The goal of this project is to eliminate electroosmotic flow (EOF) in a microfluidic chip. EOF is a naturally occurring phenomenon at the fluid-surface interface in microfluidic chips when an electric field is applied across the fluid. When isoelectric focusing (IEF) is carried out to separate proteins based on their surface charge, the analytes must remain in the separation chamber, and not migrate to adjacent features in the microfluidic chip, which happens with EOF. For this project, a microfluidic chip was designed and commissioned to be photolithographically transferred onto a Si wafer. A PDMS component was then casted on the Si wafer and plasma bonded to a glass substrate. This chip was initially designed to carry out continuous IEF, and the focus of the project was shifted to the analysis of eliminating EOF in a microfluidic chamber. Per previous research test methods, methylcellulose will be used to analyze the phenomenon of electroosmotic flow in the chamber. A COMSOL model is used a theoretical basis of comparison when analyzing the flow velocities of the treated versus untreated microfluidic chips. The purpose of this project is to use the research performed in on this chip as a precursor to future analyses of continuous IEF on microfluidic chips in the Cal Poly Microfluidics group.

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Thesis (PhD)--Macquarie University, Division of Environmental & Life Sciences, Dept. of Chemistry & Biomolecular Sciences, 2009. / Bibliography: p. 200-212. / Introduction -- Shotgun proteomic analysis of rat liver membrane proteins -- A combination of immobilised pH gradients improve membrane proteomics -- Affects of tumor-induced inflammation on membrane proteins abundance in the mouse liver -- Affects of tumor-induced inflammation on biochemical pathways in the mouse liver -- General discussion -- References. / The aim of this thesis was to develop a proteomics methodology that improves the identification of membrane proteomes from mammalian liver. Shotgun proteomics is a method that allows the analysis of proteins from cells, tissues and organs and provides comprehensive characterisation of proteomes of interest. The method developed in this thesis uses separation of peptides from trypsin digested membrane proteins by immobilised pH gradient isoelectric focusing (IPG-IEF) as the first dimension of two dimensional shotgun proteomics. In this thesis, peptide IPG-IEF was shown to be a highly reproducible, high resolution analytical separation that provided the identification of over 4,000 individual protein identifications from rat liver membrane samples. Furthermore, this shotgun proteomics strategy provided the identification of approximately 1,100 integral membrane proteins from the rat liver. The advantages of using peptide IPG-IEF as a shotgun proteomics separation dimension in conjunction with label-free quantification was applied to a biological question: namely, does the presence of a spatially unrelated benign tumor affect the abundance of mouse liver proteins. IPG-IEF shotgun proteomics provided comprehensive coverage of the mouse liver membrane proteome with 1,569 quantified proteins. In addition, the presence of an Englebreth-Holm-Swarm sarcoma induced changes in abundance of proteins in the mouse liver, including many integral membrane proteins. Changes in the abundance of liver proteins was observed in key liver metabolic processes such as fatty acid metabolism, fatty acid transport, xenobiotic metabolism and clearance. These results provide compelling evidence that the developed shotgun proteomics methodology allows for the comprehensive analysis of mammalian liver membrane proteins and detailed some of the underlying changes in liver metabolism induced by the presence of a tumor. This model may reflect changes that could occur in the livers of cancer patients and has implications for drug treatments. / Mode of access: World Wide Web. / 609 p. ill. (some col.)

The dependencies of electrophoretic mobility on pH were measured for a set of 14 markers used for isoelectric focusing that were developed by the group of Šlais and that are based on substitutions on the nitrophenol core, and for a kit consisting of 5 pI markers developed by Shimura, which have an oligopeptide structure. The dissociation constants and limiting electrophoretic mobilities of these compounds were obtained from the dependencies with the use of the program AnglerFish. The isoelectric point values of the compounds were consequently calculated using the obtained data. A comparison of the obtained pI values with the values that have been declared in literature, albeit gained by different analytical methods, has been made. Key Words capillary zone electrophoresis, isoelectric focusing, pI markers, isoelectric point, thermodynamic dissociation constant, limiting ionic mobility

Master of Science / Department of Chemistry / Christopher T. Culbertson / Capillary isoelectric focusing (cIEF) is one of several electrophoretic separation techniques for proteins and various other bio - molecules widely used in biochemistry laboratories. A wide range of analytes separable by the different modes of Capillary Electrophoresis (CE) includes from a small organic or an inorganic molecule to the complex bio-molecules such as protein, peptides, cell organelles, and live microorganisms (e.g. bacteria and viruses). Of the various modes of electrophoresis, Isoelectric focusing (IEF) is a good method for the separation of large amphoteric molecules such as peptides and proteins because of the attainment of overall surface charge depending up on its environment pH. This thesis mainly focuses on application of cIEF for proteins separation and viruses’ detection, which is one of the biggest concerns of human and animal health because of viral outbreak causing loss of thousands of lives and property every year. In chapter one of this thesis, the principles and mechanisms of separation of CE, cIEF, comparative advantages of dynamic coatings over static coating, and advantages of Whole Column Imaging Detection (WCID) over On - olumn Single Point Detection have been discussed. Chapter two includes experimental procedure and calculations for EOF determination. The results of cIEF experiments with standard proteins to develop calibration curve followed by UV absorbance detection of two bacteriophage viruses TR4 and T1 are presented in the chapter three. Final chapter four includes the conclusion and discussion on future direction for the project. The main motivation for this work was to develop a method which is less labor intensive and requires shorter detection time compared to traditional detection methods such as virus culture in serology (7days), polymerase chain reaction (PCR) and gel electrophoresis (6hrs to 2days). A commercially available dynamic coating reagent, EoTrol LN® copolymer used our CE experiments found to be more convenient and efficient than commonly used surface modifiers for example silane-based reagents. Preliminary determination of the pIs of these T1 and TR4 by cIEF was 3.1 ± 1.0 and 6.8 ± 1.0 respectively. The pI of viruses can differ by their strains and the phase of virus - growth. The viruses, though closely related, are easily distinguishable by their different pIs.

Analysis of low-abundance components in small samples remains a challenge within bioanalytical chemistry, and new techniques for sample pretreatments followed by sensitive and informative detection are required. In this thesis, procedures for preconcentration and separation of proteins and peptides in open microchannels fabricated on silicon microchips are presented. Analyte electromigration was induced by applying a voltage along the channel length, and detection was performed either by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) within the open channel, or by sampling a nL fraction containing the preconcentrated analytes from the channel for subsequent nano-electrospray ionization- (nESI-) or MALDI-MS. Utilizing solvent evaporation from the open system during sample supply, sample volumes exceeding the 25-75 nL channel volume could be analyzed. For preconcentration/separation of components in the discrete channel volume a lid of inert fluorocarbon liquid was used for evaporation control. In Papers I and II, aqueous, carrier-free solutions of proteins and peptides were analyzed, and the method was successfully applied for fast and simple preconcentration of amyloid beta (Aβ) peptides, related to Alzheimer’s disease. The impact of possible impurities in the analysis of carrier-free solutions was investigated in Paper III with the 1D simulation software GENTRANS, and a method for open-channel isoelectric focusing in a tailor-made pH gradient was developed. The latter approach was used in Paper IV for preconcentration and purification of Aβ peptides after immunoprecipitation from cerebrospinal fluid and blood plasma, followed by MALDI-MS from a micropillar chip. Paper V includes simulations of an isotachophoretic strategy for selective enrichment of Aβ peptides. GENTRANS simulations were used to select the electrolyte composition, and 2D simulations in a geometry suitable for on-chip implementation were performed using COMSOL Multiphysics. / <p>QC 20160930</p>

Proteins play a major role in living systems and present a wide spectrum of functionalities. Many different types of proteins are involved into biological processes, such as the catalysis of biochemical reactions, cellular membrane transport, immune system response and DNA replication. However, some proteins and peptides might become harmful to living organisms; for example, their abnormal aggregation causes neurodegenerative disorders including Alzheimer disease (AD). One of the causes of AD is the presence of amyloid beta peptides Aβ(1-42), Aβ(1-40), which self-assemble into insoluble fibrils and plaques, which surround neuronal cells impeding synapsis. The number of AD patients is increasing, but a cure has not been founded yet. Therefore, it is crucial to investigate the mechanisms underlying amyloid aggregation and screening for compounds able to prevent this irreversible process. Microfluidics permits characterising the physicochemical properties of proteins, investigate their aggregation and study their interactions with other molecules. Chemical kinetics allows studying the microscopic events occurring during protein self-assembly. The combination of these two techniques provides a powerful tool for the identification of compounds inhibiting the aggregation process. In this thesis by using microfluidics, chemical kinetics and other biophysical assays, I have investigated the proteins isoelectric point (pI) and the inhibition of aberrant Aβ(1-42) self-assembly process. Firstly, I describe the development of a microfluidic platform allowing for the measurement of the protein pI, in a gradient-free manner. This approach overcomes a fundamental limitation of convectional techniques that is the achievement of a stable and well-controlled pH gradient. Secondly, I investigate the inhibiting effect of llama nanobodies on Aβ(1-42) aggregation. The findings from this study show that nanobodies target monomeric species with high affinity whereas interactions with fibril surfaces are weak. Finally, I discuss the use of other compounds inhibiting specific nucleation stages. These include the chaperones clusterin and brichos, as well as soot and pure carbon nanoparticles. Importantly, the addition of both chaperones to Aβ(1-42) solutions has an additive inhibitory effect on aggregation. My findings will improve the characterization of the physicochemical properties of proteins as well as providing promising candidates for the inhibition of specific stages of amyloid beta aggregation opening the way to possible cures for AD disease.

Environmental exposures causing ingestions of toxic chemicals, such as the polycyclic aromatic hydrocarbon 2-aminoanthracene (2-AA), may increase the risk of developing cancer and other diseases such as diabetes. To understand the mode of action of 2-AA as it relates to diabetogenic processes and pancreatic cancer, 2-AA binding to soluble protein mixtures was investigated using a novel technique called dynamic isoelectric anisotropy ligand binding assay (DIABLA). Twenty four post-weaning 3-4 week old Fischer-344 (F-344) male rats were fed 0 mg/kg (control), 50 mg/kg (low dose), 75 mg/kg (medium dose) and 100 mg/kg (high dose) 2-AA diet for 14 and 28 days. Total proteins extracted from the pancreas and liver were evaluated for their binding potential using DIABLA. This technique utilizes capillary isoelectric focusing and fluorescence anisotropy to separate proteins in their active form as well as evaluate the chemical interactions. Isoelectric point (pI) values for protein binding as well as experimental mass spectra data were determined. Investigation of 2-AA binding through screening a complex mixture of proteins is a step towards understanding the mode of action and the biological activities.

Orientadores: Everson Alves Miranda, Pedro de Alcantara Pessoa Filho / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica / Made available in DSpace on 2018-08-09T04:41:28Z (GMT). No. of bitstreams: 1 Tashima_AlexandreKeiji_D.pdf: 2449482 bytes, checksum: a1d1f605f59d627bdb98b47161d1f15d (MD5) Previous issue date: 2007 / Resumo: A técnica de precipitação é freqüentemente utilizada na recuperação de proteínas de soluções aquosas. Uma das formas de se realiza-la é através do processo de precipitação isoelétrica, que consiste no ajuste do pH do meio ao valor em que a proteína tem carga global nula, ou seja, no ponto isoelétrico, pI. Ácidos e bases minerais são normalmente utilizados para ajustar o pH do meio ao pI e provocar a precipitação de proteínas. Contudo, para se obter proteínas de alta pureza e evitar a poluição do meio com resíduos indesejáveis, há a necessidade de um processo adicional para a neutralização da solução e remoção dos sais gerados. Além disso, concentrações locais elevadas dos ácidos podem causar a desnaturação da proteína de interesse. Estudos recentes vêm apontando a utilização de eletrólitos voláteis como uma alternativa promissora aos agentes de precipitação convencionalmente empregados na recuperação de proteínas. Eletrólitos voláteis são obtidos pela dissolução de gases como o dióxido de carbono em solução aquosa; nesta dissolução formam-se íons, cujas concentrações dependem da temperatura e pressão do sistema. Biomoléculas de interesse farmacêutico, como a insulina, por exemplo, podem ser potencialmente recuperadas por processos de precipitação isoelétrica com o CO2. Assim, neste projeto realizou-se um estudo experimental e teórico da precipitação isoelétrica da insulina suína com dióxido de carbono, avaliando-se a influência dos parâmetros de processo como a temperatura, pressão e concentrações de eletrólitos e de proteínas sobre a precipitação. A cinética de variação de pH devida à acidificação das soluções contendo a insulina foi determinada, assim como a cinética de precipitação da proteína. A utilização do bicarbonato de sódio como agente tamponante, em conjunto com o ácido carbônico formado em solução, permitiu que os estudos de equilíbrio fossem realizados sem a necessidade de nenhum componente adicional para o controle do pH do sistema. Dados de solubilidade da insulina suína foram obtidos entre as temperaturas de 5 e 25oC, até a pressão de 16 bar de CO2. Estes dados foram correlacionados por um modelo termodinâmico em que a proteína em solução foi considerada como um eletrólito, o que permitiu uma análise do efeito de forças eletrostáticas sobre a solubilidade da proteína / Abstract: Precipitation is a technique frequently employed in downstream process for the recovery of proteins from aqueous solutions. One example of such technique is the isoelectric precipitation, which consists of the adjustment of solution pH to the value where the protein has zero net charge, the isoelectric point, pI. Commonly, mineral acids and bases are used for pH adjustment and to induce protein precipitation. However, in order to obtain high purity proteins and avoid environmental pollution, an additional process is needed to neutralize and remove residual salts. It is also necessary to take into account the fact that local pH extremes can cause denaturation of the targeted protein. Recent works have pointed the use of volatile electrolytes as promising alternatives to the precipitating agents conventionally utilized in protein recovery. Volatile electrolytes are obtained by dissolution of gases as carbon dioxide in aqueous solutions. In this process, the volatile electrolyte dissociates into ions, whose concentrations depend on system pressure and temperature. Biomolecules of pharmaceutical interest as insulin, for instance, may be potentially recovered by isoelectric precipitation process with carbon dioxide. Thus, in this project an experimental and theoretical study of the isoelectric precipitation of porcine insulin with carbon dioxide was conducted, in order to evaluate the influence of parameters such as temperature, pressure and concentrations of electrolytes and protein over the precipitation process. Kinetics of pH variation due to acidification of the insulin solutions was determined, as well as protein precipitation kinetics. The use of sodium bicarbonate as buffer agent with carbonic acid produced in solution allowed the equilibrium studies be conducted without the need of any additional component to control system pH. Solubility data of porcine insulin were obtained in the temperature range of 5 to 25oC and up to CO2 pressures of 16 bar. These data were correlated by a thermodynamic model in which the protein in solution was considered as an electrolyte, which allowed an analysis of electrostatic force effects over protein solubility / Doutorado / Engenharia de Processos / Doutor em Engenharia Química

submitted by Liu Dan. / Thesis (M.Sc.)--Chinese University of Hong Kong, 1998. / Includes bibliographical references (leaves 66-80). / Abstract also in Chinese. / CONTENTS --- p.i / LIST OF TABLES --- p.iii / LIST OF FIGURES --- p.iv / LIST OF ABBREVIATIONS --- p.v / ACKNOWLEDGEMENTS --- p.vi / ABSTRACT --- p.vii / Chapter Chapter 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- History --- p.1 / Chapter 1.2 --- Immunoglobulins --- p.3 / Chapter 1.2.1 --- Structure --- p.3 / Chapter 1.2.2 --- Properties of immunoglobulins --- p.7 / Chapter 1.3 --- Monoclonal proteins and monoclonal gammopathies --- p.12 / Chapter 1.3.1 --- Monoclonal proteins --- p.12 / Chapter 1.3.2 --- Monoclonal gammopathies --- p.14 / Chapter 1.4 --- Laboratory investigation of monoclonal immunoglobulin --- p.17 / Chapter 1.4.1 --- The current procedure of investigation in laboratory --- p.17 / Chapter 1.4.2 --- Problems in identifying monoclonal immunolgobuin --- p.19 / Chapter 1.5 --- Comparison of different techniques --- p.20 / Chapter 1.5.1 --- Immunoelectrophoresis --- p.20 / Chapter 1.5.2 --- Immunofixation electrophoresis --- p.22 / Chapter 1.5.3 --- Isoelectric focusing and immunoisoelectric focusing --- p.24 / Chapter 1.6 --- Aim of the present study --- p.27 / Chapter 1.7 --- Design of experiment --- p.27 / Chapter Chapter 2 --- MATERIALS AND METHODS --- p.30 / Chapter 2.1 --- Study subjects --- p.30 / Chapter 2.2 --- Apparatus --- p.30 / Chapter 2.2 --- Apparatus --- p.30 / Chapter 2.3 --- Reagents and materials --- p.32 / Chapter 2.4 --- Preparation of gels --- p.35 / Chapter 2.5 --- Isoelectric focusing procedure --- p.36 / Chapter 2.6 --- Acid fixation and staining --- p.37 / Chapter 2.7 --- Technical factors affecting results --- p.38 / Chapter Chapter 3 --- RESULTS --- p.40 / Chapter 3.1 --- Interpretation of results in isoelectric focusing --- p.40 / Chapter 3.2 --- Affecting factors --- p.47 / Chapter 3.3 --- Comparison of the results between IEF and IFE --- p.53 / Chapter Chapter 4 --- DISCUSSION --- p.59 / Chapter Chapter 5 --- CONCLUSION --- p.65 / References --- p.66