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At least 1,351 records · Page 75Linked to original sources
PubMed2002

The ultimate chip shot: can microarray technology deliver for neuroscience?

The use of cDNA and oligonucleotide microarrays, or 'chips', is emerging as a powerful, new technology in the field of neuroscience for examining gene expression in a high-throughput fashion. The application of microarray technology to the study of brain and behavior has lagged behind other areas of biology such as cancer and yeast genetics due to the challenges presented by the heterogeneous and complex organization of the nervous system. This review provides a brief overview of available microarray technology as well as a description of experimental considerations in planning and implementing a neuroscience-based array study. Successful implementation of microarray technology within the field of neuroscience will provide a molecular approach to studying systems neurobiology, leading to insights into areas ranging from fundamental questions of developmental neurobiology to neurological and psychiatric disorders.

Computational Biology↗
PubMed2004

Microthermoforming of flexible, not-buried hollow microstructures for chip-based life sciences applications.

A new method is presented for the manufacturing of flexible, not buried and thin-walled hollow microstructures from polymer films. This low-cost method seems to be especially suited for the fabrication of plastic microstructures for fluidic one-way applications in the field of life sciences. It is based on a thermoforming process adapted to microstructure technology and is called 'microthermoforming'. Inside a hot embossing press, a heated thin thermoplastic film is formed into the evacuated microcavities of a plate-shaped metal mould using a compressed gas. The film may be heat-sealed on to a thicker plastic film substrate inside the same press without demoulding the thermoformed film. To demonstrate the performance of the new manufacturing method, flexible capillary electrophoresis and cell culture chips from polystyrene, polycarbonate and a cyclo-olefin polymer with 16 and 625 parallel microstructures each, respectively, have been fabricated.

Journal Article↗
PubMed2005

On-chip high-speed sorting of micron-sized particles for high-throughput analysis.

A new design of particle sorting chip is presented. The device employs a dielectrophoretic gate that deflects particles into one of two microfluidic channels at high speed. The device operates by focussing particles into the central streamline of the main flow channel using dielectrophoretic focussing. At the sorting junction (T- or Y-junction) two sets of electrodes produce a small dielectrophoretic force that pushes the particle into one or other of the outlet channels, where they are carried under the pressure-driven fluid flow to the outlet. For a 40 microm wide and high channel, it is shown that 6 microm diameter particles can be deflected at a rate of 300/s. The principle of a fully automated sorting device is demonstrated by separating fluorescent from non-fluorescent latex beads.

Cell Separation↗
PubMed2001

Acetabular revision with impacted freeze-dried cancellous bone chips and a cemented cup: a report of 7 cases at 5 to 9 years' follow-up.

The long-term results of bone impaction grafting with fresh-frozen femoral head allografts and a cemented cup are favorable. Because of intermittent shortage of fresh-frozen femoral heads at our local bone bank, we used processed freeze-dried bone in 7 acetabular revisions operated between 1989 and 1994. All 7 consecutive patients were followed annually. At final review (March 2000), 1 patient had died after 8.5 years of follow-up of a cause not related to the surgery. In 1 hip, a rerevision was performed for septic loosening 5 years after the previous septic loosening. Radiographically the freeze-dried allografts seemed to incorporate in all cases but the reinfected one; progressive radiolucent lines were not seen, although 1 case had a stable line in 1 zone. The overall survival rate for the 7 acetabular reconstructions at an average follow-up of 7 years (range, 5-9 years) was 86%. At midterm follow-up, there was no aseptic loosening. In this limited case report, the results at midterm for freeze-dried allograft bone chips in acetabular reconstructions are acceptable.

Acetabulum↗
PubMed1989

[Chip fracture of the lateral tibial condyle--a roentgenologic sign of anterior cruciate ligament injury].

A case report serves as basis for describing the importance of the so-called chip fracture as the first roentgenological pointer to a rupture of the anterior cruciate ligament in a handball player. The paper discusses the biomechanical changes resulting from an ACL rupture and underlines the importance of early arthroscopic diagnosis or of arthroscopic surgery for regaining knee stability and for preventing secondary subsequent damage.

Adult↗
PubMed2003

Direct detection of antibody-antigen binding using an on-chip artificial pore.

We demonstrate a rapid and highly sensitive all-electronic technique based on the resistive pulse method of particle sizing with a pore to detect the binding of unlabeled antibodies to the surface of latex colloids. Here, we use an on-chip pore to sense colloids derivatized with streptavidin and measure accurately their diameter increase on specific binding to several different types of antibodies. We show the sensitivity of this technique to the concentration of free antibody and that it can be used to perform immunoassays in both inhibition and sandwich configurations. Overall, our technique does not require labeling of the reactants and is performed rapidly by using very little solution, and the pore itself is fabricated quickly and inexpensively by using soft lithography. Finally, because this method relies only on the volume of bound ligand, it can be generally applied to detecting a wide range of ligand-receptor binding reactions.

Antigen-Antibody Reactions↗
PubMed2005

Metabolizing enzyme toxicology assay chip (MetaChip) for high-throughput microscale toxicity analyses.

The clinical progression of new chemical entities to pharmaceuticals remains hindered by the relatively slow pace of technology development in toxicology and clinical safety evaluation, particularly in vitro approaches, that can be used in the preclinical and early clinical phases of drug development. To alleviate this bottle-neck, we have developed a metabolizing enzyme toxicology assay chip (MetaChip) that combines high-throughput P450 catalysis with cell-based screening on a microscale platform. The MetaChip concept is demonstrated by using sol-gel encapsulated P450s to activate the prodrug cyclophosphamide, which is the major constituent of the anticancer drug Cytoxan, as well as other compounds that are activated by P450 metabolism. The MetaChip provides a high-throughput microscale alternative to currently used in vitro methods for human metabolism and toxicology screening based on liver slices, cultured human hepatocytes, purified microsomal preparations, or isolated and purified P450s. This technology creates opportunities for rapid and inexpensive assessment of ADME/Tox (absorption, distribution, metabolism, excretion/toxicology) at very early phases of drug development, thereby enabling unsuitable candidates to be eliminated from consideration much earlier in the drug discovery process.

Biotransformation↗
PubMed2004

Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips.

The TOR (target of rapamycin) proteins play important roles in nutrient signaling in eukaryotic cells. Rapamycin treatment induces a state reminiscent of the nutrient starvation response, often resulting in growth inhibition. Using a chemical genetic modifier screen, we identified two classes of small molecules, small-molecule inhibitors of rapamycin (SMIRs) and small-molecule enhancers of rapamycin (SMERs), that suppress and augment, respectively, rapamycin's effect in the yeast Saccharomyces cerevisiae. Probing proteome chips with biotinylated SMIRs revealed putative intracellular target proteins, including Tep1p, a homolog of the mammalian PTEN (phosphatase and tensin homologue deleted on chromosome 10) tumor suppressor, and Ybr077cp (Nir1p), a protein of previously unknown function that we show to be a component of the TOR signaling network. Both SMIR target proteins are associated with PI(3,4)P2, suggesting a mechanism of regulation of the TOR pathway involving phosphatidylinositides. Our results illustrate the combined use of chemical genetics and proteomics in biological discovery and map a path for creating useful therapeutics for treating human diseases involving the TOR pathway, such as diabetes and cancer.

Humans↗
PubMed2004

A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.

The soil-dwelling alpha-proteobacterium Sinorhizobium meliloti engages in a symbiosis with legumes: S. meliloti elicits the formation of plant root nodules where it converts dinitrogen to ammonia for use by the plant in exchange for plant photosynthate. To study the coordinate differentiation of S. meliloti and its legume partner during nodule development, we designed a custom Affymetrix GeneChip with the complete S. meliloti genome and approximately 10,000 probe sets for the plant host, Medicago truncatula. Expression profiling of free-living S. meliloti grown with the plant signal molecule luteolin in defined minimal and rich media or of strains altered in the expression of key regulatory proteins (NodD1, NodD3, and RpoN) confirms previous data and identifies previously undescribed regulatory targets. Analyses of root nodules show that this Symbiosis Chip allows the study of gene expression in both partners simultaneously. Our studies detail nearly 5,000 transcriptome changes in symbiosis and document complex transcriptional profiles of S. meliloti in different environments.

Bacterial Proteins↗
PubMed2005

A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation.

Phosphorus, one of the essential elements for plants, is often a limiting nutrient because of its low availability and mobility in soils. Significant changes in plant morphology and biochemical processes are associated with phosphate (Pi) deficiency. However, the molecular bases of these responses to Pi deficiency are not thoroughly elucidated. Therefore, a comprehensive survey of global gene expression in response to Pi deprivation was done by using Arabidopsis thaliana whole genome Affymetrix gene chip (ATH1) to quantify the spatio-temporal variations in transcript abundance of 22,810 genes. The analysis revealed a coordinated induction and suppression of 612 and 254 Pi-responsive genes, respectively. The functional classification of some of these genes indicated their involvement in various metabolic pathways, ion transport, signal transduction, transcriptional regulation, and other processes related to growth and development. This study is a detailed analysis of Pi starvation-induced changes in gene expression of the entire genome of Arabidopsis correlated with biochemical processes. The results not only enhance our knowledge about molecular processes associated with Pi deficiency, but also facilitate the identification of key molecular determinants for improving Pi use by crop species.

Arabidopsis↗
PubMed2001

High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

We describe here a system for the rapid identification, assay development, and characterization of gene-based single nucleotide polymorphisms (SNPs). This system couples informatics tools that mine candidate SNPs from public expressed sequence tag resources and automatically designs assay reagents with detection by a chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry platform. As a proof of concept of this system, a genomewide collection of reagents for 9,115 gene-based SNP genetic markers was rapidly developed and validated. These data provide preliminary insights into patterns of polymorphism in a genomewide collection of gene-based polymorphisms.

Alleles↗
PubMed2006

Acute pulmonary aspergillosis in immunocompetent subjects after exposure to bark chippings.

We describe 2 cases of immunocompetent males with acute community-acquired invasive pulmonary aspergillosis developing shortly after spreading bark chippings. One patient with a fatal outcome was initially diagnosed as allergic alveolitis rather than infection and received steroid treatment illustrating the obvious challenges in the differential diagnosis between these disease entities.

Adult↗
PubMed2001

A laboratory evaluation of the accuracy and precision of the photovac snapshot portable gas chromatograph and the Dräger Chip Measurement System monitor for benzene in air measurements.

A laboratory evaluation of the accuracy and precision of two field instruments, the Photovac Snapshot Gas Chromatograph and the Dräger Chip Measurement System (CMS) Monitor, both capable of specific determination of benzene, was carried out. The evaluation was based on the generation of a test atmosphere of known concentration of benzene in a stainless steel calibration chamber and simultaneous sampling of the test atmosphere by each instrument. At the same time, the chamber atmosphere was continuously monitored by one or two data logging photoionization detector (PID) hydrocarbon analysers. A series of six, 10-minute charcoal tube air samples of the test atmosphere was also collected over the 1-hour run and analyzed by gas chromatography. Nine different concentrations ranging from 0.25 ppm to 8 ppm were used. Accuracy was evaluated using National Institute for Occupational Safety and Health (NIOSH) criteria. The Photovac GC consistently met the NIOSH recommended accuracy criteria of +/- 25 percent at or below 1 ppm of benzene, whereas the Drager CMS results generally fell slightly outside this criteria. Compared against less stringent accuracy criteria of +/- 35 percent, all Photovac GC results were acceptable but about 40 percent of Drager CMS results were not. The precision of Photovac GC (CV +/- 10%) is better than Drager CMS (CV = +/- 20% to 40%). Both instruments are, however, good field instruments provided their limitations are taken into account in their use.

Air Pollutants↗
PubMed1996

Laboratory and analytical method performance of lead measurements in paint chips, soils, and dusts.

The National Lead Laboratory Accreditation Program (NLLAP) recognizes laboratories capable of analyzing lead in paints, soils, and dusts. NLLAP requires successful participation in the Environmental Lead Proficiency Analytical Testing (ELPAT) program. For paint chip analyses, laboratory-to-laboratory variability is about 10% relative standard deviation (RSD) for lead levels near 0.5%, the HUD definition of lead-based paint. For soil analyses, RSDs are about 9 to 10% near relevant federal soil standards and 16% near the lowest state bare soil standard that currently exists. For dust wipe analyses, RSDs range from 10 to 16% for lead levels near relevant HUD standards. Of participating laboratories, 92 to 93% consistently meet ELPAT performance limits. A variety of analytical methods gives similar results. No conclusive significant differences were found among most frequently used hotplate and microwave sample preparation techniques. In addition, several participating laboratories have successfully used ultrasonic extraction methods, a method suitable for use at abatement sites. The three most frequently used instrumental techniques, flame atomic absorption (FAA), inductively coupled plasma-atomic emission spectroscopy (ICP-AES), and graphite furnace atomic absorption show no statistically significant differences in ability to meet ELPAT performance limits. However, small statistically significant biases between these methods sometimes occur. The magnitude of biases is less than 5% of the corresponding laboratory mean near relevant federal standards except for lead levels near the lowest HUD lead wipe standard, where biases can be as high as 8%. Other instrumental methods that have been used successfully include ICP-mass spectroscopy, direct current plasma-atomic emission spectroscopy, dithizone spectrophotometry, and anodic stripping voltametry.

Accreditation↗
PubMedDate not supplied

Labeling during cleavage of nucleic acids for their detection on DNA chips.

A new and efficient strategy for labeling of nucleic acids prior to their hybridization on high density DNA chip has been developed. Our approach which combines the fragmentation and the labeling is based on the reactivity of the terminal phosphates of cleaved DNA and RNA fragments with a reporter molecule bearing aryldiazomethane group.

DNA↗
PubMed2005

Characterisation of protein microheterogeneity and protein complexes using on-chip immunoaffinity purification-mass spectrometry.

Post-translational modification of proteins may influence their interactions with other plasma proteins, as well as having an effect on many aspects of the metabolism of the protein, such as receptor binding, tissue uptake, degradation and excretion. Many post-translational modifications occur in a physiological context, while others are specific for certain diseases, which is why they are of diagnostic importance in clinical proteomics. Analytical approaches to the study of post-translational modifications and protein complexes through the combined use of on-chip immunological affinity purification on a surface-enhanced laser desorption/ionisation platform and subsequent mass spectrometry are illustrated in the author's own work relating to plasma transthyretin (TTR) and retinol-binding protein (RBP). In those studies, both the aspects of post-translational modifications of TTR and the formation of a protein complex between TTR and RBP have been discussed. Such aspects are of diagnostic interest in clinical proteomics, especially with regard to the modification of TTR in relation to the occurrence of amyloidotic diseases.

Amyloid↗
PubMed2002

Neural network predicts sequence of TP53 gene based on DNA chip.

UNLABELLED: We have trained an artificial neural network to predict the sequence of the human TP53 tumor suppressor gene based on a p53 GeneChip. The trained neural network uses as input the fluorescence intensities of DNA hybridized to oligonucleotides on the surface of the chip and makes between zero and four errors in the predicted 1300 bp sequence when tested on wild-type TP53 sequence. AVAILABILITY: The trained neural network is available for academic use by contacting steen@cbs.dtu.dk

Base Sequence↗
PubMed2005

Design of a DNA chip for detection of unknown genetically modified organisms (GMOs).

MOTIVATION: Unknown genetically modified organisms (GMOs) have not undergone a risk evaluation, and hence might pose a danger to health and environment. There are, today, no methods for detecting unknown GMOs. In this paper we propose a novel method intended as a first step in an approach for detecting unknown genetically modified (GM) material in a single plant. RESULTS: A model is designed where biological and combinatorial reduction rules are applied to a set of DNA chip probes containing all possible sequences of uniform length n, creating probes capable of detecting unknown GMOs. The model is theoretically tested for Arabidopsis thaliana Columbia, and the probabilities for detecting inserts and receiving false positives are assessed for various parameters for this organism. From a theoretical standpoint, the model looks very promising but should be tested further in the laboratory. AVAILABILITY: The model and algorithms will be available upon request to the corresponding author.

Algorithms↗