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Science Advances

Jiyung Shin, Fuguo Jiang, Jun-Jie Liu, Nicolas L Bray, Benjamin J Rauch, Seung Hyun Baik, Eva Nogales, Joseph Bondy-Denomy, Jacob E Corn, Jennifer A Doudna
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established...
July 2017: Science Advances
Bettina Frank, Philip Kahl, Daniel Podbiel, Grisha Spektor, Meir Orenstein, Liwei Fu, Thomas Weiss, Michael Horn-von Hoegen, Timothy J Davis, Frank-J Meyer Zu Heringdorf, Harald Giessen
We experimentally and theoretically visualize the propagation of short-range surface plasmon polaritons using atomically flat single-crystalline gold platelets on silicon substrates. We study their excitation and subfemtosecond dynamics via normal-incidence two-photon photoemission electron microscopy. By milling a plasmonic disk and grating structure into a single-crystalline gold platelet, we observe nanofocusing of the short-range surface plasmon polariton. Localized two-photon ultrafast electron emission from a spot with a smallest dimension of 60 nm is observed...
July 2017: Science Advances
Ilaria Cosorich, Gloria Dalla-Costa, Chiara Sorini, Roberto Ferrarese, Maria Josè Messina, Jayashree Dolpady, Elisa Radice, Alberto Mariani, Pier Alberto Testoni, Filippo Canducci, Giancarlo Comi, Vittorio Martinelli, Marika Falcone
T helper 17 (TH17) cells are key players in multiple sclerosis (MS), and studies in animal models demonstrated that effector TH17 cells that trigger brain autoimmunity originate in the intestine. We validate in humans the crucial role of the intestinal environment in promoting TH17 cell expansion in MS patients. We found that increased frequency of TH17 cells correlates with high disease activity and with specific alterations of the gut mucosa-associated microbiota in MS patients. By using 16S ribosomal RNA sequencing, we analyzed the microbiota isolated from small intestinal tissues and found that MS patients with high disease activity and increased intestinal TH17 cell frequency showed a higher Firmicutes/Bacteroidetes ratio, increased relative abundance of Streptococcus, and decreased Prevotella strains compared to healthy controls and MS patients with no disease activity...
July 2017: Science Advances
Jeung Hun Park, Daniel A Steingart, Suneel Kodambaka, Frances M Ross
We develop a solution-based nanoscale patterning technique for site-specific deposition and dissolution of metallic nanocrystals. Nanocrystals are grown at desired locations by electron beam-induced reduction of metal ions in solution, with the ions supplied by dissolution of a nearby electrode via an applied potential. The nanocrystals can be "erased" by choice of beam conditions and regrown repeatably. We demonstrate these processes via in situ transmission electron microscopy using Au as the model material and extend to other metals...
July 2017: Science Advances
Antoine Baudrimont, Sylvia Voegeli, Eduardo Calero Viloria, Fabian Stritt, Marine Lenon, Takeo Wada, Vincent Jaquet, Attila Becskei
The rates of mRNA synthesis and decay determine the mRNA expression level. The two processes are under coordinated control, which makes the measurements of these rates challenging, as evidenced by the low correlation among the methods of measurement of RNA half-lives. We developed a minimally invasive method, multiplexed gene control, to shut off expression of genes with controllable synthetic promoters. The method was validated by measuring the ratios of the nascent to mature mRNA molecules and by measuring the half-life with endogenous promoters that can be controlled naturally or through inserting short sequences that impart repressibility...
July 2017: Science Advances
Min Xu, Daniel Baldauf, Chun Qi Chang, Robert Desimone, Li Hai Tan
A large body of previous neuroimaging studies suggests that multiple languages are processed and organized in a single neuroanatomical system in the bilingual brain, although differential activation may be seen in some studies because of different proficiency levels and/or age of acquisition of the two languages. However, one important possibility is that the two languages may involve interleaved but functionally independent neural populations within a given cortical region, and thus, distinct patterns of neural computations may be pivotal for the processing of the two languages...
July 2017: Science Advances
Michael J Gaudry, Martin Jastroch, Jason R Treberg, Michael Hofreiter, Johanna L A Paijmans, James Starrett, Nathan Wales, Anthony V Signore, Mark S Springer, Kevin L Campbell
Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia...
July 2017: Science Advances
Luis Roman Carrasco, Thi Phuong Le Nghiem, Zhirong Chen, Edward B Barbier
Global sustainability strategies require assessing whether countries' development trajectories are sustainable over time. However, sustainability assessments are limited because losses of natural capital and its ecosystem services through deforestation have not been comprehensively incorporated into national accounts. We update the national accounts of 80 nations that underwent tropical deforestation from 2000 to 2012 and evaluate their development trajectories using weak and strong sustainability criteria...
July 2017: Science Advances
W Tecumseh Fitch, Bart de Boer, Neil Mathur, Asif A Ghazanfar
Macaques do have a speech-ready vocal tract, but lack a speech-ready brain to control it.
July 2017: Science Advances
Yong Xiao, Enhua Zhang, Jingdong Zhang, Youfen Dai, Zhaohui Yang, Hans E M Christensen, Jens Ulstrup, Feng Zhao
Microorganisms exploit extracellular electron transfer (EET) in growth and information exchange with external environments or with other cells. Every microbial cell is surrounded by extracellular polymeric substances (EPS). Understanding the roles of three-dimensional (3D) EPS in EET is essential in microbiology and microbial exploitation for mineral bio-respiration, pollutant conversion, and bioenergy production. We have addressed these challenges by comparing pure and EPS-depleted samples of three representative electrochemically active strains viz Gram-negative Shewanella oneidensis MR-1, Gram-positive Bacillus sp...
July 2017: Science Advances
Lindsay L Traeger, Grzegorz Sabat, Gregory A Barrett-Wilt, Gregg B Wells, Michael R Sussman
The electric eel (Electrophorus electricus) is unusual among electric fishes because it has three pairs of electric organs that serve multiple biological functions: For navigation and communication, it emits continuous pulses of weak electric discharge (<1 V), but for predation and defense, it intermittently emits lethal strong electric discharges (10 to 600 V). We hypothesized that these two electrogenic outputs have different energetic demands reflected by differences in their proteome and phosphoproteome...
July 2017: Science Advances
Nicholas I Brodie, Konstantin I Popov, Evgeniy V Petrotchenko, Nikolay V Dokholyan, Christoph H Borchers
We present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are incorporated into rapid discrete molecular dynamics (DMD) simulations as constraints, reducing the conformational space and achieving the correct protein folding on practical time scales. We tested our approach on myoglobin and FK506 binding protein-models for α helix-rich and β sheet-rich proteins, respectively-and found that the lowest-energy structures obtained were in agreement with the crystal structure, hydrogen-deuterium exchange, surface modification, and long-distance cross-linking validation data...
July 2017: Science Advances
Jacqueline Austermann, Jerry X Mitrovica, Peter Huybers, Alessio Rovere
Estimating minimum ice volume during the last interglacial based on local sea-level indicators requires that these indicators are corrected for processes that alter local sea level relative to the global average. Although glacial isostatic adjustment is generally accounted for, global scale dynamic changes in topography driven by convective mantle flow are generally not considered. We use numerical models of mantle flow to quantify vertical deflections caused by dynamic topography and compare predictions at passive margins to a globally distributed set of last interglacial sea-level markers...
July 2017: Science Advances
Philip Lieberman
Monkey vocal tracts are capable of producing monkey speech, not the full range of articulate human speech. The evolution of human speech entailed both anatomy and brains. Fitch, de Boer, Mathur, and Ghazanfar in Science Advances claim that "monkey vocal tracts are speech-ready," and conclude that "…the evolution of human speech capabilities required neural change rather than modifications of vocal anatomy." Neither premise is consistent either with the data presented and the conclusions reached by de Boer and Fitch themselves in their own published papers on the role of anatomy in the evolution of human speech or with the body of independent studies published since the 1950s...
July 2017: Science Advances
Romain Blanc-Mathieu, Marc Krasovec, Maxime Hebrard, Sheree Yau, Elodie Desgranges, Joel Martin, Wendy Schackwitz, Alan Kuo, Gerald Salin, Cecile Donnadieu, Yves Desdevises, Sophie Sanchez-Ferandin, Hervé Moreau, Eric Rivals, Igor V Grigoriev, Nigel Grimsley, Adam Eyre-Walker, Gwenael Piganeau
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote...
July 2017: Science Advances
Kathleen F Mittendorf, Justin T Marinko, Cheri M Hampton, Zunlong Ke, Arina Hadziselimovic, Jonathan P Schlebach, Cheryl L Law, Jun Li, Elizabeth R Wright, Charles R Sanders, Melanie D Ohi
Peripheral myelin protein 22 (PMP22) is highly expressed in myelinating Schwann cells of the peripheral nervous system. PMP22 genetic alterations cause the most common forms of Charcot-Marie-Tooth disease (CMTD), which is characterized by severe dysmyelination in the peripheral nerves. However, the functions of PMP22 in Schwann cell membranes remain unclear. We demonstrate that reconstitution of purified PMP22 into lipid vesicles results in the formation of compressed and cylindrically wrapped protein-lipid vesicles that share common organizational traits with compact myelin of peripheral nerves in vivo...
July 2017: Science Advances
Viviane Slon, Bence Viola, Gabriel Renaud, Marie-Theres Gansauge, Stefano Benazzi, Susanna Sawyer, Jean-Jacques Hublin, Michael V Shunkov, Anatoly P Derevianko, Janet Kelso, Kay Prüfer, Matthias Meyer, Svante Pääbo
The presence of Neandertals in Europe and Western Eurasia before the arrival of anatomically modern humans is well supported by archaeological and paleontological data. In contrast, fossil evidence for Denisovans, a sister group of Neandertals recently identified on the basis of DNA sequences, is limited to three specimens, all of which originate from Denisova Cave in the Altai Mountains (Siberia, Russia). We report the retrieval of DNA from a deciduous lower second molar (Denisova 2), discovered in a deep stratigraphic layer in Denisova Cave, and show that this tooth comes from a female Denisovan individual...
July 2017: Science Advances
Colin Ruprecht, Rolf Lohaus, Kevin Vanneste, Marek Mutwil, Zoran Nikoloski, Yves Van de Peer, Staffan Persson
Whole-genome duplications (WGDs) or polyploidy events have been studied extensively in plants. In a now widely cited paper, Jiao et al. presented evidence for two ancient, ancestral plant WGDs predating the origin of flowering and seed plants, respectively. This finding was based primarily on a bimodal age distribution of gene duplication events obtained from molecular dating of almost 800 phylogenetic gene trees. We reanalyzed the phylogenomic data of Jiao et al. and found that the strong bimodality of the age distribution may be the result of technical and methodological issues and may hence not be a "true" signal of two WGD events...
July 2017: Science Advances
Dany Lachance-Quirion, Yutaka Tabuchi, Seiichiro Ishino, Atsushi Noguchi, Toyofumi Ishikawa, Rekishu Yamazaki, Yasunobu Nakamura
Combining different physical systems in hybrid quantum circuits opens up novel possibilities for quantum technologies. In quantum magnonics, quanta of collective excitation modes in a ferromagnet, called magnons, interact coherently with qubits to access quantum phenomena of magnonics. We use this architecture to probe the quanta of collective spin excitations in a millimeter-sized ferromagnetic crystal. More specifically, we resolve magnon number states through spectroscopic measurements of a superconducting qubit with the hybrid system in the strong dispersive regime...
July 2017: Science Advances
Cristian Proistosescu, Peter J Huybers
The latest Intergovernmental Panel on Climate Change Assessment Report widened the equilibrium climate sensitivity (ECS) range from 2° to 4.5°C to an updated range of 1.5° to 4.5°C in order to account for the lack of consensus between estimates based on models and historical observations. The historical ECS estimates range from 1.5° to 3°C and are derived assuming a linear radiative response to warming. A Bayesian methodology applied to 24 models, however, documents curvature in the radiative response to warming from an evolving contribution of interannual to centennial modes of radiative response...
July 2017: Science Advances
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