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Search Results: 1 - 10 of 5633 matches for " Roland Gerhard Heym "
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A Cytoplasmic Complex Mediates Specific mRNA Recognition and Localization in Yeast
Marisa Müller,Roland Gerhard Heym,Andreas Mayer,Katharina Kramer,Maria Schmid,Patrick Cramer,Henning Urlaub,Ralf-Peter Jansen,Dierk Niessing
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1000611
Abstract: In eukaryotes, hundreds of mRNAs are localized by specialized transport complexes. For localization, transcripts are recognized by RNA-binding proteins and incorporated into motor-containing messenger ribonucleoprotein particles (mRNPs). To date, the molecular assembly of such mRNPs is not well understood and most details on cargo specificity remain unresolved. We used ASH1-mRNA transport in yeast to provide a first assessment of where and how localizing mRNAs are specifically recognized and incorporated into mRNPs. By using in vitro–interaction and reconstitution assays, we found that none of the implicated mRNA-binding proteins showed highly specific cargo binding. Instead, we identified the cytoplasmic myosin adapter She3p as additional RNA-binding protein. We further found that only the complex of the RNA-binding proteins She2p and She3p achieves synergistic cargo binding, with an at least 60-fold higher affinity for localizing mRNAs when compared to control RNA. Mutational studies identified a C-terminal RNA-binding fragment of She3p to be important for synergistic RNA binding with She2p. The observed cargo specificity of the ternary complex is considerably higher than previously reported for localizing mRNAs. It suggests that RNA binding for mRNP localization generally exhibits higher selectivity than inferred from previous in vitro data. This conclusion is fully consistent with a large body of in vivo evidence from different organisms. Since the ternary yeast complex only assembles in the cytoplasm, specific mRNA recognition might be limited to the very last steps of mRNP assembly. Remarkably, the mRNA itself triggers the assembly of mature, motor-containing complexes. Our reconstitution of a major portion of the mRNA-transport complex offers new and unexpected insights into the molecular assembly of specific, localization-competent mRNPs and provides an important step forward in our mechanistic understanding of mRNA localization in general.
A Cytoplasmic Complex Mediates Specific mRNA Recognition and Localization in Yeast
Marisa Müller equal contributor,Roland Gerhard Heym equal contributor,Andreas Mayer,Katharina Kramer,Maria Schmid,Patrick Cramer,Henning Urlaub,Ralf-Peter Jansen,Dierk Niessing
PLOS Biology , 2011, DOI: 10.1371/journal.pbio.1000611
Abstract: In eukaryotes, hundreds of mRNAs are localized by specialized transport complexes. For localization, transcripts are recognized by RNA-binding proteins and incorporated into motor-containing messenger ribonucleoprotein particles (mRNPs). To date, the molecular assembly of such mRNPs is not well understood and most details on cargo specificity remain unresolved. We used ASH1-mRNA transport in yeast to provide a first assessment of where and how localizing mRNAs are specifically recognized and incorporated into mRNPs. By using in vitro–interaction and reconstitution assays, we found that none of the implicated mRNA-binding proteins showed highly specific cargo binding. Instead, we identified the cytoplasmic myosin adapter She3p as additional RNA-binding protein. We further found that only the complex of the RNA-binding proteins She2p and She3p achieves synergistic cargo binding, with an at least 60-fold higher affinity for localizing mRNAs when compared to control RNA. Mutational studies identified a C-terminal RNA-binding fragment of She3p to be important for synergistic RNA binding with She2p. The observed cargo specificity of the ternary complex is considerably higher than previously reported for localizing mRNAs. It suggests that RNA binding for mRNP localization generally exhibits higher selectivity than inferred from previous in vitro data. This conclusion is fully consistent with a large body of in vivo evidence from different organisms. Since the ternary yeast complex only assembles in the cytoplasm, specific mRNA recognition might be limited to the very last steps of mRNP assembly. Remarkably, the mRNA itself triggers the assembly of mature, motor-containing complexes. Our reconstitution of a major portion of the mRNA-transport complex offers new and unexpected insights into the molecular assembly of specific, localization-competent mRNPs and provides an important step forward in our mechanistic understanding of mRNA localization in general.
Unwriting manifest borders: on culture and nature in L eslie Marmon Silko, James Welch and Linda Hogan = Desconstruindo a fronteira: a cultura e a natureza em Leslie Marmon Silko, James Welch e Linda Hog an
Roland Gerhard Mike Walter
Acta Scientiarum : Human and Social Sciences , 2006,
Abstract: The themes of transculturation, multiculturalism and border -making are discussed in Gardens in the Dune, The Heartsong of Charging Elk and Solar Storms and Power respectively by Leslie Marmon Silko, James Welch and Linda Hogan, three Native American authors. The first two authors deal with a two -way transcultural and interchange procedures in community building. Intercultural activities involve not only synthesis but also rupture and symbiosis. The two novels by Hogan, on the other han d, give importance to the construction of communities through connections between the human and the natural world which, in fact, are one. In other words, the novels deconstruct the borderbetween nature and nurture. An integrated vision of reality implode s divisions and impairs the future destruction of earth. Os temas de transcultura o, multiculturalismo e forma o de fronteiras s o discutidos nos romances Gardens in the Dune, The Heartsong of Charging Elk e Solar Storms and Power, respectivamente de Leslie Marmon Silko, James Welch e Linda Hogan, três aut ores indígenas estadunidenses. Os primeiros dois autores analisam os procedimentos transculturais de vias duplas na constru o de comunidades. As atividades interculturais, de um lado, envolvem n o apenas a síntese mas também a ruptura e a simbiose. Por outro lado, os dois romances de Hogan salientam a importancia da constru o de comunidades através dos nexos entre o mundo humano e o mundo danatureza, o qual é uno. Em outras palavras, os romances desconstroem a fronteira entre a natureza e a cultura. Uma vis o integrada da realidade implode as divis es e impede a destrui o futura do planeta.
Semiflexible polymer conformation, distribution and migration in microcapillary flows
Raghunath Chelakkot,Roland G. Winkler,Gerhard Gompper
Physics , 2010, DOI: 10.1088/0953-8984/23/18/184117
Abstract: The flow behavior of a semiflexible polymer in microchannels is studied using Multiparticle Collision Dynamics (MPC), a particle-based hydrodynamic simulation technique. Conformations, distributions, and radial cross-streamline migration are investigated for various bending rigidities, with persistence lengths Lp in the range 0.5 < Lp/Lr < 30. The flow behavior is governed by the competition between a hydrodynamic lift force and steric wall-repulsion, which lead to migration away from the wall, and a locally varying flow-induced orientation, which drives polymer away from the channel center and towards the wall. The different dependencies of these effects on the polymer bending rigidity and the flow velocity results in a complex dynamical behavior. However, a generic effect is the appearance of a maximum in the monomer and the center-of-mass distributions, which occurs in the channel center for small flow velocities, but moves off-center at higher velocities.
Physics of Microswimmers - Single Particle Motion and Collective Behavior
Jens Elgeti,Roland G. Winkler,Gerhard Gompper
Physics , 2014, DOI: 10.1088/0034-4885/78/5/056601
Abstract: Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.
Migration of semiflexible polymers in microcapillary flow
Raghunath Chelakkot,Roland. G. Winkler,Gerhard Gompper
Physics , 2010, DOI: 10.1209/0295-5075/91/14001
Abstract: The non-equilibrium structural and dynamical properties of a semiflexible polymer confined in a cylindrical microchannel and exposed to a Poiseuille flow is studied by mesoscale hydrodynamic simulations. For a polymer with a length half of its persistence length, large variations in orientation and conformations are found as a function of radial distance and flow strength. In particular, the polymer exhibits U-shaped conformations near the channel center. Hydrodynamic interactions lead to strong cross-streamline migration. Outward migration is governed by the polymer orientation and the corresponding anisotropy in its diffusivity. Strong tumbling motion is observed, with a tumbling time which exhibits the same dependence on Peclet number as a polymer in shear flow.
Virial pressure in systems of active Brownian particles
Roland G. Winkler,Adam Wysocki,Gerhard Gompper
Physics , 2015,
Abstract: The pressure of suspensions of self-propelled objects is studied theoretically and by simulation of spherical active Brownian particles (ABP). We show that for certain geometries, the mechanical pressure as force/area of a confined systems can equally be expressed by bulk properties, which implies the existence of an nonequilibrium equation of state. Exploiting the virial theorem, we derive expressions for the pressure of ABPs confined by solid walls or exposed to periodic boundary conditions. In both cases, the pressure comprises three contributions: the ideal-gas pressure due to white-noise random forces, an activity-induce pressure (swim pressure), which can be expressed in terms of a product of the bare and a mean effective propulsion velocity, and the contribution by interparticle forces. We find that the pressure of spherical ABPs in confined systems explicitly depends on the presence of the confining walls and the particle-wall interactions, which has no correspondence in systems with periodic boundary conditions. Our simulations of three-dimensional APBs in systems with periodic boundary conditions reveal a pressure-concentration dependence that becomes increasingly nonmonotonic with increasing activity. Above a critical activity and ABP concentration, a phase transition occurs, which is reflected in a rapid and steep change of the pressure. We present and discuss the pressure for various activities and analyse the contributions of the individual pressure components.
Flow-Induced Helical Coiling of Semiflexible Polymers in Structured Microchannels
Raghunath Chelakkot,Roland G. Winkler,Gerhard Gompper
Physics , 2012, DOI: 10.1103/PhysRevLett.109.178101
Abstract: The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the narrow high-velocity region into the wide low-velocity region of the channel. The transient helix formation is the result of a non-equilibrium and non-stationary buckling transition of the semiflexible polymer, which is subjected to a compressive force originating from the fluid-velocity variation in the channel. The helix properties depend on the diameter ratio of the channel, the polymer bending rigidity, and the flow strength.
Cooperative Motion of Active Brownian Spheres in Three-Dimensional Dense Suspensions
Adam Wysocki,Roland G. Winkler,Gerhard Gompper
Physics , 2013, DOI: 10.1209/0295-5075/105/48004
Abstract: The structural and dynamical properties of suspensions of self-propelled Brownian particles of spherical shape are investigated in three spatial dimensions. Our simulations reveal a phase separation into a dilute and a dense phase, above a certain density and strength of self-propulsion. The packing fraction of the dense phase approaches random close packing at high activity, yet the system remains fluid. Although no alignment mechanism exists in this model, we find long-lived cooperative motion of the particles in the dense regime. This behavior is probably due to an interface-induced sorting process. Spatial displacement correlation functions are nearly scale-free for systems with densities close to or above the glass transition density of passive systems.
Non Mycobacterial Virulence Genes in the Genome of the Emerging Pathogen Mycobacterium abscessus
Fabienne Ripoll, Sophie Pasek, Chantal Schenowitz, Carole Dossat, Valérie Barbe, Martin Rottman, Edouard Macheras, Beate Heym, Jean-Louis Herrmann, Mamadou Daffé, Roland Brosch, Jean-Loup Risler, Jean-Louis Gaillard
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0005660
Abstract: Mycobacterium abscessus is an emerging rapidly growing mycobacterium (RGM) causing a pseudotuberculous lung disease to which patients with cystic fibrosis (CF) are particularly susceptible. We report here its complete genome sequence. The genome of M. abscessus (CIP 104536T) consists of a 5,067,172-bp circular chromosome including 4920 predicted coding sequences (CDS), an 81-kb full-length prophage and 5 IS elements, and a 23-kb mercury resistance plasmid almost identical to pMM23 from Mycobacterium marinum. The chromosome encodes many virulence proteins and virulence protein families absent or present in only small numbers in the model RGM species Mycobacterium smegmatis. Many of these proteins are encoded by genes belonging to a “mycobacterial” gene pool (e.g. PE and PPE proteins, MCE and YrbE proteins, lipoprotein LpqH precursors). However, many others (e.g. phospholipase C, MgtC, MsrA, ABC Fe(3+) transporter) appear to have been horizontally acquired from distantly related environmental bacteria with a high G+C content, mostly actinobacteria (e.g. Rhodococcus sp., Streptomyces sp.) and pseudomonads. We also identified several metabolic regions acquired from actinobacteria and pseudomonads (relating to phenazine biosynthesis, homogentisate catabolism, phenylacetic acid degradation, DNA degradation) not present in the M. smegmatis genome. Many of the “non mycobacterial” factors detected in M. abscessus are also present in two of the pathogens most frequently isolated from CF patients, Pseudomonas aeruginosa and Burkholderia cepacia. This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicity shared by unrelated organisms in CF patients.
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