Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “ChIP”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,207 records · Page 67Linked to original sources
PubMed2005

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays.

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiments showed that the elongation temperature of 50 degrees C and the Mg(2+) concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.

Carbocyanines↗
PubMed2006

Human papillomaviruses in oral squamous cell carcinoma and pre-cancerous lesions detected by PCR-based gene-chip array.

Human papillomavirus (HPV) infection is a significant risk factor for uterine cervical carcinoma. Many studies have also demonstrated the presence of HPV in oral epithelia tissue, but the role of HPV infection in oral squamous cell carcinoma (OSCC) is still controversial. The aim of this study was to determine the frequency and type of HPV in OSCC and oral pre-cancerous lesions. DNA samples were collected by cytobrushing from 51 patients with OSCC, 46 with oral pre-cancerous lesions and 90 normal controls. Nested polymerase chain reaction and gene-chip arrays were used to identify the HPV types in the samples. In pre-cancerous lesions, there was a higher frequency of HPV of any type (14/46, OR = 2.844, CI = 1.186-6.816, P = 0.0216) and of low-risk HPV types (9/46, OR = 5.529, CI = 1.597-19.14, P = 0.0096) than in control samples. The prevalence of high-risk types was significantly higher in OSCC than in control lesions (11/51 vs 8/90, OR = 2.819, CI = 1.051-7.558, P = 0.0420) but this was not the case for HPV of any type (13/51 vs 12/90, OR = 2.244, CI = 0.9266-5.337, P = 0.1066). High-risk HPV types are prevalent in OSCC and may play a role in its progression, while low-risk types are associated with oral pre-cancerous lesions.

Adult↗
PubMed2004

DNA microarrays: from structural genomics to functional genomics. The applications of gene chips in dermatology and dermatopathology.

The human genome project was successful in sequencing the entire human genome and ended earlier than expected. The vast genetic information now available will have far-reaching consequences for medicine in the twenty-first century. The knowledge gained from the mapping and sequencing of human genes on a genome-wide scale--commonly referred to as structural genomics--is prerequisite for studies that focus on the functional aspects of genes. A recently invented technique, known as gene chip, or DNA microarray, technology, allows the study of the function of thousands of genes at once, thereby opening the door to the new field of functional genomics. At its core, the DNA microarray utilizes a unique feature of DNA known as complementary hybridization. As such, it is not different from Southern (DNA) blot or northern (RNA) blot hybridizations, or the polymerase chain reaction, with the exception that it allows expression profiling of the entire human genome in a single hybridization experiment. The article highlights the principles, technology, and applications of DNA microarrays as they pertain to the field of dermatology and dermatopathology. The most important applications are the gene expression profiling of skin cancer, especially of melanoma. Other potential applications include gene expression profiling of inflammatory skin diseases, the mutational analysis of genodermatoses, and polymorphism screening, as well as drug development and chemosensitivity prediction. cDNA microarrays will shape the diagnostic approach of the dermatology and the dermatopathology of the future and may lead to new therapeutic options.

Dermatology↗
PubMed2005

Capture of a monoclonal antibody and prediction of separation conditions using a synthetic multimodal ligand attached on chips and beads.

A synthetic ligand called 2-mercapto-5-benzimidazolesulfonic acid has been successfully used for the specific chromatographic capture of antibodies from a cell culture supernatant. Adsorption occurred at physiological ionic strength and pH range between 5.0 and 6.0, with some binding capacity variations within this pH range: antibody uptake increased when the pH decreased. With very dilute feedstocks, as was the case with the cell culture supernatant under investigation, it was found that the pH had to be slightly lowered to get a good antibody sorption capacity. To optimize separation conditions, a preliminary study was made using ProteinChip Arrays that displayed the same chemical functionalities as the resin. Arrays were analyzed using SELDI-MS. By this mean, it was possible to cross-over simultaneously different pH conditions at the adsorption and the desorption steps. Best conditions were implemented for preparative separation using regular lab-scale columns. At pH 5.2, antibody adsorption was not complete, while at pH 5.0 the antibody was entirely captured. pH 9 was selected at elution, rather than pH 8.0 or 10.0, and resulted in a complete desorption of antibodies from the column. Benefits of the prediction of separation conditions of antibodies on MBI beads using SELDI-MS were a significant reduction in analysis time and in sample volume. This was possible because the separation of IgG on the chip surface did mimic very well the separation on beads.

Adsorption↗
PubMed2006

Electrocardiogram on a chip: overview and first experiences of an electrocardiogram manufacturer of medium size.

The integration of an electrocardiogram (ECG) device into a chip is already well known in the field of implanted devices, such as pacemakers. For noninvasive electrocardiology, this approach has not been used on a broad scale commercially. The extension of electrocardiology to telemetry, home care, and special applications as in magnetic resonance imaging has spawned a new interest in highly miniaturized ECG devices. In our company, we are aiming for using highly integrated devices exactly in these fields. On one hand, the home monitoring market ("eHealth," "pHealth") requires small and lightweight devices ("ECG in an electrode"); on the other hand, the use of an ECG device within a hostile environment as in an magnetic resonance imaging machine with strong electromagnetic fields requires small dimensions of the device. Of these 2 fields, the one of home monitoring is the most promising. There is a large population in need of such monitoring (eg, patients with congestive heart failure), and the cost issue in medical care drives the market in this direction. Projects in both fields will be presented as well as the first experiences as a middle-sized manufacturer in trying to produce an integrated ECG "device."

Biotechnology↗
PubMed2006

Insuring children or insuring families: do parental and sibling coverage lead to improved retention of children in Medicaid and CHIP?

Recent research indicates that 3 million children leave Medicaid or the Children's Health Insurance Program (CHIP) each year and become uninsured, despite continuing eligibility. This paper explores the effect of family coverage on drop-out among children in these two programs, using instrumental variables to address the endogeneity of parental and sibling coverage in Medicaid/CHIP. Using the Current Population Survey March Supplement (1999-2004), I find that having a parent (primarily a mother) or sibling in public insurance is associated with a significantly lower risk of drop-out; after instrumenting with parental and sibling eligibility, only parental coverage remains a significant predictor of retention. I conclude that policy attempts to expand health insurance to the 8.5 million uninsured children in the U.S. would be much more effective if they covered parents and children in the same program.

Adolescent↗
PubMed2005

A novel high-throughput automated chip-based nanoelectrospray tandem mass spectrometric method for PAMPA sample analysis.

Parallel artificial membrane permeability assay (PAMPA) has recently gained popularity as a novel, high-throughput assay capable of rapidly screening compounds for their permeability characteristics in early drug discovery. The analytical techniques typically used for PAMPA sample analysis are HPLC-UV, LC/MS or more recently UV-plate reader. The LC techniques, though sturdy and accurate, are often labor and time intensive and are not ideal for high-throughput. On the other hand, UV-plate reader technique is amenable to high-throughput but is not sensitive enough to detect the lower concentrations that are often encountered in early drug discovery work. This article investigates a novel analytical method, a chip-based automated nanoelectrospray mass spectrometric method for its ability to rapidly analyze PAMPA permeability samples. The utility and advantages of this novel analytical method is demonstrated by comparing PAMPA permeability values obtained from nanoelectrospray to those from conventional analytical methods. Ten marketed drugs having a broad range of structural space, physico-chemical properties and extent of intestinal absorption were selected as test compounds for this investigation. PAMPA permeability and recovery experiments were conducted with model compounds followed by analysis by UV-plate reader, UV-HPLC as well as the automated nanoelectrospray technique (nanoESI-MS/MS). There was a very good correlation (r(2) > 0.9) between the results obtained using nanoelectrospray and the other analytical techniques tested. Moreover, the nanoelectrospray approach presented several advantages over the standard techniques such as higher sensitivity and ability to detect individual compounds in cassette studies, making it an attractive high-throughput analytical technique. Thus, it has been demonstrated that nanoelectrospray analysis provides a highly efficient and accurate analytical methodology to analyze PAMPA samples generated in early drug discovery.

Automation↗
PubMed2005

FISH and chips: marine bacterial communities analyzed by flow cytometry based on microfluidics.

To unveil the structure of natural marine pelagic bacterial communities, PCR-based techniques as well as fluorescence in situ hybridizations (FISH) were successfully performed in the past. Using fluorescence microscopes or confocal laser scanning microscopes (CLSM) for the analysis of FISH experiments, it was possible to differentiate bacterial communities, but most attempts to combine flow cytometry and FISH for this purpose have failed till now. Here we present a successful analysis of FISH experiments of natural marine pelagic bacterial communities using a flow cytometer based on microfluidics (Agilent 2100 bioanalyzer). Marine water samples were enriched on polycarbonate filters and hybridized with Cy5 labeled gene probes of different phylogenetic depth. Bacteria were detached from the filters and subsequently analyzed in the Cell Chip of the Agilent 2100 Bioanalyzer. Samples were counter-stained using SYTOX. In all samples the EUB338 positive signals could be clearly differentiated from those of the NON probe. Furthermore a dominance of alpha-protebacteria (as indicated by the probes ALF968 and G rB) could be observed. Microfluidics based flow cytometry is a promising technique for the analysis of natural bacterial communities from the marine environment.

Bacteria↗
PubMed2006

A DNA chip-based spoligotyping method for the strain identification of Mycobacterium tuberculosis isolates.

The clinical efficacy of a spoligotyping method for discriminating Mycobacterium tuberculosis strains was evaluated. Among the strains other than Beijing or Beijing like family, 30 different spoligotypes out of 39 strains were produced, which included 4 strains not having IS6110 sequence. The oligonucleotide chip-based spoligotyping technique is useful for early screening and detection of clonal proximity of M. tuberculosis isolates.

DNA Fingerprinting↗
PubMed2004

Retrograde transport of the glucocorticoid receptor in neurites requires dynamic assembly of complexes with the protein chaperone hsp90 and is linked to the CHIP component of the machinery for proteasomal degradation.

Here, we have used a chimera of green fluorescent protein (GFP) and the glucocorticoid receptor (GR) to study retrograde movement of a model soluble (i.e., non-vesicle-associated) protein in axons and dendrites of cultured NT2-N neurons. It is known that in non-neuronal cells, the GFP-GR moves from cytoplasm to the nucleus in a steroid-dependent manner by a rapid, hsp90-dependent mechanism. When rapid movement is inhibited by geldanamycin (GA), a specific inhibitor of the protein chaperone hsp90, the GFP-GR translocates slowly to the nucleus by diffusion. Here we show that GFP-GR expressed in hormone-free neurons is localized in both cytoplasm and neurites, and upon treatment with dexamethasone (DEX), it moves to the nucleus. In neurites, movement by diffusion is not possible, and we show that movement of the GFP-GR from neurites is blocked by geldanamycin, suggesting that the hsp90-dependent movement machinery is required for retrograde movement. In cells treated with both dexamethasone and geldanamycin, the GFP-GR becomes concentrated in fluorescent globules located periodically along the neurites. Carboxyl terminus of Hsc70-interacting protein (CHIP), the E3 ubiquitin ligase for the GR, also concentrates in the same loci in a steroid-dependent and geldanamycin-dependent manner. If geldanamycin is removed, the GFP-GR exits the globules and continues its retrograde movement. However, in the continued presence of geldanamycin, the GFP-GR in the globules undergoes proteasomal degradation, suggesting that the globules function as degradasomes. This is the first evidence for a linkage between receptor trafficking along neurites and receptor degradation by the proteasome.

Axons↗
PubMed2006

Gene-gene interaction analysis of personality traits in a Japanese population using an electrochemical DNA array chip analysis.

It has been suggested that genes involved in the central dopaminergic pathway may contribute to personality traits. However, the results of association studies for these genes have not been consistent. The present study investigated the relationship between the specific polymorphisms of MAO-A, COMT, DRD2, DRD3 and personality traits in Japanese women using a novel genotyping method involving electrochemical DNA array (ECA) chip analysis. Single marker association analysis for each mutation revealed no significant association between scores for Neuroticism Extraversion Openness-Five Factor Inventory (NEO-FFI) items. Gene-gene interaction analysis showed that a MAO-A 30-bp repeatxCOMT (Val158Met)xDRD3 (Ser9Gly) had a marginally significant association with Agreeableness (P=0.0547). The present results suggest that a combination of polymorphisms of MAO-A, COMT, and DRD3 might affect personality traits in Japanese women.

Adolescent↗
PubMed2006

Characterization of mRNA species that are associated with postsynaptic density fraction by gene chip microarray analysis.

We previously reported the partial identification by random sequencing of mRNA species that are associated with the postsynaptic density (PSD) fraction prepared from the rat forebrain [Tian et al., 1999. Mol. Brain Res. 72, 147-157]. We report here further characterization by gene chip analysis of the PSD fraction-associated mRNAs, which were prepared in the presence of RNase inhibitor. We found that mRNAs encoding various postsynaptic proteins, such as channels, receptors for neurotransmitters and neuromodulators, proteins involved in signaling, scaffold and adaptor proteins and cytoskeletal proteins, were highly concentrated in the PSD fraction, whereas those encoding housekeeping proteins, such as enzymes in the glycolytic pathway, were not. We extracted approximately 1900 mRNA species that were highly concentrated in the PSD fraction. mRNAs related to certain neuronal diseases were also enriched in the PSD fraction. We also constructed a cDNA library using the PSD fraction-associated mRNAs as templates, and identified 1152 randomly selected clones by sequencing. Our data suggested that the PSD fraction-associated mRNAs are a very useful resource, in which a number of as yet uncharacterized mRNAs are concentrated. Identification and functional characterization of them are essential for complete understanding of synaptic function.

Animals↗
PubMed2005

Detection of immunotoxicity using T-cell based cytokine reporter cell lines ("Cell Chip").

Safety assessment of chemicals and drugs is an important regulatory issue. The evaluation of potential adverse effects of compounds on the immune system depends today on animal experiments. An increasing demand, however, exists for in vitro alternatives. Cytokine measurement is a promising tool to evaluate chemical exposure effects on the immune system. Fortunately, this type of measurement can be performed in conjunction with in vitro exposure models. We have taken these considerations as the starting point to develop an in vitro method to efficiently screen compounds for potential immunotoxicity. The T-cell lymphoma cell line EL-4 was transfected with the regulatory sequences of interleukin (IL)-2, IL-4, IL-10, interferon (IFN)-gamma or actin fused to the gene for enhanced green fluorescent protein (EGFP) in either a stabile or a destabilised form. Consequently, changes in fluorescence intensity represent changes in cytokine expression with one cell line per cytokine. We used this prototype "Cell Chip" to test, by means of flow cytometry, the immunomodulatory potential of 13 substances and were able to detect changes in cytokine expression in 12 cases (successful for cyclosporine, rapamycin, pentamidine, thalidomide, bis(tri-n-butyltin)oxide, house dust mite allergen (Der p I), 1-chloro-2,4-dinitrobenzene, benzocaine, tolylene 2,4-diisocyanate, potassium tetrachloroplatinate, sodium dodecyl sulphate and mercuric chloride; unsuccessful for penicillin G). In conclusion, this approach seems promising for in vitro screening for potential immunotoxicity, especially when additional cell lines besides T-cells are included.

Animals↗
PubMed2005

Fluorescent Cell Chip a new in vitro approach for immunotoxicity screening.

The Fluorescent Cell Chip (FCC) has been developed specifically for immunotoxicity screening of chemical compounds. This in vitro test is based on a panel of genetically modified reporter cell lines that regulate the expression of fluorescent protein in the same way as they regulate expression of cytokines. Thus, changes in fluorescence intensity represent changes in cytokine expression. Consequently, this technique conforms to efficiency expected from high throughput screening assay. In a pre-validation effort we analyzed 46 compounds. The experimental protocol employed five reporter cell lines derived from murine EL-4 T cells. Reporter cells were exposed to tested chemicals on a 96 well plate and analyzed for EGFP-mediated fluorescence using automated flow cytometric assay. Tested compounds reproducibly generated compound-specific patterns of changes in fluorescence that allows for the hierarchical clustering of their expected activities based on pattern similarity analysis. Resultant classification revealed correlation with available in vivo immunotoxicity data. In conclusion, FCC is a new promising approach for in vitro screening of chemicals for their immunotoxicity.

Animals↗
PubMed2005

Protective effect of endotoxin preconditioning in pancreas: analysis with DNA chip arrays.

Recently we demonstrated a protective effect of endotoxin preconditioning 24 hours before pancreatic ischemia-reperfusion injury, which has also been described for other organs. The mechanisms underlying this phenomenon, such as differential gene expression, are poorly investigated. We chose to approach this question by investigating differential gene expression in the rat pancreas over the time course of endotoxin pretreatment. Male Wistar rats (5 groups, 5 animals per group) were pretreated with endotoxin intraperitoneally (1 mg/kg of body weight). After treatment at 30 minutes, and at 3 and 24 hours the pancreas was removed. Untreated animals and animals with injection of saline solution served as controls. After RNA isolation, RNA was pooled and hybridized to Affymetrix chips to measure the relative mRNA levels of 7000 genes and 1000 expression sequence tags. Three hours after administration of endotoxin there was an activation of proinflammatory transcription factors and other proinflammatory genes. After 24 hours there was a clear decrease of these proinflammatory genes, but a remaining and increasing upregulation of important antiapoptotic genes, antiproteases, and other probably protective genes. There was also a significant upregulation of complement factors. It was surprising that heat-shock proteins and other typical immediate early genes of the AP-1 complex were not upregulated. Our data show that 24 hours after endotoxin stress there is a regulation of a network of genes that represents a multifaceted preconditioning. As most important factors, inhibition of apoptosis and antiproteatic strategies are identified. Heat-shock proteins seem to play no important role in the mechanism of endotoxin preconditioning.

Animals↗
PubMed2004

Development of a SAW duplexer with one-chip isolation circuits.

We propose new structures of one-chip type SAW duplexers where Tx and Rx SAW ladder filters as well as isolation networks are fabricated together on a single 36 degrees LiTaO(3) piezoelectric substrate. The new SAW duplexer can overcome the difficulty in fabrication of conventional SAW duplexers while providing the performance matching that of conventional duplexers. Validity of the structure is verified through numerical simulation and experiments.

Journal Article↗
PubMed2004

A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips.

A comparison study of short SAGE versus GeneChip and long SAGE was conducted to determine if data were interchangeable between the techniques. Although SAGE and Affymetrix chip expression levels showed a significant correlation using the set of genes for which there was reliable and unambiguous mapping from tag-to-gene identification, correlation coefficients were low (0.51 for the Spearman's correlation coefficient with p < 0.0001). A quantitative analysis comparing the use of 10-bp SAGE tags to 17-bp SAGE tags indicated that the short SAGE technology was more efficient at identifying differentially expressed tags. However, 4-7% of the 10-bp tags were redundancies that could have been resolved by long SAGE and 10-20% of the short SAGE tags had no obvious match to currently annotated human transcript sequences.

DNA, Complementary↗
PubMed1998

Coronary risk reduction through intensive community-based lifestyle intervention: the Coronary Health Improvement Project (CHIP) experience.

Vigorous cholesterol lowering with diet, drugs, or a combination has been shown to slow, arrest, or even reverse atherosclerosis. Residential lifestyle intervention programs have successfully lowered serum cholesterol levels and other coronary risk factors, but they have the disadvantages of high cost and difficulty with long-term adherence. Community-based risk-reduction programs have the potential to effect change at low cost and improve long-term adherence. To assess the effectiveness of, and to develop a model for, such programs, the community-based Coronary Health Improvement Project (CHIP) was developed in Kalamazoo, Michigan. In the intensive (30-day, 40-hour), hospital-based educational program, participants are encouraged to exercise 30 minutes a day and to embrace a largely unrefined plant-food-centered diet that is high in complex carbohydrates and fiber; very low in fat, animal protein, sugar, and salt; and virtually free of cholesterol. A total of 304 enrollees in the first program were at elevated risk of coronary artery and related diseases: 70% were > or =10% above their ideal weight, 14% had diabetes, 47% had hypertension, and 32% had a history of coronary artery disease. Of the enrollees, 288 "graduated" from the program (123 men, 165 women; mean age was 55+/-11 years). Various markers of disease risk, including serum blood lipids and fasting blood glucose concentrations, were measured before and after the program. At 4 weeks, overall improvements in the participants' laboratory test results, blood pressures, weights, and body mass indexes were highly significant (p <0.001). Triglyceride levels decreased significantly (p <0.05) in participants who had elevated triglyceride levels (>200 mg/dL in men, 200-299 mg/dL in women).

Blood Glucose↗