Quantum dot encoded magnetic beads for multiplexed fluorescence biosensing

In recent years, the use of encoded beads has received considerable attention due to their potential for measuring multiple analytes in solution.(1-4) This can be achieved without the need for knowledge of their spatial position, as in the case of microarray technology. Encoded bead technology also relies on the solution kinetics rather than diffusion to a fixed surface as in the case of microarray technology, offering the possibility of developing rapid high throughput screening methods. This thesis describes the production, characterisation and application of quantum dot encoded beads prepared using layer-by-layer assembly of different colour quantum dots around a magnetic bead. To achieve this, two different strategies were used to make “coloured” barcodes. The first strategy used thiol chemistry to immobilise quantum dots in a layer-by-layer assembly onto magnetic beads whereas the second strategy uses the interaction between quantum dot-biotin and quantum dot-streptavidin conjugates to create constructs on the magnetic bead surface. The development of both of these immobilisation strategies was characterisation using X-ray photoelectron spectroscopy and fluorescence spectroscopy of immobilised quantum dot structures onto a plain glass substrate. After the preparation of encoded beads, they were characterised using single bead fluorescence spectroscopy. It was found that attempts to prepare barcodes by layer-by-layer assembly of CdSe/ZnS quantum dots using thiol chemistry onto magnetic beads did not comply with the necessary barcode characteristics i.e., different colour coded beads could not be distinguished from each other. However, the encoded beads prepared using layer-by-layer assembly of quantum dot-biotin and quantum dot-streptavidin conjugates onto streptavidin coated magnetic beads gave distinct multicolour coded bead spectra. These barcodes were characterised in terms of different spectral responses, stability at raised temperatures, stability in biotin solutions, and long-term stability after storage. Encoded beads prepared using layer-by-layer assembly of quantum dot-biotin and quantum dot-streptavidin conjugates onto streptavidin coated magnetic beads were then used to develop multiplexed immunoassays. Four different barcodes were prepared and used to perform model multiplexed immunoassays. The barcodes were identified upon the basis of different spectral response measured using single bead fluorescence spectroscopy. Finally, a quantitative immunoassay for human IgG was performed using these barcodes, which showed that different concentrations of human IgG can be determined in solution

Surveillance photonique des activités biologiques de bactéries immobilisées sur des surfaces des semiconducteurs quantiques biofunctionnalisées

Le suivi de la viabilitié, la croissance et le métabolisme cellulaire des bactéries peut contribuer de manière significative au diagnostic précoce de la maladie, mais peut aussi aider à améliorer le rendement des produits bactériens dans des expériences industrielle ou à petite echelle. Les méthodes conventionnelles utilisées pour l'étude de la sensibilité des bactéries aux antibiotiques sont basées principalement sur la culture, une technique qui prend au moins 12 heures pour rendre un résultat. Ce retard conduit au surtraitement d'un large éventail d'infections par des antibiotiques à large spectre, ce qui est coûteux et peut conduire à l'apparition de résistance à ces antibiotiques précieux, tandis que la détection rapide d'une infection virale ou l'absence de bactéries pourrait prévenir de tels traitements et, dans le cas d'une infection bactérienne, l'identification de la sensibilité aux antibiotiques pourrait permettre l'utilisation d'antibiotiques à spectre étroit. Le projet décrit dans le présent document vise à surveiller les activités biologiques des bactéries vivantes immobilisées sur les surfaces biofonctionnalisées de microstructures composées de semi-conducteurs quantiques (QS). Le procédé dépend de la sensibilité de la photoluminescence (PL) émise par des semi-conducteurs à la perturbation du champ électrique induit par la charge électrique des bactéries immobilisées sur la surface de ces structures. Dans la première phase du projet, nous avons étudié une méthode innovante impliquant la surveillance par PL de l'effet de photocorrosion dans des hétérostructures GaAs/AlGaAs. Le maintien d'un équilibre entre la sensibilité et la stabilité du biocapteur dans l'environnement aqueux nous a permis de détecter Escherichia coli K12 dans des solutions salines tamponnées au phosphate (PBS) avec une limite de détection attrayante de 103 UFC/ml en moins de 2 heures. Suite à cette recherche, nous avons émis l'hypothèse que ces hétérostructures pourraient être utilisés pour développer une méthode à faible coût et quasiment en temps reel de la croissance et de la sensibilité des bactéries aux antibiotiques. L'un des éléments clés dans le développement de cette plate-forme de biocapteurs était de démontrer que le GaAs (001), normalement utilisé pour recouvrir les hétérostructures de GaAs/AlGaAs, ne nuira pas à la croissance des bactéries. Dans la deuxième phase du projet, nous avons exploré la capture et la croissance de E. coli K12 sur des surfaces nues et biofonctionnalisées de GaAs (001). Il a été déterminé que la couverture initiale et les taux de croissance de bactéries dépendent de l'architecture de biofonctionnalisation utilisée pour capturer les bactéries: les surfaces biofonctionnalisées avec d'anticorps présentaient une efficacité de capture significativement plus élevée. En outre, on a trouvé que pour des suspensions contenant des bactéries à moins de 105 UFC/ml, la surface des plaquettes de GaAs ne supportait pas la croissance des bactéries, quel que soit le type d'architecture de biofonctionnalisation. Dans la troisième phase du projet, nous avons suivi la croissance et la sensibilité aux antibiotiques de E. coli K12 et E. coli HB101. Tandis que la présence de bactéries retardaient d’apparition du maximum de PL, la croissance des bactéries retardaient encore plus ce maximum. Par contre, en presence d’antibiotiques efficaces, la croissance des bactéries était arrêtée et le maximum de PL est arrivé plus tôt. Ainsi, nous avons pu distinguer entre des E. coli sensibles ou résistantes à la pénicilline ou à la ciprofloxacine en moins de 3h. En raison de la petite taille, du faible coût et de la réponse rapide du biocapteur, l'approche proposée a le potentiel d'être appliquée dans les laboratoires de diagnostic clinique pour le suivi rapide de la sensibilité des bactéries aux antibiotiques.Abstract : Monitoring the viability, growth and cellular metabolism of bacteria can contribute significantly to the early diagnosis of disease, but can also help improve yield of bacterial products in industrial- or small-scale experiments. Conventional methods applied for investigation of antibiotic sensitivity of bacteria are mostly culture-based techniques that are time-consuming and take at least 12 h to reveal results. This delay leads to overtreatment of a wide range of infections with broad spectrum antibiotics which is costly and may lead to the development of resistance to these precious antibiotics, whereas rapid detection of a viral infection or absence of bacteria could prevent such treatments and, in the case of bacterial infection, identification of antibiotic susceptibility could allow use of narrow spectrum antibiotics. The project outlined in this document aims at monitoring biological activities of live bacteria immobilized on biofunctionalized surfaces of quantum semiconductor (QS) microstructures. The method takes advantage of the sensitivity of photoluminescence (PL) emitting semiconductors to the perturbation of the electric field induced by the electric charge of bacteria immobilized on the surface of these structures. Our hypothesis was that bacteria growing on the surface of biofunctionalized QS biochips would modify their PL in a different, and measurable way in comparison with inactivated bacteria. In the first phase of the project, we investigated an innovative method involving PL monitoring of the photocorrosion effect in GaAs/AlGaAs heterostructures. Maintaining the balance between device sensitivity and stability in the biosensing (aqueous) environment allowed us to detect Escherichia coli K12 in phosphate buffered saline solutions (PBS) at an attractive limit of detection of 103 CFU/mL in less than 2 hours. Following this research, we hypothesised that these heterostructures could be employed to develop a method for inexpensive and quasi-real time monitoring of the growth and antibiotic susceptibility of bacteria. One of the key elements in the development of this biosensing platform was to demonstrate that GaAs (001), normally used for capping PL emitting GaAs/AlGaAs heterostructures, would not inhibit the growth of bacteria. In the second phase of the project, we explored the capture and growth of E. coli K12 on bare and biofunctionalized surfaces of GaAs (001). It has been determined that the initial coverage, and the subsequent bacterial growth rates are dependent on the biofunctionalization architecture used to capture bacteria, with antibody biofunctionalized surfaces exhibiting significantly higher capture efficiencies. Moreover, for suspensions containing bacteria at less than 105 CFU/mL, it has been found that the surface of GaAs wafers could not support the growth of bacteria, regardless of the type of biofunctionalization architecture. In the third phase of the project, we used PL to monitor the growth and antibiotic susceptibility of E. coli K12 and E. coli HB101 bacteria. While immobilization of bacteria on the surface of GaAs/AlGaAs heterostructures retards the PL monitored photocorrosion, growth of these bacteria further amplifies this effect. By comparing the photocorrosion rate of QS wafers exposed to bacterial solutions with and without antibiotics, the sensitivity of bacteria to the specific antibiotic could be determined in less than 3 hours. Due to the small size, low cost and rapid response of the biosensor, the proposed approach has the potential of being applied in clinical diagnostic laboratories for quick monitoring of antibiotic susceptibility of different bacteria

Porous Bead-Based Diagnostic Platforms: Bridging the Gaps in Healthcare

Advances in lab-on-a-chip systems have strong potential for multiplexed detection of a wide range of analytes with reduced sample and reagent volume; lower costs and shorter analysis times. The completion of high-fidelity multiplexed and multiclass assays remains a challenge for the medical microdevice field; as it struggles to achieve and expand upon at the point-of-care the quality of results that are achieved now routinely in remote laboratory settings. This review article serves to explore for the first time the key intersection of multiplexed bead-based detection systems with integrated microfluidic structures alongside porous capture elements together with biomarker validation studies. These strategically important elements are evaluated here in the context of platform generation as suitable for near-patient testing. Essential issues related to the scalability of these modular sensor ensembles are explored as are attempts to move such multiplexed and multiclass platforms into large-scale clinical trials. Recent efforts in these bead sensors have shown advantages over planar microarrays in terms of their capacity to generate multiplexed test results with shorter analysis times. Through high surface-to-volume ratios and encoding capabilities; porous bead-based ensembles; when combined with microfluidic elements; allow for high-throughput testing for enzymatic assays; general chemistries; protein; antibody and oligonucleotide applications

Advances in Optofluidics

Optofluidics a niche research field that integrates optics with microfluidics. It started with elegant demonstrations of the passive interaction of light and liquid media such as liquid waveguides and liquid tunable lenses. Recently, the optofluidics continues the advance in liquid-based optical devices/systems. In addition, it has expanded rapidly into many other fields that involve lightwave (or photon) and liquid media. This Special Issue invites review articles (only review articles) that update the latest progress of the optofluidics in various aspects, such as new functional devices, new integrated systems, new fabrication techniques, new applications, etc. It covers, but is not limited to, topics such as micro-optics in liquid media, optofluidic sensors, integrated micro-optical systems, displays, optofluidics-on-fibers, optofluidic manipulation, energy and environmental applciations, and so on

Modern Applications in Optics and Photonics: From Sensing and Analytics to Communication

Optics and photonics are among the key technologies of the 21st century, and offer potential for novel applications in areas such as sensing and spectroscopy, analytics, monitoring, biomedical imaging/diagnostics, and optical communication technology. The high degree of control over light fields, together with the capabilities of modern processing and integration technology, enables new optical measurement systems with enhanced functionality and sensitivity. They are attractive for a range of applications that were previously inaccessible. This Special Issue aims to provide an overview of some of the most advanced application areas in optics and photonics and indicate the broad potential for the future

Optically Induced Nanostructures

Nanostructuring of materials is a task at the heart of many modern disciplines in mechanical engineering, as well as optics, electronics, and the life sciences. This book includes an introduction to the relevant nonlinear optical processes associated with very short laser pulses for the generation of structures far below the classical optical diffraction limit of about 200 nanometers as well as coverage of state-of-the-art technical and biomedical applications. These applications include silicon and glass wafer processing, production of nanowires, laser transfection and cell reprogramming, optical cleaning, surface treatments of implants, nanowires, 3D nanoprinting, STED lithography, friction modification, and integrated optics. The book highlights also the use of modern femtosecond laser microscopes and nanoscopes as novel nanoprocessing tools

Glassy Materials Based Microdevices

Microtechnology has changed our world since the last century, when silicon microelectronics revolutionized sensor, control and communication areas, with applications extending from domotics to automotive, and from security to biomedicine. The present century, however, is also seeing an accelerating pace of innovation in glassy materials; as an example, glass-ceramics, which successfully combine the properties of an amorphous matrix with those of micro- or nano-crystals, offer a very high flexibility of design to chemists, physicists and engineers, who can conceive and implement advanced microdevices. In a very similar way, the synthesis of glassy polymers in a very wide range of chemical structures offers unprecedented potential of applications. The contemporary availability of microfabrication technologies, such as direct laser writing or 3D printing, which add to the most common processes (deposition, lithography and etching), facilitates the development of novel or advanced microdevices based on glassy materials. Biochemical and biomedical sensors, especially with the lab-on-a-chip target, are one of the most evident proofs of the success of this material platform. Other applications have also emerged in environment, food, and chemical industries. The present Special Issue of Micromachines aims at reviewing the current state-of-the-art and presenting perspectives of further development. Contributions related to the technologies, glassy materials, design and fabrication processes, characterization, and, eventually, applications are welcome

Laser-induced forward transfer (LIFT) of water soluble polyvinyl alcohol (PVA) polymers for use as support material for 3D-printed structures

The additive microfabrication method of laser-induced forward transfer (LIFT) permits the creation of functional microstructures with feature sizes down to below a micrometre [1]. Compared to other additive manufacturing techniques, LIFT can be used to deposit a broad range of materials in a contactless fashion. LIFT features the possibility of building out of plane features, but is currently limited to 2D or 2½D structures [2–4]. That is because printing of 3D structures requires sophisticated printing strategies, such as mechanical support structures and post-processing, as the material to be printed is in the liquid phase. Therefore, we propose the use of water-soluble materials as a support (and sacrificial) material, which can be easily removed after printing, by submerging the printed structure in water, without exposing the sample to more aggressive solvents or sintering treatments. Here, we present studies on LIFT printing of polyvinyl alcohol (PVA) polymer thin films via a picosecond pulsed laser source. Glass carriers are coated with a solution of PVA (donor) and brought into proximity to a receiver substrate (glass, silicon) once dried. Focussing of a laser pulse with a beam radius of 2 µm at the interface of carrier and donor leads to the ejection of a small volume of PVA that is being deposited on a receiver substrate. The effect of laser pulse fluence , donor film thickness and receiver material on the morphology (shape and size) of the deposits are studied. Adhesion of the deposits on the receiver is verified via deposition on various receiver materials and via a tape test. The solubility of PVA after laser irradiation is confirmed via dissolution in de-ionised water. In our study, the feasibility of the concept of printing PVA with the help of LIFT is demonstrated. The transfer process maintains the ability of water solubility of the deposits allowing the use as support material in LIFT printing of complex 3D structures. Future studies will investigate the compatibility (i.e. adhesion) of PVA with relevant donor materials, such as metals and functional polymers. References: [1] A. Piqué and P. Serra (2018) Laser Printing of Functional Materials. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA. [2] R. C. Y. Auyeung, H. Kim, A. J. Birnbaum, M. Zalalutdinov, S. A. Mathews, and A. Piqué (2009) Laser decal transfer of freestanding microcantilevers and microbridges, Appl. Phys. A, vol. 97, no. 3, pp. 513–519. [3] C. W. Visser, R. Pohl, C. Sun, G.-W. Römer, B. Huis in ‘t Veld, and D. Lohse (2015) Toward 3D Printing of Pure Metals by Laser-Induced Forward Transfer, Adv. Mater., vol. 27, no. 27, pp. 4087–4092. [4] J. Luo et al. (2017) Printing Functional 3D Microdevices by Laser-Induced Forward Transfer, Small, vol. 13, no. 9, p. 1602553

Multiplexed profiling of extracellular vesicles for biomarker development

Extracellular vesicles (EVs) are cell-derived membranous particles that play a crucial role in molecular trafficking, intercellular transport and the egress of unwanted proteins. They have been implicated in many diseases including cancer and neurodegeneration. EVs are detected in all bodily fluids, and their protein and nucleic acid content offers a means of assessing the status of the cells from which they originated. As such, they provide opportunities in biomarker discovery for diagnosis, prognosis or the stratification of diseases as well as an objective monitoring of therapies. The simultaneous assaying of multiple EV-derived markers will be required for an impactful practical application, and multiplexing platforms have evolved with the potential to achieve this. Herein, we provide a comprehensive overview of the currently available multiplexing platforms for EV analysis, with a primary focus on miniaturized and integrated devices that offer potential step changes in analytical power, throughput and consistency