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Region Consisting (region + consisting)
Selected AbstractsThe role of the interdomain B linker in the activation of the XylR protein of Pseudomonas putidaMOLECULAR MICROBIOLOGY, Issue 2 2000Junkal Garmendia In the presence of toluene and other structural analogues, the enhancer binding protein XylR activates the ,54 promoter Pu of the TOL (toluene degradation) plasmid pWW0 of Pseudomonas putida. Introduction of amino acid changes Val-219Asp and Ala-220Pro, which enter a proline kink at the interdomain region (B linker) between the A (signal reception) module and the central portion of XylR, originated a protein with unforeseen properties. These included a minor ability to activate Pu in the absence of aromatic effectors, a much higher responsiveness to m- xylene and a significant response to a large collection of aromatic inducers. Such changes could not be attributed to variations in XylR expression levels or to the fortuitous creation of a novel promoter, but to a genuine change in the properties of the activator. Structural predictions suggested that the mutation entirely disrupted an otherwise probable coiled-coil structure. A second directed mutant within the same region consisting of a major replacement of amino acids A220,N221 by the peptide HHHR produced an even more exacerbated phenotype. These data support a model in which the linker B region influences the effector profile by modifying at a distance the operative shape of the effector pocket and fixing the protein in an intermediate step of the activation process. [source] Effects of species diversity on the primary productivity of ecosystems: extending our spatial and temporal scales of inferenceOIKOS, Issue 3 2004Bradley J. Cardinale The number of studies examining how species diversity influences the productivity of ecosystems has increased dramatically in the past decade as concern about global loss of biodiversity has intensified. Research to date has greatly improved our understanding of how, when, and why species loss alters primary production in ecosystems. However, because experiments have been performed at rather small spatial and short temporal scales, it is unclear whether conclusions can be readily extrapolated to the broader scales at which natural communities are most likely to influence ecosystem functioning. Here we develop a simple patch-dynamics model to examine some of the scale-dependent and independent qualities of the diversity-productivity relationship. We first simulate a typical diversity-productivity experiment and show that the influence of species richness on productivity is temporally dynamic, growing stronger through successional time. This holds true irrespective of whether resource partitioning or a sampling effect is the underlying mechanism. We then increase the spatial scale of the simulation from individual patches to a region consisting of many patch types. Results suggest that the diversity-productivity relationship is not influenced by spatial scale per se, but that the mechanism producing the relationship can change from sampling effects within individual patches to resource partitioning across patch types composing the region. This change occurs even though model dynamics are the same at both scales, suggesting that sampling effects and resource partitioning can represent different descriptions of the same biological processes operating concurrently at differing scales of observation. Lastly, we incorporate regional processes of dispersal and disturbance into the model and show that these processes can amplify the effect of species richness on productivity, resulting in patterns not easily anticipated from experiments. We conclude that the relative control of community structure by local versus regional processes may be a primary determinant of the diversity-productivity relationship in natural ecosystems. Therefore, past experiments having focused only on local processes might not reflect patterns and processes underlying diversity-productivity relationships in communities where disturbance and dispersal regulate species biomasses. [source] M -plane InGaN/GaN light emitting diodes fabricated by MOCVD regrowth on c -plane patterned templatesPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 9 2008Christopher A. Schaake Abstract In this work we demonstrate a light emitting diode (LED) with m -plane quantum wells fabricated on a (000) template. N-polar, n-type GaN was grown by MOCVD on vicinal sapphire substrates. Stripes, measuring 500 nm wide, 500 nm tall and spaced 2 ,m apart, were etched parallel to the ,110, direction leading to sidewalls that are approximately {100}. Sputtered AlN was used as a regrowth mask on the c -plane surfaces. An active region consisting of 5 InGaN quantum wells and GaN barriers followed by p-type was grown. The regrowth occurred mostly on the exposed m -plane sidewalls, leading to lateral growth in the ,100, direction. The LED was processed using conventional methods. A thick metal contact was used to connect the p-regions together. Current vs. voltage measurements showed good rectifying behavior with a turn on of about 6 volts. On-wafer electroluminescence measurements revealed a peak wavelength of 422 nm. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] An extended Escherichia coli "Selenocysteine Insertion Sequence" (SECIS) as a multifunctional RNA structureBIOFACTORS, Issue 1-4 2001Hanna Engelberg-Kulka Abstract The genetic code, once thought to be rigid, has been found to permit several alternatives in its reading. Interesting alternative relates to the function of the UGA codon. Usually, it acts as a stop codon, but it can also direct the incorporation of the amino acid selenocysteine into a polypeptide. UGA-directed selenocysteine incorporation requires a cis-acting mRNA element called the "selenocysteine insertion sequence" (SECIS) that can form a stem-loop RNA structure. Here we discuss our investigation on the E. coli SECIS. This includes the follows: 1) The nature of the minimal E. coli SECIS. We found that in E. coli only the upper-stem and loop of 17 nucleotides of the SECIS is necessary for selenocysteine incorporation on the condition that it is located in the proper distance from the UGA [34]; 2) The upper stem and loop structure carries a bulged U residue that is required for selenocysteine incorporation [34] because of its interaction with SelB; and 3) We described an extended fdhF SECIS that includes the information for an additional function: The prevention of UGA readthrough under conditions of selenium deficiency [35]. This information is contained in a short mRNA region consisting of a single C residue adjacent to the UGA on its downstream side, and an additional segment consisting of the six nucleotides immediately upstream from it. These two regions act independently and additively and probably through different mechanisms. The single C residue acts as itself; the upstream region acts at the level of the two amino acids, arginine and valine, for which it codes. These two codons at the 5, side of the UGA correspond to the ribosomal E and P sites. Finally, we present a model for the E. coli fdhF SECIS as a multifunctional RNA structure containing three functional elements. Depending on the availability of selenium the SECIS enables one of two alternatives for the translational machinery: Either selenocysteine incorporation into a polypeptide or termination of the polypeptide chain. [source] | ||||||||||