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The Cellular and Molecular Properties of Flavinoids in Prostate Cancer ChemopreventionHaddad, Ahmed Qais 31 July 2008 (has links)
Flavonoids are a large class of dietary polyphenols that have emerged as candidate agents for chemoprevention in prostate cancer. Despite the large number of known flavonoids (over 9000), only a few have been studied in prostate cancer to date. The work presented in this thesis describes the identification of novel anti-proliferative flavonoids, their molecular effects on cell cycle and related proliferation and survival pathways, and their chemopreventive properties in a murine model of prostate carcinogenesis.
We identified several novel flavonoids with potent anti-proliferative effects in human prostate cancer cells in vitro. Non-prostate cell lines were generally resistant to the effect of these flavonoids. Two of the most potent flavonoids identified, 2,2-dihydroxychalcone (DHC) and fisetin, induced S and G2 phase cell cycle arrest in LNCaP and PC3 prostate cancer cells. Gene expression studies employing oligonucleotide microarray demonstrated profound down-regulation in gene expression of 75 key cell cycle (predominantly G2 and M phase) genes by DHC and fisetin, and the enhanced expression of 50 stress-response genes with important roles in cell proliferation and survival. DHC and fisetin induced apoptosis, but not accelerated senescence, in prostate cancer cells.
The chemopreventive effect of 4 flavonoids identified from the in vitro studies was examined in an autochthonous murine model of prostate cancer (TRAMP). Mice were administered diets supplemented with 1% DHC, 1% fisetin or a combination of flavonoids (0.25% DHC, 0.25% fisetin, 0.25% quercetin, 0.25% luteolin) for 32 weeks. We demonstrated a significant reduction in genitourinary weight, and a reduction in prostate cancer grade in mice administered 1% DHC and combination diets. Flavonoid supplementation was, however, associated with gastrointestinal toxicity in some mice. Liquid chromatography-mass spectrometry demonstrated the accumulation of high levels of flavonoid in the prostates of TRAMP mice. These findings lay the foundation for further studies of flavonoids in clinical chemoprevention trials.
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The Plant Transcriptome and Its Response to Envrionmental StimuliWilkins, Olivia 02 September 2010 (has links)
The relationship between an organism’s genome, developmental stage, and environment is complex. The aim of the research presented herein was to provide experimental evidence to contribute to the annotation of the P. trichocarpa genome and to test two major hypotheses addressing the interaction between drought and time of day in A. thaliana and in two hybrid Populus clones. In order to generate data to address these aims, three separate experiments were undertaken.
First, all members of the R2R3-MYB family of transcription factors in the P. trichocarpa genome were characterised by phylogenetic analysis and their transcript accumulation patterns across a range of tissues and organs were assessed using whole genome poplar microarrays. Results of this analysis indicated that expansion and diversification of the R2R3-MYB family may have contributed to phenotypic innovation in the Populus lineage.
Second, drought-responsive transcriptome adjustments of two hybrid poplar clones, DN34 (P. deltoides X P. nigra) and NM6 (P. nigra X P. maxiomowiczii) were assessed for time-of-day and genotype dependent patterns. For each genotype, each of four time points was characterised by discrete sets of drought-responsive genes. Furthermore, while a number of genes were identified that were responsive to drought in both genotypes, a much larger number of genotype-dependent, drought-responsive transcriptome changes were detected.
Finally, the drought-responsive transcriptome adjustments A. thaliana plants were assessed for time-of-day dependent accumulation patterns. Results of this analysis indicate that time-of-day-dependent differences in the drought response were manifest as changes of different magnitudes for a conserved set of genes across the four time points measured. These results emphasise the complex interplay of a plant’s genome, developmental stage, and environment in shaping the observed transcriptome.
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Aberrant epigenetics in the molecular pathogenesis of human acute myeloid leukemiaScott, Stuart Alexander 30 May 2005
Promoter hypermethylation mediated gene silencing is a frequent epigenetic finding in many cancers that affects genes known to have important roles in several aspects of cell biology. Hematological malignancies have been reported to harbor multiple genes aberrantly silenced by promoter hypermethylation and as a result, cytosine analogs known to inhibit the DNA methylation machinery are currently being evaluated in clinical trials. As such, the general goal of this thesis was to identify genes silenced by promoter hypermethylation in human acute myeloid leukemia (AML) and to study the mechanism of promoter hypermethylation mediated gene silencing. Interestingly, the cyclin dependent kinase inhibitor p15 was found to be methylated at a high frequency in AML patients and cell lines in association with a lack of detectable p15 mRNA. Treatment with the cytosine analog 5-Aza-2-deoxycytidine (5-Aza-dC) in vitro resulted in promoter demethylation and p15 mRNA re-expression, which was associated with a release of a transcriptionally repressive complex at the p15 promoter. Importantly, 5-Aza-dC treatment also reversed specific histone amino-terminal modifications at the p15 promoter which are normally associated with transcriptionally inactive chromatin regions, implicating chromatin remodeling in promoter hypermethylation mediated gene silencing. The recently discovered DNA methylation inhibitor, zebularine considered more stable than 5-Aza-dC was also able to reconstitute p15 mRNA in vitro in association with promoter demethylation, regional enrichment of histone acetylation, and growth inhibition.
To identify novel genes silenced by promoter hypermethylation in AML, cDNA microarray analysis was employed following in vitro pharmacological inhibition of DNA methylation and histone deacetylation. Of note, four genes from the metallothionein family of cysteine rich small molecules were consistently upregulated following drug treatment and further evaluation identified the gene MT1H to be hypermethylated at a high frequency in AML patients and cell lines. Taken together, the data suggests that aberrant promoter hypermethylation mediated gene silencing occurs in multiple genes from different gene families during the molecular pathogenesis of human AML. Furthermore, the mechanism of promoter methylation mediated transcriptional silencing acts in concert with specific histone modifications which, importantly, can be reversed by treatment with pharmacological inhibitors of DNA methylation.
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Functional Characterization of the Arginine Transaminase Pathway in Pseudomonas aeruginosa PAO1Yang, Zhe 27 November 2007 (has links)
Arginine utilization in Pseudomonas aeruginosa with multiple catabolic pathways represents one of the best examples of metabolic versatility of this organism. To identify genes of this complex arginine network, we employed DNA microarray to analyze the transcriptional profiles of this organism in response to L-arginine. While most genes in arginine uptake, regulation and metabolism have been identified as members of the ArgR regulon in our previous study, eighteen putative transcriptional units of 38 genes including the two known genes of the arginine dehydrogenase (ADH) pathway, kauB and gbuA, were found inducible by exogenous L-arginine but independent of ArgR. The potential physiological functions of those candidate genes in L-arginine utilization were studied by growth phenotype analysis in knockout mutants. The insertion mutation of aruH encoding an L-arginine:pyruvate transaminase abolished the capability to grow on L-arginine of an aruF mutant devoid of a functional arginine succinyltransferase (AST) pathway, the major route of arginine utilization. The aruH gene was cloned and over-expressed in E. coli. Taking L-arginine and pyruvate as the substrates, the reaction products of recombinant enzyme were identified by MS and HPLC as 2-ketoarginine and L-alanine. Lineweaver-Burk plots of the data revealed a series of parallel lines characteristic of ping-pong kinetics mechanism, and the apparent Km and catalytic efficiency (Kcat/Km) were 1.6 ± 0.1 mM and 24.1 mM-1 s-1 for pyruvate and 13.9 ± 0.8 mM and 2.8 mM-1 s-1 for L-arginine. Recombinant AruH showed an optimal pH at 9.0 and substrate specificity with an order of preference being Arg > Lys > Met > Leu > Orn > Gln. These data led us to propose the arginine transaminase (ATA) pathway that removes the α-amino group of L-arginine via transamination instead of oxidative deamination by dehydrogenase or oxidase as originally proposed. In the same genetic locus, we also identified a two-component system, AruRS, for the regulation of arginine-responsive induction of the ATA pathway. Our latest DNA microarray experiments under D-arginine conditions also revealed PA3863 as the candidate gene encoding D-arginine dehydrogenase which might lead to the recognition of a wider network of arginine metabolism than we previously recognized.
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Bartonella Bacilliformis: Understanding The Underlying Causes Of Verruga Peruana Formation During Carrion’s DiseaseKohlhorst, Drew Eric 29 April 2008 (has links)
Bartonella, a group of Gram negative facultative intracellular bacteria, are known to cause diseases, such as Cat Scratch Disease, Trench Fever and Carrion’s Disease, that involve angiogenesis during the infective cycle. B. bacilliformis, the etiological agent of Carrion’s Disease, causes a bi-phasic infection resulting in the formation of blood-filled angiogenic proliferative cutaneous nodules called verruga peruana. The work presented here was undertaken to characterize the mechanism by which these nodules are produced. Previous work in our laboratory suggested that the Bartonella henselae genome contains a homologue to the virB operon, a set of genes coding for a Type IV Secretion System (TFSS) that has been implicated in the pathogenesis of other α-2-proteobacteria. We identified virB operons in two additional Bartonella pathogens, B. quintana and B. clarridgeiae. No corresponding operon sequences were detected in B. bacilliformis DNA, however. This finding suggests that virB gene products are not required for verruga peruana formation. To continue our search for factors involved in B. bacilliformis-induced angiogenesis, we conducted a microarray analysis of differential gene expression in infected and uninfected endothelial cells. The results suggest similarities between later stage (36 hours) B. bacilliformis infection and that of HHV-8, the causative agent of Kaposi’s Sarcoma, particularly in relation to the host immune response. Finally, our research focused on the secreted factors that B. bacilliformis produces during its host infective cycle. Our data suggest that the B. bacilliformis homologue to the molecular chaperone GroEL not only induces angiogenesis in endothelial cells, but also protects endothelial cell tubule from the degradation seen when these cells are in the presence of live B. bacilliformis. In summary, the induction of verruga peruana nodules via B. bacilliformis may be the result of multiple factors over the course of persistent infection. Early infection may cause vascular damage, which induces VEGF and hypoxia factors. As infection persists, bacterial secretion of a unique GroEL may result in continued angiogenesis and the ensuing activation of immune cells, producing a localized environment of continual incomplete angiogenesis in areas of cutaneous infection.
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Endothelial Cell Factors Involved in Bartonella Bacilliformis PathogenesisSoni, Tanushree 30 April 2009 (has links)
The genus Bartonella comprises emerging pathogens that are causative agents of a wide range of clinical manifestations such as cat scratch disease, bacillary angiomatosis, and Carrion’s disease. All species are transmitted by blood-sucking arthropods and infect erythrocytes and endothelial cells of hosts. Carrion’s disease is a bi-phasic infection caused by Bartonella bacilliformis which is characterized by hemolysis of infected erythrocytes followed by invasion of the vascular endothelium. This provokes pronounced cellular proliferation, angiogenesis and skin eruptions called verruga peruana. Endothelial cells are thought to be the primary niche wherein bacteria reside between inoculation and erythrocyte infection. This study aims to elucidate some of the endothelial factors involved during the verruga peruana phase of Carrion’s disease. In order to adhere to and invade human microvascular endothelial cells (HMEC-1), B. bacilliformis engages a family of cell receptors called integrins. We used anti-integrin antibodies to show that the primary integrin involved is the fibronectin receptor á5â1, although the vitronectin receptor áVâ3 also plays a minor role. We show B. bacilliformis invasion is also dependent on integrin ligands, fibronectin and vitronectin as antibodies against these proteins decreased invasion and attachment, whereas pre-treatment of the bacteria with these molecules enhanced infection of endothelial cells. Bacterial uptake requires various host cytoplasmic signaling pathways to work in tandem, and our study identified three mitogen activated protein kinases involved. Apart from MAPKs, phosphotidylinositol 3 kinase plays a role during invasion and cell survival. PI3K inhibitors blocked bacterial internalization and B. bacilliformis infected cells showed accelerated apoptosis. Lastly, microarray analysis was performed to study the gene expression profile of B. bacilliformis infected HMEC-1 cells. Numerous molecules of the integrin signaling pathways are involved, suggesting integrins as the major receptor recruited for the successful infection by B. bacilliformis. In summary this is the first study to demonstrate the role of integrins as B. bacilliformis receptors and integrin ligands as facilitators of infection. Gene expression analysis suggests the possibility that integrin mediated signaling pathways are the key modulators of cellular alterations during B. bacilliformis infection. This hypothesis is supported by the identification of some members of the integrin signaling pathway necessary for B. bacilliformis entry into endothelial cells.
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MTSR is a Dual Regulator that Controls Virulence Genes and Metabolic Functions in Addition to Metal Homeostasis in Group A StreptococcusToukoki, Chadia 01 December 2009 (has links)
Group A Streptococcus (GAS) is a common pathogen of the human skin and mucosal surfaces and is capable of producing a variety of diseases. This dissertation investigates the function of a metalloregulator named MtsR in GAS physiology and disease process. An mtsR mutant was constructed and analyzed. Consistent with MtsR role in iron uptake regulation, the mtsR mutant accumulates more iron (80 ± 22.5%) than the wild type strain. Inactivation of mtsR results in constitutive transcription of the sia (Streptococcal Iron Acquisition) operon, which is negatively regulated by iron in the parent strain. We identified the promoter that controls the expression of the sia operon (Pshr) and used it as a model to study MtsR interaction with DNA. Electrophoretic mobility gel shift assays (EMSAs) demonstrated that MtsR binds to the shr upstream region specifically and in an iron and manganese dependent manner. DNase I footprint analysis revealed that MtsR protects a 69 bp segment in Pshr that includes 2 inverted repeats, overlapping the core promoter elements. A global transcriptional analysis determined that MtsR modulates the expression of 64 genes, of which 44 were upregulated and 20 were downregulated in the mtsR mutant. MtsR controls genes with diverse functions including immune evasion, colonization, dissemination, metal homeostasis, nucleic acid and amino acid metabolism, and protein stability. MtsR functions as a dual regulator as it binds to the promoters of the repressed genes ska, aroE, and nrdF.2, as well as the upstream region of the positively regulated genes mga, emm49, and pyrF. A 16 bp MtsR-binding consensus region was identified in all of the promoters that are directly regulated by MtsR. In conclusion, we have demonstrated that MtsR is a global regulator in GAS that controls the expression of vital virulence factors and genes involved in metal transport, virulence and metabolic pathways.
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Influence of Estradiol on In vitro Maturation of Porcine OocytesLeavins, Nikki Lee 06 October 2011
<p><i>In vitro</i> production of embryos allows efficient management of herd genetics, reduction of disease impact, and if used in combination with other reproductive technologies it could aid in preserving the threatened genetic diversity of swine. <i>In vitro</i> maturation (IVM) is identified as a deficient step in porcine in vitro production (IVP) of embryo systems, which decreases the overall success of IVP. There are problems encountered in each step of IVP; chromosomal abnormalities and decreased cell numbers in blastocysts during <i>in vitro</i> culturing (IVC), and low monospermic fertilization rates during <i>in vitro</i> fertilization (IVF) may be a result of insufficient IVM. As an addition to maturation media, porcine follicular fluid (pFF) can affect IVM. Estrogen can be found in high concentrations in pFF; possibly contributing to the effects seen when pFF is added to IVM. The objective of this thesis was to investigate the effects of estrogen supplementation during IVM on IVP of porcine embryos.</p>
<p>The first objective was to evaluate the <i>in vitro</i> maturation rates of porcine oocytes in two maturation media: protein-free and 10% pFF supplemented. Nuclear maturation of oocytes was evaluated using Lamin/Dapi staining of oocytes matured in protein-free and 10% pFF maturation media to ensure the efficiency of the protein-free media. Protein-free and 10% pFF media mature oocytes at similar rates (91% and 89% respectively).</p>
<p>The transcripts within the oocyte can be altered based on the <i>in vitro</i> maturation environment, so the second objective was to observe the expression of four chosen maternal effect genes: Basonuclin-1 (<i>BNC1</i>), Nucleoplasmin 2 (<i>NPM2</i>), Zygote arrest 1 (<i>ZAR1</i>), and Tripartite-motif protein-24 (<i>TRIM24</i>), using oocytes matured in 50 ng/ml, 100 ng/ml, or 1000 ng/ml of estradiol 17-β (E<sub>2</sub>), 10% pFF, or protein-free maturation media. Expression of maternal effect genes, was shown by the ΔCt (cycle threshold) values, obtained from the difference between the Ct values of the normalizing gene (<i>GAPDH</i>) and the genes of interest evaluated through QRT-PCR. Values of ΔCt were analyzed in place of fold change to avoid data manipulation. The ΔCt expression of <i>TRIM24</i> in 0 ng/ml E<sub>2</sub> maturation medium and the 10% pFF maturation medium were significantly different (p<0.05) from the non-matured control, the other maternal determinant genes did not differ in their expression under any treatment.</p>
<p>We hypothesized that estradiol's effects on IVM would be evident when analyzing cleavage and blastocyst formation rates. Cleavage and blastocyst formation rates were examined following <i>in vitro</i> fertilization of oocytes matured in 100 ng/ml E<sub>2</sub>, 10% pFF, or a protein-free maturation medium to investigate the effect of estradiol on IVP embryos. Cleavage rates for the E<sub>2</sub> (n= 252; 60.2%) or 10% pFF (n= 256; 55.7%) additions to the maturation media did not differ (p>0.05) when compared to the protein-free maturation media (n=264; 54.9%). Both 10% pFF and E<syb>2</sub> groups had significantly higher blastocyst formation rates (p≤0.05) than the protein-free maturation media (n=264; 3.5%), although no statistical difference was observed between the blastocyst formation rates of the 10% pFF (n=256; 12.4%) and E2 (n=252; 14.6%) groups.</o>
<p>As a final study, the global gene expression of oocytes matured in a control protein-free media and the protein-free media supplemented with 100 ng/ml E<sub>2</sub> or 10% pFF was investigated using microarray analysis. Genes were not differentially expressed among the matured groups with the outlined threshold values of -2 ≥ log2(fold change) ≥ 2, and adjusted p-value ≤0.05. A total of 16 differentially expressed genes between the non-matured and all matured groups exceeded this threshold. Of these genes, 6 are novel transcribed regions with evidence of being an embryonic EST, and 1 is a novel protein-coding gene. The other genes are FBJ murine osteosarcoma viral oncogene homolog (<i>FOS</i>), Vimentin (<i>VIM</i>), Capthesin C (<i>CTSC</i>), Selenium binding protein 1 (<i>SELENBP1</i>), Poly(A) binding protein cytoplasmic 1 (<i>PABPC1</i>), Tissue factor pathway inhibitor 2 (<i>TFPI2</i>), Cysteine-rich, angiogenic inducer 61 (<i>CYR61</i>), Acyl-CoA synthetase long-chain family member 6 (<i>ACSL6</i>), and Phospholipase A2 group VII (<i>PLA2G7</i>).</p>
<p>In conclusion, successful nuclear maturation of oocytes derived of prepubertal gilt abbatoire derived ovaries can be achieved without pFF or hormone supplementation. The expression of maternal determinant genes is not affected in a dose dependant manner, and removal of E<sub>2</sub> or supplementation of pFF during maturation may alter the expression of <i>TRIM24</i> from the non-matured control; where no other maternal effect gene changes through maturation. Estradiol has a similar effect as pFF during <i>in vitro</i> maturation of porcine oocytes as seen by cleavage and blastocyst formation rates. And media does not affect the global gene expression of porcine oocytes, though there is a temporal control of gene expression through maturation.</p>
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Analysis Of 3' / Utr Shortening Events In Breast CancerBaloglu, Onur 01 January 2013 (has links) (PDF)
Cancer is the collective term used to describe a diverse group of diseases that share certain hallmarks, which in turn enables the affected cells to sustain an uncontrolled cell growth. Despite the increasing efforts and advances in cancer therapies, cancers are still responsible for approximately 10% of all the deaths worldwide. Furthermore, the increase in the average human lifespan will further contribute to the cancer incidences. This brings the necessity to focus our efforts on early detection and effective diagnosis methods. With the advances in high-throughput genomics technologies, gene expression signatures have gained attention as a novel method in cancer diagnostics. These signatures are identified by simply comparing the expression levels of genes in tumor and control samples. Here, we propose an alternative method based on the probe expression level measurement of 3&rsquo / UTR of candidate genes. We chose breast cancer as a model and performed an in silico analysis on publicly available gene expression datasets of Affymetrix chips to analyse 3&rsquo / UTR shortening during breast cancer situation. Overall, our analysis suggests that shortening of 3&rsquo / UTR is a significant mechanism observed in breast cancer .
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The Cellular and Molecular Properties of Flavinoids in Prostate Cancer ChemopreventionHaddad, Ahmed Qais 31 July 2008 (has links)
Flavonoids are a large class of dietary polyphenols that have emerged as candidate agents for chemoprevention in prostate cancer. Despite the large number of known flavonoids (over 9000), only a few have been studied in prostate cancer to date. The work presented in this thesis describes the identification of novel anti-proliferative flavonoids, their molecular effects on cell cycle and related proliferation and survival pathways, and their chemopreventive properties in a murine model of prostate carcinogenesis.
We identified several novel flavonoids with potent anti-proliferative effects in human prostate cancer cells in vitro. Non-prostate cell lines were generally resistant to the effect of these flavonoids. Two of the most potent flavonoids identified, 2,2-dihydroxychalcone (DHC) and fisetin, induced S and G2 phase cell cycle arrest in LNCaP and PC3 prostate cancer cells. Gene expression studies employing oligonucleotide microarray demonstrated profound down-regulation in gene expression of 75 key cell cycle (predominantly G2 and M phase) genes by DHC and fisetin, and the enhanced expression of 50 stress-response genes with important roles in cell proliferation and survival. DHC and fisetin induced apoptosis, but not accelerated senescence, in prostate cancer cells.
The chemopreventive effect of 4 flavonoids identified from the in vitro studies was examined in an autochthonous murine model of prostate cancer (TRAMP). Mice were administered diets supplemented with 1% DHC, 1% fisetin or a combination of flavonoids (0.25% DHC, 0.25% fisetin, 0.25% quercetin, 0.25% luteolin) for 32 weeks. We demonstrated a significant reduction in genitourinary weight, and a reduction in prostate cancer grade in mice administered 1% DHC and combination diets. Flavonoid supplementation was, however, associated with gastrointestinal toxicity in some mice. Liquid chromatography-mass spectrometry demonstrated the accumulation of high levels of flavonoid in the prostates of TRAMP mice. These findings lay the foundation for further studies of flavonoids in clinical chemoprevention trials.
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