HIV Status and Risk Factors for Hypertension in South African Adults

Thesis (Master's)--University of Washington, 2016-06

Utility of cotyledon and detached leaf assays for assessing root reactions of lucerne to Phytophthora root rot caused by Phytophthora medicaginis

Phytophthora root rot, caused by Phytophthora medicaginis, is a major limitation to lucerne production but it can be managed through the use of resistant cultivars. Current resistance screening methods, using mature plants or post-emergence seedling assays, are costly and time consuming. The use of zoospore inoculum on detached leaves and intact cotyledons as an assay for plant resistance was assessed using genetically defined segregating populations. The detached leaf assay was a reproducible test, but this test could not be used for accurately predicting root ratings. The cotyledon tests using zoospores gave results at the population level that were indicative of the root responses of 19 cultivars and lines tested. The cotyledon reaction of individual plants also showed a strong association with root response. The cotyledon test, while not completely predictive of mature root responses, allowed the selection of Phytophthora resistant plants at a higher frequency than could be achieved by random selection.

Genetic risk factors and age-related macular degeneration (AMD)

Age related macular degeneration (AMD) is the leading cause of blindness in individuals older than 65 years of age. It is a multifactorial disorder and identification of risk factors enables individuals to make lifestyle choices that may reduce the risk of disease. Collaboration between geneticists, ophthalmologists, and optometrists suggests that genetic risk factors play a more significant role in AMD than previously thought. The most important genes are associated with immune system modulation and the complement system, e.g., complement factor H (CFH), factor B (CFB), factor C3, and serpin peptidase inhibitor (SERPING1). Genes associated with membrane transport, e.g., ATP-binding cassette protein (ABCR) and voltage-dependent calcium channel gamma 3 (CACNG3), the vascular system, e.g., fibroblast growth factor 2 (FGF2), fibulin-5, lysyl oxidase-like gene (LOXL1) and selectin-P (SELP), and with lipid metabolism, e.g., apolipoprotein E (APOE) and hepatic lipase (LIPC) have also been implicated. In addition, several other genes exhibit some statistical association with AMD, e.g., age-related maculopathy susceptibility protein 2 (ARMS2) and DNA excision repair protein gene (ERCC6) but more research is needed to establish their significance. Modifiable risk factors for AMD should be discussed with patients whose lifestyle and/or family history place them in an increased risk category. Furthermore, calculation of AMD risk using current models should be recommended as a tool for patient education. It is likely that AMD management in future will be increasingly influenced by assessment of genetic risk as such screening methods become more widely available. © 2013 Spanish General Council of Optometry.

Atmospheric plasma treatment of porous polymer constructs for tissue engineering applications

Porous 3D polymer scaffolds prepared by TIPS from PLGA (53:47) and PS are intrinsically hydrophobic which prohibits the wetting of such porous media by water. This limits the application of these materials for the fabrication of scaffolds as supports for cell adhesion/spreading. Here we demonstrate that the interior surfaces of polymer scaffolds can be effectively modified using atmospheric air plasma (AP). Polymer films (2D) were also modified as control. The surface properties of wet 2D and 3D scaffolds were characterised using zeta-potential and wettability measurements. These techniques were used as the primary screening methods to assess surface chemistry and the wettability of wet polymer constructs prior and after the surface treatment. The surfaces of the original polymers are rather hydrophobic as highlighted but contain acidic functional groups. Increased exposure to AP improved the water wetting of the treated surfaces because of the formation of a variety of oxygen and nitrogen containing functions. The morphology and pore structure was assessed using SEM and a liquid displacement test. The PLGA and PS foam samples have central regions which are open porous interconnected networks with maximum pore diameters of 49 μm for PLGA and 73 μm for PS foams. (Figure Presented) © 2007 Wiley-VCH Verlag GmbH & Co. KGaA.

Biosynthesis and analysis of plant oxylipins

The term oxylipin is applied to the generation of oxygenated products of polyunsaturated fatty acids that can arise either through non-enzymatic or enzymatic processes generating a complex array of products, including alcohols, aldehydes, ketones, acids and hydrocarbon gases. The biosynthetic origin of these products has revealed an array of enzymes involved in their formation and more recently a radical pathway. These include lipoxygenases and α-dioxygenase that insert both oxygen atoms in to the acyl chain to initiate the pathways, to specialised P450 monooxygenases that are responsible for their downstream processing. This latter group include enzymes at the branch points such as allene oxide synthase, leading to jasmonate signalling, hydroperoxide lyase, responsible for generating pathogen/pest defensive volatiles and divinyl ether synthases and peroxygenases involved in the formation of antimicrobial compounds. The complexity of the products generated raises significant challenges for their rapid identification and quantification using metabolic screening methods. Here the current developments in oxylipin metabolism are reviewed together with the emerging technologies required to expand this important field of research that underpins advances in plant-pest/pathogen interactions.

The integration of ProxiMAX randomisation with CIS display for the production of novel peptides

Saturation mutagenesis is a powerful tool in modern protein engineering, which permits key residues within a protein to be targeted in order to potentially enhance specific functionalities. However, the creation of large libraries using conventional saturation mutagenesis with degenerate codons (NNN or NNK/S) has inherent redundancy and consequent disparities in codon representation. Therefore, both chemical (trinucleotide phosphoramidites) and biological methods (sequential, enzymatic single codon additions) of non-degenerate saturation mutagenesis have been developed in order to combat these issues and so improve library quality. Large libraries with multiple saturated positions can be limited by the method used to screen them. Although the traditional screening method of choice, cell-dependent methods, such as phage display, are limited by the need for transformation. A number of cell-free screening methods, such as CIS display, which link the screened phenotype with the encoded genotype, have the capability of screening libraries with up to 1014 members. This thesis describes the further development of ProxiMAX technology to reduce library codon bias and its integration with CIS display to screen the resulting library. Synthetic MAX oligonucleotides are ligated to an acceptor base sequence, amplified, and digested, subsequently adding a randomised codon to the acceptor, which forms an iterative cycle using the digested product of the previous cycle as the base sequence for the next. Initial use of ProxiMAX highlighted areas of the process where changes could be implemented in order to improve the codon representation in the final library. The refined process was used to construct a monomeric anti-NGF peptide library, based on two proprietary dimeric peptides (Isogenica) that bind NGF. The resulting library showed greatly improved codon representation that equated to a theoretical diversity of ~69%. The library was subsequently screened using CIS display and the discovered peptides assessed for NGF-TrkA inhibition by ELISA. Despite binding to TrkA, these peptides showed lower levels of inhibition of the NGF-TrkA interaction than the parental dimeric peptides, highlighting the importance of dimerization for inhibition of NGF-TrkA binding.

Comprehensive forensic toxicological analysis of designer drugs

New designer drugs are constantly emerging onto the illicit drug market and it is often difficult to validate and maintaincomprehensive analytical methods for accurate detection of these compounds. Generally, toxicology laboratories utilize a screening method, such as immunoassay, for the presumptive identification of drugs of abuse. When a positive result occurs, confirmatory methods, such as gas chromatography (GC) or liquid chromatography (LC) coupled with mass spectrometry (MS), are required for more sensitive and specific analyses. In recent years, the need to study the activities of these compounds in screening assays as well as to develop confirmatory techniques to detect them in biological specimens has been recognized. Severe intoxications and fatalities have been encountered with emerging designer drugs, presenting analytical challenges for detection and identification of such novel compounds. The first major task of this research was to evaluate the performance of commercially available immunoassays to determine if designer drugs were cross-reactive. The second major task was to develop and validate a confirmatory method, using LC-MS, to identify and quantify these designer drugs in biological specimens.^ Cross-reactivity towards the cathinone derivatives was found to be minimal. Several other phenethylamines demonstrated cross-reactivity at low concentrations, but results were consistent with those published by the assay manufacturer or as reported in the literature. Current immunoassay-based screening methods may not be ideal for presumptively identifying most designer drugs, including the "bath salts." For this reason, an LC-MS based confirmatory method was developed for 32 compounds, including eight cathinone derivatives, with limits of quantification in the range of 1-10 ng/mL. The method was fully validated for selectivity, matrix effects, stability, recovery, precision, and accuracy. In order to compare the screening and confirmatory techniques, several human specimens were analyzed to demonstrate the importance of using a specific analytical method, such as LC-MS, to detect designer drugs in serum as immunoassays lack cross-reactivity with the novel compounds. Overall, minimal cross-reactivity was observed, highlighting the conclusion that these presumptive screens cannot detect many of the designer drugs and that a confirmatory technique, such as the LC-MS, is required for the comprehensive forensic toxicological analysis of designer drugs.^

Development of a surface-enhanced raman spectroscopy method for the detection of benzodiazepines in urine

Benzodiazepines are among the most prescribed compounds for anti-anxiety and are present in many toxicological screens. These drugs are also prominent in the commission of drug facilitated sexual assaults due their effects on the central nervous system. Due to their potency, a low dose of these compounds is often administered to victims; therefore, the target detection limit for these compounds in biological samples is 10 ng/mL. Currently these compounds are predominantly analyzed using immunoassay techniques; however more specific screening methods are needed. ^ The goal of this dissertation was to develop a rapid, specific screening technique for benzodiazepines in urine samples utilizing surface-enhanced Raman spectroscopy (SERS), which has previously been shown be capable of to detect trace quantities of pharmaceutical compounds in aqueous solutions. Surface enhanced Raman spectroscopy has the advantage of overcoming the low sensitivity and fluorescence effects seen with conventional Raman spectroscopy. The spectra are obtained by applying an analyte onto a SERS-active metal substrate such as colloidal metal particles. SERS signals can be further increased with the addition of aggregate solutions. These agents cause the nanoparticles to amass and form hot-spots which increase the signal intensity. ^ In this work, the colloidal particles are spherical gold nanoparticles in aqueous solution with an average size of approximately 30 nm. The optimum aggregating agent for the detection of benzodiazepines was determined to be 16.7 mM MgCl2, providing the highest signal intensities at the lowest drug concentrations with limits of detection between 0.5 and 127 ng/mL. A supported liquid extraction technique was utilized as a rapid clean extraction for benzodiazepines from urine at a pH of 5.0, allowing for clean extraction with limits of detection between 6 and 640 ng/mL. It was shown that at this pH other drugs that are prevalent in urine samples can be removed providing the selective detection of the benzodiazepine of interest. ^ This technique has been shown to provide rapid (less than twenty minutes), sensitive, and specific detection of benzodiazepines at low concentrations in urine. It provides the forensic community with a sensitive and specific screening technique for the detection of benzodiazepines in drug facilitated assault cases.^

Causes of Childhood Blindness in North Ghana: Results From a School for the Blind in Wa, Upper West Region

Background: Because most developing countries lack sufficient resources and infrastructure to conduct population-based studies on childhood blindness, it can be difficult to obtain epidemiologically reliable data available for planning public health strategies to effectively address the major determinants of childhood blindness. The major etiologies of blindness can differ regionally and intra-regionally. The objective of this retrospective study was to determine (1) the major causes of childhood blindness (BL) and severe visual impairment (SVI) in students who attend Wa Methodist School for the Blind in Upper West Region, North Ghana, and (2) any potential temporal trends in the causes of blindness for this region.

Methods: In this retrospective study, demographic data and clinical information from an eye screening at Wa Methodist School for the Blind were coded according to the World Health Organization/Prevention of Blindness standardized reporting methodology. Causes of BL and SVI were categorized anatomically and etiologically. We determined the major causes of BL/SVI over time using information provided about the age at onset of visual loss for each student.

Results: The major anatomical causes of BL/SVI among the 190 students screened were corneal opacity and phthisis bulbi (n=28, 15%), optic atrophy (n=23, 13%), glaucoma (n=18, 9%), microphthalmos (n=18, 9%), and cataract (n=18, 9%). Within the first year of life, students became blind mainly due to whole globe causes (n=23, 26%), cataract (n=15, 17%), and optic atrophy (n=11, 13%). Those who became blind after age one year had whole globe causes (n=26, 26%), corneal opacity (n=24, 24%), and optic atrophy (n=13, 13%).

Conclusion: At the Wa Methodist School for the Blind, the major anatomical causes of BL/SVI were corneal opacity and phthisis bulbi. About half of all students became blind within the first year of life, and were disproportionately affected by cataract and retinal causes in comparison to the other students who became blind after age one year. While research in blind schools has a number of implicit disadvantages and limitations, considering the temporal trends and other epidemiological factors of blindness may increase the usefulness and/or implications of the data that come from blind school studies in order to improve screening methods for newborns in hospitals and primary care centers, and to help tailor preventative and treatment programs to reduce avoidable childhood blindness in neonates and schoolchildren.

Development of a Surface-Enhanced Raman Spectroscopy Method for the Detection of Benzodiazepines in Urine

Benzodiazepines are among the most prescribed compounds for anti-anxiety and are present in many toxicological screens. These drugs are also prominent in the commission of drug facilitated sexual assaults due their effects on the central nervous system. Due to their potency, a low dose of these compounds is often administered to victims; therefore, the target detection limit for these compounds in biological samples is 10 ng/mL. Currently these compounds are predominantly analyzed using immunoassay techniques; however more specific screening methods are needed. The goal of this dissertation was to develop a rapid, specific screening technique for benzodiazepines in urine samples utilizing surface-enhanced Raman spectroscopy (SERS), which has previously been shown be capable of to detect trace quantities of pharmaceutical compounds in aqueous solutions. Surface enhanced Raman spectroscopy has the advantage of overcoming the low sensitivity and fluorescence effects seen with conventional Raman spectroscopy. The spectra are obtained by applying an analyte onto a SERS-active metal substrate such as colloidal metal particles. SERS signals can be further increased with the addition of aggregate solutions. These agents cause the nanoparticles to amass and form hot-spots which increase the signal intensity. In this work, the colloidal particles are spherical gold nanoparticles in aqueous solution with an average size of approximately 30 nm. The optimum aggregating agent for the detection of benzodiazepines was determined to be 16.7 mM MgCl2, providing the highest signal intensities at the lowest drug concentrations with limits of detection between 0.5 and 127 ng/mL. A supported liquid extraction technique was utilized as a rapid clean extraction for benzodiazepines from urine at a pH of 5.0, allowing for clean extraction with limits of detection between 6 and 640 ng/mL. It was shown that at this pH other drugs that are prevalent in urine samples can be removed providing the selective detection of the benzodiazepine of interest. This technique has been shown to provide rapid (less than twenty minutes), sensitive, and specific detection of benzodiazepines at low concentrations in urine. It provides the forensic community with a sensitive and specific screening technique for the detection of benzodiazepines in drug facilitated assault cases.

ERIC recommendations on TP53 mutation analysis in chronic lymphocytic leukemia.

Recent evidence suggests that - in addition to 17p deletion - TP53 mutation is an independent prognostic factor in chronic lymphocytic leukemia (CLL). Data from retrospective analyses and prospective clinical trials show that ∼5% of untreated CLL patients with treatment indication have a TP53 mutation in the absence of 17p deletion. These patients have a poor response and reduced progression-free survival and overall survival with standard treatment approaches. These data suggest that TP53 mutation testing warrants integration into current diagnostic work up of patients with CLL. There are a number of assays to detect TP53 mutations, which have respective advantages and shortcomings. Direct Sanger sequencing of exons 4-9 can be recommended as a suitable test to identify TP53 mutations for centers with limited experience with alternative screening methods. Recommendations are provided on standard operating procedures, quality control, reporting and interpretation. Patients with treatment indications should be investigated for TP53 mutations in addition to the work-up recommended by the International workshop on CLL guidelines. Patients with TP53 mutation may be considered for allogeneic stem cell transplantation in first remission. Alemtuzumab-based regimens can yield a substantial proportion of complete responses, although of short duration. Ideally, patients should be treated within clinical trials exploring new therapeutic agents.

Optimised wheat root architecture for increased yield and yield stability in the face of a changing climate.

This project provided information, selection techniques and strategies to facilitate the development of high-yielding, stay-green wheat varieties for Australian growers through: a) Improved understanding of the relationships between seminal root traits and other root- and shoot-related traits in determining high-yielding, stay-green phenotypes. b). Molecular markers and rapid phenotypic screening methods that allow selection in breeding programs and identification of genetic regions controlling favourable traits. c). Identification of traits leading to high-yielding, stay-green phenotypes for particular target populations of environments using computer simulation studies.

DEVELOPMENT AND VALIDATION OF THE ANTERIOR CRUCIATE LIGAMENT INJURY-RISK-ESTIMATION QUIZ (ACL-IQ)

Over 2 million Anterior Cruciate Ligament (ACL) injuries occur annually worldwide resulting in considerable economic and health burdens (e.g., suffering, surgery, loss of function, risk for re-injury, and osteoarthritis). Current screening methods are effective but they generally rely on expensive and time-consuming biomechanical movement analysis, and thus are impractical solutions. In this dissertation, I report on a series of studies that begins to investigate one potentially efficient alternative to biomechanical screening, namely skilled observational risk assessment (e.g., having experts estimate risk based on observations of athletes movements). Specifically, in Study 1 I discovered that ACL injury risk can be accurately and reliably estimated with nearly instantaneous visual inspection when observed by skilled and knowledgeable professionals. Modern psychometric optimization techniques were then used to develop a robust and efficient 5-item test of ACL injury risk prediction skill—i.e., the ACL Injury-Risk-Estimation Quiz or ACL-IQ. Study 2 cross-validated the results from Study 1 in a larger representative sample of both skilled (Exercise Science/Sports Medicine) and un-skilled (General Population) groups. In accord with research on human expertise, quantitative structural and process modeling of risk estimation indicated that superior performance was largely mediated by specific strategies and skills (e.g., ignoring irrelevant information), independent of domain general cognitive abilities (e.g., metal rotation, general decision skill). These cognitive models suggest that ACL-IQ is a trainable skill, providing a foundation for future research and applications in training, decision support, and ultimately clinical screening investigations. Overall, I present the first evidence that observational ACL injury risk prediction is possible including a robust technology for fast, accurate and reliable measurement—i.e., the ACL-IQ. Discussion focuses on applications and outreach including a web platform that was developed to house the test, provide a repository for further data collection, and increase public and professional awareness and outreach (www.ACL-IQ.org). Future directions and general applications of the skilled movement analysis approach are also discussed.

Detection of Carbapenemase Production in a Collection of Enterobacteriaceae with Characterized Resistance Mechanisms from Clinical and Environmental Origins by Use of Both Carba NP and Blue-Carba Tests

Rapid-screening methods to confirm the presence of resistance mechanisms in multidrug-resistant bacteria are currently recommended. Carba NP and Blue-Carba tests were evaluated in carbapenemase-producing Enterobacteriaceae from hospital (n = 102) and environmental (n = 57) origins for detecting the different molecular classes among them. Both methods showed to be fast and cost-effective, with high sensitivity (98% to 100%) and specificity (100%), and may be easily introduced in the routine laboratory.

Analytical instrumental approaches and strategies to support the sensory assessment of virgin olive oils

At the beginning, this Ph.D. project led to an overview of the most common and emerging types of fraud and possible countermeasures in the olive oil sector. Furthermore, possible weaknesses in the current conformity check system for olive oil were highlighted. Among those, despite the organoleptic assessment is a fundamental tool for establishing the virgin olive oils (VOOs) quality grade, the scientific community has evidenced some drawbacks in it. In particular, the application of instrumental screening methods to support the panel test could reduce the work of sensory panels and the cost of this analysis (e.g. for industries, distributors, public and private control laboratories), permitting the increase in the number and the efficiency of the controls. On this basis, a research line called “Quantitative Panel Test” is one of the main expected outcomes of the OLEUM project that is also partially discussed in this doctoral dissertation. In this framework, analytical activities were carried out, within this PhD project, aimed to develop and validate analytical protocols for the study of the profiles in volatile compounds (VOCs) of the VOOs headspace. Specifically, two chromatographic approaches, one targeted and one semi-targeted, to determine VOCs were investigated in this doctoral thesis. The obtained results, will allow the possible establishment of concentration limits and ranges of selected volatile markers, as related to fruitiness and defects, with the aim to support the panel test in the commercial categorization of VOOs. In parallel, a rapid instrumental screening method based on the analysis of VOCs has been investigated to assist the panel test through a fast pre-classification of VOOs samples based on a known level of probability, thus increasing the efficiency of quality control.