Matching Items (12)

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Optimization and ultimate limitations for immunoassay and clinical diagnostics

Description

Biological fluids, in particular blood plasma, provide a vital source of information on the state of human health. While specific detection of biomarker species can aid in disease diagnostics, the complexity of plasma makes analysis challenging. Despite the challenge of

Biological fluids, in particular blood plasma, provide a vital source of information on the state of human health. While specific detection of biomarker species can aid in disease diagnostics, the complexity of plasma makes analysis challenging. Despite the challenge of complex sample analysis, biomarker quantification has become a primary interest in biomedical analysis. Due to the extremely specific interaction between antibody and analyte, immunoassays are attractive for the analysis of these samples and have gained popularity since their initial introduction several decades ago. Current limitations to diagnostics through blood testing include long incubation times, interference from non-specific binding, and the requirement for specialized instrumentation and personnel. Optimizing the features of immunoassay for diagnostic testing and biomarker quantification would enable early and accurate detection of disease and afford rapid intervention, potentially improving patient outcomes. Improving the limit of quantitation for immunoassay has been the primary goal of many diverse experimental platforms. While the ability to accurately quantify low abundance species in a complex biological sample is of the utmost importance in diagnostic testing, models illustrating experimental limitations have relied on mathematical fittings, which cannot be directly related to finite analytical limits or fundamental relationships. By creating models based on the law of mass action, it is demonstrated that fundamental limitations are imposed by molecular shot noise, creating a finite statistical limitation to quantitative abilities. Regardless of sample volume, 131 molecules are necessary for quantitation to take place with acceptable levels of uncertainty. Understanding the fundamental limitations of the technique can aid in the design of immunoassay platforms, and assess progress toward the development of optimal diagnostic testing. A sandwich-type immunoassay was developed and tested on three separate human protein targets: myoglobin, heart-type fatty acid binding protein, and cardiac troponin I, achieving superior limits of quantitation approaching ultimate limitations. Furthermore, this approach is compatible with upstream sample separation methods, enabling the isolation of target molecules from a complex biological sample. Isolation of target species prior to analysis allows for the multiplex detection of biomarker panels in a microscale device, making the full optimization of immunoassay techniques possible for clinical diagnostics.

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2015

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Exploiting bioparticles: from new properties of liposomes to novel applications of bioaerosol analysis

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Bioparticles comprise a diverse amount of materials ubiquitously present in nature. From proteins to aerosolized biological debris, bioparticles have important roles spanning from regulating cellular functions to possibly influencing global climate. Understanding their structures, functions, and properties provides

Bioparticles comprise a diverse amount of materials ubiquitously present in nature. From proteins to aerosolized biological debris, bioparticles have important roles spanning from regulating cellular functions to possibly influencing global climate. Understanding their structures, functions, and properties provides the necessary tools to expand our fundamental knowledge of biological systems and exploit them for useful applications. In order to contribute to this efforts, the work presented in this dissertation focuses on the study of electrokinetic properties of liposomes and novel applications of bioaerosol analysis. Using immobilized lipid vesicles under the influence of modest (less than 100 V/cm) electric fields, a novel strategy for bionanotubule fabrication with superior throughput and simplicity was developed. Fluorescence and bright field microscopy was used to describe the formation of these bilayer-bound cylindrical structures, which have been previously identified in nature (playing crucial roles in intercellular communication) and made synthetically by direct mechanical manipulation of membranes. In the biological context, the results of this work suggest that mechanical electrostatic interaction may play a role in the shape and function of individual biological membranes and networks of membrane-bound structures. A second project involving liposomes focused on membrane potential measurements in vesicles containing trans-membrane pH gradients. These types of gradients consist of differential charge states in the lipid bilayer leaflets, which have been shown to greatly influence the efficacy of drug targeting and the treatment of diseases such as cancer. Here, these systems are qualitatively and quantitatively assessed by using voltage-sensitive membrane dyes and fluorescence spectroscopy. Bioaerosol studies involved exploring the feasibility of a fingerprinting technology based on current understanding of cellular debris in aerosols and arguments regarding sampling, sensitivity, separations and detection schemes of these debris. Aerosolized particles of cellular material and proteins emitted by humans, animals and plants can be considered information-rich packets that carry biochemical information specific to the living organisms present in the collection settings. These materials could potentially be exploited for identification purposes. Preliminary studies evaluated protein concentration trends in both indoor and outdoor locations. Results indicated that concentrations correlate to certain conditions of the collection environment (e.g. extent of human presence), supporting the idea that bioaerosol fingerprinting is possible.

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2011

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New developments in isoelectric focusing and dielectrophoresis for bioanalysis

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Bioanalytes such as protein, cells, and viruses provide vital information but are inherently challenging to measure with selective and sensitive detection. Gradient separation technologies can provide solutions to these challenges by enabling the selective isolation and pre-concentration of bioanalytes for

Bioanalytes such as protein, cells, and viruses provide vital information but are inherently challenging to measure with selective and sensitive detection. Gradient separation technologies can provide solutions to these challenges by enabling the selective isolation and pre-concentration of bioanalytes for improved detection and monitoring. Some fundamental aspects of two of these techniques, isoelectric focusing and dielectrophoresis, are examined and novel developments are presented. A reproducible and automatable method for coupling capillary isoelectric focusing (cIEF) and matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) based on syringe pump mobilization is found. Results show high resolution is maintained during mobilization and &beta-lactoglobulin; protein isoforms differing by two amino acids are resolved. Subsequently, the instrumental advantages of this approach are utilized to clarify the microheterogeneity of serum amyloid P component. Comprehensive, quantitative results support a relatively uniform glycoprotein model, contrary to inconsistent and equivocal observations in several gel isoelectric focusing studies. Fundamental studies of MALDI-MS on novel superhydrophobic substrates yield unique insights towards an optimal interface between cIEF and MALDI-MS. Finally, the fundamentals of isoelectric focusing in an open drop are explored. Findings suggest this could be a robust sample preparation technique for droplet-based microfluidic systems. Fundamental advancements in dielectrophoresis are also presented. Microfluidic channels for dielectrophoretic mobility characterization are designed which enable particle standardization, new insights to be deduced, and future devices to be intelligently designed. Dielectrophoretic mobilities are obtained for 1 µm polystyrene particles and red blood cells under select conditions. Employing velocimetry techniques allows models of particle motion to be improved which in turn improves the experimental methodology. Together this work contributes a quantitative framework which improves dielectrophoretic particle separation and analysis.

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2011

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New methods for biological and environmental protein fingerprinting: from traditional techniques to new technology

Description

A new challenge on the horizon is to utilize the large amounts of protein found in the atmosphere to identify different organisms from which the protein originated. Included here is work investigating the presence of identifiable patterns of different proteins

A new challenge on the horizon is to utilize the large amounts of protein found in the atmosphere to identify different organisms from which the protein originated. Included here is work investigating the presence of identifiable patterns of different proteins collected from the air and biological samples for the purposes of remote identification. Protein patterns were generated using high performance liquid chromatography (HPLC). Patterns created could identify high-traffic and low-traffic indoor spaces. Samples were collected from the air using air pumps to draw air through a filter paper trapping particulates, including large amounts of shed protein matter. In complimentary research aerosolized biological samples were collected from various ecosystems throughout Ecuador to explore the relationship between environmental setting and aerosolized protein concentrations. In order to further enhance protein separation and produce more detailed patterns for the identification of individual organisms of interest; a novel separation device was constructed and characterized. The separation device incorporates a longitudinal gradient as well as insulating dielectrophoretic features within a single channel. This design allows for the production of stronger local field gradients along a global gradient allowing particles to enter, initially transported through the channel by electrophoresis and electroosmosis, and to be isolated according to their characteristic physical properties, including charge, polarizability, deformability, surface charge mobility, dielectric features, and local capacitance. Thus, different types of particles are simultaneously separated at different points along the channel distance given small variations of properties. The device has shown the ability to separate analytes over a large dynamic range of size, from 20 nm to 1 μm, roughly the size of proteins to the size of cells. In the study of different sized sulfate capped polystyrene particles were shown to be selectively captured as well as concentrating particles from 103 to 106 times. Qualitative capture and manipulation of β-amyloid fibrils were also shown. The results demonstrate the selective focusing ability of the technique; and it may form the foundation for a versatile tool for separating complex mixtures. Combined this work shows promise for future identification of individual organisms from aerosolized protein as well as for applications in biomedical research.

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2011

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Photo-chemical and microbial degradation of dissolved organic carbon in the Colorado River system

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The focus of this thesis is to study dissolved organic carbon composition and reactivity along the Colorado and Green Rivers. Dissolved organic carbon (DOC) in large-scale, managed rivers is relatively poorly studied as most literature has focused on pristine unmanaged

The focus of this thesis is to study dissolved organic carbon composition and reactivity along the Colorado and Green Rivers. Dissolved organic carbon (DOC) in large-scale, managed rivers is relatively poorly studied as most literature has focused on pristine unmanaged rivers. The Colorado River System is the 7th largest in the North America; there are seventeen large dams along the Colorado and Green River. DOC in rivers and in the lakes formed by dams (reservoirs) undergo photo-chemical and bio-degradation. DOC concentration and composition in these systems were investigated using bulk concentration, optical properties, and fluorescence spectroscopy. The riverine DOC concentration decreased from upstream to downstream but there was no change in the specific ultraviolet absorbance at 254 nm (SUVA254). Total fluorescence also decreased along the river. In general, the fluorescence index (FI) increased slightly, the humification index (HIX) decreased, and the freshness index (β/α) increased from upstream to downstream. Photo-oxidation and biodegradation experiments were used to determine if the observed changes in DOC composition along the river could be driven by these biogeochemical alteration processes.

In two-week natural sunlight photo-oxidation experiments the DOC concentration did not change, while the SUVA254 and TF decreased. In addition, the FI and ‘freshness’ increased and HIX decreased during photo-oxidation. Photo-oxidation can explain the upstream to downstream trends for TF, FI, HIX, and freshness observed in river water. Serial photo-oxidation and biodegradation experiments were performed on water collected from three sites along the Colorado River. Bulk DOC concentration in all samples decreased during the biodegradation portion of the study, but DOC bioavailability was lower in samples that were photo-oxidized prior to the bioavailability study.

The upstream to downstream trends in DOC concentration and composition along the river can be explained by a combination of photo-chemical and microbial degradation. The bulk DOC concentration change is primarily driven by microbial degradation, while the changes in the composition of the fluorescent DOC are driven by photo-oxidation.

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2015

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Adapting electrophoretic exclusion to a microdevice

Description

Complex samples, such as those from biological sources, contain valuable information indicative of the state of human health. These samples, though incredibly valuable, are difficult to analyze. Separation science is often used as the first step when studying these samples.

Complex samples, such as those from biological sources, contain valuable information indicative of the state of human health. These samples, though incredibly valuable, are difficult to analyze. Separation science is often used as the first step when studying these samples. Electrophoretic exclusion is a novel separations technique that differentiates species in bulk solution. Due to its ability to isolate species in bulk solution, it is uniquely suited to array-based separations for complex sample analysis. This work provides proof of principle experimental results and resolving capabilities of the novel technique. Electrophoretic exclusion is demonstrated at a single interface on both benchtop and microscale device designs. The benchtop instrument recorded absorbance measurements in a 365 μL reservoir near a channel entrance. Results demonstrated the successful exclusion of a positively-charged dye, methyl violet, with various durations of applied potential (30 - 60 s). This was the first example of measuring absorbance at the exclusion location. A planar, hybrid glass/PDMS microscale device was also constructed. One set of experiments employed electrophoretic exclusion to isolate small dye molecules (rhodamine 123) in a 250 nL reservoir, while another set isolated particles (modified polystyrene microspheres). Separation of rhodamine 123 from carboxylate-modified polystyrene spheres was also shown. These microscale results demonstrated the first example of the direct observation of exclusion behavior. Furthermore, these results showed that electrophoretic exclusion can be applicable to a wide range of analytes. The theoretical resolving capabilities of electrophoretic exclusion were also developed. Theory indicates that species with electrophoretic mobilities as similar as 10-9 cm2/Vs can be separated using electrophoretic exclusion. These results are comparable to those of capillary electrophoresis, but on a very different format. This format, capable of isolating species in bulk solution, coupled with the resolving capabilities, makes the technique ideal for use in a separations-based array.

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2012

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Ultrafine dielectrophoresis-based technique for virus and biofluid manipulation

Description

Microfluidics has shown great potential in rapid isolation, sorting, and concentration of bioparticles upon its discovery. Over the past decades, significant improvements have been made in device fabrication techniques and microfluidic methodologies. As a result, considerable microfluidic-based isolation and concentration

Microfluidics has shown great potential in rapid isolation, sorting, and concentration of bioparticles upon its discovery. Over the past decades, significant improvements have been made in device fabrication techniques and microfluidic methodologies. As a result, considerable microfluidic-based isolation and concentration techniques have been developed, particularly for rapid pathogen detection. Among all microfluidic techniques, dielectrophoresis (DEP) is one of the most effective and efficient techniques to quickly isolate and separate polarizable particles under inhomogeneous electric field. To date, extensive studies have demonstrated that DEP devices are able to precisely manipulate cells ranging from over 10 μm (mammalian cells) down to about 1 μm (small bacteria). However, very limited DEP studies on manipulating submicron bioparticles, such as viruses, have been reported.

In this dissertation, rapid capture and concentration of two different and representative types of virus particles (Sindbis virus and bacteriophage M13) with gradient insulator-based DEP (g-iDEP) has been demonstrated. Sindbis virus has a near-spherical shape with a diameter ~68 nm, while bacteriophage M13 has a filamentous shape with a length ~900 nm and a diameter ~6 nm. Under specific g-iDEP experimental conditions, the concentration of Sindbis virus can be increased two to six times within only a few seconds, using easily accessible voltages as low as 70 V. A similar phenomenon is also observed with bacteriophage M13. Meanwhile, their different DEP behavior predicts the potential of separating viruses with carefully designed microchannels and choices of experimental condition.

DEP-based microfluidics also shows great potential in manipulating blood samples, specifically rapid separations of blood cells and proteins. To investigate the ability of g-iDEP device in blood sample manipulation, some proofs of principle work was accomplished including separating two cardiac disease-related proteins (myoglobin and heart-type fatty acid binding protein) and red blood cells (RBCs). Consistent separation was observed, showing retention of RBCs and passage of the two spiked protein biomarkers. The numerical concentration of RBCs was reduced (~70 percent after one minute) with the purified proteins available for detection or further processing. This study explores and extends the use of the device from differentiating similar particles to acting as a sample pretreatment step.

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Date Created
2017

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Higher order electrokinetic effects for applied biological analytics

Description

Microfluidic systems have gained popularity in the last two decades for their potential applications in manipulating micro- and nano- particulates of interest. Several different microfluidics devices have been built capable of rapidly probing, sorting, and trapping analytes of interest. Microfluidics

Microfluidic systems have gained popularity in the last two decades for their potential applications in manipulating micro- and nano- particulates of interest. Several different microfluidics devices have been built capable of rapidly probing, sorting, and trapping analytes of interest. Microfluidics can be combined with separation science to address challenges of obtaining a concentrated and pure distinct analyte from mixtures of increasingly similar entities. Many of these techniques have been developed to assess biological analytes of interest; one of which is dielectrophoresis (DEP), a force which acts on polarizable analytes in the presence of a non-uniform electric fields. This method can achieve high resolution separations with the unique attribute of concentrating, rather than diluting, analytes upon separation. Studies utilizing DEP have manipulated a wide range of analytes including various cell types, proteins, DNA, and viruses. These analytes range from approximately 50 nm to 1 µm in size. Many of the currently-utilized techniques for assessing these analytes are time intensive, cost prohibitive, and require specialized equipment and technical skills.

The work presented in this dissertation focuses on developing and utilizing insulator-based dielectrophoresis (iDEP) to probe a wide range of analytes; where the intrinsic properties of an analyte will determine its behavior in a microchannel. This is based on the analyte’s interactions with the electrokinetic and dielectrophoretic forces present. Novel applications of this technique to probe the biophysical difference(s) between serovars of the foodborne pathogen, Listeria monocytogenes, and surface modified Escherichia coli, are investigated. Both of these applications demonstrate the capabilities of iDEP to achieve high resolution separations and probe slight changes in the biophysical properties of an analyte of interest. To improve upon existing iDEP strategies a novel insulator design which streamlines analytes in an iDEP device while still achieving the desirable forces for separation is developed, fabricated, and tested. Finally, pioneering work to develop an iDEP device capable of manipulating larger analytes, which range in size 10-250 µm, is presented.

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Date Created
2018

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Electrocatalytic Comparison of [FeFe]-Hydrogenases

Description

Oxidoreductases catalyze transformations important in both bioenergetics and microbial technologies. Nonetheless, questions remain about how to tune them to modulate properties such as preference for catalysis in the oxidative or reductive direction, the potential range of activity, or coupling of

Oxidoreductases catalyze transformations important in both bioenergetics and microbial technologies. Nonetheless, questions remain about how to tune them to modulate properties such as preference for catalysis in the oxidative or reductive direction, the potential range of activity, or coupling of multiple reactions. Using protein film electrochemistry, the features that control these properties are defined by comparing the activities of five [FeFe]-hydrogenases and two thiosulfate reductases. Although [FeFe]-hydrogenases are largely described as hydrogen evolution catalysts, the catalytic bias of [FeFe]-hydrogenases, i.e. the ratio of maximal reductive to oxidative activities, spans more than six orders of magnitude. At one extreme, two [FeFe]-hdyrogenases, Clostridium pasteuriaunum HydAII and Clostridium symbiosum HydY, are far more active for hydrogen oxidation than hydrogen evolution. On the other extreme, Clostridium pasteurianum HydAI and Clostridium acetobutylicum HydA1 have a neutral bias, in which both proton reduction and hydrogen oxidation are efficient. By investigating a collection of site-directed mutants, it is shown that the catalytic bias of [FeFe]-hydrogenases is not trivially correlated with the identities of residues in the primary or secondary coordination sphere. On the other hand, the catalytic bias of Clostridium acetobutylicum HydAI can be modulated via mutation of an amino acid residue coordinating the terminal [FeS] cluster. Simulations suggest that this change in catalytic bias may be linked to the reduction potential of the cluster.

Two of the enzymes examined in this work, Clostridium pasteurianum HydAIII and Clostridium symbiosum HydY, display novel catalytic properties. HydY is exclusively a hydrogen oxidizing catalyst, and it couples this activity to peroxide reduction activity at a rubrerythrin center in the same enzyme. On the other hand, CpIII operates only in a narrow potential window, inactivating at oxidizing potentials. This suggests it plays a novel physiological role that has not yet been identified. Finally, the electrocatalytic properties of Pyrobaculum aerophilum thiosulfate reductase with either Mo or W in the active site are compared. In both cases, the onset of catalysis corresponds to reduction of the active site. Overall, the Mo enzyme is more active, and reduces thiosulfate with less overpotential.

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2020

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High Resolution Identification of Bioparticle Subpopulations with Electrophysical Properties

Description

There is increasing interest and demand in biology studies for identifying and characterizing rare cells or bioparticle subtypes. These subpopulations demonstrate special function, as examples, in multipotent proliferation, immune system response, and cancer diagnosis. Current techniques for separation and identification

There is increasing interest and demand in biology studies for identifying and characterizing rare cells or bioparticle subtypes. These subpopulations demonstrate special function, as examples, in multipotent proliferation, immune system response, and cancer diagnosis. Current techniques for separation and identification of these targets lack the accuracy and sensitivity needed to interrogate the complex and diverse bioparticle mixtures. High resolution separations of unlabeled and unaltered cells is an emerging capability. In particular, electric field-driven punctuated microgradient separations have shown high resolution separations of bioparticles. These separations are based on biophysical properties of the un-altered bioparticles. Here, the properties of the bioparticles were identified by ratio of electrokinetic (EK) to dielectrophoretic (DEP) mobilities.

As part of this dissertation, high-resolution separations have been applied to neural stem and progenitor cells (NSPCs). The abundance of NSPCs captured with different range of ratio of EK to DEP mobilities are consistent with the final fate trends of the populations. This supports the idea of unbiased and unlabeled high-resolution separation of NSPCs to specific fates is possible. In addition, a new strategy to generate reproducible subpopulations using varied applied potential were employed for studying insulin vesicles from beta cells. The isolated subpopulations demonstrated that the insulin vesicles are heterogenous and showed different distribution of mobility ratios when compared with glucose treated insulin vesicles. This is consistent with existing vesicle density and local concentration data. Furthermore, proteins, which are accepted as challenging small bioparticles to be captured by electrophysical method, were concentrated by this technique. Proteins including IgG, lysozyme, alpha-chymotrypsinogen A were differentiated and characterized with the ratio factor. An extremely narrow bandwidth and high resolution characterization technique, which is experimentally simple and fast, has been developed for proteins. Finally, the native whole cell separation technique has also been applied for Salmonella serotype identification and differentiation for the first time. The technique generated full differentiation of four serotypes of Salmonella. These works may lead to a less expensive and more decentralized new tool and method for transplantation, proteomics, basic research, and microbiologists, working in parallel with other characterization methods.

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2020