Graphene-Based FET Detector for E. coli K12 Real-Time Monitoring and Its Theoretical Analysis

This paper presents a theoretical analysis for a graphene-based FET real-time detector of the target bacteria E. coli K12. The motivation for this study is to design a sensor device for detection of bacteria in food and water in order to guarantee food safety. Graphene is chosen as our material for sensor design, which has outstanding electrical, physical, and optical performance. In our sensor structure, graphene-based solution gate field effect transistor (FET) is the device model; fabrication and functionalization protocol are presented together in this paper. What is more, a real-time signal display system is the accompanied equipment for our designed biosensor device. In this system, the sensor bias current signal would change obviously when the target bacteria are attached to the sensor surface. And the bias current increases when the E. coli concentration increases. In the latter part, a theoretical interpretation of the sensor signal is to explain the bias current increasing after the E. coli K12 attachment.published_or_final_versio

Biosensor Platforms for Rapid Detection of <i>E. coli</i> Bacteria

Risks of contamination with the well-known food pathogen Escherichia coli are increasing over the years. Therefore, rapid and portable technologies using different types of advanced devices named biosensors with various transduction capabilities (electrochemical, optical, or acoustic) were developed and seem to offer the most elegant solutions for research communities and final users-humans. Thus, integration of microfluidic biochips/biosensors into smartphones offer the real-time detection of any infection with E. coli, helping doctors in proceeding immediately with the clinical treatment. The present chapter will discuss about the analytical performances of biosensors and microfluidics such as selection of substrates, type of (bio)functionalization, low limit of detection, specificity, and response time for monitoring different E. coli strains. Thus, it is possible to rapidly identify (30–90 s) very low concentrations of E. coli (101 CFU/mL) down to a single bacterium in real samples (water, urine, milk, beef-meat) by simple integration of an angle scatter method and microfluidic-cellulosic pads (μPAD) loaded with micro-/nanoparticles functionalized with either polyclonal anti E. coli antibodies or with DNA strains into a portable device—a smartphone. Such biosensor configuration can also be used for the detection of other types of microorganisms with potential human and animal health concerns

Digital photocorrosion of quantum semiconductor microstructures: a method for structural diagnostics and sensing of electrically charged molecules

La fabrication de dispositifs à base de structures multicouches de semi-conducteurs exige une mesure de routine des épaisseurs et de la localisation des interfaces des couches formées. Ceci est souvent réalisé en utilisant des techniques coûteuses et compliquées telles que la microscopie à force atomique (AFM) ou la spectroscopie de photoélectrons à rayons X (XPS). Dans ce travail, la métrologie à température ambiante dans un environnement aqueux a été développée pour des tests de post-croissance des nano-hétérostructures (NHs) semi-conductrices. La méthode utilise le procédé de photocorrosion numérique (DIP) et la sensibilité de l'émission de photoluminescence (PL) aux états de surface révélés pendant la photocorrosion. Le processus de photocorrosion des NHs semi-conducteurs GaAs/AlGaAs a été étudié en présence d'une excitation la bande interdite d'échantillons immergés dans différentes solutions aqueuses. Une photo-excitation de faible intensité au-dessus de la bande interdite (<105 mW/cm2) a été appliquée en mode pulsé caractérisée par un duty cycle (DC) donné par TON/(TON + TOFF). Ceci a produit des vitesses moyennes de gravure du matériau enleves à la précision de la sous-monocouche pendant chaque cycle DIP. En utilisant les techniques d’AFM et de XPS, il a été démontré que l'émission de la PL d'une NH GaAs/AlGaAs au cours de la DIP oscille en raison des couches de GaAs et d’AlGaAs révélées. Ces oscillations sont causées par la sensibilité de l'émission PL à la vitesse de recombinaison de surface des porteurs, qui diffère considérablement pour GaAs et AlGaAs. Le processus DIP a révélé une épaisseur de 1 nm de GaAs dans une structure de GaAs/AlGaAs, mais cela ne semble pas être une limite de résolution de cette approche. Le potentiel de circuit ouvert (OCP) mesuré au cours du DIP diffère entre les jonctions d'électrolyte-GaAs et électrolyte-AlGaAs formées au cours du processus de la photocorrosion. Les différences de OCP sont interprétées comme pouvant provenir des photo-oxydes superficiels qui portent la charge électrique. Le dipôle formé par ces oxydes superficiels définit l'OCP mesuré. L'oscillation de l’OCP pourrait également être utilisée pour la métrologie des NHs. Cela ouvre la perspective d'étendre la métrologie DIP aux NHs semi-conducteurs avec un signal PL non existant ou négligeable. Enfin, les entités chargées proches du voisinage d'une surface semi-conductrice affectent le taux de DIP. Cette propriété a été utilisée pour détecter la Legionella pneumophila qui est normalement chargée négativement au pH> 4. Les mesures de FTIR ont indiqué que les monocouches auto-assemblées (SAM) d’alkanethiol restent sur la surface semi-conductrice pendant le DIP. Cela a permis la détection de la Legionella pneumophila vivante à une concentration de 105 CFU/mL avec une architecture simple à base d'anticorps. Une discussion a été proposée suggérant des protocoles de biocapteurs possibles pour atteindre des limites de détection améliorées avec le biocapteur DIP.Fabrication of devices based on semiconductor multilayer structures demands routine measurement of thicknesses and location of the interfaces of the constituent layers. This is often achieved using expensive and complicated techniques such as scanning electron microscopy, secondary ion mass spectroscopy, atomic force microscopy (AFM) or x-ray photoelectron spectroscopy (XPS). In this work, room temperature metrology in water environment has been developed for post-growth testing of semiconductor nanoheterostructures (NHs). The method utilizes the process of digital photocorrosion (DIP) and the sensitivity of photoluminescence (PL) emission to surface states revealed during photocorrosion. The photocorrosion process of GaAs/AlGaAs semiconductor NHs has been investigated in the presence of above bandgap excitation of samples immersed in different aqueous solutions. In order to achieve precise control over photocorrosion rates, the NH samples were placed in a flow cell with controlled aqueous environment. A low intensity above-bandgap photoexcitation (< 105 mW/cm2) was incident in a pulse mode and characterized by a duty cycle (DC) given by TON/(TON + TOFF). This has produced average etch rates of material removed at sub-monolayer precision during each DIP cycle. Using AFM and XPS, it has been demonstrated that the PL emission from a GaAs/AlGaAs NH during DIP oscillates owing to revealed GaAs and AlGaAs layers. These oscillations are caused by the sensitivity of the PL emission to the carrier surface recombination velocity, which drastically differs for GaAs and AlGaAs. The DIP process has revealed a 1 nm thick GaAs in a GaAs/AlGaAs NH structure, but this does not seem to be the resolution limit of this approach. Open circuit potential (OCP) measured during DIP differs amongst GaAs-electrolyte and AlGaAs-electrolyte junctions formed during the photocorrosion process. The OCP oscillations were found in-phase with the PL oscillations measured during DIP. The differences of OCP are theorized to originate from the surficial photo-oxides that carry electric charge. The dipole formed by these surficial oxides define the measured OCP. The OCP oscillation could also be used for metrology of NHs. This opens the prospect of extending the DIP metrology to semiconductor NHs with non-existing or negligible PL signal. Lastly, charged entities near the vicinity of a semiconductor surface affects the rate of DIP. This property has been utilized to detect Legionella pneumophila that normally are negatively charged at pH > 4. Fourier transform infrared spectroscopy measurements have indicated that alkanethiol self-assembled monolayers (SAMs) remain on the semiconductor surface during DIP. This has allowed for the detection of live Legionella pneumophila at 105 CFU/mL with a simple antibody-based architecture. A discussion has been provided suggesting possible biosensing protocols for achieving enhanced detection limits with the DIP biosensor

Single-molecule studies of nucleic acid dynamics using carbon nanotube-based field-effect transistors

This thesis describes the development and implementation of single-molecule carbon nanotube-based field-effect transistors (smFETs) for studies of nucleic acid dynamics. Single-molecule techniques, most notably fluorescence resonance energy transfer (smFRET) and single-molecule force spectroscopy, have been employed to investigate biomolecular dynamics due to their ability to directly observe discrete, rare events, as well as to characterize structural motions in a diverse ensemble. However, these techniques are hampered by difficulties in measuring millisecond-scale dynamics, such as base pair rearrangements, as well as the inability to observe unperturbed individual molecules for long times. Alternatively, smFETs allow observation of the dynamics of charged biomolecules, such as charged amino acids in proteins or the phosphate groups of nucleic acid backbones, with microsecond temporal resolution. Structural rearrangements of a single charged molecule on the surface of a single-walled carbon nanotube (CNT) transistor can lead to measureable fluctuations in conductance through the CNT. Thus, this technique allows for simultaneous characterization of fast events and, due to the label-free and minimally-invasive nature of smFET technology, the quantification of how the frequency of these events change over long time-scales. A portion of this work describes smFET fabrication, focusing on improvements to the functionalization method, a critical step to reliably generate individual attachment sites on the CNT for subsequent single-molecule studies. A new synthetic chemistry approach is performed in ultraminiaturized, nanofabricated reaction chambers; using lithographically-defined nanowells, single-point attachments are achieved on hundreds of individual carbon nanotube transistors, providing robust statistics and unprecedented spatial control in adduct positioning. Each device acts as a sensor to detect, in real-time and through quantized changes in conductance, single-point functionalization of the nanotube, as well as consecutive chemical reactions and subsequent molecular interactions molecular conformational changes. In particular, this thesis is focused on studying the dynamics of nucleic acids using smFET technology. First, the smFET technique presented is verified by studying the thermodynamics and kinetics of DNA hybridization, the results of which compare favorably both with predicted values and previous smFET studies using alternative device architectures. Next, the reversible folding of a single-stranded telomeric DNA sequence known to form a G-quadruplex structure is studied, revealing the characteristic increased stability of the G-quadruplex structure in the presence of potassium ions relative to sodium ions. Finally, smFET studies of the dynamics of the adenine-sensing pbuE riboswitch aptamer found in Bacillus subtilis are discussed. These results demonstrate how long-lived, ligand-dependent intermediates form at a base-pair level and suggest that these intermediates have consequences for riboswitch-regulation by adenine binding to the aptamer. With the increased time resolution of smFET technology, this work has achieved the first observation of RNA zipping and unzipping at the single-molecule level, as well as label-free observations of the effects of a three-way junction motif on helix zipping and unzipping

Interfacial Interactions between Implant Electrode and Biological Environment

Electrodes implanted into neural systems are known to degrade due to encapsulation by surrounding tissues. The mechanisms of electrode-tissue interactions and prediction of the behavior of electrode are yet to be achieved. This research will aim at establishing the fundamental knowledge of interfacial interactions between the host biological environment and an implanted electrode. We will identify the dynamic mechanisms of such interfacial interactions. Quantitative analysis of the electrical properties of interface will be conducted using Electrochemical Impedance Spectroscopy (EIS). Results will be used to develop a general model to interpret electrical circuitry of the interface. This is expected to expand our understanding in the effects of interfacial interactions to the charge transport. The interfacial interactions of an implanted electrode with neural system will be studied in two types of electrodes: silver and graphene coated. The interfacial impedance of both samples will be studied using EIS. The development of the cellular interaction will be investigated using histological procedure. X-ray photoemission spectroscopy (XPS) will be employed to study the chemical effects on the silver electrodes. Atomic force microscopy and Raman spectroscopy will be used for material characterization of graphene-coated electrodes. In the study of silver electrode, two mechanisms affecting the interfacial impedance are proposed. First is the formation of silver oxide. The other is the immuno-response of tissue encapsulation. Histological results suggest that higher cell density cause higher impedance magnitude at the interface. It is also found that the cellular encapsulation dominates the increase in impedance for longer implanted time. In the study of graphene-coated electrode, it is found that the graphene can strongly prevent the metal substrate from being oxidized. It not only provides good electrical conductivity for signal transport, but also reduces the speed of the accumulation of tissue around the electrode. Such characteristics of graphene have great potential in the application of neural implant. Finally, the dynamic mechanisms of biological interaction are proposed. A model is also developed to represent the general circuitry of the interface between an implanted electrode and the neural system. The model has three major components, which are interfacial double layer, cellular encapsulation, and the substrate. The model presented in this study can compensate for selection and prediction of materials and their behaviors

Assessment of novel Advanced Oxidation Processes for the Simultaneous Disinfection and Decontamination of Water

[ES] El mundo se enfrenta a una profunda crisis asociada al agua y la reutilización de aguas residuales urbanas (UWW), especialmente en agricultura, se presenta como una posible solución para abordar este problema. No obstante, la reutilización se debe promover dentro de unos límites mínimos de calidad del agua, los cuales pueden alcanzarse mediante la implementación de eficientes tratamientos terciaros en las actuales plantas de tratamiento de aguas residuales urbanas. En las últimas décadas, los Procesos de Oxidación Avanzada (POA), basados en la generación de especies reactivas del oxígeno altamente oxidantes y no selectivas, se han planteado como alternativa a los tratamientos convencionales para desinfección y descontaminación de agua residual. El objetivo general de este estudio es, por tanto, la evaluación de nuevos POA para desinfección y descontaminación simultánea de agua, investigando: (i) fotocatálisis heterogénea solar con ZnO modificado (Ce, Yb y Fe) y TiO2-P25 de referencia, (ii) peroximonosulfato (PMS) bajo radiación solar natural (PMS/Solar), (iii) POA basados en radical sulfato utilizando PMS y radiación UV-C (PMS/UV-C) y (iv) combinación de ZnO modificado con PMS como estrategia de tratamiento. Los objetivos biológicos y químicos analizados en este estudio fueron: tres patógenos de impacto en salud humana (dos bacterias gram-negativas Escherichia coli, Pseudomonas spp y una gram-positiva Enterococcus spp) y tres Contaminantes de Preocupación Emergente (CE) (Diclofenaco-DCF, Sulfametoxazol-SMX y Trimetoprim-TMP). La fotoactividad de ZnO modificado con Ce, Yb o Fe se evaluó a escala de laboratorio (200 mL), obteniendo buenas cinéticas de inactivación bacteriana y degradación de CE. El ZnO-Ce mostró el mejor rendimiento, no obstante, se descartó el escalado de este proceso tanto su aplicación directa, considerando su similar eficiencia en comparación con TiO2-P25 y por el alto coste del tratamiento, como en combinación con PMS, por la la liberación de Zn2+ al agua tratada. El uso directo de PMS como agente oxidante para el tratamiento de agua y UWW se ha demostrado en este estudio, aumentado su eficiencia al ser el sistema irradiado tanto con lámparas UV-C como con luz solar natural. Se han postulado diferentes mecanismos de inactivación y degradación de CE para cada tipo de irradiación: activación de PMS para generar radicales (con fotones UV-C) y la no activación o mecanismo de oxidación directo (con luz solar natural). La capacidad de los procesos PMS/Solar y PMS/UV-C se evaluó en UWW a escala de planta piloto en un Colector Parabólico Compuesto (10 L) y en una planta piloto de UV-C (80 L), respectivamente. El mejor rendimiento de tratamiento se alcanzó con una concentración de PMS de 1 mM en ambos casos, logrando una inactivación exitosa de todos los objetivos microbianos (incluyendo bacterias resistentes a antibióticos), sin observar recrecimiento bacteriano tras 48 h y eliminando de manera eficiente los CE. Por otro lado, la eliminación eficiente de genes de resistentes a antibióticos y productos de transformación se obtuvo con PMS/UV-C, mientras que éstos parámetros siguen siendo un reto a abordar en el caso del proceso PMS/Solar. En ningún caso se observó toxicidad del agua tratada para Aliivibrio fischeri, excluyendo un efecto nocivo para el medio ambiente receptor del efluente, y solo un leve efecto fitotóxico en el crecimiento de dos de las tres semillas analizadas (L. sativum y S. alba), indicando la idoneidad del efluente para su reutilización en riego. Finalmente, el análisis de costes demostró que este factor clave podría ser una barrera importante para la implementación del proceso PMS/Solar en plantas centralizadas de tratamiento de UWW. No obstante, su consideración como sistemas descentralizados asociados a pequeños volúmenes de agua en zonas con alta incidencia de radiación solar, ahorrando costes energéticos mediante el aprovechamiento de la luz solar, podría ser una opción real y asequible.[CA] El món s'enfronta a una profunda crisi associada a l'aigua i la reutilització d'aigües residuals urbanes (UWW), especialment en agricultura, es presenta com una possible solució per a abordar aquest problema. No obstant això, la reutilització s'ha de promoure dins d'uns límits mínims de qualitat de l'aigua, els quals poden aconseguir-se mitjançant la implementació d'eficients tractaments terciaris en les actuals plantes de tractament d'aigües residuals urbanes. En les últimes dècades, els Processos Avançats d'Oxidació (PAO), basats en la generació d'espècies reactives d'oxigen altament oxidants i no selectives, s'han plantejat com a alternativa als tractaments convencionals per a desinfecció i descontaminació d'aigua residual. L'objectiu general d'aquest estudi és, per tant, l'avaluació de nous POA per a desinfecció i descontaminació simultània d'aigua, investigant: (i) fotocatàlisi heterogènia solar amb ZnO modificat (Ce, Yb i Fe) i TiO2-P25 de referència, (ii) peroximonosulfat (PMS) baix radiació solar natural (PMS/Solar), (iii) POA basats en radical sulfat utilitzant PMS i radiació UV-C (PMS/UV-C) i (iv) combinació de ZnO modificat amb PMS com a estratègia de tractament. Els objectius biològics i químics analitzats en aquest estudi van ser: tres patògens d'impacte en salut humana (dos bacteris gram-negatius Escherichia coli, Pseudomonas spp i un gram-positiu Enterococcus spp) i tres Contaminants de Preocupació Emergent (CE) (Diclofenac-DCF, Sulfametoxazol-SMX i Trimetoprim-TMP). La fotoactivitat de ZnO modificat amb Ce, Yb o Fe es va avaluar a escala de laboratori (200 mL), obtenint bones cinètiques d'inactivació bacteriana i degradació de CE. El ZnO-Ce va mostrar el millor rendiment, no obstant això, es va descartar l'escalat d'aquest procés tant mitançant la seua aplicació directa o com en combinació amb PMS, considerant la seua similar eficiència en comparació amb TiO2-P25, l'alt cost del tractament i l'alliberament de Zn2+ a l'aigua tractada. L'ús directe de PMS com a agent oxidant per al tractament d'aigua i UWW s'ha demostrat en aquest estudi, augmentat la seua eficiència quan el sistema és irradiat tant amb llums UV-C com amb llum solar natural. S'han postulat diferents mecanismes d'inactivació i degradació de CE per a cada tipus d'irradiació: activació de PMS per a generar radicals (amb fotons UV-C) i la no activació o mecanisme d'oxidació directe (amb llum solar natural). La capacitat dels processos PMS/Solar i PMS/UV-C es va avaluar en UWW a escala de planta pilot en un Col·lector Parabòlic Compost (10 L) i en una planta pilot d'UV-C (80 L), respectivament. El millor rendiment de tractament es va aconseguir amb una concentració de PMS d'1 mm en tots dos casos, aconseguint una inactivació reeixida de tots els objectius microbians (incloent bacteris resistents a antibiòtics), sense observar recreixement bacterià després de 48 h i eliminant de manera eficient els CE. D'altra banda, l'eliminació eficient de gens de resistents a antibiòtics i productes de transformació es va obtindre amb PMS/UV-C, mentre que aquests paràmetres continuen sent un repte a abordar en el cas del procés PMS/Solar. En cap cas es va observar toxicitat a l'aigua tractada per a Aliivibrio fischeri, excloent un efecte nociu per al medi ambient receptor de l'efluent, i només un lleu efecte fitotòxic en el creixement de dos de les tres llavors analitzades (L. sativum i S. alba), indicant la idoneïtat de l'efluent per a la seua reutilització en reg. Finalment, l'anàlisi de costos va demostrar que aquest factor clau podria ser una barrera important per a la implementació del procés PMS/Solar en plantes centralitzades de tractament de UWW. No obstant això, la seua consideració com a sistemes descentralitzats associats a xicotets volums d'aigua en zones amb alta incidència de radiació solar, estalviant costos energètics mitjançant l'aprofitament de la llum solar, podria ser una opció real i assequible.[EN] It is well recognized that the world is facing a water crisis and the reuse of urban wastewater (UWW) in agriculture, has been gaining attention as a reliable solution to address this problem. It is mandatory to promote the safe water reuse and minimum water quality limits could be achieved by upgrading the Urban Wastewater Treatment Plants, through the addition of an efficient tertiary treatment. In the last decades, Advanced Oxidation Processes (AOPs), relying on the potential generation of highly oxidant, reactive and non-selective Reactive Oxygen Species (ROS), have been raised as alternative to conventional treatments for both water disinfection and decontamination. The general aim of this study is the assessment of novel AOPs for the simultaneous disinfection and decontamination of water, investigating (i) solar heterogeneous photocatalysis, involving modified ZnO with Ce, Yb and Fe and the benchmark TiO2-P25, (ii) peroxymonosulfate (PMS) under natural solar radiation (PMS/Solar), (iii) Sulfate radical-based AOPs (SR-AOPs) involving PMS and UV-C radiation (PMS/UV-C) and (iv) combination of the best-performing photocatalytic material with PMS (PMS/modified ZnO). The involved biological and chemical targets in this study were: three human health impact pathogens (two gram-negative bacteria Escherichia coli, Pseudomonas spp. and the gram-positive Enterococcus spp.) and three Contaminants of Emerging Concern (CECs, Diclofenac-DCF, Sulfamethoxazole-SMX and Trimethoprim-TMP). Photoactivity of modified ZnO with Ce, Yb or Fe was assessed in 200-mL vessel reactors, attaining good target's removal kinetic rates. Best performing material was ZnO-Ce, but its feasibility for a further up-scaling was discarded both as photocatalyst alone, considering the similar performances obtained, compared to TiO2-P25 and the high treatment cost, and in combination with PMS, due to the release of high amount of Zn2+. PMS alone has been proven to be an effective oxidant agent for water and UWW treatment, increasing its effectiveness when illuminated with photons from UV-C lamps and natural sunlight. Nevertheless, different inactivation and CECs degradation mechanisms have been postulated for each type of irradiation, and according to the activation of PMS (with UV-C photons) or non-activation (under natural sunlight). The capability of PMS/Solar and PMS/UV-C processes were evaluated in actual UWW at pilot plant scale in 10-L Compound Parabolic Collector and in 80L UV-C pilot plant, respectively. Optimal load of PMS was found to be 1 mM in both cases, achieving successful inactivation of natural occurring bacteria and their antibiotic resistant counterparts, without observing bacterial regrowth after 48h and efficiently eliminating CECs. Efficient removal of antibiotic resistant genes (ARGs) and transformation products (TPs) was obtained by PMS/UV-C, while their elimination is still a challenge to be addressed in PMS/Solar process. Reclaimed UWW obtained by both PMS/Solar and PMS/UV-C process showed no toxicity towards Aliivibrio fischeri, excluding a harmful effect towards the receiving aquatic environment after effluent discharge, and a very slightly phytotoxic effect for growth of two out of the three tested seeds (L. sativum and S. alba), indicating the suitability of this water for its subsequent reuse for agriculture. The analysis of the treatment cost revealed that this key factor could be an important barrier for implementation of PMS/Solar process in large centralized UWW treatment plants. Nevertheless, its consideration as decentralized systems associated to small volume of water in areas with a high solar radiation incidence, saving energy costs by using natural solar radiation, could be a real and affordable option.Berruti, I. (2022). Assessment of novel Advanced Oxidation Processes for the Simultaneous Disinfection and Decontamination of Water [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/183052TESI