Glyphosate-resistant (GR) giant ragweed (Ambrosia trifida L.) has been confirmed in several states across the mid-western and mid-southern U.S. Greenhouse and lab studies were conducted to investigate possible mechanism of glyphosate resistance in a suspect population from Monroe County, Mississippi. Translocation of 14C-glyphosate in the susceptible biotype was 77%, compared to 12% in the resistant biotype at 120 hours after treatment, suggesting that the glyphosate resistance mechanism for this giant ragweed biotype is reduced translocation. Dose response studies were conducted to confirm and characterize glyphosate resistance in suspect biotypes from Mississippi (MS-R) and Tennessee (TN-R). The ED50 for MS-R and TN-R were 3.9- and 6.3-fold higher than a susceptible biotype. Results from a fallow field study conducted in 2016 in Monroe County revealed PRE and POST treatments containing dicamba and mesotrione alone and in various combinations provided effective control of GR giant ragweed. Studies were conducted to measure fitness, phenotypic, and genetic variation among GR biotypes from MS-R, TN-R, and Ohio (OH-R). Non-destructive measurements of plants over an eight-week period revealed rapid early growth of two GR accessions from MS in the absence of glyphosate. However, no differences in vegetative biomass were recorded after eight weeks with the exception of OH-R biotype which exhibited lower biomass due to photoperiod sensitivity. Vegetative biomass and fecundity were similar. Multivariate and PCA analysis of traits grouped biotypes based on state of origin. Groupings by state of origin can be significant as managers could design similar methods of control to address giant ragweed in these areas. Simple sequence repeat (SSR) markers were used to record genetic diversity among and within biotypes. Genetic diversity values were high at 0.514, 0.502, and 0.525 within biotypes from MS, TN, and OH, respectively. However, genetic diversity did not differ due to glyphosate response or level of glyphosate resistance. High levels of genetic variation can be an indicator of the ability of giant ragweed biotypes to adapt to changing environments and conditions.

Nineteen heifers (274 ± 24 kg) were blocked into two treatment groups based upon DNAm; heifers with no DNAm (noQG), and heifers with one or more DNAm (1+QG). Prior to challenge (24 h), heifers were fitted with indwelling jugular catheters and indwelling vaginal temperature (VT) monitoring devices. Blood samples were collected at 30-min intervals while RT were collected at 1-min intervals from -2 to 8 h relative to a lipopolysaccride (LPS) challenge (0.5 ìg/kg BW) at 0 h. Serum was analyzed for concentrations of cortisol and pro-inflammatory cytokines. All physical, endocrine, and immune measurements increased relative to LPS challenge. No differences observed for IL-6 or TNF-á; however, 1+QG heifers had a greater circulating INF-ã (P < 0.001). Furthermore, 1+QG heifers had an elevated VT (P = 0.04). This would suggest a different immune system approach to an LPS challenge.

N/A / Thesis / Master of Science (MS)

Published Article / The objective of this study was to examine the relationship between external markers typically used in external motion capturing devices and the true vertebral kinematics in the cervical spine. Twenty one healthy subjects were subjected to low dosage X-rays in five different positions, while radio opaque markers were attached to the skin at each vertebral level. Distance and angle parameters were constructed for vertebral prediction from skin surface markers. The causes of variation in these parameters were identified by investigating the correlations of these parameters with anthropometrical variables. Strong correlations of the parameters were observed in flexion, but in extension, especially full extension, the correlations were poor to insignificant. In neutral, half flexion, and full flexion it is possible to predict the vertebral position from surface markers by using the parameters and anthropometrical variables. In half extension this prediction is less accurate and in full extension alternative methods should be investigated for external motion capturing.

Background: Pancreatic disease is a global problem. Severe acute pancreatitis (AP) carries a 30-50% mortality. Current scoring systems fall short in predictive accuracy, sensitivity, specificity and availability. Pancreatic cancer (PC) is a leading cause of cancer-related mortality, most patients die within one year of diagnosis. Late presentation and lack of effective oncological treatment determine a desperate need to focus on early detection of the pancreatic cancer. Current biomarkers fall short in accessibility, sensitivity and specificity and ability to distinguish malignant from benign conditions. Metabolomics aims to decipher molecular signatures that will distinguish disease from controls, ultimately leading to novel targets for diagnosis and treatment. Initial studies are discovery-based, hypothesis-generating and typically aim to establish a snapshot of the metabolism of an individual by metabolite profile. Aims: Establish a prospective phenotypic and demographic database of patients with acute pancreatitis. Determine urinary and serum metabolomic profiles of AP and PC in comparison to controls and establish if metabolomic profiling can distinguish severity of each disease in order to identify potential novel bio-markers. Methods: Urine and serum samples from 73 AP, 32 PC, 62 Healthy Controls, 8 Chronic pancreatitis and 8 Benign jaundice participants were analysed using GC-MS and UPLCMS. Metabolite identification was subject to univariate and multivariate analysis (p<0.05). Results: The differentiation of metabolite profiles was most distinct with AP. There was no differentiation by AP aetiology. AP severity was distinquished by metabolite profile. Profiles of resectable patients were distinct form non-resectable PC. Fatty acids(FA), glycerophoshocholines, eicosanoids, TCA cycle intermediates and melatonin levels were altered in AP. PC was defined by altered concentrations of FAs, eicosanoids, glycerophoshocholines, sphingomyelins, folates and amino acids and peptides (e.g. glutamine). Altered levels of UFAs, neuromedins, Vitamin D3 determined stage of PC. Conclusion: Urinary and serum metabolomic signatures may provide future biomarker panels for grading AP and PC.

Background: The use of novel targeted anticancer drugs in clinical practice is rapidly increasing. As the use of these drugs increases, so does the need to develop biomarkers to optimise the drugs' clinical and cost effectiveness. The attitudes and views of all stakeholders regarding the optimal use of predictive biomarkers in guiding personalised medicine are crucial for identifying acceptable criteria of predictive biomarker tests to guide future biomarker development. To gain insight into these views, we aimed to develop and validate a survey tool that would aid in assessing attitudes of cancer physicians and patients regarding the utilisation of biomarkers in tailoring treatment according to individual patient needs. Methods: Two questionnaires (one for oncologists and one for patients) based on emerging clinical data about novel targeted anticancer agents were designed to capture information about acceptable sensitivity, specificity, invasiveness and cost of a predictive biomarker test. A hypothetical scenario was provided that described a newly developed, targeted anticancer drug that was found to be more beneficial to certain patient subgroups identified through a predictive biomarker test. Questions in the patient survey were based on the results of the oncologist survey. Results: The response rates to these surveys were 20% (n=67) for the oncologists and 59% (n=100) for the patients. The oncologists' attitudes regarding the predictive biomarker test's false negative (FN) and false positive (FP) rates varied with the level of health outcome generated by the hypothetical drug. The acceptable FN rate for predictive biomarker test results detected in the current study was similar to many current predictive biomarkers, but the FP rate considered acceptable was much lower. The majority of the patients (90%) accepted the median acceptable FN rate of 10% reported by the oncologists. A significant minority of the oncologists (27%) refused a tumour biopsy (in addition to the diagnostic biopsy) to collect samples for the purpose of predictive biomarker testing. A much higher percentage of patients (68%) refused a biopsy under such conditions. Interestingly, our data also suggest that oncologists' expectations for the outcome of therapy have changed little in recent years, while patients' expectations have increased dramatically. Conclusions: Our data suggest that oncologists and patients agree that a FN rate of 10% is acceptable. However, based on the oncologists' responses, the FP rates associated with current predictive biomarkers are far from ideal. This may reflect oncologists' pragmatic approach in the absence of alternative choices for predictive biomarker tests. However, it also suggests that future biomarker development and implementation must focus on decreasing the FP rate without increasing the FN rate. Recent results demonstrating molecular heterogeneity in tumours suggest that, considering our data on acceptable test accuracy, serial/repeated tumour biopsies may be required. However, based on the attitudes of physicians and patients reported here, such ‘biopsy-driven' clinical trials may not be acceptable, and, without further investigation or education, this may be a barrier to the successful implementation of such potentially valuable investigational strategies. These results should certainly be taken into account when planning biopsy-dependent trials, and emphasises the importance of pursuing non-invasive biomarker assays. We believe that the survey questionnaires originating from the current study are valid tools for assessing stakeholders' attitudes and views about the appropriate application of predictive biomarkers in personalised medicine.

No description available.

Thesis (PhD)--Stellenbosch University, 2001. / ENGLISH ABSTRACT: Given the organisation of the maize genome as well as demands placed on the saturation of molecular linkage maps it would be desirable to identify informative molecular markers that is located or linked to genic rich areas. Sequences of gene products from different gene classes were investigated. Proteins containing a nucleotide binding site (NBS) and leucine-rich repeat (LRR) region comprise the largest class of disease resistance proteins. Resistant gene analogue (RGA) primers belonging to this specific class were derived from previous published literature studies. By means of similarity studies of short stretches of conserved amino acid and DNA sequences, primers were developed that belonged to the peroxidase and reductase gene classes. A novel class of transposable element was identified, that occurred in the gene rich areas of a diverse range of grass genomes. Of all the MITE families described so far, the Heartbreaker (Hbr) and Hb2 family elements were of particular interest. The unique properties of MITEs, especially their high copy number, polymorphism, stability and preference for genic areas together with the RGA primers, were exploited to develop a new marker technique for the isolation of a class of molecular marker with a strong preference for genic areas. Using the publicly available recombinant inbred population, Tx303 x C0159, 196 MITE/RGA markers were added to the existing recombinant inbred linkage map consisting of ±1033 already established markers. It became apparent that just like loci for disease resistance, the 196 MITE/RGA fragments were not randomly distributed across the maize genome but occurred in clusters spread across the ten maize chromosomes. Ninety-two (92) of the MITE/RGA fragments showed significant correlation to previously mapped maize resistance genes. To establish the conservation and specificity of both the Hbr and Hb2 elements, sequences of 19 MITE/RGA fragments were ascertained. When comparing the partial MITE element sequences from these fragments, a high degree of element conservation was observed. One fragment showed good sequence correlation to a NADPH He Toxin reductase protein product and mapped to the same chromosomal location as the hm1 gene locus in maize. This fragment can be considered a candidate gene for resistance against the pathogen, Helminthosporium carbonum. The Hbr primer used proved to be very specific for the Heartbreaker MITE element, this was in contrast to the non-specificity of the Hb2 primer. The applicability of this technique was tested on two maize diseases that cause immense damage in the maize production industries in South Africa. Fourteen MITE/RGA markers were used to fine map the putative chromosomal locations for the HtN1, Ht1, Ht2 and Ht3 genes that confer resistance. against Setosphaeria turcica, the northern corn leaf blight (NelS) pathogen in maize. Three MITE/RGA fragments were identified that aided in the saturation of the linkage map for quantitative trait resistance (QTl) against gray leaf spot (GlS) in maize. This novel MITE/RGA technique presented a unique opportunity to search for additional candidate genes by using polymerase chain reaction (peR) analysis. When compared to the conventional amplified fragment length polymorphism (AFLP) technique, the MITE/RGA technique proved to be just as efficient but was more cost effective and less time consuming. / AFRIKAANSE OPSOMMING: Die organisasie van die mielie genoom as ook die vereistes wat daar geplaas word op die versadiging van koppelingskaarte, vereis dat daar meer klem geplaas word op die ontwikkeling van molekulêre tegnieke wat merkers in geenryke areas identifiseer. Die volgordes van geenprodukte, wat behoort tot verskillende geenklasse, is deeglik bestudeer. Proteïenprodukte wat bestaan uit 'n nukleotiedbindingsarea (NBA) en 'n leusienryke herhalende (LRH) area is een van die grootste klasse waaronder siekteweerstandsproteïene sorteer. Polimerase kettingreaksie (PKR) inleiers wat behoort tot hierdie spesifieke klas, is verkry vanuit vorige publikasies. Deur kort gekonserveerde aminosuur en DNS volgordes te vergelyk is inleiers ontwikkel wat behoort tot die peroksidase en reduktase gene klasse. 'n Nuwe klas transponeerbare elemente wat voorkom in die geenryke areas van diverse gras genome, is geïdentifiseer. Van al die miniatuur inversie herhalende transponeerbare elemente (MITE) wat al geïdentifiseer is, is die twee elemente, Heartbreaker (Hbr) en Hb2, van groot belang. Unieke eienskappe van die MITEs, veral hul hoë kopie aantal, polimorfiese-indeks, stabiliteit asook voorkeur vir geenryke areas, tesame met die weerstandsgeen analoë (WGA) inleiers, is gebruik om 'n nuwe merker tegniek te ontwikkel. Hierdie nuwe tegniek identifiseer 'n klas merker wat 'n sterk voorkeur het vir geenryke areas. Deur gebruik te maak van die openbare beskikbare rekombinante ingeteelde (RI) populasie, Tx303 x C0159, is 196 MITE/WGA-merkers gekarteer op die bestaande RIL koppelingskaart, wat alreeds bestaan uit ±1033 gevestigde merkers. Net soos die lokusse vir siekteweerstand het dit geblyk dat hierdie 196 merkers in groepe voorkom wat verspreid is oor die tien mielie chromosome. Twee-en-negentig (92) van die 196 gekarteerde MITE/WGA-merkers het betekenisvolle korrelasie gewys met reeds gekarteerde mielie weerstandsgene. Die volgordes van 19 MITE/WGAfragmente is bepaal om sodoende die spesifisiteit en mate van konservering van die Hbr and Hb2 elemente te bereken. 'n Hoë mate van element konservering is waargeneem. Een fragment het In baie goeie volgorde korrelasie gewys met In NADPH HG toksien reduktase proteïen produk en karteer op dieselfde chromosomale posisie as die hm1 geen lokus. Hierdie fragment kan gesien word as In kandidaatgeen vir weerstand teen die mielie patogeen, Helminthosporium carbonum. Die toepasbaarheid van hierdie tegniek is getoets op twee siekte toestande, wat lei tot groot verliese in die mielie industrie, in Suid-Afrika. Veertien van die MITE/WGAmerkers is gebruik om die waarskynlike chromosomale posisies van die HtN1, Ht1, Ht2 en Ht3 gene, wat weerstand bied teen Setosphaeria turcica, die noordelike mielie blaarvlek (NMBV) patogeen, fyner te karteer. Drie MITE/WGA fragmente is geïdentifiseer wat gehelp het in die versadiging van die koppelingskaart vir die kwantitatiewe kenmerk weerstandbiedenheid (KKW) teen grys blaarvlek (GBV) in mielies. Deur gebruik te maak van polimerase kettingreaksie (PKR) analise, verskaf hierdie tegniek die moontlikheid om te soek vir addisionele kandidaatgene. Hierdie tegniek is ook vergelyk met die konvensionele geamplifiseerde fragment lengte polimorfisme (AFLP) tegniek. Daar is gevind dat die nuwe tegniek net so informatief is, maar wel meer koste effektief en tyd besparend.

published_or_final_version / abstract / Zoology / Doctoral / Doctor of Philosophy

published_or_final_version / Surgery / Master / Master of Philosophy