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Item Potential of Beetroot and Blackcurrant Compounds to Improve Metabolic Syndrome Risk Factors(MDPI (Basel, Switzerland), 25/05/2021) Haswell C; Ali A; Page R; Hurst R; Rutherfurd-Markwick KMetabolic syndrome (MetS) is a group of metabolic abnormalities, which together lead to increased risk of coronary heart disease (CHD) and type 2 diabetes mellitus (T2DM), as well as reduced quality of life. Dietary nitrate, betalains and anthocyanins may improve risk factors for MetS and reduce the risk of development of CHD and T2DM. Beetroot is a rich source of dietary nitrate, and anthocyanins are present in high concentrations in blackcurrants. This narrative review considers the efficacy of beetroot and blackcurrant compounds as potential agents to improve MetS risk factors, which could lead to decreased risk of CHD and T2DM. Further research is needed to establish the mechanisms through which these outcomes may occur, and chronic supplementation studies in humans may corroborate promising findings from animal models and acute human trials.Item Targeting DNA secondary structures using chemically modified oligonucleotides : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Chemistry, Massey University, Palmerston North, New Zealand(Massey University, 2021) Su, YongdongChemical modifications bring in additional features to oligonucleotides (ONs), including enhanced stability against nucleases, increased binding affinity towards DNA or RNA, improved cellular uptake, etc. This Thesis describes several strategies and chemical modifications used for targeting DNA duplexes and G-quadruplexes. We introduced a pyrene analogue, (R)-1-O-[2-(1-pyrenylethynyl)phenylmethyl]-glycerol, called ortho-TINA (twisted intercalating nucleic acid) monomer into a native duplex DNA. The affinity of ortho-TINA modified strands was low to each other, whereas the affinity of ortho-TINA sequence towards complementary DNA was increased. This property of ortho-TINA duplex was applied for targeting native duplexes in a sequence-specific manner using a process called dual duplex invasion (DDI). The speed of DDI is increased with the increased number of ortho-TINA pairs present in the duplex, as well as with the rise of temperature from 4 to 37 ℃. However, DDI against duplexes longer than the probe is compromised. To improve the kinetics of DDI, we designed and synthesised DNA probes with zwitterionic moieties, 4‐(trimethylammonium)butylsulfonyl phosphoramidate groups (N+), in which the negatively charged phosphate is neutralised by the positively charged quaternary amine. We assume that several N+ moieties in the DNA probe should reduce the electrostatic repulsion between the probe and the target duplex, and in this way, enhance DDI. However, no improvement of kinetics was achieved using N+ modifications in the probe alone and in combination with ortho-TINA monomers. Application of ONs bearing N+ modifications was explored further in parallel DNA triplexes and G-quadruplex. The initial stage of assembly of N+TG₄T proceeded faster in the presence of Na⁺ than K⁺ ions, which contrasted the trend observed for unmodified sequences, and this process was independent of the ionic strength in solution. We also evaluated several other phosphate modifications alongside for a comparison with our N+ modified DNA. Finally, several directions of future work are proposed based on the results obtained in the present Thesis.Item Relative orientation of collagen molecules within a fibril: A homology model for homo sapiens type I collagen.(Taylor & Francis, 30/01/2018) Collier TA; Nash A; Birch HL; de Leeuw NHType I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule’s size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril. Through the use of the homology model and implementation of a novel simulation technique, we have ascertained the orientations of the collagen molecules within a fibril, which is currently below the resolution limit of experimental techniques. The longitudinal orientation of collagen molecules within a fibril has a significant effect on the mechanical and biological properties of the fibril, owing to the different amino acid side-chains available at the interface between the molecules.Item Robust SERS Platforms Based on Annealed Gold Nanostructures Formed on Ultrafine Glass Substrates for Various (Bio)Applications(MDPI (Basel, Switzerland), 2019-06) Zhou L; Poggesi S; Casari Bariani G; Mittapalli R; Adam P-M; Manzano M; Ionescu REIn this study, stable gold nanoparticles (AuNPs) are fabricated for the first time on commercial ultrafine glass coverslips coated with gold thin layers (2 nm, 4 nm, 6 nm, and 8 nm) at 25 °C and annealed at high temperatures (350 °C, 450 °C, and 550 °C) on a hot plate for different periods of time. Such gold nanostructured coverslips were systematically tested via surface enhanced Raman spectroscopy (SERS) to identify their spectral performances in the presence of different concentrations of a model molecule, namely 1,2-bis-(4-pyridyl)-ethene (BPE). By using these SERS platforms, it is possible to detect BPE traces (10-12 M) in aqueous solutions in 120 s. The stability of SERS spectra over five weeks of thiol-DNA probe (2 µL) deposited on gold nano-structured coverslip is also reported.Item In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes(Oxford University Press, 25/07/2013) Daly TK; Sutherland-Smith AJ; Penny EDVaults are very large oligomeric ribonucleoproteins conserved among a variety of species. The rat vault 3D structure shows an ovoid oligomeric particle, consisting of 78 major vault protein monomers, each of approximately 861 amino acids. Vaults are probably the largest ribonucleoprotein structures in eukaryote cells, being approximately 70 nm in length with a diameter of 40 nm--the size of three ribosomes and with a lumen capacity of 50 million Å(3). We use both protein sequences and inferred ancestral sequences for in silico virtual resurrection of tertiary and quaternary structures to search for vaults in a wide variety of eukaryotes. We find that the vault's phylogenetic distribution is widespread in eukaryotes, but is apparently absent in some notable model organisms. Our conclusion from the distribution of vaults is that they were present in the last eukaryote common ancestor but they have apparently been lost from a number of groups including fungi, insects, and probably plants. Our approach of inferring ancestral 3D and quaternary structures is expected to be useful generally.Item Comparison of the effects of 7.2% hypertonic saline and 20% mannitol on whole blood coagulation and platelet function in dogs with suspected intracranial hypertension - a pilot study(BioMed Central, 19/06/2017) Yozova ID; Howard J; Henke D; Dirkmann D; Adamik KNHyperosmolar therapy with either mannitol or hypertonic saline (HTS) is commonly used in the treatment of intracranial hypertension (ICH). In vitro data indicate that both mannitol and HTS affect coagulation and platelet function in dogs. The aim of this study was to compare the effects of 20% mannitol and 7.2% HTS on whole blood coagulation using rotational thromboelastometry (ROTEM®) and platelet function using a platelet function analyzer (PFA®) in dogs with suspected ICH. Thirty client-owned dogs with suspected ICH needing osmotherapy were randomized to receive either 20% mannitol (5 ml/kg IV over 15 min) or 7.2% HTS (4 ml/kg IV over 5 min). ROTEM® (EXTEM® and FIBTEM® assays) and PFA® analyses (collagen/ADP cartridges) were performed before (T0), as well as 5 (T5), 60 (T60) and 120 (T120) minutes after administration of HTS or mannitol. Data at T5, T60 and T120 were analyzed as a percentage of values at T0 for comparison between groups, and as absolute values for comparison between time points, respectively.No significant difference was found between the groups for the percentage change of any parameter at any time point except for FIBTEM® clotting time. Within each group, no significant difference was found between time points for any parameter except for FIBTEM® clotting time in the HTS group, and EXTEM® and FIBTEM® maximum clot firmness in the mannitol group. Median ROTEM® values lay within institutional reference intervals in both groups at all time points, whereas median PFA® values were above the reference intervals at T5 (both groups) and T60 (HTS group).Using currently recommended doses, mannitol and HTS do not differ in their effects on whole blood coagulation and platelet function in dogs with suspected ICH. Moreover, no relevant impairment of whole blood coagulation was found following treatment with either solution, whereas a short-lived impairment of platelet function was found after both solutions.Item Complex patterns of admixture across the Indonesian archipelago(1/10/2017) Hudjashov G; Karafet TM; Lawson DJ; Downey S; Savina O; Sudoyo H; Lansing JS; Hammer MF; Cox MPIndonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.Item Proteins isolated with TRIzol are compatible with two-dimensional electrophoresis and mass spectrometry analyses(Elsevier Masson, 2012) Young C; Truman PTRIzol is used for RNA isolation but also permits protein recovery. We investigated whether proteins prepared with TRIzol were suitable for two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization mass spectrometry. Proteins from TRIzol-treated SH-SY5Y cells produced 2-DE spot patterns similar to those from an equivalent untreated sample. Subsequent identification of TRIzol-treated proteins using peptide mass fingerprinting was successful. TRIzol exposure altered neither the mass of myoglobin extracted from sodium dodecyl sulfate (SDS) gels nor the masses of myoglobin peptides produced by in-gel trypsin digestion. These findings suggest that proteins isolated with TRIzol remain amenable to proteomic analyses.Item Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant.(15/10/2015) Burgess SA; Cox MP; Flint SH; Lindsay D; Biggs PJThree strains of Geobacillus stearothermophilus (designated A1, P3, and D1) were isolated from a New Zealand milk powder manufacturing plant. Here, we describe their draft genome sequences. This information provided the first genomic insights into the nature of G. stearothermophilus strains present in the milk powder manufacturing environment.Item Collagen dehydration(Elsevier BV, 1/09/2022) Haverkamp RG; Sizeland KH; Wells HC; Kamma-Lorger CType I collagen is a ubiquitous structural protein in animal tissues. It is normally present in a hydrated form. However, collagen is very dependent on associated water for its mechanical properties. In skin, where type I collagen is dominant, there is a longstanding concern that the skin and therefore collagen may partially dry out and result in structural degradation. Here we show that dehydration of type I collagen fibrils, using 2-propanol, results in a two-stage dehydration process. Initially, the fibrils do not change length, i.e. the D-period remains constant, but shrinkage occurs within the fibrils by an increase in the gap region and a decrease in the overlap region within a D-band and a shortening of the helical turn distance and fibril diameter. Only with further dehydration does the length of the collagen fibril decrease (a decrease in D-period). This mechanism explains why collagen materials are resistant to gross structural change in the early stages of dehydration and shows why they may then suffer from sudden external shrinkage with further dehydration.