abstract: Biosensors offer excellent diagnostic methods through precise quantification of bodily fluid biomarkers and could fill an important niche in diagnostic screening. The long term goal of this research is the development of an impedance immunosensor for easy-to-use, rapid, sensitive and selective simultaneously multiplexed quantification of bodily fluid disease biomarkers. To test the hypothesis that various cytokines induce empirically determinable response frequencies when captured by printed circuit board (PCB) impedance immunosensor surface, cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) methods were used to test PCB biosensors versus multiple cytokine biomarkers to determine limits of detection, background interaction and response at all sweep frequencies. Results indicated that sensors for cytokine Interleukin-12 (IL-12) detected their target over three decades of concentration and were tolerant to high levels of background protein. Further, the hypothesis that cytokine analytes may be rapidly detected via constant frequency impedance immunosensing without sacrificing undue sensitivity, CV, EIS, impedance-time (Zt) methods and modeling were used to test CHITM gold electrodes versus IL-12 over different lengths of time to determine limits of detection, detection time, frequency of response and consistent cross-platform sensor performance. Modeling and Zt studies indicate interrogation of the electrode with optimum frequency could be used for detection of different target concentrations within 90 seconds of sensor exposure and that interrogating the immunosensor with fixed, optimum frequency could be used for sensing target antigen. This informs usability of fixed-frequency impedance methods for biosensor research and particularly for clinical biosensor use. Finally, a multiplexing impedance immunosensor prototype for quantification of biomarkers in various body fluids was designed for increased automation of sample handling and testing. This enables variability due to exogenous factors and increased rapidity of assay with eased sensor fabrication. Methods were provided for simultaneous multiplexing through multisine perturbation of a sensor, and subsequent data processing. This demonstrated ways to observe multiple types of antibody-antigen affinity binding events in real time, reducing the number of sensors and target sample used in the detection and quantification of multiple biomarkers. These features would also improve the suitability of the sensor for clinical multiplex detection of disease biomarkers. / Dissertation/Thesis / Ph.D. Bioengineering 2012

A obesidade tem aumentado dramaticamente nos últimos anos, tornando-se o maior fator de risco para o desenvolvimento de doenças cardiovasculares, vários tipos de câncer, e também do Diabetes mellitus tipo 2 (DM 2). A associação da obesidade com o desenvolvimento do DM 2 pode ser explicada, em parte, pela secreção alterada pelo tecido adiposo de adipocinas, como a adiponectina, um hormônio com propriedades antiinflamatórias e de sensibilização à insulina. O excesso do tecido adiposo regula negativamente a secreção de adiponectina, o que ocorre de 10 a 20 anos antes da hiperglicemia crônica, fazendo com que este hormônio seja um bom indicador para o diagnóstico preditivo de DM 2. A concentração de adiponectina em plasma é usualmente aferida por ELISA, método não amplamente utilizado devido ao seu alto preço, necessidade de pessoal qualificado e material e, dessa maneira, ainda praticamente inacessível à grande parcela da população. Sendo assim, o desenvolvimento de novas metodologias e de ferramentas de diagnóstico confiáveis e de baixo custo (que possam ser implementados pelo Sistema Único de Saúde SUS) é imprescindível. Aqui, desenvolvemos um biossensor simples e de baixo custo para detecção de adiponectina baseado na espectroscopia de impedância eletroquímica (EIS) ou voltametría cíclica (CV) usando plataformas nanoestruturadas contendo receptores transmembrana de adiponectina (AdipoR1 e AdipoR2) ou anticorpos anti-AdipoQ imobilizados em eletrodos de ouro. Os melhores resultados foram obtidos através do uso dos receptores AdipoR1/R2 em conjunto com CV. Neste caso, os biossensores foram capazes de detectar concentrações de adiponectina tão baixas quanto 7 nmol L-1 com uma faixa linear entre 0,01 a 0,75 mol L-1 de adiponectina, R²=0,992. O dispositivo apresentou ótima seletividade, estabilidade e reprodutibilidade (ca. 1,7% para n=3). Além disso, em amostras de plasma humano, o biossensor obteve resultados muito próximos aos obtidos pelo método pardão ELISA, com desvio de 14%. Esperamos que este estudo propicie maior acessibilidade ao diagnóstico preditivo do DM 2 através de dispositivos mais baratos, rápidos e portáteis e que um maior número indivíduos possam ser alertados e orientados, evitando o desenvolvimento posterior da doença. / Obesity has increased dramatically in the last few years, becoming the biggest risk factor for development of cardiovascular diseases, several types of cancer and also the type 2 diabetes mellitus (DM 2). The association between obesity and DM 2 can be partially explained by the altered secretion of adiponectin hormone by the adipose tissue, which presents anti-inflammatory and insulin sensitizing properties. The excess of adipose tissue regulates negatively adiponectin secretion, which occurs 10 to 20 years before chronic hyperglycemia, making this hormone a great biomarker for predictive DM 2 diagnosis. Adiponectin plasma concentration is usually measured by ELISA, a method not widely used due to its high cost, personal and material demand, being, therefore, not accessible to part of the population. Therefore, the development of new diagnostic methodologies and tools trustable and low-cost (that can be implemented by Sistema Único de Saúde SUS) is crucial. Here we developed a simple and low-cost biosensor for adiponectin detection based on electrochemical impedance spectroscopy (EIS) or cyclic voltammetry (CV) using nanostructured platforms containing adiponectin transmembrane receptors (AdipoR1 and AdipoR2) or anti-AdipoQ antibodies immobilized on gold electrodes. The best results were achieved using AdipoR1/R2 receptors among with CV. In this case, biosensors were able to detect adiponectin at concentrations down to 7 nmol L-1 in a linear detection range from 0.01 to 0.75 mol L-1 of adiponectin, R²=0.992. The device displayed great selectivity, stability and reproducibility (ca. 1.7% for n=3). For human plasma samples, analyses using the biosensor and the ELISA technique presented similar results, with deviations of 14%. Therefore, we expect that this study leads to a greater accessibility to predictive DM 2 diagnoses through cheaper, faster and portable devices, so that a higher number of patients may be alerted and oriented, avoiding further disease development.

Neste trabalho é apresentado um estudo da imobilização da enzima horseradish peroxidase (HRPO) em matriz polimérica através de dois métodos diferentes. O primeiro consiste em um método de uma etapa, no qual a HRPO é imobilizada por eletropolimerização de pirrol em meio aquoso com eletrodo de platina – técnica esta denominada entrapment – visando a confecção de biossensores enzimáticos para a detecção amperométrica de peróxido de hidrogênio (H2O2). A matriz polimérica com a enzima imobilizada foi analisada por reação colorimétrica, confirmando as afirmações de alguns autores sobre a baixa quantidade de enzima imobilizada, e FTIR mostrando espectros bastante semelhantes entre os filmes de polipirrol (PPy) puro e de PPY + HRPO. Foram realizados estudos do efeito das concentrações de monômero, enzima e eletrólito, assim como dos parâmetros eletroquímicos para a otimização da preparação do biossensor. Os valores dos parâmetros otimizados serviram de referência para o estudo do segundo método de imobilização, no qual é utilizado um anticorpo específico para a enzima HRPO, o V3.5R3, imobilizado via entrapment com a HRPO inoculada ao sistema através da imersão do substrato formado (PPy-V3.5R3) em uma solução de HRPO. Os dois métodos de confecção dos biossensores para a determinação quantitativa de H2O2 são comparados: em relação ao parâmetro comportamento linear, verificou-se uma faixa de concentração de 0 a 15 mmol/L de H2O2 para o método via entrapment, enquanto que através do método com inoculação foi verificado um comportamento linear de 2 a 8 mmol/L de H2O2. Em relação à resposta do biossensor, tem-se para a concentração de 8 mmol/L de H2O2, uma corrente de aproximadamente 600 nA utilizando biossensores preparados pelo método de entrapment e 300 nA pelo método com inoculação. Apesar do baixo desempenho da imobilização do anticorpo V3.5R3 para a detecção de H2O2, o sucesso na imobilização de diferentes biocomponentes e o desenvolvimento de mecanismos como a inoculação amplia o espectro de possibilidades para o estudo de biossensores. / In this work is presented a study of the immobilization of the enzyme horseradish peroxidase (HRPO) in polymeric matrix by two different methods. The first one consist in a one-step method, in which the HRPO is immobilized by electropolymerization of pyrrole in aqueous solution onto platin electrode – techniques denominated entrapment – aiming the confection of enzymatic biosensors for the amperometric detection of hydrogen peroxide (H2O2). The polymeric matrix with the immobilized enzyme (substrate PPy-HRPO) was analyzed by colorimetric reaction, confirming the affirmations of some authors about the low quantities of enzymatic immobilization, and FTIR, what shows very similar specters for the polypyrrole (PPy) film and the PPy + HRPO. Studies of the concentrations of monomer, enzyme and electrolyte, as well as of the electrochemical parameters, have been carried through for the optimization of the biossensor. The values of the optimized parameters were used as reference for the study of the second immobilization method, in which is used a specific antibody for enzyme HRPO, the V3.5R3, immobilized via entrapment. The HRPO is, then, inoculated to the system by immersion of the PPy-V3.5R3 substrate in HRPO solution. The results of the biossensores confectioned by the two methods are compared: about the linear behavior it was verified a range of concentration form 0 to 15 mmol/L of H2O2, while through the second method was verified a linear range of 2 to 8 mmol/L of H2O2. About the signal response, for the same concentration of 8 mmol/L of H2O2, an electric current of 600 nA was reached, against 300 nA with the biosensors constructed by the second method. Although the low performance of the immobilization of the antibody V3.5R3 for the H2O2 detection, the success in different biocomponents immobilization and the development of mechanisms as the inoculation increases the possibilities specter for biosensors research.

>Magister Scientiae - MSc / HIV and AIDS are among the world's pandemics that pose serious concern to almost every individual in the world. With the current level of availability of anti-retroviral (ARV) drugs and the ease of accessibility of treatment in many countries such as South Africa, the disease can be controlled by suppressing the viral load of an infected individual. These anti HIV drugs such as delavirdine are metabolised by enzymes which are found in the liver microsomes, particularly those of the cytochrome P450 family. Due to the fact that the metabolic rate of a patient determines the effect of the drug, the drug could either have a beneficial or an adverse effect once it is administered. It is therefore imperative that the metabolic profile of a patient is determined at point-of-care is necessary for proper dosing of the ARV drugs. In this project a nanobiosensor system was devised and used for the determination of the metabolism of delavirdine, a non-nucleoside reverse transcriptase inhibitor (NNRTI) ARV drug. The nanobiosensor was prepared by the entrapment of the isoenzyme CYP3A4 into a pre-formed electro active carrier matrice consisting of a dendrimeric copper generation-2 poly (propylene imine)-co-polypyrrole star copolymer (Cu(G2PPI)-co-PPy). The metallo-dendrimer was used as a host for the enzyme and provided thenecessary bio-compatible environment that allowed the direct transfer of electrons between the enzyme's active centres and platinum electrode surface. Copper was the choice of metal used in the study due to its properties. Copper is a malleable, ductile and a good conductor of both heat and electricity. It is a better conductor than most metals. Silver which also belongs to group 1b in the periodic table is a better electrical conductor than copper but copper has better corrosion resistance and is a more abundant and hence it is a cheaper material to use. Cu(G2PPI)-co-PPy was prepared by the incorporation of the copper metal into the G2PPI and the electropolymerization of pyrrole onto the Cu(G2PPI). The incorporation of Cu into G2PPI was determined by FTIR which did not show the presence of the Cu but showed an increase in the intensities of the peaks after the incorporation. The surface morphology of Cu (G2PPI) was confirmed by the use of HRSEM which showed a difference in the surface morphology of the dendrimer moiety with the addition of the copper metal. The HRSEM images after Cu incorporation resulted in the change from rough surface to smooth surface with open cavities which were essential for the entrapment of the biological systems (CYP3A4). Energy dispersive spectrometry (EDS) and HRTEM were used to confirm the presence of spherically shaped copper nanoparticles in the Cu (G2PPI) and were found to have a size distribution of 12-17 nm with an average particle size of 15nm. The star copolymer (Cu(G2PPI)-co-PPy) was characterised using cyclic voltammetrywhere it was confirmed that the material was electroactive and conducting due to electron movement along the polymer chain. A diffusion co-efficient (D₀) value of 8.64 x 10⁻⁵ cm²/s was determined for the material indicating a slow electron transfer kinetics within the diffusion layer. The constructed nanobiosensor was developed using copper poly (propylene imine) – polypyrrole star copolymer, bovine serum albumin and glutaraldehyde coupled to the enzyme CYP3A4. The resultant nanobiosensor parameters include a dynamic linear range (DLR) of 0.01-0.06 nM, a limit of detection (LOD) of 0.025 nM and a sensitivity value of0.379 μA/nM.

Specific detection of biological matter is one of the key elements in a wide range of modern fields such as food industry, medicine, environmental and pharmaceutical industries. Generally, current common methods of detection (e.g. ELISA) involve molecular labelling, requirements for well-trained personnel and lengthy experimental procedures such as bacteria culture. All of the above issues result in high costs for biological analysis, and consequently, high costs for medical service, therapeutic drugs and various food products. Biosensors, on the other hand, can provide quick and cheap solutions to these problems. The field of optical biosensors is dominated by the method of surface plasmon resonance, which so far has attracted a lot of attention in the pharmaceutical industry. Investigation of long-range surface plasmon-polariton waveguides as an application for biosensing is still very novel, and most of it exists in the venue of theoretical discussions and modelling. The objective of this thesis is to demonstrate the capability of the novel optical biosensor based on plasmonic waveguides to selectively detect various biological entities in solutions. The experiments were conducted on photolithographically fabricated sensors consisting of straight gold waveguides embedded in low-refractive index fluoropolymer CYTOP and a microfluidic channel. As a proof-of-concept, a demonstration of basic sensing experiments such as detection of change in refractive index of bulk solution and non-specific adsorption of bovine serum albumin is provided. Further investigation of the sensor capabilities involved specific detection of human red blood cells and leukemia markers. Red blood cell detection was based on ABO blood grouping and included the estimation of limit of detection and signal-to-noise ratio for single cell detection. Finally, a clinically relevant problem of B-cell leukemia marker detection was targeted. The sensor demonstrated the ability to detect the relative abundance of similar proteins (immunoglobulin kappa and lambda) in a complex fluid (human serum). In addition, an experimental study on the optimization of the sensor for sensitivity was conducted.

Detection and quantification of small peptides, such as yeast pheromones, are often challenging. We developed a highly sensitive and robust affinity-assay for the quantification of the α-factor pheromone of Saccharomyces cerevisiae based on recombinant hydrophobins. These small, amphipathic proteins self-assemble into highly stable monolayers at hydrophilic-hydrophobic interfaces. Upon functionalization of solid supports with a combination of hydrophobins either lacking or exposing the α-factor, pheromone-specific antibodies were bound to the surface. Increasing concentrations of the pheromone competitively detached the antibodies, thus allowing for quantification of the pheromone. By adjusting the percentage of pheromone-exposing hydrophobins, the sensitivity of the assay could be precisely predefined. The assay proved to be highly robust against changes in sample matrix composition. Due to the high stability of hydrophobin layers, the functionalized surfaces could be repeatedly used without affecting the sensitivity. Furthermore, by using an inverse setup, the sensitivity was increased by three orders of magnitude, yielding a novel kind of biosensor for the yeast pheromone with the lowest limit of detection reported so far. This assay was applied to study the pheromone secretion of diverse yeast strains including a whole-cell biosensor strain of Schizosaccharomyces pombe modulating α-factor secretion in response to an environmental signal.

Having evolved longer than any other group of organisms, bacteria have been perfecting mechanisms of sensing their environments for billions of years. Recent advances in the field of biosensing have enabled miniaturization of existing biosensors, but the number of characterized biosensor elements remains limited. Sensing parts derived from bacteria make promising targets for integration into biosensor devices and could expand the repertoire of easily detectable compounds. Here, RNA sequencing screening was used to identify a novel TetR family 3-ketosteroid inducible transcription factor called SRTF1 (Steroid Responsive Transcription Factor 1) from the Gram-positive soil bacterium Pimelobacter simplex. This is the first transcription factor confirmed to be inducible by these steroids in-vitro. A potential regulon was identified using in-vitro chromatin immunoprecipitation sequencing, revealing a conserved 20 base pair long palindrome within several promoters in a region of the P. simplex genome highly differentially expressed on exposure to steroids. Biolayer interferometry and intrinsic tryptophan fluorescence were used to quantitatively characterize the transcription factor’s DNA binding strength and hormone induction specificity. Circular dichroism study of SRTF1 revealed it is primarily alpha-helical like almost all other TetR family transcription factors. Bases in a core GCCG repeat within the palindrome were identified as important for SRTF1 binding and a disrupted palindrome was generated that greatly increased a quantum-dot based SRTF1 biosensor’s sensitivity for progesterone. As the transcription factor displays cross reactivity to cortisol and aldosterone that is undesirable in a diagnostic device, a fluorescent reporter assay based on the transcription factor was constructed. This reporter assay showed a similar steroid induction profiles as purified SRTF1, and was used to select for mutant SRTF1 variants generated using error-prone polymerase chain reaction with reduced inducibility by these 11-hydroxy steroids. This pipeline for identifying novel transcription factors, characterizing their DNA and ligand binding profiles, and altering them through mutation of DNA and protein sequences could allow for an expanded number of biosensor parts.

Detection and quantification of small peptides, such as yeast pheromones, are often challenging. We developed a highly sensitive and robust affinity-assay for the quantification of the α-factor pheromone of Saccharomyces cerevisiae based on recombinant hydrophobins. These small, amphipathic proteins self-assemble into highly stable monolayers at hydrophilic-hydrophobic interfaces. Upon functionalization of solid supports with a combination of hydrophobins either lacking or exposing the α-factor, pheromone-specific antibodies were bound to the surface. Increasing concentrations of the pheromone competitively detached the antibodies, thus allowing for quantification of the pheromone. By adjusting the percentage of pheromone-exposing hydrophobins, the sensitivity of the assay could be precisely predefined. The assay proved to be highly robust against changes in sample matrix composition. Due to the high stability of hydrophobin layers, the functionalized surfaces could be repeatedly used without affecting the sensitivity. Furthermore, by using an inverse setup, the sensitivity was increased by three orders of magnitude, yielding a novel kind of biosensor for the yeast pheromone with the lowest limit of detection reported so far. This assay was applied to study the pheromone secretion of diverse yeast strains including a whole-cell biosensor strain of Schizosaccharomyces pombe modulating α-factor secretion in response to an environmental signal.

Guanosine tetraphosphate (ppGpp) is a bacterial signaling molecule involved in activating the stringent response, a cellular reaction to environmental stress that downregulates cell division and metabolism processes to conserve nutrients. The stringent response is implicated in some instances of antibiotic persistence, so broadening the current understanding of ppGpp signaling is useful. This thesis seeks to generate a ppGpp biosensor that will bind ppGpp and emit fluorescent light in its presence, which will allow for improved research into the pathways and functions of the signaling molecule. To generate a novel ppGpp biosensor, I converted a biosensor previously used to detect cyclic di-GMP (a different signaling molecule) to contain a binding site transformed to now bind specifically with ppGpp. The genetic sequence for the cyclic di-GMP binding site was replaced with the ppGpp hydrolase domain which has a specific affinity for ppGpp; however, hydrolase activity would provide unwanted breakdown of the ppGpp, so it is mutated further to neutralize hydrolase activity. The desired outcome of this thesis results in a biosensor with a binding site that has a specific and sufficient binding affinity for the ppGpp molecule. Using this, we can determine how ppGpp levels are regulated in bacteria under conditions of stress, and how this signaling molecule is related to the survival of bacteria in response to antibiotic treatment.

Arsenic is a notorious poison due to its high toxicity, worldwide distribution, and lack of any taste and colour once dissolved. The abundance of arsenic in Earth’s crust makes that it can naturally find its way into food and drinking water. Rapid and reliable detection of arsenic, directly in the field, is critical to support evidence-based decision-making in choosing irrigation or drinking water sources. Current cost-effective colourimetric techniques are associated with poor accuracy, health risks, and unacceptable levels of false negatives. Arsenic-specific cellular sensors, or biosensors, may present an inexpensive, safe, and renewable alternative, yet they have long been criticized for unsatisfactory sensing performance, and inconsistency of the outcome. This, in addition to the lack of suitable instruments capable of measuring the signals produced by these biosensors, has led to very few solutions reaching market. The goal of my thesis research was to test hypotheses that improve our fundamental understanding of As species biogeochemistry in simple and complex environmental matrices to then develop a new arsenic monitoring interface, one that would be both simple and accessible to the general public. Using a combination of wild-type and mutant strains, I managed to detail both the internal regulation of arsenic, and the external drivers of arsenic bioavailability. I started by designing a defined exposure protocol that achieved, for the first time, equimolar uptake of over 94% of the added As(III) and As(V) into the cells. By developing this control early into my thesis, I then worked to reintroduce commonly found constituents of environmental waters that are thought to impact arsenic uptake. This direct testing approach uncovered fundamentals of environmental arsenic redox chemistry such as As(III) photooxidation in solution, environmental ligand exchanges, and biological transport pathways. Simplifying a complex exposure protocol for use by the general public required automation of the data analysis steps. This consists of several hundred lines of code, capable of analyzing, normalizing and stabilizing biosensor output to improve the consistency and robustness of this system. These algorithms were then integrated into a new arsenic monitoring interface, one that was built and designed specifically for dehydrated biosensors. This portable, low-cost spectrometer achieved a fluorescent detection range that rivals expensive and sophisticated laboratory equipment at a fraction of the price, and without the need for a computer to compile the measurements. In contrast to highly criticized colorimetric techniques, the biosensor exposure protocol exceeds in operational use, reliability and detection limit. At its core, my thesis research provides a new and complete arsenic testing solution, one capable of measuring both As(III) and As(V) at levels relevant to the World Health Organization and Canadian guidelines for arsenic content in water (10 µg/L). It also provides a new method capable of selectively discriminating between arsenic species, thereby providing an inexpensive and high-throughput arsenic speciation method. I hope this work will help kickstart development of a marketable solution that empowers individuals to test and to monitor the quality of their water sources.