A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation, Retrieval, Classification and Interpretation

Thesis (Ph.D.)--University of Washington, 2016-06

Modulation of Translation Efficiency in S. cerevisiae by Codon Pairs and mRNA Structure

Thesis (Ph.D.)--University of Washington, 2016-06

Molecular dynamics simulation of organic-inorganic nanocomposites: Layering behavior and interlayer structure of organoclays

Isothermal-isobaric (NPT) molecular dynamics simulation has been performed to investigate the layering behavior and structure of nanoconfined quaternary alkylammoniums in organoclays. This work is focused on systems consisting of two clay layers and a number of alkylammoniums, and involves the use of modified Dreiding force field. The simulated basal spacings of organoclays agree satisfactorily with the experimental results in the literature. The atomic density profiles in the direction normal to the clay surface indicate that the alkyl chains within the interlayer space of montmorillonite exhibit an obvious layering behavior. The headgroups of long alkyl chains are distributed within two layers close to the clay surface, whereas the distributions of methyl and methylene groups are strongly dependent on the alkyl chain length and clay layer charge. Monolayer, bilayer, and pseudo-trilayer structures are found in organoclays modified with single long alkyl chains, which are identical to the structural models based on the measured basal spacings. A pseudo-quadrilayer structure, for the first time to our knowledge, is also identified in organoclays with double long alkyl chains. In the mixture structure of paraffin-type and multilayer, alkyl chains do not lie flat within a single layer but interlace, and also jump to the next layer in pseudo-trilayer as well as next nearest layer in pseudo-quadrilayer.

Testing the sediment-trapping paradigm of seagrass: Do seagrasses influence nutrient status and sediment structure in tropical intertidal environments?

Seagrass meadows are considered important for sediment trapping and sediment stabilisation. Deposition of fine sediments and associated adsorbed nutrients is considered an important part of the chemical and biological processes attributed to seagrass communities. This paradigm was based on work in temperate regions on Zostera marina and in tropical regions on Thalassia testudinum, two species that maintain relatively high biomass, stable meadows. The current study investigates this concept for three species of intertidal tropical seagrass meadows in northeastern Australia. Sediment structure and nutrient status did not differ between vegetated and unvegated habitats in intertidal areas within the central region of the Great Barrier Reef World Heritage Area. The 'trapping' functions that have been attributed to seagrasses need to be re-assessed for a variety of locations and species before they can be accepted as dogma. In tropical Australia, intertidal meadows are predominantly ephemeral and comprised of structurally small species of low biomass. Consequently, sediment trapping within these meadows is largely insignificant.

Enzymatic cyclization of a potent Bowman-Birk protease inhibitor, sunflower trypsin inhibitor-1, and solution structure of an acyclic precursor peptide

The most potent known naturally occurring Bowman-Birk inhibitor, sunflower trypsin inhibitor-1 (SFTI-1), is a bicyclic 14-amino acid peptide from sunflower seeds comprising one disulfide bond and a cyclic backbone. At present, little is known about the cyclization mechanism of SFTI-1. We show here that an acyclic permutant of SFTI-1 open at its scissile bond, SFTI-1[ 6,5], also functions as an inhibitor of trypsin and that it can be enzymatically backbone-cyclized by incubation with bovine beta-trypsin. The resulting ratio of cyclic SFTI-1 to SFTI1[6,5] is similar to9:1 regardless of whether trypsin is incubated with SFTI-1[ 6,5] or SFTI-1. Enzymatic resynthesis of the scissile bond to form cyclic SFTI-1 is a novel mechanism of cyclization of SFTI-1[ 6,5]. Such a reaction could potentially occur on a trypsin affinity column as used in the original isolation procedure of SFTI-1. We therefore extracted SFTI-1 from sunflower seeds without a trypsin purification step and confirmed that the backbone of SFTI-1 is indeed naturally cyclic. Structural studies on SFTI-1[ 6,5] revealed high heterogeneity, and multiple species of SFTI-1[ 6,5] were identified. The main species closely resembles the structure of cyclic SFTI-1 with the broken binding loop able to rotate between a cis/trans geometry of the I7-P8 bond with the cis conformer being similar to the canonical binding loop conformation. The non-reactive loop adopts a beta-hairpin structure as in cyclic wild-type SFTI-1. Another species exhibits an isoaspartate residue at position 14 and provides implications for possible in vivo cyclization mechanisms.

Mitochondrial control region diversity of the houbara bustard Chlamydotis undulata complex and genetic structure along the Atlantic seaboard of North Africa

The houbara bustard, Chlamydotis undulata, is a declining cryptic desert bird whose range extends from North Africa to Central Asia. Three subspecies are currently recognized by geographical distribution and morphology: C.u.fuertaventurae, C.u.undulata and C.u.macqueenii. We have sequenced 854 bp of mitochondrial control region from 73 birds to describe their population genetic structure with a particular sampling focus on the connectivity between C.u.fuertaventurae and C.u.undulata along the Atlantic seaboard of North Africa. Nucleotide and haplotypic diversity varied among the subspecies being highest in C.u.undulata, lowest in C.u.fuertaventurae and intermediate in C.u.macqueenii. C.u.fuertaventurae and C.u.undulata are paraphyletic and an average nucleotide divergence of 2.08% splits the later from C.u.macqueenii. We estimate that C.u.fuertaventurae and C.u.undulata split from C.u.macqueenii approximately 430 000 years ago. C.u.fuertaventurae and C.u.undulata are weakly differentiated (F-ST = 0.27, N-m = 1.3), indicative of a recent shared history. Archaeological evidence indicates that houbara bustards have been present on the Canary Islands for 130-170 000 years. However, our genetic data point to a more recent separation of C.u.fuertaventurae and C.u.undulata at around 20-25 000 years. Concordant archaeological, climatic opportunities for colonization and genetic data point to a scenario of: (i) initial colonization of the Canary Islands about 130 000 years ago; (ii) a period of secondary contact 19-30 000 years ago homogenizing any pre-existing genetic structure followed by; (iii) a period of relative isolation that persists today.

Sustained swimming performance and muscle structure are altered by thermal acclimation in male mosquitofish

Males of the eastern mosquito fish (Gambusia holbrooki) possess one of the widest reproductively active temperature ranges for any ectotherm, ranging across seasons from at least 18degreesC to 34degreesC. In this study, we tested the ability of male G. holbrooki to acclimate their sustained swimming performance following long-term exposure to 18degreesC or 30degreesC. We also investigated some of the possible physiological mechanisms associated with thermal acclimation responses in swimming performance, including changes in slow muscle fibre size and abundance and the expression of myosin heavy chains (MyHC). We found that U-crit, of 18degreesC-acclimated G. holbrooki was 20% greater at 18degreesC than 30degreesC-acclimated fish, and the Ucrit of the 30degreesC-acclimated group was more than 15% greater at 30degreesC. Slow, fast and intermediate muscle fibres were identified on the basis of their myosin ATPase staining reaction. Although the number of slow and intermediate muscle fibres was similar between groups, the total cross-sectional area of aerobic fibre types was 40% greater in 18degrees-than 30degreesC-acclimated fish, reflecting an increase in the average fibre diameter. An S58 antibody raised against chicken slow skeletal muscle myosin stained a sub-set of the slow fibres identified by myosin ATPase staining. The number of S58-positive muscle fibres was 50% greater in 30degreesC-than 18degreesC-acclimated fish, implying that different MyHCs are being expressed in cold and warm acclimated individuals. Given the sexually coercive mating system of this species, increases in the sustained swimming performance via thermal acclimation may benefit the ability of males to maintain a high rate of sneaky copulations. (C) 2004 Elsevier Ltd. All rights reserved.

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise F-ST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise F-ST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

Disulfide bond mutagenesis and the structure and function of the head-to-tail macrocyclic trypsin inhibitor SFTI-1

SFTI-1 is a novel 14 amino acid peptide comprised of a circular backbone constrained by three proline residues, a hydrogen-bond network, and a single disulfide bond. It is the smallest and most potent known Bowman-Birk trypsin inhibitor and the only one with a cyclic peptidic backbone. The solution structure of [ABA(3,11)]SFTI-1, a disulfide-deficient analogue of SFTI-1, has been determined by H-1 NMR spectroscopy. The lowest energy structures of native SFTI-1 and [ABA(3,11)]SFTI-1 are similar and superimpose with a root-mean-square deviation over the backbone and heavy atoms of 0.26 +/- 0.09 and 1.10 +/- 0.22 Angstrom, respectively. The disulfide bridge in SFTI-1 was found to be a minor determinant for the overall structure, but its removal resulted in a slightly weakened hydrogen-bonding network. To further investigate the role of the disulfide bridge, NMR chemical shifts for the backbone H-alpha protons of two disulfide-deficient linear analogues of SFTI-1, [ABA(3,11)]SFTI-1[6,5] and [ABA(3,11)]SFTI-1[1,14] were measured. These correspond to analogues of the cleavage product of SFTI-1 and a putative biosynthetic precursor, respectively. In contrast with the cyclic peptide, it was found that the disulfide bridge is essential for maintaining the structure of these open-chain analogues. Overall, the hydrogen-bond network appears to be a crucial determinant of the structure of SFTI-1 analogues.

Mesoporous nanocrystalline zirconia with lamellar and MSU structure

Without introduction of any stabilizer, the mesoporous nanocrystalline zirconia with lamellar and MSU structure was obtained via solid state reaction coupled with surfactant templating method. The phase, surface area and pore structure of zirconia prepared with this novel method could be designed, tailored and controlled by varying synthesis parameters. The phase transformation was controlled by particle size. The mesostructure possesses nanocrystalline pore wall, which renders it more thermally stable than amorphous framework. The results suggest strongly that in solid state synthesis system mesostructure formation still follow the supramolecular self-assembly mechanism. The lamellar and reverse hexagonal structure could be transformed at different OH-/Zr molar ratios in order to sustain the low surface energy of the mesophases. The lamellar structure was preferred at higher OH-/Zr molar ratios but reverse hexagonal was at low ratios.

The relationships between microstructure and crystal structure in zincite solid solutions

Single phase (Zn,Fe)(1-x) O zincite solid solution samples have been prepared by high temperature equilibration in air and in reducing atmospheres, followed by quenching to room temperature. The Fe2+/Fe3+ concentrations in the samples have been determined using wet chemical and XPS techniques. Iron is found to be present in zincite predominantly in the form of Fe3+ ions. The transition from an equiaxed grain morphology to plate-like zincite crystals is shown to be associated with increasing Fe3+ concentration, increasing elongation in < 001 > of the hexagonal crystals and increasing anisotropic strain along the c-axis. The plate-like crystals are shown to contain planar defects and zincite polytypes at high iron concentrations.