Nathan Cowieson

Bio: Nathan Cowieson is an academic researcher from Australian Synchrotron. The author has contributed to research in topics: Protein structure & Beamline. The author has an hindex of 26, co-authored 65 publications receiving 2779 citations. Previous affiliations of Nathan Cowieson include University of Queensland & Monash University.

A low-background-intensity focusing small-angle X-ray scattering undulator beamline

Abstract: The SAXS/WAXS beamline at the Australian Synchrotron is an advanced and flexible undulator X-ray scattering beamline used for small- and wide-angle X-ray scattering analysis on a wide variety of solids, fluids and surfaces across a diverse range of research and development fields. The beamline has numerous features that minimize the intensity of the instrument background, provide automated stable optics, and allow accurate analysis of very weakly scattering samples. The geometric and intensity requirements of a three-slit collimation system are described in detail for conventional metal and single-crystal germanium slits. Straightforward ray tracing and simple linear projections describe the observed direct beam as well as parasitic background scattering geometry of the beamline at its longest camera length, providing a methodology for the design and operation of similar beamlines. As an aid to instrument design, the limit of background intensity determined by the intensity incident on single-crystal germanium guard slit edges and its q dependence was quantified at 11 keV. Details of the beamline's implementation, underlying optical concept and measured performance are given.

MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron.

Abstract: MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented.

MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron

Abstract: MX2 is an in-vacuum undulator-based crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range 4.8–21 keV to a focal spot of 22 × 12 µm FWHM (H × V). At 13 keV the flux at the sample is 3.4 × 1012 photons s−1. The beamline endstation allows robotic handling of cryogenic samples via an updated SSRL SAM robot. This beamline is ideal for weakly diffracting hard-to-crystallize proteins, virus particles, protein assemblies and nucleic acids as well as smaller molecules such as inorganic catalysts and organic drug molecules. The beamline is now mature and has enjoyed a full user program for the last nine years. This paper describes the beamline status, plans for its future and some recent scientific highlights.

Protein-phytate interactions in pig and poultry nutrition: a reappraisal.

Abstract: Protein-phytate interactions are fundamental to the detrimental impact of phytate on protein/amino acid availability. The inclusion of exogenous phytase in pig and poultry diets degrades phytate to more innocuous esters and attenuates these negative influences. The objective of the present review is to reappraise the underlying mechanisms of these interactions and reassess their implications in pig and poultry nutrition. Protein digestion appears to be impeded by phytate in the following manner. Binary protein-phytate complexes are formed at pH levels less than the isoelectric point of proteins and complexed proteins are refractory to pepsin digestion. Once the protein isoelectric points are exceeded binary complexes dissociate; however, the isoelectric point of proteins in cereal grains may be sufficiently high to permit these complexes to persist in the small intestine. Ternary protein-phytate complexes are formed at pH levels above the isoelectric point of proteins where a cationic bridge links the protein and phytate moieties. The molecular weights of protein and polypeptides in small-intestinal digesta may be sufficient to allow phytate to bind nutritionally important amounts of protein in ternary complexes. Thus binary and ternary complexes may impede protein digestion and amino acid absorption in the small intestine. Alternatively, phytate may interact with protein indirectly. Myo-inositol hexaphosphate possesses six phosphate anionic moieties (HPO(4)(2-)) that have strong kosmotropic effects and can stabilise proteins by interacting with the surrounding water medium. Phytate increases mucin secretions into the gut, which increases endogenous amino acid flows as the protein component of mucin remains largely undigested. Phytate promotes the transition of Na(+) into the small-intestinal lumen and this suggests that phytate may interfere with glucose and amino acid absorption by compromising Na(+)-dependent transport systems and the activity of the Na pump (Na(+)-K(+)-ATPase). Starch digestion may be depressed by phytate interacting with proteins that are closely associated with starch in the endosperm of cereal grains. While elucidation is required, the impacts of dietary phytate and exogenous phytase on the site, rate and synchrony of glucose and amino acid intestinal uptakes may be of importance to efficient protein deposition. Somewhat paradoxically, the responses to phytase in the majority of amino acid digestibility assays in pigs and poultry are equivocal. A brief consideration of the probable reasons for these inconclusive outcomes is included in this reappraisal.

Translating the Histone Code

Abstract: Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a “histone code” that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.

Abstract: Heterochromatin protein 1 (HP1) is localized at heterochromatin sites where it mediates gene silencing. The chromo domain of HP1 is necessary for both targeting and transcriptional repression. In the fission yeast Schizosaccharomyces pombe, the correct localization of Swi6 (the HP1 equivalent) depends on Clr4, a homologue of the mammalian SUV39H1 histone methylase. Both Clr4 and SUV39H1 methylate specifically lysine 9 of histone H3 (ref. 6). Here we show that HP1 can bind with high affinity to histone H3 methylated at lysine 9 but not at lysine 4. The chromo domain of HP1 is identified as its methyl-lysine-binding domain. A point mutation in the chromo domain, which destroys the gene silencing activity of HP1 in Drosophila, abolishes methyl-lysine-binding activity. Genetic and biochemical analysis in S. pombe shows that the methylase activity of Clr4 is necessary for the correct localization of Swi6 at centromeric heterochromatin and for gene silencing. These results provide a stepwise model for the formation of a transcriptionally silent heterochromatin: SUV39H1 places a 'methyl marker' on histone H3, which is then recognized by HP1 through its chromo domain. This model may also explain the stable inheritance of the heterochromatic state.

Mechanisms of Endocytosis

Abstract: Endocytic mechanisms control the lipid and protein composition of the plasma membrane, thereby regulating how cells interact with their environments. Here, we review what is known about mammalian endocytic mechanisms, with focus on the cellular proteins that control these events. We discuss the well-studied clathrin-mediated endocytic mechanisms and dissect endocytic pathways that proceed independently of clathrin. These clathrin-independent pathways include the CLIC/GEEC endocytic pathway, arf6-dependent endocytosis, flotillin-dependent endocytosis, macropinocytosis, circular doral ruffles, phagocytosis, and trans-endocytosis. We also critically review the role of caveolae and caveolin1 in endocytosis. We highlight the roles of lipids, membrane curvature-modulating proteins, small G proteins, actin, and dynamin in endocytic pathways. We discuss the functional relevance of distinct endocytic pathways and emphasize the importance of studying these pathways to understand human disease processes.