Shock wave–induced permeabilization of mammalian cells Phys. Life Rev. (IF 13.84) Pub Date : 2018-03-21 Luz M. López–Marín, Ana Leonor Rivera, Francisco Fernández, Achim M. Loske
Controlled permeabilization of mammalian cell membranes is fundamental to develop gene and cell therapies based on macromolecular cargo delivery, a process that emerged against an increasing number of health afflictions, including genetic disorders, cancer and infections. Viral vectors have been successfully used for macromolecular delivery; however, they may have unpredictable side effects and have been limited to life–threatening cases. Thus, several chemical and physical methods have been explored to introduce drugs, vaccines, and nucleic acids into cells. One of the most appealing physical methods to deliver genes into cells is shock wave–induced poration. High–speed microjets of fluid, emitted due to the collapse of microbubbles after shock wave passage, represent the most significant mechanism that contributes to cell membrane poration by this technique. Herein, progress in shock wave–induced permeabilization of mammalian cells is presented. After covering the main concepts related to molecular strategies whose applications depend on safer drug delivery methods, the physics behind shock wave phenomena are described. Insights into the use of shock waves for cell membrane permeation are discussed, along with an overview of the two major biomedical applications thereof–i.e., genetic modification and anti–cancer shock wave–assisted chemotherapy. The aim of this review is to summarize 30 years of data showing underwater shock waves as a safe, noninvasive method for macromolecular delivery into mammalian cells, encouraging the development of further research, which is still required before the introduction of this promising tool into clinical practice.
Publisher Correction: Ultrafast quantum beats of anisotropic excitons in atomically thin ReS2 Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Sangwan Sim, Doeon Lee, Artur V. Trifonov, Taeyoung Kim, Soonyoung Cha, Ji Ho Sung, Sungjun Cho, Wooyoung Shim, Moon-Ho Jo, Hyunyong Choi
In the originally published HTML and PDF versions of this article, Figs. 3g and 4d contained typesetting errors affecting the way the data points were displayed. This has now been corrected in the HTML and PDF versions.
Engineering enhanced cellobiohydrolase activity Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Larry E. Taylor, Brandon C. Knott, John O. Baker, P. Markus Alahuhta, Sarah E. Hobdey, Jeffrey G. Linger, Vladimir V. Lunin, Antonella Amore, Venkataramanan Subramanian, Kara Podkaminer, Qi Xu, Todd A. VanderWall, Logan A. Schuster, Yogesh B. Chaudhari, William S. Adney, Michael F. Crowley, Michael E. Himmel, Stephen R. Decker, Gregg T. Beckham
Glycoside Hydrolase Family 7 cellobiohydrolases (GH7 CBHs) catalyze cellulose depolymerization in cellulolytic eukaryotes, making them key discovery and engineering targets. However, there remains a lack of robust structure–activity relationships for these industrially important cellulases. Here, we compare CBHs from Trichoderma reesei (TrCel7A) and Penicillium funiculosum (PfCel7A), which exhibit a multi-modular architecture consisting of catalytic domain (CD), carbohydrate-binding module, and linker. We show that PfCel7A exhibits 60% greater performance on biomass than TrCel7A. To understand the contribution of each domain to this improvement, we measure enzymatic activity for a library of CBH chimeras with swapped subdomains, demonstrating that the enhancement is mainly caused by PfCel7A CD. We solve the crystal structure of PfCel7A CD and use this information to create a second library of TrCel7A CD mutants, identifying a TrCel7A double mutant with near-equivalent activity to wild-type PfCel7A. Overall, these results reveal CBH regions that enable targeted activity improvements.
Ruthenium(II)-enabled para-selective C–H difluoromethylation of anilides and their derivatives Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Chunchen Yuan, Lei Zhu, Changpeng Chen, Xiaolan Chen, Yong Yang, Yu Lan, Yingsheng Zhao
Transition-metal-catalyzed direct site-selective functionalization of arene C–H bonds has emerged as an innovative approach for building the core structure of pharmaceutical agents and other versatile complex compounds. However, para-selective C–H functionalization has seldom been explored, only a few examples, such as steric-hindered arenes, electron-rich arenes, and substrates with a directing group, have been reported to date. Here we describe the development of a ruthenium-enabled para-selective C–H difluoromethylation of anilides, indolines, and tetrahydroquinolines. This reaction tolerates various substituted arenes, affording para-difluoromethylation products in moderate to good yields. Results of a preliminary study of the mechanism indicate that chelation-assisted cycloruthenation might play a role in the selective activation of para-CAr–H bonds. Furthermore, this method provides a direct approach for the synthesis of fluorinated drug derivatives, which has important application for drug discovery and development.
US science agencies set to win big in budget deal Nature (IF 40.137) Pub Date : 2018-03-22 Lauren Morello
US science agencies set to win big in budget deal US science agencies set to win big in budget deal, Published online: 22 March 2018; doi:10.1038/d41586-018-03700-9 Lawmakers are set to vote this week on legislation that includes significant funding increases for many science agencies.
High-capacity optical long data memory based on enhanced Young’s modulus in nanoplasmonic hybrid glass composites Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Qiming Zhang, Zhilin Xia, Yi-Bing Cheng, Min Gu
Emerging as an inevitable outcome of the big data era, long data are the massive amount of data that captures changes in the real world over a long period of time. In this context, recording and reading the data of a few terabytes in a single storage device repeatedly with a century-long unchanged baseline is in high demand. Here, we demonstrate the concept of optical long data memory with nanoplasmonic hybrid glass composites. Through the sintering-free incorporation of nanorods into the earth abundant hybrid glass composite, Young’s modulus is enhanced by one to two orders of magnitude. This discovery, enabling reshaping control of plasmonic nanoparticles of multiple-length allows for continuous multi-level recording and reading with a capacity over 10 terabytes with no appreciable change of the baseline over 600 years, which opens new opportunities for long data memory that affects the past and future.
Early birds may have been too hefty to sit on their eggs Nature (IF 40.137) Pub Date : 2018-03-22 John Pickrell
Early birds may have been too hefty to sit on their eggs Early birds may have been too hefty to sit on their eggs , Published online: 22 March 2018; doi:10.1038/d41586-018-03447-3 Fossil pelvises suggest brooding might have evolved late in modern birds.
Adsorption-based atmospheric water harvesting device for arid climates Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Hyunho Kim, Sameer R. Rao, Eugene A. Kapustin, Lin Zhao, Sungwoo Yang, Omar M. Yaghi, Evelyn N. Wang
Water scarcity is a particularly severe challenge in arid and desert climates. While a substantial amount of water is present in the form of vapour in the atmosphere, harvesting this water by state-of-the-art dewing technology can be extremely energy intensive and impractical, particularly when the relative humidity (RH) is low (i.e., below ~40% RH). In contrast, atmospheric water generators that utilise sorbents enable capture of vapour at low RH conditions and can be driven by the abundant source of solar-thermal energy with higher efficiency. Here, we demonstrate an air-cooled sorbent-based atmospheric water harvesting device using the metal−organic framework (MOF)-801 [Zr6O4(OH)4(fumarate)6] operating in an exceptionally arid climate (10–40% RH) and sub-zero dew points (Tempe, Arizona, USA) with a thermal efficiency (solar input to water conversion) of ~14%. We predict that this device delivered over 0.25 L of water per kg of MOF for a single daily cycle.
Emulsion patterns in the wake of a liquid-liquid phase separation front [Physics] PNAS (IF 9.661) Pub Date : 2018-03-21 Pepijn G. Moerman, Pierre C. Hohenberg, Eric Vanden-Eijnden, Jasna Brujic
Miscible liquids can phase separate in response to a composition change. In bulk fluids, the demixing begins on molecular-length scales, which coarsen into macroscopic phases. By contrast, confining a mixture in microfluidic droplets causes sequential phase separation bursts, which self-organize into rings of oil and water to make multilayered emulsions. The spacing in these nonequilibrium patterns is self-similar and scale-free over a range of droplet sizes. We develop a modified Cahn–Hilliard model, in which an immiscibility front with stretched exponential dynamics quantitatively predicts the spacing of the layers. In addition, a scaling law predicts the lifetime of each layer, giving rise to a stepwise release of inner droplets. Analogously, in long rectangular capillaries, a diffusive front yields large-scale oil and water stripes on the time scale of hours. The same theory relates their characteristic length scale to the speed of the front and the rate of mass transport. Control over liquid–liquid phase separation into large-scale patterns finds potential material applications in living cells, encapsulation, particulate design, and surface patterning.
An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Xiaonan Liu, Kari Salokas, Fitsum Tamene, Yaming Jiu, Rigbe G. Weldatsadik, Tiina Öhman, Markku Varjosalo
Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein’s molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome.
Spatially disaggregated population estimates in the absence of national population and housing census data [Perspectives] PNAS (IF 9.661) Pub Date : 2018-03-21 N. A. Wardrop, W. C. Jochem, T. J. Bird, H. R. Chamberlain, D. Clarke, D. Kerr, L. Bengtsson, S. Juran, V. Seaman, A. J. Tatem
Population numbers at local levels are fundamental data for many applications, including the delivery and planning of services, election preparation, and response to disasters. In resource-poor settings, recent and reliable demographic data at subnational scales can often be lacking. National population and housing census data can be outdated, inaccurate, or missing key groups or areas, while registry data are generally lacking or incomplete. Moreover, at local scales accurate boundary data are often limited, and high rates of migration and urban growth make existing data quickly outdated. Here we review past and ongoing work aimed at producing spatially disaggregated local-scale population estimates, and discuss how new technologies are now enabling robust and cost-effective solutions. Recent advances in the availability of detailed satellite imagery, geopositioning tools for field surveys, statistical methods, and computational power are enabling the development and application of approaches that can estimate population distributions at fine spatial scales across entire countries in the absence of census data. We outline the potential of such approaches as well as their limitations, emphasizing the political and operational hurdles for acceptance and sustainable implementation of new approaches, and the continued importance of traditional sources of national statistical data.
BEARscc determines robustness of single-cell clusters using simulated technical replicates Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 D. T. Severson, R. P. Owen, M. J. White, X. Lu, B. Schuster-Böckler
Single-cell messenger RNA sequencing (scRNA-seq) has emerged as a powerful tool to study cellular heterogeneity within complex tissues. Subpopulations of cells with common gene expression profiles can be identified by applying unsupervised clustering algorithms. However, technical variance is a major confounding factor in scRNA-seq, not least because it is not possible to replicate measurements on the same cell. Here, we present BEARscc, a tool that uses RNA spike-in controls to simulate experiment-specific technical replicates. BEARscc works with a wide range of existing clustering algorithms to assess the robustness of clusters to technical variation. We demonstrate that the tool improves the unsupervised classification of cells and facilitates the biological interpretation of single-cell RNA-seq experiments.
Genetic mapping of species differences via in vitro crosses in mouse embryonic stem cells [Genetics] PNAS (IF 9.661) Pub Date : 2018-03-21 Stefano Lazzarano, Marek Kučka, João P. L. Castro, Ronald Naumann, Paloma Medina, Michael N. C. Fletcher, Rebecka Wombacher, Joost Gribnau, Tino Hochepied, Marc Van Montagu, Claude Libert, Yingguang Frank Chan
Discovering the genetic changes underlying species differences is a central goal in evolutionary genetics. However, hybrid crosses between species in mammals often suffer from hybrid sterility, greatly complicating genetic mapping of trait variation across species. Here, we describe a simple, robust, and transgene-free technique to generate “in vitro crosses” in hybrid mouse embryonic stem (ES) cells by inducing random mitotic cross-overs with the drug ML216, which inhibits the DNA helicase Bloom syndrome (BLM). Starting with an interspecific F1 hybrid ES cell line between the Mus musculus laboratory mouse and Mus spretus (∼1.5 million years of divergence), we mapped the genetic basis of drug resistance to the antimetabolite tioguanine to a single region containing hypoxanthine–guanine phosphoribosyltransferase (Hprt) in as few as 21 d through “flow mapping” by coupling in vitro crosses with fluorescence-activated cell sorting (FACS). We also show how our platform can enable direct study of developmental variation by rederiving embryos with contribution from the recombinant ES cell lines. We demonstrate how in vitro crosses can overcome major bottlenecks in mouse complex trait genetics and address fundamental questions in evolutionary biology that are otherwise intractable through traditional breeding due to high cost, small litter sizes, and/or hybrid sterility. In doing so, we describe an experimental platform toward studying evolutionary systems biology in mouse and potentially in human and other mammals, including cross-species hybrids.
Surface tension-assisted additive manufacturing Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Héloïse Ragelle, Mark W. Tibbitt, Shang-Yun Wu, Michael A. Castillo, George Z. Cheng, Sidharta P. Gangadharan, Daniel G. Anderson, Michael J. Cima, Robert Langer
The proliferation of computer-aided design and additive manufacturing enables on-demand fabrication of complex, three-dimensional structures. However, combining the versatility of cell-laden hydrogels within the 3D printing process remains a challenge. Herein, we describe a facile and versatile method that integrates polymer networks (including hydrogels) with 3D-printed mechanical supports to fabricate multicomponent (bio)materials. The approach exploits surface tension to coat fenestrated surfaces with suspended liquid films that can be transformed into solid films. The operating parameters for the process are determined using a physical model, and complex geometric structures are successfully fabricated. We engineer, by tailoring the window geometry, scaffolds with anisotropic mechanical properties that compress longitudinally (~30% strain) without damaging the hydrogel coating. Finally, the process is amenable to high cell density encapsulation and co-culture. Viability (>95%) was maintained 28 days after encapsulation. This general approach can generate biocompatible, macroscale devices with structural integrity and anisotropic mechanical properties.
Analysis of oscillatory rocking curve by dynamical diffraction in protein crystals [Physics] PNAS (IF 9.661) Pub Date : 2018-03-21 Ryo Suzuki, Haruhiko Koizumi, Keiichi Hirano, Takashi Kumasaka, Kenichi Kojima, Masaru Tachibana
High-quality protein crystals meant for structural analysis by X-ray diffraction have been grown by various methods. The observation of dynamical diffraction in protein crystals is an interesting topic because dynamical diffraction generally occurs in perfect crystals such as Si crystals. However, to our knowledge, there is no report yet on protein crystals showing clear dynamical diffraction. We wonder whether the perfection of protein crystals might still be low compared with that of high-quality Si crystals. Here, we present observations of the oscillatory profile of rocking curves for protein crystals such as glucose isomerase crystals. The oscillatory profiles are in good agreement with those predicted by the dynamical theory of diffraction. We demonstrate that dynamical diffraction occurs even in protein crystals. This suggests the possibility of the use of dynamical diffraction for the determination of the structure and charge density of proteins.
Cryo-EM structure of the polycystic kidney disease-like channel PKD2L1 Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Qiang Su, Feizhuo Hu, Yuxia Liu, Xiaofei Ge, Changlin Mei, Shengqiang Yu, Aiwen Shen, Qiang Zhou, Chuangye Yan, Jianlin Lei, Yanqing Zhang, Xiaodong Liu, Tingliang Wang
PKD2L1, also termed TRPP3 from the TRPP subfamily (polycystic TRP channels), is involved in the sour sensation and other pH-dependent processes. PKD2L1 is believed to be a nonselective cation channel that can be regulated by voltage, protons, and calcium. Despite its considerable importance, the molecular mechanisms underlying PKD2L1 regulations are largely unknown. Here, we determine the PKD2L1 atomic structure at 3.38 Å resolution by cryo-electron microscopy, whereby side chains of nearly all residues are assigned. Unlike its ortholog PKD2, the pore helix (PH) and transmembrane segment 6 (S6) of PKD2L1, which are involved in upper and lower-gate opening, adopt an open conformation. Structural comparisons of PKD2L1 with a PKD2-based homologous model indicate that the pore domain dilation is coupled to conformational changes of voltage-sensing domains (VSDs) via a series of π–π interactions, suggesting a potential PKD2L1 gating mechanism.
Schema learning for the cocktail party problem [Psychological and Cognitive Sciences] PNAS (IF 9.661) Pub Date : 2018-03-21 Kevin J. P. Woods, Josh H. McDermott
The cocktail party problem requires listeners to infer individual sound sources from mixtures of sound. The problem can be solved only by leveraging regularities in natural sound sources, but little is known about how such regularities are internalized. We explored whether listeners learn source “schemas”—the abstract structure shared by different occurrences of the same type of sound source—and use them to infer sources from mixtures. We measured the ability of listeners to segregate mixtures of time-varying sources. In each experiment a subset of trials contained schema-based sources generated from a common template by transformations (transposition and time dilation) that introduced acoustic variation but preserved abstract structure. Across several tasks and classes of sound sources, schema-based sources consistently aided source separation, in some cases producing rapid improvements in performance over the first few exposures to a schema. Learning persisted across blocks that did not contain the learned schema, and listeners were able to learn and use multiple schemas simultaneously. No learning was evident when schema were presented in the task-irrelevant (i.e., distractor) source. However, learning from task-relevant stimuli showed signs of being implicit, in that listeners were no more likely to report that sources recurred in experiments containing schema-based sources than in control experiments containing no schema-based sources. The results implicate a mechanism for rapidly internalizing abstract sound structure, facilitating accurate perceptual organization of sound sources that recur in the environment.
Asymmetric synthesis of γ-branched amines via rhodium-catalyzed reductive amination Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Zhao Wu, Summer D. Laffoon, Kami L. Hull
Amines bearing γ-stereocenters are highly important structural motifs in many biologically active compounds. However, reported enantioselective syntheses of these molecules are indirect and often require multiple steps. Herein, we report a general asymmetric route for the one-pot synthesis of chiral γ-branched amines through the highly enantioselective isomerization of allylamines, followed by enamine exchange and subsequent chemoselective reduction. This protocol is suitable for establishing various tertiary stereocenters, including those containing dialkyl, diaryl, cyclic, trifluoromethyl, difluoromethyl, and silyl substituents, which allows for a rapid and modular synthesis of many chiral γ-branched amines. To demonstrate the synthetic utility, Terikalant and Tolterodine are synthesized using this method with high levels of enantioselectivity.
Identifying migratory birds’ population bottlenecks in time and space [Commentaries] PNAS (IF 9.661) Pub Date : 2018-03-21 Thomas W. Sherry
The annual disappearance and reappearance of billions of migratory animals from seasonal environments across the planet is a stunning natural phenomenon. Naturalists have marveled for more than 2,000 y at these migrations, at least since Aristotle pondered birds’ seasonal disappearance. Birds are the preeminent seasonal commuters because of their physiological capacity for sustained long-distance flight, extraordinary navigational adaptations, and diversity of movement patterns; and since Aristotle’s time we have learned much about how and why birds migrate (1). What’s been tougher to decipher is how and where migrants’ populations are controlled. Sampling and tracking the millions of individuals in many species is challenging because of far-flung seasonal movements that can span entire continents and shuttle between them, the baffling array of ways to migrate, and the potential for population limitation in summer, winter, spring or fall transits, or some combination thereof. Overcoming many of these challenges, Kramer et al. (2) in PNAS contribute significantly to understanding migratory birds’ population bottlenecks by linking different distribution patterns in two closely related Vermivora wood warblers (Parulidae) to ecological conditions precipitating decline in a geographically distinctive population of one of the two species.
Studying an antiaromatic polycyclic hydrocarbon adsorbed on different surfaces Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Zsolt Majzik, Niko Pavliček, Manuel Vilas-Varela, Dolores Pérez, Nikolaj Moll, Enrique Guitián, Gerhard Meyer, Diego Peña, Leo Gross
Antiaromatic and open-shell molecules are attractive because of their distinct electronic and magnetic behaviour. However, their increased reactivity creates a challenge for probing their properties. Here, we describe the on-surface and in-solution generation and characterisation of a highly reactive antiaromatic molecule: indeno[1,2-b]fluorene (IF). In solution, we generated IF by KI-induced dehalogenation of a dibromo-substituted precursor molecule and found that IF survives for minutes at ambient conditions. Using atom manipulation at low temperatures we generated IF on Cu(111) and on bilayer NaCl. On these surfaces, we characterised IF by bond-order analysis using non-contact atomic force microscopy with CO-functionalised tips and by orbital imaging using scanning tunnelling microscopy. We found that the closed-shell configuration and antiaromatic character predicted for gas-phase IF are preserved on the NaCl film. On Cu(111), we observed significant bond-order reorganisation within the s-indacene moiety because of chemisorption, highlighting the importance of molecule surface interactions on the π-electron distribution.
Strategies for microbial synthesis of high-value phytochemicals Nat. Chem. (IF 25.87) Pub Date : 2018-03-22 Sijin Li, Yanran Li, Christina D. Smolke
Phytochemicals are of great pharmaceutical and agricultural importance, but often exhibit low abundance in nature. Recent demonstrations of industrial-scale production of phytochemicals in yeast have shown that microbial production of these high-value chemicals is a promising alternative to sourcing these molecules from native plant hosts. However, a number of challenges remain in the broader application of this approach, including the limited knowledge of plant secondary metabolism and the inefficient reconstitution of plant metabolic pathways in microbial hosts. In this Review, we discuss recent strategies to achieve microbial biosynthesis of complex phytochemicals, including strategies to: (1) reconstruct plant biosynthetic pathways that have not been fully elucidated by mining enzymes from native and non-native hosts or by enzyme engineering; (2) enhance plant enzyme activity, specifically cytochrome P450 activity, by improving efficiency, selectivity, expression or electron transfer; and (3) enhance overall reaction efficiency of multi-enzyme pathways by dynamic control, compartmentalization or optimization with the host’s metabolism. We also highlight remaining challenges to — and future opportunities of — this approach.
Protonation underlies tonic vs. use-dependent block [Commentaries] PNAS (IF 9.661) Pub Date : 2018-03-21 Vincenzo Carnevale
Eukaryotic voltage gated sodium-selective channels (VGSCs) enable influx of Na+ into excitable cells in response to a change in the transmembrane potential. This movement of ions causes the membrane depolarization occurring during the rising phase of the action potential and, as such, underlies propagation of electrical signals in neurons. The transmembrane region of VGSCs is characterized by a fourfold pseudosymmetrical architecture. In particular, the channel is constituted of four homologous repeats (referred to as domains, DI through DIV), each comprising six helical segments (S1 through S6). The first four helices (S1–S4) of each domain assemble into a separate helix bundle, the so-called voltage sensor domain, which undergoes a conformational transition in response to membrane depolarization. The remaining S5 and S6 helices from all of the domains form a tetrameric assembly, the pore domain, containing a lumen in its center. The latter constitutes a pathway connecting the extracellular and intracellular compartments, enabling diffusion of water molecules and ions across the membrane. Crucial milestones along this pathway are the selectivity filter, a section permeable to Na+ but not K+, and the activation gate, a hydrophobic plug that hinders the passage of waters and ions when the channel is in the closed state.
Molecular basis of binding between the global post-transcriptional regulator CsrA and the T3SS chaperone CesT Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Fei Ye, Fanli Yang, Ruijie Yu, Xi Lin, Jianxun Qi, Zhujun Chen, Yu Cao, Yuquan Wei, George F. Gao, Guangwen Lu
The T3SS chaperone CesT is recently shown to interact with the post-transcriptional regulator CsrA to modulate post-attachment signaling in enteropathogenic and enterohemorrhagic Escherichia coli. The molecular basis of the CesT/CsrA binding, however, remains elusive. Here, we show that CesT and CsrA both created two ligand binding sites in their homodimers, forming irregular multimeric complexes in solution. Through construction of a recombinant CsrA-dimer (Re-CsrA) that contains a single CesT binding site, the atomic binding features between CesT and CsrA are delineated via the structure of the CesT/Re-CsrA complex. In contrast to a previously reported N-terminally swapped dimer-form, CesT adopts a dimeric architecture with a swapped C-terminal helix for CsrA engagement. In CsrA, CesT binds to a surface patch that extensively overlaps with its mRNA binding site. The binding mode therefore justifies a mechanism of CsrA-modulation by CesT via competitive inhibition of the CsrA/mRNA interactions.
Low ocean-floor rises regulate subpolar sea surface temperature by forming baroclinic jets Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 H. Mitsudera, T. Miyama, H. Nishigaki, T. Nakanowatari, H. Nishikawa, T. Nakamura, T. Wagawa, R. Furue, Y. Fujii, S. Ito
Sea surface temperature (SST) fronts in mid- to high-latitude oceans have significant impacts on extratropical atmospheric circulations and climate. In the western subarctic Pacific, sharp SST fronts form between the cold subarctic water and the recently found quasi-stationary jets that advect warm waters originating in the Kuroshio northeastward. Here we present a new mechanism of the jet formation paying attention to the propagation of baroclinic Rossby waves that is deflected by eddy-driven barotropic flows over bottom rises, although their height is low (~500 m) compared with the depth of the North Pacific Ocean (~6000 m). Steered by the barotropic flows, Rossby waves bring a thicker upper layer from the subtropical gyre and a thinner upper layer from the subarctic gyre, thereby creating a thickness jump, hence a surface jet, where they converge. This study reveals an overlooked role of low-rise bottom topography in regulating SST anomalies in subpolar oceans.
Value of ecosystem-based management [Commentaries] PNAS (IF 9.661) Pub Date : 2018-03-21 Heather M. Leslie
Taking the pulse of an ecosystem is not quite as straightforward as taking the pulse of a person, especially when that ecosystem is the Chesapeake Bay. At 195 miles long and 3,237 square miles in area, the size and complexity of the bay’s coupled social and ecological systems has challenged efforts to assess its health. Building on more than 30 y of research, Lefcheck et al. (1) offer an innovative way to take the pulse of this much loved and debilitated coastal estuary. By developing a model of the bay ecosystem that brings data from long-term, large-scale monitoring together with knowledge of the mechanisms underlying those patterns, Lefcheck et al. make a compelling case that ecosystem restoration initiatives of the last 30+ y are paying off.
Foldamers wave to the ribosome Nat. Chem. (IF 25.87) Pub Date : 2018-03-22 Alanna Schepartz
Foldamers wave to the ribosome Foldamers wave to the ribosome, Published online: 22 March 2018; doi:10.1038/s41557-018-0036-5 Ribosomes have now been shown to accept certain initiator tRNAs acylated with aromatic foldamer–dipeptides thereby enabling the translation of a peptide or protein with a short aromatic foldamer at the N-terminus. Some foldamer–peptide hybrids could be cyclized to generate macrocycles that present conformationally restricted peptide loops.
Isolation of diborenes and their 90°-twisted diradical congeners Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Julian Böhnke, Theresa Dellermann, Mehmet Ali Celik, Ivo Krummenacher, Rian D. Dewhurst, Serhiy Demeshko, William C. Ewing, Kai Hammond, Merlin Heß, Eckhard Bill, Eileen Welz, Merle I. S. Röhr, Roland Mitrić, Bernd Engels, Franc Meyer, Holger Braunschweig
Molecules containing multiple bonds between atoms—most often in the form of olefins—are ubiquitous in nature, commerce, and science, and as such have a huge impact on everyday life. Given their prominence, over the last few decades, frequent attempts have been made to perturb the structure and reactivity of multiply-bound species through bending and twisting. However, only modest success has been achieved in the quest to completely twist double bonds in order to homolytically cleave the associated π bond. Here, we present the isolation of double-bond-containing species based on boron, as well as their fully twisted diradical congeners, by the incorporation of attached groups with different electronic properties. The compounds comprise a structurally authenticated set of diamagnetic multiply-bound and diradical singly-bound congeners of the same class of compound.
Facile bottom-up synthesis of partially oxidized black phosphorus nanosheets as metal-free photocatalyst for hydrogen evolution [Chemistry] PNAS (IF 9.661) Pub Date : 2018-03-21 Bin Tian, Bining Tian, Bethany Smith, M. C. Scott, Qin Lei, Ruinian Hua, Yue Tian, Yi Liu
Few-layer black phosphorus (BP) nanosheets were first reported as a 2D material for the application of field-effect transistors in 2014 and have stimulated intense activity among physicists, chemists, and material and biomedical scientists, driving research into novel synthetic techniques to produce BP nanosheets. At present, exfoliation is the main route toward few-layer BP nanosheets via employing bulk BP as raw material. However, this is a complicated and time-consuming process, which is difficult for the large-scale synthesis of BP nanosheets. Moreover, BP degrades rapidly when exfoliated to nanoscale dimensions, resulting in the rapid loss of semiconducting properties. Here, we report the direct wet-chemical synthesis of few-layer BP nanosheets in gram-scale quantities in a bottom-up approach based on common laboratory reagents at low temperature, showing excellent stability due to partial oxidation of surface. Solvent and temperature are two critical factors, controlling not only the formation of BP nanosheets but also the thickness. The as-prepared BP nanosheets can extract hydrogen from pure water (pH = 6.8), exhibiting more than 24-fold higher activity than the well-known C3N4 nanosheets. Our results reporting the ability to prepare few-layer BP nanosheets with a facile, scalable, low-cost approach take us a step closer to real-world applications of phosphorene including next-generation metal-free photocatalysts for photosynthesis.
PHA-4/FoxA senses nucleolar stress to regulate lipid accumulation in Caenorhabditis elegans Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Jieyu Wu, Xue Jiang, Yamei Li, Tingting Zhu, Jingjing Zhang, Zhiguo Zhang, Linqiang Zhang, Yuru Zhang, Yanli Wang, Xiaoju Zou, Bin Liang
The primary function of the nucleolus is ribosome biogenesis, which is an extremely energetically expensive process. Failures in ribosome biogenesis cause nucleolar stress with an altered energy status. However, little is known about the underlying mechanism linking nucleolar stress to energy metabolism. Here we show that nucleolar stress is triggered by inactivation of RSKS-1 (ribosomal protein S6 kinase), RRP-8 (ribosomal RNA processing 8), and PRO-2/3 (proximal proliferation), all of which are involved in ribosomal RNA processing or inhibition of rDNA transcription by actinomycin D (AD), leading to excessive lipid accumulation in Caenorhabditis elegans. The transcription factor PHA-4/FoxA acts as a sensor of nucleolar stress to bind to and transactivate the expression of the lipogenic genes pod-2 (acetyl-CoA carboxylase), fasn-1 (fatty acid synthase), and dgat-2 (diacylglycerol O-acyltransferase 2), consequently promoting lipid accumulation. Importantly, inactivation of pha-4 or dgat-2 is sufficient to abolish nucleolar stress-induced lipid accumulation and prolonged starvation survival. The results revealed a distinct PHA-4-mediated lipogenesis pathway that senses nucleolar stress and shifts excessive energy for storage as fat.
Hormone modulates protein dynamics to regulate plant growth [Commentaries] PNAS (IF 9.661) Pub Date : 2018-03-21 Yonglun Zeng, Jinbo Shen, Baiying Li, Liwen Jiang
Endosomal traffic in the plant endomembrane system is a fundamental and complex process that controls many essential cellular, developmental, and physiological functions in plants, including cellular polarization, cytokinesis, metal ion homeostasis, pathogen defense, and hormone transport (1). The secretory and endocytic pathways represent two major anterograde protein transport routes for protein delivery into the vacuole in plant cells (Fig. 1A). In the secretory pathway, transportation of newly synthesized soluble vacuolar cargo proteins is mediated by the vacuolar sorting receptors (VSRs) (2). After delivery of the soluble cargos into an intermediate compartment, receptors are recycled by the attachment of conserved sorting nexins (SNXs) and the core subunits of retromer complex (VPS26, VPS29, and VPS35) to the membrane. Nevertheless, the precise localization of the SNXs and the retromer subunits, as well as the identity of the organelles from which VSRs are recycled, remains in debate (3, 4). During endocytosis, plasma membrane (PM) proteins are internalized and delivered into the trans-Golgi network (TGN)/early endosomes in plants (5). Ubiquitinated PM proteins are further sorted into the intralumenal vesicles of multivesicular bodies, previously identified as a prevacuolar compartment (6), by the endosomal sorting complex required for transport machinery for vacuolar degradation (7). Alternatively, PM proteins without a ubiquitin tag (or after removal of ubiquitin by a deubiquitinating enzyme) are recycled back to the PM from the TGN or recycling endosome (RE) (1, 8). In plants, numerous PM proteins undergo endocytosis and endosomal recycling, with the PIN-FORMED (PINs) transporters for the plant hormone auxin being the most studied (9). Polarized PM localization of PINs has a profound developmental importance and is tightly regulated by multiple endosomal trafficking routes, including endocytosis, endosomal recycling, and vacuolar degradation. PINs are internalized via clathrin-mediated endocytosis and then recycled back to the PM via the GNOM-positive putative RE …
Data-driven model for the assessment of Mycobacterium tuberculosis transmission in evolving demographic structures [Medical Sciences] PNAS (IF 9.661) Pub Date : 2018-03-21 Sergio Arregui, María José Iglesias, Sofía Samper, Dessislava Marinova, Carlos Martin, Joaquín Sanz, Yamir Moreno
In the case of tuberculosis (TB), the capabilities of epidemic models to produce quantitatively robust forecasts are limited by multiple hindrances. Among these, understanding the complex relationship between disease epidemiology and populations’ age structure has been highlighted as one of the most relevant. TB dynamics depends on age in multiple ways, some of which are traditionally simplified in the literature. That is the case of the heterogeneities in contact intensity among different age strata that are common to all airborne diseases, but still typically neglected in the TB case. Furthermore, while demographic structures of many countries are rapidly aging, demographic dynamics are pervasively ignored when modeling TB spreading. In this work, we present a TB transmission model that incorporates country-specific demographic prospects and empirical contact data around a data-driven description of TB dynamics. Using our model, we find that the inclusion of demographic dynamics is followed by an increase in the burden levels predicted for the next decades in the areas of the world that are most hit by the disease today. Similarly, we show that considering realistic patterns of contacts among individuals in different age strata reshapes the transmission patterns reproduced by the models, a result with potential implications for the design of age-focused epidemiological interventions.
Dop1 enhances conspecific olfactory attraction by inhibiting miR-9a maturation in locusts Nat. Commun. (IF 12.124) Pub Date : 2018-03-22 Xiaojiao Guo, Zongyuan Ma, Baozhen Du, Ting Li, Wudi Li, Lingling Xu, Jing He, Le Kang
Dopamine receptor 1 (Dop1) mediates locust attraction behaviors, however, the mechanism by which Dop1 modulates this process remains unknown to date. Here, we identify differentially expressed small RNAs associated with locust olfactory attraction after activating and inhibiting Dop1. Small RNA transcriptome analysis and qPCR validation reveal that Dop1 activation and inhibition downregulates and upregulates microRNA-9a (miR-9a) expression, respectively. miR-9a knockdown in solitarious locusts increases their attraction to gregarious volatiles, whereas miR-9a overexpression in gregarious locusts reduces olfactory attraction. Moreover, miR-9a directly targets adenylyl cyclase 2 (ac2), causing its downregulation at the mRNA and protein levels. ac2 responds to Dop1 and mediates locust olfactory attraction. Mechanistically, Dop1 inhibits miR-9a expression through inducing the dissociation of La protein from pre-miR-9a and resulting in miR-9a maturation inhibition. Our results reveal a Dop1–miR-9a–AC2 circuit that modulates locust olfactory attraction underlying aggregation. This study suggests that miRNAs act as key messengers in the GPCR signaling.
Made in translation Nat. Chem. (IF 25.87) Pub Date : 2018-03-22 John C. Chaput
Made in translation Made in translation, Published online: 22 March 2018; doi:10.1038/s41557-018-0034-7 Evolution of highly functionalized DNA could enable the discovery of artificial nucleic acid sequences with different properties to natural DNA. Now, an artificial translation system has been designed that can support the evolution of non-natural sequence-defined nucleic acid polymers carrying eight different functional groups on 32 codons.
Organic synthesis provides opportunities to transform drug discovery Nat. Chem. (IF 25.87) Pub Date : 2018-03-22 David C. Blakemore, Luis Castro, Ian Churcher, David C. Rees, Andrew W. Thomas, David M. Wilson, Anthony Wood
Despite decades of ground-breaking research in academia, organic synthesis is still a rate-limiting factor in drug-discovery projects. Here we present some current challenges in synthetic organic chemistry from the perspective of the pharmaceutical industry and highlight problematic steps that, if overcome, would find extensive application in the discovery of transformational medicines. Significant synthesis challenges arise from the fact that drug molecules typically contain amines and N-heterocycles, as well as unprotected polar groups. There is also a need for new reactions that enable non-traditional disconnections, more C–H bond activation and late-stage functionalization, as well as stereoselectively substituted aliphatic heterocyclic ring synthesis, C–X or C–C bond formation. We also emphasize that syntheses compatible with biomacromolecules will find increasing use, while new technologies such as machine-assisted approaches and artificial intelligence for synthesis planning have the potential to dramatically accelerate the drug-discovery process. We believe that increasing collaboration between academic and industrial chemists is crucial to address the challenges outlined here.
Spindle cell sarcoma: a SEER population-based analysis Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Lei Feng, Meng Wang, Feiluore Yibulayin, Hao Zhang, Yin-Long Yang, Fei Ren, Alimujiang Wushou
Due to the substantial limitation of study population, Spindle cell sarcoma (SCS) was unexplored comprehensively. In this study, we investigated the clinical characteristics and disease specific prognostic factors of SCS. 3299 SCS cases were identified and extracted from Surveillance, Epidemiology, and End Results (SEER) database (1973–2017). White people account for 79.1% with median age of 57 years without predominance in any gender. Significant disease specific survival (DSS) and overall survival (OS) were found differentiated in age, T stage, N stage, M stage, AJCC stage, SEER historic stage, tumor locations, surgery, and pathologic grade. In the multivariate Cox analysis, the age >64 years (for DSS, P < 0.001 and for OS, P < 0.001; Reference age ≤64 years), AJCC stage III (for DSS, P = 0.006 and for OS, P = 0.04; Reference: AJCC stage I), and non-surgical treatment (for DSS, P < 0.001 and for OS, P < 0.001; Reference: surgery) were independently associated with worse DSS and OS. In brief, our study demonstrated that SCS mostly found in white people at fifth to seventh decades of life without gender predilection. The patient’s age, AJCC stage, tumor location and surgery were independent prognostic indicators for both DSS and OS of SCS.
Operating length and velocity of human vastus lateralis muscle during walking and running Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 S. Bohm, R. Marzilger, F. Mersmann, A. Santuz, A. Arampatzis
According to the force-length-velocity relationships, the muscle force potential during locomotion is determined by the operating fibre length and velocity. We measured fascicle and muscle-tendon unit length and velocity as well as the activity of the human vastus lateralis muscle (VL) during walking and running. Furthermore, we determined the VL force-length relationship experimentally and calculated the force-length and force-velocity potentials (i.e. fraction of maximum force according to the force-length-velocity curves) for both gaits. During the active state of the stance phase, fascicles showed significantly (p < 0.05) smaller length changes (walking: 9.2 ± 4.7% of optimal length (L0); running: 9.0 ± 8.4%L0) and lower velocities (0.46 ± 0.36 L0/s; 0.03 ± 0.83 L0/s) compared to the muscle-tendon unit (walking: 19.7 ± 5.3%L0, −0.94 ± 0.32 L0/s; running: 34.5 ± 5.8%L0, −2.59 ± 0.41 L0/s). The VL fascicles operated close to optimum length (L0 = 9.4 ± 0.11 cm) in both walking (8.6 ± 0.14 cm) and running (10.1 ± 0.19 cm), resulting in high force-length (walking: 0.92 ± 0.08; running: 0.91 ± 0.14) and force-velocity (0.91 ± 0.08; 0.97 ± 0.13) potentials. For the first time we demonstrated that, in contrast to the current general conception, the VL fascicles operate almost isometrically and close to L0 during the active state of the stance phase of walking and running. The findings further verify an important contribution of the series-elastic element to VL fascicle dynamics.
Frequency of Esophageal Eosinophilia in a Pediatric Population from Central Brazil Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Daniel Strozzi, Marco Aurélio Silveira Botacin, Marilia Adriano Mekdessi, Luciana Ximenes Salustiano, Pedro H. de Paula Silva, Lysa Bernardes Minasi, Gesmar Rodrigues Silva Segundo, Aparecido Divino da Cruz
Here we report a retrospective cross-sectional study on Esophageal eosinophilia (EsEo) frequency in Brazil, for 2, 425 pediatric patients with symptoms associated with gastroesophageal diseases in 2012. EsEo is defined by ≥15 eosinophils per high power field (400x) and confirmed through histological analyses of esophageal biopsies. Overall, 126 patients had EsEo equating to a frequency of 5.2%. There was a significant difference between the endoscopic features of patients with EsEo, where 10.7% had erosive esophagitis, 3.0% had non-erosive esophagitis and 1% showed normal esophageal mucosa. According to the interaction of the variables in the Classification and Regression Tree Analysis, most patients diagnosed with EsEo were older males with erosive esophagitis. On the other hand, the lowest frequency of EsEo was found among younger females with non-erosive esophagitis/normal mucosa. Environmental conditions, including climate variation and changes, were observed in association with EsEo, supporting a potential role for environmental factors in its pathogenesis. There was an inverse correlation between the number of EsEo, rainfall and humidity. EsEo is a relatively frequent finding in the pediatric population of Brazil with symptoms of gastroesophageal diseases. Both clinical and histological examinations of patients are important for a reliable diagnostic of EsEo cases and to patient care.
Tracing intensive fish and meat consumption using Zn isotope ratios: evidence from a historical Breton population (Rennes, France) Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Klervia Jaouen, Rozenn Colleter, Anita Pietrzak, Marie-Laure Pons, Benoît Clavel, Norbert Telmon, Éric Crubézy, Jean-Jacques Hublin, Michael P. Richards
Here we report Sr and Zn isotope ratios of teeth of medieval to early modern Breton people a population whose diet is known from historical, archeological and collagen isotope data. Most of the population, buried in the Dominican convent of Rennes, France, consists of parliamentary nobles, wealthy commoners and ecclesiastics, who had a diet rich in animal products. Our aim is to assess how the Zn isotope ratios of their teeth compare to those of other French historical populations previously studied, which were characterized by cereal-based diets, and those of modern French individuals, who daily eat animal products. We describe a clear offset (∼0.35‰) between local and non-local human individuals in Zn isotope ratios. The δ66Zntooth values of local individuals overlap that of modern French people, and are lower than those of local carnivores. Non-local δ66Zn values are similar to those of historical individuals analyzed previously. We conclude the lower Zn isotope ratios of local humans relative to the associated fauna can be explained by the consumption of carnivorous fish and pork, in agreement with historical, zooarchaeological and collagen (C, N, S) isotope data. Zn isotopes could therefore be a tracer of fish and/or substantial meat consumption in ancient populations.
Hidden hassium Nat. Chem. (IF 25.87) Pub Date : 2018-03-22 Michael A. Tarselli
Hidden hassium Hidden hassium, Published online: 22 March 2018; doi:10.1038/s41557-018-0037-4 From its scarcity to political intrigue over naming conventions, element 108’s story describes how international cooperation overcame the limits of nuclear science, says Michael Tarselli.
Kinematic features in patients with lateral discoid meniscus injury during walking Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Zefeng Lin, Wenhan Huang, Limin Ma, Lingling Chen, Zhiqiang Huang, Xiaolong Zeng, Hong Xia, Yu Zhang
At present, there few studies on the kinematic features of lateral discoid meniscus injury. In this study, a motion capture system was used to investigate the motion characteristics of knees with lateral discoid meniscus after injury, and the differences between the knees with lateral meniscus and intact knees were compared. Fourteen patients diagnosed with unilateral lateral discoid meniscus injury, fourteen patients diagnosed with unilateral lateral meniscus injury, and fourteen normal subjects with healthy knees were recruited and grouped. Through kinematic gait analysis, it was found that the subjects in the two groups with meniscus injuries exhibited significantly smaller ranges of rotation and translation than those with healthy knees on the sagittal, coronal, and horizontal planes, but not in proximal-distal translation. Maximum lateral tibial translation and maximum internal tibial rotation in the knees with lateral discoid meniscus injury were significantly decreased compared to those with lateral meniscus injury. The results show that the kinematic features of knees with lateral discoid meniscus injury are statistically different than those of healthy knees and knees with lateral meniscus injury. This study provides an important reference for the dynamic function of knees with lateral discoid meniscus injury.
Repeatability and degree of territorial aggression differs among urban and rural great tits (Parus major) Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Samuel I. Hardman, Sarah Dalesman
Animals in urban habitats face many novel selection pressures such as increased human population densities and human disturbance. This is predicted to favour bolder and more aggressive individuals together with greater flexibility in behaviour. Previous work has focussed primarily on studying these traits in captive birds and has shown increased aggression and reduced consistency between traits (behavioural syndromes) in birds from urban populations. However, personality (consistency within a behavioural trait) has not been well studied in the wild. Here we tested whether urban free-living male great tits show greater territorial aggression than rural counterparts. We also tested predictions that both behavioural syndromes and personality would show lower consistency in urban populations. We found that urban populations were more aggressive than rural populations and urban birds appeared to show lower levels of individual behavioural repeatability (personality) as predicted. However, we found no effect of urbanisation on behavioural syndromes (correlations between multiple behavioural traits). Our results indicate that urban environments may favour individuals which exhibit increased territorial aggression and greater within-trait flexibility which may be essential to success in holding urban territories. Determining how urban environments impact key fitness traits will be important in predicting how animals cope with ongoing urbanisation.
Multi-Target Tracking of Human Spermatozoa in Phase-Contrast Microscopy Image Sequences using a Hybrid Dynamic Bayesian Network Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Abdollah Arasteh, Bijan Vosoughi Vahdat, Reza Salman Yazdi
Male infertility is mostly related to semen and spermatozoa, and any diagnosis or treatment requires the investigation of the motility patterns of spermatozoa. The movements of spermatozoa are fast and involve collision and occlusion with each other. In order to extract the motility patterns of spermatozoa, multi-target tracking (MTT) of spermatozoa is necessary. One of the most important steps of MTT is data association, in which the newly arrived observations are used to update the previous tracks. Dynamic Bayesian network (DBN) is a powerful tool for modeling and solving various types of problems such as tracking and classification. There can also be a hybrid-DBN (HDBN), in which both continuous and discrete nodes are present. HDBN has a suitable structure for modeling problems that have both discrete and continuous parameters like MTT. In this research, the data association for MTT of human spermatozoa has been studied. The proposed algorithm was tested over hundreds of manually extracted spermatozoa tracks and evaluated using several standard measures. The superior results of the proposed algorithm in comparison to the other well-known algorithms, show that it could be considered as an improved alternative to traditional computer assisted sperm analysis (CASA) algorithms.
Diffuse Myocardial Injuries are Present in Subclinical Hypothyroidism: A Clinical Study Using Myocardial T1-mapping Quantification Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Zhi Yao, Xia Gao, Min Liu, Zhe Chen, Ning Yang, Yu-Mei Jia, Xiao-Meng Feng, Yuan Xu, Xin-Chun Yang, Guang Wang
Subclinical hypothyroidism (SHT) is a common disorder that may represent early thyroid dysfunction and is related to adverse cardiovascular events. However, myocardial injuries induced by SHT are difficult to detect. Our previous study demonstrated that the cardiac magnetic resonance (CMR) myocardial longitudinal relaxation time (T1) mapping technique is a useful tool for assessing diffuse myocardial injuries in overt hypothyroidism patients. This study was designed to detect whether diffuse myocardial injuries were present in SHT by using the T1 mapping technique. We found that SHT participants had significantly increased native T1 values within four segments of the left ventricle (all p < 0.01), especially patients with thyroid-stimulating hormone (TSH) levels ≥10 µIU/mL, compared with those in the controls. In addition, the native T1 values were negatively correlated with free thyroxine (FT4) (r = −0.476, p = 0.003) and were positively correlated with TSH (r = 0.489, p = 0.002). Furthermore, left ventricular diastolic function estimated by the peak filling rate (PFR) was significantly lower in patients with TSH levels ≥10 µIU/mL than that in the controls (p < 0.05). In conclusion, diffuse myocardial injuries were present in SHT, and T1 mapping may be a useful tool for evaluating mild myocardial injuries in SHT at an early stage. Our study is the first to confirm myocardial injuries in SHT patients using T1 mapping.
Author Correction: Ultra-fast Hygrometer based on U-shaped Optical Microfiber with Nanoporous Polyelectrolyte Coating Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 George Y. Chen, Xuan Wu, Yvonne Qiongyue Kang, Li Yu, Tanya M. Monro, David G. Lancaster, Xiaokong Liu, Haolan Xu
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Pattern Formation through Temporal Fractional Derivatives Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Hongwei Yin, Xiaoqing Wen
It is well known that temporal first-derivative reaction-diffusion systems can produce various fascinating Turing patterns. However, it has been found that many physical, chemical and biological systems are well described by temporal fractional-derivative reaction-diffusion equations. Naturally arises an issue whether and how spatial patterns form for such a kind of systems. To address this issue clearly, we consider a classical prey-predator diffusive model with the Holling II functional response, where temporal fractional derivatives are introduced according to the memory character of prey’s and predator’s behaviors. In this paper, we show that this fractional-derivative system can form steadily spatial patterns even though its first-derivative counterpart can’t exhibit any steady pattern. This result implies that the temporal fractional derivatives can induce spatial patterns, which enriches the current mechanisms of pattern formation.
Cellular response to persistent foot-and-mouth disease virus infection is linked to specific types of alterations in the host cell transcriptome Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Lingling Han, Xiu Xin, Hailong Wang, Jiadai Li, Yao Hao, Mingzhen Wang, Congyi Zheng, Chao Shen
Food-and-mouth disease virus (FMDV) is a highly contagious virus that seriously threatens the development of animal husbandry. Although persistent FMDV infection can dramatically worsen the situation, the mechanisms involved in persistent FMDV infection remain unclear. In the present study, we identified the presence of evolved cells in the persistently FMDV-infected cell line. These cells exhibited resistance to the parent FMDV and re-established persistent infection when infected with FMDV-Op (virus supernatant of persistent infection cell lines), emphasizing the decisive role of evolved host cells in the establishment of persistent FMDV infection. Using RNA-seq, we identified the gene expression profiles of these evolved host cells. In total, 4,686 genes were differentially expressed in evolved cells compared with normal cells, with these genes being involved in metabolic processes, cell cycle, and cellular protein catabolic processes. In addition, 1,229 alternative splicing events, especially skipped exon events, were induced in evolved cells. Moreover, evolved cells exhibited a stronger immune defensive response and weaker MAPK signal response than normal cells. This comprehensive transcriptome analysis of evolved host cells lays the foundation for further investigations of the molecular mechanisms of persistent FMDV infection and screening for genes resistant to FMDV infection.
Drivers of solar radiation variability in the McMurdo Dry Valleys, Antarctica Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 M. K. Obryk, A. G. Fountain, P. T. Doran, W. B. Lyons, R. Eastman
Annually averaged solar radiation in the McMurdo Dry Valleys, Antarctica has varied by over 20 W m−2 during the past three decades; however, the drivers of this variability are unknown. Because small differences in radiation are important to water availability and ecosystem functioning in polar deserts, determining the causes are important to predictions of future desert processes. We examine the potential drivers of solar variability and systematically eliminate all but stratospheric sulfur dioxide. We argue that increases in stratospheric sulfur dioxide increase stratospheric aerosol optical depth and decrease solar intensity. Because of the polar location of the McMurdo Dry Valleys (77–78°S) and relatively long solar ray path through the stratosphere, terrestrial solar intensity is sensitive to small differences in stratospheric transmissivity. Important sources of sulfur dioxide include natural (wildfires and volcanic eruptions) and anthropogenic emission.
Diverse Assemblage of Ediacaran fossils from Central Iran Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Seyed Hamid Vaziri, Mahmoud Reza Majidifard, Marc Laflamme
Reinvestigation of the Kushk and Chahmir areas (Bafq and Behabad regions) of central Iran has yielded a diverse assemblage of Ediacaran fossils, including several new species, just prior to the Cambrian explosion of complex animals. The Kushk series consists mainly of shallow marine carbonate deposits followed by deep-water calcareous marine shales. Ediacaran fossils occur commonly in the shale deposits and include biostratigraphically-important taxa Cloudina and Corumbella, which confirms a latest Ediacaran age for these deposits, the youngest examples of Kimberellomorphs (stem-group molluscs) that helps bridge the gap between their first occurrence in the middle-Ediacaran and the crown diversification in the Cambrian, and likely sponges, which are rare prior to the Cambrian.
Identification of highly effective target genes for RNAi-mediated control of emerald ash borer, Agrilus planipennis Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Thais B. Rodrigues, Jian J. Duan, Subba R. Palli, Lynne K. Rieske
Recent study has shown that RNA interference (RNAi) is efficient in emerald ash borer (EAB), Agrilus planipennis, and that ingestion of double-stranded RNA (dsRNA) targeting specific genes causes gene silencing and mortality in neonates. Here, we report on the identification of highly effective target genes for RNAi-mediated control of EAB. We screened 13 candidate genes in neonate larvae and selected the most effective target genes for further investigation, including their effect on EAB adults and on a non-target organism, Tribolium castaneum. The two most efficient target genes selected, hsp (heat shock 70-kDa protein cognate 3) and shi (shibire), caused up to 90% mortality of larvae and adults. In EAB eggs, larvae, and adults, the hsp is expressed at higher levels when compared to that of shi. Ingestion of dsHSP and dsSHI caused mortality in both neonate larvae and adults. Administration of a mixture of both dsRNAs worked better than either dsRNA by itself. In contrast, injection of EAB.dsHSP and EAB.dsSHI did not cause mortality in T. castaneum. Thus, the two genes identified cause high mortality in the EAB with no apparent phenotype effects in a non-target organism, the red flour beetle, and could be used in RNAi-mediated control of this invasive pest.
Author Correction: Interferometric rotating point spread function Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Wei Wang, Guohai Situ
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Magnetic field effect on the energy levels of an exciton in a GaAs quantum dot: Application for excitonic lasers Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 K. Luhluh Jahan, A. Boda, I. V. Shankar, Ch. Narasimha Raju, Ashok Chatterjee
The problem of an exciton trapped in a Gaussian quantum dot (QD) of GaAs is studied in both two and three dimensions in the presence of an external magnetic field using the Ritz variational method, the 1/N expansion method and the shifted 1/N expansion method. The ground state energy and the binding energy of the exciton are obtained as a function of the quantum dot size, confinement strength and the magnetic field and compared with those available in the literature. While the variational method gives the upper bound to the ground state energy, the 1/N expansion method gives the lower bound. The results obtained from the shifted 1/N expansion method are shown to match very well with those obtained from the exact diagonalization technique. The variation of the exciton size and the oscillator strength of the exciton are also studied as a function of the size of the quantum dot. The excited states of the exciton are computed using the shifted 1/N expansion method and it is suggested that a given number of stable excitonic bound states can be realized in a quantum dot by tuning the quantum dot parameters. This can open up the possibility of having quantum dot lasers using excitonic states.
Coherent all-optical transistor based on frustrated total internal reflection Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 A. Goodarzi, M. Ghanaatshoar
This study aims to design an all-optical transistor based on tunneling of light through frustrated total internal reflection. Under total internal reflection, the electromagnetic wave penetrates into the lower index medium. If a medium with high refractive index is placed close to the boundary of the first one, a portion of light leaks into the second medium. The penetrated electromagnetic field distribution can be influenced by another coherent light in the low refractive index medium via interference, leading to light amplification. Upon this technique, we introduce coherent all-optical transistors based on photonic crystal structures. Subsequently, we inspect the shortest pulse which is amplified by the designed system and also its terahertz repetition rate. We will show that such a system can operate in a cascade form. Operating in terahertz range and the amplification efficiency of around 20 are of advantages of this system.
A complete, homozygous CRX deletion causing nullizygosity is a new genetic mechanism for Leber congenital amaurosis Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 M. T. Ibrahim, T. Alarcon-Martinez, I. Lopez, N. Fajardo, J. Chiang, R. K. Koenekoop
CRX is a transcription factor required for activating the expression of many photoreceptor-neuron genes. CRX may be mutated in three forms of human blindness; Leber congenital amaurosis (LCA), cone-rod degeneration (CRD) and retinitis pigmentosa (RP). The pathogenic mechanism in most cases is likely dominant negative, with gain of function. We report a novel, complete homozygous CRX deletion in LCA. We identified a Lebanese family with 3 affected LCA cases. The proband was sequenced by NGS. Quantitative PCR, array comparative genomic hybridization, and long range PCR were performed. Full eye examinations, OCT and photography were performed. We identified a homozygous 56,000 bp deletion of CRX, which co-segregates and is heterozygous in four parents, who report normal vision. The blind children with LCA manifest severe retinal degeneration, a phenotype typical for CRX and LCA. We hypothesized that a single copy of CRX (haplo-insufficiency) in the causes mild abnormal foveal development, but not LCA. Two parents had significant inner and outer foveal and photoreceptor abnormalities. This is the first reported case of a homozygous, complete CRX deletion. Nullizygosity of CRX thus causes LCA while haplo-insufficiency of CRX causes abnormal foveal development, but not LCA. Our data suggest a new disease mechanism for CRX.
Ocimum flavone Orientin as a countermeasure for thrombocytopenia Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Marshleen Yadav, Feifei Song, Jason Huang, Arnab Chakravarti, Naduparambil K. Jacob
Thrombocytopenia or chronic depletion of platelets in blood, could create life-threatening conditions in patients who receive aggressive systemic radiation and chemotherapy. Currently there are no approved agents for the rapid treatment of thrombocytopenia. In the present study, we demonstrate that administration of Orientin, a glycosidic flavonoid or dietary administration of Orientin containing Tulsi (Holy Basil) leaves, results in a significant increase in circulating platelets in a clinically relevant mouse model. No noticeable effects were observed on red blood cells, white blood cells or other hematologic parameters in treated animals indicating that Orientin specificity enhances platelet formation. The gene expression and immunophenotyping of bone marrow revealed that Orientin stimulates megakaryopoiesis specific transcriptional program. A significant increase in colony formation in bone marrow cells from Orientin pretreated mice further complemented the effect of Orientin on progenitor cells. The ex-vivo differentiation of irradiated human peripheral blood CD34+ stem cells demonstrated stimulatory effects of Orientin on megakaryocyte erythrocyte progenitors (MEP). The results show that Orientin, a non-toxic readily available natural product can counter platelet imbalances. Thrombocytopenia also develop as a consequence of multiple hematologic malignancies and side effects of treatments. Dietary supplementation of Orientin containing phytochemicals could be effective as countermeasures and viable therapeutics.
Atomistic scale investigation of cation ordering and phase stability in Cs-substituted Ba1.33Zn1.33Ti6.67O16, Ba1.33Ga2.66Ti5.67O16 and Ba1.33Al2.66Ti5.33O16 hollandite Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Yi Wen, Yun Xu, Kyle S. Brinkman, Lindsay Shuller-Nickles
The titanate-based hollandite structure is proposed as an effective ceramic waste form for Cs-immobilization. In this study, quantum-mechanical calculations were used to quantify the impact of A-site and B-site ordering on the structural stability of hollandite with compositions BaxCsy(MzTi8-z)O16, where M = Zn2+, Ga3+, and Al3+. The calculated enthalpy of formation agrees with experimental measurements of related hollandite phases from melt solution calorimetry. Ground state geometry optimizations show that, for intermediate compositions (e.g., CsBaGa6Ti18O48), the presence of both Cs and Ba in the A-site tunnels is not energetically favored. However, the decay heat generated during storage of the Cs-containing waste form may overcome the energetics of Ba and Cs mixing in the tunnel structure of hollandite. The ability of the hollandite structure to accommodate the radioparagenesis of Cs to Ba is critical for long term performance of the waste. For the first time, B-site ordering was observed along the tunnel direction ( zone axis) for the Ga-hollandite compositions, as well as the intermediate Al-hollandite composition. These compositionally dependent structural features, and associated formation enthalpies, are of importance to the stability and radiation damage tolerance of ceramic waste forms.
Author Correction: High-pressure versus low-pressure home non-invasive positive pressure ventilation with built-in software in patients with stable hypercapnic COPD: a pilot study Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Luqian Zhou, Lili Guan, Weiliang Wu, Xiaoying Li, Xin Chen, Bingpeng Guo, Yating Huo, Jiawen Xu, Yuqiong Yang, Rongchang Chen
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 R. Pérez-Portela, A. Bumford, B. Coffman, S. Wedelich, M. Davenport, A. Fogg, M. K. Swenarton, F. Coleman, M. A. Johnston, D. L. Crawford, M. F. Oleksiak
Despite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand genetic trends relevant to the lionfish’s long-term persistence. We found no significant differences in genetic structure or diversity between the two areas (FST p-values > 0.01, and t-test p-values > 0.05). In fact, our genomic analyses showed genetic homogeneity, with enough gene flow between the east coast of Florida and Gulf of Mexico to erase previous signals of genetic divergence detected between these areas, secondary spreading, and bottlenecks in the Gulf of Mexico. These findings suggest rapid genetic changes over space and time during the invasion, resulting in one panmictic population with no signs of divergence between areas due to local adaptation.
Modulation of the Neuregulin 1/ErbB system after skeletal muscle denervation and reinnervation Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Michela Morano, Giulia Ronchi, Valentina Nicolò, Benedetta Elena Fornasari, Alessandro Crosio, Isabelle Perroteau, Stefano Geuna, Giovanna Gambarotta, Stefania Raimondo
Neuregulin 1 (NRG1) is a growth factor produced by both peripheral nerves and skeletal muscle. In muscle, it regulates neuromuscular junction gene expression, acetylcholine receptor number, muscle homeostasis and satellite cell survival. NRG1 signalling is mediated by the tyrosine kinase receptors ErbB3 and ErbB4 and their co-receptors ErbB1 and ErbB2. The NRG1/ErbB system is well studied in nerve tissue after injury, but little is known about this system in skeletal muscle after denervation/reinnervation processes. Here, we performed a detailed time-course expression analysis of several NRG1 isoforms and ErbB receptors in the rat superficial digitorum flexor muscle after three types of median nerve injuries of different severities. We found that ErbB receptor expression was correlated with the innervated state of the muscle, with upregulation of ErbB2 clearly associated with the denervation state. Interestingly, the NRG1 isoforms were differently regulated depending on the nerve injury type, leading to the hypothesis that both the NRG1α and NRG1β isoforms play a key role in the muscle reaction to injury. Indeed, in vitro experiments with C2C12 atrophic myotubes revealed that both NRG1α and NRG1β treatment influences the best-known atrophic pathways, suggesting that NRG1 might play an anti-atrophic role.
Evidence for a dyadic motor plan in joint action Sci. Rep. (IF 4.259) Pub Date : 2018-03-22 Lucia Maria Sacheli, Elisa Arcangeli, Eraldo Paulesu
What mechanisms distinguish interactive from non-interactive actions? To answer this question we tested participants while they took turns playing music with a virtual partner: in the interactive joint action condition, the participants played a melody together with their partner by grasping (C note) or pressing (G note) a cube-shaped instrument, alternating in playing one note each. In the non-interactive control condition, players’ behavior was not guided by a shared melody, so that the partner’s actions and notes were irrelevant to the participant. In both conditions, the participant’s and partner’s actions were physically congruent (e.g., grasp-grasp) or incongruent (e.g., grasp-point), and the partner’s association between actions and notes was coherent with the participant’s or reversed. Performance in the non-interactive condition was only affected by physical incongruence, whereas joint action was only affected when the partner’s action-note associations were reversed. This shows that task interactivity shapes the sensorimotor coding of others’ behaviors, and that joint action is based on active prediction of the partner’s action effects rather than on passive action imitation. We suggest that such predictions are based on Dyadic Motor Plans that represent both the agent’s and the partner’s contributions to the interaction goal, like playing a melody together.
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