Microfluidic platforms for the characterization of in meso membrane protein crystallization

Membrane proteins, which reside in the membranes of cells, play a critical role in many important biological processes including cellular signaling, immune response, and material and energy transduction. Because of their key role in maintaining the environment within cells and facilitating intercellular interactions, understanding the function of these proteins is of tremendous medical and biochemical significance. Indeed, the malfunction of membrane proteins has been linked to numerous diseases including diabetes, cirrhosis of the liver, cystic fibrosis, cancer, Alzheimer's disease, hypertension, epilepsy, cataracts, tubulopathy, leukodystrophy, Leigh syndrome, anemia, sensorineural deafness, and hypertrophic cardiomyopathy.1-3 However, the structure of many of these proteins and the changes in their structure that lead to disease-related malfunctions are not well understood. Additionally, at least 60% of the pharmaceuticals currently available are thought to target membrane proteins, despite the fact that their exact mode of operation is not known.4-6 Developing a detailed understanding of the function of a protein is achieved by coupling biochemical experiments with knowledge of the structure of the protein. Currently the most common method for obtaining three-dimensional structure information is X-ray crystallography. However, no a priori methods are currently available to predict crystallization conditions for a given protein.7-14 This limitation is currently overcome by screening a large number of possible combinations of precipitants, buffer, salt, and pH conditions to identify conditions that are conducive to crystal nucleation and growth.7,9,11,15-24 Unfortunately, these screening efforts are often limited by difficulties associated with quantity and purity of available protein samples. While the two most significant bottlenecks for protein structure determination in general are the (i) obtaining sufficient quantities of high quality protein samples and (ii) growing high quality protein crystals that are suitable for X-ray structure determination,7,20,21,23,25-47 membrane proteins present additional challenges. For crystallization it is necessary to extract the membrane proteins from the cellular membrane. However, this process often leads to denaturation. In fact, membrane proteins have proven to be so difficult to crystallize that of the more than 66,000 structures deposited in the Protein Data Bank,48 less than 1% are for membrane proteins, with even fewer present at high resolution (< 2Å)4,6,49 and only a handful are human membrane proteins.49 A variety of strategies including detergent solubilization50-53 and the use of artificial membrane-like environments have been developed to circumvent this challenge.43,53-55 In recent years, the use of a lipidic mesophase as a medium for crystallizing membrane proteins has been demonstrated to increase success for a wide range of membrane proteins, including human receptor proteins.54,56-62 This in meso method for membrane protein crystallization, however, is still by no means routine due to challenges related to sample preparation at sub-microliter volumes and to crystal harvesting and X-ray data collection. This dissertation presents various aspects of the development of a microfluidic platform to enable high throughput in meso membrane protein crystallization at a level beyond the capabilities of current technologies. Microfluidic platforms for protein crystallization and other lab-on-a-chip applications have been well demonstrated.9,63-66 These integrated chips provide fine control over transport phenomena and the ability to perform high throughput analyses via highly integrated fluid networks. However, the development of microfluidic platforms for in meso protein crystallization required the development of strategies to cope with extremely viscous and non-Newtonian fluids. A theoretical treatment of highly viscous fluids in microfluidic devices is presented in Chapter 3, followed by the application of these strategies for the development of a microfluidic mixer capable of preparing a mesophase sample for in meso crystallization at a scale of less than 20 nL in Chapter 4. This approach was validated with the successful on chip in meso crystallization of the membrane protein bacteriorhodopsin. In summary, this is the first report of a microfluidic platform capable of performing in meso crystallization on-chip, representing a 1000x reduction in the scale at which mesophase trials can be prepared. Once protein crystals have formed, they are typically harvested from the droplet they were grown in and mounted for crystallographic analysis. Despite the high throughput automation present in nearly all other aspects of protein structure determination, the harvesting and mounting of crystals is still largely a manual process. Furthermore, during mounting the fragile protein crystals can potentially be damaged, both from physical and environmental shock. To circumvent these challenges an X-ray transparent microfluidic device architecture was developed to couple the benefits of scale, integration, and precise fluid control with the ability to perform in situ X-ray analysis (Chapter 5). This approach was validated successfully by crystallization and subsequent on-chip analysis of the soluble proteins lysozyme, thaumatin, and ribonuclease A and will be extended to microfluidic platforms for in meso membrane protein crystallization. The ability to perform in situ X-ray analysis was shown to provide extremely high quality diffraction data, in part as a result of not being affected by damage due to physical handling of the crystals. As part of the work described in this thesis, a variety of data collection strategies for in situ data analysis were also tested, including merging of small slices of data from a large number of crystals grown on a single chip, to allow for diffraction analysis at biologically relevant temperatures. While such strategies have been applied previously,57,59,61,67 they are potentially challenging when applied via traditional methods due to the need to grow and then mount a large number of crystals with minimal crystal-to-crystal variability. The integrated nature of microfluidic platforms easily enables the generation of a large number of reproducible crystallization trials. This, coupled with in situ analysis capabilities has the potential of being able to acquire high resolution structural data of proteins at biologically relevant conditions for which only small crystals, or crystals which are adversely affected by standard cryocooling techniques, could be obtained (Chapters 5 and 6). While the main focus of protein crystallography is to obtain three-dimensional protein structures, the results of typical experiments provide only a static picture of the protein. The use of polychromatic or Laue X-ray diffraction methods enables the collection of time resolved structural information. These experiments are very sensitive to crystal quality, however, and often suffer from severe radiation damage due to the intense polychromatic X-ray beams. Here, as before, the ability to perform in situ X-ray analysis on many small protein crystals within a microfluidic crystallization platform has the potential to overcome these challenges. An automated method for collecting a "single-shot" of data from a large number of crystals was developed in collaboration with the BioCARS team at the Advanced Photon Source at Argonne National Laboratory (Chapter 6). The work described in this thesis shows that, even more so than for traditional structure determination efforts, the ability to grow and analyze a large number of high quality crystals is critical to enable time resolved structural studies of novel proteins. In addition to enabling X-ray crystallography experiments, the development of X-ray transparent microfluidic platforms also has tremendous potential to answer other scientific questions, such as unraveling the mechanism of in meso crystallization. For instance, the lipidic mesophases utilized during in meso membrane protein crystallization can be characterized by small angle X-ray diffraction analysis. Coupling in situ analysis with microfluidic platforms capable of preparing these difficult mesophase samples at very small volumes has tremendous potential to enable the high throughput analysis of these systems on a scale that is not reasonably achievable using conventional sample preparation strategies (Chapter 7). In collaboration with the LS-CAT team at the Advanced Photon Source, an experimental station for small angle X-ray analysis coupled with the high quality visualization capabilities needed to target specific microfluidic samples on a highly integrated chip is under development. Characterizing the phase behavior of these mesophase systems and the effects of various additives present in crystallization trials is key for developing an understanding of how in meso crystallization occurs. A long term goal of these studies is to enable the rational design of in meso crystallization experiments so as to avoid or limit the need for high throughput screening efforts. In summary, this thesis describes the development of microfluidic platforms for protein crystallization with in situ analysis capabilities. Coupling the ability to perform in situ analysis with the small scale, fine control, and the high throughput nature of microfluidic platforms has tremendous potential to enable a new generation of crystallographic studies and facilitate the structure determination of important biological targets. The development of platforms for in meso membrane protein crystallization is particularly significant because they enable the preparation of highly viscous mixtures at a previously unachievable scale. Work in these areas is ongoing and has tremendous potential to improve not only current the methods of protein crystallization and crystallography, but also to enhance our knowledge of the structure and function of proteins which could have a significant scientific and medical impact on society as a whole. The microfluidic technology described in this thesis has the potential to significantly advance our understanding of the structure and function of membrane proteins, thereby aiding the elucidation of human biology, the development of pharmaceuticals with fewer side effects for a wide range of diseases. References (1) Quick, M.; Javitch, J. A. P Natl Acad Sci USA 2007, 104, 3603. (2) Trubetskoy, V. S.; Burke, T. J. Am Lab 2005, 37, 19. (3) Pecina, P.; Houstkova, H.; Hansikova, H.; Zeman, J.; Houstek, J. Physiol Res 2004, 53, S213. (4) Arinaminpathy, Y.; Khurana, E.; Engelman, D. M.; Gerstein, M. B. Drug Discovery Today 2009, 14, 1130. (5) Overington, J. P.; Al-Lazikani, B.; Hopkins, A. L. Nat Rev Drug Discov 2006, 5, 993. (6) Dauter, Z.; Lamzin, V. S.; Wilson, K. S. Current Opinion in Structural Biology 1997, 7, 681. (7) Hansen, C.; Quake, S. R. Current Opinion in Structural Biology 2003, 13, 538. (8) Govada, L.; Carpenter, L.; da Fonseca, P. C. A.; Helliwell, J. 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Brucella Non-Neutrocytic Bacterascites in a Patient with Chronic Liver Disease

Objectives: To report a case of Brucella peritonitis. Patient and methods: We describe the case of a patient and present a brief review of the few published reports. Results: The patient had alcoholic cirrhosis of the liver and was diagnosed with Brucella non-neutrocytic bacterascites. Conclusion: Brucellosis is a common zoonosis with worldwide distribution. It is a systemic disease with the potential to predominantly affect one organ or a specific system (focal brucellosis). However, peritoneal focalization of this disease is a very rare presentation.

Intravascular Lymphoma as an Uncommon Cause of Anasarca

Objectives: To report a case of intravascular lymphoma (IVL) in a Caucasian patient who presented with anasarca as his sole clinical sign. Material and Methods: A man presented with anasarca-type oedema and fatigue. After excluding heart failure, hepatic cirrhosis, nephrotic syndrome, hypothyroidism, AL-amyloidosis and adverse drug reaction which can all cause oedema, we turned our attention to capillary permeability disorders. Results: Closer review of the bone marrow aspirate demonstrated haemophagocytic histiocytosis, while core, renal and duodenal biopsies showed a B-cell IVL. Conclusion: The differential diagnosis of anasarca, a relatively common clinical sign, should include IVL although the diagnosis may still be challenging.

Proton-pump inhibitors adverse effects: a review of the evidence and position statement by the Sociedad Española de Patología Digestiva

Introduction: In the last few years a significant number of papers have related the use of proton-pump inhibitors (PPIs) to potential serious adverse effects that have resulted in social unrest. Objective: The goal of this paper was to provide a literature review for the development of an institutional position statement by Sociedad Española de Patología Digestiva (SEPD) regarding the safety of long-term PPI use. Material and methods: A comprehensive review of the literature was performed to draw conclusions based on a critical assessment of the following: a) current PPI indications; b) vitamin B12 deficiency and neurological disorders; c) magnesium deficiency; d) bone fractures; e) enteric infection and pneumonia; f) interactions with thienopyridine derivatives; e) complications in cirrhotic patients. Results: Current PPI indications have remained unchanged for years now, and are well established. A general screening of vitamin B12 levels is not recommended for all patients on a PPI; however, it does seem necessary that magnesium levels be measured at therapy onset, and then monitored in subjects on other drugs that may induce hypomagnesemia. A higher risk for bone fractures is present, even though causality cannot be concluded for this association. The association between PPIs and infection with Clostridium difficile is mild to moderate, and the risk for pneumonia is low. In patients with cardiovascular risk receiving thienopyridines derivatives it is prudent to adequately consider gastrointestinal and cardiovascular risks, given the absence of definitive evidence regardin potential drug-drug interactions; if gastrointestinal risk is found to be moderate or high, effective prevention should be in place with a PPI. PPIs should be cautiously indicated in patients with decompensated cirrhosis. Conclusions: PPIs are safe drugs whose benefits outweigh their potential side effects both short-term and long-term, provided their indication, dosage, and duration are appropriate.

Implication of gut microbiota in nonalcoholic fatty liver disease

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Reduced lipoapoptosis, hedgehog pathway activation and fibrosis in caspase-2 deficient mice with non-alcoholic steatohepatitis

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Screening of esophageal varices by esophageal capsule endoscopy: results of a French multicenter prospective study

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Extraction, identification, fractionation and isolation of phenolic compounds in plants with hepatoprotective effects

The liver is one of the most important organs of human body, being involved in several vital functions and regulation of physiological processes. Given its pivotal role in the excretion of waste metabolites and drugs detoxification, the liver is often subjected to oxidative stress that leads to lipid peroxidation and severe cellular damage. The conventional treatments of liver diseases such as cirrhosis, fatty liver and chronic hepatitis are frequently inadequate due to side effects caused by hepatotoxic chemical drugs. To overcome this problematic paradox, medicinal plants, owing to their natural richness in phenolic compounds, have been intensively exploited concerning their extracts and fraction composition in order to find bioactive compounds that could be isolated and applied in the treatment of liver ailments. The present review aimed to collect the main results of recent studies carried out in this field and systematize the information for a better understanding of the hepatoprotective capacity of medicinal plants in in vitro and in vivo systems. Generally, the assessed plant extracts revealed good hepatoprotective properties, justifying the fractionation and further isolation of phenolic compounds from different parts of the plant. Twenty-five phenolic compounds, including flavonoids, lignan compounds, phenolic acids and other phenolic compounds, have been isolated and identified, and proved to be effective in the prevention and/or treatment of chemically induced liver damage. In this perspective, the use of medicinal plant extracts, fractions and phenolic compounds seems to be a promising strategy to avoid side effects caused by hepatotoxic chemicals.

One-year follow-up of the nutritional status of patients undergoing liver transplantation

Background: Choosing the method of nutritional assessment is essential for proper follow-up of the nutritional status of patients undergoing liver transplantation. Objectives: Evaluate and compare the nutritional status of cirrhotic patients before and after liver transplantation over a year by different methods of nutritional assessment. Methods: Patients undergoing liver transplantation were assessed in five phases: pre-transplant, 1, 3, 6 and 12 months after transplantation at the hospital Santa Casa de Misericordia de Porto Alegre, RS, Brazil. The methods used for nutritional assessment were anthropometry, grip strength of the non-dominant hand (HGS) by dynamometry, thickness of the adductor pollicis muscle (APM) and phase angle (PA) by bioelectrical impedance analysis (BIA). In all evaluations, the same measurements were taken. Results: Evaluations were performed in 22 patients. Methods that showed a higher prevalence of malnourished patients before transplantation were PA by BIA (25%), arm muscle circumference (AMC) (21.9%) and arm circumference (AC) (18.8%). When comparing the nutritional status of patients during follow-up, there was a significant difference only in the evaluation methods AC, triceps skinfold thickness and PA by BIA. At the end, the methods of nutritional assessment were compared again. They showed a significant statistical difference, with HGS being the best method for detecting malnutrition. Conclusions: In conclusion, it is suggested that the method PA by BIA could be widely used with this population since the results are consistent with other findings in the literature and they are significant, reliable, and reproducible.

Esofagite a citomegalovirus em cirrose hepática auto-imune : a propósito de um caso clínico

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Automated morphometry provides accurate and reproducible virtual staging of liver fibrosis in chronic hepatitis C

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Determinación del comportamiento del riesgo cardiovascular en paciente postrasplante hepatico en Fundacion Cardioinfantil

El trasplante hepático es una opción terapéutica para enfermedad hepática avanzada cada vez más frecuente en Colombia. La sobrevida del 80% a 5 años conlleva a un aumento del riesgo cardiovascular y de eventos cardiovasculares, por esta razón esta investigación determina el comportamiento del riesgo cardiovascular en los pacientes con trasplante hepático de la Fundación Cardioinfantil, realizado en 3 años de seguimiento . Lo encontrado en esta investigación es que existe un aumento del riesgo cardiovascular a tres años en pacientes post trasplante hepático, estadísticamente significativo, principalmente secundario a hipertensión, diabetes e hipertrigliceridemia. El aumento es mayor a lo descrito en la población general, y similar a otros pacientes trasplantados, en un periodo de 5 años

Factores de riesgo asociados al desarrollo de bacteriemia en pacientes adultos cirróticos hospitalizados

Introducción: La Bacteriemia en pacientes cirróticos es una causa importante de morbimortalidad, en gran parte favorecida por la especial vulnerabilidad de esta población ante procesos infecciosos. El objetivo fue determinar los factores asociados al desarrollo de bacteriemia primaria y secundaria en pacientes con Cirrosis, hospitalizados en la Fundación Cardioinfantil – Instituto de Cardiología entre 01 enero de 2010 y 31 enero de 2016. Materiales y Métodos: Estudio de casos y controles en pacientes mayores de 18 años con cirrosis hepática conocida o confirmada durante la hospitalización. Se realizó un análisis descriptivo, un análisis bivariado para determinar las diferencias entre los casos y los controles con respecto a las variables independientes un análisis de asociación mediante un modelo de regresión logística no condicional con variable dependiente bacteriemia. Los resultados se expresan en odds ratios con intervalos de confianza al 95%. Resultados: Las condiciones asociadas a bacteriemia como factores de riesgo fueron: Enfermedad renal crónica OR 9,1 (IC 95% 2,4-34), Escala Meld > 10 puntos OR 4,0 (IC 95% 2,-34), Infección previa OR 7,2 (IC 95% 2,1-24), presencia de catéter central OR 12,0 (IC 95% 1,8-80), presencia de sonda vesical OR 21,1 (IC 95% 1,6-276), estudio endoscópico OR 3,9 (IC 95% 1,1-14). Discusión: Factores relacionados con las condiciones clínicas del paciente evaluadas por las escalas Meld y Child-Pugh, el antecedente de infección previa y la presencia de dispositivos para monitorear el estado del paciente aumentan el riesgo de bacteriemia en pacientes hospitalizados con cirrosis.

Experiencia y porcentaje de complicaciones de las derivaciones portosistémicas intrahepáticas transyugulares en la Fundación Cardioinfantil

La derivación portosistémica intrahepática transyugular (TIPS) es una técnica importante en el manejo de las complicaciones de la hipertensión portal, en especial en aquellos pacientes candidatos a trasplante hepático. Se trata de un estudio observacional analítico, sin riesgo, en el cual se emplearon técnicas y métodos de investigación documental retrospectivo, y no se realizó ningún tipo de intervención sobre las variables fisiológicas, psicológicas y sociales de la población incluida. Se realizó la descripción demográfica de los pacientes, características clínicas, hallazgos imageneológicos y aspectos técnicos asociados al procedimiento de los pacientes con hipertensión portal que han sido manejados con TIPS en la Fundación CardioInfantil desde Enero 1 de 2007 hasta Junio 30 de 2016. Se incluyeron 54 pacientes de los cuales el 66,7% no presentaron complicaciones inmediatas, tenidas en cuenta desde la terminación del procedimiento y hasta las siguientes 24 horas; sin embargo, 16,9% debutaron con encefalopatía durante este periodo. De las complicaciones tardías, la más frecuente fue la ascitis con un 66,7%, con una mortalidad de 20,4% de los cuales, el 45% de estos fue por shock séptico y falla orgánica secundaria. Aunque el porcentaje de complicaciones asociadas al procedimiento fue alto en nuestros pacientes, se encuentra dentro de los valores reportados en la literatura. Los resultados presentados son un punto de partida para la evaluación del procedimiento en nuestra población y permiten implementar estrategias de mejora que conlleven a incidir de manera positiva en el porcentaje de complicaciones y mortalidad derivadas del procedimiento.