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Function Study (function + study)
Selected AbstractsGene Knockdown: A Powerful Tool for Gene Function Study in FishJOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 3 2008Surintorn Boonanuntanasarn So far, there are a number of fish genome projects, including experimental and economically important fish that provide available DNA sequence information. However, the function of a gene cannot be deduced only by its DNA sequence. Therefore, a technique with which to investigate the function of the fish gene is needed. Gene knockdown (GKD), or antisense technology, is now being used as a powerful technique to study gene functions in living organisms. GKD effects result from the introduction of an antisense molecule into living cells. The antisense agents bind to target messenger RNA, thus inactivating the target gene expression. The appropriately spatial inhibitory effects on protein production from corresponding gene resulted in the phenotypic change. Therefore, the function of the gene can be understood. To date, there are a number of antisense molecules that can affect efficient GKD in fish. These include antisense oligonucleotides, small interfering RNA, and ribozyme. These antisense molecules cause specific gene inhibitor effects with different mechanisms. The various antisense mechanism types facilitate a number of GKD applications with various approaches in animals. In this review, we demonstrate the characteristics of each antisense molecule, its mechanism, and its application, especially for gene functional analysis in fish. [source] Crustal structure of central and northern Iceland from analysis of teleseismic receiver functionsGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 1 2000Fiona A. Darbyshire We present results from a teleseismic receiver function study of central and northern Iceland, carried out during the period 1995,1998. Data from eight broad-band seismometers installed in the SIL network operated by the Icelandic Meteorological Office were used for analysis. Receiver functions for each station were generated from events for a wide range of backazimuths and a combination of inversion and forward modelling was used to infer the crustal structure below each station. The models generated show a considerable variation in the nature and thickness of the crust across Iceland. The thinnest crust (20,21 km) is found in the northern half of the Northern Volcanic Zone approximately 120 km north of the centre of the Iceland mantle plume. Thicker crust (24,30 km) is found elsewhere in northern and central Iceland and the thickest crust (37 km) is found close to the plume centre. Velocity,depth profiles show a distinct division of the crust into two main sections, an upper high-velocity-gradient section of thickness 2,8 km and a lower crustal section with small or zero overall velocity gradient. The thickness of the upper crust correlates with the tectonic structure of Iceland; the upper crust is thickest on the flanks of the northern and central volcanic rift zones and thinnest close to active or extinct central volcanoes. Below the Krafla central volcano in northeastern Iceland the receiver function models show a prominent low-velocity zone at 10,15 km depth with minimum shear wave velocities of 2.0,2.5 km s,1. We suggest that this feature results from the presence of partially molten sills in the lower crust. Less prominent low-velocity zones found in other regions of Iceland may arise from locally high temperatures in the crust or from acidic intrusive bodies at depth. A combination of the receiver function results and seismic refraction results constrains the crustal thickness across a large part of Iceland. Melting by passive decompression of the hot mantle below the rift zone in northern Iceland forms a crust of thickness ,20 km. In contrast, the larger crustal thickness below central Iceland probably arises from enhanced melt production due to active upwelling in the plume core. [source] Crystallization and preliminary X-ray analysis of the chemokine-binding protein from orf virus (Poxviridae)ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Rafael Miguez Couñago The parapoxvirus orf virus (ORFV) encodes a chemokine-binding protein (CBP) that functions to downregulate the host's immune response at the site of infection by blocking the chemokine-induced recruitment of immune cells. In order to shed light on the structural determinants of CBP,chemokine binding, ORFV CBP was crystallized as part of an ongoing structure,function study on this protein. ORFV CBP crystals were obtained by the sitting-drop vapour-diffusion technique using ammonium citrate as a precipitant. The crystal quality was greatly improved through the addition of small-molecule additives to the crystallization mother liquor. ORFV CBP crystals diffracted X-rays to 2.50,Å resolution and belonged to the hexagonal space group P6122 or its enantiomorph P6522, with unit-cell parameters a = b = 75.62, c = 282.49,Å, , = 90, , = 90, , = 120°. [source] Ion channel activity of transmembrane segment 6 of Escherichia coli proton-dependent manganese transporterBIOPOLYMERS, Issue 8 2010uková Abstract Synthetic peptides corresponding to the sixth transmembrane segment (TMS6) of secondary-active transporter MntH (Proton-dependent Manganese Transporter) from Escherichia coli and its two mutations in the functionally important conserved histidine residue were used as a model for structure,function study of MntH. The secondary structure of the peptides was estimated in different environments using circular dichroism spectroscopy. These peptides interacted with and adopted helical conformations in lipid membranes. Electrophysiological experiments demonstrated that TMS6 was able to form multi-state ion channels in model biological membranes. Electrophysiological properties of these weakly cation-selective ion channels were strongly dependent on the surrounding pH. Manganese ion, as a physiological substrate of MntH, enhanced the conductivity of TMS6 channels, influenced the transition between closed and open states, and affected the peptide conformations. Moreover, functional properties of peptides carrying two different mutations of His211 were analogous to in vivo functional characteristics of Nramp/MntH proteins mutated at homologous residues. Hence, a single functionally important TMS can retain some of the functional properties of the full-length protein. These findings could contribute to understanding the structure,function relationship at the molecular level. However it remains unclear to what extent the peptide-specific channel activity represents a functional aspect of the full-length membrane carrier protein. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 718,726, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Selenium Derivatization of Nucleic Acids for X-Ray Crystal-Structure and Function StudiesCHEMISTRY & BIODIVERSITY, Issue 4 2010Jia Sheng Abstract It is estimated that over two thirds of all new crystal structures of proteins are determined via the protein selenium derivatization (selenomethionine (Se-Met) strategy). This selenium derivatization strategy via MAD (multi-wavelength anomalous dispersion) phasing has revolutionized protein X-ray crystallography. Through our pioneer research, similarly, Se has also been successfully incorporated into nucleic acids to facilitate the X-ray crystal-structure and function studies of nucleic acids. Currently, Se has been stably introduced into nucleic acids by replacing nucleotide O-atom at the positions 2,, 4,, 5,, and in nucleobases and non-bridging phosphates. The Se derivatization of nucleic acids can be achieved through solid-phase chemical synthesis and enzymatic methods, and the Se-derivatized nucleic acids (SeNA) can be easily purified by HPLC, FPLC, and gel electrophoresis to obtain high purity. It has also been demonstrated that the Se derivatization of nucleic acids facilitates the phase determination via MAD phasing without significant perturbation. A growing number of structures of DNAs, RNAs, and protein,nucleic acid complexes have been determined by the Se derivatization and MAD phasing. Furthermore, it was observed that the Se derivatization can facilitate crystallization, especially when it is introduced to the 2,-position. In addition, this novel derivatization strategy has many advantages over the conventional halogen derivatization, such as more choices of the modification sites via the atom-specific substitution of the nucleotide O-atom, better stability under X-ray radiation, and structure isomorphism. Therefore, our Se-derivatization strategy has great potentials to provide rational solutions for both phase determination and high-quality crystal growth in nucleic-acid crystallography. Moreover, the Se derivatization generates the nucleic acids with many new properties and creates a new paradigm of nucleic acids. This review summarizes the recent developments of the atomic site-specific Se derivatization of nucleic acids for structure determination and function study. Several applications of this Se-derivatization strategy in nucleic acid and protein research are also described in this review. [source] A structure/function study of polyaminoamide dendrimers as silica scale growth inhibitorsJOURNAL OF CHEMICAL TECHNOLOGY & BIOTECHNOLOGY, Issue 6 2005Konstantinos D Demadis Abstract Dendrimers have attracted immense attention during the last decade due to their interesting properties both from a basic and an applied research viewpoint. Encapsulation of metal nanoparticles for catalysis, drug delivery and light harvesting are only some applications of dendrimers that are breaking new ground. A novel application of dendrimer technology is described in the present paper that relates to industrial water treatment. Industrial water systems often suffer from undesirable inorganic deposits. These can form either in the bulk or on metallic surfaces, such as heat exchangers or pipelines. Silica (SiO2) scale formation and deposition is a major problem in high-silica-containing cooling waters. Scale prevention rather than removal is highly desired. In this paper, benchtop screening tests on various silica inhibition chemistries are reported, with emphasis on materials with a dendrimeric structure. Specifically, the inhibition properties of commercially available STARBURST® polyaminoamide (PAMAM) dendrimers generations 0.5, 1, 1.5, 2, and 2.5 are investigated in detail together with other commonly-used scale inhibitors. Experimental results show that inhibition efficiency largely depends on structural features of PAMAM dendrimers such as generation number and nature of the end groups. PAMAM dendrimers are effective inhibitors of silica scale growth at 40 ppm dosage levels. PAMAM dendrimers also act as silica nucleators, forming SiO2,PAMAM composites. This occurs because the SiO2 formed by incomplete inhibition interacts with cationic PAMAM-1 and -2. The general scope of silica formation and inhibition in industrial waters is also discussed. Copyright © 2005 Society of Chemical Industry [source] Characterization of conantokin Rl -A: molecular phylogeny as structure/function studyJOURNAL OF PEPTIDE SCIENCE, Issue 8 2010Konkallu H. Gowd Abstract A multidisciplinary strategy for discovery of new Conus venom peptides combines molecular genetics and phylogenetics with peptide chemistry and neuropharmacology. Here we describe application of this approach to the conantokin family of conopeptides targeting NMDA receptors. A new conantokin from Conus rolani, ConRl -A, was identified using molecular phylogeny and subsequently synthesized and functionally characterized. ConRl -A is a 24-residue peptide containing three ,-carboxyglutamic acid residues with a number of unique sequence features compared to conantokins previously characterized. The HPLC elution of ConRl -A suggested that this peptide exists as two distinct, slowly exchanging conformers. ConRl -A is predominantly helical (estimated helicity of 50%), both in the presence and absence of Ca++. The order of potency for blocking the four NMDA receptor subtypes by ConRl -A was NR2B > NR2D > NR2A > NR2C. This peptide has a greater discrimination between NR2B and NR2C than any other ligand reported so far. In summary, ConRl -A is a new member of the conantokin family that expands our understanding of structure/function of this group of peptidic ligands targeted to NMDA receptors. Thus, incorporating phylogeny in the discovery of novel ligands for the given family of ion channels or receptors is an efficient means of exploring the megadiverse group of peptides from the genus Conus. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. [source] | |||||||||||||