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, 2015. / Surface enhanced Raman spectroscopy (SERS) has emerged as a surface sensitive vibrational technique that leads to the enhancement of the Raman scattering molecules on or close to the surface of a plasmonic nanostructure. The enhancement is found to be in orders of 104 to 1015, which allows the technique to be sensitive enough to detect a single molecule. In this study, we report on the synthesis of different sizes of gold and silver nanoparticles (AuNPs and AgNPs) and gold nanorods (AuNRs). These are functionalized or co-stabilized with different stoichiometric ratios of HS-(CH2)11-PEG-COOH and alkanethiols (Raman reporters), i.e.; HS-(CH2)11-NHCO-coumarin(C), HS-(CH2)11-triphenylimidazole (TPI), HS- (CH2)11-indole (HSI), HS-(CH2)11-hydroquinone (HQ) to form mixed monolayer protected clusters (MMPCs). The alkanethiols were chosen as Raman reporters to facilitate the selfassembled formation of monolayers on the metal surface, thus resulting in stable MMPCs. The optical properties and stability of MMPCs were obtained using ultraviolet-visible (UVvis) spectrophometry and a zeta sizer. Size and shape of the as-synthesized nanoparticles were obtained using transmission electron microscopy (TEM). The tendency of thiolcapped nanoparticles to form self-assembled ordered superlattices was observed. Their Raman activities were evaluated using Raman spectroscopy, with the enhancement factor (EF) being calculated from the intensities of symmetric stretch vibrations of C-H observed in the region of about 2900 to 3000 cm-1 in all SERS spectra. In all four different alkanethiols (Raman reporters), smaller size metal nanoparticles (14 nm for AuNPs and 16 nm AgNPs) showed higher EF compared to 30 and 40 nm metal nanoparticles. The EF was observed to increase proportionally with stoichiometric ratios of alkanethiols from 1% iv | P a g e to 50%. The prepared MMPCs with small sizes were used as a SERS probe for the detection of malaria and tuberculosis biomarkers.

Diffuse gliomas, the most common primary brain cancer, are classified into astrocytomas, oligodendrogliomas and oligoastrocytomas according to morphological similarity to glial cell, and categorized into grade II to IV according to histological features. While standard-of-care of surgery followed by chemo-radiotherapy exists for grade IV glioblastomas, lower grade gliomas (grades II and III) remain as a heterogeneous entity with variable treatment and outcome. The current WHO classification of lower grade glioma is purely based on histology and subject to interobserver variation, which can be aggravated by sampling error or small tissue biopsy. Objective prognostic biomarker guiding patient risk stratification is also relatively inadequate in lower grade gliomas. Since molecular markers will be supplemented into the future classification system of gliomas in order to facilitate clinico-pathological prediction and therapeutic planning in patient management and clinical trials, identification of clinically relevant biomarker is of paramount importance in neuro-oncology. In this study, we evaluated the clinical significance of several important molecular markers in a very large cohort of 453 lower grade gliomas (including 244 diffuse astrocytomas, 73 anaplastic astrocytomas, 31 oligodendrogliomas, 17 anaplastic oligodendrogliomas, 76 oligoastrocytomas and 12 anaplastic oligoastrocytomas) from Prince of Wales Hospital (Hong Kong) and Huashan Hospital (Shanghai). Mutational analysis was conducted in IDH, CIC, FUBP1 and TERT promoter by direct sequencing and 1p/19q codeletion and EGFR amplification were evaluated by fluorescent in-situ hybridization. Protein expressions of IDH1-R132H, CIC, FUBP1, EGFR, INA, p53 and PDGFRA were examined by immunohistochemistry. IDH mutation, detected in 69% of lower grade gliomas, represented a crucial marker in classifying the tumors into two groups with distinct prognosis, the favorable IDH mutated group and unfavorable IDH wild type group. 1p/19q codeletion, present in 20% of lower grade gliomas, identified tumors with oligodendroglial histology and favorable prognosis within the IDH mutated group. This IDH mutated-1p/19q codeleted genetic signature was frequently found in incidentally-discovered low grade gliomas, a clinical subgroup of tumors with excellent prognosis. CIC and FUBP1 mutations, detected in 47% and 16% of oligodendroglial tumors respectively, were oligodendroglial markers which conferred unfavorable prognosis to patients within IDH mutated-1p/19q codeleted oligodendroglial tumors. Among IDH mutated-1p/19q intact gliomas, p53 positive expressing tumors exhibited worse prognosis and PDGFRA positive expressing tumors showed better prognosis. TERT promoter mutation, identified in 28% of lower grade gliomas, exhibited as an oligodendroglial marker and favorable prognostic factor within the IDH mutated group and highlighted a subgroup of aggressive astrocytic tumors with short survival within the IDH wild type group. EGFR amplification, observed in 7% of lower grade gliomas, occurred exclusively in IDH wild type tumors, correlated with TERT promoter mutation and contributed a subset of tumors with fatal prognosis. Taken together, this study identifies objective and clinically relevant biomarkers which define lower grade gliomas into molecular subgroups with distinct clinico-pathological features. The biomarkers not only provide adjuncts to tumor classification beyond histology but potentially facilitate standardization of treatment strategy. With continuous efforts, I believe that this information will ultimately contribute to patient care in neuro-oncology in the era of personalized medicine. / 瀰漫性腦膠質瘤是最常見的原發性腦癌，可根據形態學分為星形細胞瘤、少枝膠質細胞瘤和少枝星形細胞瘤，並根據惡性特徵分為II至IV級。雖然膠質母細胞瘤(Ⅳ級)有標準的手術和術後化放療方案，低級別膠質瘤(Ⅱ和Ⅲ級)在治療方案和臨床結果上仍有很大的變異。目前世界衛生組織就膠質瘤的分類是純基於組織學，因此存在著觀察者間的變異，而抽樣誤差和活檢組織樣本太小亦加劇此問題。客觀和俱臨床價值的標誌物在低級別膠質瘤亦相對缺乏。為了改善腫瘤診斷和治療，未來膠質瘤分類將會加入分子標誌物，因此探討預後標誌物在神經腫瘤研究領域極為重要。我們從香港威爾斯親王醫院和上海華山醫院採集了453例低級別膠質瘤樣本，並對幾個重要的分子標誌物的臨床意義進行評估。我們以直接測序分析IDH，CIC，FUBP1和TERT啟動子突變，以熒光原位雜交技術檢測染色體1p/19q雜合性缺失和EGFR基因擴增，並以免疫組化檢測IDH1-R132H，CIC，FUBP1，EGFR，INA，p53和PDGFRA蛋白表達。IDH的突變率為69%，它把膠質瘤分成兩組: 預後好的IDH突變型組和預後差的IDH野生型組。1p/19q雜合性缺失的發生率為20%，主要是IDH突變型組內的少枝膠質細胞瘤，有較好的預後。IDH突變-1p/19q雜合性缺失這個基因特徵經常出現在偶發低級別膠質瘤，是一組預後良好的臨床亞組。CIC和FUBP1在少枝膠質腫瘤的突變率分別為47%和16%，在IDH突變-1p/19q雜合性缺失的少枝膠質腫瘤有不良的預後。在IDH突變-1p/19q完整的膠質瘤，p53陽性表達的腫瘤預後較差，PDGFRA陽性表達的腫瘤則預後較好。TERT啟動子的突變率為28%。在IDH突變型組，TERT啟動子突變表現為少枝膠質標誌物，出現在預後良好的腫瘤;在IDH野生型組，TERT啟動子突變則出現在一組生存期很短的星形細胞腫瘤亞組。EGFR基因擴增的發生率為7%，只出現在IDH野生型腫瘤，與TERT啟動子突變有相關性，並有致命性的預後。綜上所述，本研究確定了客觀的臨床標誌物，為膠質瘤分類提供組織學以外的參考，更為制定標準治療方案奠定基礎。在這個體化醫療時代，本人相信這些資訊最終將有助於神經腫瘤病人的治理。 / Chan, Ka Yin. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 159-186). / Abstracts also in Chinese. / Title from PDF title page (viewed on 02, December, 2016). / Detailed summary in vernacular field only.

Conventional treatments for depression, such as pharmacological interventions, are often ineffective. Up to half of patients do not respond, resulting in a poor prognosis for depression. Therefore, treatment options can be invaluable for increasing rates of remission. It is generally assumed that aerobic exercise benefits affective state. However, exercise remains a controversial treatment, possibly due to inconsistent evidence and unknown mechanisms. It is hypothesised variable results (literature is conflicting) are due to/because of heterogeneity in exercise interventions and subjective reports of exercise and mood state. If a biomarker for depression can be identified, the effects of exercise on depression could be objectively assessed. Neuroimaging research has elucidated numerous biomarkers, but has had little benefit on the diagnosis, prognosis or treatment of depression. However, if research can identify which biomarkers respond to treatments, can stratify patients and which can predict response outcome, targets for new interventions can be developed. Therefore, this thesis first establishes the effect of ECT treatment on emotionally salient brain regions in MDD, establishing the basis of a treatment responsive biomarker and potential targets for other interventions. The same functional connectivity methods are then used to analyse the effects of a single bout of aerobic exercise in a healthy population. Similar reductions in functional connectivity were observed in brain structures relevant to depression, suggesting exercise might target relevant brain structures. Finally, using the same functional connectivity methods, a long-term aerobic exercise intervention is shown to reduce functional hyperconnectivity in mildly depressed participants compared to healthy controls. This supports two primary hypotheses: that hyperconnectivity may underlie depressive disorders, constituting a biomarker for depression; and that aerobic exercise is an effective treatment for milder forms of depression.

A number of major crop species, such as allohexaploid wheat and autotetraploid potato are polyploid. Potato is the fourth most important crop in terms of production and has become an important food source in many countries. Therefore, the molecular analysis was directed towards investigating ways to develop markers to assist the potato breeding process; for example breeding for powdery scab disease resistance, and tolerance to cold induced sweetening. Polyploids have more possible genotypes per population, allele dosage effects and increased marker complexity compared to diploids. Potato is also outcrossing and therefore highly heterozygous. Various methods for detecting marker-trait associations including, linkage, quantitative trait locus (QTL) and association mapping were studied and protocols developed. A mapping population was produced and a number of traits were measured including powdery scab resistance. Powdery scab disease assays were carried out over six seasons and markers associated with disease resistance were identified. Markers associated with resistance to powdery scab were identified on chromosomes I, IV, V, VI, VIII and IX using analysis of variance (ANOVA). Linkage maps were produced for each parent of the population and QTL associated with resistance and susceptibility to disease were identified using interval mapping, which revealed QTL on chromosomes II, V, VII , VIII, IX and an unanchored linkage group. QTL were detected across years on regions of chromosomes VIII and IX. These QTL results had some overlap with the marker-trait associations that were identified using ANOVA analysis. Another marker identification technique was tested, known as association or linkage disequilibrium mapping. Alleles of candidate genes were tested for association with cold-induced sweetening using a germplasm collection. The alleles identified as important were of the apoplastic invertase and UGPase genes and a unique interaction between alleles of the apoplastic invertase and apoplastic invertase inhibitor was also detected. This thesis describes the first study into the genetics of powdery scab resistance and the markers identified as associated with resistance will be validated for use in a marker-assisted selection (MAS) programme. The tools and resources developed as part of this thesis are vital to the potato breeding programme that requires the identification of associated molecular markers.

Molecular DNA markers have become widely used in all areas of genetic research. The objectives of this thesis were to develop polymorphic markers in sunflower and utilize the markers for genetic and candidate gene analyses. Amplified fragment length polymorphism (AFLP) markers were used to estimate genetic similarities and assess the genetic diversity among 24 public oilseed inbred lines of sunflower (Helianthus annuus L.). A total of 359 AFLP markers were scored by using six AFLP primer combinations. Genetic similarities ranged from 0.70 to 0.91, polymorphism rate ranged from 7 to 24%, and polymorphic information contents (PICs) ranged from 0.0 to 0.5. Principal coordinate and cluster analysis separated the lines into two groups, B-lines and R-lines, illustrating breeding history, basic heterotic pattern and the widespread practice of using each group to develop new lines. ��9 stearoyl-ACP desaturase (SAD) and ��l2 oleate desaturase (OLD) cDNAs were cloned and sequenced. DNA fragment length polymorphism (DFLP), single strand conformational polymorphism (SSCP), and simple sequence repeat (SSR) markers were developed for the SAD6 and SAD17 genes among eight elite inbred lines. PICs for DFLP, SSCP, and SSR markers were 0.18, 0.37, and 0.30, respectively. Length variants were due to long monomeric repeats, insertions, and deletions in intron sequences, thereby producing polymorphic markers. OLD desaturates 18:1-PC (oleoyl phosphatidylcholine) to 18:2-PC, thereby converting oleic to linoleic acid. It is a likely candidate gene to be causing the high oleic phenotype in mutant sunflower. The expression of OLD7 in developing seeds was greatly reduced in mutant as opposed to wildtype backcross-derived lines. The restriction fragment length polymorphism (RFLP) patterns suggest that OLD7 is duplicated and rearranged in mutant lines. Utilizing sunflower SAD gene sequences and 27 inbred lines, intron fragment length polymorphism (IFLP) markers were developed for automated genotyping. These IFLP markers with ~470 to ~850 bp in length had a mean PIC score of 0.414, versus 0.336 for DFLP markers, and 0.582 for SSCP markers. One and two nucleotide length polymorphisms were reliably detected in PCR fragments up to ~150 and ~680 bp, respectively. / Graduation date: 1998

Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004. / Includes bibliographical references. Also available in electronic version. Access restricted to campus users.

Thesis (Ph.D.) -- University of Texas at Arlington, 2008.

Thesis (Ph.D.) -- University of Texas at Arlington, 2008.

Thesis (Ph.D.)--Ohio University, August, 2009. / Release of full electronic text on OhioLINK has been delayed until September 1, 2012. Includes bibliographical references (p. 253-288)

Thesis (Ph.D.)--Ohio University, August, 2009. / Title from PDF t.p. Release of full electronic text on OhioLINK has been delayed until September 1, 2012. Includes bibliographical references (p. 253-288)