Therapeutic proteins have become a cornerstone of modern medicine since the FDA approval of recombinant human insulin in 1982. Likewise, biosensors transform chemical detection and disease diagnostics by identifying biomarkers, chemical contaminants, and infective agents. Long-standing methods for creating therapeutics and biosensors employ whole cells such as Escherichia coli (E. coli). Alternatively, cell-free protein synthesis (CFPS) employs the enzymatic reactions necessary for protein production and biosensing within a cell, but in an engineered reactor environment facilitating unprecedented access to and control over biochemical machinery, preservation by cryodesiccation for portable deployment, and functionality in cytotoxic applications. This dissertation reports advances in an E. coli CFPS production platform toward creating therapeutic proteins by this means. First, an endotoxin-free CFPS platform is created by optimizing fermentation and cell-extract harvest of an endotoxin-free E. coli strain. Next, liquid cell growth culture media is specially formulated to change chemical composition during cell culture and provide a streamlined method for producing high-yielding, endotoxin-free E. coli CFPS. Then, novel CFPS bioreactor formats are mathematically validated and developed which employ "hydrofoam" and oxygen to increase therapeutic protein production yield. Additionally, advances are reported in CFPS biosensing technology. First, a chimeric fusion protein incorporating the ligand binding domain of the human estrogen receptor is expressed in CFPS to detect estrogenic chemicals in the presence of human blood and urine. Next, the molecular mechanism of this protein construct is elucidated and the assay readout is optimized with mathematical simulations and CFPS. Then, CFPS is metabolically engineered to create a biosensor of L-glutamine, the most abundant amino acid in the body. Finally, this dissertation reports the development of a synergistic platform for potentially treating Acute Lymphoblastic Leukemia wherein CFPS is engineered to both produce the therapeutic protein crisantaspase and assess its activity in the presence of human serum for improved, potentially even personalized treatment of the disease. It is anticipated that the advances reported herein will contribute to the utility of in vitro or cell-free protein synthesis for therapeutic and diagnostic applications.

Ce travail s’inscrit dans le cadre de la recherche relative au développement de biosenseurs à ADN électrochimiques. Des aspects fondamentaux, ainsi que des aspects d’application de la détection d’hybridation d’ADN sont envisagés. Dans un premier temps, le comportement interfacial et le processus d’hybridation d’oligonucléotides d’ADN linéaires et ADN hairpin (structure en épingle à cheveux) nonmarqués sont étudiés en formant des monocouches auto-assemblées mixtes de monobrins d’ADN (ssADN) thiolés et d’un hydroxyalcanethiol (4-mercaptobutan-1-ol) par coadsorption spontanée sur des électrodes d’or polycristallin. L’immobilisation de monocouches mixtes ssADN/MCB est caractérisée par voie électrochimique et par spectroscopie des photoélectrons X. Des mesures de chronocoulométrie, en présence de [Ru(NH3)6]3+ (RuHex), permettent de déterminer la quantité d’ADN dans la monocouche mixte formée. Les résultats montrent que l’excès superficiel d’ADN linéaire est plus important que l’excès superficiel d’ADN hairpin sous des conditions de formation identiques. La réaction de reconnaissance moléculaire d’hybridation est détectée par des mesures d’impédance en présence de [Fe(CN)6]3-/4-. L’hybridation se traduit dans le cas de l’ADN linéaire par une augmentation de la résistance au transfert d’électron Rct tandis que dans le cas de l’ADN hairpin, Rct diminue. Ces différences sont dues au plus faible recouvrement et au changement de conformation des molécules d’ADN hairpin lors de l’hybridation. Des mesures de réflectivité de neutrons nous ont permis de mettre en évidence l’augmentation de l’épaisseur du film d’ADN hairpin et de confirmer le changement conformationel ces sondes lors de la reconnaissance moléculaire. Dans la seconde partie, nous présentons une nouvelle méthode électrochimique de détection d’hybridation, basée sur les interactions électrostatiques entre le complexe cationique RuHex et les groupements phosphates de l’ADN. Afin d’améliorer la détection des molécules de PNA (peptide nucleic acid) ont été immobilisées comme sondes de reconnaissance moléculaire. Après hybridation des sondes PNA avec le brin complémentaire, RuHex s’adsorbe sur l’ADN hybridé et un signal de réduction de ces complexes redox, enregistré par voltampérométrie alternative, constitue une signature claire de l’hybridation d’ADN à l’interface modifiée. Les interactions RuHex/PNA-ADN ont été étudiées. La constante d’adsorption de RuHex sur l’électrode modifiée PNA/MCB après hybridation est évaluée à 2,9 (±0,3) 105 M-1 en milieu Tris-HCl 0,01M, selon une isotherme de Langmuir. Les performances analytiques de la méthode de détection (sensibilité, sélectivité et reproductibilité) ont été évaluées et optimisées pour la détection des séquences d’ADN du gène de l’ARNr 23S d’Helicobacter pylori. La méthode de détection électrochimique présentée est assez sélective pour permettre de discriminer les mutations ponctuelles A2143G et A2144C de la séquence de type sauvage. La diminution significative des signaux d’admittance enregistrés en présence des séquences mutées est attribuée à la capacité accrue de discrimination de mutations ponctuelles des molécules PNA. La réponse de détection est linéaire en fonction du logarithme de la concentration de la cible d’ADN sur plus de quatre ordres de grandeur (10-6 M à 10-10 M). La limite de détection de l’oligonucléotide d’ADN complémentaire de 80 pM est très bonne. La méthode a été appliquée avec succès à la détection de fragments PCR complémentaires de 100 et 400 paires de bases, amplifiés à partir de souches SS1 d’H.pylori.

As electronics reach nanometer size scales, new avenues of integrating biology and electronics become available. For example, nanoscale field-effect transistors have been integrated with single neurons to detect neural activity. Researchers have also used nanoscale materials to build electronic ears and noses. Another exciting development is the use of nanoscale biosensors for the point-of-care detection of disease biomarkers. This thesis addresses many issues that are relevant for electrical sensing applications in biological environments. As an experimental platform we have used carbon nanotube field-effect transistors for the detection of biological proteins. Using this experimental platform we have probed many of properties that control sensor function, such as surface potentials, the response of field effect transistors to absorbed material, and the mass transport of proteins. Field effect transistor biosensors are a topic of active research, and were first demonstrated in 1962. Despite decades of research, the mass transport of proteins onto a sensor surface has not been quantified experimentally, and theoretical modeling has not been reconciled with some notable experiments. Protein transport is an important issue because signals from low analyte concentrations can take hours to develop. Guided by mass transport modeling we modified our sensors to demonstrate a 2.5 fold improvement in sensor response time. It is easy to imagine a 25 fold improvement in sensor response time using more advanced existing fabrication techniques. This improvement would allow for the detection of low concentrations of analyte on the order of minutes instead of hours, and will open the door point-of-care biosensors. / Graduation date: 2011

No description available.

Current biofuel production methods use engineered bacteria to break down cellulose and convert it to biofuel. However, this production is limited by the toxicity of the biofuel to the organism that is producing it. Therefore, to increase yields, microbial biofuel tolerance must be increased. Tolerant strains of bacteria use a wide range of mechanisms to counteract the detrimental effects of toxic solvents. Previous research demonstrates that efflux pumps are effective at increasing tolerance to various biofuels. However, when overexpressed, efflux pumps burden cells, which hinders growth and slows biofuel production. Therefore, the toxicity of the biofuel must be balanced with the toxicity of pump overexpression. We have developed a mathematical model and experimentally characterized parts for a synthetic feedback loop to control efflux pump expression so that it is proportional to the concentration of biofuel present. In this way, the biofuel production rate will be maximal when the concentration of biofuel is low because the cell does not expend energy expressing efflux pumps when they are not needed. Additionally, the microbe is able to adapt to toxic conditions by triggering the expression of efflux pumps, which allows it to continue biofuel production. The mathematical model shows that this feedback loop increases biofuel production relative to a model that expresses efflux pumps at a constant level by delaying pump expression until it is needed. This result is more pronounced when there is variability in biofuel production rates because the system can use feedback to adjust to the actual production rate. To complement the mathematical model, we also constructed a whole cell biosensor that responds to biofuel by expressing a fluorescent reporter protein from a promoter under the control of the sensor.

The silicon based sensor is able to detect part per trillion ionic silver in 0.0098% hydrofluoric acid based on the open circuit potential (OCP) measurement. The OCP jump of 100 ppt ionic silver solution is up to 120 mV. The complex agent can effectively suppress the ionic silver concentration and suppress the OCP signal. The ability of complex agent to suppress the OCP signal depends on the formation constant of the complex with silver. The complex adsorbed on the sensor surface induces a second OCP jump, the height of the second jump depends on the formation constant of the complex. The MINEQL chemical equilibrium modeling program is used to calculate the ionic silver concentration when complex agent presents, a discrepancy is found between the MINEQL simulation result and the OCP signal of the silicon based sensor. The toxicity of ionic silver to C. dubia is studied parallel to the OCP signal of silicon based sensor. Less toxicity is found when the complex agent is present similar to the OCP signal. Another discrepancy is found between the MINEQL simulation and the toxicity test when MINEQL simulation is used to predict and control the ionic silver concentration. The data from both biosensor C. dubia and silicon based sensor support each other and both are not in agreement with MINEQL simulation prediction.

For applications from biosensor generation to synthetic biology, the ability to accurately and quantitatively generate input-output data from biological systems over a wide dynamic range is becoming increasingly important. This study has demonstrated that a simple approach utilising multiple promoters, recognising the same transcriptional activator but with differing affinities, linked to compatible reporter genes can achieve this goal. This simple system highlights that even for complex promoters with multiple binding sites we can use the ratio of two reporters to obtain accurate and reproducible input-output data for reporters contained on a high copy number plasmid without the need for any background subtraction or accurate determination of cell number. It has also demonstrated that the precise promoter strengths are not too crucial to the design, provided they are significantly different, as taking the ratio of either the high affinity/low affinity or medium affinity/low affinity channels give similar improvements over any single channel alone. The modularity of this system means that it should be possible to exchange the IPTG inducible promoter and hence place the ntrC* gene under the regulation of any environmentally important promoter. It should also be possible to simply construct different strength promoters for the same transcriptional activator by standard DNA synthesis techniques, therefore allowing direct ratiometric detection of specific active transcription factors. Finally, there is considerable interest in the biosensor field in the use of immobilised cells for field based applications. In these cases, determining the exact number of viable cells present at the time of use may be problematic and obtaining high signal levels may also be essential. In this regard, the use of ratiometric reporters from constructs on high copy number plasmids could alleviate many of these potential problems and significantly simplify the required biosensor detection equipment.

Pressure ischemia is a medical condition characterised by the necrosis of the skin and underlying tissues in body areas exposed to prolonged pressure. This condition leads to the development of bedsores and affects 9% of hospitalised patients, costing the NHS between £1.4 and £2.1 billion per year. The severity of pressure ischemia has been linked to the concentration of sweat lactate, a product of sweat gland metabolism under anaerobic conditions, such as hypoxia. Normal levels of lactate in human sweat are 20±7 mM, but under ischemic conditions these can rise up to approximately 70 mM. This project presents the development of a novel flexible electrochemical enzyme-based biosensor for the continuous and non-invasive monitoring of sweat lactate with the potential for becoming a body-worn device for the early detection of pressure ischemia onset. The core of the recognition system is a flexible laminate, comprising two highly porous polycarbonate membranes, which provide support for the lactate oxidase enzyme, immobilised via covalent cross-linking. Oxidation of lactate produces H2O2, which is subsequently determined electrochemically. The transducer comprises a two-electrode system on a single flexible polycarbonate membrane, sputter-coated with gold (CE/RE) and platinum (WE) to render it conductive. The developed design has been improved through investigation into different factors regarding the immobilisation method of the enzyme in the laminate and the lowering of interferences from oxidising compounds present in sweat. The sensing system exhibits lactate selectivity at physiologically relevant concentrations in sweat for pressure ischemia (0–70 mM), with good reproducibility (7.2–12.2% RSD) for a hand-manufactured device. The reliability of the sensor’s performance and the capability to detect lactate fluctuations on human sweat samples has been demonstrated. The sensing system showed excellent operational and mechanical stability. The application of Nafion® on the WE lowered interferences from ascorbic acid and uric acid by 96.7 and 81.7% respectively. These results show promise towards the further development of a body-­‐worn monitoring device for determining lactate levels in undiluted human sweat samples in a reproducible, fast and accurate manner.

BACKGROUND: It is well known that those taking chronic opioid pain medications often become tolerant to the medications and require escalating doses over time (Drewes, 2017). No objective method to identify tolerance currently exists. OBJECTIVE: The objective of this study is to determine the usability and feasibility of a wearable biosensor technology to determine a transition point between opioid naivety and tolerance. METHODS: Participant’s were recruited in the Emergency Department setting and were being admitted with a treatment plan that includes opioid analgesics. Participants were instructed to wear the sensor at all times and to ‘tag’ the sensor when opioid pain medications were administered. This data was analyzed for trends and changes in sensor data before and after opioid administration. Research staff also conducted formative interviews during and after hospital admission to gather information on the participants’ perception of the wearable biosensor and of opioid tolerance. RESULTS: The sample included 17 participants who received, on average, 21.2 morphine equivalents per day during admission. Over 90% of participants stated that they would wear the sensor again, and 70% would even wear two. Data analysis from the E4 biosensor indicated a difference between baseline physiological signaling and post-opioid administration. CONCLUSIONS: In this study, feasibility of wearable mHealth technology was assured, and the preliminary findings of the biosensor data suggest that the features from activity data at different axes can predict opioid use. Future studies will evaluate the development of tolerance among these participants. / 2021-06-17T00:00:00Z

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.