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 811 records · Page 45Linked to original sources
PubMed2001

Analysis of recombinant adenoviruses using an integrated microfluidic chip-based system.

The use of recombinant virus for gene therapy requires rigorous quality control methods to ensure that the viral vector preparations are functional and safe. A viral identity test is performed in which the viral payload, or transgene, is PCR amplified, followed by digestion with restriction enzymes that yields a characteristic "fingerprint." These DNA fragments are typically analyzed by agarose gel electrophoresis. The ethidium bromide-stained gels are photographed or scanned and the results are sufficient for a qualitative or semiquantitative identity confirmation of the viral product. We have investigated the use of an integrated microfluidic chip-based system as a new tool in the quality control testing of a recombinant, adenoviral, gene therapy product. The chip-based method was found to be very sensitive, requiring 100-fold less sample and only one-third the time compared to the agarose gel method. The automated data analysis sizes and quantitates the DNA fragments, thus yielding a more thorough, reproducible, sensitive, and rapid analysis.

Adenoviruses, Human↗
PubMed2002

Adsorption characteristics of bisphenol A onto carbonaceous materials produced from wood chips as organic waste.

Many organic by-products have been discharged by humans, and the development of technology for recycling organic by-products has attracted much interest. In this paper, the techniques for producing carbonaceous adsorbents from an organic by-product and an application to remove endocrine disruptors are described. Wood chips as an organic by-product were carbonized at 873 to 1073 K. The iodine adsorption capacity of the obtained carbonaceous materials increased with increasing carbonization temperature. The amount of bisphenol A adsorbed on the carbonized materials produced from Sugi and Hinoki at a 1073 K carbonization temperature was higher than that of activated carbon. The Freundlich constant, 1/N, of the carbonaceous materials produced from Sugi chips, Sugi sawdust, and Hinoki sawdust was similar to that of the activated carbon. This result indicated that the affinity between bisphenol A and the carbonaceous materials or the activated carbon was similar. Their Freundlich constant, K, was greater than that of the activated carbon. Hence, bisphenol A could be efficiently removed by the carbonaceous materials.

Adsorption↗
PubMed2005

Controlling acrylamide in French fry and potato chip models and a mathematical model of acrylamide formation: acrylamide: acidulants, phytate and calcium.

We previously reported that in potato chip and French fry models, the formation of acrylamide can be reduced by controlling pH during processing steps, either by organic (acidulants) or inorganic acids. Use of phytate, a naturally occurring chelator, with or without Ca++ (or divalent ions), can reduce acrylamide formation in both models. However, since phytate itself is acidic, the question remains as to whether the effect of phytate is due to pH alone or to additional effects. In the French fry model, the effects on acrylamide formation of pH, phytate, and/or Ca++ in various combinations were tested in either blanching or soaking (after blanching) steps. All treatments significantly reduced acrylamide levels compared to control. Among variables tested, pH may be the single most important factor for reducing acrylamide levels, while there were independent effects of phytate and/or Ca++ in this French fry model. We also developed a mathematical formula to estimate the final concentration of acrylamide in a potato chip model, using variables that can affect acrylamide formation: glucose and asparagine concentrations, cut potato surface area and shape, cooking temperature and time, and other processing conditions.

Acids↗
PubMed2005

Pilot study on the impact of potato chips consumption on biomarkers of acrylamide exposure.

Food is assumed to be one major source of acrylamide exposure in the general population. Acrylamide exposure is usually assessed by measuring hemoglobin adducts of acrylamide and its primary metabolite glycidamide as biomarkers. Little is known about the impact of acrylamide in food on biomarkers of acrylamide exposure. Therefore, CDC is conducting a feeding study to investigate the effect of consumption of endogenous acrylamide in food on biomarkers of acrylamide exposure. As part of this study, we performed a pilot study to obtain further information on the magnitude of the changes in biomarker levels after consumption of high amounts of potato chips (21 ounces) over a short period of time (1 week) in non-smokers. After 1 week, biomarkers levels increased up to 46% for acrylamide adducts and 79% for glycidamide adducts. The results indicate that changes in biomarker levels due to consumption of potato chips can be detected. However, because of the design of this pilot study, the observed magnitude of change cannot be. generalized and needs to be confirmed in the main study.

Acrylamide↗
PubMed1987

Bone and joint disorders in the upper extremities of chipping and grinding operators.

X-ray examinations of the wrists, the elbows and the shoulders were carried out on 67 vibration-exposed foundry workers and on 46 comparable referents performing heavy manual work. Both groups had a mean age of 39.6 years. Musculoskeletal symptoms, such as arthralgias of the wrist and elbow joints, muscle pain and decreased muscular force, were found to be significantly increased in the chipping and grinding workers compared with the referents. After adjustment for age, the prevalence of cysts in the metacarpal and carpal bones was almost the same in the two groups, whereas radiological signs of osteoarthritis in the wrist joint were more frequent among the vibration-exposed workers (P less than 0.025). The overall prevalence of radiographic abnormalities in the elbow joint was higher in the vibration group than in the reference group (P less than 0.025). Olecranon spurs were observed in 50.7% of the exposed operators and in 28.2% of the referents (P less than 0.025). No difference in the prevalence of radiological changes in the should could be demonstrated between the populations studied. In both groups injuries of bones and joints were not associated with age. Among the chipping and grinding operators, a slight but not significant trend in the prevalence of skeletal abnormalities with increasing vibration exposure was observed. The results of this study indicate that the foundry workers using vibrating tools were affected with bone and joint disorders in the elbow and, to a lesser extent, in the wrist, which occurred more frequently than was observed in unexposed referents, who performed solely heavy manual activity. Among the vibration-exposed workers, no relationship between radiological changes in the upper limbs and symptoms of vibration white finger was found, pointing out that different pathogenic mechanisms are involved.

Adult↗
PubMed1996

Immobilization of Saccharomyces diastaticus on wood chips for ethanol production.

Saccharomyces diastaticus cells were immobilized onto beech wood chips of different particle size and three pH values. pH values in the range 5.0-6.0, and 1.84-1.92 mm particle size had a positive effect on the immobilization process. The chosen carrier--1.84 mm-sized wood chips adsorbed 150 mg dry cell mass per g dry carrier mass. The Gibbs free energy and the activation energy for the first (monolayer) and second (multilayer) immobilization stages was 4581, 19,090 and 8590 J g mol-1, respectively. The kinetics of immobilized cell systems in ethanol production have been studied in a packed bed-reactor. Ethanol production and the respiration quotient (RQ) were at a maximum at a dilution rate of 0.16/h. The reactor was operated under steady-state conditions for 30 d at the dilution rate 0.16/h.

Bioreactors↗
PubMed2002

On-chip absorption measurements using an integrated waveguide.

Square hollow waveguides are used to integrate measurement of absorption with chip-based electrophoresis. The 50x50 microm liquid channel and 50x50 microm waveguide are etched as a negative pattern into a silicon master and replicated as a positive in poly-dimethylsiloxane (PDMS). The uniform refractive index of the chip prevents guiding by total internal reflection. Instead, light at 488 nm is guided by reflection at the air-PDMS interface. The waveguide has a 60% efficiency over a distance of 3.2 cm. Separation of fluorescein and the dye BODIPY is demonstrated. A detection limit (S/N=3) of 200 microM fluorescein is obtained using a 50 microm pathlength and a simple photocell detector.

Absorption↗
PubMed2004

Lab-on-a-chip systems for biomedical and environmental monitoring.

During the last decade, pocket-sized analytical equipment based on the "lab-on-a-chip" approach has become available. These chips, in combination with portable electronic equipment, are applicable in, for example, "point-of-care" ion analysis of body fluids, forensics, identification of explosives, tracking of pollution in environmental or waste waters, monitoring nutrients in agricultural or horticultural water, controlling quality in food production, or process control in chemical industry. This paper discusses several demonstrator systems with applications in these fields.

Environmental Monitoring↗
PubMed2004

Double-chip protein arrays: force-based multiplex sandwich immunoassays with increased specificity.

Protein assays provide direct access to biologically and pharmacologically relevant information. To obtain a maximum of information from the very smallest amounts of complex biological samples, highly multiplexed protein assays are needed. However, at present, cross-reactions of binding reagents restrict the use of such assays to selected cases and severely limit the potential for up-scaling the technology. Here we describe a double-chip format, which can effectively overcome this specificity problem for sandwich immunoassays. This format consists of a capture array and a reference array with fluorescent labeled detection antibodies coupled to the reference array via DNA duplexes. This format allows for the local application of the labeled detection antibodies onto their corresponding specific spots on the capture array. Here we show that this double-chip format allows for the use of cross-reactive antibodies without generating false positive signals, and an assay for the parallel detection of seven different cytokines was set up. Even without further optimization, the dynamic range and the limit of detection for interleukin 8 were found to be comparable to those obtained with other types of multiplexed sandwich immunoassays.

Animals↗
PubMed2005

DNA separation with low-viscosity sieving matrix on microfabricated polycarbonate microfluidic chips.

Microfluidic devices have been fabricated on polycarbonate (PC) substrates by use of a hot embossing method using a silicon master template. By adding auxiliary lines around the functional channel on the silicon master, its lifetime was significantly prolonged and the bonding strength of the PC cover plate to the microfluidic chip was greatly improved. More than 300 polycarbonate microfluidic chips have been replicated with the same silicon mold. CE separation of Phi X-174/HaeIII DNA restriction fragments, with high resolution efficiency and good reproducibility, was achieved on these devices using the low-viscosity sieving matrix HPMC-50. Temperature was found to have a significant effect on separation efficiency.

Bacteriophage phi X 174↗
PubMed2005

Feature characterization of microfabricated microfluidic chips by PDMS replication and CCD imaging.

This paper presents a new approach for the metrological characterization of microfabricated features on microfluidic chips, based on a combination of poly(dimethylsiloxane) (PDMS) replication and charge-coupled device (CCD) imaging. A PDMS replicate was cast from the original chip sample, and a 2-mm thick sample slice was cut from the replica at the cross-section to be studied. The digital image of the revealed structural profile was captured by a CCD camera under a microscope, and the image was processed using specially-developed algorithms for CCD image calibration and edge detection. Depth and width measurements obtained using the method agreed well with those gained using a stylus profiler and universal measuring microscope, with a deviation of below 0.9 mum, while profile distortions of deeper structures using stylus profilers were avoided. The method is reliable, non-destructive, and cheap and simple to implement in any analytical laboratory.

Journal Article↗
PubMed2005

Determination of reactive oxygen species in single human erythrocytes using microfluidic chip electrophoresis.

Reactive oxygen species (ROS) are known to not only mediate the damage of cellular constituents but also to regulate cellular signaling. Analysis of ROS is essential if we wish to understand the mechanisms of cellular alterations. In this paper, a microfluidic chip-based approach to the determination of ROS in single erythrocyte was developed by using a simple crossed-channel glass chip with integrated operational functions, including cell sampling, single cell loading, docking, lysing, and capillary electrophoretic (CE) separation with laser-induced fluorescence (LIF) detection. Non-fluorescent dihydrorhodamine 123 (DHR 123), which can be oxidized intracellularly by ROS to the fluorescent rhodamine 123 (Rh 123), was used as the fluorogenic reagent. The effect of pH on the migration time of Rh 123 and detection sensitivity was discussed. The present method minimized dilution of intracellular ROS during reaction with DHR 123 and determination. As a result, an extremely low detection limit of 0.8 amol has been achieved. The time required for complete analysis of one human erythrocyte was less than 3 min. A migration time precision of 4.1% RSD was obtained for six consecutively-injected cells. Upon stimulation with 4 mmol/l H2O2 for 10 min, the intracellular ROS concentration was found to increase on average by about a factor of 8.4.

Calibration↗
PubMed2001

Chips and Qi: microcomponent-based analysis in traditional Chinese medicine.

Over the last 50 years or so Traditional Chinese medicine (TCM) has been subject to intensive basic and clinical research. Although the effectiveness and remarkable safety of TCM have been documented after controlled clinical studies, there are several herbal and animal parts that are toxic or difficult to identify. DNA polymorphism-based assays have recently been developed for the identification of herbal medicines. In this approach, small amounts of DNA are amplified by the polymerase chain reaction and the reactions products are analyzed by gel electrophoresis, sequencing, or hybridization with species-specific probes. With the DNA based identification of TCM materials as an example, chip-based analytical micro devices were developed with the goal of fabricating an integrated device that will enable sample preparation, amplification, and analysis on a single microchip-based device ("lab-on-a-chip"). The application of a silicon-based polymerase chain reaction microreactor and a DNA microarray for the DNA sequence-based identification of toxic medicinal plants is reported here.

DNA, Plant↗
PubMed2001

Lab-on-a-chip sample preparation using laminar fluid diffusion interfaces--computational fluid dynamics model results and fluidic verification experiments.

Microfluidic structures for the generation of laminar fluid diffusion interfaces (LFDIs) for sample preparation and analysis are discussed. Experimental data and the results of fluid modeling are shown. LFDIs are generated when two or more streams flow in parallel in a single microfluidic structure without any mixing of the fluids other than by diffusion of particles across the diffusion interface. It has been shown that such structures can be used for diffusion-based separation and detection applications. The method has been applied to DNA desalting, the extraction of small proteins from whole blood samples, and the detection of various constituents in whole blood, among other examples. In this paper the design and manufacture of self-contained microfluidic cartridges for the extraction of small molecules from a mixture of small and large molecules by diffusion is demonstrated. The cards are operated without any external instrumentation, and use hydrostatic pressure as the driving force. The performance of the cartridges is illustrated by separating fluorescein from a mixture of fluorescein and dextran of molecular weight 2 x 10(6). In a single pass, 98.6% of dextran was retained in the product whereas 43.1% of fluorescein was removed. The method is adjustable for different separation requirements, and computational fluid dynamics (CFD) models are shown that demonstrate the tuning of various microfluidic parameters to optimize separation performance. Other applications of LFDIs for establishment of stable concentration gradients, and the exposure of chemical constituents or biological particles to these concentration gradients are shown qualitatively. Microfluidic chips have been designed for high-throughput screening applications that enable the uniform and controlled exposure of cells to lysing agents, thus enabling the differentiation of cells by their sensitivity to specific agents in an on-chip cytometer coupled directly to the lysing structure.

Chemistry Techniques, Analytical↗
PubMed2001

Multi-layer microfluidic glass chips for microanalytical applications.

A new, versatile architecture is presented for microfluidic devices made entirely from glass, for use with reagents which would prove highly corrosive for silicon. Chips consist of three layers of glass wafers bonded together by fusion bonding. On the inside wafer faces a network of microfluidic channels is created by photolithography and wet chemical etching. Low dead-volume fluidic connections between the layers are fabricated by spark-assisted etching (SAE), a computer numerical controlled (CNC)-like machining technique new to microfluidic system fabrication. This method is also used to form a vertical, long path-length, optical cuvette through the middle wafer for optical absorbance detection of low-concentration compounds. Advantages of this technique compared with other, more standard, methods are discussed. When the new glass-based device for flow-injection analysis of ammonia was compared with our first-generation chips based on silicon micromachining, concentration sensitivity was higher, because of the longer path-length of the optical cuvette. The dependence of dispersion on velocity profile and on channel cross-sectional geometry is discussed. The rapid implementation of the devices for an organic synthesis reaction, the Wittig reaction, is also briefly described.

Journal Article↗
PubMed2006

Novel immunoassay for carcinoembryonic antigen based on protein A-conjugated immunosensor chip by surface plasmon resonance and cyclic voltammetry.

In this study, an immunosensor chip utilizing surface plasmon resonance (SPR) and cyclic voltammetry (CV) was fabricated for detecting carcinoembryonic antigen (CEA). Specifically, we applied in parallel an SPR instrument and a CV device to monitor the assembly of carcinoembryonic antibody (anti-CEA) on a protein A-conjugated surface and the subsequent ligand reaction. The immunosensor chips were constructed by various concentrations of protein A. To determine the surface characteristics of different self-assembly monolayers (SAMs), several quantitative and kinetic measurements were carried out. The extent of immobilization of anti-CEA and the immune response of anti-CEA antibody against CEA were measured using the SPR instrument and CV device. The terminal functional groups of protein A have different effects on the adsorption and covalent binding of immunoprotein depending on the steric hindrance. Through the parallel measurements, we demonstrate that SPR and CV are sensitive to measure the antigen-antibody binding capacity.

Biosensing Techniques↗
PubMed2002

Reconstruction of suboccipital craniectomy with autologous bone chips.

BACKGROUND: In patients submitted to suboccipital craniectomy in whom the bone is not repositioned, there may be a significant aesthetic defect due to lack of bone tissue, sometimes accompanied by paresthaesia and painful symptoms. METHOD: In 15 patients submitted to suboccipital craniectomy, the bone chips were repositioned during wound closure. FINDINGS: At a mean follow up of 19 months (from 6 to 36 months), 2 patients (13%) complained of mild wound discomfort or occasional local pain. Twelve patients underwent control CT-scan. In three cases (25%) the bone fragments had been partly reabsorbed whereas in the other 9 (75%) they either formed a thin (4 patients) or consistent (5 patients) bony wall, with variable degree of adaptation to the contour of the contralateral occipital bone. The best cosmetic and functional results were obtained in young patients in whom the cerebellar parenchyma was well-preserved, as opposed to those in whom a CSF collection had replaced areas of cerebellar tissue. INTERPRETATION: In the majority of cases in whom an osteoplastic suboccipital craniotomy is not possible, repositioning of the bone chips from suboccipital craniectomy is able to restore a bone table, thus allowing morphological and functional recovery of the occipital region.

Arnold-Chiari Malformation↗
PubMed2002

[Opportunities and chances for tissue chip microarrays in head and neck surgery. A novel technique for the rapid evaluation of potentially novel biomarkers].

Oral squamous cell carcinomas (OSCC) are malignant tumors with a poor prognosis and low long-term survival rates, even when using modern adjuvant and neoadjuvant therapy forms in addition to surgery. For the clinical estimation of each tumor, it is necessary to define stage-dependent molecular and/or cellular parameters as it is known that OSCC develop along a multistep pathway including the loss of tumor suppressor genes and the amplification of oncogenes which result in changes in protein expression. In order to establish a reliable pattern of molecular and cellular biomarkers, a large number of tumor specimens from different stages of the disease need to be analysed. In this study, biopsies of a collective of 293 OSCC in different stages were screened with the novel technique of tissue chip microarrays by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC). FISH-analysis was performed on the oncogene cyclin D1 and IHC-analysis on the proteins cyclin D1, p53, p16, cdk4, bcl2, mdm2 and rb. Tissue chip technology was shown to facilitate rapid screening for molecular and cellular alterations in different stages of OSCC and revealed reliable and reproducible results that may allow the definition of a multistep pathway model for tumor progression in OSCC.

Aged↗