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At least 1,189 records · Page 66Linked to original sources
PubMed2006

SNPs on chips: the hidden genetic code in expression arrays.

Gene expression microarray analysis in postmortem brains is one of the fastest growing fields of psychiatric research. Here we show that common polymorphisms (SNPs) present on probe sets can masquerade as significant "gene expression" differences. After first observing this artifact in the Catechol-O-methyl transferase (COMT) gene, we replicate the finding in two additional genes predicted to show this artifact. Many Affymetrix chips contain thousands of SNPs that are both common and in the central probe region affecting hybridization, and thus have the potential to confound expression analysis.

Analysis of Variance↗
PubMed2004

Optimization of a biological process for treating potato chips industry wastewater using a mixed culture of Aspergillus foetidus and Aspergillus niger.

Potato chips industry wastewater was collected and analyzed for biochemical oxygen demand (BOD), chemical oxygen demand (COD), total suspended solids (TSS) and total carbohydrates. Two Aspergillus species, A. foetidus and A. niger, were evaluated for their ability to grow and produce biomass and reduce the organic load of the wastewater. A. foetidus MTCC 508 and A. niger ITCC 2012 were able to reduce COD by about 60% and produce biomass 2.4 and 2.85 gl(-1), respectively. Co-inoculation of both Aspergillus strains resulted in increased fungal biomass production and higher COD reduction than in individual culture at different culture pH. pH 6 was optimum for biomass production and COD reduction. Amendment of the wastewater with different N and P sources, increased the biomass production and COD reduction substantially. Under standardized conditions of pH 6 and amendment of wastewater with 0.1% KH2PO4 and 0.1% (NH4)2 SO4, a mixed culture gave 90% reduction in COD within 60 h of incubation.

Aspergillus↗
PubMed2004

Assessment of wood-inhabiting Basidiomycetes for biokraft pulping of softwood chips.

Wood-inhabiting Basidiomycetes have been screened for various applications in the pulp and paper industry and it is evident that different fungi need to be used to suit the specific requirements of each application. This study assessed the suitability of 278 strains of South African wood-decay fungi for the pre-treatment of softwood chips for kraft pulping. The influence of these fungi on kappa number, yield and strength properties of pulp was evaluated. A number of these strains were more efficient in reducing kappa number than the frequently used strains of Phanerochaete chrysosporium and Ceriporiopsis subvermispora. Six strains of Stereum hirsutum and a strain of an unidentified species were able to reduce the kappa number significantly without a significant influence on the pulp yield. Treatment of wood with two strains of S. hirsutum, one strain of Peniophora sp. and a strain of an unidentified species resulted in paper with improved strength properties.

Basidiomycota↗
PubMed2004

Segmented flow generation by chip reactors for highly parallelized cell cultivation.

Micro system technology offers convenient tools for the production of handling devices for small liquid volumes which can be used in cell cultivation. Here, a modular system for the rapid generation of cell suspension aliquots is presented. The system is used to produce and analyze high numbers of well-separated culture volumes. Selected clones may be retrieved from the system. Therefore, the principle of segmented flow is applied. Portions of aqueous culture medium containing one cell or very small cell ensembles are separated from each other by a nonmiscible liquid like dodecane, tetradecane or mineral oil. In addition, the alkane separates the culture droplets from the innerside of the walls of chip channels and capillaries. This way, compatibility problems between cell wall surfaces and the chemical character of walls are excluded. The separated culture droplets are guided by micro flow transportation in different channel and chamber topologies. The whole system has the character of a serially operating cell processing system. The aliquot generation can be sped up to frequencies of about 30 Hz in each microchannel. That means, that about 10(5) individual cultural volumes can be produced per hour or about 2 million per day. The survival and the growth of microorganisms has been shown for model organisms as well as for organisms from a natural sample (soil).

Cell Culture Techniques↗
PubMed2005

On-chip PCR amplification of very long templates using immobilized primers on glassy surfaces.

In this paper we describe a novel method for visualizing very long DNA fragments (for example >6 kb) which are difficult to spot with commonly used arrayers or capillary samplers with very small nanoliter volumes, using directly bound primers on "on-chip" polymerase chain reaction (PCR). We have used the genomes of the M13 bacteriophage (7.2 kb) the human mitochondrion (16.5 kb) as examples of long DNA templates to test the PCR and were able to elicit robust reactivity. Over 75% of the immobilized primers could be elongated to their fullest extent. In addition we were able to elicit the PCR reaction with double stranded templates in which one primer was immobilized and the other suspended in the reaction solution. These synthesized PCR products were visualized by either confocal microarray scanning or fluorescence microscopy using Cy5-dye fluorescence of the modified free primer, or the fluorescence of intercalating dyes.

Adsorption↗
PubMed2005

Unique supramolecular assembly of a redox protein with nucleic acids onto hybrid bilayer: towards a dynamic DNA chip.

Highly controlled supramolecular assemblies combining a genetically engineered redox protein, cytochrome b5, and modified oligonucleotides are presented. Modified b5 and DNA are covalently assembled through a hetero bifunctional cross-linker to give a unique hybrid molecular species. Moreover, the assembly includes a histidine tag head able to bind to modified phospholipids which lead to a new generation of self-assembled dynamic DNA chips. The interaction of the construction with a complementary oligonucleotide sequence can be monitored in real time by surface plasmon resonance using Biacore technology. The biochip, presented herein, features unique properties including tunable surface density of probes, very low non-specific interactions and optimization of hybridization efficiency. In addition, we demonstrated that the phase transition of the lipidic layer can modulate the dynamic of the association of the complex to the supported membrane. Potential applications of this new device are multiple including high sensitivity and high selectivity biochips, especially for studies of the DNA-ligands interactions in a biomimetic environment.

Cytochromes b5↗
PubMed2005

Amperometric detection of the bacterial metabolic regulation with a microbial array chip.

A microbial array chip with collagen gel spots entrapping living bacterial cells has been applied to investigate the metabolic regulation in Paracoccus denitrificans. Scanning electrochemical microscopy (SECM) was used to monitor the ferrocyanide production that reflects the electron flow in the respiratory chain located within the internal membrane of P. denitrificans. The ferrocyanide production from P. denitrificans largely depends on the types of the carbon source (glucose or lactate), suggesting that the electron flow rate in the respiratory chain depends on the activity of the metabolic pathway located up-stream of the respiratory chain. More importantly, it was found that the enzymes affecting glucose catabolic reactions were significantly up-regulated in cultures with a nutrient agar medium containing D-(+)-glucose as a sole carbon source. Enzyme assays using crude extracts of P. denitrificans were carried out to identify the enzymes expressed at a higher level in cultures supplemented with D-(+)-glucose. It was confirmed that the pyruvate kinase and enzymes of the overall Entner-Doudoroff pathway were highly induced in cultures containing D-(+)-glucose.

Electrochemistry↗
PubMed2005

Constraining the connectivity of neuronal networks cultured on microelectrode arrays with microfluidic techniques: a step towards neuron-based functional chips.

In vitro culture of small neuronal networks with pre-defined topological features is particularly desirable when the electrical activity of such assemblies can be monitored for long periods of time. Indeed, it is hoped that such networks, with pre-determined connectivity, will provide unique insights into the structure/function relationship of biological neural networks and their properties of self-organization. However, the experimental techniques that have been developed so far for that purpose have either failed to provide very long-term pattern definition and retention, or they have not shown potential for integration into more complex microfluidic devices. To address this problem, three-dimensional microfluidic systems in poly(dimethylsiloxane) (PDMS) were fabricated and used in conjunction with both custom-made and commercially available planar microelectrode arrays (pMEAs). Various types of primary neuronal cell cultures were established inside these systems. Extracellular electrical signals were successfully recorded from all types of cells placed inside the patterns, and this bioelectrical activity was present for several weeks. The advantage of this approach is that it can be further integrated with microfluidic devices and pMEAs to yield, for example, complex neuron-based biosensors or chips for pharmacological screening.

Action Potentials↗
PubMed2005

Sample flow switching techniques on microfluidic chips.

This paper presents an experimental investigation into electrokinetically focused flow injection for bio-analytical applications. A novel microfluidic device for microfluidic sample handling is presented. The microfluidic chip is fabricated on glass substrates using conventional photolithographic and chemical etching processes and is bonded using a high-temperature fusion method. The proposed valve-less device is capable not only of directing a single sample flow to a specified output port, but also of driving multiple samples to separate outlet channels or even to a single outlet to facilitate sample mixing. The experimental results confirm that the sample flow can be electrokinetically pre-focused into a narrow stream and guided to the desired outlet port by means of a simple control voltage model. The microchip presented within this paper has considerable potential for use in a variety of applications, including high-throughput chemical analysis, cell fusion, fraction collection, sample mixing, and many other applications within the micro-total-analysis systems field.

Biosensing Techniques↗
PubMed2006

Multiple detection of food-borne pathogenic bacteria using a novel 16S rDNA-based oligonucleotide signature chip.

There have been many attempts to develop sensitive and accurate techniques for the detection and diagnosis of pathogenic bacteria using nucleic acid-based technology. To achieve efficient multiple detection of seven selected food-borne pathogens, we assessed the respective 16S rDNA pathogen specific sequences using an oligonucleotide-based signature array. Strategic optimal design of specific capture probes was achieved by using the characteristic first variable region. To assess the specificity of this pathogen detection system, we employed a two-step experimental strategy. Under conditions established through experiments with chemically synthesized model targets comprising both conserved and variable regions of 16S rDNA, we confirmed the validity of this system using real 16S rDNA targets. Detection with real targets was successfully performed using our system, and better specificity was obtained compared to experiments with model targets. Moreover, the subtypes of Vibrio pathogens were successfully classified. We developed a two-dimensional visualization plot tool for positive control and specific spots, which allowed facile and minute differentiation between spot intensities. Repeated array formats were employed to ensure experimental uniformity, and included the statistical p-value criterion for pathogen discrimination. The present results thus indicate that our novel oligonucleotide-based signature chip detection system can be employed for the effective detection of multiple pathogens.

Bacteria↗
PubMed2006

A method of binding kinetics of a ligand to micropatterned proteins on a microfluidic chip.

A combination of microfluidic protein patterning and quantitative microfluidic handling has been used to analyze the binding kinetics of protein-ligand interactions on the nanoliter scale. The microfluidic handling method employing hydrophobic valving and pneumatic control allowed us to control nanoliter volumes of ligand or protein on a microfluidic chip. A hydrophobic and inert fluorocarbon thin film was patterned on a silicon nitride substrate to prevent non-specific binding on the background. Selectively patterned protein patterns of various sizes were used for quantitative analysis of the kinetic parameters of immobilized proteins on the circular patterns. As a model system, a streptavidin-patterned array of the same-sized pattern, i.e. 150 microm diameter, was used to capture FITC-BSA-biotin present in solution. The fluorescence intensity was well matched with the Langmuir isotherm model results, showing a dissociation constant of 2.43x10(-8)M. Similar streptavidin arrays with different-sized spots, ranging from 50 to 200 microm, showed a consistent dissociation constant of FITC-BSA-biotin with streptavidin pattern. Therefore, the reduction of pattern size of an immobilized protein did not change the dissociation rate of the ligand.

Biosensing Techniques↗
PubMed2006

Modeling micropatterned antigen-antibody binding kinetics in a microfluidic chip.

The reaction kinetics of antigen-antibody binding in the electrokinetically controlled microfluidic heterogeneous immunoassays has been investigated by numerical simulations. A two-dimensional computational model was employed to include the mass transport (convection and diffusion) and binding reaction between the antigen in the bulk flow and the immobilized antibody at the channel surface. The influence of the bulk velocity, the concentrations of the antibody and antigen, and the geometry of the microchips was studied for a variation of conditions and the guidance for designing of microfluidic immunoassay was provided. The model also shows that electrokinetically driven immunoassays have better reaction kinetics than pressure-driven ones, resulting from the plug-like velocity profile. Finally, a multi-patch immunoassay chip was analyzed and the reaction kinetics was optimized by rearranging the reaction patches at the channel surfaces.

Antigen-Antibody Complex↗
PubMed2006

On-chip microdialysis system with flow-through sensing components.

Microdialysis probes have been used for diabetes treatment as continuous monitoring system coupled to a glucose sensor. An on-chip microdialysis system with in-line sensing electrodes is demonstrated. As a first step towards greater biosensor integration with this miniaturized microdialysis system, a stacked system with in-line sensing electrodes was developed. Impedance electrodes sputtered within the microchannels were used to determine fluid electrical resistance from a dialyzed phosphate buffered saline (PBS) solution, which characterizes solution conductivity as a function of PBS concentration. The permeability of the membrane to the salt ions was obtained as 0.246+/-0.028 microm/s (15 nm pores). Subsequently, experiments measuring PBS dialysis in the time-domain at 64.4% recovery were conducted. The PBS concentration of the reservoir was changed in both a step response and sinusoidally with an 800 s period. The subsequently measured impedance indicates that the system is able to continuously track concentration changes in the reservoir with a 210 s system response delay. Most of this delay is due to the dead volume within the tubing between the syringe pumps and the microsystem. In addition, the predicted response was modeled using linear systems theory and matches the experimental measurements (r=0.98). This system is expected to have the proper sensitivity to track physiologically relevant concentration changes of biomolecules such as glucose (which has a physiological maximum change rate of approximately 4 mg/dl min with a periodicity of 1h or greater) with minimal lag time and amplitude reduction.

Electrochemistry↗
PubMed2006

Single-chip microelectronic system to interface with living cells.

A high degree of connectivity and the coordinated electrical activity of neural cells or networks are believed to be the reason that the brain is capable of highly sophisticated information processing. Likewise, the effectiveness of an animal heart largely depends on such coordinated cell activity. To advance our understanding of these complex biological systems, high spatiotemporal-resolution techniques to monitor the cell electrical activity and an ideally seamless interaction between cells and recording devices are desired. Here we present a monolithic microsystem in complementary metal oxide semiconductor (CMOS) technology that provides bidirectional communication (stimulation and recording) between standard electronics technology and cultured electrogenic cells. The microchip can be directly used as a substrate for cell culturing, it features circuitry units per electrode for stimulation and immediate cell signal treatment, and it provides on-chip signal transformation as well as a digital interface so that a very fast, almost real-time interaction (2 ms loop time from event recognition to, e.g., a defined stimulation) is possible at remarkable signal quality. The corresponding spontaneous and stimulated electrical activity recordings with neuronal and cardiac cell cultures will be presented. The system can be used to, e.g., study the development of neural networks, reveal the effects of neuronal plasticity and study cellular or network activity in response to pharmacological treatments.

Action Potentials↗
PubMed2005

Determination of total sulfite in wine. Zone electrophoresis-isotachophoresis quantitation of sulfate on a chip after an in-sample oxidation of total sulfite.

This work deals with the determination of total sulfite in wine. The determination combines an in-sample hydrogen peroxide oxidation of total sulfite in alkalized wine to sulfate with the separation and quantitation of the latter anion by zone electrophoresis (ZE) on-line coupled with isotachophoresis (ITP) on a column-coupling chip. Sample clean up, integrated into the ITP-ZE separation, eliminated wine matrix in an extent comparable to that provided by a highly selective distillation isolation of sulfite. At the same time, conductivity detection, employed to the detection of sulfate in the ZE stage of the ITP-ZE combination, provided for sulfate the concentration limit of detection corresponding to a 90 microg/l concentration of sulfite in the loaded sample (0.9 microl). Such a detectability allowed a reproducible quantitation of total sulfite when its concentration in wine was 15 mg/l. Formaldehyde binding of free sulfite in wine, included into the pre-column sample preparation, prevented an uncontrolled oxidation of this sulfite form. This step contributed to an unbiased determination of sulfate present in the original wine sample (this determination corrected for the concentration of sulfate determined in the sample after the peroxide oxidation of sulfite to the value equivalent to the total sulfite). The 99-101% recoveries of sulfite, determined for appropriately spiked wine samples, indicate a very good accuracy of the present method. Such a statement also supports excellent agreements of the results of quantitation based on the in-sample peroxide oxidation of the total sulfite (bound sulfite released at a high pH) with those in which this analyte was isolated from wine by distillation (bound sulfite released at a very low pH).

Electrophoresis, Microchip↗
PubMed2005

Determination of acrylamide in potato chips and crisps by high-performance liquid chromatography.

A simple and rapid method using liquid chromatography coupled to diode array detection (LC-DAD) was developed for the determination of acrylamide in potato-based foods at low levels. The method entails extraction of acrylamide with methanol, purification with Carrez I and II solutions, evaporation and solvent change to water, and cleanup with a Oasis HLB solid-phase extraction (SPE) cartridge. The final extract was analyzed by LC-DAD for quantification and by liquid chromatography coupled to mass spectrometry (LC-MS) for confirmation. The chromatographic separations were performed on a hydrophilic and a hydrophobic interaction columns having good retention of acrylamide under 100% aqueous flow conditions (k' 3.67 and 2.54, respectively). The limit of quantitation was estimated to be 4.0 microg/kg based on the signal-to-noise ratio of 3 recorded at 226 nm. Recoveries of acrylamide from potato chips samples spiked at levels of 250, 500 and 1000 (n = 4 for each level) microg/kg ranged between 92.8 and 96.2% with relative standard deviations of less than 5%. The results of this study revealed that a conventional LC instrument coupled to DAD can also be used accurately and precisely, as an alternative to tandem LC-MS methods for the determination of acrylamide in potato-based foods.

Acrylamide↗
PubMed2005

Integrated microfabricated systems including a purification module and an on-chip nano electrospray ionization interface for biological analysis.

We report here on an integrated microfabricated device dedicated to the preparation of biological samples prior to their on-line analysis by electrospray ionization-mass spectrometry (ESI-MS). This microfluidic device is fabricated using the negative photoresist SU-8 by microtechnology techniques. The device includes a chromatographic module plus an ESI interface for MS. The chromatographic module is dedicated to sample purification and is based on a polymer monolithic phase which includes hydrophobic moieties. The ESI interface is integrated onto the chip and is based on a capillary slot. We present here the integration of these different modules onto a single system that is fabricated via a SU-8-based microtechnology route. We present also their testing for the purification of peptide samples. This started with a partial integration step with the combination of at least two of the modules (microsystem + monolith; microsystem + nib) and their test before the fabrication and testing of fully integrated microsystems.

Microscopy, Electron, Scanning↗
PubMed2005

Toward million-fold sensitivity enhancement by sweeping in capillary electrophoresis combined with thermal lens microscopic detection using an interface chip.

This paper reports a thermal lens microscope (TLM) detection coupled with capillary electrophoresis (CE) by using an interface chip (IFChip) to achieve highly sensitive detection with high reproducibility. Fused silica capillaries with an inner diameter of 50 microm were directly connected to a microchannel on the IFChip. In comparison with an on-capillary detection method in CE-TLM, ca. 10-fold improvements in the reproducibility for peak height were obtained by using IFChips. The detection limit of an azo dye was estimated to be 3.6 x 10(-7)M (100 ppb), which was above 100-times lower than that of conventional absorbance detection. Toward further improvement of the detectability for nonfluorescent compounds, on-line sample preconcentration by sweeping was applied to the CE-TLM using the IFChip. Due to the sweeping effect, 3900000-fold increase in the sensitivity was successfully achieved.

Electrophoresis, Capillary↗