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  • Correction for Chen et al., Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13 [Corrections]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    National Academy of Sciences

    MEDICAL SCIENCES Correction for “Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13,” by Zhong Chen, Dayong Wu, Jennifer M. …

    更新日期:2018-09-19
  • Linking economic growth pathways and environmental sustainability by understanding development as alternate social-ecological regimes [Sustainability Science]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Graeme S. Cumming, Stephan von Cramon-Taubadel

    Scientists understand how global ecological degradation is occurring but not why it seems to be so difficult to reverse. We used national-level data and a mathematical model to provide an empirical test of the hypothesis that national economies display two distinct economic regimes that are maintained by self-reinforcing feedbacks between natural resources and society. Our results not only support previous findings that two distinct groups exist, but also show that countries move toward one of these two different equilibrium points because of their different patterns of natural resource use and responses to population growth. At the less economically developed equilibrium point maintained by “green-loop” feedbacks, human populations depend more directly on ecosystems for income. At the more economically developed equilibrium point maintained by “red-loop” feedbacks, nonecosystem services (e.g., technology, manufacturing, services) generate the majority of national gross domestic product (GDP), but increasing consumption of natural resources means that environmental impacts are higher and are often exported (via cross-scale feedbacks) to other countries. Feedbacks between income and population growth are pushing countries farther from sustainability. Our analysis shows that economic growth alone cannot lead to environmental sustainability and that current trajectories of resource use cannot be sustained without breaking feedback loops in national and international economies.

    更新日期:2018-09-19
  • Americans’ occupational status reflects the status of both of their parents [Social Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Michael Hout

    American workers’ occupational status strongly reflects the status of their parents. Men and women who grew up in a two-earner or father-breadwinner family achieved occupations that rose 0.5 point for every one-point increase in their parents’ statuses (less if their father was absent). Gender differences were small in two-earner families and mother-only families, but men’s status persisted more when the father was the sole breadwinner. Intergenerational persistence did not change in the time the data cover (1994–2016). Absolute mobility declined for recent birth cohorts; barely half the men and women born in the 1980s were upwardly mobile compared with two-thirds of those born in the 1940s. The results as described hold for a socioeconomic index (SEI) that scores occupation according to the average pay and credentials of people in the occupation. Most results were the same when occupations were coded by different criteria, but SEI produced the smallest gender differences.

    更新日期:2018-09-19
  • Perspective taking can promote short-term inclusionary behavior toward Syrian refugees [Political Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Claire L. Adida, Adeline Lo, Melina R. Platas

    Social scientists have shown how easily individuals are moved to exclude outgroup members. Can we foster inclusion instead? This study leverages one of the most significant humanitarian crises of our time to test whether, and under what conditions, American citizens adopt more inclusionary behavior toward Syrian refugees. We conduct a nationally representative survey of over 5,000 American citizens in the weeks leading up to the 2016 presidential election and experimentally test whether a perspective-taking exercise increases inclusionary behavior in the form of an anonymous letter supportive of refugees to be sent to the 45th President of the United States. Our results indicate that the perspective-taking message increases the likelihood of writing such a positive letter by two to five percentage points. By contrast, an informational message had no significant effect on letter writing. The effect of the perspective-taking exercise occurs in the short run only, manifests as a behavioral rather than an attitudinal response, and is strongest among Democrats. However, this effect also appears in the subset of Republican respondents, suggesting that efforts to promote perspective taking may move to action a wide cross-section of individuals.

    更新日期:2018-09-19
  • Plastid terminal oxidase requires translocation to the grana stacks to act as a sink for electron transport [Plant Biology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Piotr Stepien, Giles N. Johnson

    The plastid terminal oxidase (PTOX) has been shown to be an important sink for photosynthetic electron transport in stress-tolerant plants. However, overexpression studies in stress-sensitive species have previously failed to induce significant activity of this protein. Here we show that overexpression of PTOX from the salt-tolerant brassica species Eutrema salsugineum does not, alone, result in activity, but that overexpressing plants show faster induction and a greater final level of PTOX activity once exposed to salt stress. This implies that an additional activation step is required before activity is induced. We show that that activation involves the translocation of the protein from the unstacked stromal lamellae to the thylakoid grana and a protection of the protein from trypsin digestion. This represents an important activation step and opens up possibilities in the search for stress-tolerant crops.

    更新日期:2018-09-19
  • Metal-insulator-transition engineering by modulation tilt-control in perovskite nickelates for room temperature optical switching [Physics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Zhaoliang Liao, Nicolas Gauquelin, Robert J. Green, Knut Müller-Caspary, Ivan Lobato, Lin Li, Sandra Van Aert, Johan Verbeeck, Mark Huijben, Mathieu N. Grisolia, Victor Rouco, Ralph El Hage, Javier E. Villegas, Alain Mercy, Manuel Bibes, Philippe Ghosez, George A. Sawatzky, Guus Rijnders, Gertjan Koster

    In transition metal perovskites ABO3, the physical properties are largely driven by the rotations of the BO6 octahedra, which can be tuned in thin films through strain and dimensionality control. However, both approaches have fundamental and practical limitations due to discrete and indirect variations in bond angles, bond lengths, and film symmetry by using commercially available substrates. Here, we introduce modulation tilt control as an approach to tune the ground state of perovskite oxide thin films by acting explicitly on the oxygen octahedra rotation modes—that is, directly on the bond angles. By intercalating the prototype SmNiO3 target material with a tilt-control layer, we cause the system to change the natural amplitude of a given rotation mode without affecting the interactions. In contrast to strain and dimensionality engineering, our method enables a continuous fine-tuning of the materials’ properties. This is achieved through two independent adjustable parameters: the nature of the tilt-control material (through its symmetry, elastic constants, and oxygen rotation angles), and the relative thicknesses of the target and tilt-control materials. As a result, a magnetic and electronic phase diagram can be obtained, normally only accessible by A-site element substitution, within the single SmNiO3 compound. With this unique approach, we successfully adjusted the metal–insulator transition (MIT) to room temperature to fulfill the desired conditions for optical switching applications.

    更新日期:2018-09-19
  • Structural fluctuations cause spin-split states in tetragonal (CH3NH3)PbI3 as evidenced by the circular photogalvanic effect [Physics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Daniel Niesner, Martin Hauck, Shreetu Shrestha, Ievgen Levchuk, Gebhard J. Matt, Andres Osvet, Miroslaw Batentschuk, Christoph Brabec, Heiko B. Weber, Thomas Fauster

    Lead halide perovskites are used in thin-film solar cells, which owe their high efficiency to the long lifetimes of photocarriers. Various calculations find that a dynamical Rashba effect could significantly contribute to these long lifetimes. This effect is predicted to cause a spin splitting of the electronic bands of inversion-symmetric crystalline materials at finite temperatures, resulting in a slightly indirect band gap. Direct experimental evidence of the existence or the strength of the spin splitting is lacking. Here, we resonantly excite photocurrents in single crystalline (CH3NH3)PbI3 with circularly polarized light to clarify the existence of spin splittings in the band structure. We observe a circular photogalvanic effect, i.e., the photocurrent depends on the light helicity, in both orthorhombic and tetragonal (CH3NH3)PbI3. At room temperature, the effect peaks for excitation photon energies ΔE=110 meV below the direct optical band gap. Temperature-dependent measurements reveal a sign change of the effect at the orthorhombic–tetragonal phase transition, indicating different microscopic origins in the two phases. Within the tetragonal phase, both ΔE and the amplitude of the circular photogalvanic effect increase with temperature. Our findings support a dynamical Rashba effect in this phase, i.e., a spin splitting caused by thermally induced structural fluctuations which break inversion symmetry.

    更新日期:2018-09-19
  • Nontrivial superconductivity in topological MoTe2-xSx crystals [Physics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Yanan Li, Qiangqiang Gu, Chen Chen, Jun Zhang, Qin Liu, Xiyao Hu, Jun Liu, Yi Liu, Langsheng Ling, Mingliang Tian, Yong Wang, Nitin Samarth, Shiyan Li, Tong Zhang, Ji Feng, Jian Wang

    Topological Weyl semimetals (TWSs) with pairs of Weyl points and topologically protected Fermi arc states have broadened the classification of topological phases and provide superior platform for study of topological superconductivity. Here we report the nontrivial superconductivity and topological features of sulfur-doped Td-phase MoTe2 with enhanced Tc compared with type-II TWS MoTe2. It is found that Td-phase S-doped MoTe2 (MoTe2−xSx, x ∼ 0.2) is a two-band s-wave bulk superconductor (∼0.13 meV and 0.26 meV), where the superconducting behavior can be explained by the s+− pairing model. Further, measurements of the quasi-particle interference (QPI) patterns and a comparison with band-structure calculations reveal the existence of Fermi arcs in MoTe2−xSx. More interestingly, a relatively large superconducting gap (∼1.7 meV) is detected by scanning tunneling spectroscopy on the sample surface, showing a hint of topological nontrivial superconductivity based on the pairing of Fermi arc surface states. Our work demonstrates that the Td-phase MoTe2−xSx is not only a promising topological superconductor candidate but also a unique material for study of s+− superconductivity.

    更新日期:2018-09-19
  • Universal quantum Hamiltonians [Physics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Toby S. Cubitt, Ashley Montanaro, Stephen Piddock

    Quantum many-body systems exhibit an extremely diverse range of phases and physical phenomena. However, we prove that the entire physics of any quantum many-body system can be replicated by certain simple, “universal” spin-lattice models. We first characterize precisely what it means for one quantum system to simulate the entire physics of another. We then fully classify the simulation power of all two-qubit interactions, thereby proving that certain simple models can simulate all others, and hence are universal. Our results put the practical field of analogue Hamiltonian simulation on a rigorous footing and take a step toward justifying why error correction may not be required for this application of quantum information technology.

    更新日期:2018-09-19
  • Floquet quantum criticality [Physics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    William Berdanier, Michael Kolodrubetz, S. A. Parameswaran, Romain Vasseur

    We study transitions between distinct phases of one-dimensional periodically driven (Floquet) systems. We argue that these are generically controlled by infinite-randomness fixed points of a strong-disorder renormalization group procedure. Working in the fermionic representation of the prototypical Floquet Ising chain, we leverage infinite randomness physics to provide a simple description of Floquet (multi)criticality in terms of a distinct type of domain wall associated with time translational symmetry-breaking and the formation of “Floquet time crystals.” We validate our analysis via numerical simulations of free-fermion models sufficient to capture the critical physics.

    更新日期:2018-09-19
  • Designing antiphase boundaries by atomic control of heterointerfaces [Physics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Zhen Wang, Hangwen Guo, Shuai Shao, Mohammad Saghayezhian, Jun Li, Rosalba Fittipaldi, Antonio Vecchione, Prahald Siwakoti, Yimei Zhu, Jiandi Zhang, E. W. Plummer

    Extended defects are known to have critical influences in achieving desired material performance. However, the nature of extended defect generation is highly elusive due to the presence of multiple nucleation mechanisms with close energetics. A strategy to design extended defects in a simple and clean way is thus highly desirable to advance the understanding of their role, improve material quality, and serve as a unique playground to discover new phenomena. In this work, we report an approach to create planar extended defects—antiphase boundaries (APB) —with well-defined origins via the combination of advanced growth, atomic-resolved electron microscopy, first-principals calculations, and defect theory. In La2/3Sr1/3MnO3 thin film grown on Sr2RuO4 substrate, APBs in the film naturally nucleate at the step on the substrate/film interface. For a single step, the generated APBs tend to be nearly perpendicular to the interface and propragate toward the film surface. Interestingly, when two steps are close to each other, two corresponding APBs communicate and merge together, forming a unique triangle-shaped defect domain boundary. Such behavior has been ascribed, in general, to the minimization of the surface energy of the APB. Atomic-resolved electron microscopy shows that these APBs have an intriguing antipolar structure phase, thus having the potential as a general recipe to achieve ferroelectric-like domain walls for high-density nonvolatile memory.

    更新日期:2018-09-19
  • ASCT1 (Slc1a4) transporter is a physiologic regulator of brain d-serine and neurodevelopment [Neuroscience]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Eitan Kaplan, Salman Zubedat, Inna Radzishevsky, Alec C. Valenta, Ohad Rechnitz, Hagit Sason, Clara Sajrawi, Oded Bodner, Kohtarou Konno, Kayoko Esaki, Dori Derdikman, Takeo Yoshikawa, Masahiko Watanabe, Robert T. Kennedy, Jean-Marie Billard, Avi Avital, Herman Wolosker

    d-serine is a physiologic coagonist of NMDA receptors, but little is known about the regulation of its synthesis and synaptic turnover. The amino acid exchangers ASCT1 (Slc1a4) and ASCT2 (Slc1a5) are candidates for regulating d-serine levels. Using ASCT1 and ASCT2 KO mice, we report that ASCT1, rather than ASCT2, is a physiologic regulator of d-serine metabolism. ASCT1 is a major d-serine uptake system in astrocytes and can also export l-serine via heteroexchange, supplying neurons with the substrate for d-serine synthesis. ASCT1-KO mice display lower levels of brain d-serine along with higher levels of l-alanine, l-threonine, and glycine. Deletion of ASCT1 was associated with neurodevelopmental alterations including lower hippocampal and striatal volumes and changes in the expression of neurodevelopmental-relevant genes. Furthermore, ASCT1-KO mice exhibited deficits in motor function, spatial learning, and affective behavior, along with changes in the relative contributions of d-serine vs. glycine in mediating NMDA receptor activity. In vivo microdialysis demonstrated lower levels of extracellular d-serine in ASCT1-KO mice, confirming altered d-serine metabolism. These alterations are reminiscent of some of the neurodevelopmental phenotypes exhibited by patients with ASCT1 mutations. ASCT1-KO mice provide a useful model for potential therapeutic interventions aimed at correcting the metabolic impairments in patients with ASCT1 mutations.

    更新日期:2018-09-19
  • A pan-mammalian map of interhemispheric brain connections predates the evolution of the corpus callosum [Neuroscience]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Rodrigo Suárez, Annalisa Paolino, Laura R. Fenlon, Laura R. Morcom, Peter Kozulin, Nyoman D. Kurniawan, Linda J. Richards

    The brain of mammals differs from that of all other vertebrates, in having a six-layered neocortex that is extensively interconnected within and between hemispheres. Interhemispheric connections are conveyed through the anterior commissure in egg-laying monotremes and marsupials, whereas eutherians evolved a separate commissural tract, the corpus callosum. Although the pattern of interhemispheric connectivity via the corpus callosum is broadly shared across eutherian species, it is not known whether this pattern arose as a consequence of callosal evolution or instead corresponds to a more ancient feature of mammalian brain organization. Here we show that, despite cortical axons using an ancestral commissural route, monotremes and marsupials share features of interhemispheric connectivity with eutherians that likely predate the origin of the corpus callosum. Based on ex vivo magnetic resonance imaging and tractography, we found that connections through the anterior commissure in both fat-tailed dunnarts (Marsupialia) and duck-billed platypus (Monotremata) are spatially segregated according to cortical area topography. Moreover, cell-resolution retrograde and anterograde interhemispheric circuit mapping in dunnarts revealed several features shared with callosal circuits of eutherians. These include the layered organization of commissural neurons and terminals, a broad map of connections between similar (homotopic) regions of each hemisphere, and regions connected to different areas (heterotopic), including hyperconnected hubs along the medial and lateral borders of the cortex, such as the cingulate/motor cortex and claustrum/insula. We therefore propose that an interhemispheric connectome originated in early mammalian ancestors, predating the evolution of the corpus callosum. Because these features have been conserved throughout mammalian evolution, they likely represent key aspects of neocortical organization.

    更新日期:2018-09-19
  • Clinical and veterinary trypanocidal benzoxaboroles target CPSF3 [Microbiology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Richard J. Wall, Eva Rico, Iva Lukac, Fabio Zuccotto, Sara Elg, Ian H. Gilbert, Yvonne Freund, M. R. K. Alley, Mark C. Field, Susan Wyllie, David Horn

    African trypanosomes cause lethal and neglected tropical diseases, known as sleeping sickness in humans and nagana in animals. Current therapies are limited, but fortunately, promising therapies are in advanced clinical and veterinary development, including acoziborole (AN5568 or SCYX-7158) and AN11736, respectively. These benzoxaboroles will likely be key to the World Health Organization’s target of disease control by 2030. Their mode of action was previously unknown. We have developed a high-coverage overexpression library and use it here to explore drug mode of action in Trypanosoma brucei. Initially, an inhibitor with a known target was used to select for drug resistance and to test massive parallel library screening and genome-wide mapping; this effectively identified the known target and validated the approach. Subsequently, the overexpression screening approach was used to identify the target of the benzoxaboroles, Cleavage and Polyadenylation Specificity Factor 3 (CPSF3, Tb927.4.1340). We validated the CPSF3 endonuclease as the target, using independent overexpression strains. Knockdown provided genetic validation of CPSF3 as essential, and GFP tagging confirmed the expected nuclear localization. Molecular docking and CRISPR-Cas9-based editing demonstrated how acoziborole can specifically block the active site and mRNA processing by parasite, but not host CPSF3. Thus, our findings provide both genetic and chemical validation for CPSF3 as an important drug target in trypanosomes and reveal inhibition of mRNA maturation as the mode of action of the trypanocidal benzoxaboroles. Understanding the mechanism of action of benzoxaborole-based therapies can assist development of improved therapies, as well as the prediction and monitoring of resistance, if or when it arises.

    更新日期:2018-09-19
  • Distinct antiviral signatures revealed by the magnitude and round of influenza virus replication in vivo [Microbiology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Louisa E. Sjaastad, Elizabeth J. Fay, Jessica K. Fiege, Marissa G. Macchietto, Ian A. Stone, Matthew W. Markman, Steven Shen, Ryan A. Langlois

    Influenza virus has a broad cellular tropism in the respiratory tract. Infected epithelial cells sense the infection and initiate an antiviral response. To define the antiviral response at the earliest stages of infection we used a series of single-cycle reporter viruses. These viral probes demonstrated cells in vivo harbor a range in magnitude of virus replication. Transcriptional profiling of cells supporting different levels of replication revealed tiers of IFN-stimulated gene expression. Uninfected cells and cells with blunted replication expressed a distinct and potentially protective antiviral signature, while cells with high replication expressed a unique reserve set of antiviral genes. Finally, we used these single-cycle reporter viruses to determine the antiviral landscape during virus spread, which unveiled disparate protection of epithelial cell subsets mediated by IFN in vivo. Together these results highlight the complexity of virus–host interactions within the infected lung and suggest that magnitude and round of replication tune the antiviral response.

    更新日期:2018-09-19
  • High-resolution repertoire analysis reveals a major bystander activation of Tfh and Tfr cells [Immunology and Inflammation]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Paul-Gydeon Ritvo, Ahmed Saadawi, Pierre Barennes, Valentin Quiniou, Wahiba Chaara, Karim El Soufi, Benjamin Bonnet, Adrien Six, Mikhail Shugay, Encarnita Mariotti-Ferrandiz, David Klatzmann

    T follicular helper (Tfh) and regulatory (Tfr) cells are terminally differentiated cells found in germinal centers (GCs), specialized secondary lymphoid organ structures dedicated to antibody production. As such, follicular T (Tfol) cells are supposed to be specific for immunizing antigens, which has been reported for Tfh cells but is debated for Tfr cells. Here, we used high-throughput T cell receptor (TCR) sequencing to analyze the repertoires of Tfh and Tfr cells, at homeostasis and after immunization with self- or foreign antigens. We observed that, whatever the conditions, Tfh and Tfr cell repertoires are less diverse than those of effector T cells and Treg cells of the same tissues; surprisingly, these repertoires still represent thousands of different sequences, even after immunization with a single antigen that induces a 10-fold increase in Tfol cell numbers. Thorough analysis of the sharing and network of TCR sequences revealed that a specific response to the immunizing antigen can only, but hardly, be detected in Tfh cells immunized with a foreign antigen and Tfr cells immunized with a self-antigen. These antigen-specific responses are obscured by a global stimulation of Tfh and Tfr cells that appears to be antigen-independent. Altogether, our results suggest a major bystander Tfol cell activation during the immune response in the GCs.

    更新日期:2018-09-19
  • Cancer-driving H3G34V/R/D mutations block H3K36 methylation and H3K36me3-MutS{alpha} interaction [Genetics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Jun Fang, Yaping Huang, Guogen Mao, Shuang Yang, Gadi Rennert, Liya Gu, Haitao Li, Guo-Min Li

    Somatic mutations on glycine 34 of histone H3 (H3G34) cause pediatric cancers, but the underlying oncogenic mechanism remains unknown. We demonstrate that substituting H3G34 with arginine, valine, or aspartate (H3G34R/V/D), which converts the non-side chain glycine to a large side chain-containing residue, blocks H3 lysine 36 (H3K36) dimethylation and trimethylation by histone methyltransferases, including SETD2, an H3K36-specific trimethyltransferase. Our structural analysis reveals that the H3 “G33-G34” motif is recognized by a narrow substrate channel, and that H3G34/R/V/D mutations impair the catalytic activity of SETD2 due to steric clashes that impede optimal SETD2–H3K36 interaction. H3G34R/V/D mutations also block H3K36me3 from interacting with mismatch repair (MMR) protein MutSα, preventing the recruitment of the MMR machinery to chromatin. Cells harboring H3G34R/V/D mutations display a mutator phenotype similar to that observed in MMR-defective cells. Therefore, H3G34R/V/D mutations promote genome instability and tumorigenesis by inhibiting MMR activity.

    更新日期:2018-09-19
  • Global estimates of mortality associated with long-term exposure to outdoor fine particulate matter [Environmental Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Richard Burnett, Hong Chen, Mieczysław Szyszkowicz, Neal Fann, Bryan Hubbell, C. Arden Pope, Joshua S. Apte, Michael Brauer, Aaron Cohen, Scott Weichenthal, Jay Coggins, Qian Di, Bert Brunekreef, Joseph Frostad, Stephen S. Lim, Haidong Kan, Katherine D. Walker, George D. Thurston, Richard B. Hayes, Chris C. Lim, Michelle C. Turner, Michael Jerrett, Daniel Krewski, Susan M. Gapstur, W. Ryan Diver, Bart Ostro, Debbie Goldberg, Daniel L. Crouse, Randall V. Martin, Paul Peters, Lauren Pinault, Michael Tjepkema, Aaron van Donkelaar, Paul J. Villeneuve, Anthony B. Miller, Peng Yin, Maigeng Zhou, Lijun Wang, Nicole A. H. Janssen, Marten Marra, Richard W. Atkinson, Hilda Tsang, Thuan Quoc Thach, John B. Cannon, Ryan T. Allen, Jaime E. Hart, Francine Laden, Giulia Cesaroni, Francesco Forastiere, Gudrun Weinmayr, Andrea Jaensch, Gabriele Nagel, Hans Concin, Joseph V. Spadaro

    Exposure to ambient fine particulate matter (PM2.5) is a major global health concern. Quantitative estimates of attributable mortality are based on disease-specific hazard ratio models that incorporate risk information from multiple PM2.5 sources (outdoor and indoor air pollution from use of solid fuels and secondhand and active smoking), requiring assumptions about equivalent exposure and toxicity. We relax these contentious assumptions by constructing a PM2.5-mortality hazard ratio function based only on cohort studies of outdoor air pollution that covers the global exposure range. We modeled the shape of the association between PM2.5 and nonaccidental mortality using data from 41 cohorts from 16 countries—the Global Exposure Mortality Model (GEMM). We then constructed GEMMs for five specific causes of death examined by the global burden of disease (GBD). The GEMM predicts 8.9 million [95% confidence interval (CI): 7.5–10.3] deaths in 2015, a figure 30% larger than that predicted by the sum of deaths among the five specific causes (6.9; 95% CI: 4.9–8.5) and 120% larger than the risk function used in the GBD (4.0; 95% CI: 3.3–4.8). Differences between the GEMM and GBD risk functions are larger for a 20% reduction in concentrations, with the GEMM predicting 220% higher excess deaths. These results suggest that PM2.5 exposure may be related to additional causes of death than the five considered by the GBD and that incorporation of risk information from other, nonoutdoor, particle sources leads to underestimation of disease burden, especially at higher concentrations.

    更新日期:2018-09-19
  • Wetting controls of droplet formation in step emulsification [Engineering]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Maximilian L. Eggersdorfer, Hansjörg Seybold, Alessandro Ofner, David A. Weitz, André R. Studart

    The formation of droplets is ubiquitous in many natural and industrial processes and has reached an unprecedented level of control with the emergence of milli- and microfluidics. Although important insight into the mechanisms of droplet formation has been gained over the past decades, a sound understanding of the physics underlying this phenomenon and the effect of the fluid’s flow and wetting properties on the droplet size and production rate is still missing, especially for the widely applied method of step emulsification. In this work, we elucidate the physical controls of microdroplet formation in step emulsification by using the wetting of fluidic channels as a tunable parameter to explore a broad set of emulsification conditions. With the help of high-speed measurements, we unequivocally show that the final droplet pinch-off is triggered by a Rayleigh–Plateau-type instability. The droplet size, however, is not determined by the Rayleigh–Plateau breakup, but by the initial wetting regime, where the fluid’s contact angle plays a crucial role. We develop a physical theory for the wetting process, which closely describes our experimental measurements without invoking any free fit parameter. Our theory predicts the initiation of the Rayleigh–Plateau breakup and the transition from dripping to jetting as a function of the fluid’s contact angle. Additionally, the theory solves the conundrum why there is a minimal contact angle of α = 2π/3 = 120° for which droplets can form.

    更新日期:2018-09-19
  • Dynamic amplification of extreme precipitation sensitivity [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Ji Nie, Adam H. Sobel, Daniel A. Shaevitz, Shuguang Wang

    A useful starting hypothesis for predictions of changes in precipitation extremes with climate is that those extremes increase at the same rate as atmospheric moisture does, which is ∼7% K−1 following the Clausius–Clapeyron (CC) relation. This hypothesis, however, neglects potential changes in the strengths of atmospheric circulations associated with precipitation extremes. As increased moisture leads to increased precipitation, the increased latent heating may lead to stronger large-scale ascent and thus, additional increase in precipitation, leading to a super-CC scaling. This study investigates this possibility in the context of the 2015 Texas extreme precipitation event using the Column Quasi-Geostrophic (CQG) method. Analogs to this event are simulated in different climatic conditions with varying surface temperature (Ts) given the same adiabatic quasigeostrophic forcing. Precipitation in these events exhibits super-CC scaling due to the dynamic contribution associated with increasing ascent due to increased latent heating, an increase with importance that increases with Ts. The thermodynamic contribution (attributable to increasing water vapor; assuming no change in vertical motion) approximately follows CC as expected, while vertical structure changes of moisture and diabatic heating lead to negative but secondary contributions to the sensitivity, reducing the rate of increase.

    更新日期:2018-09-19
  • Striking stationarity of large-scale climate model bias patterns under strong climate change [Earth, Atmospheric, and Planetary Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Gerhard Krinner, Mark G. Flanner

    Because all climate models exhibit biases, their use for assessing future climate change requires implicitly assuming or explicitly postulating that the biases are stationary or vary predictably. This hypothesis, however, has not been, and cannot be, tested directly. This work shows that under very large climate change the bias patterns of key climate variables exhibit a striking degree of stationarity. Using only correlation with a model’s preindustrial bias pattern, a model’s 4xCO2 bias pattern is objectively and correctly identified among a large model ensemble in almost all cases. This outcome would be exceedingly improbable if bias patterns were independent of climate state. A similar result is also found for bias patterns in two historical periods. This provides compelling and heretofore missing justification for using such models to quantify climate perturbation patterns and for selecting well-performing models for regional downscaling. Furthermore, it opens the way to extending bias corrections to perturbed states, substantially broadening the range of justified applications of climate models.

    更新日期:2018-09-19
  • Toward the first quantum simulation with quantum speedup [Computer Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Andrew M. Childs, Dmitri Maslov, Yunseong Nam, Neil J. Ross, Yuan Su

    With quantum computers of significant size now on the horizon, we should understand how to best exploit their initially limited abilities. To this end, we aim to identify a practical problem that is beyond the reach of current classical computers, but that requires the fewest resources for a quantum computer. We consider quantum simulation of spin systems, which could be applied to understand condensed matter phenomena. We synthesize explicit circuits for three leading quantum simulation algorithms, using diverse techniques to tighten error bounds and optimize circuit implementations. Quantum signal processing appears to be preferred among algorithms with rigorous performance guarantees, whereas higher-order product formulas prevail if empirical error estimates suffice. Our circuits are orders of magnitude smaller than those for the simplest classically infeasible instances of factoring and quantum chemistry, bringing practical quantum computation closer to reality.

    更新日期:2018-09-19
  • Decreased water activity in nanoconfinement contributes to the folding of G-quadruplex and i-motif structures [Chemistry]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Sagun Jonchhe, Shankar Pandey, Tomoko Emura, Kumi Hidaka, Mohammad Akter Hossain, Prakash Shrestha, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao

    Due to the small size of a nanoconfinement, the property of water contained inside is rather challenging to probe. Herein, we measured the amount of water molecules released during the folding of individual G-quadruplex and i-motif structures, from which water activities are estimated in the DNA nanocages prepared by 5 × 5 to 7 × 7 helix bundles (cross-sections, 9 × 9 to 15 × 15 nm). We found water activities decrease with reducing cage size. In the 9 × 9-nm cage, water activity was reduced beyond the reach of regular cosolutes such as polyethylene glycol (PEG). With this set of nanocages, we were able to retrieve the change in water molecules throughout the folding trajectory of G-quadruplex or i-motif. We found that water molecules absorbed from the unfolded to the transition states are much fewer than those lost from the transition to the folded states. The overall loss of water therefore drives the folding of G-quadruplex or i-motif in nanocages with reduced water activities.

    更新日期:2018-09-19
  • Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Christopher R. Benson, Christopher Maffeo, Elisabeth M. Fatila, Yun Liu, Edward G. Sheetz, Aleksei Aksimentiev, Abhishek Singharoy, Amar H. Flood

    The coordinated motion of many individual components underpins the operation of all machines. However, despite generations of experience in engineering, understanding the motion of three or more coupled components remains a challenge, known since the time of Newton as the “three-body problem.” Here, we describe, quantify, and simulate a molecular three-body problem of threading two molecular rings onto a linear molecular thread. Specifically, we use voltage-triggered reduction of a tetrazine-based thread to capture two cyanostar macrocycles and form a [3]pseudorotaxane product. As a consequence of the noncovalent coupling between the cyanostar rings, we find the threading occurs by an unexpected and rare inchworm-like motion where one ring follows the other. The mechanism was derived from controls, analysis of cyclic voltammetry (CV) traces, and Brownian dynamics simulations. CVs from two noncovalently interacting rings match that of two covalently linked rings designed to thread via the inchworm pathway, and they deviate considerably from the CV of a macrocycle designed to thread via a stepwise pathway. Time-dependent electrochemistry provides estimates of rate constants for threading. Experimentally derived parameters (energy wells, barriers, diffusion coefficients) helped determine likely pathways of motion with rate-kinetics and Brownian dynamics simulations. Simulations verified intercomponent coupling could be separated into ring–thread interactions for kinetics, and ring–ring interactions for thermodynamics to reduce the three-body problem to a two-body one. Our findings provide a basis for high-throughput design of molecular machinery with multiple components undergoing coupled motion.

    更新日期:2018-09-19
  • Remote electrochemical modulation of pKa in a rotaxane by co-conformational allostery [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Giulio Ragazzon, Christian Schäfer, Paola Franchi, Serena Silvi, Benoit Colasson, Marco Lucarini, Alberto Credi

    Allosteric control, one of Nature’s most effective ways to regulate functions in biomolecular machinery, involves the transfer of information between distant sites. The mechanistic details of such a transfer are still an object of intensive investigation and debate, and the idea that intramolecular communication could be enabled by dynamic processes is gaining attention as a complement to traditional explanations. Mechanically interlocked molecules, owing to the particular kind of connection between their components and the resulting dynamic behavior, are attractive systems to investigate allosteric mechanisms and exploit them to develop functionalities with artificial species. We show that the pKa of an ammonium site located on the axle component of a [2]rotaxane can be reversibly modulated by changing the affinity of a remote recognition site for the interlocked crown ether ring through electrochemical stimulation. The use of a reversible ternary redox switch enables us to set the pKa to three different values, encompassing more than seven units. Our results demonstrate that in the axle the two sites do not communicate, and that in the rotaxane the transfer of information between them is made possible by the shuttling of the ring, that is, by a dynamic intramolecular process. The investigated coupling of electron- and proton-transfer reactions is reminiscent of the operation of the protein complex I of the respiratory chain.

    更新日期:2018-09-19
  • Reversible photoswitching of encapsulated azobenzenes in water [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Dipak Samanta, Julius Gemen, Zonglin Chu, Yael Diskin-Posner, Linda J. W. Shimon, Rafal Klajn

    Efficient molecular switching in confined spaces is critical for the successful development of artificial molecular machines. However, molecular switching events often entail large structural changes and therefore require conformational freedom, which is typically limited under confinement conditions. Here, we investigated the behavior of azobenzene—the key building block of light-controlled molecular machines—in a confined environment that is flexible and can adapt its shape to that of the bound guest. To this end, we encapsulated several structurally diverse azobenzenes within the cavity of a flexible, water-soluble coordination cage, and investigated their light-responsive behavior. Using UV/Vis absorption spectroscopy and a combination of NMR methods, we showed that each of the encapsulated azobenzenes exhibited distinct switching properties. An azobenzene forming a 1:1 host–guest inclusion complex could be efficiently photoisomerized in a reversible fashion. In contrast, successful switching in inclusion complexes incorporating two azobenzene guests was dependent on the availability of free cages in the system, and it involved reversible trafficking of azobenzene between the cages. In the absence of extra cages, photoswitching was either suppressed or it involved expulsion of azobenzene from the cage and consequently its precipitation from the solution. This finding was utilized to develop an information storage medium in which messages could be written and erased in a reversible fashion using light.

    更新日期:2018-09-19
  • Structure of a monolayer of molecular rotors on aqueous subphase from grazing-incidence X-ray diffraction [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Jiří Kaleta, Jin Wen, Thomas F. Magnera, Paul I. Dron, Chenhui Zhu, Josef Michl

    In situ grazing-incidence X-ray scattering shows that a monolayer of artificial rod-shaped dipolar molecular rotors produced on the surface of an aqueous subphase in a Langmuir trough has a structure conducive to a 2D ferroelectric phase. The axes of the rotors stand an average of 0.83 nm apart in a triangular grid, perpendicular to the surface within experimental error. They carry 2,3-dichlorophenylene rotators near rod centers, between two decks of interlocked triptycenes installed axially on the rotor axle. The analysis is based first on simultaneous fitting of observed Bragg rods and second on fitting the reflectivity curve with only three adjustable parameters and the calculated rotor electron density, which also revealed the presence of about seven molecules of water near each rotator. Dependent on preparation conditions, a minor and variable amount of a different crystal phase may also be present in the monolayer.

    更新日期:2018-09-19
  • Triangular cyclic rotaxanes: Size, fluctuations, and switching properties [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Prithvi Reddy, Edith M. Sevick, David R. M. Williams

    We examine one of the simplest cyclic rotaxanes—a molecule made from three rods with variable length between 0 and L. This [3]rotaxane, unlike a traditional molecule, shows significant size and shape fluctuations. We quantify these using a number of different measures. In particular, we show that the average angles are 100∘,52∘, and 28∘ and the most populated lengths lie at L,2L/3, and L/3. The triangles are usually obtuse. We discuss the area allowed within the triangle for inclusion compounds. Inspired by the linear rotaxane switches, we also consider the statistical mechanics of switching when stations with attractive interactions promote small-cycle areas.

    更新日期:2018-09-19
  • Dynamic force spectroscopy of synthetic oligorotaxane foldamers [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Damien Sluysmans, Floriane Devaux, Carson J. Bruns, J. Fraser Stoddart, Anne-Sophie Duwez

    Wholly synthetic molecules involving both mechanical bonds and a folded secondary structure are one of the most promising architectures for the design of functional molecular machines with unprecedented properties. Here, we report dynamic single-molecule force spectroscopy experiments that explore the energetic details of donor–acceptor oligorotaxane foldamers, a class of molecular switches. The mechanical breaking of the donor–acceptor interactions responsible for the folded structure shows a high constant rupture force over a broad range of loading rates, covering three orders of magnitude. In comparison with dynamic force spectroscopy performed during the past 20 y on various (bio)molecules, the near-equilibrium regime of oligorotaxanes persists at much higher loading rates, at which biomolecules have reached their kinetic regime, illustrating the very fast dynamics and remarkable rebinding capabilities of the intramolecular donor–acceptor interactions. We focused on one single interaction at a time and probed the stochastic rupture and rebinding paths. Using the Crooks fluctuation theorem, we measured the mechanical work produced during the breaking and rebinding to determine a free-energy difference, ΔG, of 6 kcal·mol−1 between the two local conformations around a single bond.

    更新日期:2018-09-19
  • News Feature: What’s the best way to build a molecular machine? [Chemistry]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Stephen Ornes

    Some of the smallest, most useful machines known to science are the biological molecules that keep living things living. The protein myosin drives the contraction and relaxation of muscle. Kinesin drags cellular cargo around the cell. Motor enzymes unwind, rewind, and maintain DNA, and bacteria use a molecular motor to rotate their whip-like flagella up to 100,000 times per minute, propelling them forward. These machines turn chemical energy into motion. They’re very efficient at their jobs.

    更新日期:2018-09-19
  • Genetic screen identifies adaptive aneuploidy as a key mediator of ER stress resistance in yeast [Cell Biology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Carine Beaupere, Leticia Dinatto, Brian M. Wasko, Rosalyn B. Chen, Lauren VanValkenburg, Michael G. Kiflezghi, Mitchell B. Lee, Daniel E. L. Promislow, Weiwei Dang, Matt Kaeberlein, Vyacheslav M. Labunskyy

    The yeast genome becomes unstable during stress, which often results in adaptive aneuploidy, allowing rapid activation of protective mechanisms that restore cellular homeostasis. In this study, we performed a genetic screen in Saccharomyces cerevisiae to identify genome adaptations that confer resistance to tunicamycin-induced endoplasmic reticulum (ER) stress. Whole-genome sequencing of tunicamycin-resistant mutants revealed that ER stress resistance correlated significantly with gains of chromosomes II and XIII. We found that chromosome duplications allow adaptation of yeast cells to ER stress independently of the unfolded protein response, and that the gain of an extra copy of chromosome II alone is sufficient to induce protection from tunicamycin. Moreover, the protective effect of disomic chromosomes can be recapitulated by overexpression of several genes located on chromosome II. Among these genes, overexpression of UDP-N-acetylglucosamine-1-P transferase (ALG7), a subunit of the 20S proteasome (PRE7), and YBR085C-A induced tunicamycin resistance in wild-type cells, whereas deletion of all three genes completely reversed the tunicamycin-resistance phenotype. Together, our data demonstrate that aneuploidy plays a critical role in adaptation to ER stress by increasing the copy number of ER stress protective genes. While aneuploidy itself leads to proteotoxic stress, the gene-specific effects of chromosome II aneuploidy counteract the negative effect resulting in improved protein folding.

    更新日期:2018-09-19
  • The chaperonin TRiC/CCT is essential for the action of bacterial glycosylating protein toxins like Clostridium difficile toxins A and B [Cell Biology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Marcus Steinemann, Andreas Schlosser, Thomas Jank, Klaus Aktories

    Various bacterial protein toxins, including Clostridium difficile toxins A (TcdA) and B (TcdB), attack intracellular target proteins of host cells by glucosylation. After receptor binding and endocytosis, the toxins are translocated into the cytosol, where they modify target proteins (e.g., Rho proteins). Here we report that the activity of translocated glucosylating toxins depends on the chaperonin TRiC/CCT. The chaperonin subunits CCT4/5 directly interact with the toxins and enhance the refolding and restoration of the glucosyltransferase activities of toxins after heat treatment. Knockdown of CCT5 by siRNA and HSF1A, an inhibitor of TRiC/CCT, blocks the cytotoxic effects of TcdA and TcdB. In contrast, HSP90, which is involved in the translocation and uptake of ADP ribosylating toxins, is not involved in uptake of the glucosylating toxins. We show that the actions of numerous glycosylating toxins from various toxin types and different species depend on TRiC/CCT. Our data indicate that the TRiC/CCT chaperonin system is specifically involved in toxin uptake and essential for the action of various glucosylating protein toxins acting intracellularly on target proteins.

    更新日期:2018-09-19
  • Chemical control over membrane-initiated steroid signaling with a DNA nanocapsule [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Aneesh T. Veetil, Maulik S. Jani, Yamuna Krishnan

    Membrane-initiated steroid signaling (MISS) is a recently discovered aspect of steroidal control over cell function that has proved highly challenging to study due to its rapidity and ultrasensitivity to the steroid trigger [Chow RWY, Handelsman DJ, Ng MKC (2010) Endocrinology 151:2411–2422]. Fundamental aspects underlying MISS, such as receptor binding, kinetics of ion-channel opening, and production of downstream effector molecules remain obscure because a pristine molecular technology that could trigger the release of signaling steroids was not available. We have recently described a prototype DNA nanocapsule which can be programmed to release small molecules upon photoirradiation [Veetil AT, et al. (2017) Nat Nanotechnol 12:1183–1189]. Here we show that this DNA-based molecular technology can now be programmed to chemically trigger MISS, significantly expanding its applicability to systems that are refractory to photoirradiation.

    更新日期:2018-09-19
  • Mechanics of diseased red blood cells in human spleen and consequences for hereditary blood disorders [Biophysics and Computational Biology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    He Li, Lu Lu, Xuejin Li, Pierre A. Buffet, Ming Dao, George E. Karniadakis, Subra Suresh

    In red blood cell (RBC) diseases, the spleen contributes to anemia by clearing the damaged RBCs, but its unique ability to mechanically challenge RBCs also poses the risk of inducing other pathogenic effects. We have analyzed RBCs in hereditary spherocytosis (HS) and hereditary elliptocytosis (HE), two typical examples of blood disorders that result in membrane protein defects in RBCs. We use a two-component protein-scale RBC model to simulate the traversal of the interendothelial slit (IES) in the human spleen, a stringent biomechanical challenge on healthy and diseased RBCs that cannot be directly observed in vivo. In HS, our results confirm that the RBC loses surface due to weakened cohesion between the lipid bilayer and the cytoskeleton and reveal that surface loss may result from vesiculation of the RBC as it crosses IES. In HE, traversing IES induces sustained elongation of the RBC with impaired elasticity and fragmentation in severe disease. Our simulations thus suggest that in inherited RBC disorders, the spleen not only filters out pathological RBCs but also directly contributes to RBC alterations. These results provide a mechanistic rationale for different clinical outcomes documented following splenectomy in HS patients with spectrin-deficient and ankyrin-deficient RBCs and offer insights into the pathogenic role of human spleen in RBC diseases.

    更新日期:2018-09-19
  • Machining protein microcrystals for structure determination by electron diffraction [Biophysics and Computational Biology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Helen M. E. Duyvesteyn, Abhay Kotecha, Helen M. Ginn, Corey W. Hecksel, Emma V. Beale, Felix de Haas, Gwyndaf Evans, Peijun Zhang, Wah Chiu, David I. Stuart

    We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure determination, bridging the crystal size gap between the nanometer scale of conventional electron diffraction and micron scale of synchrotron microfocus beamlines. The demonstration that atomic information can be retained suggests that milling could provide such detail on sections cut from vitrified cells.

    更新日期:2018-09-19
  • Simultaneous polymerization and adhesion under hypoxia in sickle cell disease [Biophysics and Computational Biology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Dimitrios P. Papageorgiou, Sabia Z. Abidi, Hung-Yu Chang, Xuejin Li, Gregory J. Kato, George E. Karniadakis, Subra Suresh, Ming Dao

    Polymerization and adhesion, dynamic processes that are hallmarks of sickle cell disease (SCD), have thus far been studied in vitro only separately. Here, we present quantitative results of the simultaneous and synergistic effects of adhesion and polymerization of deoxygenated sickle hemoglobin (HbS) in the human red blood cell (RBC) on the mechanisms underlying vasoocclusive pain crisis. For this purpose, we employ a specially developed hypoxic microfluidic platform, which is capable of inducing sickling and unsickling of RBCs in vitro, to test blood samples from eight patients with SCD. We supplemented these experimental results with detailed molecular-level computational simulations of cytoadherence and biorheology using dissipative particle dynamics. By recourse to image analysis techniques, we characterize sickle RBC maturation stages in the following order of the degree of adhesion susceptibility under hypoxia: sickle reticulocytes in circulation (SRs) → sickle mature erythrocytes (SMEs) → irreversibly sickled cells (ISCs). We show that (i) hypoxia significantly enhances sickle RBC adherence; (ii) HbS polymerization enhances sickle cell adherence in SRs and SMEs, but not in ISCs; (iii) SRs exhibit unique adhesion dynamics where HbS fiber projections growing outward from the cell surface create multiple sites of adhesion; and (iv) polymerization stimulates adhesion and vice versa, thereby establishing the bidirectional coupling between the two processes. These findings offer insights into possible mechanistic pathways leading to vasoocclusion crisis. They also elucidate the processes underlying the onset of occlusion that may involve circulating reticulocytes, which are more abundant in hemolytic anemias due to robust compensatory erythropoiesis.

    更新日期:2018-09-19
  • Franck-Condon picture of incoherent neutron scattering [Biophysics and Computational Biology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Gerald R. Kneller

    A spectroscopic interpretation of incoherent neutron scattering experiments is presented which is based on Franck–Condon-type probabilities for scattering-induced transitions between quantum states of the target. The resulting expressions for the scattering functions enable an energy landscape-oriented analysis of neutron scattering spectra as well as a physical interpretation of Van Hove’s space–time correlation functions in the quantum regime that accounts for the scattering kinematics. They suggest moreover a combined analysis of quasi- and inelastic scattering that becomes inseparable for complex systems with slow power-law relaxation.

    更新日期:2018-09-19
  • GEF mechanism revealed by the structure of SmgGDS-558 and farnesylated RhoA complex and its implication for a chaperone mechanism [Biochemistry]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Hikaru Shimizu, Sachiko Toma-Fukai, Kenji Kontani, Toshiaki Katada, Toshiyuki Shimizu

    SmgGDS has dual functions in cells and regulates small GTPases as both a guanine nucleotide exchange factor (GEF) for the Rho family and a molecular chaperone for small GTPases possessing a C-terminal polybasic region followed by four C-terminal residues called the CaaX motif, which is posttranslationally prenylated at its cysteine residue. Our recent structural work revealed that SmgGDS folds into tandem copies of armadillo-repeat motifs (ARMs) that are not present in other GEFs. However, the precise mechanism of GEF activity and recognition mechanism for the prenylated CaaX motif remain unknown because SmgGDS does not have a typical GEF catalytic domain and lacks a pocket to accommodate a prenyl group. Here, we aimed to determine the crystal structure of the SmgGDS/farnesylated RhoA complex. We found that SmgGDS induces a significant conformational change in the switch I and II regions that opens up the nucleotide-binding site, with the prenyl group fitting into the cryptic pocket in the N-terminal ARMs. Taken together, our findings could advance the understanding of the role of SmgGDS and enable drug design strategies for targeting SmgGDS and small GTPases.

    更新日期:2018-09-19
  • Mammalian STT3A/B oligosaccharyltransferases segregate N-glycosylation at the translocon from lipid-linked oligosaccharide hydrolysis [Biochemistry]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Hua Lu, Charles S. Fermaintt, Natalia A. Cherepanova, Reid Gilmore, Nan Yan, Mark A. Lehrman

    Oligosaccharyltransferases (OSTs) N-glycosylate proteins by transferring oligosaccharides from lipid-linked oligosaccharides (LLOs) to asparaginyl residues of Asn-Xaa-Ser/Thr acceptor sequons. Mammals have OST isoforms with STT3A or STT3B catalytic subunits for cotranslational or posttranslational N-glycosylation, respectively. OSTs also hydrolyze LLOs, forming free oligosaccharides (fOSs). It has been unclear whether hydrolysis is due to one or both OSTs, segregated from N-glycosylation, and/or regulated. Transfer and hydrolysis were assayed in permeabilized HEK293 kidney and Huh7.5.1 liver cells lacking STT3A or STT3B. Transfer by both STT3A-OST and STT3B-OST with synthetic acceptors was robust. LLO hydrolysis by STT3B-OST was readily detected and surprisingly modulated: Without acceptors, STT3B-OST hydrolyzed Glc3Man9GlcNAc2-LLO but not Man9GlcNAc2-LLO, yet it hydrolyzed both LLOs with acceptors present. In contrast, LLO hydrolysis by STT3A-OST was negligible. STT3A-OST however may be regulatory, because it suppressed STT3B-OST–dependent fOSs. TREX1, a negative innate immunity factor that diminishes immunogenic fOSs derived from LLOs, acted through STT3B-OST as well. In summary, only STT3B-OST hydrolyzes LLOs, depending upon LLO quality and acceptor site occupancy. TREX1 and STT3A suppress STT3B-OST–dependent fOSs. Without strict kinetic limitations during posttranslational N-glycosylation, STT3B-OST can thus moonlight for LLO hydrolysis. In contrast, the STT3A-OST/translocon complex preserves LLOs for temporally fastidious cotranslational N-glycosylation.

    更新日期:2018-09-19
  • Ultrahigh-throughput functional profiling of microbiota communities [Biochemistry]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Stanislav S. Terekhov, Ivan V. Smirnov, Maja V. Malakhova, Andrei E. Samoilov, Alexander I. Manolov, Anton S. Nazarov, Dmitry V. Danilov, Svetlana A. Dubiley, Ilya A. Osterman, Maria P. Rubtsova, Elena S. Kostryukova, Rustam H. Ziganshin, Maria A. Kornienko, Anna A. Vanyushkina, Olga N. Bukato, Elena N. Ilina, Valentin V. Vlasov, Konstantin V. Severinov, Alexander G. Gabibov, Sidney Altman

    Microbiome spectra serve as critical clues to elucidate the evolutionary biology pathways, potential pathologies, and even behavioral patterns of the host organisms. Furthermore, exotic sources of microbiota represent an unexplored niche to discover microbial secondary metabolites. However, establishing the bacterial functionality is complicated by an intricate web of interactions inside the microbiome. Here we apply an ultrahigh-throughput (uHT) microfluidic droplet platform for activity profiling of the entire oral microbial community of the Siberian bear to isolate Bacillus strains demonstrating antimicrobial activity against Staphylococcus aureus. Genome mining allowed us to identify antibiotic amicoumacin A (Ami) as responsible for inhibiting the growth of S. aureus. Proteomics and metabolomics revealed a unique mechanism of Bacillus self-resistance to Ami, based on a subtle equilibrium of its deactivation and activation by kinase AmiN and phosphatase AmiO, respectively. We developed uHT quantitative single-cell analysis to estimate antibiotic efficacy toward different microbiomes and used it to determine the activity spectra of Ami toward human and Siberian bear microbiota. Thus, uHT microfluidic droplet platform activity profiling is a powerful tool for discovering antibiotics and quantifying external influences on a microbiome.

    更新日期:2018-09-19
  • Ragulator and SLC38A9 activate the Rag GTPases through noncanonical GEF mechanisms [Biochemistry]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Kuang Shen, David M. Sabatini

    The mechanistic target of rapamycin complex 1 (mTORC1) growth pathway detects nutrients through a variety of sensors and regulators that converge on the Rag GTPases, which form heterodimers consisting of RagA or RagB tightly bound to RagC or RagD and control the subcellular localization of mTORC1. The Rag heterodimer uses a unique “locking” mechanism to stabilize its active (GTPRagA–RagCGDP) or inactive (GDPRagA–RagCGTP) nucleotide states. The Ragulator complex tethers the Rag heterodimer to the lysosomal surface, and the SLC38A9 transmembrane protein is a lysosomal arginine sensor that upon activation stimulates mTORC1 activity through the Rag GTPases. How Ragulator and SLC38A9 control the nucleotide loading state of the Rag GTPases remains incompletely understood. Here we find that Ragulator and SLC38A9 are each unique guanine exchange factors (GEFs) that collectively push the Rag GTPases toward the active state. Ragulator triggers GTP release from RagC, thus resolving the locked inactivated state of the Rag GTPases. Upon arginine binding, SLC38A9 converts RagA from the GDP- to the GTP-loaded state, and therefore activates the Rag GTPase heterodimer. Altogether, Ragulator and SLC38A9 act on the Rag GTPases to activate the mTORC1 pathway in response to nutrient sufficiency.

    更新日期:2018-09-19
  • Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo [Biochemistry]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Robert M. Yarrington, Surbhi Verma, Shaina Schwartz, Jonathan K. Trautman, Dana Carroll

    Genome editing with CRISPR-Cas nucleases has been applied successfully to a wide range of cells and organisms. There is, however, considerable variation in the efficiency of cleavage and outcomes at different genomic targets, even within the same cell type. Some of this variability is likely due to the inherent quality of the interaction between the guide RNA and the target sequence, but some may also reflect the relative accessibility of the target. We investigated the influence of chromatin structure, particularly the presence or absence of nucleosomes, on cleavage by the Streptococcus pyogenes Cas9 protein. At multiple target sequences in two promoters in the yeast genome, we find that Cas9 cleavage is strongly inhibited when the DNA target is within a nucleosome. This inhibition is relieved when nucleosomes are depleted. Remarkably, the same is not true of zinc-finger nucleases (ZFNs), which cleave equally well at nucleosome-occupied and nucleosome-depleted sites. These results have implications for the choice of specific targets for genome editing, both in research and in clinical and other practical applications.

    更新日期:2018-09-19
  • Origin of the emergent fragile-to-strong transition in supercooled water [Applied Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Rui Shi, John Russo, Hajime Tanaka

    Liquids can be broadly classified into two categories, fragile and strong ones, depending on how their dynamical properties change with temperature. The dynamics of a strong liquid obey the Arrhenius law, whereas the fragile one displays a super-Arrhenius law, with a much steeper slowing down upon cooling. Recently, however, it was discovered that many materials such as water, oxides, and metals do not obey this simple classification, apparently exhibiting a fragile-to-strong transition far above Tg. Such a transition is particularly well known for water, and it is now regarded as one of water’s most important anomalies. This phenomenon has been attributed to either an unusual glass transition behavior or the crossing of a Widom line emanating from a liquid–liquid critical point. Here by computer simulations of two popular water models and through analyses of experimental data, we show that the emergent fragile-to-strong transition is actually a crossover between two Arrhenius regimes with different activation energies, which can be naturally explained by a two-state description of the dynamics. Our finding provides insight into the fragile-to-strong transition observed in a wide class of materials.

    更新日期:2018-09-19
  • Morphological transitions of elastic filaments in shear flow [Applied Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Yanan Liu, Brato Chakrabarti, David Saintillan, Anke Lindner, Olivia du Roure

    The morphological dynamics, instabilities, and transitions of elastic filaments in viscous flows underlie a wealth of biophysical processes from flagellar propulsion to intracellular streaming and are also key to deciphering the rheological behavior of many complex fluids and soft materials. Here, we combine experiments and computational modeling to elucidate the dynamical regimes and morphological transitions of elastic Brownian filaments in a simple shear flow. Actin filaments are used as an experimental model system and their conformations are investigated through fluorescence microscopy in microfluidic channels. Simulations matching the experimental conditions are also performed using inextensible Euler–Bernoulli beam theory and nonlocal slender-body hydrodynamics in the presence of thermal fluctuations and agree quantitatively with observations. We demonstrate that filament dynamics in this system are primarily governed by a dimensionless elasto-viscous number comparing viscous drag forces to elastic bending forces, with thermal fluctuations playing only a secondary role. While short and rigid filaments perform quasi-periodic tumbling motions, a buckling instability arises above a critical flow strength. A second transition to strongly deformed shapes occurs at a yet larger value of the elasto-viscous number and is characterized by the appearance of localized high-curvature bends that propagate along the filaments in apparent “snaking” motions. A theoretical model for the as yet unexplored onset of snaking accurately predicts the transition and explains the observed dynamics. We present a complete characterization of filament morphologies and transitions as a function of elasto-viscous number and scaled persistence length and demonstrate excellent agreement between theory, experiments, and simulations.

    更新日期:2018-09-19
  • Molecular rotary motors: Unidirectional motion around double bonds [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Diederik Roke, Sander J. Wezenberg, Ben L. Feringa

    The field of synthetic molecular machines has quickly evolved in recent years, growing from a fundamental curiosity to a highly active field of chemistry. Many different applications are being explored in areas such as catalysis, self-assembled and nanostructured materials, and molecular electronics. Rotary molecular motors hold great promise for achieving dynamic control of molecular functions as well as for powering nanoscale devices. However, for these motors to reach their full potential, many challenges still need to be addressed. In this paper we focus on the design principles of rotary motors featuring a double-bond axle and discuss the major challenges that are ahead of us. Although great progress has been made, further design improvements, for example in terms of efficiency, energy input, and environmental adaptability, will be crucial to fully exploit the opportunities that these rotary motors offer.

    更新日期:2018-09-19
  • New molecular switch architectures [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Jared D. Harris, Mark J. Moran, Ivan Aprahamian

    In this paper we elaborate on recently developed molecular switch architectures and how these new systems can help with the realization of new functions and advancement of artificial molecular machines. Progress in chemically and photoinduced switches and motors is summarized and contextualized such that the reader may gain an appreciation for the novel tools that have come about in the past decade. Many of these systems offer distinct advantages over commonly employed switches, including improved fidelity, addressability, and robustness. Thus, this paper serves as a jumping-off point for researchers seeking new switching motifs for specific applications, or ones that address the limitations of presently available systems.

    更新日期:2018-09-19
  • Stochastically pumped adaptation and directional motion of molecular machines [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    R. Dean Astumian

    Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment—walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium.

    更新日期:2018-09-19
  • Molecular machines with bio-inspired mechanisms [Physical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Liang Zhang, Vanesa Marcos, David A. Leigh

    The widespread use of molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular machines—which by and large function as switches—and the machines of the macroscopic world, which utilize the synchronized behavior of integrated components to perform more sophisticated tasks than is possible with any individual switch. Should we try to make molecular machines of greater complexity by trying to mimic machines from the macroscopic world or instead apply unfamiliar (and no doubt have to discover or invent currently unknown) mechanisms utilized by biological machines? Here we try to answer that question by exploring some of the advances made to date using bio-inspired machine mechanisms.

    更新日期:2018-09-19
  • Growing community of artificial molecular machinists [Introductions]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Damien Sluysmans, J. Fraser Stoddart

    Over the past decades, chemists have been pursuing the creation of man-made molecular machines with either designed engineering-like operations or with higher performances compared with biological machines. The promise of creating an artificial molecular world traces its origins in the well-known lecture of Richard Feynman, There’s plenty of room at the bottom (1). Feynman’s insights into the immense possibilities of such small artificial machines, assembled in a straightforward manner, were deeply inspiring for the scientific community. The design of machines on the molecular scale is not an easy task to accomplish. Instead of gravity and inertia, which are omnipresent in the macroscopic world, random thermal fluctuations are prevalent and dominate movements on the molecular scale. Two main approaches are being considered for the construction of artificial molecular machines (AMMs): namely, bio-inspiration and miniaturization. The former consists of integrating concepts from naturally occurring machines and unnatural building blocks into AMMs, while the latter involves engineering nano-devices based on the mechanical actions of macroscopic machines. Perhaps a better way to design AMMs with unprecedented functions would be to follow neither of these routes, but rather to construct molecularly precise architectures based on recent advances in supramolecular chemistry: explore what has not been built by Nature. This unnatural route would only share with the biological world its fundamental laws at small scales, but differentiates it from its working processes.

    更新日期:2018-09-19
  • Mid-level visual features underlie the high-level categorical organization of the ventral stream [Psychological and Cognitive Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Bria Long, Chen-Ping Yu, Talia Konkle

    Human object-selective cortex shows a large-scale organization characterized by the high-level properties of both animacy and object size. To what extent are these neural responses explained by primitive perceptual features that distinguish animals from objects and big objects from small objects? To address this question, we used a texture synthesis algorithm to create a class of stimuli—texforms—which preserve some mid-level texture and form information from objects while rendering them unrecognizable. We found that unrecognizable texforms were sufficient to elicit the large-scale organizations of object-selective cortex along the entire ventral pathway. Further, the structure in the neural patterns elicited by texforms was well predicted by curvature features and by intermediate layers of a deep convolutional neural network, supporting the mid-level nature of the representations. These results provide clear evidence that a substantial portion of ventral stream organization can be accounted for by coarse texture and form information without requiring explicit recognition of intact objects.

    更新日期:2018-09-19
  • Glutamate-activated BK channel complexes formed with NMDA receptors [Physiology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Jiyuan Zhang, Xin Guan, Qin Li, Andrea L. Meredith, Hui-Lin Pan, Jiusheng Yan

    The large-conductance calcium- and voltage-activated K+ (BK) channel has a requirement of high intracellular free Ca2+ concentrations for its activation in neurons under physiological conditions. The Ca2+ sources for BK channel activation are not well understood. In this study, we showed by coimmunopurification and colocalization analyses that BK channels form complexes with NMDA receptors (NMDARs) in both rodent brains and a heterologous expression system. The BK–NMDAR complexes are broadly present in different brain regions. The complex formation occurs between the obligatory BKα and GluN1 subunits likely via a direct physical interaction of the former’s intracellular S0–S1 loop with the latter’s cytosolic regions. By patch-clamp recording on mouse brain slices, we observed BK channel activation by NMDAR-mediated Ca2+ influx in dentate gyrus granule cells. BK channels modulate excitatory synaptic transmission via functional coupling with NMDARs at postsynaptic sites of medial perforant path-dentate gyrus granule cell synapses. A synthesized peptide of the BKα S0–S1 loop region, when loaded intracellularly via recording pipette, abolished the NMDAR-mediated BK channel activation and effect on synaptic transmission. These findings reveal the broad expression of the BK–NMDAR complexes in brain, the potential mechanism underlying the complex formation, and the NMDAR-mediated activation and function of postsynaptic BK channels in neurons.

    更新日期:2018-09-19
  • PKCϵ contributes to lipid-induced insulin resistance through cross talk with p70S6K and through previously unknown regulators of insulin signaling [Physiology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Brandon M. Gassaway, Max C. Petersen, Yulia V. Surovtseva, Karl W. Barber, Joshua B. Sheetz, Hans R. Aerni, Jane S. Merkel, Varman T. Samuel, Gerald I. Shulman, Jesse Rinehart

    Insulin resistance drives the development of type 2 diabetes (T2D). In liver, diacylglycerol (DAG) is a key mediator of lipid-induced insulin resistance. DAG activates protein kinase C ε (PKCε), which phosphorylates and inhibits the insulin receptor. In rats, a 3-day high-fat diet produces hepatic insulin resistance through this mechanism, and knockdown of hepatic PKCε protects against high-fat diet-induced hepatic insulin resistance. Here, we employed a systems-level approach to uncover additional signaling pathways involved in high-fat diet-induced hepatic insulin resistance. We used quantitative phosphoproteomics to map global in vivo changes in hepatic protein phosphorylation in chow-fed, high-fat–fed, and high-fat–fed with PKCε knockdown rats to distinguish the impact of lipid- and PKCε-induced protein phosphorylation. This was followed by a functional siRNA-based screen to determine which dynamically regulated phosphoproteins may be involved in canonical insulin signaling. Direct PKCε substrates were identified by motif analysis of phosphoproteomics data and validated using a large-scale in vitro kinase assay. These substrates included the p70S6K substrates RPS6 and IRS1, which suggested cross talk between PKCε and p70S6K in high-fat diet-induced hepatic insulin resistance. These results identify an expanded set of proteins through which PKCε may drive high-fat diet-induced hepatic insulin resistance that may direct new therapeutic approaches for T2D.

    更新日期:2018-09-19
  • Elimination of the error signal in the superior colliculus impairs saccade motor learning [Neuroscience]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Yoshiko Kojima, Robijanto Soetedjo

    When movements become dysmetric, the resultant motor error induces a plastic change in the cerebellum to correct the movement, i.e., motor adaptation. Current evidence suggests that the error signal to the cerebellum is delivered by complex spikes originating in the inferior olive (IO). To prove a causal link between the IO error signal and motor adaptation, several studies blocked the IO, which, unfortunately, affected not only the adaptation but also the movement itself. We avoided this confound by inactivating the source of an error signal to the IO. Several studies implicate the superior colliculus (SC) as the source of the error signal to the IO for saccade adaptation. When we inactivated the SC, the metrics of the saccade to be adapted were unchanged, but saccade adaptation was impaired. Thus, an intact rostral SC is necessary for saccade adaptation. Our data provide experimental evidence for the cerebellar learning theory that requires an error signal to drive motor adaptation.

    更新日期:2018-09-19
  • Ehrlichia type IV secretion system effector Etf-2 binds to active RAB5 and delays endosome maturation [Microbiology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Qi Yan, Mingqun Lin, Weiyan Huang, Omid Teymournejad, Jennifer M. Johnson, Franklin A. Hays, Zhimin Liang, Guangpu Li, Yasuko Rikihisa

    Ehrlichia chaffeensis, an obligatory intracellular bacterium, infects monocytes/macrophages by sequestering a regulator of endosomal traffic, the small GTPase RAB5, on its membrane-bound inclusions to avoid routing to host-cell phagolysosomes. How RAB5 is sequestered on ehrlichial inclusions is poorly understood, however. We found that native Ehrlichia translocated factor-2 (Etf-2), a previously predicted effector of the Ehrlichia type IV secretion system, and recombinant Etf-2 (cloned into the Ehrlichia genome) are secreted into the host-cell cytoplasm and localize to ehrlichial inclusions. Ectopically expressed Etf-2–GFP also localized to inclusions and membranes of early endosomes marked with RAB5 and interacted with GTP-bound RAB5 but not with a GDP-bound RAB5. Etf-2, although lacking a RAB GTPase-activating protein (GAP) Tre2-Bub2-Cdc16 (TBC) domain, contains two conserved TBC domain motifs, namely an Arg finger and a Gln finger, and site-directed mutagenesis revealed that both Arg188 and Gln245 are required for Etf-2 localization to early endosomes. The yeast two-hybrid assay and microscale thermophoresis revealed that Etf-2 binds tightly to GTP-bound RAB5 but not to GDP-bound RAB5. However, Etf-2 lacks RAB5-specific GAP activity. Etf-2 localized to bead-containing phagosomes as well as endosomes containing beads coated with the C-terminal fragment of EtpE (entry-triggering protein of Ehrlichia), an Ehrlichia outer-membrane invasin, and significantly delayed RAB5 dissociation from and RAB7 localization to phagosomes/endosomes and RABGAP5 localization to endosomes. Thus, binding of Etf-2 to RAB5-GTP appears to delay RAB5 inactivation by impeding RABGAP5 localization to endosomes. This suggests a unique mechanism by which RAB5 is sequestered on ehrlichial inclusions to benefit bacterial survival and replication.

    更新日期:2018-09-19
  • Enterotoxigenic E. coli virulence gene regulation in human infections [Microbiology]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Alexander A. Crofts, Simone M. Giovanetti, Erica J. Rubin, Frédéric M. Poly, Ramiro L. Gutiérrez, Kawsar R. Talaat, Chad K. Porter, Mark S. Riddle, Barbara DeNearing, Jessica Brubaker, Milton Maciel, Ashley N. Alcala, Subhra Chakraborty, Michael G. Prouty, Stephen J. Savarino, Bryan W. Davies, M. Stephen Trent

    Enterotoxigenic Escherichia coli (ETEC) is a global diarrheal pathogen that utilizes adhesins and secreted enterotoxins to cause disease in mammalian hosts. Decades of research on virulence factor regulation in ETEC has revealed a variety of environmental factors that influence gene expression, including bile, pH, bicarbonate, osmolarity, and glucose. However, other hallmarks of the intestinal tract, such as low oxygen availability, have not been examined. Further, determining how ETEC integrates these signals in the complex host environment is challenging. To address this, we characterized ETEC’s response to the human host using samples from a controlled human infection model. We found ETEC senses environmental oxygen to globally influence virulence factor expression via the oxygen-sensitive transcriptional regulator fumarate and nitrate reduction (FNR) regulator. In vitro anaerobic growth replicates the in vivo virulence factor expression profile, and deletion of fnr in ETEC strain H10407 results in a significant increase in expression of all classical virulence factors, including the colonization factor antigen I (CFA/I) adhesin operon and both heat-stable and heat-labile enterotoxins. These data depict a model of ETEC infection where FNR activity can globally influence virulence gene expression, and therefore proximity to the oxygenated zone bordering intestinal epithelial cells likely influences ETEC virulence gene expression in vivo. Outside of the host, ETEC biofilms are associated with seasonal ETEC epidemics, and we find FNR is a regulator of biofilm production. Together these data suggest FNR-dependent oxygen sensing in ETEC has implications for human infection inside and outside of the host.

    更新日期:2018-09-19
  • Phylogenetic approach to recover integration dates of latent HIV sequences within-host [Medical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Bradley R. Jones, Natalie N. Kinloch, Joshua Horacsek, Bruce Ganase, Marianne Harris, P. Richard Harrigan, R. Brad Jones, Mark A. Brockman, Jeffrey B. Joy, Art F. Y. Poon, Zabrina L. Brumme

    Given that HIV evolution and latent reservoir establishment occur continually within-host, and that latently infected cells can persist long-term, the HIV reservoir should comprise a genetically heterogeneous archive recapitulating within-host HIV evolution. However, this has yet to be conclusively demonstrated, in part due to the challenges of reconstructing within-host reservoir establishment dynamics over long timescales. We developed a phylogenetic framework to reconstruct the integration dates of individual latent HIV lineages. The framework first involves inference and rooting of a maximum-likelihood phylogeny relating plasma HIV RNA sequences serially sampled before the initiation of suppressive antiretroviral therapy, along with putative latent sequences sampled thereafter. A linear model relating root-to-tip distances of plasma HIV RNA sequences to their sampling dates is used to convert root-to-tip distances of putative latent lineages to their establishment (integration) dates. Reconstruction of the ages of putative latent sequences sampled from chronically HIV-infected individuals up to 10 y following initiation of suppressive therapy revealed a genetically heterogeneous reservoir that recapitulated HIV’s within-host evolutionary history. Reservoir sequences were interspersed throughout multiple within-host lineages, with the oldest dating to >20 y before sampling; historic genetic bottleneck events were also recorded therein. Notably, plasma HIV RNA sequences isolated from a viremia blip in an individual receiving otherwise suppressive therapy were highly genetically diverse and spanned a 20-y age range, suggestive of spontaneous in vivo HIV reactivation from a large latently infected cell pool. Our framework for reservoir dating provides a potentially powerful addition to the HIV persistence research toolkit.

    更新日期:2018-09-19
  • Expansion of cancer stem cell pool initiates lung cancer recurrence before angiogenesis [Medical Sciences]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Lei Li, Jiang-Chao Li, Hong Yang, Xu Zhang, Lu-Lu Liu, Yan Li, Ting-Ting Zeng, Ying-Hui Zhu, Xiao-Dong Li, Yan Li, Dan Xie, Li Fu, Xin-Yuan Guan

    Angiogenesis is essential in the early stage of solid tumor recurrence, but how a suspensive tumor is reactivated before angiogenesis is mostly unknown. Herein, we stumble across an interesting phenomenon that s.c. xenografting human lung cancer tissues can awaken the s.c. suspensive tumor in nude mice. We further found that a high level of insulin-like growth factor 1 (IGF1) was mainly responsible for triggering the transition from suspensive tumor to progressive tumor in this model. The s.c. suspensive tumor is characterized with growth arrest, avascularity, and a steady-state level of proliferating and apoptotic cells. Intriguingly, CD133+ lung cancer stem cells (LCSCs) are highly enriched in suspensive tumor compared with progressive tumor. Mechanistically, high IGF1 initiates LCSCs self-renewal from asymmetry to symmetry via the activation of a PI3K/Akt/β-catenin axis. Next, the expansion of LCSC pool promotes angiogenesis by increasing the production of CXCL1 and PlGF in CD133+ LCSCs, which results in lung cancer recurrence. Clinically, a high level of serum IGF1 in lung cancer patients after orthotopic lung cancer resection as an unfavorable factor is strongly correlated with the high rate of recurrence and indicates an adverse progression-free survival. Vice versa, blocking IGF1 or CXCL1/PlGF with neutralizing antibodies can prevent the reactivation of a suspensive tumor induced by IGF1 stimulation in the mouse model. Collectively, the expansion of LCSC pool before angiogenesis induced by IGF1 is a key checkpoint during the initiation of cancer relapse, and targeting serum IGF1 may be a promising treatment for preventing recurrence in lung cancer patients.

    更新日期:2018-09-19
  • Lack of Sprouty 1 and 2 enhances survival of effector CD8+ T cells and yields more protective memory cells [Immunology and Inflammation]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Hesham M. Shehata, Shahzada Khan, Elise Chen, Patrick E. Fields, Richard A. Flavell, Shomyseh Sanjabi

    Identifying novel pathways that promote robust function and longevity of cytotoxic T cells has promising potential for immunotherapeutic strategies to combat cancer and chronic infections. We show that sprouty 1 and 2 (Spry1/2) molecules regulate the survival and function of memory CD8+ T cells. Spry1/2 double-knockout (DKO) ovalbumin (OVA)-specific CD8+ T cells (OT-I cells) mounted more vigorous autoimmune diabetes than WT OT-I cells when transferred to mice expressing OVA in their pancreatic β-islets. To determine the consequence of Spry1/2 deletion on effector and memory CD8+ T cell development and function, we used systemic infection with lymphocytic choriomeningitis virus (LCMV) Armstrong. Spry1/2 DKO LCMV gp33-specific P14 CD8+ T cells survive contraction better than WT cells and generate significantly more polyfunctional memory T cells. The larger number of Spry1/2 DKO memory T cells displayed enhanced infiltration into infected tissue, demonstrating that absence of Spry1/2 can result in increased recall capacity. Upon adoptive transfer into naive hosts, Spry1/2 DKO memory T cells controlled Listeria monocytogenes infection better than WT cells. The enhanced formation of more functional Spry1/2 DKO memory T cells was associated with significantly reduced mTORC1 activity and glucose uptake. Reduced p-AKT, p-FoxO1/3a, and T-bet expression was also consistent with enhanced survival and memory accrual. Collectively, loss of Spry1/2 enhances the survival of effector CD8+ T cells and results in the formation of more protective memory cells. Deleting Spry1/2 in antigen-specific CD8+ T cells may have therapeutic potential for enhancing the survival and functionality of effector and memory CD8+ T cells in vivo.

    更新日期:2018-09-19
  • Chemokine receptors CCR2 and CX3CR1 regulate viral encephalitis-induced hippocampal damage but not seizures [Immunology and Inflammation]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Christopher Käufer, Chintan Chhatbar, Sonja Bröer, Inken Waltl, Luca Ghita, Ingo Gerhauser, Ulrich Kalinke, Wolfgang Löscher

    Viral encephalitis is a major risk factor for the development of seizures, epilepsy, and hippocampal damage with associated cognitive impairment, markedly reducing quality of life in survivors. The mechanisms underlying seizures and hippocampal neurodegeneration developing during and after viral encephalitis are only incompletely understood, hampering the development of preventive treatments. Recent findings suggest that brain invasion of blood-born monocytes may be critically involved in both seizures and brain damage in response to encephalitis, whereas the relative role of microglia, the brain’s resident immune cells, in these processes is not clear. CCR2 and CX3CR1 are two chemokine receptors that regulate the responses of myeloid cells, such as monocytes and microglia, during inflammation. We used Ccr2-KO and Cx3cr1-KO mice to understand the role of these receptors in viral encephalitis-associated seizures and neurodegeneration, using the Theiler’s virus model of encephalitis in C57BL/6 mice. Our results show that CCR2 as well as CX3CR1 plays a key role in the accumulation of myeloid cells in the CNS and activation of hippocampal myeloid cells upon infection. Furthermore, by using Cx3cr1-creER+/−tdTomatoSt/Wt reporter mice, we show that, with regard to CD45 and CD11b expression, some microglia become indistinguishable from monocytes during CNS infection. Interestingly, the lack of CCR2 or CX3CR1 receptors was associated with almost complete prevention of hippocampal damage but did not prevent seizure development after viral CNS infection. These data are compatible with the hypothesis that CNS inflammatory mechanism(s) other than the infiltrating myeloid cells trigger the development of seizures during viral encephalitis.

    更新日期:2018-09-19
  • Defective cortex glia plasma membrane structure underlies light-induced epilepsy in cpes mutants [Genetics]
    PNAS (IF 9.504) Pub Date : 2018-09-18
    Govind Kunduri, Daniel Turner-Evans, Yutaka Konya, Yoshihiro Izumi, Kunio Nagashima, Stephen Lockett, Joost Holthuis, Takeshi Bamba, Usha Acharya, Jairaj K. Acharya

    Seizures induced by visual stimulation (photosensitive epilepsy; PSE) represent a common type of epilepsy in humans, but the molecular mechanisms and genetic drivers underlying PSE remain unknown, and no good genetic animal models have been identified as yet. Here, we show an animal model of PSE, in Drosophila, owing to defective cortex glia. The cortex glial membranes are severely compromised in ceramide phosphoethanolamine synthase (cpes)-null mutants and fail to encapsulate the neuronal cell bodies in the Drosophila neuronal cortex. Expression of human sphingomyelin synthase 1, which synthesizes the closely related ceramide phosphocholine (sphingomyelin), rescues the cortex glial abnormalities and PSE, underscoring the evolutionarily conserved role of these lipids in glial membranes. Further, we show the compromise in plasma membrane structure that underlies the glial cell membrane collapse in cpes mutants and leads to the PSE phenotype.

    更新日期:2018-09-19
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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