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Schizophrenia, bipolar disorder and major depression are common, heritable neuropsychiatric conditions and yet the source of the inherited risk remains largely unknown. This thesis focuses on two complementary strategies for identifying and characterising the genetic component of these illnesses: homozygosity mapping in consanguineous pedigrees, and genetic and neurobiological investigations of candidate genes identified by the analysis of structural chromosomal abnormalities carried by patients with psychiatric diagnoses. In a family of a cousin marriage, five of six offspring presented with a rare combination of schizophrenia, sensori-neural hearing impairment and epilepsy. Two loci were located on chromosomes 22q13 and 2p24-25 where a series of markers were homozygous by descent (HBD). Five further HBD loci were identified in a second, related family where four of five offspring had hearing loss. However, there was no overlap of the HBD intervals in the two families, and sequencing coding regions of candidate genes failed to identify causative mutations. A second study investigated the candidate gene ABCA13 identified at a breakpoint region on chromosome 7 in a patient with schizophrenia who carried a complex chromosomal rearrangement. Re-sequencing exons encoding the highly conserved functional domains identified eight potentially pathogenic, rare coding variants. Case control association studies involving cohorts of schizophrenia, bipolar disorder and major depression revealed significant associations of these variants with all three clinical phenotypes, and follow-up in relatives displayed familial inheritance patterns. Disruption of ABCA13, expressed in human hippocampus and frontal cortex, implicates aberrant lipid biology as a pathological pathway in mental illness. A third study focused on GRIK4, a candidate gene previously reported disrupted in a patient with schizophrenia who carried a chromosome abnormality. A deletion in the 3’UTR of GRIK4, encoding the kainate receptor subunit KA1, was identified as a protective factor for bipolar disorder. Using post mortem human brain tissue from control subjects, KA1 protein expression patterns were characterized in the hippocampal formation, amygdala, frontal cortex and cerebellum. KA1 expression was found significantly increased in subjects with the protective allele, supporting the hypothesis that reduced glutamatergic neurotransmission is a risk factor in major psychiatric illnesses. Together, these novel discoveries define aspects of the genetic contribution to mental illness, implicate specific dysfunctional processes and suggest new directions for research in the quest to find rationally based treatments and preventative strategies for some of the most common and disabling psychiatric disorders.

Dissertation submitted to the Faculty of Science, University of the Witswatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. May 2015 in Johannesburg / Claudins are a large gene family found in all vertebrates. Claudins encode tetraspan membrane proteins, involved in the structure and function of the tight junctions. This association of cells leads to the formation of the epithelial sheet which is involved in many functions such as embryo morphogenesis. The NCBI database shows 27 claudins identified in humans; 23 in mice and 17 in Xenopus. This suggests that an increase in gene family size may correlate with the evolution of more complex vertebrates. In this study claudins from the most basal extant vertebrate, the sea lamprey, were investigated. RNA used to build up the lamprey genome by Jeramiah Smith (Smith et al., 2012), was used for lamprey claudin sequences. Additionally this study identified 2 more claudins (Cldn B & Cldn F). The phylogenetic tree constructed using claudins from higher vertebrate model organisms and the invertebrates Ciona intestinalis and Drosophila melanogaster; showed that lamprey claudins are evolutionarily more distantly related to their orthologs in higher vertebrates. Furthermore some claudins in lamprey did not show any homologs in higher vertebrates and vice versa, indicating the emergence of novel members in higher vertebrates. However lamprey Cldn A was found to be homologous to CLDN 3 in higher vertebrates. This is interesting since CLDN 3 is involved in the development of two vertebrate specific traits; one of which is the ear placode. Thus Cldn A (renamed Cldn 3B), was made a focus of this study. RNA in situ hybridization using probes designed from individual UTRs showed localised expression of Cldn 3B in the ear placode, pharyngeal pouch, pericardial cavity and the fin fold whereas Cldn B (renamed Cldn 8B) was mostly expressed in the pharyngeal pouch and ear placode much like its orthologs in higher vertebrates. Knockout experiments showed that Cldn 3B is involved in sealing and expansion of the ear placode and pharyngeal arches during development whereas Cldn 8B is involved in determining ear placode development. Thus claudins are seen to be heavily involved in the morphology of vertebrate specific traits therefore an expansion in this gene family would affect the complexity of vertebrates during evolution.

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. / FOXP2 is the gene product of the so-called “language gene” and is the only protein known to be involved in a monogenetic autosomally inherited language disorder. This disorder has been termed Speech-Language Disorder 1. In addition to the role it plays in language, FOXP2 is thought to be involved in cancer, autism and schizophrenia. FOXP2 is a member of the P subfamily of FOX transcription factors, the DNA-binding domain of which is the forkhead domain. The aim of this work was to investigate the binding mechanism of the FOXP2 forkhead domain and various DNA sequences in order to assess affinity and specificity. It was shown by surface plasmon resonance that the FOXP2 forkhead domain can recognise a variety of DNA sequences, including a novel sequence, identified by systematic evolution of ligands by exponential enrichment. This motif has not previously been reported as a binding motif of the FOXP2 forkhead domain. Kinetic analysis by surface plasmon resonance showed that the novel sequence, as well as other published cognate sequences, each binds to the FOXP2 forkhead domain with different rates and affinities. Molecular docking of the DNA sequences to the FOXP2 forkhead domain revealed that electrostatic interactions between positively charged amino acids and the DNA backbone, as well as basespecific interactions between His554 and the DNA appear to be key in determining rates and affinities of binding interactions of the FOXP2 forkhead domain and DNA. Based on these findings, three types of DNA-binding are proposed for the FOXP2 forkhead domain. These types are: low affinity, nonfunctional binding; moderate affinity, non-functional binding and high affinity, functional binding. It is probable that each type of binding serves to control the vii spatial location of the protein within the nucleus, as well as the local concentration of protein. The proposed mechanism of binding for the forkhead domain of FOXP2 may have a future impact on the binding and function of full length FOXP2.

Thesis (Ph. D.), Faculty of Health Sciences, University of the Witwatersrand, 2009 / With the high prevalence and high mortality rate of cancer in the global community, it is increasingly essential to accelerate our understanding of the disease, to identify new genetic targets for therapy, and to pursue avenues for improving on the therapies in development and in current use. The aim of this study is to identify cell cycle-related genes whose expression is influenced by the chemotherapeutic drugs curcumin, SAHA, lycopene and thalidomide in breast and colon cancer and normal cell lines. These drugs are currently not in clinical use for cancer in South Africa, and while there have been investigative studies of these chemotherapeutic agents, this study aims to identify the specific genes that are influenced by the drugs. The result of this is that several genes that were not previously documented as targets of these drugs are highlighted. The cell cycle pathway is the area of focus as loss of regulation in the cell cycle is one of the important factors involved in promoting cancer initiation and progression. In the first instance, flow cytometry was used to identify optimal drug concentrations relative to the cell cycle stages. Following this, alterations in gene expression were assessed using a PCR-based differential display after each drug treatment. Subsequently, a more focussed approach was taken in a PCR-array analysis of panels of cell cyclerelated genes. A subset of genes is identified that is implicated in oncogenic transformation in breast cancer. This has the potential to inhibit the genetic pathways involved in breast malignancy by providing targets that perhaps may not be manipulated in current therapies. The gene expression studies here suggest that lycopene and thalidomide function in inhibiting this transformation, and play significant roles in suppressing the oncogenic state of breast cancer. Curcumin and SAHA also exhibit important functions in inhibiting tumourigenesis in colon cancer. While the results propose that the drugs have clear roles in inhibiting breast and colon cancer, they are also implicated in promoting cancer. This research has defined the genes that must be carefully monitored during drug administering as they may promote these and other cancers. The availability of these results to researchers will aid in selecting the criteria for assessing the success rate of these drugs.

A pesquisa teve como objetivo avaliar a possibilidade de obtenção de segregantes transgressivos precoces e produtivos através de 12 cruzamentos envolvendo 6 parentais exóticos (Pella, Williams, Century, Maple Presto, Maple Amber e Maccall) com dois parentais adaptados (BR80-6989 e Primavera). Foram estudadas as 12 progênies F 2 em 12 experimentos delineados em blocos casualizados com quatro repetições. Foram avaliados os seguintes caracteres: número de dias para início de florescimento, número de dias para maturidade, altura da planta no florescimento, altura da planta na maturidade, acamamento, valor agronômico, produtividade de planta individual e produtividade de parcela. Os resultados permitiram as seguintes conclusões: a) os parentais possuem características complementares de interesse para o melhoramento; b) houve uma grande variação de heterose e heterobeltiose porém nem sempre as maiores médias estavam associadas as maiores variâncias; c) a avaliação das progênies F2 através da frequência de genótipos superiores, demonstrou a existência de segregantes transgressivos que reuniam simultaneamente a precocidade, altura adequada a colheita mecanizada e produtividade / This research aimed to evaluate the potential of crosses between exotic and adapted parents for development of transgressive segregates having high levels of earliness and seed yielding. Six exotics parents (Century, Maple Amber, Maple Presto, McCall, Pella and Williams) were chosen based on their earliness and seed yielding; such parents exhibited the disadvantage of to be very sensitives to photoperiodic variations. Two adapted parents (BR 80-6989 and Primavera) were chosen based on their small sensitivity to variation and high seed yielding. However, they exhibited lower earliness than necessary. In 1985, handled hibridizations were made to obtaining 12 crosses (six exotic x two adapted). Natural selfing originated the F 2, that were evaluated at 12 experiments establishe in randomized block design with four replications. The results allowed the following conclusions: a) the parents were significantly different them selves; consequently, complementary traits were combined in all crosses; b) a large heterosis and heterobeltiosis variation were found for all traits evaluated, however, the higher means were not always related to higher variances; c) the combination of high earliness from exotic parents with long-juvenile trait from adapted parents was a promissing strategy for development of transgressive segregates appropriated to rotation crop with sugarcane

三十五肽重複蛋白是線粒體和葉綠體中與RNA轉錄后加工相關的一個家族蛋白。PPR蛋白特異性的和RNA結合，在RNA編輯，剪接，形成成熟的5’端以及蛋白質翻譯等方面起著重要作用。由於PPR蛋白家族很龐大，目前很多PPR蛋白的功能還未知。在這個論文里，我們對兩個三十五肽重複蛋白 PPR1703和 PPR87進行了分子水平上的功能分析。 / PPR1703基因編碼一個含有17個重複結構的P型PPR蛋白。GFP螢光定位的結果顯示，這個蛋白定位於線粒體。爲了研究這個蛋白的功能，我們從UniformMu突變群中分離了ppr1703-1突變體。在ppr1703-1突變體中，PPR1703基因的表達完全喪失。這個基因的突變抑制了胚和胚乳的發育，導致空果皮（emp）表型。這個基因的突變導致部份花粉的發育不良，從而破壞了3:1的分離比。通過比較野生型和突變體線粒體基因的表達發現，nad7第二個內含子的剪接功能在突變體中幾乎喪失。隨後的研究發現，PPR1703基因缺失突變體無法組裝線粒體複合物一，喪失線粒體複合物一活性進而誘導了與交替氧化途徑相關的基因的表達。我們的實驗結果證明，PPR1703基因負責線粒體基因nad7第二個內含子的剪接，並且影響了玉米胚和胚乳的發育。 / PPR87基因編碼一個定位於線粒體的E型PPR蛋白。在PPR87基因缺失型突變體中，有3個線粒體編輯位點的功能消失，他們分別是：NADH脫氫酶1的740編輯位點，NADH脫氫酶7的739編輯位點和膜定位和轉運蛋白的139位點。還有3個編輯位點的功能減低，他們分別是：NADH脫氫酶4L的110位點，膜定位和轉運蛋白的138位點和细胞色素C成熟蛋白亚基的1492位點。在PPR1703突變體中，胚和胚乳的發育受到抑制。我們的工作證明PPR87基因負責多個線粒體RNA位點的編輯，這個基因的突變破壞了線粒體的正常功能，進而影響了種子發育。 / Pentatricopeptide repeat proteins (PPR) are a large family of proteins in land plants with functions implicated in RNA processing in mitochondria and chloroplasts. Each PPR protein is believed to recognize and bind specifically its target sequence in the transcript, performing the function of RNA editing, splicing, 5’ and 3’ end maturation and protein translation regulation. Because of the family size, functions of many PPRs are unknown. In this thesis, we demonstrate the molecular characterization of PPR1703 and PPR87 in maize. / PPR1703 is a P subclass PPR protein, containing 17 PPR repeats. PPR1703-GFP analysis indicated that PPR1703 is targeted to the mitochondrion, which is consistent with bioinformatics prediction. To reveal its function, we isolated a Mutator (Mu) insertional mutant from the UniformMu population in maize, named ppr1703-1. The insertion abolishes the expression of PPR1703, constituting a null allele. The mutant shows severely arrested embryo and endosperm development, causing an empty pericarp phenotype. Its pollen development is partially affected, causing a distortion from 3:1 segregation. Comparative study of the entire mitochondrial transcripts between the WT and the mutant revealed that the nad7 intron 2 splicing is dramatically reduced in the mutant. This deficiency is accompanied by reduced mitochondrial complex I assembly and its activity. These results indicate that PPR1703 is required for mitochondrial nad7 intron 2 splicing and embryogenesis and endosperm development in maize. / PPR87 is an E subclass of the PLS subfamily PPR protein, which was showed to be targeted to mitochondria as well. The Mu-insertional mutant showed embryo and endosperm development arrest at coleoptilar stage. Analysis of the mitochondrial transcripts revealed that loss function of the PPR87 abolishes the C-to-U editing of multiple sites including nad1-740, nad7-739 and mttB(orfX)-139; and also significantly decreases the editing in nad4L-110, mttB(orfX)-138 and ccmFn-1492. These results indicate that PPR87 functions in the C-to-U editing of multiple sites in several transcripts and such editing is essential to the mitochondrial function, thus the embryogenesis and endosperm development in maize. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Yang, Yanzhuo. / Thesis (Ph.D.) Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 79-98). / Abstracts also in Chinese. / Yang, Yanzhuo.

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