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 1,333 records · Page 74Linked to original sources
PubMed2004

Acoustic control of suspended particles in micro fluidic chips.

A method to separate suspended particles from their medium in a continuous mode at microchip level is described. The method combines an ultrasonic standing wave field with the extreme laminar flow properties obtained in a silicon micro channel. The channel was 750 microm wide and 250 microm deep with vertical side walls defined by anisotropic wet etching. The suspension comprised "Orgasol 5 microm" polyamide spheres and distilled water. The channel was perfused by applying an under pressure (suction) to the outlets. The channel was ultrasonically actuated from the back side of the chip by a piezoceramic plate. When operating the acoustic separator at the fundamental resonance frequency the acoustic forces were not strong enough to focus the particles into a well defined single band in the centre of the channel. The frequency was therefore changed to about 2 MHz, the first harmonic with two pressure nodes in the standing wave, and consequently two lines of particles were formed which were collected via the side outlets. Two different microchip separator designs were investigated with exit channels branching off from the separation channel at angles of 90 degrees and 45 degrees respectively. The 45 degrees separator displayed the most optimal fluid dynamic properties and 90% of the particles were gathered in 2/3 of the original fluid volume.

Acoustics↗
PubMed2004

Principles of droplet electrohydrodynamics for lab-on-a-chip.

Electrically controlled droplet-based labs-on-a-chip operate under the principles of electro-capillarity and dielectrophoresis. The microfluidic mechanics of manipulating electrified droplets are complex and not entirely understood. In this article, we analyse these operating principles, especially electrowetting on dielectric (a form of electro-capillarity) and dielectrophoresis, under a unified framework of droplet electrohydrodynamics. We differentiate them by their electric origins and their energy transduction mechanisms. Our study shows that both electrowetting on dielectric and dielectrophoresis are effective for droplet generation and manipulation. In addition, our study demonstrates: (1) the presence of a wetting contribution to dielectrophoresis; and (2) contact angle reduction is merely an observable consequence of, not a condition for, the occurrence of electrowetting on dielectric. Simulations are used extensively in this article to illustrate device operation, to expose underlying physics, and to validate our conclusions. Simulations of electrically driven droplet generation, droplet translocation, droplet fusion, and droplet fission are presented.

Electrophoresis, Capillary↗
PubMed2004

Microfluidic channel fabrication in dry film resist for production and prototyping of hybrid chips.

Microfluidic networks are patterned in a dry film resist (Ordyl SY300/550) that is sandwiched in between two substrates. The technique enables fabrication of complex biochips with active elements both in the bottom and the top substrate (hybrid chips). The resist can be double bonded at relatively low temperatures without the use of extra adhesives. A postbake transfers the resist into a rigid structure. The resist is qualified in terms of resolution, biocompatibility and fluidic sealing. Fabrication in both a fully equipped cleanroom setting as well as a minimally equipped laboratory is described. The technique is applied for dielectrophoresis-based cell separation systems and a fuel cell reaction chamber with micropillars. The dry film resist can be considered a cheap and fast alternative to SU-8.

Journal Article↗
PubMed2005

Gentle cell trapping and release on a microfluidic chip by in situ alginate hydrogel formation.

Microfluidic devices are increasingly used to perform biological experiments on a single-cell basis. However, long-term stability of cell positions is still an issue. A novel biocompatible method for cell entrapment and release on a microchip is presented. It is based on the controlled formation of an alginate hydrogel by bringing two laminar flows of alginate and calcium ions in the range of 2 mM to 40 mM into contact. The resulting growth of a gel bar is used to enclose and immobilize yeast cells. Adding ethylenediaminetetraacetic acid (EDTA) to the alginate solution allows for control of the hydrogel growth, and by varying the ratio of Ca(2+) to EDTA concentrations gel growth or gel shrinkage can be induced at will. Trapped cells are released during shrinkage of the gel. The trapping efficiency for different cell speeds is investigated and the properties of gel growth are discussed using a diffusion model. Precise positioning of a single cell is demonstrated. The technique presented allows not only the reversible immobilization of cells under gentle conditions but also offers the potential of long-term cell cultures as shown by on-chip incubation of yeast cells. The procedure may provide a simple and fully biocompatible technique for a multitude of innovative experiments on cells in microsystems.

Alginates↗
PubMed2005

Direct optical emission spectroscopy of liquid analytes using an electrolyte as a cathode discharge source (ELCAD) integrated on a micro-fluidic chip.

Atomic emission detection of metallic species in aqueous solutions has been performed using a miniaturised plasma created within a planar, glass micro-fluidic chip. Detection was achieved using an Electrolyte as a Cathode Discharge source (ELCAD) in which the sample solution itself is used as the cathode for the discharge. To realise the ELCAD technique within a micro-fluidic device, a parallel liquid-gas flow was set up in a micro-channel and a glow discharge ignited between the flowing liquid sample surface and a metal wire anode. The detection of copper and sodium was achieved, using atmospheric pressure air as a carrier gas, by observation of atomic emission lines of copper at 324 nm, 327 nm, 511 nm, 515 nm and 522 nm and an atomic emission line of sodium at 589 nm using a commercially available miniaturised spectrometer. A total electrical power of less than 70 mW was required to sustain the discharge. A semi-quantitative, absolute detection limit of 17 nmol s(-1) was obtained for sodium with a sample flow rate of 100 microL min(-1) and an integration time of 100 ms in air at atmospheric pressure. The volume required for such detection is approximately 170 nL. Further analysis was performed with an Echelle spectrometer using both argon and air as a carrier gas. The geometry and flow rates used demonstrate the feasibility of integrating such micro-plasmas into other micro-fluidic devices, such as miniaturised CE devices, as a method of detection. The potential for using such micro-plasmas within highly portable miniaturised systems and mu-TAS devices is presented and discussed.

Journal Article↗
PubMed2005

Shear-driven pumping and Fourier transform detection for on chip circular chromatography applications.

A circular, shear-driven pumping system combined with Fourier Transform detection has been developed for the application of chip based cyclic chromatography. Using this system, it is possible to perform an injection of a sample plug into a circular micro-channel and then drive the sample through the channel, using shear flow induced by a rotation stage. High pumping rates at uniform speeds are attainable with this system with very little heat production. Typical pumping rates of up to 1.423 mm s(-1) +/- 2 microm s(-1) were used in experiments although much higher rates >14 mm s(-1) are also possible with this system. Fluorescence detection was used to detect a sample plug of Coumarin dyes, flowing around the channel. A coating of porous polymethacrylate was used to immobilise RP-HPLC beads onto the glass surface and was applied to the glass micro-channel by selective photopolymerisation. This coating acted as a stationary phase and differences in retention time were observed for an injection of Coumarin dyes for different methanol-water, mobile phase ratios. Full sample retention occurred for 30 : 70 (v/v) methanol-water whereas no retention occurred for 92 : 8 (v/v) methanol-water which can be expected for such a reverse phase, open tubular system. Fourier transform detection applied to the fully retained and non-retained cases showed frequency domain data from a single detection point corresponding to that which may be expected from shear flow theory.

Journal Article↗
PubMed2005

Bio-sensing on a chip with compact discs and nanofibers.

This paper describes a novel, sensitive detection system for biomolecules (DNA and proteins etc.) that is integrated in a lab-on-a-chip utilizing optical compact discs (CDs) and bio-nanofibers. The new method comprises a microchannel containing CD grating that confines fragments of unique bacterial cellulose fibrils (BC), which have nanometre scale fibers and holes. A maximum of six times higher sensitivity to detect DNA was obtained with this CD and BC system compared to a conventional method. We also demonstrate an effective light-confining effect for biological application with the new method.

Biosensing Techniques↗
PubMed2005

Analysis of chloride, bromide and iodide using miniaturised isotachophoresis on a planar polymer chip.

A new method has been developed to allow the determination of the halide anions chloride, bromide and iodide using isotachophoresis. This method employs a new electrolyte system which incorporates the novel application of indium(III) as a complexing agent. This electrolyte system was devised based on the findings of an investigation into the potential for using indium(III) as a complexing counter ion to selectively manipulate the effective mobilities of halide ions. A leading electrolyte incorporating 3.5 mmol dm(-3) of indium(III) allowed the simultaneous determination of chloride, bromide and iodide to be successfully achieved. The new procedure allows such separations to be made without interference from common inorganic anions such as sulfate and nitrate. Separations were performed using a miniaturised planar poly(methyl methacrylate) chip with integrated platinum wire conductivity detection electrodes. Using this instrumentation the limits of detection were calculated to be 0.7 mg dm(-3), 1.7 mg dm(-3) and 2.2 mg dm(-3) for chloride, bromide and iodide respectively.

Anions↗
PubMed2005

Continuous monitoring with microfabricated capillary electrophoresis chip devices.

We report on the direct coupling of hydrodynamically flowing stream to a microchip capillary electrophoresis (CE) for continuous assays of liquid samples. The new interface relies on mounting the sample tubing onto a sharp inlet tip and allows rapid, convenient and reproducible electrokinetic loading from a continuously flowing stream directly into the narrow separation microchannel. The sharp inlet interface is characterized by its efficiency, stability and simplicity. The effect of the sample flow rate, applied voltages and other relevant variables, is described. It was found that the peak intensity is independent of the flow rate. The performance of the new interface is illustrated for on-line CE-electrochemical monitoring of phenolic and explosive compounds. Conditions simulating continuous long-term monitoring, led to a highly stable response for a 15 ppm 1,3,5-trinitrobenzene solution (RSD = 3.7%, n= 40). Such ability to continuously introduce flowing samples into micrometer channels makes 'lab-on-a-chip' devices highly compatible with real-life monitoring applications.

Electrophoresis, Microchip↗
PubMed2005

A lab-on-a-chip compatible bioaffinity assay method for human alpha-fetoprotein.

A new lab-on-a-chip compatible binding assay platform is introduced. The platform combines dry-chemistry bioaffinity reagents and the recently introduced ArcDia TPX binding assay technique. The technique employs polymer microspheres as a solid phase reaction carrier, fluorescently labeled antibody conjugates, and detection of fluorescence emission from the surface of individual microspheres by two-photon excitation fluorescence. Signal response of the technique is independent of the reaction volume, thus the technique is particularly well suited for detection of bioaffinity reactions from miniature volumes. Performance of the new assay platform is studied by means of an immunometric assay of human alpha-fetoprotein (hAFP) in 384-plate format, and the results are compared to those of a corresponding wet-chemistry assay method. The results show that the ArcDia TPX detection technique can be combined with dry-chemistry reagents without compromises in assay performance. The microchip field has so far been characterized with a lack of microchip-compatible detection platforms which would allow cost-effective microchip design and sensitive bioaffinity detection. The presented detection technique is expected to provide a solution for this shortage.

Humans↗
PubMed2006

An actuated pump on-chip powered by cultured cardiomyocytes.

Cellular functions are frequently exploited as processing components for integrated chemical systems such as biochemical reactors and bioassay systems. Here, we have created a new cell-based microsystem exploiting the intrinsic pulsatile mechanical functions of cardiomyocytes to build a cellular micropump on-chip using cardiomyocyte sheets as prototype bio-microactuators. We first demonstrate cell-based control of fluid motion in a model microchannel without check valves and evaluate the potential performance of the bio-actuation. For this purpose, a poly(dimethylsiloxane) (PDMS) microchip with a microchannel equipped with a diaphragm and a push-bar structure capable of harnessing collective cell fluid mechanical forces was coupled to a cultured pulsating cardiomyocyte sheet, activating cell-based fluid movement in the microchannel by actuating the diaphragm. Cell oscillation frequency and correlated fluid displacement in this system depended on temperature. When culture temperature was increased, collective cell contraction frequency remained cooperative and synchronous but increased, while displacement was slightly reduced. We then demonstrated directional fluid pumping within microchannels using cantilever-type micro-check valves made of polyimide. A directional flow rate of nL min(-1) was produced. This cell micropump system could be further developed as a self-actuated and efficient mechanochemical transducer requiring no external energy sources for various purposes in the future.

Animals↗
PubMed2006

X-ray microfocussing combined with microfluidics for on-chip X-ray scattering measurements.

This work describes the fabrication of thin microfluidic devices in Kapton (polyimide). These chips are well-suited to perform X-ray scattering experiments using intense microfocussed beams, as Kapton is both relatively resistant to the high intensities generated by a synchrotron, and almost transparent to X-rays. We show networks of microchannels obtained using laser ablation of Kapton films, and we also present a simple way to perform fusion bonding between two Kapton films. The possibilities offered using such devices are illustrated with X-ray scattering experiments. These experiments demonstrate that structural measurements in the 1 A-20 nm range can be obtained with spatial resolutions of a few microns in a microchannel.

Microarray Analysis↗
PubMed2006

On-chip pressure injection for integration of infrared-mediated DNA amplification with electrophoretic separation.

Poly(dimethylsiloxane) (PDMS) membrane valves were utilized for diaphragm pumping on a PDMS-glass hybrid microdevice in order to couple infrared-mediated DNA amplification with electrophoretic separation of the products in a single device. Specific amplification products created during non-contact, infrared (IR) mediated polymerase chain reaction (PCR) were injected via chip-based diaphragm pumping into an electrophoretic separation channel. Channel dimensions were designed for injection plug shaping via preferential flow paths, which aided in minimizing the plug widths. Unbiased injection of sample could be achieved in as little as 190 ms, decreasing the time required with electrokinetic injection by two orders of magnitude. Additionally, sample stacking was promoted using laminar or biased-laminar loading to co-inject either water or low ionic strength DNA marker solution along with the PCR-amplified sample. Complete baseline resolution (Res = 2.11) of the 80- and 102-bp fragments of pUC-18 DNA marker solution was achieved, with partially resolved 257- and 267-bp fragments (Res = 0.56), in a separation channel having an effective length of only 3.0 cm. This resolution was deemed adequate for many PCR amplicon separations, with the added advantage of short separation time-typically complete in <120 s. Decreasing the amount of glass surrounding the PCR chamber reduced the DNA amplification time, yielding a further enhancement in analysis speed, with heating and cooling rates as high as 13.4 and -6.4 degrees C s(-1), respectively. With the time requirements greatly reduced for each step, it was possible to seamlessly couple IR-mediated amplification, sample injection, and separation/detection of a 278-bp fragment from the invA gene of <1000 starting copies of Salmonella typhimurium DNA in approximately 12 min on a single device, representing the fastest PCR-ME integration achieved to date.

DNA Replication↗
PubMed2006

Electrokinetic flow control in microfluidic chips using a field-effect transistor.

A field-effect transistor is developed to control flow in microfluidic chips by modifying the surface charge condition. In this investigation, zeta potential at a particular location is altered locally by applying a gate voltage, while zeta potential at other locations is maintained at its original value. This non-uniform zeta potential results in a secondary electroosmotic flow in the lateral direction, which is used for flow control in microgeometries. Here, microchannel structures and field-effect transistors are formed on polydimethylsiloxane (PDMS) using soft lithography techniques, and a micro particle image velocimetry technique is used to obtain high resolution velocity distribution in the controlled region. The flow control is observed at relatively low gate voltage (less than 50 V), and this local flow control is primarily due to current leakage through the interface between PDMS and glass layers. A leakage capacitance model is introduced to estimate the modified zeta potential for the straight channel case, and excellent agreement is obtained between the predicted and experimental zeta potential results. This leakage-current based field-effect is then applied to a T-channel junction to control flow in the branch channel. Experiments show that the amount of discharge in the branch channel can be controlled by modulating gate voltage.

Kinetics↗
PubMed2006

Grafting epoxy-modified hydrophilic polymers onto poly(dimethylsiloxane) microfluidic chip to resist nonspecific protein adsorption.

In order to achieve a simple covalent hydrophilic polymer coating on poly(dimethylsiloxane) (PDMS) microfluidic chip, epoxy modified hydrophilic polymers were synthesized in aqueous solution with a persulfate radical initiation system, and crosslinked onto PDMS pretreated by oxygen plasma and silanized with 3-aminopropyl-triethoxysilanes (APTES). Glycidyl methacrylate (GMA) was copolymerized with acrylamide (poly(AAM-co-GMA)) or dimethylacrylamide (poly(DAM-co-GMA)), and graft polymerized with polyvinylpyrrolidone (PVP-g-GMA) or polyvinylalcohol (PVA-g-GMA). The epoxy groups in the polymers were determined by UV spectra after derivation with benzylamine. Reflection absorption infrared spectroscopy (RAIRS) confirmed covalent grafting of GMA-modified polymers onto PDMS surface. Electroosmotic flow (EOF) in the polymer grafted microchannel was strongly suppressed within the range pH 3-11. Surface adsorption of lysozyme and bovine serum albumin (BSA) was reduced to less than 10% relative to that on the native PDMS surface. On the GMA-modified polymer coated PDMS microchip, basic proteins, peptides, and sodium dodecyl sulfate (SDS) denatured proteins were separated successfully.

Acrylamides↗
PubMed2005

Synaptic vesicle chips to assay botulinum neurotoxins.

BoNTs (botulinum neurotoxins), considered to be the most toxic of all biological substances, inhibit neurotransmission through proteolytic cleavage of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins [VAMP (vesicle-associated membrane protein, or synaptobrevin), SNAP-25 (25 kDa synaptosome-associated protein) or syntaxin]. Expansion in the use of BoNTs as therapeutic and cosmetic agents, and the potential threat they constitute as biological weapons, underlines the need for rapid and sensitive in vitro assays. Here, we present new automatized bioassays to detect VAMP cleavage by BoNT/B and F. Western blotting and SPR (surface plasmon resonance) methods revealed that BoNT/B and F totally cleave their substrate on immunoisolated SVs (synaptic vesicles). Real-time monitoring of the immunocapture of native SVs from crude lysates on SPR sensor chips enabled the detection of picogram amounts of different SV proteins. Pre-incubation of a membrane fraction containing SVs with BoNT specifically inhibited capture by anti-VAMP antibodies, and amounts as low as 0.1 pg of BoNT/B were detected. This automated SPR assay is approx. 200 times more sensitive, and 25 times more rapid, than the in vivo BoNT/B test currently used. Moreover, the method can be performed using a few thousand cultured neurons and constitutes a new screening assay for inhibitors. Our data indicate that native VAMP is an optimal substrate for in vitro BoNT assays that can be monitored by SPR.

Animals↗
PubMed2003

Coupling gene chip analyses and rat genetic variances in identifying potential target genes that may contribute to neuropathic allodynia development.

Genetic factors and nerve injury-induced changes of gene expression in sensory neurons are potential contributors to tactile allodynia, a neuropathic pain state manifested as hypersensitivity to innocuous mechanical stimulation. To uncover genes relevant to neuropathic allodynia, we analyzed gene expression profiles in dorsal root ganglia (DRG) of spinal nerve-ligated Harlan and Holtzman Sprague Dawley rats, strains with different susceptibilities to neuropathic allodynia. Using Affymetrix gene chips, we identified genes showing differential basal-level expression in these strains without injury-induced regulation. Of more than 8000 genes analyzed, less than 180 genes in each strain were regulated after injury, and 19-22% of that was regulated in a strain-specific manner. Importantly, we identified functionally related genes that were co-regulated post injury in one or both strains. In situ hybridization and real-time PCR analyses of a subset of identified genes confirmed the patterns of the microarray data, and the former also demonstrated that injury-induced changes occurred, not only in neurons, but also in non-neuronal cells. Together, our studies provide a global view of injury plasticity in DRG of these rat stains and support a plasticity-based mechanism mediating variations in allodynia susceptibility, thus providing a source for further characterization of neuropathic pain-relevant genes and potential pathways.

Animals↗