Biochip Research Papers - Academia.edu (original) (raw)

1,3-Dinitrobenzene (1,3-DNB) specifically injures Sertoli cells and induces testicular toxicity by disrupting the key function of these cells. To clarify the molecular mechanism underlying 1,3-DNB’s action on Sertoli cells, we analyzed gene expression profiles of TM4 mouse Sertoli cells after chemical treatment. In total, 1,203 genes were identified as either up- or down-regulated, with greater than 1.5-fold changes (P<0.05). Based on k-means clustering, genes that were differentially expressed in a time-dependent manner were identified; then biofunction and canonical pathways were analyzed using Ingenuity Pathways Analysis. Genes related to axonal guidance, Nrf2-mediated oxidative stress response, protein ubiquitination, and tight junction signaling pathways were identified in either time-specifically or time-dependently regulated groups. The transcription levels of genes related to tight junction signaling pathways (Mpp5, F11r, Prkcz, Magi2, and Tgfb2) and genes encoding junction proteins (Ocln, Tjp1, Tjp2, Gja1, and Gjd2) were validated in 1,3-DNB-treated and 2,5-hexanedione-treated TM4 cells by quantitative real-time polymerase chain reaction. Comprehensive gene expression profiling of 1,3-DNB-treated TM4 cells and subsequent canonical pathway analyses provided valuable information regarding the molecular mechanism of cell death and cell interaction in TM4 mouse Sertoli cells after 1,3-DNB exposure.

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- Molecular Mechanics, Biochip, Cell Death, Axon Guidance

In this paper, we compare the biotransformation capacities of cryopreserved primary human hepatocytes cultivated in a liver microfluidic biochip and in plates. The hepatocytes were exposed to the CIME cocktail (Carte d'Identité MEtabolique), a mixture of seven probes (acetaminophen, amodiaquine, caffeine, dextromethorphan, midazolam, omeprazole and tolbutamide) for key enzymes involved in the xenobiotic metabolism and pharmacokinetics. The purpose of the cocktail was to give an overview of the metabolic profile of the hepatocytes due to concomitant exposure and a simultaneous mass spectrometric detection method of the metabolites. The results showed a greater activity for CYP1A2, CYP2C9, CYP2C19 CYP2D6, CYP3A and UGT1A1 after 4 h of incubation in the microfluidic biochip when compared to the plate cultures. Furthermore, the metabolic ratio time-course measured at 1 h, 3 h and 4 h indicated that the enzymatic activity increased when the hepatocytes were cultivated in the microflu...

- by Cécile Legallais
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- Metabolism, Pharmaceutics, Humans, Biochip
- by Sandro Carrara and +1
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- Analytical Chemistry, Biomedical Engineering, Privacy, Biotechnology

Recent advances in the convergence of the biological, chemical, physical, and engineering sciences have opened new avenues of research into the interfacing of diverse biological moieties with inanimate platforms. A main aspect of this field, the integration of live cells with micro-machined platforms for high throughput and bio-sensing applications, is the subject of the present review. These unique hybrid systems are configured in a manner that ensures positioning of the cells in designated patterns, and enables cellular viability maintenance, and monitoring of cellular functionality. Here we review both animate and inanimate surface properties and how they affect cellular attachment, describe relevant modifications of both types of surfaces, list technologies for platform engineering and for cell deposition in the desired configurations, and discuss the influence of various deposition and immobilization methods on the viability and performance of the immobilized cells.

- by Hadar Ben-Yoav and +1
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- Biochip
- by Mohamad Sawan
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- Medical Imaging, Brain Imaging, Biochip, Fnirs
- by Luiz Carlos Kretly
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- Robotics, Technology, Architecture, Nanomedicine

This work presents a novel micro-fluidic whole cell biosensor for water toxicity analysis. The biosen- sor presented here is based on bacterial cells that are genetically “tailored” to generate a sequence of biochemical reactions that eventually generate an electrical signal in the presence of genotoxicants. The bacterial assay was affected by toxicant contaminated water for an induction time that ranged between 30 min and 120 min. Enzymatic substrate (pAPP) was added to the assay generating the electrochemi- cal active material (pAP) only when toxicants are sensed by the bacteria. The bacteria were integrated onto a micro-chip that was manufactured by MEMS technology and comprises various micro-chambers with volume ranging between 2.5 nl and 157 nl with electrode radius between 37.5 m and 300 m. We describe the biochip operation, its electrochemical response to calibration solutions as well as to the whole cell assays. The potential use of the whole cell biochip for toxicity detection of two different geno- toxicants, nalidixic acid (NA) and 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), is demonstrated. We demonstrate minimal toxicant detection of 10 g/ml for NA using 30 min for induction and 0.31 M for IQ using 120 min for induction, both 3 min after the addition of the substrate material.

- by Hadar Ben-Yoav and +3
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- Bioelectrochemistry, Biosensors, Electrochemistry, Lab On A Chip
- by Andrea Gallotta and +1
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- Nanotechnology, Antibodies, Humans, Biochip
- by Colette McDonagh and +1
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- Technology, Modeling, Fluorescence, Chemical Physics

Proprietary mixture of polyurethane methacrylate (PUMA) and off-stoichiometry thiol-ene (OSTE-80) are evaluated as two possible polymeric substrates to prototype microfluidic biochips. Because of their lack of biocompatibility, PUMA and OSTE-80 are modified by argon (Ar) or nitrogen (N 2) plasma treatment to introduce nitrogen moieties that are highly polar and conducive for cell attachment and growth. XPS and water contact angle measurement show that these nitrogen groups are relatively stable in the plasma-treated PUMA and OSTE-80 in spite of the hydrophobic recovery and volatilization of nitrogen moieties during air ageing for 15 days. This stability can be attributed to their high degree crosslinking that is reflected by the increase of elastic modulus of PUMA and OSTE-80 during their air ageing. These results show that Ar and N 2 plasma-treated PUMA and OSTE-80 possess the necessary physical and chemical properties to be evaluated further to develop microfluidic biochips for biological applications.

- by Kim S Siow
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- Microfluidics, Plasma Engineering, Surface Chemistry, Surface modification
- by Sunil Shah
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- Engineering, Materials Engineering, Materials Science, Organic Chemistry
- by Lawrence Shah
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- Optics, Glass, Femtosecond Laser, Fiber Lasers
- by Shiuh-Bin Fang
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- Materials Science, Microfluidics, Industrial Biotechnology, Medicine

The heart may be a mirror of the soul, but the human mind is more than its heart rate variability (HRV). Many techniques to quantify HRV promise to give a view of what is going on in the body or even the psyche of the subject under study. This "Hypothesis" paper gives, on the one hand, a critical view on the field of HRV-analysis and, on the other hand, points out a possible direction of future applications. In view of the inherent variability of HRV and the underlying processes, as lined out here, the best use may be found in serial analysis in a subject/patient, to find changes over time that may help in early discovery of developing pathology. Not every future possibility is bright and shining, though, as demonstrated in a fictional diary excerpt from a future subject, living in a society geared toward preventive medicine. Here implanted biochips watch over the health of the population and artificial intelligence (AI) analyses the massive data flow to support the diagnostic process.

- by John M Karemaker
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- Artificial Intelligence, Preventive medicine, Personalized Medicine, Futurology

The isolation and characterization of six polymorphic loci from a Testudo hermanni genomic library is reported. Enrichment was performed for AC but four of the character- ized microsatellites present also an additional motif. Variability was tested on populations of the two recognized subspecies, Testudo hermanni hermanni and Testudo hermanni boett- geri. For one locus, a size range specific for the

- by Barbara Livoreil
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- Chemical Engineering, Genetics, Food Science, Conservation Genetics
- by Yangseok Kim and +2
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- Biochip
- by Sahar Melamed and +2
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- Technology, Cell Adhesion, Biological Sciences, Biochip

The electrode geometry and material have a significant effect on the electrochemical biochip transduction of chemical signals into electrical current or voltage. In this work we focus on the working electrode aiming to improve the signal level of live cell sensors integrated on solid-state microchips. We present here a model and measurements describing the effect of the electrode material and dimensions on the biochip performance. The research hypothesis was that the electrode transduction efficiency increases as its effective area increases. Therefore, we investigated two methods to increase the electrode effective area: 3D structures and a polymer modified electrode. An electrochemical microchip was fabricated with a working electrode that was further modified, resulting in two structure types: 3D metallic pillar-based and polypyrrole-coated. The electrochemical performance of both modified electrodes was characterized and their utilization as working electrodes in whole-cell biochips for toxicity sensing was studied. Bio- detection efficiency analysis demonstrated higher biosensing performance for the metallic (e.g. Cu/Au) pillar-based microchip than for the polypyrrole-modified and the non-modified microchips. Therefore, we conclude that the enhanced signal of the modified geometry electrode is most probably due to the increased effective surface area and the improved charge transfer efficiency.

- by Hadar Ben-Yoav and +2
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- Conducting Polymers, Microfabrication, Biochip, Whole Cell Bacterial Biosensor

This study developed a method of detecting bioparticles such as Salmonella that exist in the biological samples. The method employed a substrate with interlaced comb-like electrodes into which the mixtures of biological samples and antibody-coated gold nanoparticles were added. The alternative signals with appropriate frequency bands were then conducted into the comb-like electrodes to change the dielectrophoresis force. The gold-modified Salmonella can be adsorbed on the edges of the electrodes and isolated from various biological samples. The impedance of the adsorbed Salmonella on the edges of the electrodes was measured and comparison of the impedance between the electrodes with and without Salmonella can quantify the amount of the adsorbed Salmonella.

- by Shiuh-Bin Fang
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- Electrochemistry, Industrial Biotechnology, Dielectrophoresis, Metal Nanoparticles

Early detection of kinetic, metabolic, and toxicity (ADME-Tox) profiles for new drug candidates is of crucial importance during drug development. This article describes a novel in vitro system for the incubation of precision-cut liver slices (PCLS) under flow conditions, based on a poly(dimethylsiloxane) (PDMS) device containing 25-µL microchambers for integration of the slices. The microdevice is coupled to a perifusion system, which enables a constant delivery of nutrients and oxygen and a continuous removal of waste products. Both a highly controlled incubation environment and high metabolite detection sensitivity could be achieved using microfluidics. Liver slices were viable for at least 24 h in the microdevice. The compound, 7-ethoxycoumarin (7-EC), was chosen to test metabolism, since its metabolism includes both phase I and phase II metabolism and when tested in the conventional well plate system, correlates well with the in vivo situation (De Kanter et al. 2004. Xenobiotica 34(3): 229–241.). The metabolic rate of 7-EC was found to be 214 ± 5 pmol/min/mg protein in the microdevice, comparable to well plates, and was constant over time for at least 3 h. This perifusion system better mimics the in vivo situation, and has the potential to significantly contribute to drug metabolism and toxicology studies of novel chemical entities. Biotechnol. Bioeng. 2010;105: 184–194. © 2009 Wiley Periodicals, Inc.

- by Paul van Midwoud
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- Fluid Mechanics, Microfluidics, Metabolism, Toxicology
- by Maan Alkaisi
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- Microfluidics, Electrokinetics in Microfluidics, Dielectrophoresis, Microelectronic

This paper presents a whole-cell bio-chip system where viable, functioning cells are deposited onto solid surfaces that are a part of a micro-machined system. The development of such novel hybrid functional sensors depends on the cell deposition methods; in this work new approach integrating live bacterial cells on a bio-chip using electrophoretic deposition is presented. The bio-material deposition technique was characterized under various driving potential and chamber configurations. The deposited bio-mass included genetically engineered bacterial cells generating electrochemically active byproduct upon exposure to toxic materials in the aqueous solution. In this paper we present the deposition apparatus and methods, as well as the characterization results, e.g. signal vs. time and induction factor, of such chips and discussing the highlight and problems of the new deposition method.

- by Hadar Ben-Yoav and +2
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- Biochip, Electrophoretic Deposition
- by Young-Su Jeong
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- Biochip

Our studies focused on improving the biocompatibility properties of two microfluidic prototyping substrates i.e. polyurethane methacrylate (PUMA) and off-stoichiometry thiol-ene (OSTE-80) polymer by Ar and N 2 plasma treatment. The contact angle (CA) measurement showed that both plasma treatments inserted oxygen and nitrogen moieties increased the surface energy and hydrophilicity of PUMA and OSTE-80 polymer which corresponded to an increase of nitrogen to carbon ratios (N/C), as measured by XPS, to provide a conducive environment for cell attachments and proliferation. Under the SEM observation, the surface topography of PUMA and OSTE-80 polymer showed minimal changes after the plasma treatments. Furthermore, ageing studies showed that plasma-treated PUMA and OSTE-80 polymer had stable hydrophilicity and nitrogen composition during storage in ambient air for 15 days. After in vitro cell culture of human umbilical vein endothelial cells (HUVECs) on these surfaces for 24 h and 72 h, both trypan blue and alamar blue assays indicated that PUMA and OSTE-80 polymer treated with N 2 plasma had the highest viability and proliferation. The polar nitrogen moi-eties, specifically amide groups, encouraged the HUVECs adhesion on the plasma-treated PUMA and OSTE-80 surfaces. Interestingly, PUMA polymer treated with Ar and N 2 plasma showed different HUVECs morphology which was spindle and cobblestone-shaped respectively after 72 h of incubation. On the contrary, a monolayer of well-spread HUVECs formed on the Ar and N 2 plasma-treated OSTE-80 polymers. These variable morphologies observed can be ascribed to the adherence HUVECs on the different elastic moduli of these surfaces whereby further investigation might be needed. Overall, Ar and N 2 plasma treatment had successfully altered the surface properties of PUMA and OSTE-80 polymer by increasing its surface energy, hydrophilicity and chemical function-alities to create a biocompatible surface for HUVECs adhesion and proliferation.

- by Kim S Siow
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- Biomaterials, Microfluidics, Bio MEMS, Biochip
- by Joong Yull Park
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- Extracellular Matrix, Cell Culture, Biochip, Survival Rate
- by Yun Tae Nam
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- Chemical Engineering, Genetics, Nanobiotechnology, Environmental Pollution
- by Quamrul Hasan
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- Analytical Chemistry, Microfluidics, Biotechnology, Self Assembly
- by Alan Arai
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- Optics, Glass, Femtosecond Laser, Fiber Lasers
- by Kuldeep Lal
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- Chemical Engineering, Genetics, Food Science, Conservation Genetics

ABSTRACT Cell death is the ultimate endpoint of the cellular life cycle, and the ability to distinguish different types of cell death (e.g., apoptosis and necrosis) has been a subject of intensive research. This paper demonstrates the suitability and efficiency of a microfluidics-based method for characterization of cell death events. A multicompartmented microfluidic device was used to examine the types of cell death induced by cadmium ions at various concentrations. Annexin V-FITC in combination with propidium iodide was used to distinguish between viable, apoptotic, and necrotic cells. The microfluidics-based method facilitates the performance of analysis of cell death on the basis of membrane alteration as well as morphological discrimination. In addition, this method shows high sensitivity and specificity, as evidenced by the quantification of the ratio of apoptotic and necrotic cells in the total population of cells.

- by sanjeev kumar mahto
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- Biochip
- by Jae-chun Ryu
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- Immune response, Real-time RT-PCR, Biochip, Cell Death
- by Jae-chun Ryu
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- Proteomics, Biochip, Rat, Proteome analysis
- by Peter Solar
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- Plant Biology, Membrane Proteins, Apoptosis, Gene expression

A nanolaboratory is proposed to realize the capabilities of nanofabrication, nanoinstrumentation and nanoassembly to make three-dimensional structures, devices and systems in the nanoworld. A nanorobotic manipulation system is introduced to realize these capabilities inside a scanning electron microscope or a transmission electron microscope. Some precursors are introduced into the small working space in the nanoworld, so that cutting, bending, peeling and fixing operations in the nanoworld could be realized using nanomanipulators, electron-bean-induced deposition and other methodologies as in the macroworld. After making the three-dimensional structures, the nanodevices such as nanosensors and nanoactuators are fabricated using carbon nanotubes and a focused ion beam chemical vapor deposition process. Some nanodevices for bioapplications are also presented.

- by Haitham ELSHIMY
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- Engineering, Mechanical Engineering, Computer Science, Architecture
- by Carla Zotti
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- Microbiology, Medical Microbiology, Humans, Legionella pneumophila

Miniaturized and parallelized ligand binding assays are of great interest in postgenomic research because microarray technology allows the simultaneous determination of a large number of parameters from a minute amount of sample within a single experiment. Assay systems based on this technology are used for the identification and quantification of proteins as well as for the study of protein interactions. Protein affinity assays have been implemented that allow the analysis of interactions between proteins with other proteins, peptides, low molecular weight compounds, oligosaccharides or DNA. Microarray technology is an emerging technology used in global analytical approaches and has a considerable impact on proteomic research.

- by Thomas O Joos
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- Proteomics, Biological Sciences, Antibodies, Cell line
- by Luiz Carlos Kretly
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- Robotics, Technology, Architecture, Nanomedicine
- by peter gascoyne
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- Biomedical Engineering, Microfluidics, Genomics, Cancer

Autophagy is a cellular homeostatic mechanism where proteins and organelles are digested and recycled to provide an alternative source of building blocks and energy to cells. The role of autophagy in cancer microenvironment is still poorly understood. Here, we present a microfluidic system allowing monitoring of the crosstalk between single cells. We used this system to study how tumor cells induced autophagy in the stromal niche. Firstly, we could confirm that transforming growth factor β1 (TGFβ1) secreted from breast tumor cells is a paracrine mediator of tumor-stroma interaction leading to the activation of autophagy in the stroma component fibroblasts. Through proof of concept experiments using TGFβ1 as a model factor, we could demonstrate real time monitoring of autophagy induction in fibroblasts by single tumor cells. Retrieval of individual tumor cells from the microfluidic system and their subsequent genomic analysis was possible, allowing us to determine the nature of the factor mediating tumor-stroma interactions. Therefore, our microfluidic platform might be used as a promising tool for quantitative investigation of tumor–stroma interactions, especially for and high-throughput screening of paracrine factors that are secreted from heterogeneous tumor cell populations. Interactions between cancer cells and the neighboring stroma play a critical role in tumorigenesis, and an in-depth understanding of intercellular communication is of great significance for the development of novel therapeutic strategies 1–3. Heterogeneity of tumor cells is evident, and its profound impact in clinical applications is highly recognized 4. However, conventional tools used to study cell-to-cell interactions only deliver averaged information from a population of cells and fail to provide information on the distribution of responses reflecting the heterogeneity of individual cells. Microfluidic devices have emerged as useful tools for single-cell analysis 5–7. Phenotype heterogeneity 8 , par-acrine secretion 9 , and DNA repair capacities with different genetic backgrounds 10 are among the cellular properties that have been analyzed using single-cell based systems. Cell-to-cell interactions may also be studied at a single-cell level. For example, using single-cell pairing techniques, effects of cell-to-cell interaction on migration and proliferation patterns 11 and contact-dependent organoid formation 12 have been analyzed. In addition, the heterogeneous dynamics of CD8 T-cells during their interaction with lymphocytes have been investigated 13. However, to the best of our knowledge, single-cell-based techniques have been rarely used for studying the interactions of tumor cells with tissues surrounding them, i.e., the stroma. Furthermore, the retrieval of individual

- by Devrim Gozuacik
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- Breast Cancer, Cytokines, Cancer Biology, Autophagy
- by Lucy E Lee
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- Cell line, Chemicals, Toxicity, Biochip

Diethylstilbestrol (DES), a synthetic estrogen, was examined for genotoxicity in mouse testicular Sertoli TM4 cells using an in vitro micronucleus assay and microarray analysis to clarify the molecular mechanisms underlying the genotoxicity of estrogenic compounds on the male reproductive system. The micronucleus test showed that DES induced genotoxic effects on TM4 cells with S9 activation. Gene expression profiles were studied in DES-treated cells and positive controls, which were cyclophosphamide (CPA)-treated TM4 cells, as compared to the negative controls. In total, 349 and 328 genes were identified as being either up- or down-regulated, with over 2-fold changes, in DES- and CPA-treated TM4 cells, respectively. Biofunction and canonical pathways of differentially expressed genes were analyzed using Ingenuity Pathways Analysis, which were mainly categorized as cellular development and growth/proliferation. In addition, genes related to cell cycle regulation, such as Egr1, Far1, Cd44, Wint16, Sox6, Sox14, Dnmt3a, and Hdac11, were differentially expressed in DES-treated TM4 cells. A gene network analysis was also performed. Comprehensive gene expression profiling of DES-treated TM4 cells provides valuable information to better understand the genotoxic events of estrogenic chemicals in testicular Sertoli cells.

- by Han-Jin Park
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- Molecular Mechanics, Male Reproduction Health, Biochip, Gene Network

- by Han-Jin Park
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- Molecular Mechanics, Male Reproduction Health, Biochip, Gene Network

- by Han-Jin Park
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- Molecular Mechanics, Biochip, Cell Death, Axon Guidance
- by Sungkyu Seo
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- Nanofabrication, Electron Beam Lithography, Biochip, Bacteria
- by Sahar Melamed and +5
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- Electronics, Humans, Medical Biotechnology, Biochip

ABSTRACT In this work, the formation of functional synapses between compartmentalized cortical neurons cultured inside three-compartment microfluidic devices in a controlled fashion is described. The proposed device can direct axons in an isolated compartment and, thus, facilitates isolated axons forming functional synapses with dendrites of other neurons in an isolated microenvironment. This microfluidic approach allows continuous real-time monitoring of neuronal processes and fluorescently tagged biomolecules involved in synapse formation, and provides an easy, simple, cost effective, and efficient method to develop and manipulate synapses in an isolated microenvironment without using surface patterning techniques or electrical stimulation. The results presented here suggest that this microfluidic approach could be used as an alternative method for the formation of functional synapses and their exhaustive examinations.

- by sanjeev kumar mahto
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- Biochip

The use of on-chip cellular activity monitoring for biological/chemical sensing is promising for environmental, medical and pharmaceutical applications. The miniaturization revolution in microelectronics is harnessed to provide on-chip detection of cellular activity, opening new horizons for miniature, fast, low cost and portable screening and monitoring devices. In this chapter we survey different on-chip cellular activity detection technologies based on electrochemical, bio-impedance and optical detection. Both prokaryotic and eukaryotic cell-on-chip technologies are mentioned and reviewed.

- by Hadar Ben-Yoav
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- Biochip
- by Narsis Daftarian
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- Ophthalmology, Medicine, Biochip, Retinal

Sample preconcentration is an important step that increases the accuracy of subsequent detection, especially for samples with extremely low concentrations. Due to the overlap of electrical double layers in a nanofluidic channel, the concentration polarization effect can be generated by applying an electric field. A nonlinear electrokinetic flow is induced, which results in the fast accumulation of proteins in front of the induced ionic depletion zone, the so-called exclusion- enrichment effect. In this way, a protein sample can be driven by electroosmotic flow and accumulated at a specific location. In the present study, a nanofluidic preconcentrator fabricated with the help of junction gap electric breakdown was integrated with microelectrodes for immunoassay. The preconcentration chip for proteins was fabricated using simple standard soft lithography with a polydimethylsiloxane replica. Human galectin-1 proteins from the cell lysate of T24 cells were concentrated and immunoassayed in the proposed microchip. The capability of the proposed microchip for concentrating multiple proteins from cell lysates and immunoassays after preconcentration was demonstrated. Immunosensing was evaluated by measurements of both fluorescence intensities and impedance, which proved the enhancement of preconcentration for immunoassay.

- by Chun-Ping Jen
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- Chemistry, Biochip

The heart may be a mirror of the soul, but the human mind is more than its heart rate variability (HRV). Many techniques to quantify HRV promise to give a view of what is going on in the body or even the psyche of the subject under study. This “Hypothesis” paper gives, on the one hand, a critical view on the field of HRV-analysis and, on the other hand, points out a possible direction of future applications. In view of the inherent variability of HRV and the underlying processes, as lined out here, the best use may be found in serial analysis in a subject/patient, to find changes over time that may help in early discovery of developing pathology. Not every future possibility is bright and shining, though, as demonstrated in a fictional diary excerpt from a future subject, living in a society geared toward preventive medicine. Here implanted biochips watch over the health of the population and artificial intelligence (AI) analyses the massive data flow to support the diagnostic process.