Specificity of DNA methylation in the hypertensive kidney

Background: Evidence suggests that DNA methylation (5mC) is important in the development of essential hypertension (EH). The 5mC percentage, a measurement for global methylation studies, in peripheral blood leukocytes (PBL) has been previously associated with hypertension. Methylation patterns are tissue-specific, contributing to differences in transcriptional regulation and cellular differentiation. So far, there have been no studies of 5mC in the kidney – an important effector organ in EH. Furthermore, there has been no investigation of the relationship between 5mC patterns in the hypertensive kidney and PBLs. Aims: (i) To determine if global 5mC in the kidney is correlated to hypertension diagnosis and blood pressure (BP) regulation. (ii) To determine whether PBLs provide a surrogate for cross-tissue patterns of 5mC in the kidney. Methods: We used 96 human kidney and 76 human PBL samples from the TRANSLATE study to investigate global 5mC percentage. TRANSLATE consists of carefully characterized collections of "apparently healthy" specimens of human kidneys. Global methylation was determined using the 5mC ELISA kit (Zymo Research) that measures the total amount of 5mC present in a sample. Results: We found no association of global 5mC percentage in kidney (P=0.18) and PBL (P=0.54) with hypertension diagnosis, nor between PBL 5mC percentage and BP. However, a negative correlation was found between kidney 5mC percentage and systolic BP (r= –0.246; P <0.05), and diastolic BP (r= –0.319; P <0.01). This association was still evident after adjustment for antihypertensive medication for systolic BP (r= –0.210; P <0.05) and diastolic BP (r= –0.273; P <0.01). Furthermore, we found a strong positive correlation between normotensive kidneys and leukocyte 5mC percentages (r=0.864; P<0.01). Similarly, a strong positive correlation was evident for hypertensive kidneys and leukocyte 5mC percentages (r=0.916; P <0.01). Conclusion: Our findings show that kidney 5mC, but not PBL 5m C, is correlated to BP regulation. No relationship was evident for global 5mC and hypertension diagnosis, regardless of the tissue type studied. Furthermore, PBL 5mC global methylation percentage was highly correlated to kidney 5mC percentage. These results highlight the importance of further studies on the involvement of kidney DNA methylation in hypertension, as well as further investigation of the relationship between methylation patterns in the kidney and blood

In silico explorations of gold–biomolecule interactions for the engineering of biomedical gold nanomaterials

This thesis employs computational molecular modelling techniques to explore the physicochemical interactions occurring at the interface between gold nanomaterials and their biological coatings in order to better understand, predict, and ultimately design the properties of novel biomedical devices. In direct collaboration with experimental research, atomistic classical molecular dynamics (MD) simulations are used to investigate ligand conformational behaviour, reveal structure&amp;ndash;property relationships, and guide the effective engineering of three distinct functionalised gold nanomaterial systems. A general introduction is given in Chapter 1 to provide a background into the appeal of gold nanomaterials for biological applications, including an outline of the unique size-dependent properties these fascinating materials possess and examples of how nanogold-based devices are revolutionising diagnostic methods and the treatment of disease. In the subsequent Chapter 2, the current successes and challenges associated with multiscale computational strategies for simulating Au&amp;ndash;bio systems, from electronic structure calculations to force field methods, are given to illustrate links between different approaches and their relationship to experiment and applications. In Chapter 3, a methodological overview of physics-based computational techniques is presented, focusing on gold interfacial all-atom classical MD due to its application in this thesis. Chapter 4 utilises MD to clarify the conformations adopted by different peptide-monolayers on Au(111) surfaces and explores how these relate to the experimental efficacy of an in vitro diagnostic approach, which identifies and quantifies the presence of disease marking antibody molecules in solution. The peptide-monolayers formed on Au(111) are found to be intimately related to the inclusion and location of particular amino acids in individual peptide chains of the monolayers, with certain residues strongly influencing the conformational landscapes exhibited. The complex gold&amp;ndash;peptide topographies and solvent exposure of antibody-specific residues correlate well with empirical performance and provide non-intuitive characterisations of the assemblies unattainable through experiments. To study how peptide-ligand conformations affect the photoluminescence (PL) properties of Au25 nanoclusters that are capable of in vivo bioimaging, MD is used in conjunction with quantum mechanical calculations in Chapter 5. Following the systematic MD modelling of different Au25(SP)18 nanoclusters (where P = hexapeptide), properties such as peptide arrangement, hydrodynamic radii, distribution of chemical groups around the gold core, water structuring, and hydrogen bond networking are each correlated with experimentally measured AuNC PL. Key findings from this chapter present design principles to optimise the PL of these systems and postulate potential mechanisms for PL quenching. Next, Chapter 6 employs MD to examine octanethiol-protected Au25 nanoclusters, which are inherently hydrophobic and form an integral component in a composite gold&amp;ndash;silica theranostic material. Simulations in explicit water and ethanol solvents reveal significant structural differences in the alkanethiol ligand layers on Au25(SC8H17)18 and these differences are then used to hypothesise a steric&amp;ndash;kinetic mechanism to explain performance issues that these materials face in their drug delivery applications. The outcomes of this thesis contribute to the overall understanding of organic&amp;ndash;inorganic materials in targeted applications through exploring the intricate interactions that occur on the nanoscale. This work also highlights how the synergistic union of theoretical and experimental approaches can be used to produce translational research, improve insight, and facilitate the development of biocompatible gold nanomaterials for applications in the fields of bioimaging, biosensing, drug delivery, and biomedicine in general

Genetic Diversity in the Anthracnose Pathogen Infecting \u3ci\u3eStylosanthes\u3c/i\u3e in Brazil, India and China

This work aimed to determine the genetic diversity of Colletotrichum gloeosporioides infecting Stylosanthes spp. in Brazil, China and India. A total of 132 isolate originating from S. seabrana, S. macrocephala, S. capitata, S. scabra, and S. guianensis were used. Four major genetic groups were identified from an analysis of genetic diversity using selection-neutral DNA markers. Group 1 contained 20 isolates and this may represent a genotype that migrated from the center of diversity in Brazil and Colombia to Australia, Thailand and India. Group 2 consisted of 66 Brazilian isolates and group 3 had 19 isolates from Australia, Burundi, Brazil, China, Colombia, Ivory Coast and Peru. The 27 isolates in group 4 were very diverse with \u3e50% dissimilarity between some isolates. Genetic diversity in Brazil and China was more extensive than in the Indian pathogen population

Strain‐Promoted Cycloadditions in Lipid Bilayers Triggered by Liposome Fusion

Due to the variety of roles served by the cell membrane, its composition and structure are complex, making it difficult to study. Bioorthogonal reactions, such as the strain promoted azide-alkyne cycloaddition (SPAAC), are powerful tools for exploring the function of biomolecules in their native environment but have been largely unexplored within the context of lipid bilayers. Here, we developed a new approach to study the SPAAC reaction in liposomal membranes using azide- and strained alkyne-functionalized Förster resonance energy transfer (FRET) dye pairs. This study represents the first characterization of the SPAAC reaction between diffusing molecules inside liposomal membranes. Potential applications of this work include in situ bioorthogonal labeling of membrane proteins, improved understanding of membrane dynamics and fluidity, and the generation of new probes for biosensing assays

Surface dynamics and ligand-core interactions of quantum sized photoluminescent gold nanoclusters

Quantum-sized metallic clusters protected by biological ligands represent a new class of luminescent materials; yet the understanding of structural information and photoluminescence origin of these ultrasmall clusters remains a challenge. Herein we systematically study the surface ligand dynamics and ligand–metal core interactions of peptide-protected gold nanoclusters (AuNCs) with combined experimental characterizations and theoretical molecular simulations. We show that the peptide sequence plays an important role in determining the surface peptide structuring, interfacial water dynamics and ligand–Au core interaction, which can be tailored by controlling peptide acetylation, constituent amino acid electron donating/withdrawing capacity, aromaticity/hydrophobicity and by adjusting environmental pH. Specifically, emission enhancement is achieved through increasing the electron density of surface ligands in proximity to the Au core, discouraging photoinduced quenching, and by reducing the amount of surface-bound water molecules. These findings provide key design principles for understanding the surface dynamics of peptide-protected nanoparticles and maximizing the photoluminescence of metallic clusters through the exploitation of biologically relevant ligand properties

Selection of High Yielding and Anthracnose Resistant \u3ci\u3eStylosanthes\u3c/i\u3e for Brazil, India and China

Resistance to anthracnose, dry matter yield (DMY) and seed yield (SY) was assessed for germplasm and breeding lines of Stylosanthes in Brazil, India and China. Overall, Stylosanthes guianensis produced higher DMY than S. scabra, S. capitata and S. macrocephala at most sites in Brazil. Data from China suggest that there are high yielding anthracnose resistant S. guianensis lines that can reduce the reliance on CIAT 184. S. seabrana might also prove successful. S. seabrana in India produced the highest DMY and SY and it can form nodules with native Bradyrhizobium strains. Regional differences in resistance within accessions stress the importance of targeting germplasm to combat the suite of pathogen races present at a local level

Surface enhanced raman scattering artificial nose for high dimensionality fingerprinting

Label-free surface-enhanced Raman spectroscopy (SERS) can interrogate systems by directly fingerprinting its components’ unique physicochemical properties. In complex biological systems however, this can yield highly overlapping spectra that hinder sample identification. Here, we present an artificial-nose inspired SERS fingerprinting approach where spectral data is obtained as a function of sensor surface chemical functionality. Supported by molecular dynamics modelling, we show that mildly selective self-assembled monolayers can influence the strength and configuration in which analytes interact with plasmonic surfaces, diversifying the resulting SERS fingerprints. Since each sensor generates a modulated signature, the implicit value of increasing the dimensionality of datasets is shown using cell lysates for all possible combinations of up to 9 fingerprints. Reliable improvements in mean discriminatory accuracy towards 100% is achieved with each additional surface functionality. This arrayed label-free platform illustrates the wide-ranging potential of high dimensionality artificial-nose based sensing systems for more reliable assessment of complex biological matrices