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At least 883 records · Page 49Linked to original sources
PubMed2003

A modified sensor chip for surface plasmon resonance enables a rapid determination of sequence specificity of DNA-binding proteins.

A novel method is described which rapidly determines specificity of DNA-binding proteins using a surface plasmon resonance (SPR) sensor chip. An oligohistidine-tagged DNA-binding domain of a transcription factor, NtERF2, was immobilised via nitrilotriacetic acid ligands to a sensor chip with an attenuated degree of carboxymethylation. DNA molecules were selected from a pool of randomised oligomers through binding to the immobilised protein and amplified by PCR. After several cycles of selection, during which binding was monitored by SPR, DNA sequences containing a consensus sequence were determined. The time necessary for one cycle is approximately 50 min, which is shorter than existing methods.

Base Sequence↗
PubMed2001

Application of complementary DNA microarray (DNA chip) technology in the study of gene expression profiles during folliculogenesis.

OBJECTIVE: Using oligonucleotide microarray (DNA chip)-based hybridization analysis to gain a comprehensive view of gene expression and regulation involved in folliculogenesis. DESIGN: Prospective randomized study. SETTING: Academic institution. ANIMAL(S): B6D2F1 female mice. INTERVENTION(S): Superovulation. MAIN OUTCOME MEASURE(S): Preantral follicles isolated from day 14 B6D2F-1 mice were stimulated in vitro to form Graafian follicles. Total RNA extracted from the mouse preantral and Graafian follicles were reverse transcribed, labeled with digoxigenin-11-dUTP, and then hybridized with Clontech Atlas mouse cDNA expression arrays for comparison. RESULT(S): Of 588 known studied genes, 39 and 61 were detected in preantral follicles and in Graafian follicles, respectively, and 17 were highly expressed consistently in both preantral and Graafian follicles. Performing clustering analysis, we found that 15 detected genes were down-regulated and 46 were up-regulated as the follicles advanced to mature stages. CONCLUSION(S): We have successfully developed a sensitive DNA chip technology that is able to simultaneously and quantitatively study gene expression profiles in a small number of follicles (1.5-15 follicles). Several folliculogenesis-related genes have been identified. Some of these genes were expressed, indicating that they may be essential for follicle growth and maturation, whereas others were up-regulated only during late follicular development, indicating stage-specific roles.

Animals↗
PubMed2000

Rapid, parallel separations of d1S80 alleles in a plastic microchannel chip.

We have performed fast, parallel separations of alleles of the D1S80 locus in a plastic, multi-channel chip, replicated from a microfabricated master and laminated with a plastic film. The array of 16 channels was filled with a replaceable sieving polymer, and a size-dependent, electrophoretic separation of the DNA fragments was performed in all channels in less than 10 min, representing a 30-fold increase in throughput compared to that on a single-capillary instrument. To detect the fragments in all 16 channels in parallel during the run, we designed and built a scanning, confocal, laser-induced fluorescence system. The electropherograms were then used to determine the sample genotype. To demonstrate the use of multiplexed, microchannel arrays for real-life samples, we amplified D1S80 alleles from genomic DNA extracted from whole blood and separated these alleles by electrophoresis in the plastic chip. Evaluation of the electrophoretic data showed that, using a 300- and a 1,000-base pair fragment as internal mobility markers, 83% of the alleles were assigned correctly, using the allele identification from a single capillary instrument as a reference. This work demonstrates that, with improvements in the microchannel electrophoresis system, it is feasible to perform rapid, parallel genotyping in mass-produced, inexpensive, disposable plastic devices for large-scale applications in medicine and the life sciences.

Alleles↗
PubMed2001

Comparison of the properties of phospholipid surfaces formed on HPA and L1 biosensor chips for the binding of the coagulation factor VIII.

Binding of a coagulation factor VIII to phosphatidylserine-containing membranes is critical for exerting its cofactor activity. The use of surface plasmon resonance allows studying factor VIII interaction with immobilized phospholipids. In the present study we compared factor VIII-binding properties of phospholipid surfaces immobilized on L1 and HPA Biacore chips in the form of a flexible bilayer and rigid monolayer, respectively. We demonstrated that immobilized phospholipid surfaces with physiological contents of PS and PE formed on L1 but not on HPA chip closely mimic intact phospholipid vesicles in their factor VIII and thrombin-activated factor VIII (factor VIIIa) binding properties.

Biosensing Techniques↗
PubMed2001

Sample stacking in laboratory-on-a-chip devices.

Sample stacking is a very important sample concentration technique. It has been used widely in capillary electrophoresis (CE). There are many different stacking techniques. One of the most popular techniques is called "field-amplified sample stacking" where an electric field discontinuity is set up across a concentration boundary. Charged analytes will then automatically stacked due to velocity changes after they cross the concentration boundary. There are several different strategies to perform sample stacking in microfluidic laboratory-on-a-chip devices. One could simply inject a plug of low concentration buffer containing sample into a channel surrounded by high concentration buffer. The electric field is then applied to stack the sample and move the whole plug into the separation channel. One could also stack the sample in a side channel adjacent to the separation channel. The disadvantage of this sample stacking technique is the difficulty in control of the precise location of stacked sample. We present a new sample stacking technique applied specifically to microfluidic laboratory-on-a-chip devices. Up to hundreds of fold increases in sample concentration can be achieved. We have also combined this stacking with electrophoretic separation in the same device.

Electrophoresis, Capillary↗
PubMed2003

Protein proteolysis and the multi-dimensional electrochromatographic separation of histidine-containing peptide fragments on a chip.

This paper reports a system for three-dimensional electrochromatography in a chip format. The steps involved included trypsin digestion, copper(II)-immobilized metal affinity chromatography [Cu(II)-IMAC] selection of histidine-containing peptides, and reversed-phase capillary electrochromatography of the selected peptides. Trypsin digestion and affinity chromatography were achieved in particle-based columns with a microfabricated frit whereas reversed-phase separations were executed on a column of collocated monolithic support structures. Column frits were designed to maintain constant cross sectional area and path length in all channels and to retain particles down to a size of 3 microm. Cu(II)-IMAC selection of histidine-containing peptides from standard peptide mixtures and protein digests followed by reversed-phase chromatography of the selected peptides was demonstrated in the electrochromatography mode. The possibility to run a comprehensive proteomic analysis by combining trypsin digestion, affinity selection, and a reversed-phase separation on chips was shown using fluorescein isothiocyanate-labeled bovine serum albumin as an example.

Histidine↗
PubMed2002

Mr. Chips 2002: new insights from an ideal-observer model of reading.

The integration of visual, lexical, and oculomotor information is a critical part of reading. Mr. Chips is an ideal-observer model that combines these sources of information optimally to read simple texts in the minimum number of saccades. This model provides a computational framework for interpreting human reading saccades in both normal and low vision. The purpose of this paper is to report performance of the model for conditions emulating reading with normal vision--a visual span of nine characters, multiplicative saccade noise with a standard deviation of 30%, and texts based on three full-length children's books. Comparison of fixation locations by humans and Mr. Chips revealed: (1) that both exhibit very similar word-skipping behavior; (2) both show initial fixations near the center of words, but with a systematic difference suggestive of an asymmetry in the human visual span; and (3) differences in the pattern of refixations within words that may uncover non-optimal lexical inference by human readers. A human context effect--30% difference in mean saccade size between continuous text and random sequences of words--was very similar to the 25% effect for the model associated with a corresponding difference in the predictability of text words. Overall, our findings show that many of the complicated aspects of human reading saccades can be explained concisely by early information-processing constraints.

Computer Simulation↗
PubMed2003

Detoxification of semisolid olive-mill wastes and pine-chip mixtures using Phanerochaete flavido-alba.

Semisolid olive-mill residues, pine chips, and mixtures of both residues contain phytotoxic components capable of inhibiting germination and vegetative growth in plants. Solid-state cultures of Phanerochate flavido-alba on pine chips or mixtures of both residues reduce these phytotoxic effects in fermented substrates. The phenol and lipid contents in cultures detoxified by this fungus also decreases.

Biodegradation, Environmental↗
PubMed2002

DNA chips for yeast biotechnology. The case of wine yeasts.

The yeast Saccharomyces cerevisiae is one of the most popular model organisms. It was the first eukaryote whose genome was sequenced. Since then many functional analysis projects have tried to find the function of many genes and to understand its metabolism in a holistic way. Apart from basic science this microorganism is of great interest in several biotechnology processes, such as winemaking. Only global studies of the cell as a whole can help us to understand many of the technical problems facing winemaking. DNA chip technology is one of the most promising tools for the analysis of cell physiology. Yeast has been the model organism for the development of this technique. Many of the studies can be applied to improve our knowledge of wine strains. Nevertheless wine strains are quite different in some aspects from the laboratory reference strains so a particular study of wine strains and especially during the winemaking process is needed. During the past two years some groups have started this study and the first results have been published. We review here the current state of the knowledge of wine yeast and the capacity of DNA chip technology for its improvement.

Biological Evolution↗
PubMedDate not supplied

[Spanish version of the Child Health and Illness Profile-Child Edition Parent Report Form [CHIP-CE/PRF]].

OBJECTIVES: To analyze the reliability and validity of the domains of the Child Health and Illness Profile-Child Edition Parent Report Form (CHIP-CE/PRF) included in the Barcelona Health Survey conducted in 2000 and to obtain population-based reference values. METHODS: Data were obtained from proxy-respondent interviews of children aged 5-14 years old (n = 836) participating in the Barcelona Health Survey 2000. The 4 subdomains of the parent version of the CHIP-PRF included in the health survey were: satisfaction with health, and physical discomfort, emotional discomfort, and limitation of activities of the discomfort domain. Internal consistency was assessed using Cronbach's alpha coefficients. An exploratory factor analysis was carried out and analysis of covariance was performed to assess the construct validity of the subdomains. RESULTS: In all the subdomains assessed, Cronbach's alpha was above 0.70 (range, 0.76-0.98). In the factorial analysis, almost all the items (31/35) presented the highest load in their corresponding subdomain. Most of the expected mean differences among groups were confirmed. Girls aged 10-14 years old scored the lowest, both in satisfaction with health (48.93; 95% confidence interval [CI 95%], 47.40-50.47) and in discomfort (48.87; CI 95%, 47.51-50.22). No differences were found according to the social class of the head of the family. CONCLUSIONS: The present study provides a useful measure of perceived health status in a child health survey.

Adolescent↗
PubMed2003

Microphysiological testing for chemosensitivity of living tumor cells with multiparametric microsensor chips.

A constraint in the reliability of predictive chemosensitivity assays is linked to the fact that they analyze only a single cellular or biochemical parameter. A multiparametric test system using microsensor chips has been developed which can detect online microphysiological changes in living cells. Tumor cells were grown directly on glass- or silicon-based electronic sensor chips. Changes in extracellular pH and pO(2), reflecting metabolic activities, and changes in impedance, reflecting morphological properties, were monitored. In this study, colon and breast cancer cells as well as doxorubicin-sensitive and doxorubicin-resistant sarcoma cell lines were exposed to cytochalasin B, chloroacetaldehyde, or doxorubicin. Results show (1) reduction in medium acidification, (2) marked and rapid changes in O(2) consumption, and (3) modulations in impedance correlating with morphological changes observed in the microscope. Drug-resistant cells do not show these changes. Therefore, this microphysiological monitoring is a versatile tool for chemosensitivity testing of tumor cells.

Antineoplastic Agents↗
PubMed2001

Electrical properties of a light-addressable microelectrode chip with high electrode density for extracellular stimulation and recording of excitable cells.

A light-addressable microelectrode chip with 3600 TiN electrodes was fabricated. Amorphous silicon (a-Si:H) serves as a photo conductor. The electrodes on the chip are addressed by a laser spot and electrical properties of the system are determined. DC measurements show a dark to bright dynamic of 10(6)-10(7). The AC impedance dynamic @ 1 kHz/100 mV and thus the signal-to-noise-ratio is determined to 60. This value is quite sufficient for electrophysiological measurements. For the first time, recordings from cardiac myocytes are reported using the principle of light-addressing. Measurements were done with a standard laser scan microscope (Zeiss LSM 410).

Electric Stimulation↗
PubMed2003

A micromachined capillary electrophoresis chip with fully integrated electrodes for separation and electrochemical detection.

A novel analytical microsystem with fully integrated electrodes for electrophoresis and amperometrical detection is described. With respect to the lab-on-a-chip concept a capillary electrophoresis (CE) microsystem has been fabricated with a total of six gold electrodes for sample injection, separation and electrochemical detection using standard microfabrication technologies. The device is a ready-to-use system that does not need any extra mechanical apparatus for electrode insertion. The CE-chip has successfully been tested by measuring hydrogen peroxide, ascorbic acid and uric acid simultaneously. All three oxidizable species could be detected in less than 70 s. Glucose was detected by performing an enzymatic reaction along the separation channel. The microsystem showed a very good reproducibility.

Ascorbic Acid↗
PubMed2003

Fractionation of Eucalyptus grandis chips by dilute acid-catalysed steam explosion.

Steam explosion of Eucalyptus grandis has been carried out under various pretreatment conditions (200-210 degrees C, 2-5 min) after impregnation of the wood chips with 0.087 and 0.175% (w/w) H2SO4. This study, arranged as a 2(3) factorial design, indicated that pretreatment temperature is the most critical variable affecting the yield of steam-treated fractions. Pretreatment of 0.175% (w/w) H2SO4-impregnated chips at 210 degrees C for 2 min was the best condition for hemicellulose recovery (mostly as xylose) in the water soluble fraction, reaching almost 70% of the corresponding xylose theoretical yield. By contrast, lower pretreatment temperatures of 200 degrees C were enough to yield steam-treated substrates from which a 90% cellulose conversion was obtained in 48 h, using low enzyme loadings of a Celluclast 1.5 1 plus Novozym 188 mixture (Novo Nordisk). Release of water-soluble chromophores was monitored by UV spectroscopy and their concentration increased with pretreatment severity. The yield of alkali-soluble lignin increased at higher levels of acid impregnation and pretreatment temperatures. Thermoanalysis of these lignin fractions indicated a pattern of lignin fragmentation towards greater pretreatment severities but lignin condensation prevailed at the most drastic pretreatment conditions.

Catalysis↗
PubMed1999

DNA chips: promising toys have become powerful tools.

DNA chips are glass surfaces that represent thousands of DNA fragments arrayed at discrete sites. Hybridization of RNA or DNA-derived samples to DNA chips allows us to monitor expression of mRNAs or the occurrence of polymorphisms in genomic DNA. The technology holds great promise for identifying gene polymorphisms that predispose man to disease, gene regulation events involved in disease progression, and more-effective disease treatments.

DNA Mutational Analysis↗
PubMed2005

The DNA-Chip technology as a new molecular tool for the detection of HBV mutants.

Genetic variability of the Hepatitis B virus (HBV) strongly impacts the natural history of infection and the efficiency of diagnosis, vaccination and treatment. A genotypc assay able to provide genetic information on all HBV genes would be a very important tool for clinicians and epidemiologists. The DNA-Chip technology has proved to be powerful and convenient for the diagnosis of infectious diseases due to bacteria and viruses. We have designed a genotyping assay based on polymerase chain reaction and DNA-Chip for HBV Starting from a unique specimen, analysis of polymorphisms at 150 positions along the genome and 383 mutations is possible as well as the determination of the genotype. Preliminary experiments with plasmas from infected patients show that results obtained with this reagent are strongly correlated with those obtained with sequencing.

Genetic Techniques↗
PubMed2002

Protein chips: from concept to practice.

A series of exciting reports over the past two years has established the usefulness of protein chips and made important advances in preparing protein arrays. However, several technical challenges must still be addressed to make these tools available to the wider community of researchers. Here, we discusses these challenges and survey recent opportunities for creating quantitative assays, preparing and immobilizing large numbers of proteins, using detection methods to analyze the results of chip-based experiments, and using informatics tools to interpret these results.

Biotechnology↗
PubMed2006

Posterolateral lumbar spinal fusion with autogenous bone chips from laminectomy extended with OsteoSet.

BACKGROUND: This study was conducted to evaluate posterolateral lumbar fusion with autogenous corticocancellous bone chips from the laminae and spinous processes extended with OsteoSet instead of cancellous bone from the iliac crest. METHODS: A total of 124 patients who underwent posterior decompression and posterolateral fusion with instrumentation between May 2001 and December 2003 were analyzed retrospectively. The study population comprised 49 males and 75 females with a mean age of 66 +/- 9.5 years. In all the patients, corticocancellous bone chips from laminectomy and OsteoSet were used as the graft material. There was no cancellous bone harvested from the iliac crest. The follow-up period was 28 +/- 7.1 months. RESULTS: The overall union rate was 91%, and the average union time was 3.9 months. There were 3 complications, including 2 patients with dura tear, and 1 with deep infection. At the final follow-up, the good and excellent results were up to 83.9%. CONCLUSION: Graft material from laminae and spinous processes extended with OsteoSet is reliable and effective enough to replace the graft from the posterior iliac crest.

Aged↗