A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 1996 / The electric field strength and pH gradients generated in isotachophoretic systems may be used for the separation of biomolecules. Poly (2 acrylamido 2-methyl-1-propanesulfonic acid) polymers of a uniform distribution of molecular mass were synthesized and used as spacers in isotachophoresis in order to generate linear electric field strength gradients in which biomolecules could be focused. These novel spacers are designed to operate within sieving media, and hence are useful for the separation of nucleic acids. [Abbreviated Abstract. Open document to view full version]

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published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

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No abstract available. / Thesis (Ph.D.)-University of Natal, Pietermaritzburg, 1996.

Finally, based on theoretical calculations and experiments, we present a development model (DDRA model) to describe the interaction between the protein and its solvent molecule. The parameters derived from this model provide good fits to the experimentally determined complex dielectric constant, making it of the model valuable benchmarks for other theoretical treatments of bio-molecular system. / Secondly, we focus our aims on investigating protein molecules due to the possibility of being able to explain the mechanism of molecular interactions more clearly. Two lands of labeled immunoglobulin G were investigated using a reflective THz-IDS system. The dielectric properties were sensitive to the conjugation of the antibody. Additionally, terahertz spectroscopy is able to evaluate the depth of the hydrogen shell and shows that the hydrogen-bonded networks of charged protein solutions play an important role in determining the dielectric. / The bio-molecular interaction has been one of the most challenging subjects to probe due to its complexity. In the thesis, we have been attempting to answer fundamental questions about bio-molecular interactions in the terahertz (THz) region from the macroscopic to microscopic level. Terahertz radiation (defined as 0.1--10 THz) can excite intermolecular interactions such as the librational and vibrational modes. These attributes make it feasible to probe the dynamic characteristics of the bio-molecular system. Furthermore, it is worth investigating whether terahertz technology could potentially be used as a novel tool in the biomedical diagnosis field in the near future. / Thirdly, using a transmission THz-TDS system we investigated a biomarker protein and observed distinct spectral differences at various temperatures. This work demonstrates that terahertz spectroscopy can be used to evaluate the anharmonicity of the vibrational potential. By comparing the absorption spectra of the THz-TDS and Synchrotron results it is possible to deduce the approximate localization of the vibrational modes within the molecular chain. / We develop a controlled study to investigate the effects of formalin fixing on the THz properties of two different tissue types. The optical properties are measured using THz reflection spectroscopy. The results present how the fixing process can affect image contrast in THz images of biological samples. / Sun, Yiwen. / Advisers: Emma MacPherson; Yuan-ting Zhang. / Source: Dissertation Abstracts International, Volume: 73-03, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 120-140). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

High-throughput technologies have continuously driven the generation of different biomolecular data, including the genomics, epigenomics, transcriptomics, and other omics data in the last two decades. The developments and advances have revolutionized medical research. In this dissertation, a collection of computational analyses and tools, based on different types of biomolecular data with particular applications on human diseases are presented including 1) a cascade ensemble model based on the Dirichlet process mixture model for reconstructing tumor subclonality from tumor DNA sequencing data; 2) a meta-analysis of gene expression and DNA methylation data from prefrontal cortex samples of patients with neuropsychiatric disorders indicating a stress-related epigenetic mechanism; 3) 2DImpute, an imputation algorithm that is designed to alleviate the sparsity problem in single-cell RNA-sequencing data; and 4) a pan-cancer transformation from adipose-derived stromal cells to metastasis-associated fibroblasts revealed by single cell analysis.

The conformational dynamics of RNA are crucial to its role in numerous essential biological functions, requiring a comprehensive view of masses of individual molecular motions in order to fully understand these processes. Obtaining such a unified view, however, presents many challenges. Even the simplest RNA structures undergo rearrangements within an intricate three-dimensional network of secondary and tertiary interactions, resulting in motions that span a broad range of timescales. This complexity gives rise to a large number of experimental techniques sampling different aspects of the folding process, leaving a rather fragmented picture of RNA folding overall. In order to address the divergence and limitations of existing ensemble and single-molecule methods, this work describes the application of carbon nanotube (CNT)-based single-molecule field-effect transistors (smFET) as a platform for studying the folding and unfolding dynamics of RNA. smFET is capable of measuring individual biomolecular dynamics for long durations, while at a sufficiently high time resolution to capture the relevant timescales for RNA folding. This technique, moreover, avoids potential sources of interference or damage to the molecule as found in other available methods, and capitalizes on the detailed information that can be garnered from studying a single molecule as opposed to an ensemble. By taking advantage of the highly sensitive electronic properties and nanoscale dimensions of CNTs, and tethering a comparably sized and charged single biomolecule like RNA, it is possible to monitor the folding and unfolding of the molecule and characterize the kinetics associated with these motions. This thesis describes the optimization and application of such smFET technology to RNA stem-loops, which are extremely prevalent and thermodynamically stable elements of RNA secondary structure. Chapter 1 introduces the biological context of these molecules as well as the mechanisms of CNT-based smFET sensing. In Chapter 2, the methods used to fabricate smFET devices are described along with the experiments conducted to optimize single-molecule tethering. These methods and protocols were then applied to the studies detailed in Chapter 3, which examines the implications of the thermodynamic and kinetic analyses of RNA stem-loop folding and unfolding as investigated with smFET. Chapter 4 concludes with a brief overview of what has been accomplished and potential future directions for this platform. The work expressed here thus presents a cohesive view of RNA stem-loop folding, integrating the past results of both experimental and computational studies. With this improved smFET methodology, this technique can be applied to many other essential and increasingly complex biological systems to achieve a fuller and richer understanding of the processes that govern life.

The ability to identify and confirm a compound using mass spectrometry usually involves time consuming sample preparation and method development. The open-air ion source DART (Direct Analysis in Real Time) can ionize compounds in the gas, solid, or liquid phase without chromatography or sample preparation due to the interactions of helium metastable atoms with gas molecules commonly found in air. The coupling of the DART to a time-of-flight (TOF) mass spectrometer allows the rapid determination of an analyte's elemental composition based on accurate mass measurement and isotope peak intensities. Mass spectrometric fragmentation data can aid in the structural identification of an analyte as compounds produce characteristic fragment-ions based on their structure. The TOP's ability to produce fragmentation spectra was compared to the more traditional tandem mass spectral method (MS/MS) considering the TOF lacks the ability to select pre-cursor ions. The TOF produced in-source CAD (collisionally activated dissociation) spectra comparable to MS/MS spectra for three well known pharmaceuticals acetaminophen, phenylbutazone and clenbuterol. Further structural confirmation was explored through a determination of the number of active hydrogen atoms in an analyte molecule achieved by hydrogen/deuterium (H/D) exchange by treatment with deuterium oxide (D20) in the DART sample gap. Mass spectra acquired in the presence of D20 of analytes containing active hydrogen atoms associated with hydroxyl, amino and carboxylic acid groups showed that H/D exchange was predictable and reproducible. Using accurate mass measurement and isotope peak intensities, the elemental composition of an unknown captured on filter paper was identified as dipropylene glycol (DPG) analyzed directly from the surface of the filter paper. Data from in-source CAD and H/D exchange of both the unknown and authentic standards confirmed that the unknown was DPG. The cross-correlation of accurate mass measurement and isotope peak intensities, in-source CAD and HID exchange data provided an unambiguous identification of the contaminant melamine in dog food without the need for any sample preparation. Once analytes are identified and confirmed, quantitation of the analyte is desirable. The calibration curves here are constructed using the net extracted ion-current associated with the analyte relative to the internal standard. In cough syrup, a complicated matrix, the linearity, R2, is shown to be 0.992.