Blood is a complex mixture of formed cellular elements, proteins, and ions dissolved in a solution. It is a difficult fluid to model because it is a shear-thinning, viscoelastic fluid that stress- relaxes. In this study, a new mathematical model for whole blood is developed from a general equation for a fluid with a shear dependent viscosity. The model is then used as a backdrop for 28 different biochemical factors interacting to form a clot. The full intrinsic and extrinsic pathways are both used in the simulation; the inclusion of the full intrinsic pathway is something that had not been done prior to this work. The model is executed in one spatial direction in an infinite domain as well as within a rigid walled cylinder using a finite volume scheme. The rigid wall, similar to the new mathematical equation for blood, is an oversimplification of actual in-vitro conditions. The results of both simulations show the formation and dissolution of the clot. Sensitivity analysis is then performed in the finite domain model by adjusting the initial levels of factors Va and Xa. The results show that by increasing the initial level of one or both of these factors leads to the quicker formation of a clot.

<p>Thrombosis is associated with the occlusion of a blood vessel and can be triggered by a number of types of injury, such as the rupture of an atherosclerotic plaque on the artery wall, changes in blood composition, or blood stasis. The resulting thrombosis can cause major diseases such as myocardial infarction, stroke, and venous thromboembolic disorders that, collectively, account for the most common cause of death in the developed world. Anticoagulants are used to treat and prevent these thrombotic diseases in a number of clinical and surgical settings. Although commonly prescribed, currently approved anticoagulants have a major limitation of severe drug-induced bleeding that contributes to the high levels of morbidity and mortality associated with use. The "holy grail" for antithrombotic therapy is to identify a drug that inhibits thrombus formation without promoting bleeding. Understanding the differences between thrombosis and hemostasis in the vascular system is critical to developing these safe and effective anticoagulants, as this depends on striking the correct balance between inhibiting thrombus formation (efficacy) and reducing the risk of severe bleeding (safety). While it is commonly thought that the same factors play a similar role in hemostasis and thrombosis, recent evidence points to differing functions for FXI and FXII in each of these settings. Importantly, these factors seem to contribute to pathological thrombus formation without being involved in normal hemostasis.</p><p> The overall goal of this project was to evaluate the inhibition of the intrinsic pathway of coagulation as a potential anticoagulant strategy utilizing the aptamer platform. Aptamers are short, highly structured nucleic acids that act as antagonists by binding to large surface areas on their target protein and thus tend to inhibit protein-protein interactions. High affinity binding aptamers have been isolated that specifically target a diverse range of proteins, including transcription factors, proteases, viral proteins, and growth factors, as well as other coagulation factors. As synthetic molecules, aptamers have a small molecular weight, are highly amenable to modifications that can control their bioavailability, and have not been found to elicit an immune response, thus making them ideal drug candidates. Importantly, aptamers can be rapidly and effectively reversed with either a sequence specific antidote that recognizes the primary sequence of the aptamer or a universal antidote that binds to their backbone and reverses all aptamer activity independent of sequence. This ability lends itself well to their therapeutic application in coagulation, as rapid reversal of a drug upon the onset of bleeding is a key property for increasing the safety of this class of drugs.</p><p> Aptamers targeting FXI/FXIa and FXII/FXIIa were isolated in two separate SELEX (systematic evolution of ligands by exponential enrichment) procedures: the FXII aptamer was isolated in a convergent SELEX approach and the FXIa aptamer was isolated from a purified protein selection. In both processes, 2'fluoropyrimindine modified RNA with a 40-nucleotide random region was incubated with either the plasma proteome (in initial rounds of the convergent SELEX) or the purified protein target (FXII or FXIa). The nucleic acids that did not bind to the target were separated from those that bound, and these molecules were then amplified to generate an enriched pool with increased binding affinity for the target. This process was repeated under increasingly stringent conditions to isolate the aptamer that bound with the highest affinity to the purified target protein. Utilizing biochemical and in vitro coagulation assays, specific, high-affinity binding and functional anticoagulant aptamers were identified for both protein targets, and the mechanism of anticoagulation was ascertained for each aptamer. </p><p> Overall, both aptamers bound to an exosite on their target protein that was able to inhibit downstream activation of the next protein in the coagulation cascade. In order to specifically examine aptamer effects on several parameters of thrombin generation, a new assay was developed and fully characterized using aptamer anticoagulants targeting other coagulation factors. Aptamer inhibition of both FXI and FXII was able to decrease thrombin generation in human plasma. However, limited cross-reactivity in other animal species by both aptamers hindered our ability to assess aptamer inhibition in an in vivo setting. Moving forward, screening aptamers against a larger selection of animal plasmas will hopefully allow us to identify an animal species in which we can analyze aptamer inhibition of the intrinsic pathway for effectiveness and safety in inhibiting thrombosis. The further characterization and use of these aptamers in plasma and blood based settings will allow us to study the diverging functions of the intrinsic pathway in thrombosis and hemostasis.</p><p> A critical need exists for safe and effective anticoagulants to treat and prevent numerous thrombotic procedures and diseases. An ideal anticoagulant is one that strikes the correct balance between inhibiting thrombus formation and reducing drug-induced bleeding. Inhibition or depletion of factors XI and XII of the intrinsic pathway of coagulation have shown reduced thrombus formation without interruption of normal hemostasis in several models of thrombosis. By developing novel RNA aptamer anticoagulants to these factors, we have set the stage for evaluating the net therapeutic benefit of intrinsic pathway inhibition to effectively control coagulation, manage thrombosis, and improve patient outcome. As well as developing a safe anticoagulation, these agents can lead to important biological discoveries concerning the fundamental difference between hemostasis and thrombosis.</p> / Dissertation

The inner surface of the stomach is lined by a mucous membrane known as the gastric mucosa. The integrity of the gastric mucosa is critical for protecting the stomach from the low pH and proteolytic environment within the lumen. Both clinically and experimentally, exposure of gastric mucosal cells to bile salts is known to cause injury. Bile salts present in duodenogastric reflux are thought to play a significant role in gastric ulcer formation and alkaline gastritis. In vitro, studies using physiologic concentrations of the secondary bile salt, deoxycholic acid, indicate that bile salts can induce apoptosis in cultured human gastric epithelial cells in a caspase-dependent manner. Therefore, there is interest in developing approaches that can protect gastric cells from bile salt-induced damage. It has been shown that induction of the stress protein, heme oxygenase-1, can provide protection against apoptosis. Therefore, the objective of this study was to test the hypotheses that heme oxygenase-1 expression could be induced in human gastric epithelial cells and that furthermore; this would provide protection from deoxycholic acid-induced apoptosis. Heme oxygenase-1 expression was induced pharmacologically or by introduction of a plasmid expressing heme oxygenase-1 into the gastric epithelial cell line, AGS. Induction of heme oxygenase-1 prior to challenge with deoxycholate reduced apoptotic-associated morphological changes, DNA fragmentation, the appearance of oligonucleosomes in the cytoplasm, and activation of caspase-3 and caspase-9. Based on these results, it was concluded that expression of heme oxygenase-1, or the introduction of its products, can provide protection to human gastric epithelial cells against sodium deoxycholic acid induced-apoptosis.

A desregulação da apoptose, principalmente da via mitocondrial, exerce papel na progressão tumoral, resistência à quimioterapia, além de favorecer a formação de metástases por permitir a sobrevivência de células tumorais na circulação e outros microambientes teciduais. No presente estudo, foram avaliados 58 mastocitomas cutâneos caninos, provenientes de 50 animais submetidos à cirurgia excisional como única forma de tratamento. Os tumores foram graduados de acordo com o sistemas de estabelecidos por Patnaik, Ehler e MacEwen (1984) e Kiupel et al. (2011). As expressões das proteínas relacionadas à via intrínseca da apoptose, BCL2, BAX, APAF1, Caspase 9 e Caspase 3, foram caracterizadas por meio de imuno-histoquímica. Os resultados obtidos das imunomarcações foram comparados às graduações histopatológicas, bem como à mortalidade em função do tumor e ao tempo de sobrevida pós-cirúrgico. Observamos maior expressão de BAX em mastocitomas de grau III, bem como menor expressão de BCL2 em tumores de alto grau. A detecção imuno-histoquímica de BAX foi considerada um indicador prognóstico para sobrevida e mortalidade em função da doença, enquanto que as de APAF1 e BCL2 adicionaram valor prognóstico às graduações histopatológicas melhorando a previsão da sobrevida pós-cirurgia / Deregulation of apoptosis, especially in the mitochondrial pathway, plays a role in tumor progression, resistance to chemotherapy, and favor the formation of metastases by allowing the survival of tumor cells in the blood stream and other tissue microenvironments. In the present study, we evaluated 58 canine cutaneous mast cell tumors, from 50 dogs, which were submitted to excisional surgery alone. The tumors were graded according to the systems proposed by Patnaik, Ehler and MacEwen (1984) and Kiupel et al. (2011). The expression of the apoptosis-related proteins BCL2, BAX, APAF1, caspase 9 and caspase 3 was characterized by immunohistochemistry. Immunohistochemical results were compared with the histopathological grades, mortality due to the tumor and post-surgical survival time. We observed increased expression of BAX in grade III mast cell tumors and lower expression of BCL2 in high-grade tumors. Immunohistochemical detection of BAX was considered an independent indicator of prognosis for survival and mortality due to the disease, whereas APAF1 and BCL2 added prognostic value to the histopathological grading systems improving the prediction of survival post surgery

A desregulação da apoptose, principalmente da via mitocondrial, exerce papel na progressão tumoral, resistência à quimioterapia, além de favorecer a formação de metástases por permitir a sobrevivência de células tumorais na circulação e outros microambientes teciduais. No presente estudo, foram avaliados 58 mastocitomas cutâneos caninos, provenientes de 50 animais submetidos à cirurgia excisional como única forma de tratamento. Os tumores foram graduados de acordo com o sistemas de estabelecidos por Patnaik, Ehler e MacEwen (1984) e Kiupel et al. (2011). As expressões das proteínas relacionadas à via intrínseca da apoptose, BCL2, BAX, APAF1, Caspase 9 e Caspase 3, foram caracterizadas por meio de imuno-histoquímica. Os resultados obtidos das imunomarcações foram comparados às graduações histopatológicas, bem como à mortalidade em função do tumor e ao tempo de sobrevida pós-cirúrgico. Observamos maior expressão de BAX em mastocitomas de grau III, bem como menor expressão de BCL2 em tumores de alto grau. A detecção imuno-histoquímica de BAX foi considerada um indicador prognóstico para sobrevida e mortalidade em função da doença, enquanto que as de APAF1 e BCL2 adicionaram valor prognóstico às graduações histopatológicas melhorando a previsão da sobrevida pós-cirurgia / Deregulation of apoptosis, especially in the mitochondrial pathway, plays a role in tumor progression, resistance to chemotherapy, and favor the formation of metastases by allowing the survival of tumor cells in the blood stream and other tissue microenvironments. In the present study, we evaluated 58 canine cutaneous mast cell tumors, from 50 dogs, which were submitted to excisional surgery alone. The tumors were graded according to the systems proposed by Patnaik, Ehler and MacEwen (1984) and Kiupel et al. (2011). The expression of the apoptosis-related proteins BCL2, BAX, APAF1, caspase 9 and caspase 3 was characterized by immunohistochemistry. Immunohistochemical results were compared with the histopathological grades, mortality due to the tumor and post-surgical survival time. We observed increased expression of BAX in grade III mast cell tumors and lower expression of BCL2 in high-grade tumors. Immunohistochemical detection of BAX was considered an independent indicator of prognosis for survival and mortality due to the disease, whereas APAF1 and BCL2 added prognostic value to the histopathological grading systems improving the prediction of survival post surgery

Medical devices, such as catheters and heart valves, are an important part of patient care. However, blood-contacting devices can activate the blood coagulation cascade to produce factor (f) Xa, the clotting enzyme that induces thrombin generation. By activating platelets and converting soluble fibrinogen to fibrin, thrombin leads to blood clot formation. Blood clots that form on medical devices create problems because they may foul the device and/or serve as a nidus for infection. In addition, clots can break off from the device, travel through the circulation and lodge in distant organs; a process known as embolization. This is particularly problematic with central venous catheters because clots that form on them can break off and lodge in pulmonary arteries, thereby producing a pulmonary embolism. Similarly, clots that form on heart valves can break off and lodge in cerebral arteries, thereby producing a stroke. Therefore, anticoagulants, blood thinning drugs, are frequently used to prevent clotting on medical devices. Conventional anticoagulants, such as heparin and warfarin, target multiple clotting factors. Heparin binds to antithrombin in plasma and accelerates the rate at which it inhibits fXa, thrombin and many other clotting enzymes. Warfarin, which is a vitamin K antagonist, attenuates thrombin generation by interfering with the synthesis of the vitamin K-dependent clotting factors, which include fX and prothrombin, the precursor of thrombin. In contrast to heparin and warfarin, more recent anticoagulants inhibit only a single clotting enzyme. For example, fondaparinux, a synthetic heparin fragment, only inhibits fXa and dabigatran, an oral thrombin inhibitor, only targets thrombin. Although effective for many indications, fondaparinux was less effective than heparin for preventing clotting on catheters in patients undergoing heart interventions and dabigatran was less effective than warfarin for preventing strokes in patients with mechanical heart valves. The failure of these new anticoagulants highlights the need for a better understanding into the drivers of clotting on medical devices. Therefore, the overall purpose of this thesis is to gain this understanding so that more rational approaches to its prevention can be identified. In the classical model of blood coagulation, clotting is triggered via two distinct pathways; the tissue factor (TF) pathway or extrinsic pathway and the contact pathway or intrinsic pathway; pathways which are initiated by fVIIa and fXIIa, respectively. The mechanism by which medical devices initiate clotting is uncertain. Platelet and complement activation and microparticle formation have been implicated, which would drive clotting via the TF pathway. Alternatively, medical devices can bind and activate fXII, thereby initiating the contact pathway. We hypothesized that medical devices trigger clotting via the contact pathway and induce the local generation of fXa and thrombin in concentrations that exceed the capacity of fondaparinux and dabigatran to inhibit them. To test this hypothesis, we used catheters as a prototypical medical device and we used a combination of in vitro and rabbit models. Several lines of evidence indicate that catheters initiate clotting via the contact pathway. First, catheter segments shortened the clotting time of human plasma, and this activity was attenuated in fXII- or fXI-deficient plasma, which are key components of the contact pathway, but not in fVII-deficient plasma, which is the critical component of the extrinsic pathway. Second, corn trypsin inhibitor (CTI), a potent and specific inhibitor of fXIIa, attenuates catheter thrombosis. Third, selective knockdown of fXII or fXI with antisense oligonucleotides attenuated catheter-induced thrombosis in rabbits, whereas knockdown of fVII had no effect. Therefore, these results revealed the importance of the contact pathway in device-associated thrombosis, and identified CTI or fXII or fXI knockdown as novel strategies for preventing this problem. Focusing on fXIIa as the root cause of medical device associated clotting, we coated catheters with CTI using a polyethylene glycol (PEG) spacer. In addition to unmodified catheters, other controls included catheters coated with albumin via a PEG spacer or catheters coated with PEG alone. Compared with unmodified catheters or with the other controls, CTI-coated catheters attenuated clotting in buffer or plasma systems and were resistant to occlusion in rabbits. These findings support the concept that catheter-induced clotting is driven via the contact pathway and identify CTI coating as a viable strategy for its prevention. We next set out to test the hypothesis that fondaparinux and dabigatran, which inhibit fXa and thrombin, respectively, are less effective than heparin, which inhibits multiple clotting enzymes. Fondaparinux and dabigatran were less effective than heparin at preventing catheter induced clotting and thrombin generation, respectively. Likewise, in a rabbit model of catheter thrombosis, fondaparinux was less effective than heparin and dabigatran was only effective when administered at doses that yielded plasma dabigatran levels similar to those found at peak in human given the drug; at trough levels, dabigatran was no better than placebo. Finally, we also showed synergy between heparin and either fondaparinux or dabigatran. Thus, when co-administered to rabbits in doses that on their own had no effect, the combination of fondaparinux or dabigatran plus heparin extended the time to catheter thrombosis. These findings support the hypothesis that when catheters trigger clotting via the contact pathway, fXa and thrombin are generated in concentrations that overwhelm the capacity of fondaparinux or dabigatran to inhibit them. Furthermore, the synergy between heparin and fondaparinux or dabigatran has clinical implications because it explains why supplemental heparin attenuated the risk of catheter thrombosis in patients treated with fondaparinux who underwent cardiac procedures and it identifies the potential role of supplemental heparin in dabigatran-treated patients who require such interventions. In summary, we have shown that catheters trigger clotting via the contact pathway and have identified CTI coating or fXII or fXI knockdown as viable strategies for prevention of this problem. In addition, for prevention of catheter thrombosis, we also have shown that heparin, which inhibits multiple coagulation enzymes, is more effective than fondaparinux or dabigatran, which only inhibit fXa or thrombin, respectively; findings consistent with the clinical observations. Moreover, the synergy that we observed between fondaparinux or dabigatran and heparin identifies supplemental heparin as strategy for preventing catheter thrombosis in patients receiving these drugs. Taken together, these studies provide insight into the mechanisms of catheter thrombosis and potential strategies for its prevention. / Thesis / Doctor of Philosophy (PhD)