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PubMed1994

Mutations in aquaporin-1 in phenotypically normal humans without functional CHIP water channels.

The gene aquaporin-1 encodes channel-forming integral protein (CHIP), a member of a large family of water transporters found throughout nature. Three rare individuals were identified who do not express CHIP-associated Colton blood group antigens and whose red cells exhibit low osmotic water permeabilities. Genomic DNA analyses demonstrated that two individuals were homozygous for different nonsense mutations (exon deletion or frameshift), and the third had a missense mutation encoding a nonfunctioning CHIP molecule. Surprisingly, none of the three suffers any apparent clinical consequence, which raises questions about the physiological importance of CHIP and implies that other mechanisms may compensate for its absence.

Animals↗
PubMed1988

Delignification of Wood Chips and Pulps by Using Natural and Synthetic Porphyrins: Models of Fungal Decay.

Kraft pulps, prepared from softwoods, and small chips of birch wood were treated with heme and tert-butyl hydroperoxide in aqueous solutions at reflux temperature. Analyses of treated pulps showed decreases in kappa number (a measure of lignin content) from about 36 to less than 2, with concomitant increases in brightness (80% increase in the better samples). Analyses of treated wood chips revealed selective delignification and removal of hemicelluloses. After 48 h of treatment, lignin losses from the wood chips approached 40%, and xylose/mannose (hemicellulose) losses approached 70%, while glucose (cellulose) losses were less than 10%. Examination of delignified chips by transmission electron microscopy showed that the removal of lignin occurred in a manner virtually indistinguishable from that seen after decay by white rot fungi. Various metalloporphyrins, which act as biomimetic catalysts, were compared to horseradish peroxidase and fungal manganese peroxidase in their abilities to oxidize syringaldazine in an organic solvent, dioxane. The metalloporphyrins and peroxidases behaved similarly, and it appeared that the activities of the peroxidases resulted from the extraction of heme into the organic phase, rather than from the activities of the enzymes themselves. We concluded that heme-tert-butyl hydroperoxide systems in the absence of a protein carrier mimic the decay of lignified tissues by white rot fungi.

Journal Article↗
PubMed2006

Comparison of a conventional antimicrobial susceptibility assay to an oligonucleotide chip system for detection of drug resistance in Mycobacterium tuberculosis isolates.

An oligonucleotide chip (Combichip Mycobacteria chip) detecting specific mutations in the rpoB, katG, and inhA genes of Mycobacterium tuberculosis was compared with conventional antimicrobial susceptibility results. The probes detecting drug resistance were as follows: 7 wild-type and 13 mutant probes for rifampin and 2 wild-type and 3 mutant probes for isoniazid. Target DNA of M. tuberculosis was amplified by PCR, followed by hybridization and scanning. Direct sequencing was performed to verify the results of the oligonucleotide chip. One-hundred seven of 115 rifampin-resistant strains (93%) had mutations in the rpoB gene. Eighty-five of 119 isoniazid-resistant strains (71%) had mutations in the katG gene or inhA gene. The diagnostic oligonucleotide chip with mutation-specific probes is a reliable and useful tool for the rapid and accurate diagnosis of resistance against rifampin and isoniazid in M. tuberculosis isolates.

Antibiotics, Antitubercular↗
PubMed1999

Real time image processing with an analog vision chip system.

A linear analog network model is proposed to characterize the function of the outer retinal circuit in terms of the standard regularization theory. Inspired by the function and the architecture of the model, a vision chip has been designed using analog CMOS Very Large Scale Integrated circuit technology. In the chip, sample/hold amplifier circuits are incorporated to compensate for statistic transistor mismatches. Accordingly, extremely low noise outputs were obtained from the chip. Using the chip and a zero-crossing detector, edges of given images were effectively extracted in indoor illumination.

Adaptation, Ocular↗
PubMed2006

Assay development and screening of a serine/threonine kinase in an on-chip mode using caliper nanofluidics technology.

Kinases are key targets for drug discovery. In the field of screening in general and especially in the kinase area, because of considerations of efficiency and cost, radioactivity-based assays tend to be replaced by alternative, mostly fluorescence-based, assays. Today, the limiting factor is rarely the number of data points that can be obtained but rather the quality of the data, enzyme availability, and cost. In this article, the authors describe the development of an assay for a kinase screen based on the electrophoretic separation of fluorescent product and substrate using a Caliper-based nanofluidics environment in on-chip incubation mode. The authors present the results of screening a focused set of 32,000 compounds together with confirmation data obtained in a filtration assay. In addition, they have made a small-scale comparison between the on-chip and off-chip nanofluidics screening modes. In their hands, the screen in on-chip mode is characterized by high precision most likely due to the absence of liquid pipetting; an excellent confirmation rate (62%) in an independent assay format, namely, filtration; and good sensitivity. This study led to the identification of 4 novel chemical series of inhibitors.

Drug Evaluation, Preclinical↗
PubMedDate not supplied

DNA chips: the future of biomarkers.

DNA chips are small, solid supports such as microscope slides onto which thousands of cDNAs or oligonucleotides are arrayed, representing known genes or simply EST clones, or covering the entire sequence of a gene with all its possible mutations. Fluorescently labeled DNA or RNA extracted from tissues is hybridized to the array. Laser scanning of the chip permits quantitative evaluation of each individual complementary sequence present in the sample. DNA chip technology is currently being proposed for qualitative and quantitative applications, firstly for the detection of point mutations, small deletions and insertions in genes involved in human diseases or affected during cancer progression; secondly, to determine on a genome-wide basis the pattern of gene expression in tumors, as well as in a number of experimental situations. The extraordinary power of DNA chips will have a strong impact on medicine in the near future, both in the molecular characterization of tumors and genetic diseases and in drug discovery and evaluation. Quantitative applications will soon spread through all fields of biology.

Biomarkers↗
PubMed2005

Harshlight: a "corrective make-up" program for microarray chips.

BACKGROUND: Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects. RESULTS: We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects: localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip. CONCLUSION: We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle changes between samples. For the widely used MAS5 algorithm, we show that compact blemishes cause an average of 8 gene expression values per chip to change by more than 50%, two of them by more than twofold; our masking algorithm restores about two thirds of this damage. Large-scale artifacts are successfully detected and eliminated.

Algorithms↗
PubMed2003

CHIP: a link between the chaperone and proteasome systems.

CHIP, carboxy terminus of Hsc70 interacting protein, is a cytoplasmic protein whose amino acid sequence is highly conserved across species. It is most highly expressed in cardiac and skeletal muscle and brain. The primary amino acid sequence is characterized by 3 domains, a tetratricopeptide repeat (TPR) domain at its amino terminus, a U-box domain at its carboxy terminus, and an intervening charged domain. CHIP interacts with the molecular chaperones Hsc70-Hsp70 and Hsp90 through its TPR domain, whereas its U-box domain contains its E3 ubiquitin ligase activity. Its interaction with these molecular chaperones results in client substrate ubiquitylation and degradation by the proteasome. Thus, CHIP acts to tilt the folding-refolding machinery toward the degradative pathway, and it serves as a link between the two. Because protein degradation is required for healthy cellular function, CHIP's ability to degrade proteins that are the signature of disease, eg, ErbB2 in breast and ovarian cancers, could prove to be a point of therapeutic intervention.

Animals↗
PubMed2005

Nanosystems for biosensing: multianalyte immunoassay on a protein chip.

This chapter describes the construction of addressable two-dimensional (2D) microarrays via the random fluidic self-assembly of metallic particles and the use of these arrays as platforms for constructing protein chips for bioassays. These arrays will be useful as platforms for constructing protein chips for bioassays in a broad range of applications. The basic units in the assembly are microfabricated particles, which carry a straightforward visible code, and the corresponding array template patterned on a glass substrate. On one face, the particles consist of a hydrophobic and magnetic Ni-polytetrafluoroethylene (Ni-PTFE) composite layer; the other face has a gold layer that was modified for biomolecular attachment. We use photoresist patterning to create an array template with spatially discrete microwells into which an Ni-PTFE hydrophobic composite layer and a hydrophobic photoadhesive coating are electrodeposited. After biomaterial attachment and binding processes in bulk, the particles are randomly self-assembled onto the lubricated bonding sites on the chip substrate. This self-assembly process is driven by a combination of magnetic, hydrophobic, and capillary interactions. The encoding symbol carried by each particle is used to identify the target attached to the particle surface. This model system demonstrates the utility of the protein chip array for conducting simultaneous multianalyte immunoassays of human immunoglobulins (IgA, IgG, and IgM).

Animals↗
PubMed2006

Effect of a controlled-release chlorhexidine chip on clinical and microbiological parameters and prostaglandin E2 levels in gingival crevicular fluid.

BACKGROUND: The aim of the present study was to determine the effect of a chlorhexidine chip on crevicular prostaglandin E2 (PGE2) levels and on the clinical and microbiological parameters of periodontitis when used as adjunctive therapy to scaling and root planing (SRP) in patients with chronic periodontitis. METHODS: This randomized single-blind study was carried out in parallel design. The test group received SRP plus chlorhexidine chip, whereas the control group received SRP alone. Thirty-four subjects, aged 20 to 55 years, with chronic periodontitis were recruited. Clinical indices, microbiological samples, and gingival crevicular fluid (GCF) samples were evaluated at baseline and after 1, 3, and 6 months. Microbiological samples were evaluated under a light microscope. GCF PGE2 levels were determined using radioimmunoassay. RESULTS: Significant improvements could be found for all clinical variables in both groups over the study period. The mean changes in probing depth obtained by SRP plus chlorhexidine chip were greater than those obtained by the SRP alone group at 3 and 6 months. In the test group, there was also significant gain in clinical attachment level at 6 months. When data were combined from all groups, significant reductions in GCF PGE2 levels and number of microorganisms were noted at all time points. However, in the test group, reduction was greater at 6 months for crevicular PGE2 level and at 3 and 6 months for proportions of spirochetes. CONCLUSION: Based on the findings of this study, the chlorhexidine chip reduced GCF PGE2 levels and had positive effects on clinical parameters and subgingival flora when used as adjunctive therapy to SRP in patients with chronic periodontitis.

Adult↗
PubMed2003

Channel shape effects on the solution-flow characteristics and the liquid/liquid extraction efficiency in polymer microchannel chips.

A polymer microchannel chip with a symmetrical or unsymmetrical zigzag-side-walled structure was fabricated by an imprinting method, and applied to study shape effects on solution flow characteristics as well as on the liquid/liquid extraction efficiency of an aluminium(III) chelate complex (Al-DHAB: DHAB = o,o'-dihydroxyazobenzene) in a microchannel chip. In an unsymmetrical zigzag-side-walled channel chip (us-channel), an oil/water interface was sinusoidal, while that in a symmetrical zigzag-side-walled channel chip (s-channel) was flat as long as the observation was made under an optical microscope. It was demonstrated that the efficiency of the water-to-oil (1-butanol) extraction of Al-DHAB in the microchannel was governed by the contact time between the two phases. As the most important results, furthermore, the extraction efficiency was higher in the us-channel, as compared with that in the s-channel, owing to the sinusoidal liquid/liquid interfacial structure and, therefore, to the high interfacial area between the two phases.

Journal Article↗
PubMed2005

Optimization of an interface chip for coupling capillary electrophoresis with thermal lens microscopic detection.

This paper presents a capillary-to-microchip connection, which can be used as an interface for coupling capillary electrophoresis (CE) with a thermal lens microscope (TLM). It is difficult to directly apply TLM to samples in a capillary with a curved surface, and such an interface chip at the end of a CE separation column is needed for reliable TLM measurements. The dependence of the TLM signal intensity on the TLM detection point in the interface chip and the dependence of the theoretical plate number of CE separation on the channel dimensions of the interface chip were investigated and optimized with a mixture of 4-dimethylaminoazobenze-4'-sulfonyl (DABSYL)-derivatized amino acids (glycine, alanine, methionine, and proline) as a model sample. By using an optimized interface chip, theoretical plate numbers of DABSYL-glycine, -methionine, -alanine, and -proline were obtained to be 104000, 95000, 104000, and 95000, respectively.

Amino Acids↗
PubMed2006

Use of a Peltier chip with a newly devised local brain-cooling system for neocortical seizures in the rat. Technical note.

Local cortical cooling for termination of epileptic discharges (EDs) has recently become a focus of research. The authors report on a newly devised cooling system that uses a thermoelectric (Peltier) chip and examine the system's performance in experimental neocortical seizures. Experiments were performed in adult male Sprague-Dawley rats after induction of halothane anesthesia. The Peltier chip was attached to a heat sink with a water channel. Two silicon tubes were connected to the heat sink, and water at 37 degrees C was circulated in the channel. The newly designed device was placed on the surface of the cortex. Kainic acid (KA) was injected into the cortex to provoke EDs. In the nonepileptic cortex, the temperature of the cortical surface decreased to 14.8 +/- 1.5 degrees C and that 2 mm below the surface to 27.1 +/- 3.1 degrees C within 30 seconds after the start of cooling. The temperature of the heated side of the chip was maintained at approximately 36.9 degrees C. Without water circulation, the temperature of the cortical surface decreased to 20 degrees C but soon began to increase, peaking at 30 degrees C. The temperature of the heated side of the chip rose to more than 60 degrees C. The EDs, which appeared within 20 minutes after KA injection, began to decrease in amplitude immediately after cooling began and continued to decrease as the temperature of the cortex was lowered. Sufficient miniaturization and good performance of the cooling device was demonstrated. Further efforts to develop implantable cooling systems and improve existing ones should be continued.

Animals↗
PubMed2004

Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

Lamivudine, a nucleoside analogue, has been used widely as an effective antiviral agent for the treatment of patients with chronic hepatitis B virus (HBV) infection. However, the YMDD motif mutation of HBV polymerase resistant to lamivudine occurs very frequently after long term therapy. We developed an oligonucleotide chip for the detection of YMDD motif mutants resistant to lamivudine and investigated the prevalence of the mutants in patients with chronic HBV infection who had not been treated by lamivudine before. Forty patients who had not been treated with lamivudine were included in this study. Serum samples were tested by the oligonucleotide chips designed for detection of wild-type YMDD motif, M552V and M552I. Samples were confirmed by restriction fragment length polymorphism (RFLP) and direct sequencing. M552I mutants were detected by the oligonucleotide chips in 7.5% (3/40) of chronic HBV infected patients (2 chronic hepatitis and 1 cirrhosis). The results were in accordance with those of RFLP. YMDD motif mutants occur as natural genome variabilities in patients with chronic HBV infection who had not been treated with lamivudine before. Oligonucleotide chip technology is a reliable and useful diagnostic tool for the detection of mutants resistant to antiviral therapy in chronic HBV infection.

Adolescent↗
PubMedDate not supplied

[DNA chips].

DNA chips represent a miniaturization of the classical system of reverse dot-blot. They consist of a small size support made of plastic or glass or silicium on which probes are synthesized or immobilized. It is thus possible to fix a few thousand or even a hundred of thousands of probes per cm2. Practically the chips are hybridized with the nucleic acid to be studied that has been amplified beforehand by PCR and which is generally labelled by a fluorochrome, either during amplification or after hybridization. After washing the hybrids are detected by a system which most of the time consists of a laser and a confocal microscope interfaced with a computer, but many variations exist. It is thus possible to analyse at the same time a considerable number of sequences. The diagnostic applications are only at the prototype stage. Eventually the chips should allow the identification of any point mutation, or the search for bacteria, viruses or parasites in a very short period of time without preliminary cultures. They should also allow many sorts of typing ranging from infectious agents to HLA. They should become a particularly powerful tool in the search for new medicines and in the revealing of their toxicity. A considerable potential market is also the diagnosis of the predisposition to polygenic diseases or to a particular sensitivity to any chemical substance. In fact the chips are only just beginning to be used. One of the foreseeable developments should be the possibility to study nucleic acids without preliminary amplification and we can hope to eventually have at our disposal very cheap, autonomous integrated systems. The technology could eventually extend to fields other than molecular biology such as immunology or biochemistry.

Humans↗
PubMed1997

Regulation of water channel gene (AQP-CHIP) expression by estradiol and anordiol in rat uterus.

In the present studies, we observed the regulation of water channel gene (AQP-CHIP) expression by estradiol (E2) and anordiol, an antiestrogen with agonist activity, in immature female rat uterus. Antisense and sense oligonucleotide primers corresponding to the consensus sequences of two rats AQP-CHIP water channels were synthesized and used to amplify a cDNA fragment that was reverse-transcripted from rat uterine total RNA preparation. E2 administered as a single dose of 40 micrograms.kg-1 to immature female rats induced a significant increase in AQP-CHIP mRNA expression 9 h after treatment. The lowest effective doses of E2 and anordiol were 40 and 50 micrograms.kg-1, respectively. The stimulatory effect of anordiol was more pronounced than that of E2. The present results suggest that AQP-CHIP water channel gene expression may be involved in E2- and anordiol-mediated water imbibition and luminal fluid production in the uterus.

Animals↗
PubMed2000

Intelligent DNA chips: logical operation of gene expression profiles on DNA computers.

We propose a new type of DNA chips with logical operations executable. In DNA computing researches, some methods have been developed to represent and evaluate Boolean functions on DNA strands. By employing the evaluation methods, we are able to deal with logical operations such as logical-and and logical-or for gene expressions. By combining with the DNA Coded Number method, we implement universal DNA chips which not only detect gene expressions but also find logical formulae of gene expressions. An important advantage of our intelligent DNA chip is that the intensity of the fluorescence at each element is not only proportional to the expression level of the genes in the sample but also proportional to the satisfiability level of the Boolean formula at the element with the gene expression pattern. These features of the intelligent DNA chip and the DCN method allow us more quantitative analyses of gene expression profiles and the logical operations.

Algorithms↗
PubMed1999

[The development and applications of digital signal processing (DSP)-chip].

Due to the limitation of operation speed, real time performance of digital signal processing (DSP) system is far from that of analog signal processing system in decades ago. Since early 80's, DSP chips have been greatly improved in the following aspects: operation speed, computation precision, fabrication technics, cost, chip volume, operational power supply voltage, weight and power consumption. Furthermore, development tools and methods have been developed greatly. Modern DSP chips can be operated very fast, which make the implementation of many DSP based signal processing system possible. Now DSP chips have been widely applied successfully in communication, automatic control, aerospace and medicine. DSP based technology has very promising future in manned space flight area.

Aerospace Medicine↗