BioScript: programming safe chemistry on laboratories-on-a-chip

This paper introduces BioScript, a domain-specific language (DSL) for programmable biochemistry which executes on emerging microfluidic platforms. The goal of this research is to provide a simple, intuitive, and type-safe DSL that is accessible to life science practitioners. The novel feature of the language is its syntax, which aims to optimize human readability; the technical contributions of the paper include the BioScript type system and relevant portions of its compiler. The type system ensures that certain types of errors, specific to biochemistry, do not occur, including the interaction of chemicals that may be unsafe. The compiler includes novel optimizations that place biochemical operations to execute concurrently on a spatial 2D array platform on the granularity of a control flow graph, as opposed to individual basic blocks. Results are obtained using both a cycle-accurate microfluidic simulator and a software interface to a real-world platform

Droplet routing for digital microfluidic biochips based on microelectrode dot array architecture

A digital microfluidic biochip (DMFB) is a device that digitizes fluidic samples into tiny droplets and operates chemical processes on a single chip. Movement control of droplets can be realized by using electrowetting-on-dielectric (EWOD) technology. DMFBs have high configurability, high sensitivity, low cost and reduced human error as well as a promising future in the applications of point-of-care medical diagnostic, and DNA sequencing. As the demands of scalability, configurability and portability increase, a new DMFB architecture called Microelectrode Dot Array (MEDA) has been introduced recently to allow configurable electrodes shape and more precise control of droplets. The objective of this work is to investigate a routing algorithm which can not only handle the routing problem for traditional DMFBs, but also be able to route different sizes of droplets and incorporate diagonal movements for MEDA. The proposed droplet routing algorithm is based on 3D-A* search algorithm. The simulation results show that the proposed algorithm can reduce the maximum latest arrival time, average latest arrival time and total number of used cells. By enabling channel-based routing in MEDA, the equivalent total number of used cells can be significantly reduced. Compared to all existing algorithms, the proposed algorithm can achieve so far the least average latest arrival time

Detection of Pathogens in Water Using Micro and Nano-Technology

Detection of Pathogens in Water Using Micro and Nano-Technology aims to promote the uptake of innovative micro and nano-technological approaches towards the development of an integrated, cost-effective nano-biological sensor useful for security and environmental assays.  The book describes the concerted efforts of a large European research project and the achievements of additional leading research groups. The reported knowledge and expertise should support in the innovation and integration of often separated unitary processes. Sampling, cell lysis and DNA/RNA extraction, DNA hybridisation detection micro- and nanosensors, microfluidics, together also with computational modelling and risk assessment can be integrated in the framework of the current and evolving European regulations and needs. The development and uptake of molecular methods is revolutionizing the field of waterborne pathogens detection, commonly performed with time-consuming cultural methods. The molecular detection methods are enabling the development of integrated instruments based on biosensor that will ultimately automate the full pathway of the microbiological analysis of water

Detection of Pathogens in Water Using Micro and Nano-Technology

Detection of Pathogens in Water Using Micro and Nano-Technology aims to promote the uptake of innovative micro and nano-technological approaches towards the development of an integrated, cost-effective nano-biological sensor useful for security and environmental assays.  The book describes the concerted efforts of a large European research project and the achievements of additional leading research groups. The reported knowledge and expertise should support in the innovation and integration of often separated unitary processes. Sampling, cell lysis and DNA/RNA extraction, DNA hybridisation detection micro- and nanosensors, microfluidics, together also with computational modelling and risk assessment can be integrated in the framework of the current and evolving European regulations and needs. The development and uptake of molecular methods is revolutionizing the field of waterborne pathogens detection, commonly performed with time-consuming cultural methods. The molecular detection methods are enabling the development of integrated instruments based on biosensor that will ultimately automate the full pathway of the microbiological analysis of water

Configurable and Up-Scalable Microfluidic Life Science Platform for Cell Based Assays by Gravity Driven Sequential Perfusion and Diffusion

Microfluidics has the potential to significantly change the way modern biology is performed, but for this potential to be realized several on-chip integration and operation challenges have to be addressed. Critical issues are addressed in this work by first demonstrating an integrated microfluidic tmRNA purification and real time nucleic acid sequence based amplification (NASBA) device. The device is manufactured using soft lithography and a unique silica bead immobilization method for the nucleic acid micro purification column. The integrated device produced a pathogen-specific response in < 3 min from the chip-purified RNA. Further enhancements in the device design and operation that allow the on-chip integration of mammalian cell handling and culturing produced a novel integrated NASBA array. This system demonstrated for the first time that it is possible to combine on a single micro-device cell culture and real time NASBA. In order to expand the cell based assay capabilities of the integrated NASBA array and simplify the device operation novel hydrodynamics and cell sedimentation within trench structures and gravity driven sequential perfusion and diffusion mechanisms were developed. These mechanisms were characterized and implemented within an iCell array device. iCell array can completely integrate cell based assays with bio-analytical read-out. The device is highly scalable and can enable the configurable on-chip integration of procedures such as adherent and non-adherent cell-culture, cellstimulation, cell-lysis, cell-fixing, protein-immunoassays, bright field and fluorescent microscopic monitoring, and real time detection of nucleic acid amplification. The device uses on-board gravity driven flow control which makes it simple and economical to operate with dilute samples (down to 5 cells per reaction), low reagent volumes (50 nL per reaction), highly efficient cell capture (100% capture rates) and single cell protein and gene expression sensitivity. The key results from this work demonstrate a novel technology for versatile, fully integrated microfluidic array platforms. By multiplexing this integrated functionality, the device can be used from routine applications in a biology laboratory to high content screenings

On-chip food safety monitoring: multi-analyte screening with imaging surface plasmon resonance-based biosensor

Food safety is an increasing health concern, recognised and promoted by many institutions across the globe. Food products can be contaminated with pathogenic microorganisms, environmental pollutants, veterinary drug residues, allergens and toxins. Public health concerns which have been raised in relation to hazardous agents found in food include, among others, increased cancer risk, endocrine, reproductive and neurobehavioral systems disruption, teratogenesis, antibiotic resistance and even death in cases of allergic reactions and acute poisoning. Some of the food hazardous agents (e.g. pathogenic microorganisms and toxins) can even be used as biological warfare, spread through food and agricultural chains. Thus, an adequate detection of these compounds is also important for biosecurity. In order to safeguard consumers’ health, legislations have been put in place both in the US and the EU. These laws specify for each health threatening compound the maximal acceptable amounts in different food products. Besides health issues, food safety and quality has an economical impact on the food industry, where quality control expenses amount to about 1.5 – 2 % of the total sales. Since more and more food products nowadays contain multiple and processed ingredients, which are often shipped from different parts of the world, and share common production lines and storage spaces, food safety and quality monitoring becomes a challenging task. Traditional analytical methods require dedicated laboratories, equipment and highly trained personnel for detection and identification of each type of hazardous agent (e.g. antibiotics, bacteria, allergens). These techniques are also time-consuming and often expensive. There is a growing need for multi-analyte screening methods, which will enable rapid and simultaneous detection of multiple compounds in complex food samples. In recent years, biosensors have been applied successfully to food analysis, incorporating the same bioassay principals as traditional methods with transducers (optical, electrochemical, etc) in novel, usually miniaturized, integrated analytical devices. However, most of these biosensors still lack the desired level of the multiplexicity. Recent developments in the field of Surface Plasmon Resonance (SPR) technology in the direction of high-throughput systems and multi-analyte measurements present a promising alternative for the existing systems. One of such systems is imaging SPR (iSPR); it enables real-time and label free read-out of spatially modified surfaces (e.g. microarrays). The aim of this study was to develop an iSPR–based biosensor, for simultaneous and quantitative detection of different health-threatening compounds in food. To obtain a comprehensive overview on the analytical applicability of such a system, several points were addressed. The intrinsic sensor properties, such as optical sensitivity and robustness, of the iSPR instrument were studied. Further on, both direct and competitive immunoassay formats for high and low molecular weight compounds detection using the iSPR platform were evaluated. Then, the iSPR-based biosensor was applied for detection of regulated substances in food such as antibiotic residues in milk and allergens in cookies and chocolates. Finally, the most common drawback of using SPR for screening in complex biological matrices, the nonspecific binding to the sensor chip surface, was tackled. The sensitivity of both high and low molecular weight compounds was proven to be sufficient for some of the hazardous agents detection at the maximum residue levels, established in the EU legislation, as was demonstrated by simultaneous detection of seven antibiotic residues in milk and twelve allergens in cookies and dark chocolates. The analysis time takes about 10 minutes and provides quantitative information on multiple targets, producing a fingerprint (allergenic fingerprint for instance) of the tested food. This detailed food profile contributes to the decision making process on the quality and safety of foods, basing it on the total picture of all target compounds present. In order for iSPR-based biosensing to reach its full potential and to become a widely applied routine analytical tool, the instrumental cost needs to be reduced and the analysis further simplified, becoming cost-effective and approachable to non-trained personnel. An additional drawback in analytical applications of a SPR sensor is the nonspecific binding of the matrix components of complex samples to the sensor surface. Many assays based on SPR fail due to inapplicability to measure in “real” samples. As a possible solution to this problem, sensor chip surface engineering was suggested in this thesis. A nanopatterned filter layer covering the sensor chip surface was found to be effective in reducing nonspecific binding when the measurements were performed in “raw” samples by keeping the non-soluble aggregates and big sample matrix components beyond the sensing region of the SPR. With respect to other existing biosensors, iSPR still lags behind in terms of sensitivity and portability. In summary, the results of this study demonstrate that iSPR-based biosensor is a versatile platform, which can be applied for a wide variety of fundamentally different analytes and offers several advantages over already existing methods. SPR detection principle eliminates the need in labelling and the instrumental set-up allows automated analysis. High multiplexing capabilities and short measurement times are obtained with no need for complex and time consuming sample preparation steps. By using iSPR-based biosensor, one can obtain robust and quantitative information on the target analyte concentration, in real time and with high specificity (or broad spectrum, depending on the assay). In conclusion, on-chip screening using iSPR, described here, presents a powerful analytical approach towards food safety and quality monitoring which satisfies the current need in rapid and multi-analytical devices. <br/