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PubMed2000

Biochemistry. Ligand chip helps manipulate cells.

Scientists at the University of Chicago have found an electrochemical way to control interactions between cells and a chip. It's an improvement over existing methods of influencing cell behavior, none of which allows control over cell-surface activities with chip-bound molecules. Researchers say the achievement could be a key step toward a wide variety of applications--everything from new drug assays to prosthetic aids that replace damaged neurons.

Biochemistry↗
PubMed1998

Application of the principle of marginal analysis to sampling practice using prostatic chippings as a model.

AIMS: To demonstrate an application of health economic principles in histopathology by using the sampling of transurethral resections of prostate specimens. By demonstrating how marginal costs are calculated the aim is to illustrate that the potential opportunity cost of sampling entire specimens is much greater than would be anticipated by taking average cost, or the cost of producing a histological section alone. METHOD: A mathematical model is used with data obtained from the Aberdeen pathology department files and published estimates of the likely percentage of cancerous chippings in each specimen. RESULTS: The average cost of each cancer detected remains low, between 47 Pounds and 151 Pounds, in all the scenarios examined. However, the marginal costs can become high, exceeding 10,000 Pounds in larger specimens, if all the chippings are processed. CONCLUSIONS: This study demonstrates that there are potential opportunity cost penalties to histopathological services associated with sampling strategies. Although the results are derived from a hypothetical mathematical model using local data that applies only to histopathology, the method could be widely applied. The principles of marginal analysis should be performed by multidisciplinary teams and include outcomes as well as a broader range of costs, including those that arise subsequent to diagnosis.

Costs and Cost Analysis↗
PubMed1993

Recent developments in neurodynamics and their impact on the design of neuro-chips.

Neurons can be modeled either by equations or differential equations. For the latter, a low-pass filter must be added to the analog function blocks associated with the McCullogh and Pitts type of static neuron in order to provide the time-dependent neuron solution. The low-pass filter enhances stability and enables a time-continuous analog implementation much more compact than that attained with time-discrete analog or pure digital design. A few examples of equations as well as differential equations are known for that part of learning. However, much less than for the recall mode, it is clear how to design learning neuro-chips for temporal pattern processing. It is shown here that a partial differential equation can be used to provide a unified description of both the recall and learning dynamics of a neural network as well as to investigate systematically the VLSI potential for analog time-continuous neuro-chips. It turns out that the recall and learning dynamics can be divided into causal as well as noncausal solutions. The first type of solution includes oscillating or spiking neurons. The second type of solution allows for a much simpler signal representation but leads to the problem of storing the temporal signal of each neuron for as long a time as a single pattern lasts. As this is prohibitive for larger networks and time-varying patterns, the analog VLSI implementation of causal neuron models is suggested.

Artificial Intelligence↗
PubMed2006

A single nucleotide polymorphism chip-based method for combined genetic and epigenetic profiling: validation in decitabine therapy and tumor/normal comparisons.

Progress on several unresolved issues in cancer epigenetics will benefit from rapid and standardized methods for profiling DNA methylation genome-wide. In the area of epigenetic therapy, the demethylating drug decitabine (5-aza-2'-deoxycytidine) is increasingly used to treat acute myelogenous leukemia and myelodysplastic syndrome, but the mechanisms of its anticancer activity have remained unclear. Given the clinical efficacy of decitabine and the uncertainties about its mode of action, it will be useful to optimize methods for following DNA methylation as a biochemical response in individual patients. Here, we describe a single nucleotide polymorphism (SNP) chip-based method (MSNP) for profiling DNA methylation. Using this procedure, the extent of demethylation in bone marrow aspirates from patients with leukemia receiving decitabine can be assessed genome-wide using commercially available (Affymetrix) SNP chips. We validated the accuracy of MSNP by comparing the results with combined bisulfite restriction analysis and by sequencing cloned PCR products from bisulfite-converted DNA. We further validated MSNP in a Wilms' tumor/normal kidney comparison, comparing the results with methylation-sensitive Southern blotting. MSNP simultaneously detects aberrations in DNA copy number and loss of heterozygosity, making it a generally useful approach for combined genetic and epigenetic profiling in tissue samples from cancer patients.

Antimetabolites, Antineoplastic↗
PubMed1993

Comparison of three different methods for measurement of plaque-pH in humans after consumption of soft bread and potato chips.

Three different techniques for measurement of plaque-pH--the sampling, the microtouch, and the telemetric methods--were compared after subjects had consumed different starch products. Ten volunteers, equipped with partial lower prostheses, incorporating a miniature glass pH electrode, refrained from toothbrushing for 3 days. Four products were tested: (1) soft bread, (2) potato chips, (3) 5% starch, and (4) 5% sucrose. The pH of plaque was measured for 45 min by means of all three of the methods. The results showed that the mean pH at 10 min was 1.5 units lower with the telemetric than with the sampling method and 1.0 unit lower with the telemetric than with the microtouch method. Relatively small differences were found among the effects of the four test products for all three methods, with the clearest distinctions among the pH curves being with the microtouch and telemetric methods. The main conclusions from the present investigation are: (1) that there were large differences in pH levels measured with the sampling, the microtouch, and the telemetric methods, even though they ranked the test products in about the same order, and (2) that the two starchy foods, bread and potato chips, were both easily fermented by dental plaque.

Aged↗
PubMed1986

Ototoxicity of cisplatin vs. platinum analogs CBDCA (JM-8) and CHIP (JM-9).

Cis-diamminedichloroplatinum (cisplatin), a divalent platinum compound and cell-cycle nonspecific chemotherapeutic agent, produces a permanent high-frequency sensorineural hearing loss and a dose-related cumulative renal insufficiency with tubular necrosis and interstitial nephritis. Synthetic platinum analogs are presently being tested to identify an analog with greater antitumor activity, but less ototoxicity and nephrotoxicity than cisplatin. The objectives of this study were to analyze the potential cochlear and nephrotoxic effects of two synthetic platinum analogs presently in phases I and II of clinical trials, CBDCA [JM-8 or cis-diammine, 1,1-cyclobutane dicarboxylato (2)-0,0(1)-platinum (NSC-241240)] and CHIP [JM-9 or cis-dichloro-trans-dihydroxybisisopropylamine platinum IV (NSC-256927)]. Cytocochleography, auditory brain-stem evoked response (ABR), double-blind light microscopy of renal tissues, and gamma emission analysis of 195mpt localization in viscera and inner ear were employed in the evaluation of cisplatin and platinum analogs (JM-8 and JM-9) in adult guinea pigs. Final results indicate that the investigational chemotherapeutic analogs CBDCA (JM-8) and CHIP (JM-9) do not produce the ototoxicity and nephrotoxicity characteristic of cisplatin. Furthermore, these findings demonstrate 195mpt localization in the vestibular labyrinth and confirm previous platinum distribution studies in the organ of Corti and stria vascularis tissues.

Animals↗
PubMed2001

High throughput studies of gene expression using green fluorescent protein-oxidative stress promoter probe constructs: the potential for living chips.

Green fluorescent protein fusions were constructed with several oxidative stress promoters from Escherichia coli. These promoters were chosen for their induction by reactive oxygen species (ROS) such as superoxide, hydrogen peroxide, and hydroxyl radicals. When exposed to various free radical insults, the cells fluoresced with great specificity based on the corresponding ROS. In this work, we propose a way in which these constructs could be used to study the mode of action of a variety of antitumor drugs. This approach offers the possibility of complementing gene chip technology by the creation of living chips for high throughput screening as well as studying differential gene expression.

Antineoplastic Agents↗
PubMed2005

Rapid self-assembly of DNA on a microfluidic chip.

BACKGROUND: DNA self-assembly methods have played a major role in enabling methods for acquiring genetic information without having to resort to sequencing, a relatively slow and costly procedure. However, even self-assembly processes tend to be very slow when they rely upon diffusion on a large scale. Miniaturisation and integration therefore hold the promise of greatly increasing this speed of operation. RESULTS: We have developed a rapid method for implementing the self-assembly of DNA within a microfluidic system by electrically extracting the DNA from an environment containing an uncharged denaturant. By controlling the parameters of the electrophoretic extraction and subsequent analysis of the DNA we are able to control when the hybridisation occurs as well as the degree of hybridisation. By avoiding off-chip processing or long thermal treatments we are able to perform this hybridisation rapidly and can perform hybridisation, sizing, heteroduplex analysis and single-stranded conformation analysis within a matter of minutes. The rapidity of this analysis allows the sampling of transient effects that may improve the sensitivity of mutation detection. CONCLUSIONS: We believe that this method will aid the integration of self-assembly methods upon microfluidic chips. The speed of this analysis also appears to provide information upon the dynamics of the self-assembly process.

Journal Article↗
PubMed2005

Stability of beating frequency in cardiac myocytes by their community effect measured by agarose microchamber chip.

To understand the contribution of community effect on the stability of beating frequency in cardiac myocyte cell groups, the stepwise network formation of cells as the reconstructive approach using the on-chip agarose microchamber cell microcultivation system with photo-thermal etching method was applied. In the system, the shapes of agarose microstructures were changed step by step with photo-thermal etching of agarose-layer of the chip using a 1064-nm infrared focused laser beam to increase the interaction of cardiac myocyte cells during cultivation. First, individual rat cardiac myocyte in each microstructure were cultivated under isolated condition, and then connected them one by one through newly-created microchannels by photo-thermal etching to compare the contribution of community size for the magnitude of beating stability of the cell groups. Though the isolated individual cells have 50% fluctuation of beating frequency, their stability increased as the number of connected cells increased. And finally when the number reached to eight cells, they stabilized around the 10% fluctuation, which was the same magnitude of the tissue model cultivated on the dish. The result indicates the importance of the community size of cells to stabilize their performance for making cell-network model for using cells for monitoring their functions like the tissue model.

Journal Article↗
PubMed2005

Predicting transcription factor activities from combined analysis of microarray and ChIP data: a partial least squares approach.

BACKGROUND: The study of the network between transcription factors and their targets is important for understanding the complex regulatory mechanisms in a cell. Unfortunately, with standard microarray experiments it is not possible to measure the transcription factor activities (TFAs) directly, as their own transcription levels are subject to post-translational modifications. RESULTS: Here we propose a statistical approach based on partial least squares (PLS) regression to infer the true TFAs from a combination of mRNA expression and DNA-protein binding measurements. This method is also statistically sound for small samples and allows the detection of functional interactions among the transcription factors via the notion of "meta"-transcription factors. In addition, it enables false positives to be identified in ChIP data and activation and suppression activities to be distinguished. CONCLUSION: The proposed method performs very well both for simulated data and for real expression and ChIP data from yeast and E. Coli experiments. It overcomes the limitations of previously used approaches to estimating TFAs. The estimated profiles may also serve as input for further studies, such as tests of periodicity or differential regulation. An R package "plsgenomics" implementing the proposed methods is available for download from the CRAN archive.

Algorithms↗
PubMed2005

Novel biomarkers of human growth hormone action from serum proteomic profiling using protein chip mass spectrometry.

CONTEXT: The detection of exogenous human GH (hGH) administration in athletes poses unique analytical problems, because its short circulating half-life provides only a brief opportunity to detect the administered hormone above endogenous levels. Measurement of novel GH-regulated serum protein biomarkers might provide an indirect method to detect exogenous GH. OBJECTIVE: The objective of this study was to identify new serum biomarkers of GH administration using proteomic profiling. DESIGN: Sera from a previously reported, double-blind, placebo-controlled GH administration trial were analyzed by protein chip mass spectrometry. SETTING: The study was performed at clinical research centers. SUBJECTS: Sixty healthy subjects, aged 18-40 yr, who were not elite athletes, were studied. INTERVENTIONS: Placebo or recombinant hGH treatment (0.1 or 0.2 IU/kg.d; 20 subjects/group) was administered for 4 wk, followed by an 8-wk washout period. MAIN OUTCOME MEASURES: Protein mass profiles were determined on immobilized Cu(2+) chips on d 0 and 21 of GH administration, and multivariate analysis was used to classify subjects into GH and placebo administration groups. RESULTS: When assessed by cross-validation, the classification performance of classifiers based on multivariate analysis of several GH-regulated peaks performed no better than classifiers based on the single best peak. This peak, a prominent biomarker of 15.1 kDa, was purified and identified as hemoglobin alpha-chain. The time course of the GH response of this biomarker is similar to that of other GH-dependent markers, such as IGF-I. CONCLUSION: This study demonstrates that protein mass profiling is an effective tool for the detection of GH administration and suggests that measurement of hemoglobin alpha-chain may have utility as a novel serum biomarker of GH action.

Adolescent↗
PubMed2006

Use of chromatin immunoprecipitation (ChIP) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells.

The Chromatin Immunoprecipiation (ChIP) provides a powerful technique for identifying the in vivo association of transcription factors with regulatory elements. However, obtaining meaningful information for promoter interactions is extremely challenging when the promoter is a member of a class of highly homologous elements. Use of PCR primers with small numbers of mutations can limit cross-hybridization with non-targeted sequences and distinguish a pattern of binding for factors with the regulatory element of interest. In this report, we demonstrate the selective in vivo association of NF-kappaB, p300 and CREB with the human Igamma1 promoter located in the intronic region upstream of the Cgamma1 exons in the immunoglobulin heavy chain locus. These methods have the ability to extend ChIP analysis to promoters with a high degree of homology.

Journal Article↗
PubMed2005

Far-field pattern simulation of flip-chip bonded power light-emitting diodes by a Monte Carlo photon-tracing method.

The far-field pattern of light-emitting diodes (LEDs) is an important issue in practical applications. We used a Monte Carlo photon-tracing method for the package design of flip-chip bonded power LEDs. As a first-order approximation, we propose using a plane light source model to calculate the far-field pattern of encapsulated LEDs. The far-field pattern is also studied by use of a more detailed model, which takes the structure of all epitaxial layers of a flip-chip bonded power LED into consideration. By comparing the simulation results with the experimental data, we have concluded that the plane light source model is much less time-consuming and offers fairly good precision for package design.

Journal Article↗
PubMed2004

Ultralow-threshold microcavity Raman laser on a microelectronic chip.

Using ultrahigh-Q toroid microcavities on a chip, we demonstrate a monolithic microcavity Raman laser. Cavity photon lifetimes in excess of 100 ns combined with mode volumes typically of less than 1000 (microm)3 significantly reduce the threshold for stimulated Raman scattering. In conjunction with the high ideality of a tapered optical fiber coupling junction, stimulated Raman lasing is observed at an ultralow threshold (as low as 74 microW of fiber-launched power at 1550 nm) with high efficiency (up to 45% at the critical coupling point) in good agreement with theoretical modeling. Equally important, the wafer-scale nature of these devices should permit integration with other photonic, mechanical, or electrical functionality on a chip.

Journal Article↗
PubMed2004

Beta-thalassemia microelectronic chip: a fast and accurate method for mutation detection.

BACKGROUND: beta-Thalassemia is one of the most common genetic diseases in humans. We developed an automated electronic microchip for fast and reliable detection of the nine most frequent mutations accounting for >95% of the beta-thalassemia alleles in the Mediterranean area. METHODS: We developed a microchip-based assay to identify the nine most frequent mutations (cd39C>T, IVS1-110G>A, IVS1-1G>A, IVS1-6T>C, IVS2-745C>G, cd6delA, -87C>G, IVS2-1G>A, and cd8delAA) by use of the Nanogen Workstation. The biotinylated amplicon was electronically addressed on the chip to selected pads, where it remained embedded through interaction with streptavidin in the permeation layer. The DNA at each test site was then hybridized to a mixture of fluorescently labeled wild-type or mutant probes. RESULTS: Assays conditions were established based on the analysis of 700 DNA samples from compound heterozygotes or homozygotes for the nine mutations. The assays were blindly validated on 250 DNA samples previously genotyped by other methods, with complete concordance of results. Alternative multiplexed formats were explored: the combination of multiplex PCR with multiple addressing and/or hybridization allowed analysis of all nine mutations in the same sample on one test site of the chip. CONCLUSIONS: The open flexible platform can be designed by the user according to the local prevalence of mutations in each geographic area and can be rapidly extended to include the remaining mutations causing beta-thalassemia in other regions of the world.

Fluorometry↗
PubMed2004

Protein chip array profiling analysis in patients with severe acute respiratory syndrome identified serum amyloid a protein as a biomarker potentially useful in monitoring the extent of pneumonia.

BACKGROUND: A new strain of coronavirus (CoV) has caused an outbreak of severe acute respiratory syndrome (SARS), with 8098 individuals being infected and 774 deaths worldwide. We carried out protein chip array profiling analysis in an attempt to identify biomarkers that might be useful in monitoring the clinical course of SARS patients. METHODS: We performed surface-enhanced laser desorption ionization time-of-flight mass spectrometry on 89 sera collected from 28 SARS patients, 72 sera from 51 control patients with various viral or bacterial infections, and 10 sera from apparently healthy individuals. RESULTS: Nine significantly increased and three significantly decreased serum biomarkers were discovered in the SARS patients compared with the controls. Among these biomarkers, one (11,695 Da) was identified to be serum amyloid A (SAA) protein by peptide mapping and tandem mass spectrometric analysis. When we monitored the SAA concentrations longitudinally in 45 sera from four SARS patients, we found a good correlation of SAA concentration with the extent of pneumonia as assessed by a serial chest x-ray opacity score. Increased SAA occurred in three of four patients at the time of extensive pneumonia as indicated by high x-ray scores. Over the course of gradual recovery in two patients, as assessed clinically and radiologically, SAA concentrations gradually decreased. In the third patient, the concentrations were initially increased, but were further increased with superimposed multiple bacterial infections. SAA was not markedly increased in the fourth patient, who had low x-ray scores and whose clinical course was relatively mild. CONCLUSIONS: Protein chip array profiling analysis could be potentially useful in monitoring the severity of disease in SARS patients.

Biomarkers↗