Thesis (Ph. D.)--University of Washington, 2000. / Vita. Includes bibliographical references (leaves 111-119).

abstract: Given the process of tumorigenesis, biological signaling pathways have become of interest in the field of oncology. Many of the regulatory mechanisms that are altered in cancer are directly related to signal transduction and cellular communication. Thus, identifying signaling pathways that have become deregulated may provide useful information to better understanding altered regulatory mechanisms within cancer. Many methods that have been created to measure the distinct activity of signaling pathways have relied strictly upon transcription profiles. With advancements in comparative genomic hybridization techniques, copy number data has become extremely useful in providing valuable information pertaining to the genomic landscape of cancer. The purpose of this thesis is to develop a methodology that incorporates both gene expression and copy number data to identify signaling pathways that have become deregulated in cancer. The central idea is that copy number data may significantly assist in identifying signaling pathway deregulation by justifying the aberrant activity being measured in gene expression profiles. This method was then applied to four different subtypes of breast cancer resulting in the identification of signaling pathways associated with distinct functionalities for each of the breast cancer subtypes. / Dissertation/Thesis / M.S. Computer Science 2011

abstract: Signaling cascades transduce signals received on the cell membrane to the nucleus. While noise filtering, ultra-sensitive switches, and signal amplification have all been shown to be features of such signaling cascades, it is not understood why cascades typically show three or four layers. Using singular perturbation theory, Michaelis-Menten type equations are derived for open enzymatic systems. When these equations are organized into a cascade, it is demonstrated that the output signal as a function of time becomes sigmoidal with the addition of more layers. Furthermore, it is shown that the activation time will speed up to a point, after which more layers become superfluous. It is shown that three layers create a reliable sigmoidal response progress curve from a wide variety of time-dependent signaling inputs arriving at the cell membrane, suggesting that natural selection may have favored signaling cascades as a parsimonious solution to the problem of generating switch-like behavior in a noisy environment. / Dissertation/Thesis / Ph.D. Applied Mathematics 2013

Orientador: Kleber Gomes Franchini / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas / Made available in DSpace on 2018-08-11T13:49:24Z (GMT). No. of bitstreams: 1 Clemente_CarolinaFernandaManfrediZambon_D.pdf: 14683053 bytes, checksum: 740572fd1e2c19884bc045a5fafe828f (MD5) Previous issue date: 2008 / Resumo: Doenças do coração cursam frequentemente com hipertrofia do miocárdio. Estímulos mecânicos e neuro-humorais são sinalizadores críticos para o crescimento hipertrófico dos cardiomiócitos nos vários processos patológicos. Neste contexto, estudos indicam que a quinase de adesão focal (FAK), uma proteína tirosino-quinase que participa dos mecanismos de sinalização por integrinas, é uma mediadora importante do crescimento hipertrófico do ventrículo esquerdo (VE). Este estudo teve como objetivo avaliar a influência da FAK na indução da hipertrofia e na deterioração do VE induzidas por sobrecarga pressórica crônica em camundongos através de estratégia de interferência por RNA. A coarctação da aorta em camundongos induziu a hipertrofia do VE acompanhada pelo aumento da expressão e atividade da FAK no miocárdio. A infusão de siRNA específico para FAK (siRNAFAK), via veia jugular, levou ao silenciamento gênico prolongado da FAK (~70%) no VE normal e também no hipertrófico. O knockdown da FAK foi confirmado nos miócitos e fibroblastos cardíacos provenientes do VE de camundongos. O silenciamento da FAK foi acompanhado tanto da prevenção como regressão da hipertrofia do VE. A função do VE foi preservada e a taxa de sobrevivência foi maior nos camundongos tratados com siRNAFAK, apesar da persistência da sobrecarga pressórica. Estes achados foram paralelos a atenuação do crescimento hipertrófico dos cardiomiócitos e da expressão do marcador de hipertrofia ß-MHC no VE sob sobrecarga pressórica. O silenciamento da FAK também atenuou o aumento da fibrose intersticial, conteúdo de colágeno e atividade da metaloproteinase-2 (MMP-2) no VE submetido ao estímulo mecânico. Em fibroblastos extraídos de corações hipertróficos, o silenciamento da FAK foi concomitante à diminuição da expressão de MMP-2. Assim, estes dados indicam que a sinalização mediada pela FAK é necessária não apenas para o desenvolvimento, mas também para sustentar a hipertrofia em resposta a sobrecarga pressórica crônica / Abstract: Hypertrophy is a critical event in the onset of failure in chronically overloaded hearts. Mechanical stress and neurohumoral factors signaling factors have been considered the main triggering stimuli for the installation of hypertrophy in cardiac myocytes in a variety of pathological process. In this context, focal adhesion kinase (FAK), a key protein of the integrin signaling pathway, has attracted particular attention as a mediator of hypertrophy induced by increased load. This study was performed to address the influence of FAK in the pathophysiology of cardiac hypertrophy and failure induced by chronic pressure overload in mice using RNA interference methodology. Aortic constriction in mice induced left ventricle (LV) hypertrophy and increased expression and phosphorylation of FAK. Intrajugular delivery of specific small interfering RNA induced prolonged FAK silencing (~70%) in both normal and hypertrophic LVs. Studies in cardiac myocytes and fibroblasts harvested from LVs confirmed the ability of the systemically administered specific small interfering RNA to silence FAK in both cell types. Myocardial FAK silencing was accompanied by prevention, as well as reversal, of load-induced left ventricular hypertrophy. The function of LVs was preserved and the survival rate was higher in banded mice treated with small interfering RNA targeted to FAK, despite the persistent pressure overload. Further analysis indicated attenuation of cardiac myocyte hypertrophic growth and of the rise in the expression of ß-myosin heavy chain in overloaded LVs. Moreover, FAK silencing was demonstrated to attenuate the rise in the fibrosis, collagen content, and activity of matrix metalloproteinase-2 in overloaded LVs, as well as the rise of matrix metalloproteinase-2 protein expression in fibroblasts harvested from overloaded LVs. This study indicate that FAK is necessary not only to the development but also to sustain LV hypertrophy in response to chronic pressure overload / Doutorado / Medicina Experimental / Doutor em Fisiopatologia Medica

Peptídeos sinais determinam o crescimento, desenvolvimento e defesa das plantas. RALF (Rapid Alkalinization Factor) é um peptídeo de sinalização ubíquo no reino vegetal e que está envolvido com a expansão celular. Os peptídeos RALF em arabidopsis estão organizados em uma família multigênica de 37 membros, alguns com expressão tecido-específica, outros expressos em toda a planta. Os mecanismos envolvidos na expansão celular são regulados por vários hormônios, entre os quais as citocininas. A relação existente entre os peptídeos RALF e os demais hormônios é pouco conhecida e um melhor entendimento dessa relação poderá auxiliar na modulação dos processos de crescimento e desenvolvimento vegetal por engenharia genética. O objetivo desse trabalho foi estudar a relação entre o peptídeo AtRALF e as citocininas, principalmente no que diz respeito aos efeitos de ambos no crescimento e desenvolvimento das raízes. Para isso, selecionou-se as isoformas AtRALF1, AtRALF19 e AtRALF34 que apresentam diferentes padrões de expressão. Os resultados sugerem que AtRALF19 e AtRALF34, ambas expressas em toda a planta, contribuem mais com a transdução de sinal da citocinina do que a isoforma AtRALF1, com padrão de expressão específico de raízes. Os peptídeos AtRALF19 e 34 reprimem parcialmente a expressão dos genes reguladores de resposta, ARRs tipo-A, que são reguladores negativos da via de sinalização de citocinina. / Peptides signals influence the growth, development and plant defense. RALF (Rapid Alkalinization Factor) is a ubiquitous signaling peptide in the plant kingdom and is involved in cell expansion. The RALF peptides in arabidopsis are organized in a multigene family of 37 members, some with tissue-specific expression, others expressed throughout the plant. The mechanisms involved in cellular growth are regulated by various hormones, including cytokinins. The relationship between RALF peptides and other hormones is poorly understood and a better understanding of this relationship assists in modulating the processes of plant growth and development. The aim of this work was to study the relationship of AtRALF peptide with cytokinins, especially with regard to the effects of both in the growth and development of roots. For this, we selected the AtRALF1, AtRALF19 and AtRALF34 isoforms that have different expression patterns. The results suggest that AtRALF19 and AtRALF34, both expressed throughout the plant, contribute more to cytokinin signal transduction than isoform AtRALF1, with specific expression pattern in roots. The AtRALF19 and 34 repressed the expression of type-A Arabidopsis Response Regulators (ARRs), whose products act as negative regulators of cytokinin signaling.

Abstract Cardiac hypertrophy and remodelling are mechanisms of adaptation to increased workload and acute injuries of the heart. In the long-term, these initially beneficial mechanisms become detrimental and ultimately lead to the development of heart failure. The molecular determinant of myocardial remodelling and heart failure is altered intracellular signal transduction and a modified gene expression pattern in the individual cardiomyocyte. This study was aimed at characterising the changes in mitogen-activated protein kinases (MAPKs) and their nuclear effector, GATA-4, and their functional significance and interaction in experimental models of increased cardiac workload and remodelling. To study the effects of increased cardiac workload on MAPKs and GATA-4, isolated perfused rat hearts were subjected to increased left ventricular wall stress and their activities were determined using western blot and gel mobility shift assays. Left ventricular wall stress rapidly activated the DNA binding of GATA-4, and this activation was abolished in the presence of endothelin-1 (ET-1) and angiotensin II receptor antagonists. Furthermore, the activation of GATA-4 DNA binding was significantly attenuated by p38 MAPK and extracellular signal regulated kinase (ERK) inhibition. To gain further insights into the role of p38 MAPK as a regulator of cardiac transcription factors, gene expression and remodelling, a gene transfer protocol of increased p38 MAPK activity was established. Direct adenovirus-mediated gene transfer of wild-type p38α and constitutively active upstream kinase mitogen-activated kinase kinase 3b (MKK3b) selectively increased p38 MAPK activity in the left ventricle, which was followed by up-regulation of cardiac gene expression, myocardial inflammation and fibrosis. Using a DNA microarray approach, the cardiac target genes of p38 MAPK were identified, including several cell division, inflammation and signal transduction-associated genes. Furthermore, p38 MAPK over-expression was found to increase the DNA binding activities of several transcription factors, including GATA-4. Finally, the functional role of p38 MAPK was determined using adenovirus-mediated gene transfer in an experimental model of myocardial infarction. Post-infarction remodelling was characterised by a sustained down-regulation of p38 MAPK, while rescue of p38 MAPK activity attenuated post-infarction remodelling through anti-apoptotic and angiogenic mechanisms. These results indicate that p38 MAPK is a key regulator of GATA-4 transcription factor and cardiac gene expression during left ventricular wall stress and remodelling. They demonstrate that p38 MAPK, being cardioprotective in the infarcted heart but promoting inflammation and fibrosis in the normal heart, has a unique dual role in the myocardium.

The transduction of stress signals in plants is known to involve complex hysiological responses. In D. salina a range of stresses results in hyperaccumulation of ft-carotene and an understanding of stress responses in this organism has important biotechnological implications. In this thesis an attempt was made to elucidate the physiological components involved and establish a role for pH in response to high light stress. In order to achieve this the effect of high light stress on photosynthesis and cell productivity was measured. Results showed that photosynthetic carbon assimilation, oxygen evolution and cellular productivity was initially inhibited by exposure to high light intensities, but this inhibition was transient and was overcome by a rapid increase in all three parameters. The response of the carbon pool intermediates was also investigated. It was shown that on exposure to high light ft-carotene declined but then showed a rapid increase after about 4 hours of exposure. It was also demonstrated that the initial loss of ft-carotene was due to loss of this pigment from the photosynthetic pigment bed and that the hyper-accumulation of ft-carotene was due to accumulation of ft-carotene in lipoidal globules located in the chloroplast stroma. It was further demonstrated that there was mass movement of carbon in the xanthophyll cycle shortly after exposure to high light. This was characterized by the de-epoxidation of violaxanthin to antheraxanthin with a further de-epoxidation to zeaxanthin, thereby decreasing the epoxidation state of the cycle. Furthermore, it was shown that there was relocation of carbon from violaxanthin to the plant growth regulator abscisic acid. It was also shown for the first time in D. salina that the production of ft-carotene and operation of the epoxidation state of the xanthophyll cycle has a periodicity which is established after exposure to successive cycles of a light regime. Chlorophyll fluorescence was used together with well established ammonia stress responses to acquire a general overview of energy dissipation from the photosynthetic pigment bed. In conjunction with an understanding of xanthophyll cycle operation during exposure to high light stress it has been possible to establish a relationship between chlorophyll florescence, xanthophyll cycle operation and intracellular pH. It was also shown using chlorophyll fluorescence that after 4 hour exposure to high light a maximum fluorescence peak could no longer be induced indicating a transition at about this point from a state of reversibility to commitment of the full stress response. Nuclear magnetic resonance was used to follow intracellular pH fluxes during exposure to high light. A novel technique was developed for studying photosynthetically active organisms in the dark using nuclear magnetic resonance. These results showed that on exposure to high light stress there is rapid acidification of the chloroplast stroma and to a lesser degree of the acidic vacuole. The pH of these compartments is re-established after about 4 hours which is co-incident with the onset of fl-carotene hyper-accumulation and the loss of the induction of the chlorophyll fluorescence peak indicating an intimate relationship for fl-carotene, chlorophyll fluorescence, xanthophyll cycle operation and pH. The results from this study allow for the proposal of a general physiological stress transduction response mechanism for D. salina which is common for a range of different stresses and where intracellular pH plays a central role.

Adenylyl Cyclases (ACs) catalyze the formation of the key universal second messenger adenosine 3’, 5’-cyclic monophosphate (cAMP) from adenosine 5’- triphosphate. Cyclic AMP participates in several signal transduction pathways and is present in bacteria and higher and lower eukaryotes including higher plants. Previous studies in plants have shown a role for cAMP in signal transduction during e.g. the cell cycle, elongation of the pollen tube and stimulation of protein kinase activity. More recently cAMP has been shown to play a role in stress responses. Interestingly, cAMP has also been shown to regulate ion transport in plant cells. Here we used a similar strategy that led to the discovery of the first guanylyl cyclase in plants that was based on the alignment of conserved and functionally assigned amino acids in the catalytic centre of annotated nucleotide cyclases from lower and higher eukaryotes, to identify a novel candidate ACs in Arabidopsis (Arabidopsis thaliana K+ Uptake 5 and 7). ATKUP5 and 7 are homologous to K+ uptake permeases (KUPs) from bacteria and high-affinity K+ transporters (HAKs) from fungi. The AC activity was investigated by recombinantly expressing the ATKUP5 and 7 AC domain in vitro and by complementation of an E. coli AC mutant (cyaA). Furthermore, ATKUP5 was tested for its ability to functionally complement a yeast mutant deficient in Trk1 and Trk2 high affinity potassium uptake transporters. Site-mutagenesis in the AC domain was used to test the effect of both functions in each other. Furthermore, ATKUP5 was characterized electrophysiologically in HEK-293 cells to characterize the nature of this transporter. The localization of the ATKUP5 in Arabidopsis was examined using a Green Fluorescent Protein (GFP) fusion with the ATKUP5 to determine whether ATKUP5 is expressed at the plasma or tonoplast membrane. Arabiodpsis thaliana of the wild type, overexpressing ATKUP5 and atkup5 mutant lines were used to examine phenotypic differences.

Sessile bacterial communities which form on the solid surface or solid-liquid interface are known as biofilms. Both single species and multispecies biofilms are characterized by an extracellular matrix of polymeric substances which gives them several hundred times more antibiotic resistances than a planktonic bacterial culture. Though bacteria are the most common causative agent of various diseases, because of the high antibiotic resistance, biofilms cause complications of various diseases like cystic fibrosis, prosthetic valve endocarditis, chronic pulmonary diseases, catheter-associated urinary tract infections and several other diseases. From past studies, quorum sensing has been established as a novel target mechanism against biofilms; in this study, the two-component signal transduction systems (2CSTSs) have been focused. Once better understood, 2CSTSs can serve as a novel drug target and prevention mechanism for biofilm associated diseases. According to prior high-throughput experiments and phenotype microarray experiments by our lab, several 2CSTSs like OmpR-EnvZ, RcsCDB along with the global regulator FlhD/FlhC were hypothesized to have an important effect on various developmental stages of biofilm formation. From that past study, we postulated that acetate metabolism may be an important aspect for biofilm formation. In this study, we tested and confirmed this hypothesis. We observed biofilms formed by several mutants in 2CSTS, as well as mutants in acetate metabolism, using Scanning Electron Microscopy (SEM). We found quantitative and qualitative differences in the biofilm of the acetate mutants when compared to their isogenic parental Escherichia coli strain. An additional mutation in rcsB with acetate mutant strains forms less clumpy biofilms whereas an additional mutation in dcuR results in the formation of less biofilms. So the structural and the quantitative differences of acetate mutant biofilms depend on additional mutations in rcsB and dcuR. Though a number of studies have been done on the temporal gene expression within biofilms, spatial gene expression of the mature biofilm is a big gap of knowledge. The future aim of this study is to study the temporal as well as the spatial gene expression of different 2CSTSs in the biofilm. In my MS thesis, I have constructed selected promoter fused GFP /RFP plasmids and some other fusion plasmids were purchased from the promoter collections from Open Biosystems, lastly E. coli AJW678 bacterial strains were transformed with these GFP /RFP fused plasmids. A 96 well microtiter plate assay was performed to study the temporal expression from the promoters by quantifying the fluorescence intensity in the planktonic culture. According to this experiment, the highest expression of flhD was after 20 hours whereas, the expression of ompR increases up to 7 days, which indicates that the flhD expresses earlier than ompR. The decreasing phase of flhD expression was paralleled by the sharpest increase in ompR expression as phosphorylated OmpR is an inhibitor of flhD expression. / National Institutes of Health (NIH grant 1R15AI089403) / United States. Animal and Plant Health Inspection Service

Objective Plasma fibrinogen has been defined as a risk factor of cardiovascular disease and may play a role in the development of cardiac hypertrophy. We have previously demonstrated that the Toll-like receptor 4 (TLR4)-mediated myeloid differentiation primary response protein 88 (MyD88)-dependent nuclear factor-κB (NF-κB) pathway is involved in cardiac hypertrophy. The present study aimed to investigate whether fibrinogen will stimulate the hypertrophic response of cardiac myocytes and to examine the role of the TLR4/MyD88/NF-κB pathway in fibrinogen-induced cardiac hypertrophy. Methods and Results Cardiac hypertrophy was induced by transverse aortic banding for 5 weeks in Sprague-Dawley rats. The deposition of fibrinogen in the left ventricle, as determined by immunohistochemistry and immunoblotting, was increased. Aortic banding also significantly enhanced the association of TLR4 with MyD88 and increased NF-κB activity. In-vitro studies showed that fibrinogen induced a dose-dependent, hypertrophic response of neonatal cardiomyocytes. Fibrinogen stimulation significantly increased myocyte size, 3H-leucine incorporation and mRNA levels of atrial natriuretic peptide (ANP); fibrinogen challenge also significantly increased associations of TLR4 with MyD88 and NF-κB binding activity. Transient transfection of cardiomyocytes with a dominant-negative MyD88 plasmid significantly attenuated the fibrinogen-induced hypertrophic response of neonatal cardiac myocytes and blunted fibrinogen-increased activation of the TLR4/MyD88/NF-κB signaling pathway. Conclusion Our results suggest that fibrinogen induces hypertrophic response of cardiomyocytes partially through a TLR4-mediated, MyD88-dependent NF-κB pathway.