Cross-over electrophoresis, an immunological method for analyzing blood residues on archaeological artifacts, is tested. Artifacts from three sites were utilized in the testing of this methodology. The sites are the Dietz site in south-central Oregon (282 artifacts), Konemehu in northern California (48 artifacts tested for Winthrop Associates), and Chimney Shelter in southwestern Oregon (3 artifacts from the Umpqua National Forest).

This thesis investigates technologies directed towards developing photonic crystal display devices. A switching technology based on dye electrophoretic motion within a 1D porous photonic crystal was developed. Dissociated absorbing dye species were moved through the assembled device and reflectance was controllably altered by up to 0.4. Refinement of fabrication techniques yielded a slow switching device, whose time-resolved reflectance data was analyzed. A wavelength dependence of the device switching speed was observed. This phenomenon was described by modelling where bandgap effects match observation. These devices may be improved by employing a 3D photonic crystal. We developed a nanoimprint lithography technique for seeding films deposited by GLAD for the fabrication of 3D square spiral photonic crystals. Parameters for patterning a precisely defined mould pattern using electron beam lithography were established. A large area diamond:1 square spiral photonic crystal was fabricated on the nanoimprinted seeds, and it exhibited a visible wavelength bandgap. / Micro-Electro-Mechanical Systems (MEMS) and Nanosystems

No description available.

No description available.

B. henselae, B. bacilliformis and B. quintana are capable of causing vasoproliferative diseases in humans by modulating apoptosis and proliferation of endothelial cells. Bartonella clarridgeiae, a close relative of the pathogenic Bartonellae, has been implicated in human disease but has not yet been isolated from a human patient. Both B. bacilliformis and B. clarridgeiae have flagella and a flagellar type 3 secretion system, while B. henselae and B. quintana do not. We created 2 non-motile mutants of B. clarridgeiae by interrupting the flagellin gene, flaA, or the flagellar motor genes, motBC. We investigated whether B. clarridgeiae could invade human endothelial cells (HMECs) and if functional flagella were important for invasion. The non-motile mutants and the wild-type strain were capable of entering HMECs in vitro. The flaA mutant was deficient in attachment, but the HMECs in culture with the flaA mutant demonstrated increased proliferation. The motBC mutant showed enhanced invasion. Differential secretion of proteins was revealed by 2-D electrophoresis and MALDI-TOF analysis of secretomes from the co-cultures compared to uninfected HMECs. HMECS infected with wild-type B. clarridgeiae secreted proteins indicative of proliferation. The flaA mutant induced the secretion of proteins involved in cytoskeletal rearrangement, cell migration, and proliferation. The motBC-infected HMECs showed signs of hypoxia. The co-chaperonin GroES was found in higher concentration in the supernatant of the hyper-invasive motBC strain/HMEC co-culture than the wild-type co-culture and was found at a very low concentration in the flaA culture supernatant. Cross-talk between secretion systems is suggested.

Salmonella species continue to be commonly associated with cases of food-borne disease in developed countries. In the United States in 2001, the incidence per 100,000 people was highest for salmonellosis (15.1), followed by campylobacteriosis (13.8) and shigellosis (6.4). Enteric pathogens usually contaminate the surface of raw animal products during slaughter and primary processing (scalding, defeathering or dehiding, rinsing, cutting, mixing, and grinding, etc.) and can attach and/or reside in the regular and irregular surfaces of the skin, multiply and, thereafter, contaminate food preparation surfaces, hands and utensils. Trisodium phosphate (TSP) has been approved by the USDA as a sanitizer to reduce surface loads of Salmonella on chicken carcasses. A number of studies had demonstrated that TSP effectively removes surface contamination of carcasses by food-borne pathogens. However, very little scientific evidence is available which identifies the actual mechanisms of TSP antimicrobial activity and the response of food-borne pathogens exposed to TSP. This study examined both the physiological and molecular response of Salmonella enterica serovar Enteritidis to TSP treatment. The role of high pH during TSP treatment on its antimicrobial activity was examined. Adaptation of S. enterica serovar Enteritidis to TSP treatment was also examined by analyzing the proteome of serovar Enteritidis cells using two-dimensional gel electrophoresis and mass spectrometry. The role of high pH on the antimicrobial activity of TSP was examined using comparative studies involving treatment solutions containing different concentrations of TSP, treatment solutions adjusted to the equivalent pH as in each of the TSP treatments and TSP solutions pH adjusted to 7.0. Direct and indirect indices of cell survival, membrane damage, and cellular leakage were also employed to examine specific antimicrobial effects. Cell viability, loss of membrane integrity, cellular leakage, release of lipopolysaccharides and cell morphology were accordingly examined and quantified under the above treatment conditions. Exposure of serovar Enteritidis cells to TSP or equivalent alkaline pH made with NaOH resulted in the loss of cell viability and membrane integrity in a TSP concentration- or NaOH-alkaline pH-dependent manner. In contrast, cells treated with different concentrations of TSP whose pH was adjusted to 7.0 did not show any loss of cell viability or membrane integrity. These results indicate that TSP is a potent membrane-acting agent, and provide compelling evidence that high pH during TSP treatment was responsible for its antimicrobial activity. Adaptation of S. enterica serovar Enteritidis with a sublethal concentration of TSP resulted in the induction of the alkaline stress response. Alkaline stress response involves induced thermotolerance, resistance to higher concentrations of TSP, high pH and sensitivity to acid. Examination of the proteome of TSP-adapted cells revealed differential expression of a number of proteins but did not include the common heat shock proteins involved in thermotolerance. However, TSP adaptation caused a shift in the membrane fatty acid composition from unsaturated to a higher saturated and cyclic fatty acid. This shift in fatty acid composition increases the melting point of the cytoplasmic membrane so that it remains functional at high temperatures. Biofilm bacteria are more resistant to sanitizers, heat and antimicrobial agents than their planktonic counterparts. Examination of the proteome of TSP-adapted biofilm cell of S. enterica serovar Enteritidis revealed little overlap in the protein profile compared to TSP-adapted planktonic cells. Proteomic examination of planktonic and biofilm cells of S. enterica serovar Enteritidis revealed differential expression of a number of proteins involved in DNA replication, stress survival and transport of newly synthesized proteins. These results clearly indicate that changes in the expression of specific genes are involved in the biofilm mode of growth, which could play a significant role in resistance to antimicrobial agents. The results of the current study provide a better understanding of the mechanisms of antimicrobial action of TSP and also elucidate the response of S. enterica serovar Enteritidis to TSP and high pH adaptation. The study also raises new questions regarding stress tolerance of S. Enteritidis following TSP or alkaline pH adaptation with relevance to food safety.

Salmonella species continue to be commonly associated with cases of food-borne disease in developed countries. In the United States in 2001, the incidence per 100,000 people was highest for salmonellosis (15.1), followed by campylobacteriosis (13.8) and shigellosis (6.4). Enteric pathogens usually contaminate the surface of raw animal products during slaughter and primary processing (scalding, defeathering or dehiding, rinsing, cutting, mixing, and grinding, etc.) and can attach and/or reside in the regular and irregular surfaces of the skin, multiply and, thereafter, contaminate food preparation surfaces, hands and utensils. Trisodium phosphate (TSP) has been approved by the USDA as a sanitizer to reduce surface loads of Salmonella on chicken carcasses. A number of studies had demonstrated that TSP effectively removes surface contamination of carcasses by food-borne pathogens. However, very little scientific evidence is available which identifies the actual mechanisms of TSP antimicrobial activity and the response of food-borne pathogens exposed to TSP. This study examined both the physiological and molecular response of Salmonella enterica serovar Enteritidis to TSP treatment. The role of high pH during TSP treatment on its antimicrobial activity was examined. Adaptation of S. enterica serovar Enteritidis to TSP treatment was also examined by analyzing the proteome of serovar Enteritidis cells using two-dimensional gel electrophoresis and mass spectrometry. The role of high pH on the antimicrobial activity of TSP was examined using comparative studies involving treatment solutions containing different concentrations of TSP, treatment solutions adjusted to the equivalent pH as in each of the TSP treatments and TSP solutions pH adjusted to 7.0. Direct and indirect indices of cell survival, membrane damage, and cellular leakage were also employed to examine specific antimicrobial effects. Cell viability, loss of membrane integrity, cellular leakage, release of lipopolysaccharides and cell morphology were accordingly examined and quantified under the above treatment conditions. Exposure of serovar Enteritidis cells to TSP or equivalent alkaline pH made with NaOH resulted in the loss of cell viability and membrane integrity in a TSP concentration- or NaOH-alkaline pH-dependent manner. In contrast, cells treated with different concentrations of TSP whose pH was adjusted to 7.0 did not show any loss of cell viability or membrane integrity. These results indicate that TSP is a potent membrane-acting agent, and provide compelling evidence that high pH during TSP treatment was responsible for its antimicrobial activity. Adaptation of S. enterica serovar Enteritidis with a sublethal concentration of TSP resulted in the induction of the alkaline stress response. Alkaline stress response involves induced thermotolerance, resistance to higher concentrations of TSP, high pH and sensitivity to acid. Examination of the proteome of TSP-adapted cells revealed differential expression of a number of proteins but did not include the common heat shock proteins involved in thermotolerance. However, TSP adaptation caused a shift in the membrane fatty acid composition from unsaturated to a higher saturated and cyclic fatty acid. This shift in fatty acid composition increases the melting point of the cytoplasmic membrane so that it remains functional at high temperatures. Biofilm bacteria are more resistant to sanitizers, heat and antimicrobial agents than their planktonic counterparts. Examination of the proteome of TSP-adapted biofilm cell of S. enterica serovar Enteritidis revealed little overlap in the protein profile compared to TSP-adapted planktonic cells. Proteomic examination of planktonic and biofilm cells of S. enterica serovar Enteritidis revealed differential expression of a number of proteins involved in DNA replication, stress survival and transport of newly synthesized proteins. These results clearly indicate that changes in the expression of specific genes are involved in the biofilm mode of growth, which could play a significant role in resistance to antimicrobial agents. The results of the current study provide a better understanding of the mechanisms of antimicrobial action of TSP and also elucidate the response of S. enterica serovar Enteritidis to TSP and high pH adaptation. The study also raises new questions regarding stress tolerance of S. Enteritidis following TSP or alkaline pH adaptation with relevance to food safety.

Electrophoresis separation corresponds to the motion and separation of dispersed particles under the influence of a constant electric field. In molecular biology, electrophoresis separation plays a major role in identifying, quantifying and studying different biological samples such as proteins, peptides, RNA acids, and DNA. In electrophoresis separation, different characteristics of particles, such as charge to mass ratio, size, and pI, can be used to separate and isolate those particles. For very complex samples, two or more characteristics can be combined to form a multi-dimensional electrophoresis separation system, significantly improving separation efficiency. Much effort has been devoted in recent years to performing electrophoresis separations in microfluidic format. Employing microfluidic technology for this purpose provides several benefits, such as improved transport control, reduced sample volumes, simplicity of operation, portability, greater accessibility, and reduced cost. The aim of this study is to develop microfluidic systems for high-performance separation of biochemical samples using electrophoresis methods. The first part of the thesis concerns the development of a fully integrated microfluidic chip for isoelectric focusing separation of proteins with whole-channel imaging detection. All the challenges posed in fabricating and integrating the chip were addressed. The chip was tested by performing protein and pI marker separations, and the separation results obtained from the chip were compared with those obtained from commercial cartridges. Side-by-side comparison of the results validated the developed chip and fabrication techniques. The research also focuses on improving the peak capacity and separation resolution of two counter-flow gradient electrofocusing methods: Temperature Gradient Focusing (TGF) and Micellar Affinity Gradient Focusing (MAGF). In these techniques, a temperature gradient across a microchannel or capillary is used to separate analytes. With an appropriate buffer, the temperature gradient creates a gradient in the electrophoretic velocity (TGF) or affinity (MAGF) of analytes and, if combined with a bulk counter-flow, ionic species concentrate at unique points where their total velocity is zero, and separate from each other. A bilinear temperature gradient is used along the separation channel to improve both peak capacity and separation resolution simultaneously. The temperature profile along the channel consists of a very sharp gradient used to pre-concentrate the sample, followed by a shallow gradient that increases separation resolution. A simple numerical model was applied to predict the improvement in resolution when using a bilinear gradient. A hybrid PDMS/glass chip integrated with planar micro-heaters for generating bilinear temperature gradients was fabricated using conventional sputtering and soft lithography techniques. A specialized design was developed for the heaters to achieve the desired bilinear profiles using both analytical and numerical modeling. To confirm the temperature profile along the channel, a two-color thermometry technique was also developed for measuring the temperature inside the chip. Separation performance was characterized by separating several different dyes, amino acids and peptides. Experiments showed a dramatic improvement in peak capacity and resolution of both techniques over the standard linear temperature gradients. Next, an analytical model was developed to investigate the effect of bilinear gradients in counter-flow gradient electrofocusing methods. The model provides a general equation for calculating the resolution for different gradients, diffusion coefficients and bulk flow scan rates. The results indicate that a bilinear gradient provides up to 100% improvement in separation resolution over the linear case. Additionally, for some scanning rates, an optimum bilinear gradient can be found that maximizes separation resolution. Numerical modeling was also developed to validate some of the results. The final part of the thesis describes the development of a two-dimensional separation system for protein separation, combining temperature gradient focusing (TGF) and sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) in a PDMS/glass microfluidic chip. An experimental study was performed on separating a mixture of proteins using two characteristics: charge to mass ratio, and size. Experimental results showed a dramatic improvement in peak capacity over each of the one-dimensional separation techniques.

La electroforesis capilar presenta menos sensibilidad en términos de concentración, comparado con la cromatografía de líquidos debido principalmente al pequeño volumen de inyección de la muestra y a la pequeña longitud del camino óptico para la detección, el cual coincide con el diámetro interno del capilar. El objetivo de la presente Tesis es el estudio y desarrollo de diferentes estrategias para disminuir los límites de detección de la electroforesis capilar, concretamente técnicas de preconcentración electroforéticas y cromatográficas. Se presentan técnica basadas en isotacoforesis y SPE acoplado en línea a electroforesis capilar para la determinación de drogas de abuso y de anti-inflamatorios no esteroidales. El desarrollo fundamental de estas estrategias va, en muchos casos, relacionado con el desarrollo de las aplicaciones, por lo cual el trabajo con muestras reales es fundamental, concretamente se ha trabajado con muestras biológicas (plasma y orina) y con muestras de agua medioambientales (agua de rio y de grifo). / Capillary electrophoresis is a highly promising analytical separation technique with a wide range of applications in biological and environmental fields. However, Capillary electrophoresis suffers from a lack of sensitivity when compared with chromatographic techniques because, in general, it is not possible to inject high sample volumes and also due to the short optical path-length for on-capillary detection. The objective of this Doctoral Thesis is the development of analytical methods to increase sensitivity in capillary electrophoresis for the determination of pharmaceuticals and drugs of abuse in environmental and biological samples. To do that, several preconcentration techniques either stacking (based on isotachophoresis principles) or chromatographic (based on in-line SPE) have been studied. The compounds selected for the different studies in this Doctoral Thesis belong to the pharmaceutical compound group (in particularly in non-steroidal anti-inflammatory drugs) and to the drugs of abuse group.

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