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Precise surgical excision of brain tumors depends on the surgeon’s ability to accurately differentiate tumors from healthy brain tissues. We have developed an automated system integrated with biochips, an actuation unit, and electronics to measure the electrical resistivity of ex vivo human brain tissues for differentiating normal and tumor. The electrical resistivity of fresh (n = 48), formalin-fixed for one week (n = 48), and long-term (six months) formalin-fixed (n = 27) healthy human brain samples from different anatomical regions and tumor samples (glioma n = 6; fresh, formalin-fixed for one week, and formalin-fixed for six months) were measured using the automated system. The resistivity of glioma (22.4 ± $1.6~\Omega$ .cm) was significantly lesser than the normal region (98.6 ± $1.4~\Omega$ .cm) for fresh tissue samples (p = 5e-8). The trend of lower resistivity of glioma compared to normal was preserved after one week and six months of formalin fixation. We also report the effects of heterogeneity of normal brain tissue and formalin-fixation on the electrical properties of tissues. White matter regions were found to have higher resistivity compared to grey matter regions. The heterogeneity associated with grey matter regions was lower than the white matter regions. Formalin-fixation was observed to increase the magnitude of resistivity measured while retaining the observed trend across the different regions of the brain and tumors. The study shows that the electrical resistivity could potentially be used as an additional biomarker for delineating normal from the tumor.

Surface plasmon resonance devices typically rely on the use of gold-coated surfaces, but the use of more abundant metals is desirable for the long-term development of plasmonic biochips. As a substitute for gold, thin copper films have been deposited on glass coverslips by thermal evaporation. As expected, these films immersed in a water solution initially exhibit an intense plasmonic resonance comparable to gold. However, without protection, an angle-resolved optical analysis shows a rapid degradation of the copper, characterized by a continuous angular shift of the plasmonic resonance curve. We show that copper films protected with a thin layer of aluminum oxide of a few nanometers can limit the oxidation rate for a sufficient time to perform some standard measurements. As the process is simple and compatible with the current biochip production technique, such an approach could pave the way for the production of alternative and more sustainable biochips.

Objetivo: Analizar las tendencias de la aplicación convencional de los biochips, para lo cual se realizó una revisión documental en torno a las tendencias en la creación de biochips a partir de una búsqueda y análisis de los trabajos publicados desde el año 2012 hasta el 2017 en la base de datos de la National Center for Biotechnology Information (NCBI). Resultados: Se encontró que las tendencias en la creación de biochips se han configurado como una innovación relativamente nueva en el campo de la Ingeniería Bioinformática aplicada en otras áreas, y en particular la medicina, para el tratamiento y diagnóstico de enfermedades como el cáncer. Asimismo, se encontró que desde la química y la genética se han desarrollado materiales para la fabricación de los biochips, haciéndolos biocompatibles para el organismo humano. Conclusiones: El desarrollo de nuevas tecnologías, usando biochips para la detección y monitoreo de enfermedades, permite la creación de tratamientos más efectivos y puntuales en pro de la salud y la calidad de vida. Así se evitan, además, complicaciones futuras de los pacientes, dado que su implementación sugiere una técnica menos traumática e invasiva.

Since the early 2000s, extensive research has been performed to address numerous challenges in biochip and biosensor fabrication in order to use them for various biomedical applications. These biochips and biosensor devices either integrate biological elements (e.g., DNA, proteins or cells) in the fabrication processes or experience post fabrication of biofunctionalization for different downstream applications, including sensing, diagnostics, drug screening, and therapy. Scalable lithographic techniques that are well established in the semiconductor industry are now being harnessed for large-scale production of such devices, with additional development to meet the demand of precise deposition of various biological elements on device substrates with retained biological activities and precisely specified topography. In this review, the lithographic methods that are capable of large-scale and mass fabrication of biochips and biosensors will be discussed. In particular, those allowing patterning of large areas from 10 cm2 to m2, maintaining cost effectiveness, high throughput (>100 cm2 h-1), high resolution (from micrometer down to nanometer scale), accuracy, and reproducibility. This review will compare various fabrication technologies and comment on their resolution limit and throughput, and how they can be related to the device performance, including sensitivity, detection limit, reproducibility, and robustness.

The first biochip was invented by an American company namely Affymetrix, and the product of this company is GeneChip (DNA microarrays). These products comprise the number of individual DNA sensors used for sensing defects. Biochip plays an essential role in the field of biology research like systems biology as well as disease biology while the number of clinical applications is rising. It is a set of microarrays which are placed on a strong surface of a substrate to allow thousands of reactions to be performed in less time. The development of biochip mainly includes the combination of molecular biology, biochemistry, and genetics. Biochips are used for analyzing organic molecules connected with a live organism. This article discusses what is Biochip, types, biochips and their uses, disadvantages, and its applications.

This paper describes a promising micro-channel multiplex immunoassay method based on the quantum dots encoded beads which requires micro-volume sample. Briefly, Au nanoparticles coated polystyrene (PS) beads were prepared and Quantum dots (QDs) were employed to encode 4 types of the PS beads by different emission wavelength QDs and various intensities. Different coding types of the beads were immobilized with different antibodies on the surface and BSA was used to block the unsatisfied sites. The antibody linked beads were then arranged in the 150 µm diameter optical capillary where the specific reactions took place before the detections. Results showed that the antibody on the Au coated surface maintains the bioactivity for the immunoreactions. Using this system, the fluorescent intensity was linear with analyte concentration in the range of 1×10(-7)-1×10(-5) mg/mL (RSD

The early diagnostics of hepatitis C virus (HCV) infections is currently one of the most highly demanded medical tasks. This study is devoted to the development of biochips (microarrays) that can be applied for the detection of HCV. The analytical platforms of suggested devices were based on macroporous poly(glycidyl methacrylate-co-di(ethylene glycol) dimethacrylate) monolithic material. The biochips were obtained by the covalent immobilization of specific probes spotted onto the surface of macroporous monolithic platforms. Using the developed biochips, different variants of bioassay were investigated. This study was carried out using hepatitis C virus-mimetic particles (VMPs) representing polymer nanoparticles with a size close to HCV and bearing surface virus antigen (E2 protein). At the first step, the main parameters of bioassay were optimized. Additionally, the dissociation constants were calculated for the pairs &ldquo, ligand&ndash, receptor&rdquo, and &ldquo, antigen&ndash, antibody&rdquo, formed at the surface of biochips. As a result of this study, the analysis of VMPs in model buffer solution and human blood plasma was carried out in a format of direct and &ldquo, sandwich&rdquo, approaches. It was found that bioassay efficacy appeared to be similar for both the model medium and real biological fluid. Finally, limit of detection (LOD), limit of quantification (LOQ), spot-to-spot and biochip-to-biochip reproducibility for the developed systems were evaluated.

Clinical microbiology is experiencing the emergence of the syndromic approach of diagnosis. This paradigm shift will require innovative technologies to detect rapidly, and in a single sample, multiple pathogens associated with an infectious disease. Here, we report on a multiplex technology based on DNA-microarray that allows detecting and discriminating 11 bacteria implicated in respiratory tract infection. The process requires a PCR amplification of bacterial 16S rDNA, a 30 min hybridization step on species-specific oligoprobes covalently linked on dendrimers coated glass slides (DendriChips®) and a reading of the slides by a dedicated laser scanner. A diagnostic result is delivered in about 4 h as a predictive value of presence/absence of pathogens using a decision algorithm based on machine-learning method, which was constructed from hybridization profiles of known bacterial and clinical isolated samples and which can be regularly enriched with hybridization profiles from clinical samples. We demonstrated that our technology converged in more than 95% of cases with the microbiological culture for bacteria detection and identification.

We describe the design and fabrication of biochips based on 1-D photonic crystals supporting Bloch surface waves for label-free optical biosensing. The optical properties of Bloch surface waves are studied in relation to the geometry of the photonic crystals and on the properties of the dielectric materials used for the fabrication. The planar stacks of the biochips are composed of silica, tantala, and titania that were deposited using plasma-ion-assisted evaporation under high-vacuum conditions. The biochip surfaces were functionalized by silanization, and appropriate fluidic cells were designed to operate in an automated platform. An angularly resolved ellipsometric optical sensing apparatus was assembled to carry out the sensing studies. The angular operation is obtained by a focused laser beam at a fixed wavelength and detection of the angular reflectance spectrum by means of an array detector. The results of the experimental characterization of the physical properties of the fabricated biochips show that their characteristics, in terms of sensitivity and figure of merit, match those expected from the numerical simulations. Practical application of the sensor was demonstrated by detecting a specific glycoprotein, Angio-poietin 2, that is involved in angiogenesis and inflammation processes. The protocol used for the label-free detection of Angiopoietin 2 is described, and the results of an exemplary assay, carried out at a relatively high concentration of 1 µg/ml, are given and confirm that an efficient detection can be achieved. The limit of detection of the biochips for Angiopoietin 2, based on the protocol used, is 1.5 pg/mm2 in buffer solution. The efficiency of the label-free assay is confirmed by independent measurements carried out by means of confocal fluorescence microscopy.

Date of Conference: 28–29 January 2017 Miniaturized optofluidic platforms play an important role in bio-analysis, detection and diagnostic applications. The advantages of such miniaturized devices are extremely low sample requirement, low cost development and rapid analysis capabilities. Fused silica is advantageous for optofluidic systems due to properties such as being chemically inert, mechanically stable, and optically transparent to a wide spectrum of light. As a three dimensional manufacturing method, femtosecond laser scanning followed by chemical etching shows great potential to fabricate glass based optofluidic chips. In this study, we demonstrate fabrication of all-fiber based, optofluidic flow cytometer in fused silica glass by femtosecond laser machining. 3D particle focusing was achieved through a straightforward planar chip design with two separately fabricated fused silica glass slides thermally bonded together. Bioparticles in a fluid stream encounter with optical interrogation region specifically designed to allocate 405nm single mode fiber laser source and two multi-mode collection fibers for forward scattering (FSC) and side scattering (SSC) signals detection. Detected signal data collected with oscilloscope and post processed with MATLAB script file. We were able to count number of events over 4000events/sec, and achieve size distribution for 5.95μm monodisperse polystyrene beads using FSC and SSC signals. Our platform shows promise for optical and fluidic miniaturization of flow cytometry systems. © 2017 SPIE.

This paper reports on the design and fabrication of electrolyte insulator semiconductor capacitor (EISCAP) devices to detect triglycerides in the form of microreactors fabricated by bulk micromachining of silicon. We have developed a complete triglyceride biochip wherein the enzyme for hydrolysis and the counter electrode for signal transduction are integrated with a miniaturised EISCAP sensor. A compact readout system that measures the triglyceride concentration in blood serum under test has been developed and is implemented in a Programmable System on Chip (PSoC�). The miniaturised EISCAP devices are tested using blood serum samples to estimate the triglyceride concentration within the clinical range of 50 to 150 mg dL-1 and the time taken by the readout system to calibrate the sensor and to measure the triglyceride is less than 5 minutes. � The Royal Society of Chemistry 2014.

Biochips are cyber-physical system with realistic potential to improve the healthcare process, e.g., by providing faster disease diagnosis and at-home direct treatment. We review the area of biochips on its way to becoming a strong research field. However, for the real breakthrough to happen, a stronger collaboration among disciplines is needed. Thus, we organized this tutorial at Embedded Systems Week, to inform researchers about the potential of biochips. We presented the vision, the research challenges and an overview of the design automation as well as of the fabrication work. We show how the conventional methods in embedded systems can be applied to biochips to optimize their execution and design. Besides that, we conducted a hands-on lab that allowed the participants to get in direct contact with biochips. The participants were highly inspired and we hope their interest will result in fruitful collaborations.

DNA microarrays are used extensively for biochemical analysis that includes genomics and drug discovery. This increased usage demands large microarrays, thus complicating their computer aided design (CAD) and manufacturing methodologies. One such time-consuming design problem is to minimize the border length of masks used during the manufacture of microarrays. From the manufacturing point of view the border length of masks is one of the crucial parameters determining the reliability of the microarray. This article presents a novel algorithm for synthesis (placement and embedding) of microarrays, which consumes significantly less time than the best algorithm reported in the literature, while maintaining the quality (border length of masks) of the result. The proposed technique uses only a part of each probe to decide on the placement and the remaining parts for deciding on the embedding sequence. This is in contrast to the earlier methods that considered the entire probe for both placement and embedding. The second novelty of the proposed technique is the preclassification (prior to placement and embedding) of probes based on their prefixes. This decreases the complexity of the problem of deciding the next probe to be placed from that involving computation of Hamming distance between all probes (as used in earlier approaches) to the one involving searching of nonempty cells on a constant size grid array. The proposed algorithm is 43× faster than the best reported in the literature for the case of synthesizing a microarray with 250,000 probes and further exhibits linear behavior in terms of computation time for larger microarrays.

Background Immunological test systems for diagnostics of type I hypersensitivity involve the following types of antigens: whole allergen extracts, individual highly purified proteins and their recombinant analogues. The goal of this study was to compare the results obtained with whole allergen extracts (birch pollen, cat dander, and timothy grass pollen) and their respective recombinant proteins in biochip-based immunoassay. Methods Multiplex fluorescent immunoassay of 139 patients’ blood serum samples was carried out using biological microchips (biochips). sIgE concentrations for the chosen allergens and their recombinant components were measured. ROC analysis was used for comparison of the results and determination of diagnostic accuracy. Results The results for the birch pollen extract and its recombinant allergens have shown that the diagnostic accuracy of the methods utilizing the whole allergen extract, its major component Bet v 1 and the combination of major and minor components (Bet v 1 and Bet v 2) was the same. Values for diagnostic accuracy for the cat dander extract and its major recombinant component Fel d 1 were equal. In contrast with birch pollen and cat dander allergens, using of recombinant components of timothy grass pollen (Phl p 1, Phl p 5, Phl p 7 and Phl p 12) did not allow reaching the diagnostic accuracy of using natural extract. Conclusions Multiplex analysis of samples obtained from patients with allergy to birch pollen and cat dander using biological microchips has shown that comparable accuracy was observed for the assay with natural extracts and recombinant allergens. In the case of timothy grass allergen, using the recombinant components may be insufficient.

In this work we show the development and assessment of disposable, biocompatible, fully plastic microreactors, which are demonstrated to be highly efficient for performing on-chip direct PCR analyses of very diverse crude biological samples, such as human cells, whole blood, buccal scrape and hair bulbs, without requiring any purification steps before PCR analyses.

International audience; Carbohydrate and glycoconjugates play a major role in key biological events such as cell-cell recognition, pathogenesis and inflammation[1]. As a consequence, there is a need to understand the structural parameters governing the recognition of carbohydrate by their receptors. Technologies for rapid monitoring and evaluating such interactions are of great importance to provide deep insights relevant to carbohydrate involving biological events. However, most conventional approaches are cumbersome and material and time consuming. Carbohydrate microarray technology is a promising approach for probing carbohydrate/protein interactions because it permits the simultaneous screening of a number of biological interactions with only minute amounts of material. Herein, we develop a strategy to probe different glycoconjugates (different spatial configuration, linker, geometry...) toward proteins in one time on a DNA Directed Immobilization (DDI) oligosaccharide biochip.

Cell separation and sorting are essential steps in cell biology research and in many diagnostic and therapeutic methods. Recently, there has been interest in methods which avoid the use of biochemical labels; numerous intrinsic biomarkers have been explored to identify cells including size, electrical polarizability, and hydrodynamic properties. This review highlights microfluidic techniques used for label-free discrimination and fractionation of cell populations. Microfluidic systems have been adopted to precisely handle single cells and interface with other tools for biochemical analysis. We analyzed many of these techniques, detailing their mode of separation, while concentrating on recent developments and evaluating their prospects for application. Furthermore, this was done from a perspective where inertial effects are considered important and general performance metrics were proposed which would ease comparison of reported technologies. Lastly, we assess the current state of these technologies and suggest directions which may make them more accessible. Figure A wide range of microfluidic technologies have been developed to separate and sort cells by taking advantage of differences in their intrinsic biophysical properties

A mild, fast and flexible method for photoimmobilization of biomolecules based on the light-initiated thiol-ene reaction has been developed. After investigation and optimization of various surface materials, surface chemistries and reaction parameters, microstructures and microarrays of biotin, oligonucleotides, peptides, and MUC1 tandem repeat glycopeptides were prepared with this photoimmobilization method. Furthermore, MUC1 tandem repeat glycopeptide microarrays were successfully used to probe antibodies in mouse serum obtained from vaccinated mice. Dimensions of biomolecule microstructures were shown to be freely controllable through photolithographic techniques, and features down to 5 microm in size covering an area of up to 75x25 mm were created. Use of a confocal laser microscope with a UV laser as UV-light source enabled further reduction of biotin feature size opening access to nanostructured biochips.

This paper investigates technological advancements in developing reliable technologies for label free detection of cancer markers. Capacitance detection was used successfully to develop an immunosensor. Rigorous probe immobilization was implemented to obtain reliable capacitance measurements. The commonly considered alkanethiols for proteins immobilization do not allow sufficiently stable capacitance measurements. Therefore, new ethylene-glycol functionalized alkanethiols were used as more suitable materials to develop lab-on-a-chip detection of cancer markers. Results from AFM, Chemi-luminescence, Fluorescence, Cyclic Voltammetry, QCM, and capacitance measurements showed that three (ethylene-glycol) alkanethiols highly stabilized the sensing surfaces in time. The measured capacitance on the antibody layers was in the range of 60–70 nF/cm2 and 80–115 nF/cm2 for the antigen detection. The developed system was utilized to detect the Hepatocarcinoma marker SCCA, and the whole IgM fraction from Hepatocarcinoma patient’s serum. Electrode by electrode reproducibility within the same chip increased by one order of magnitude (variations were reduced from 30–40% down to less than 2%) using these new alkanethiols, while the reached limit in sensitivity was close to 2.43 μg/ml.

This paper reports the first intensified biochip system for chemiluminescence detection and the feasibility of using this system for the analysis of biological warfare agents is demonstrated. An enzyme-linked immunosorbent assay targeting Bacillus globigii spores, a surrogate species for Bacillus anthracis, using a chemiluminescent alkaline phosphatase substrate is combined with a compact intensified biochip detection system. The enzymatic amplification was found to be an attractive method for detection of low spore concentrations when combined with the intensified biochip device. This system was capable of detecting approximately 1 × 105Bacillus globigii spores. Moreover, the chemiluminescence method, combined with the self-contained biochip design, allows for a simple, compact system that does not require laser excitation and is readily adaptable to field use. Figure Schematic diagram of the miniature biochip detection system

In this work, we study the role of the organosulfur linker in the adsorption of derivatized single stranded (ss) DNA on gold. The studied oligonucleotides are the unmodified ssDNA, the ssDNA modified with a thiol linker (SH-DNA), a symmetrical disulfide carrying two identical ssDNA molecules (DNA-SS-DNA) and an asymmetric disulfide carrying the protecting group dimetoxitrityl (DNA-SS-DMTO). Surface inspection by atomic force microscopy shows that the modified oligonucleotides and the non modified oligonucleotides form monolayers on gold with similar structure and density. However, the results obtained by the cantilever bending method show that surface stress induced by the adsorption of ssDNA on gold critically depends on the organosulfur linker used. The results indicate that the surface stress measurement is mainly sensitive to the chemisorbed DNA molecules. We interpret the results using a two-step adsorption model, in which the oligonucleotides quickly phisysorb on the gold surface before chemisorption is achieved via formation of the same alkanethiolate species in the three cases studied. Surface stress upon adsorption, and subsequent cantilever bending, is related to the transition between the physisorbed and chemisorbed states, in which the disulfide linker imposes a major difficulty to achieve the chemisorbed state due to geometrical and steric constraints.

Lab-on-a-chip biological platforms have been intensively developed during the last decade since emerging technologies have offered possibilities to manufacture reliable devices with increased spatial resolution and 3D configurations. These biochips permit testing chemical reactions with nanoliter volumes, enhanced sensitivity in analysis and reduced consumption of reagents. Due to the high peak intensity that allows multiphoton absorption, ultrafast lasers can induce local modifications inside transparent materials with high precision at micro- and nanoscale. Subtractive manufacturing based on laser internal modification followed by wet chemical etching can directly fabricate 3D micro-channels in glass materials. On the other hand, additive laser manufacturing by two-photon polymerization of photoresists can grow 3D polymeric micro- and nanostructures with specific properties for biomedical use. Both transparent materials are ideal candidates for biochips that allow exploring phenomena at cellular levels while their processing with a nanoscale resolution represents an excellent opportunity to get more insights on biological aspects. We will review herein the laser fabrication of transparent microfluidic and optofluidic devices for biochip applications and will address challenges associated with their potential. In particular, integrated micro- and optofluidic systems will be presented with emphasis on the functionality for biological applications. It will be shown that ultrafast laser processing is not only an instrument that can tailor appropriate 3D environments to study living microorganisms and to improve cell detection or sorting but also a tool to fabricate appropriate biomimetic structures for complex cellular analyses. New advances open now the avenue to construct miniaturized organs of desired shapes and configurations with the goal to reproduce life processes and bypass in vivo animal or human testing.

International audience; Diamond is wide band gap semiconductor presenting many extreme properties. It is notably known as the most stable material with the highest chemical inertness, the highest mechanical hardness and the highest thermal conductivity. Since the mid 1970s it has been possible to grow synthetic diamond by several methods. High Pressure High Temperature techniques that mimic the diamond formation in the earth's crust were first developed. Then Chemical Vapour Deposition (CVD) methods enable diamond growth at laboratory scale as well as the control the P-type and N-type doping of diamond. Besides, it is possible to tune the diamond electrical properties form very resistive to metallic thanks to the P-type doping with boron. Current achievements have enabled the development of diamond sensors that can operate in extreme conditions. After being used for its mechanical and thermal properties, diamond was considered for chemical sensing. In fact the chemical stability and the close-to-metallic conductivity of diamond make it a powerful tool for electrochemical detection in various environment. Furthermore, the diamond is an ideal substrate for surface functionalization thanks to the wide and very known carbon based chemistry. Such a feature combined to the outstanding electrochemical properties of the diamond electrodes have enable the production of very efficient biosensors and biochips. Diamond is also an interesting sensor for medical imaging. Its carbon nature, well tolerated by living tissues, are actually very useful for its use as a biosensor capable of working in contact with bio-environments as well as real neuronal interfaces. Both those topics will be discussed in details in the following pages. In a first part an overview on electrochemical based biosensors and their performance is described. Then in a second half of the chapter, novel applications where diamond is directly used as an electrode for neural tissue interfacing is presented in details.

An increase in the frequency of antimicrobial resistance genes (ARGs) in bacteria including Escherichia coli could be a threat to public health. This study investigated the impact of activated sludge and physicochemical wastewater treatment processes on the prevalence of ARGs in E. coli isolates. In total, 719 E. coli were isolated from the influent and effluent (prior to disinfection) of two activated sludge and two physicochemical municipal treatment plants, and genotyped using DNA microarrays. Changes in the abundance of ARGs in the E. coli population were different for the two treatment processes. Activated sludge treatment did not change the prevalence of ARG-possessing E. coli but increased the abundance of ARGs in the E. coli genome while physicochemical treatment reduced both the prevalence of ARG-carrying E. coli as well as the frequency of ARGs in the E. coli genome. Most E. coli isolates from the four treatment plants possessed ARGs of multiple antimicrobial classes, mainly aminoglycoside, β-lactams, quinolone and tetracyclines. In addition these isolates harboured DNA insertion sequence elements including integrase and transposase. A significant positive association was found between the occurrence of ARGs and virulence genotypes. © 2013 Elsevier Ltd.

Digital microfluidics is an emerging technology that provides fluid-handling capability on a chip. Biochips based on digital microfluidics have therefore enabled the automation of laboratory procedures in biochemistry. By reducing the rate of sample and reagent consumption, digital microfluidic biochips allow continuous sampling and analysis for real-time biochemical analysis, with application to clinical diagnostics, immunoassays, and DNA sequencing. Recent advances in technology and applications serve as a powerful driver for research on computer-aided design (CAD) tools for biochips.This thesis research is focused on a design automation framework that addresses chip synthesis, droplet routing, control-pin mapping, testing and diagnosis, and error recovery. In contrast to prior work on automated design techniques for digital microfluidics, the emphasis here is on practical CAD optimization methods that can target different design problems in a unified manner. Constraints arising from the underlying technology and the application domain are directly incorporated in the optimization framework.The avoidance of cross-contamination during droplet routing is a key design challenge for biochips. As a first step in this thesis research, a droplet-routing method based on disjoint droplet routes has been developed to avoid cross-contamination during the design of droplet flow paths. A wash-operation synchronization method has been developed to synchronize wash-droplet routing steps with sample/reagent droplet-routing steps by controlling the order of arrival of droplets at cross-contamination sites.In pin-constrained digital microfluidic biochips, concurrently-implemented fluidic operations may involve pin-actuation conflicts if they are not carefully synchronized. A two-phase optimization method has been proposed to identify and synchronize these fluidic operations. The goal is to implement these fluidic operations without pin-actuation conflict, and minimize the duration of implementing the outcome sequence after synchronization.Due to the interdependence between droplet routing and pin-count reduction, this thesis presents two optimization methods to concurrently solve the droplet-routing and the pin-mapping design problems. First, an integer linear programming (ILP)-based optimization method has been developed to minimize the number of control pins. Next an efficient heuristic approach has been developed to tackle the co-optimization problem.Dependability is an important system attribute for microfluidic biochips. Robust testing methods are therefore needed to ensure correct results. This thesis presents a built-in self-test (BIST) method for digital microfluidic biochips. This method utilizes digital microfluidic logic gates to implement the BIST architecture. A cost-effective fault diagnosis method has also been proposed to locate a single defective cell, multiplerows/columns with defective cells, as well as an unknown number of rows/columns-under-test with defective cells. A BIST method for on-line testing of digital microfluidic biochips has been proposed. An automatic test pattern generation (ATPG) method has been proposed for non-regular digital microfluidic chips. A pin-count-aware online testing method has been developed for pin-constrained designs to support the execution of both fault testing and the target bioassay protocol.To better monitor and manage the execution of bioassays, control flow has been incorporated in the design and optimization framework. A synthesis method has been developed to incorporate control paths and an error-recovery mechanism during chip design. This method addresses the problem of recovering from fluidic errors that occurduring on-chip bioassay execution.In summary, this thesis research has led to a set of unified design tools for digital microfluidics. This work is expected to reduce human effort during biochip design and biochip usage, and enable low-cost manufacture and more widespread adoption for laboratory procedures.

This paper describes an innovative integrated micro flow cytometer that presents a new arrangement for the excitation/detection system. The sample liquid, containing the fluorescent marked particles/cells under analysis, is hydrodynamically squeezed into a narrow stream by two sheath flows so that the particles/cells flow individually through a detection region. The detection of the particles/cells emitted fluorescence is carried out by using a collection fiber placed orthogonally to the flow. The device is based on silicon hollow core antiresonant reflecting optical waveguides (ARROWs). ARROW geometry allows one to use the same channel to guide both the sample stream and the fluorescence excitation light, leading to a simplification of the optical configuration and to an increase of the signal-to-noise ratio. The integrated micro flow cytometer has been characterized by using biological samples marked with standard fluorochromes. The experimental investigation confirms the success of the proposed microdevice in the detection of cells.

Electroporation is a widely used technique which allows introducing into cultured cells molecules which won't enter in naturally because of the high selectivity of the cell membrane (this is called transfection). We are presenting in this paper a biochip comprising an array of microelectrodes which can be used to electroporate single cells instead than the large number of cells customarily treated with commonly used transfection techniques. In particular, we are dealing with electrical measurements of the biochip electrodes and with an accurate equivalent model.

Background A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. Results Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane) material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. Conclusion The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting technology.

10 páginas, 6 figuras.-- Trabajo presentado en la conferencia "Nanotechnology"; Maspalomas, Gran Canaria (España); 19-Mayo-2003; Editores: Robert Vajtai, Xavier Aymerich, Laszlo B. Kish, Angel Rubio., Nanomechanical biosensors have emerged as a promising platform for specific biological. Among the advantages are direct detection without need of labelling with fluorescent or radioactive molecules, very high sensitivity, reduced sensor area, and suitability for integration using silicon technology. Here we have studied the immobilization of oligonucleotide monolayers by monitoring the microcantilever bending. Oligonucleotides were derivatized with thiol molecules for self-assembly on the gold-coated side of a microcantilever. The geometry of the binding and the surface density were studied by mixing derivatized oligonucleotides with spacer self-assembled monolayers and by controlling the oligonucleotide functional group form. These results are compared with fluoresencent and chemiluminescence techniques. Furthermore, we present the first results of direct pesticide detection with microcantilever-based biosensors. Herbicide DDT was detected by performing competitive assays, in which the cantilever was coated with a synthetic DDT hapten, and it was exposured to different rations between the monoclonal antibody and the DDT. A new technique is presented for the detection of the nanomechanical response for biosensing applications, in which the resonant frequency is measured with about two orders of magnitude higher sensitivity. The low quality factor of the microcantilever in liquid is increased up by using an active feedback control, in which the cantilever oscillation is amplified and delayed and it is used as a driving force. The technique has been applied for the detection of ethanol, proteins, and pathogens., This work was supported by the Spanish Ministry of Science and Technology (MCyT), project BIO2001-1235-C03-01. Mar Álvarez acknowledge the grant from the MCyT.

A complete photonic wire molecular biosensor microarray chip architecture and supporting instrumentation is described. Chip layouts with 16 and 128 independent sensors have been fabricated and tested, where each sensor can provide an independent molecular binding curve. Each sensor is 50 μm in diameter, and consists of a millimeter long silicon photonic wire waveguide folded into a spiral ring resonator. An array of 128 sensors occupies a 2 × 2 mm2 area on a 6 × 9 mm2 chip. Microfluidic sample delivery channels are fabricated monolithically on the chip. The size and layout of the sensor array is fully compatible with commercial spotting tools designed to independently functionalize fluorescence based biochips. The sensor chips are interrogated using an instrument that delivers sample fluid to the chip and is capable of acquiring up to 128 optical sensor outputs simultaneously and in real time. Coupling light from the sensor chip is accomplished through arrays of sub-wavelength surface grating couplers, and the signals are collected by a fixed two-dimensional detector array. The chip and instrument are designed so that connection of the fluid delivery system and optical alignment are automated, and can be completed in a few seconds with no active user input. This microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria using serospecific polyclonal antibody probe molecules. © 2013 Optical Society of America.

The paper discusses the recent achievements in the development of chips with integrated sensing of biomolecules. In particular, it focuses on integrated sensing electrodes on silicon and presents innovative solutions for the enhanced robustness of the electrodes towards cleaning processes and electrolytes. In this study, a microfabrication technology for 3D-integrated disposable chip layers that enables the reusability of the overall system for many times is presented.

This paper presents an electronic system for a fast DNA label-less detection. The sensitivity of the capacitive sensor in use is improved by depositing an insulating self-assembled monolayer (SAM) over the golden electrodes. The capacitance shift due to the hybridization effect is monitored by means of a charge-sensitive amplifier and digitalized by means of a comparator and a counter. The read-out solution demonstrates the ability to identify a 0.01% variation on the capacitive value of the sensor. Results from measurements with the optimized sensor show the reliability of the electronics. The investigated solution is suitable for monolithic systems or for a micro-fabricated array of sensors. An example of the integrated front-end is described and performances and noise evaluation are reported here. (C) 2008 Elsevier Ltd. All rights reserved.

The implantable enzyme amperometric biosensor continues as the dominant in vivo format for the detection, monitoring and reporting of biochemical analytes related to a wide range of pathologies. Widely used in animal studies, there is increasing emphasis on their use in diabetes care and management, the management of trauma-associated hemorrhage and in critical care monitoring by intensivists in the ICU. These frontier opportunities demand continuous indwelling performance for up to several years, well in excess of the currently approved seven days. This review outlines the many challenges to successful deployment of chronically implantable amperometric enzyme biosensors and emphasizes the emerging technological approaches in their continued development. The foreign body response plays a prominent role in implantable biotransducer failure. Topics considering the approaches to mitigate the inflammatory response, use of biomimetic chemistries, nanostructured topographies, drug eluting constructs, and tissue-to-device interface modulus matching are reviewed. Similarly, factors that influence biotransducer performance such as enzyme stability, substrate interference, mediator selection and calibration are reviewed. For the biosensor system, the opportunities and challenges of integration, guided by footprint requirements, the limitations of mixed signal electronics, and power requirements, has produced three systems approaches. The potential is great. However, integration along the multiple length scales needed to address fundamental issues and integration across the diverse disciplines needed to achieve success of these highly integrated systems, continues to be a challenge in the development and deployment of implantable amperometric enzyme biosensor systems. (c) 2012 Elsevier B.V. All rights reserved.