Errata pasted onto back page. / Bibliography: leaves 193-228. / xv, 228 leaves : ill. (chiefly col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Physiology, 2001

<p>Hypertension is common and constitutes an increased risk of morbidity and mortality of cardiovascular disease. Antihypertensive treatment will reduce this risk; the individual patient's response to treatment, however, is difficult to predict.</p><p>Patients with hypertension and left ventricular hypertrophy were randomized to monotherapy with either the angiotensin II type 1 receptor antagonist irbesartan or the beta-adrenoreceptor blocker atenolol, and followed for three months. The aim was to determine whether gene polymorphisms in the renin-angiotensin-aldosterone system were related to the response to treatment.</p><p>The ACE II genotype was associated with the most pronounced diastolic blood pressure response, while the aldosterone synthase (CYP11B2) -344 TT genotype showed the greatest systolic blood pressure response. The angiotensinogen 174 TM genotype showed the most pronounced regression in left ventricular mass, independent of the change in blood pressure. These associations were exhibited only in response to treatment with the angiotensin II type 1 receptor antagonist irbesartan.</p><p>In a sample of apparently healthy subjects, those with both the D allele and the angiotensinogen 174 TM variant in combination showed a decreased endothelium-dependent vasodilation.</p><p>These results suggest that the response to antihypertensive treatment is associated with polymorphisms in the genes reflective of the pathophysiological pathway the drug targets. The present study is an encouragement for future investigation, such as large scale studies of multiple polymorphisms and combinations thereof in an attempt to identify a panel of genotypes that can be used as a predictor of an individual patient's response to anithypertensive treatment.</p>

<p>This thesis reports on the development of a novel comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer, DDEC) as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. More importantly, it illustrates how the biocurated genes in the database may represent a reliable starting point for divulging transcriptional regulation, diagnostic markers and the biology related to esophageal cancer.</p>

Hypertension is common and constitutes an increased risk of morbidity and mortality of cardiovascular disease. Antihypertensive treatment will reduce this risk; the individual patient's response to treatment, however, is difficult to predict. Patients with hypertension and left ventricular hypertrophy were randomized to monotherapy with either the angiotensin II type 1 receptor antagonist irbesartan or the beta-adrenoreceptor blocker atenolol, and followed for three months. The aim was to determine whether gene polymorphisms in the renin-angiotensin-aldosterone system were related to the response to treatment. The ACE II genotype was associated with the most pronounced diastolic blood pressure response, while the aldosterone synthase (CYP11B2) -344 TT genotype showed the greatest systolic blood pressure response. The angiotensinogen 174 TM genotype showed the most pronounced regression in left ventricular mass, independent of the change in blood pressure. These associations were exhibited only in response to treatment with the angiotensin II type 1 receptor antagonist irbesartan. In a sample of apparently healthy subjects, those with both the D allele and the angiotensinogen 174 TM variant in combination showed a decreased endothelium-dependent vasodilation. These results suggest that the response to antihypertensive treatment is associated with polymorphisms in the genes reflective of the pathophysiological pathway the drug targets. The present study is an encouragement for future investigation, such as large scale studies of multiple polymorphisms and combinations thereof in an attempt to identify a panel of genotypes that can be used as a predictor of an individual patient's response to anithypertensive treatment.

Gene expression analyses using native populations can provide information on the genetic and molecular mechanisms that determine intraspecific variation and contribute to the understanding of plant development and adaptation in multiple ways. Using quantitative real time – polymerase chain reaction (qRT-PCR), we analyzed the expression of 111 genes with probable roles in wood development in 400 loblolly pine individuals belonging to a population covering much of the natural range. Association mapping techniques are increasingly being used in plants to dissect complex genetic traits and identify genes responsible for the quantitative variation of these traits. We used candidate-gene based association studies to associate single nucleotide polymorphisms (SNPs) in candidate genes with the variation in gene expression. The specific objectives established for this study were to study natural variation in expression of xylem development genes in loblolly pine (Pinus taeda L.) using qRT-PCR, to associate SNPs in candidate genes with the variation in gene expression using candidate-gene based association analyses and to detect loblolly pine promoter polymorphisms and study their effect on gene expression. Out of the 111 genes analyzed using qRT-PCR, there were significant differences in expression among clones for 106 genes. Candidate-gene based association studies were performed between 3937 single nucleotide polymorphisms (SNPs) and gene expression to associate SNPs in candidate genes with the variation in gene expression. To the best of our knowledge, this is the first association genetic study where expression of a large number of genes, analyzed in a natural population, has been the phenotypic trait of interest. We cloned and sequenced promoters of 19 genes, 16 of which are transcription factors involved in wood development and drought response. SNP discovery was done in 13 of these promoters using a panel of 24 loblolly pine clones (unique genotypes). SNP genotyping is underway in the entire association population and association analyses will be done to study the effects of promoter SNPs on gene expression. The results from this project are promising and once these associations have been tested and proved, we believe that they will help in our understanding of the genetics of complex traits.

Cichlid fishes from the East African Rift lakes Victoria, Tanganyika and Malawi represent a preeminent example of replicated and rapid evolutionary radiation. In this single natural system, numerous morphological (eg. jaw and tooth shape, color patterns, visual sensitivity), behavioral (eg. bower-building) and physiological (eg. development, neural patterning) phenotypes have emerged, much akin to a mutagenic screen. This dissertation encompasses three studies that seek to decipher the underpinnings of such rapid evolutionary diversification, investigated via the genetic variation in East African cichlids. We generated a valuable cichlid genomic resource of five low-coverage Lake Malawi cichlid genomes, from which the general properties of the genome were characterized. Nucleotide diversity of Malawi cichlids was low at 0.26%, and a sample genotyping study found that biallelic polymorphisms segregate widely throughout the Malawi species flock, making each species a mosaic of ancestrally polymorphic genomes. A second genotyping study expanded our evolutionary analysis to cover the entire East African cichlid radiation, where we found that more than 40% of single nucleotide polymorphisms (SNPs) were ancestral polymorphisms shared across multiple lakes. Bayesian analysis of genetic structure in the data supported the hypothesis that riverine species had contributed significantly to the genomes of Malawi cichlids and that Lake Malawi cichlids are not monophyletic. Both genotyping studies also identified interesting loci involved in important sensory as well as developmental pathways that were well differentiated between species and lineages. We also investigated cichlid genetic variation in relation to the evolution of microRNA regulation, and found that divergent selection on miRNA target sites may have led to differential gene expression, which contributed to the diversification of cichlid species. Overall, the patterns of cichlid genetic variation seem to be dominated by the phenomena of extensive sharing of ancestral polymorphisms. We thus believe that standing genetic variation in the form of ancestrally inherited polymorphisms, as opposed to variations arising from new mutations, provides much of the genetic diversity on which selection acts, allowing for the rapid and repeated adaptive radiation of East African cichlids.

Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2003. / Includes bibliographical references (leaves 95-105). Also available in electronic version. Access restricted to campus users.

Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7281. Adviser: Lu-Yu Hwang. Includes bibliographical references.

published_or_final_version / Medicine / Doctoral / Doctor of Philosophy

Η ανάγκη εξατομίκευσης της θεραπείας ασθενών που πάσχουν από καρκίνο κρίνεται επιτακτική, λόγω του στενού θεραπευτικού εύρους των αντινεοπλασματικών φαρμάκων και των παρατηρούμενων δια-ατομικών διαφορών στη φαρμακοκινητική και στην κλινική ανταπόκριση. Ένα πολύ χρήσιμο εργαλείο στην εξατομίκευση της θεραπείας θεωρείται ότι είναι η πληθυσμιακή φαρμακοκινητική-φαρμακοδυναμική μοντελοποίηση, καθώς μπορεί να περιγράψει τις σχέσεις δόσης-ανταπόκρισης, να εξηγήσει την παρατηρούμενη μεταβλητότητα στην έκθεση στο φάρμακο ή στην κλινική ανταπόκριση και να καθοδηγήσει την επιλογή της δόσης βάσει της βέλτιστης αναλογίας οφέλους-κινδύνου για τη δεδομένη θεραπεία. Η παρούσα διδακτορική διατριβή επικεντρώθηκε στην μπεβασιζουμάμπη, ένα σχετικά καινούριο φάρμακο στοχευμένης θεραπείας για το οποίο δεν υπάρχουν αρκετά διαθέσιμα στοιχεία που αφορούν στη φαρμακοκινητική και φαρμακοδυναμική συμπεριφορά του. Σκοπός της συγκεκριμένης μελέτης ήταν ο χαρακτηρισμός της αλληλεπίδρασης της μπεβασιζουμάμπης με τον μοριακό της στόχο, VEGF165, σε ενήλικες ασθενείς με μεταστατικό ορθοκολικό καρκίνο που λαμβάνουν το φάρμακο σε συνδυασμό με χημειοθεραπεία (FOLFIRI, FOLFOX ή CAPIRI). Για αυτόν τον λόγο, προσδιορίστηκαν αρχικά οι συγκεντρώσεις της ολικής μπεβασιζουμάμπης και του ελεύθερου VEGF165 σε διάφορους κύκλους θεραπείας και στη συνέχεια, εφαρμόζοντας τη μη γραμμική μικτών επιδράσεων μοντελοποίηση με το υπολογιστικό πρόγραμμα NONMEM 7.3, αναπτύχθηκε ένα φαρμακοκινητικό μοντέλο σύνδεσης της μπεβασιζουμάμπης με τον VEGF165. Επιπλέον, διερευνήθηκε η επίδραση των δημογραφικών δεδομένων και των VEGF μονονουκλεοτιδικών πολυμορφισμών στην αλληλεπίδραση μεταξύ της φαρμακοκινητικής της μπεβασιζουμάμπης και των συγκεντρώσεων του VEGF165. Είναι η πρώτη φορά που χρησιμοποιήθηκε η TMDD προσέγγιση για τον χαρακτηρισμό της in vivo αλληλεπίδρασης μπεβασιζουμάμπης-VEGF165. Σύμφωνα με αυτή την προσέγγιση, η φαρμακοκινητική ενός φαρμάκου επηρεάζεται από την υψηλής συγγένειας δέσμευση με τον μοριακό του στόχο και την επακόλουθη αποικοδόμηση του σχηματιζόμενου συμπλόκου μέσω ενδοκυττάρωσης. Το αναπτυχθέν μοντέλο επέτρεψε την ικανοποιητική περιγραφή της φαρμακοκινητικής της μπεβασιζουμάμπης και των ιδιοτήτων σύνδεσής της με τον VEGF165. Η κάθαρση της μπεβασιζουμάμπης βρέθηκε να είναι 0.18 L/day, η τιμή αναφοράς της συγκέντρωσης του ελεύθερου VEGF165 ήταν 212 ng/L, η σταθερά του ρυθμού απομάκρυνσης του ελεύθερου VEGF165 ήταν 0.401 day-1 και η Kss ήταν 267 nM. Η επίδραση του πραγματικού σωματικού βάρους συνυπολογίστηκε στην εκτίμηση όλων των φαρμακοκινητικών παραμέτρων του μοντέλου. Κάποιες στατιστικά μη σημαντικές συσχετίσεις παρατηρήθηκαν μεταξύ της συγγένειας δέσμευσης του φαρμάκου και των VEGF-2578C/A και VEGF-634G/C πολυμορφισμών. Το αναπτυχθέν μοντέλο θα μπορούσε να αποτελέσει ένα χρήσιμο εργαλείο στην εξατομίκευση της θεραπείας και στην αξιολόγηση της κλινικής ανταπόκρισης ασθενών που λαμβάνουν μπεβασιζουμάμπη σε συνδυασμό με χημειοθεραπεία. / The need for individualized treatment in cancer patients is considered crucial due to the narrow therapeutic range of antineoplastic drugs and the observed inter-individual differences in pharmacokinetics and clinical response. Population pharmacokinetic-pharmacodynamic modeling has been recognized as a beneficial tool for personalizing treatment, as it can describe the dose-response relationships, explain the observed variability in drug exposure or response and guide dose selection based on the optimal benefit-risk ratio for a given treatment. The current doctoral thesis was focused on bevacizumab, a relatively new targeted therapy drug for which no sufficient data are available regarding its pharmacokinetic and pharmacodynamic behavior. The aim of the present study was to characterize the interaction of bevacizumab with its molecular target, VEGF165, in adult patients with metastatic colorectal cancer who receive the drug in combination with chemotherapy (FOLFIRI, FOLFOX or CAPIRI). For this reason, the concentrations of total bevacizumab and free VEGF165 were first determined in different cycles of treatment and then, a pharmacokinetic model for bevacizumab binding to VEGF165 was developed by using nonlinear mixed-effects modeling implemented in NONMEM 7.3 software. Moreover, the effect of demographic data and VEGF single nucleotide polymorphisms on the interplay between bevacizumab pharmacokinetics and VEGF165 concen-trations was investigated. This is the first time the TMDD approach was applied to characterize the in vivo bevacizumab-VEGF165 interaction. According to this approach, the pharmacokinetics of a drug is affected by its high affinity binding to its molecular target and subsequent degradation of the formed complex via endocytosis. The developed model allowed an adequate description of bevacizumab pharmacokinetics and its binding properties to VEGF165. Bevacizumab clearance was found to be 0.18 L/day, the free VEGF165 concentration at baseline was 212 ng/L, the elimination rate constant of free VEGF165 was 0.401 day-1, and Kss was 267 nM. The effect of actual body weight was taken into account in the estimation of all pharmacokinetic model parameters. Correlations, which were not statistically significant, were noticed between the binding affinity of the drug and the VEGF-2578C/A and VEGF-634G/C polymorphisms. The developed model could become a useful tool for individualizing treatment and evaluating clinical response of patients receiving bevacizumab in combination with chemotherapy.