The level to which genes are expressed depends on the rate at which the mRNA is generated, and the rate at which it is utilised and destroyed. Almost all eukaryotic mRNAs contain a stretch of adenosine nucleotides known as the poly(A) tail. The removal of the polyA tail from an mRNA, a process called deadenylation, is an important mechanism of gene expression regulation. It is the first step in the decay of the transcript, and is also linked to repression of translation. Deadenylation is predominantly catalysed by a conserved multi-protein complex called Ccr4-Not. While the poly(A) tail is a feature of almost all mRNAs, cells control the rate at which each undergoes decay by the precise targeting of Ccr4-Not in both a gene-dependent and a context-dependent fashion. Substrate-selective deadenylation is therefore a central biochemical process to the control of gene expression. It plays a pivotal role in most cellular processes including differentiation, cell cycle control and adaptation to environmental change. The inflammatory response and embryogenesis are two systems in which deadenylation has been well studied. The subject of this dissertation is the biochemical mechanisms by which mRNAs are selected for deadenylation by Ccr4-Not. Despite its importance, intact Ccr4-Not has not previously been obtained in sufficient quantity and purity for rigorous biochemical and structural analysis. Here I present the purification of recombinant Ccr4-Not. An experimental system was devised to quantify the rate and pattern of the deadenylation reaction that it catalyses in vitro. Two models of Ccr4-Not regulation were characterised in detail: the recruitment of Ccr4-Not by RNA-binding adaptor proteins, and the effect of the protein Pab1, which binds to the poly(A) tail. These have yielded insight into the features of the proteins and RNA sequences that are critical to deadenylation. In addition, a structural study of the Ccr4-Not complex was performed using electron cryomicroscopy and single-particle analysis.

Alzheimer's disease is a progressive neurodegenerative disorder of the central nervous system. One pathological characteristic is excessive neuronal loss in specific regions of the brain. Among the areas most severely affected are the basal forebrain cholinergic neurons and their projection regions, the hippocampus and cortex. Neurotrophic factors, particularly the neurotrophins nerve growth factor and brain-derived neurotrophic factor, play an important role in the development, regulation and survival of basal forebrain cholinergic neurons. Furthermore, brain-derived neurotrophic factor regulates the function of hippocampal and cortical neurons. Neurotrophins are synthesized in hippocampus and cortex and retrogradely transported to the basal forebrain. Decreased levels of neurotrophic factors are suspected to be involved in the neurodegenerative changes observed in Alzheimer's disease. We examined autopsied parietal cortex, hippocampus and nucleus basalis of Meynert samples from age- and gender-matched Alzheimer's diseased and neurologically non-impaired individuals using the quantitative technique of competitive RT-PCR. We also examined parietal cortex samples by Western blotting. We demonstrate a 3.4-fold decrease in brain-derived neurotrophic factor mRNA levels in the parietal cortex of patients with Alzheimer's disease compared to controls (p < 0.004) but fail to observe changes in BDNF protein levels in that brain region. We also demonstrate, for the first time, BDNF mRNA in the nucleus basalis of Meynert and report an age-related decline in the levels of BDNF mRNA in both control and AD samples. Using the competitive RT-PCR technique we fail to observe differences in BDNF mRNA levels in the hippocampus between AD and control subjects, conflicting with previous in situ hybridization studies and RNase protection assays. A decrease in brain-derived neurotrophic factor synthesis could have detrimental effects on hippocampal, cortical and basal forebrain cholinergic neurons and may account for their selective vulnerability in Alzheimer's disease. / Thesis / Master of Science (MS)

Epilobium hirsutum L. (Onagraceae) is a flowering, tall and perennial plant and native to Eurasia. It shows analgesic, anti-microbial and anti-proliferative activity, and it is used in our country as an alternative medicine. The pharmacological effect of Epilobium hirsutum L. could be explained by the presence of polyphenolics including steroids, tannins and flavonoids in the aerial parts. Viscum album L. (Loranthaceae) is a shrub that grows as an epiphyte on the branches of deciduous trees. It involves in the enhancement of macrophage phagocytic and cytotoxic mediated abilities as well as the strengthening the immune system. CYP24A1 and CYP27B1 are members of cytochrome P450 superfamily and the most important enzymes involved in the metabolism of vitamin D3. CYP27B1 and CYP24A1 are mitochondrial enzymes and also known as 25-hydroxyvitamin D3 1alpha-hydroxylase and 24-hydroxylase, respectively. CYP24A1 involves in 24-hydroxylation of 25-OH-D3 and 1,25-(OH)2D3 which is required for the catabolism of vitamin D3 compounds while CYP27B1 involves in 1&alpha / -hydroxylation of 25-OH-D3 into 1,25-(OH)2D3. In this study, in vivo effects of Epilobium hirsutum and Viscum album (subspecies growing on pine-trees-subsp. austriacum (Wiesb.) Vollmann) on rat liver CYP24A1 and CYP27B1 mRNA and protein expressions were investigated. To achieve this goal, 37.5 mg water extract of Epilobium hirsutum L./kg body weight/day was intraperitoneally injected to male rats for 9 days. To study the effect of Viscum album L., 10 mg water extract of Viscum album L./kg body weight/day was injected with the same conditions. After decapitation, livers were removed and S1.5 fractions were prepared. Effects of Epilobium hirsutum L. and Viscum album L. on rat liver mRNA and protein expressions were analyzed by qRT-PCR and western blotting, respectively. Epilobium hirsutum L. extract caused 31% and 18% decrease in rat liver CYP24A1 (p&lt / 0.0001) and CYP27B1 (p&lt / 0.05) protein expressions, respectively. The effect of Epilobium hirsutum L. on mRNA expression of CYP24A1 could not be observed, because CYP24A1 mRNA was almost undetectable in liver. Injection of Epilobium hirsutum L. to rats caused 2.7 fold increase in mRNA expression of CYP27B1 with respect to controls and normalized with GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) expression as an internal reference (p&lt / 0.005). Viscum album L. caused 17% decrease in CYP24A1 protein expression (p&lt / 0.05). When rats injected with plant extract of Viscum album L., 18% decrease in CYP27B1 protein expression was observed (p&lt / 0.05). The effect of Viscum album L. on mRNA expression of CYP24A1 could not be observed since CYP24A1 mRNA was almost undetectable in liver. Injection of Viscum album L. to rats caused 3.8 fold increase in mRNA expression of CYP27B1 with respect to controls and normalized with GAPDH (Glyceraldehyde 3-phosphate dehydrogenase) expression as an internal reference (p&lt / 0.005). In conclusion, vitamin D3 metabolism may be affected by medicinal plants Epilobium hirsutum L. and Viscum album L. due to the changes in mRNA and protein expressions of CYP24A1 and CYP27B1 enzymes.

Epilobium hirsutum L. (Onagraceae), a medicinal plant known as hairy willow herb, has been used by people all around the world for treatment or prevention of inflammation, adenoma, rectal bleeding, menstrual disorders, constipates, and prostate. It contains polyphenolics including steroids, tannins such as gallic, ellagic, and p-coumaric acids and flavonoids such as myricetin, isomyricetin, and quercetin. Polyphenols have been known for their multiple biological health benefits, including antioxidant activities. Viscum album L. (Loranthaceae), a species of mistletoe, contains lectins, polypeptides, mucilage, sugar alcohols, flavonoids, lignans, triterpenes, and phenylallyl alcohols. The leaves and twigs of Viscum album L., taken as tea, have been traditionally used for hypertension, stomachache, diarrhea, diabetes, dysuria and also as analgesic and cardiotonic agent in Anatolia, Turkey. In addition, in Europe, sterile extracts of Viscum album L. are among the most common herbal extracts applied in cancer treatment and have been used as prescription drugs, while in US, considered as dietary supplement. Flavin-containing monooxygenases are FAD-containing phase I enzymes responsible for the oxidation of wide-range of nucleophilic nitrogen, sulfur, phosphorus, and selenium heteroatom-containing drugs such as tamoxifen, v methimazole and imipramine, pesticides, neurotoxins, and other chemicals using NADPH as cofactor. The aim of this study was to determine the in vivo effects of Epilobium hirsutum L. and Viscum album L. (subspecies growing on pine trees-subsp. austriacum (Wiesb.) Vollmann) on FMO activity, mRNA and protein expressions in rat liver. The water extracts of Epilobium hirsutum L. (37.5 mg/kg body weight) and Viscum album L. (10 mg/kg body weight) were injected intraperitonally (i.p) into Wistar albino rats for 9 consecutive days. Following the decapitation, the livers were removed and microsomal fractions were prepared by differential centrifugation. Rat liver microsomal FMO activity using methimazole as substrate, mRNA expression by quantitative Real-Time PCR, and protein expression by Western Blot were determined. The results showed that water extract of Epilobium hirsutum L. has no significant effect on FMO activity / however, it decreased significantly (p&lt / 0.05) FMO3 protein and mRNA expression 27.71% and 1.41 fold, respectively, compared as controls. Water extract of Viscum album L. decreased mRNA (2.56 fold), and protein expressions (27.66%) as well as enzyme activity (19%) of FMO with respect to controls. In conclusion, our current data suggest that the metabolism of xenobiotics including drug molecules by FMO-catalyzed reactions may be altered due to the changes in FMO expression and activity by medicinal plants Epilobium hirsutum L. and Viscum album L.

Oocyte development in Xenopus laevis spans six morphologically distinct stages (stage I-VI), and is associated with a decrease in protein O-GlcNAc levels. As a first step in elucidating the role of O-GlcNAc in developing oocytes, initial efforts were focused on isolation and identification of fifteen modified proteins that decrease during oocyte development. Stage I oocytes due to their high amounts of these proteins, were used as starting material for purification. Multiple affinity and specific antibody based purification technique were initially used in an attempt to enrich the O-GlcNAc proteins. Due to the unique properties of the proteins ultimately identified, these techniques were unable to provide sufficient material for sequencing. However, differential centrifugation coupled with 2D-gel electrophoresis was highly successful. The majority of isolated proteins were strongly basic in nature with pIs 8-10. Coomassie stained bands from 2D-analysis were trypsin digested, and peptides were sequenced by mass spectroscopy (Finnigan LCQ). Mass data were interpreted by Bioworks software, and protein sequences were compared to multiple protein databases. Initially, six proteins were identified as Thesaurin a (42Sp50), cytoplasmic mRNA binding protein p54, y-box homolog, Xp 54 (ATP dependent RNA helicase p54), Vg1 RNA binding protein variant A, Zygote arrest 1(Zar1) and Poly (A) binding protein (PABP). Thesaurin a, the main component of 42S particle of previtellogenic oocytes (stages I-III) is involved in tRNA storage and possess low tRNA transfer activity; y-box factor homolog and Xp54 are present in oocyte mRNA storage ribonucleoprotein particles; Vg1 RBP variant A associates mVg1 RNA to microtubules in order to translocate to the vegetal cortex; Zar1 is involved in oocyte-to-embryo transition; and PABP initiates mRNA translation. This study is the first to characterize these oocyte specific proteins as O-GlcNAc modified proteins. Overall, the presence of several O-GlcNAc proteins in oocytes, the reduction in their levels/ O-GlcNAc levels, and the variation in maturation time in the presence of HBP-flux modulators in developing oocyte indicates O-GlcNAc may play important roles in metabolism, cell growth and cell division of X. laevis oocytes. Therefore, identifying the remainder of these proteins and elucidating the O-GlcNAc role in their function is a worthwhile pursuit.

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