoulos, Alexander J Murphy, Abdulkadir Ozkan, Patrick Davis, John Hatch, Rory Kirchner, Jeffrey D Macklis
The development of neural circuits relies on axon projections establishing diverse, yet well-defined, connections between areas of the nervous system. Each projection is formed by growth cones-subcellular specializations at the tips of growing axons, encompassing sets of molecules that control projection-specific growth, guidance, and target selection1 . To investigate the set of molecules within native growth cones that form specific connections, here we developed growth cone sorting and subcellular RNA-proteome mapping, an approach that identifies and quantifies local transcriptomes and proteomes from labelled growth cones of single projections in vivo...
January 9, 2019: Nature
Samuel E Weinberg, Benjamin D Singer, Elizabeth M Steinert, Carlos A Martinez, Manan M Mehta, Inmaculada Martínez-Reyes, Peng Gao, Kathryn A Helmin, Hiam Abdala-Valencia, Laura A Sena, Paul T Schumacker, Laurence A Turka, Navdeep S Chandel
Regulatory T cells (Treg cells), a distinct subset of CD4+ T cells, are necessary for the maintenance of immune self-tolerance and homeostasis1,2 . Recent studies have demonstrated that Treg cells exhibit a unique metabolic profile, characterized by an increase in mitochondrial metabolism relative to other CD4+ effector subsets3,4 . Furthermore, the Treg cell lineage-defining transcription factor, Foxp3, has been shown to promote respiration5,6 ; however, it remains unknown whether the mitochondrial respiratory chain is required for the T cell-suppression capacity, stability and survival of Treg cells...
January 9, 2019: Nature
Shunsuke Miyashima, Pawel Roszak, Iris Sevilem, Koichi Toyokura, Bernhard Blob, Jung-Ok Heo, Nathan Mellor, Hanna Help-Rinta-Rahko, Sofia Otero, Wouter Smet, Mark Boekschoten, Guido Hooiveld, Kayo Hashimoto, Ondřej Smetana, Riccardo Siligato, Eva-Sophie Wallner, Ari Pekka Mähönen, Yuki Kondo, Charles W Melnyk, Thomas Greb, Keiji Nakajima, Rosangela Sozzani, Anthony Bishopp, Bert De Rybel, Ykä Helariutta
Apical growth in plants initiates upon seed germination, whereas radial growth is primed only during early ontogenesis in procambium cells and activated later by the vascular cambium1 . Although it is not known how radial growth is organized and regulated in plants, this system resembles the developmental competence observed in some animal systems, in which pre-existing patterns of developmental potential are established early on2,3 . Here we show that in Arabidopsis the initiation of radial growth occurs around early protophloem-sieve-element cell files of the root procambial tissue...
January 9, 2019: Nature
Hande Boyaci, James Chen, Rolf Jansen, Seth A Darst, Elizabeth A Campbell
A key regulated step of transcription is promoter melting by RNA polymerase (RNAP) to form the open promoter complex1-3 . To generate the open complex, the conserved catalytic core of the RNAP combines with initiation factors to locate promoter DNA, unwind 12-14 base pairs of the DNA duplex and load the template-strand DNA into the RNAP active site. Formation of the open complex is a multi-step process during which transient intermediates of unknown structure are formed4-6 . Here we present cryo-electron microscopy structures of bacterial RNAP-promoter DNA complexes, including structures of partially melted intermediates...
January 9, 2019: Nature
Ondřej Smetana, Riikka Mäkilä, Munan Lyu, Ali Amiryousefi, Filomeno Sánchez Rodríguez, Miin-Feng Wu, Anna Solé-Gil, Marina Leal Gavarrón, Riccardo Siligato, Shunsuke Miyashima, Pawel Roszak, Tiina Blomster, Jason W Reed, Suvi Broholm, Ari Pekka Mähönen
Wood, a type of xylem tissue, originates from cell proliferation of the vascular cambium. Xylem is produced inside, and phloem outside, of the cambium1 . Morphogenesis in plants is typically coordinated by organizer cells that direct the adjacent stem cells to undergo programmed cell division and differentiation. The location of the vascular cambium stem cells and whether the organizer concept applies to the cambium are currently unknown2 . Here, using lineage-tracing and molecular genetic studies in the roots of Arabidopsis thaliana, we show that cells with a xylem identity direct adjacent vascular cambial cells to divide and function as stem cells...
January 9, 2019: Nature
Yihao Yang, Zhen Gao, Haoran Xue, Li Zhang, Mengjia He, Zhaoju Yang, Ranjan Singh, Yidong Chong, Baile Zhang, Hongsheng Chen
Confining photons in a finite volume is highly desirable in modern photonic devices, such as waveguides, lasers and cavities. Decades ago, this motivated the study and application of photonic crystals, which have a photonic bandgap that forbids light propagation in all directions1-3 . Recently, inspired by the discoveries of topological insulators4,5 , the confinement of photons with topological protection has been demonstrated in two-dimensional (2D) photonic structures known as photonic topological insulators6-8 , with promising applications in topological lasers9,10 and robust optical delay lines11 ...
January 9, 2019: Nature
M J Darnley, R Hounsell, T J O'Brien, M Henze, P Rodríguez-Gil, A W Shafter, M M Shara, N M H Vaytet, M F Bode, R Ciardullo, B D Davis, R Galera-Rosillo, D J Harman, E J Harvey, M W Healy, J-U Ness, V A R M Ribeiro, S C Williams
The accretion of hydrogen onto a white dwarf star ignites a classical nova eruption1,2 -a thermonuclear runaway in the accumulated envelope of gas, leading to luminosities up to a million times that of the Sun and a high-velocity mass ejection that produces a remnant shell (mainly consisting of insterstellar medium). Close to the upper mass limit of a white dwarf3 (1.4 solar masses), rapid accretion of hydrogen (about 10-7 solar masses per year) from a stellar companion leads to frequent eruptions on timescales of years4,5 to decades6 ...
January 9, 2019: Nature
C Pabst, R Higgins, J R Goicoechea, D Teyssier, O Berne, E Chambers, M Wolfire, S T Suri, R Guesten, J Stutzki, U U Graf, C Risacher, A G G M Tielens
Massive stars inject mechanical and radiative energy into the surrounding environment, which stirs it up, heats the gas, produces cloud and intercloud phases in the interstellar medium, and disrupts molecular clouds (the birth sites of new stars1,2 ). Stellar winds, supernova explosions and ionization by ultraviolet photons control the lifetimes of molecular clouds3-7 . Theoretical studies predict that momentum injection by radiation should dominate that by stellar winds8 , but this has been difficult to assess observationally...
January 7, 2019: Nature
Jennifer A Shusterman, Nicholas D Scielzo, Keenan J Thomas, Eric B Norman, Suzanne E Lapi, C Shaun Loveless, Nickie J Peters, J David Robertson, Dawn A Shaughnessy, Anton P Tonchev
The probability that a nucleus will absorb a neutron-the neutron capture cross-section-is important to many areas of nuclear science, including stellar nucleosynthesis, reactor performance, nuclear medicine and defence applications. Although neutron capture cross-sections have been measured for most stable nuclei, fewer results exist for radioactive isotopes, and statistical-model predictions typically have large uncertainties1 . There are almost no nuclear data for neutron-induced reactions of the radioactive nucleus 88 Zr, despite its importance as a diagnostic for nuclear security...
January 7, 2019: Nature
M Rodell, J S Famiglietti, D N Wiese, J T Reager, H K Beaudoing, F W Landerer, M-H Lo
In Fig. 2 of this Analysis, the tick-mark labels on the colour bars in the second and third images from the top were inadvertently swapped. In addition, the citation at the end of the sentence, "On a monthly basis GRACE can resolve TWS changes with sufficient accuracy over scales that range from approximately 200,000 km2 at low latitudes to about 90,000 km2 near the poles" should be to ref. 4 not ref. 1 . These errors have been corrected online.
January 3, 2019: Nature
Akira Yokoyama, Nobuyuki Kakiuchi, Tetsuichi Yoshizato, Yasuhito Nannya, Hiromichi Suzuki, Yasuhide Takeuchi, Yusuke Shiozawa, Yusuke Sato, Kosuke Aoki, Soo Ki Kim, Yoichi Fujii, Kenichi Yoshida, Keisuke Kataoka, Masahiro M Nakagawa, Yoshikage Inoue, Tomonori Hirano, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Masashi Sanada, Yoshitaka Nishikawa, Yusuke Amanuma, Shinya Ohashi, Ikuo Aoyama, Takahiro Horimatsu, Shin'ichi Miyamoto, Shigeru Tsunoda, Yoshiharu Sakai, Maiko Narahara, J B Brown, Yoshitaka Sato, Genta Sawada, Koshi Mimori, Sachiko Minamiguchi, Hironori Haga, Hiroshi Seno, Satoru Miyano, Hideki Makishima, Manabu Muto, Seishi Ogawa
Clonal expansion in aged normal tissues has been implicated in the development of cancer. However, the chronology and risk dependence of the expansion are poorly understood. Here we intensively sequence 682 micro-scale oesophageal samples and show, in physiologically normal oesophageal epithelia, the progressive age-related expansion of clones that carry mutations in driver genes (predominantly NOTCH1), which is substantially accelerated by alcohol consumption and by smoking. Driver-mutated clones emerge multifocally from early childhood and increase their number and size with ageing, and ultimately replace almost the entire oesophageal epithelium in the extremely elderly...
January 2, 2019: Nature
C Dornes, Y Acremann, M Savoini, M Kubli, M J Neugebauer, E Abreu, L Huber, G Lantz, C A F Vaz, H Lemke, E M Bothschafter, M Porer, V Esposito, L Rettig, M Buzzi, A Alberca, Y W Windsor, P Beaud, U Staub, Diling Zhu, Sanghoon Song, J M Glownia, S L Johnson
The Einstein-de Haas effect was originally observed in a landmark experiment1 demonstrating that the angular momentum associated with aligned electron spins in a ferromagnet can be converted to mechanical angular momentum by reversing the direction of magnetization using an external magnetic field. A related problem concerns the timescale of this angular momentum transfer. Experiments have established that intense photoexcitation in several metallic ferromagnets leads to a drop in magnetization on a timescale shorter than 100 femtoseconds-a phenomenon called ultrafast demagnetization2-4 ...
January 2, 2019: Nature
Aaron D Mickle, Sang Min Won, Kyung Nim Noh, Jangyeol Yoon, Kathleen W Meacham, Yeguang Xue, Lisa A McIlvried, Bryan A Copits, Vijay K Samineni, Kaitlyn E Crawford, Do Hoon Kim, Paulome Srivastava, Bong Hoon Kim, Seunghwan Min, Young Shiuan, Yeojeong Yun, Maria A Payne, Jianpeng Zhang, Hokyung Jang, Yuhang Li, H Henry Lai, Yonggang Huang, Sung-Il Park, Robert W Gereau, John A Rogers
The fast-growing field of bioelectronic medicine aims to develop engineered systems that can relieve clinical conditions by stimulating the peripheral nervous system1-5 . This type of technology relies largely on electrical stimulation to provide neuromodulation of organ function or pain. One example is sacral nerve stimulation to treat overactive bladder, urinary incontinence and interstitial cystitis (also known as bladder pain syndrome)4,6,7 . Conventional, continuous stimulation protocols, however, can cause discomfort and pain, particularly when treating symptoms that can be intermittent (for example, sudden urinary urgency)8 ...
January 2, 2019: Nature
Simonas Masiulis, Rooma Desai, Tomasz Uchański, Itziar Serna Martin, Duncan Laverty, Dimple Karia, Tomas Malinauskas, Jasenko Zivanov, Els Pardon, Abhay Kotecha, Jan Steyaert, Keith W Miller, A Radu Aricescu
Type-A γ-aminobutyric (GABAA ) receptors are ligand-gated chloride channels with a very rich pharmacology. Some of their modulators, including benzodiazepines and general anaesthetics, are among the most successful drugs in clinical use and are common substances of abuse. Without reliable structural data, the mechanistic basis for the pharmacological modulation of GABAA receptors remains largely unknown. Here we report several high-resolution cryo-electron microscopy structures in which the full-length human α1β3γ2L GABAA receptor in lipid nanodiscs is bound to the channel-blocker picrotoxin, the competitive antagonist bicuculline, the agonist GABA (γ-aminobutyric acid), and the classical benzodiazepines alprazolam and diazepam...
January 2, 2019: Nature
Duncan Laverty, Rooma Desai, Tomasz Uchański, Simonas Masiulis, Wojciech J Stec, Tomas Malinauskas, Jasenko Zivanov, Els Pardon, Jan Steyaert, Keith W Miller, A Radu Aricescu
Type A γ-aminobutyric acid (GABAA ) receptors are pentameric ligand-gated ion channels and the main drivers of fast inhibitory neurotransmission in the vertebrate nervous system1,2 . Their dysfunction is implicated in a range of neurological disorders, including depression, epilepsy and schizophrenia3,4 . Among the numerous assemblies that are theoretically possible, the most prevalent in the brain are the α1β2/3γ2 GABAA receptors5 . The β3 subunit has an important role in maintaining inhibitory tone, and the expression of this subunit alone is sufficient to rescue inhibitory synaptic transmission in β1-β3 triple knockout neurons6 ...
January 2, 2019: Nature
François-Xavier Weill, Daryl Domman, Elisabeth Njamkepo, Abdullrahman A Almesbahi, Mona Naji, Samar Saeed Nasher, Ankur Rakesh, Abdullah M Assiri, Naresh Chand Sharma, Samuel Kariuki, Mohammad Reza Pourshafie, Jean Rauzier, Abdinasir Abubakar, Jane Y Carter, Joseph F Wamala, Caroline Seguin, Christiane Bouchier, Thérèse Malliavin, Bita Bakhshi, Hayder H N Abulmaali, Dhirendra Kumar, Samuel M Njoroge, Mamunur Rahman Malik, John Kiiru, Francisco J Luquero, Andrew S Azman, Thandavarayan Ramamurthy, Nicholas R Thomson, Marie-Laure Quilici
Yemen is currently experiencing, to our knowledge, the largest cholera epidemic in recent history. The first cases were declared in September 2016, and over 1.1 million cases and 2,300 deaths have since been reported1 . Here we investigate the phylogenetic relationships, pathogenesis and determinants of antimicrobial resistance by sequencing the genomes of Vibrio cholerae isolates from the epidemic in Yemen and recent isolates from neighbouring regions. These 116 genomic sequences were placed within the phylogenetic context of a global collection of 1,087 isolates of the seventh pandemic V...
January 2, 2019: Nature
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