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At least 253 records · Page 14Linked to original sources
PubMed2004

[Rapid detection of the genotyping of hepatitis C virus using DNA chip with coloration methods].

OBJECTIVE: To develop a new DNA chip with coloration, which can be used for rapid and economical detection of the genotyping of hepatitis C virus (HCV). METHODS: Probes and primers were designed according to the sequence of HCV 5' non-coding region (5' NCR) to fabricate DNA chip. Experimental group consisted of 60 positive serum samples and control group consisted of 20 negative serum samples. To obtain the aimed gene, then they were hybridized with DNA chip. Finally, the results showed in a nylon film. The results of DNA sequencing of samples were used as the control in double blind experimental. RESULTS: Using DNA chip, HCV was detected in positive of all serum specimens of experimental group and negative in control group. The determination of HCV genotype by DNA chip showed corresponding rate of 96.7% with those by sequence assay. CONCLUSION: It showed higher specialty and sensitivity using DNA chip to detect the genotype of HCV. It would be valuable for the clinical genotyping of HCV

5' Untranslated Regions↗
PubMed1992

Prevalence of radiographic evidence of paint chip ingestion among children with moderate to severe lead poisoning, St Louis, Missouri, 1989 through 1990.

Although experts once believed that ingesting chips of lead-based paint was the major cause of lead poisoning among children, conventional wisdom now holds that lead-contaminated dust and soil are the major routes of exposure. Data from a childhood lead-poisoning treatment clinic were examined to assess the frequency with which children ingest paint chips. For this study, the reports on abdominal radiographs of 90 children with moderate to severe lead poisoning who had received their first chelation treatment during 1989 or 1990 were reviewed. According to a radiologist's evaluation, 13 of 90 abdominal radiographs (14%; 95% confidence interval [CI] 7% to 22%) showed evidence of paint chip ingestion. Of 46 children with blood lead levels greater than or equal to 55 micrograms/dL, 12 (26%) had radiographs that showed paint chips, whereas only 1 (2%) of 44 children with blood lead levels less than 55 micrograms/dL had such radiographs (prevalence ratio = 11.5; 95% CI 1.6 to 84.6). The actual proportion of children with moderate to severe lead poisoning who have consumed leaded-paint chips is likely to be higher than this estimate based on radiographic evidence. While lead-contaminated dust is a major source of lead exposure, ingestion of leaded-paint chips clearly remains an important source of exposure among children with moderate to severe lead poisoning.

Acute Disease↗
PubMed2003

[Preparation and application of gel chip].

A new method for manufacturing three-dimensional gel film-coated chips was described in this paper and its advantages were evaluated by its application. A patch of polyacrylamide gel (15mm x 15mm x 20 microm) was fixed on the glass surface with Bind-Silane treatment, then activated by glutaraldehyde. The aldehyde groups in gel provided reactive sites that allowed covalent immobilization of molecules containing amino groups. Oligonucleotides were mechanically spotted by GMS 417 Arrayer. After hybridization with Cy-3 labeled probes, fluorescence signals of perfect binding can be discriminated from mismatched ones. Compared with two-dimensional glass chip, the capacity of oligonucleotides immobilized on gel film-coated chip is over 100 times. And the gel film-coated chip have lower background and shorter hybridization time. Monoclonal antibodys of cytokine IL-4, IL-5, IL-6, IL-7, ANG, I-309 and VEGF were also immobilized on the gel film-coated chips to make protein microarrays. After incubation with serum of breast cancer patients or normal persons, the microarray reacted with biotin-labeled second antibodys of cytokines and Cy-3-labeled streptavidin sequentially. Results show IL-4, IL-5, I-309 and VEGF of patients have higher expression level than normal persons. This kind of protein microarrays can be potentially helpful to clinical diagnosis. Furthermore different oligonucleotides or proteins can be performed in parallel in a single reaction with minimal amount of binding reagents. Such gel film-coated chips can be used widely in the fabrication of oligonucleotides and proteins microarrays.

Acrylic Resins↗
PubMed2005

[Laboratory on a microfluidic chip].

The recent achievements of microfluidic chip and its applications, based on the works mainly carried out in the authors' lab are reviewed. The chip fabrication capabilities have been extended into design and fabricate chips with higher degree of complexity in different materials, such as quartz, glass, polymethyl methacrylate (PMMA), and polydimethyl siloxane (PDMS). A set of methods for surface modification of micro-channels on such materials have been developed, which results in better reproducibility and higher efficiency in protein and peptide analysis. The use of novel materials for chip fabrication is also under investigation. A series of microfluidic workstations with integrated chip manipulation as well as laser induced fluorescence (LIF), ultraviolet (UV), electrochemical and chemiluminescence detection modules have been developed to attain the abilities of complex microfluidic control and data acquisition schemes. A single cell/single molecule imagining system was built up for dynamic analysis of molecular or cellular events too. Based on the work mentioned above, different functional units, such as membrane, monolithic, isotachophoresis (ITP) etc were set up and integrated. Glycoform separation of turkey ovalbumin in a lectin monolithic column and an electrophoresis channel was performed on an integrated microchip. And a novel technique has been developed that allows for the coupling of ITP and non-gel sieving electrophoresis for protein analysis in a single microchip and resulting in - 50 fold increase of the sensitivity in comparison with the use of gel electrophoresis only. A single molecule detection (SMD) based technique was developed for simultaneously measuring both bulk flow and near-wall flow velocity in the microchannels. And more recently, an SMD based technology was developed for observing molecular interactions at single molecule level. An ultra-rapid microchip electrophoresis method was established for simultaneous determination intracellular reactive oxygen species (ROS) and reduced glutathione (GSH) related to apoptosis and oxidative stress. In an effort to develop a novel microfluidic based drug screening platform, systematic studies on the interaction between granulocyte colony-stimulating factor (G-CSF) and sulfated oligosaccharides were carried out at both molecular and cellular levels. Doxorubicin induced apoptosis of human hepatocellular carcinoma (HepG2) was studied using the integrated microfluidic device with concentration generator. In the application phase, severe acute respiratory syndrome (SARS) diagnosis based on reverse transcription-polymerase chain reaction (RT-PCR) and microfluidic chip electrophoresis (MCE) with 18 cases, methylation analysis of the P16 gene in 159 samples of patients and references for cancer diagnosis and polymorphism analysis of angiotenigen gene in 226 patients and references with essential hypertension are described. Forty-three up to date references are

Animals↗
PubMed2006

[Evaluation of gene chip technology for high risk type human papillomavirus in cervical cancer screening].

OBJECTIVE: To investigate the clinical value of gene chips technology for human papillomavirus (HPV) in cervical cancer screening. METHODS: A population-based cross-sectional screening study was conducted among 1137 women aged 15-59 in a community, Shenzhen city. Hybrid capture 2 (hc2) and gene chip technology were performed to examine the high risk type human papillomavirus in the exfoliated cervical cells. Liquid-based cytology test (LCT) was also performed at the same time. The HPV-positive women with LCT > or = atypical squamous cells of undetermined sign (ASCUS) and the HPV-negative women with LCT > or = low grade squamous intraepithelial lesion (LSIL) underwent biopsy under colposcopy. The pathological results were used as the gold standard to evaluate the two HPV test methods. RESULTS: Totally 122 biopsy specimens were obtained. Pathological examination showed no cervical cancer case, 3 cases of grade III cervical intraepithelial neoplasia (CIN), 11 cases of grade II CIN, 36 cases of grade I CIN, 69 cases of chronic cervicitis and metaplasia of squamous epithelium, and 3 cases of normal cervix. The HPV-positive rate was 14.0% by hc2 and 9.8% by gene chips with a HPV-positive rate by hc2 higher than that by gene chips (P < 0.001) and an mediocre accordance rate between these methods (kappa = 0.498). The. HPV-positive rate increased along with the increase of the grade of cervical lesions (P < 0.05). The sensitivity, specificity, accuracy, positive prevalue, negative prevalue, positive likelihood ratio and negative likelihood ratio of hc2 for high-risk HPV were 100%, 87.1%, 87.3%, 8.8%, 100%, 7.7 and 0.000, respectively; and those of gene chips were 78.6%, 91.1%, 90.9%, 9.9%, 99.7%, 8.8 and 0.235 respectively. CONCLUSION: At present hc2 high risk HPV testing is still the better method for cervical cancer screening. Gene chips technology is able to rival hc2 except that its sensitivity for cervical high grade lesions need be improved.

Adolescent↗
PubMed1994

Membrane topology of aquaporin CHIP. Analysis of functional epitope-scanning mutants by vectorial proteolysis.

CHIP is the archetypal member of the aquaporins, a widely expressed family of membrane water channels. The NH2- and COOH-terminal halves of CHIP are sequence-related, and hydropathy analysis predicted six membrane-spanning domains with five connecting loops (A-E). Here, we determined the membrane topology of CHIP expressed in Xenopus oocytes using biologically active recombinant channels. CHIP is glycosylated at Asn-42, indicating loop A is exofacial. An epitope from the coronavirus E1 glycoprotein was inserted into CHIP and localized to the outer or inner leaflet of the membrane by alpha-chymotrypsin digestion of intact oocytes or inside-out membrane vesicles. The E1 epitope at Thr-120 was protease-sensitive in intact oocytes, indicating that loop C is exofacial. The E1 epitope at Lys-6, Arg-162, or Lys-267 was protease-sensitive in inside-out membrane vesicles, confirming the cytoplasmic location of the NH2 and COOH termini and loop D. Insertions into loops B and E did not produce active water channels, but their cleavage patterns were consistent with inner (loop B) and outer (loop E) leaflet locations. This study indicates that the functional CHIP molecule is a unique structure with two internal repeats oriented 180 degrees to each other within the membrane.

Amino Acid Sequence↗
PubMed2025

A Simple Method to Analyze Context- and Tissue-Specific Cis-Regulatory Modulations of Homeotic (HOX) Genes Using ChIP.

Homeobox genes (HOX), the master regulators, deploy a unique set of target genes to coordinate and orchestrate the spatiotemporal development of an organism. HOX encoded transcriptional factors regulate the expression of target genes by binding to the specific sequences on the genome. Chromatin Immunoprecipitation (ChIP) and Chromatin Immunoprecipitation with Sequencing (ChIP-Seq) are widely used to map and understand specific gene locus and global regulatory regions on the genome. ChIP is a powerful technique of cross-linking the proteins bound to the DNA, fragmenting DNA to the desired size, and pulling them down using specific antibodies to enrich and analyze the protein-bound DNA. Based on the mapping information, a differential ChIP can be performed to understand cis-regulatory modulations at a defined locus by two developmental stages. This chapter describes the differential ChIP used to identify new targets by comparing two different developmental stages simultaneously using Drosophila melanogaster.

Animals↗
PubMed2025

Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations.

ChIP-Seq is used to study DNA-protein interactions, unraveling chromatin states and gene regulatory properties of transcription factors. ChIP-Seq involves immunoprecipitation followed by sequencing using Next-Generation sequencing approaches. The ENCODE consortium provides extensive guidelines for ChIP-Seq analysis. Meanwhile, appropriate QC metrics and knowledge to interpret outcomes are essential for a good ChIP-Seq experiment. This chapter outlines the various QC metrics and analytical tools for ChIP-Seq analysis to provide a better understanding of the results.

Chromatin Immunoprecipitation Sequencing↗
PubMed2006

A multicellular spheroid array to realize spheroid formation, culture, and viability assay on a chip.

We describe a novel multicellular spheroid culture system that facilitates the easy preparation and culture of a spheroid microarray for the long-term monitoring of cellular activity. A spheroid culture device with an array of pyramid-like microholes was constructed in a silicon chip that was equipped with elastomeric microchannels. A cell suspension was introduced via the microfluidic channel into the microstructure that comprised silicon microholes and elastomeric microwells. A single spheroid can be formed and localized precisely within each microstructure. Since the culture medium could be replaced via the microchannels, a long-term culture (of approximately 2 weeks) is available on the chip. Measurement of albumin production in the hepatoma cell line (HepG2) showed that the liver-specific functions were maintained for 2 weeks. Based on the cellular respiratory activity, the cellular viability of the spheroid array on the chip was evaluated using scanning electrochemical microscopy. Responses to four different chemical stimulations were simultaneously detected on the same chip, thus demonstrating that each channel could be evaluated independently under various stimulation conditions. Our spheroid culture system facilitated the understanding of spheroid formation, culture, and viability assay on a single chip, thus functioning as a useful drug-screening device for cancer and liver cells.

Albumins↗
PubMed2006

A disposable on-chip phosphate sensor with planar cobalt microelectrodes on polymer substrate.

Disposable microsensors on polymer substrates consisting of fully integrated on-chip planar cobalt (Co) microelectrodes, Ag/AgCl reference electrodes, and microfluidic channels have been designed, fabricated, and characterized for phosphate concentration measurement in aqueous solution. The planar Co microelectrode shows phosphate-selective potential response over the range from 10(-5) to 10(-2)M in acidic medium (pH 5.0) for both inorganic (KH(2)PO(4)) and organic (adenosine 5'-triphosphate (ATP) and adenosine 5'-diphosphates (ADP)) phosphate compounds. This microfabricated sensor also demonstrates significant reproducibility with a small repeated sensing deviation (i.e. relative standard deviation (R.S.D.)<1%) on a single chip and a small chip-to-chip deviation (i.e. R.S.D.<2.5%). Specifically, while keeping the high selectivity, sensitivity, and stability of a conventional bulk Co-wire electrode, the proposed phosphate sensor yields advantages such as ease of use, cost effectiveness, reduced analyte consumption, and ease of integrating into disposable polymer lab-on-a-chip devices. The capability to sense both inorganic and organic phosphate compounds makes this sensor applicable in diverse areas such as environmental monitoring, soil extract analysis, and clinical diagnostics.

Biosensing Techniques↗
PubMed2005

SPR sensor chip for detection of small molecules using molecularly imprinted polymer with embedded gold nanoparticles.

Molecularly imprinted polymer gel with embedded gold nanoparticle was prepared on a gold substrate of a chip for a surface plasmon resonance (SPR) sensor for fabricating an SPR sensor sensitive to a low molecular weight analyte. The sensing is based on swelling of the imprinted polymer gel that is triggered by an analyte binding event within the polymer gel. The swelling causes greater distance between the gold nanoparticles and substrate, shifting a dip of an SPR curve to a higher SPR angle. The polymer synthesis was conducted by radical polymerization of a mixture of acrylic acid, N-isopropylacrylamide, N,N'-methylenebisacrylamide, and gold nanoparticles in the presence of dopamine as model template species on a sensor chip coated with allyl mercaptan. The modified sensor chip showed an increasing SPR angle in response to dopamine concentration, which agrees with the expected sensing mechanism. Furthermore, the gold nanoparticles were shown to be effective for enhancing the signal intensity (the change of SPR angle) by comparison with a sensor chip immobilizing no gold nanoparticles. The analyte binding process and the consequent swelling appeared to be reversible, allowing one the repeated use of the presented sensor chip.

Gold↗
PubMed2002

On-chip enzymatic assays.

This article reviews different possibilities for conducting enzymatic assays on microchip platforms, along with potential advantages, limitations, and selected examples of such biochips. Enzyme-based chips combine the analytical power and reagent economy of microfluidic devices with the selectivity and amplification features of biocatalytic reactions. "Lab-on-chip" devices thus allow enzymatic assays to be performed more rapidly, easily, and economically. Such assays usually rely on on-chip mixing and reactions (of the substrates and enzymes) in connection to separations (of the substrates or products). The realization of on-chip enzymatic assays thus requires understanding of how enzymatic reactions behave on a small scale and can be interfaced with separation microchips, and how the microfluidics can be tailored to suit the requirements of particular enzymatic assays. The goal is to obtain sufficient reaction times, without compromising the quality of the analytical separation. The versatility of such on-chip enzymatic assays offers great promise for decentralized testing of clinically or environmentally important substrates.

Electrophoresis, Capillary↗
PubMed2004

Effect of initial moisture content and chip size on the bioconversion efficiency of softwood lignocellulosics.

Previous optimization strategies for the bioconversion of lignocellulosics by steam explosion technologies have focused on the effects of temperature, pH, and treatment time, but have not accounted for changes in severity brought about by properties inherent in the starting feedstock. Consequently, this study evaluated the effects of chip properties, feedstock size (40-mesh, 1.5 x 1.5 cm, 5 x 5 cm), and moisture content (12% and 30%) on the overall bioconversion process, and more specifically on the efficacy of removal of recalcitrant lignin from the lignocellulosic substrates following steam explosion. Increasing chip size resulted in an improvement in the solids recovery, with concurrent increases in the water soluble, hemicellulose-derived sugar recovery (7.5%). This increased recovery is a result of a decrease in the "relative severity" of the pretreatment as chip size increases. Additionally, the decreased relative severity minimized the condensation of the recalcitrant residual lignin and therefore increased the efficacy of peroxide fractionation, where a 60% improvement in lignin removal was possible with chips of larger initial size. Similarly, increased initial moisture content reduced the relative severity of the pretreatment, generating improved solids and hemicellulose-derived carbohydrate recovery. Both increased chip size and higher initial moisture content results in a substrate that performs better during peroxide delignification, and consequently enzymatic hydrolysis. Furthermore, a post steam-explosion refining step increased hemicellulose-derived sugar recovery and was most effectively delignified (to as low as 6.5%). The refined substrate could be enzymatically hydrolyzed to very high levels (98%) and relatively fast rates (1.23 g/L/h).

Biotransformation↗
PubMed2006

Chip-on-beads: flow-cytometric evaluation of chromatin immunoprecipitation.

BACKGROUND: Chromatin immunoprecipitation (ChIP) is a widely used technique for the detection of in vivo DNA-protein interactions underlying epigenetic regulation. The standard readout of ChIP is based on semi-quantitative or quantitative PCR measurements; however, the development of alternative platforms with high throughput potentialities is expected to facilitate the introduction of this method into routine diagnostics. METHODS: We have established a flow-cytometry-based alternative for the evaluation of ChIP data. The method is based on the capture of the products of a conventional PCR run to low cycle numbers, on microbeads. RESULTS: In vivo histone H4 acetylation and H3 lysine 4 methylation was detected at the promoter of the tissue transglutaminase type 2 gene. These results were confirmed by QPCR measurements. The levels of modifications decreased significantly upon apoptosis and were accompanied by the down-regulation of TGM2 mRNA expression. CONCLUSIONS: This method that we named ChIP-on-beads, a combination of flow cytometry and conventional PCR, is a reliable and efficient alternative in the quantitative analysis of ChIP results, especially promising when high throughput monitoring of epigenetic markers of diagnostic importance is required. The method is simple enough to be easily implemented in a routine flow-cytometric laboratory.

Acetylation↗
PubMed2004

Rapid analysis of inflammatory cytokines in cerebrospinal fluid using chip-based immunoaffinity electrophoresis.

A chip-based capillary electrophoresis system has been designed for rapidly measuring the concentrations of inflammatory cytokines in the cerebrospinal fluid of patients with head trauma. Isolation of the reactive cytokines was achieved by immunoaffinity capture using a panel of six immobilized antibodies, directly attached to the injection port of the chip. The captured cytokines were labeled in situ with a red light-emitting laser dye and electroeluted into the separation channel. Separation of the isolated cytokines was achieved by electrophoresis in under 2 min with quantification of the resolved peaks being achieved by on-line laser-induced fluorescence and integration of each peak area. Comparison of the results to commercially available high-sensitivity immunoassays demonstrates that the chip-based assay provides a fast, accurate procedure for studying the concentrations of these analytes in complex biological materials. The degree of accuracy and precision achieved by the chip-based CE is comparable to conventional immunoassays, the system being able to analyze between 10-12 samples per hour. With the ever-expanding array of antibodies that are commercially available, this chip-based system can be applied to a wide variety of different analyses.

Antibodies↗
PubMed2004

An integrated method for mutation detection using on-chip sample preparation, single-stranded conformation polymorphism, and heteroduplex analysis.

This work integrates rapid techniques for mutation detection by producing single-stranded DNA and (renatured) double-stranded DNA on-chip, labeling these with fluorescent DNA stains and then performing two complementary methods of mutation detection-single stranded conformation polymorphism (SSCP) analysis and heteroduplex analysis (HA). This involves the denaturation of double-stranded polymerase chain reaction (PCR) product into single-stranded DNA, the mutation analysis of the single-stranded DNA by SSCP and the rehybridized double-stranded DNA by HA. These steps were performed entirely on-chip within several minutes of operation. The combination of these two mutation detection methods on-chip provides a highly sensitive method of mutation detection for either genotyping or screening. Many mutation analysis methods rely upon fluorescently labeled samples from a PCR with fluorescently labeled primers. By labeling on-chip we not only attain improved signal strength, but the method is considerably more versatile. Although we used PCR products in this work, this method could be used to analyze DNA from any source. We believe that this combination of several procedures on a single chip represents a significant step in the development of higher levels of integration upon microfluidic devices.

DNA, Single-Stranded↗
PubMed2005

Static adsorptive coating of poly(methyl methacrylate) microfluidic chips for extended usage in DNA separations.

A simple and robust static adsorptive (dynamic) coating process using 2% hydroxyethylcellulose was developed for surface modification of poly(methyl methacrylate) (PMMA) microfluidic chips for DNA separations, suitable for usage over extended periods, involving hundreds of runs. The coating medium was also used as a sieving matrix for the DNA separations following the coating process. Four consecutive static treatments, by simply filling the PMMA chip channels with sieving matrix once every day, were required for obtaining a stable coating and optimum performance. The performance of the coated chips at different phases of the coating process was studied by consecutive gel electrophoretic separations with LIF detection using a PhiX-174/HaeIII DNA digest sample. The coated chip, with daily renewal of the sieving matrix, showed high stability in performance during a 25-day period of systematic study, involving more than 100 individual runs. The performance of the coated chip also remained almost the same after 3 months of continuous usage, during which over 200 separations were performed. The average precision of migration time for the 603-bp fragment was 1.31% RSD (n = 6) during the 25-day study, with a separation efficiency of 6.5 x 10(4) plates (effective separation length 5.4 cm).

Adsorption↗
PubMed2005

Chiral separations on multichannel microfluidic chips.

Chiral separations of FITC-labeled basic drugs on multichannel microfluidic chips with LIF detector were investigated. A preliminary screening procedure for seven neutral CDs was performed under optimized conditions for chiral separations of three FITC-labeled drugs (baclofen, norfenefrine, and tocainide) on a mono-channel microfluidic chip. According to the results of screening, FITC-baclofen and FITC-norfenefrine as well as two chiral selectors including gamma-CD and dimethyl-beta-CD (DM-beta-CD) were selected as models to perform chiral separations on a two-channel chip. FITC-baclofen enantiomers were separated completely by gamma-CD in one channel, while resolution of FITC-norfenefrine enantiomers was achieved by DM-beta-CD in the other channel in the same run. Furthermore, the feasibility of using one chiral selector to separate multiple chiral samples was studied on a four-channel chip. These results show that multichannel chip has a potential for chiral high-throughput screening.

Baclofen↗