Biomedical subjects

Mark A Burns

Publications and source records attributed to Mark A Burns.

At least 19 recordsLinked to original sources

PubMed2006

Low-power concentration and separation using temperature gradient focusing via Joule heating.

We present an experimental study of temperature gradient focusing (TGF) exploiting an inherent Joule heating phenomenon. A simple variable-width PDMS device delivers rapid and repeatable focusing of model analytes using significantly lower power than conventional TGF techniques. High electric potential applied to the device induces a temperature gradient within the microchannel due to the channel's variable width, and the temperature-dependent mobility of the analytes causes focusing at a specific location. The PDMS device also shows simultaneous separation and concentration capability of a mixture of two sample analytes in less than 10 min. An experiment combining Joule heating with external heating/cooling further supports the hypothesis that temperature is indeed the dominant factor in achieving focusing with this technique.

Fluorescein↗

PubMed2006

Nanopore sequencing technology: research trends and applications.

Nanopore sequencing is one of the most promising technologies being developed as a cheap and fast alternative to the conventional Sanger sequencing method. Protein or synthetic nanopores have been used to detect DNA or RNA molecules. Although none of the technologies to date has shown single-base resolution for de novo DNA sequencing, there have been several reports of alpha-hemolysin protein nanopores being used for basic DNA analyses, and various synthetic nanopores have been fabricated. This review will examine current nanopore sequencing technologies, including recent developments of new applications.

Biosensing Techniques↗

PubMed2006

Electrokinetic protein preconcentration using a simple glass/poly(dimethylsiloxane) microfluidic chip.

We discovered that a protein concentration device can be constructed using a simple one-layer fabrication process. Microfluidic half-channels are molded using standard procedures in PDMS; the PDMS layer is reversibly bonded to a glass base such as a microscope slide. The microfluidic channels are chevron-shaped, in mirror image orientation, with their apexes designed to pass within approximately 20 microm of each other, forming a thin-walled section between the channels. When an electric field is applied across this thin-walled section, negatively charged proteins are observed to concentrate on the anode side of it. About 10(3)-10(6)-fold protein concentration was achieved in 30 min. Subsequent separation of two different concentrated proteins is easily achieved by switching the direction of the electric field in the direction parallel to the thin-walled section. We hypothesize that a nanoscale channel forms between the PDMS and the glass due to the weak, reversible bonding method. This hypothesis is supported by the observation that, when the PDMS and glass are irreversibly bonded, this phenomenon is not observed until a very high E-field was applied and dielectric breakdown of the PDMS is observed. We therefore suspect that the ion exclusion-enrichment effect caused by electrical double layer overlapping induces cationic selectivity of this nanochannel. This simple on-chip protein preconcentration and separation device could be a useful component in practically any PDMS-on-glass microfluidic device used for protein assays.

Animals↗

PubMed2006

Microstencils for the patterning of nontraditional materials.

A microfabrication technique that uses a photolithographically patterned film as a microstencil has been developed. This microstencil has a bilayer structure comprised of parylene and SU-8 films with thicknesses from 4 to 100 microm. The parylene layer enables the microstencil to be mechanically peeled from hydrophilic substrates. Since no chemicals are required to release the microstencil, this technique can be used to pattern chemically and biologically sensitive materials. The amount of material deposited can be automatically controlled by the height of the SU-8 structures or externally controlled by spin coating or other thin film deposition techniques. This patterning method is very versatile and has been used to pattern features as small as 25 by 25 microm on silicon, glass, and polymer substrates. As an initial demonstration, we have patterned wax, cells, proteins, sol, and CYTOP.

Coated Materials, Biocompatible↗

PubMed2006

Optimization of dielectrophoretic DNA stretching in microfabricated devices.

We have found that the surface and bulk solution properties in a microfabricated device affect the degree and probability of electrostretching of DNA molecules. Using lambda phage DNA, we found that significantly hydrophilic surfaces between the electrodes decrease the efficiency of stretching. Surfaces treated with higher silane (trimethylchlorosilane) concentrations performed better presumably due to the decreased nonspecific adsorption of DNA on these surfaces compared to their more hydrophilic counterparts. The shape and dimensions of the electrodes also affected the efficiency of stretching. Both liftoff and metal etching methods produced electrodes with random microscopic peaks along the electrode's edge and were poorly suited for stretching. Annealing the electrodes (450 degrees C for 10 min) removed most of these peaks and allowed for more controlled stretching to be obtained. We also found that thin electrodes (65 nm) gave close to a 90% success rate of DNA stretching but stretching with thick electrodes (350 nm) produced only a 20% success rate.

DNA, Viral↗

PubMed2006

Electronic drop sensing in microfluidic devices: automated operation of a nanoliter viscometer.

We describe three droplet sensing techniques: a digital electrode, an analog electrode, and a thermal method. All three techniques use a single layer of metal lines that is easy to microfabricate and an electronic signal can be produced using low DC voltages. While the electrode methods utilize changes in electrical conductivity when the air/liquid interface of the droplet passes over a pair of electrodes, the thermal method is based on convective heat loss from a locally heated region. For the electrode method, the analog technique is able to detect 25 nL droplets while the digital technique is capable of detecting droplets as small as 100 pL. For thermal sensing, temperature profiles in the range of 36 degrees C and higher were used. Finally, we have used the digital electrode method and an array of electrodes located at preset distances to automate the operation of a previously described microfluidic viscometer. The viscometer is completely controlled by a laptop computer, and the total time for operation including setup, calibration, sample addition and viscosity calculation is approximately 4 minutes.

Electrodes↗

PubMed2006

Analysis of non-Newtonian liquids using a microfluidic capillary viscometer.

We have used a self-calibrating microfabricated capillary viscometer to analyze non-Newtonian power law fluids. The capillary viscometer can generate a wide range of shear rates during a single experimental run enabling quick and accurate analysis of non-Newtonian liquids. The measurement of viscosity is based on monitoring the capillary pressure-driven movement of fluid sample whose mean velocity and, therefore, shear rate varies with time. The device has been successfully tested for accuracy and robustness with dilute as well as semidilute solutions of flexible elastic polymers including poly(ethylene oxide) and hydrolyzed polyacrylamide to an aqueous solution of a stiff rodlike polymer molecule of xanthan gum, a popular emulsifier and food thickener, as well as with ink-jet printing inks. Viscosities in the range of 1-600 cP were measured, and shear rates varying from 5 to 1000 s(-1) have been obtained on the microfabricated viscometer with the current geometry and channel dimensions. The total measurement time varied between 2 and 8 min and less than 1 microL of sample volume was required. Such a microfabricated capillary viscometer would have possible applications in quality control and manufacturing where rapid and repeated measurements need to be made using limited sample volume.

Biopolymers↗

PubMed2005

Addressable electric fields for size-fractioned sample extraction in microfluidic devices.

Fraction collection following electrophoresis is of major importance for a variety of biological analyses. These assays typically need to identify specific fractions in the separated sample for further processing and require extraction of one or a group of fragments. In this paper, we have developed and characterized a technique to generate addressable electric fields for improved extraction during electrophoresis in microfluidic devices. The addressable electric field is achieved by applying a low bias voltage (1-2 V) to microelectrode pairs within the electrophoresis microchannel. Theoretical analysis shows the purity of the extracted sample can be improved as much as 30% over extraction without the shaped electric fields, and nearly 100% predicted yield can be achieved. We also describe the theoretical design of shaped electric fields by characterizing the optimal electrode geometry, field strength, channel configuration, and electrophoretic migration behavior needed for efficient band extraction.

DNA↗

PubMed2005

Nanoliter viscometer for analyzing blood plasma and other liquid samples.

We have developed a microfabricated nanoliter capillary viscometer that quickly, easily, and inexpensively measures the viscosity of liquids. The measurement of viscosity is based on capillary pressure-driven flow inside microfluidic channels (depth approximately 30 microm and width approximately 300 microm). Accurate and precise viscosity measurements can be made in less than 100 s while using only 600 nL of liquid sample. The silicon-glass hybrid device (18 mm by 15 mm) contains on-chip components that measure the driving capillary pressure difference and the relevant geometrical parameters; these components make the nanoliter viscometer completely self-calibrating, robust, and easy to use. Several different microfabricated viscometers were tested using solutions with viscosities ranging from 1 to 5 cP, a range relevant to biological fluids (urine, blood, blood plasma, etc.). Blood plasma samples collected from patients with the symptoms of hyperviscosity syndrome were tested on the nanoliter capillary viscometer to an accuracy of 3%. Such self-calibrating nanoliter viscometers may have widespread applications in chemical, biological, and medical laboratories as well as in personal health care.

Blood Viscosity↗

PubMed2005

Effect of buffer flow on DNA separation in a microfabricated electrophoresis system.

An adequate buffer reservoir is one essential component of an electrophoresis system, providing current carrying ions and maintaining constant pH. In a microfabricated DNA separation system with on-chip electrodes, the amount of buffer used is limited by the design of the device; the buffer continuity can be easily disturbed by the production of bubbles. Continuously flowing 1 x Tris-borate-EDTA (TBE) buffer over the electrodes at the cathodic end solves both problems. This flow increases the resolution for ssDNA primer separations (21 and 25 bases) to a maximum value of 1.4 within a distance of 1.2 cm, about four times higher than that without flow. Similar improvement has been achieved for dsDNA separation (20 bp ladder; BioRad) at a distance of only 0.4 cm, giving baseline resolution for bands from 20 to 240 bp. We have also investigated the effect of buffer concentration on resolution, and no similar improvement can be obtained by merely increasing the buffer concentration without flow.

Buffers↗

PubMed2004

Polymerase chain reaction in high surface-to-volume ratio SiO2 microstructures.

We have performed the Taqman beta-actin PCR system in high-surface-to-volume ratio (0.02-0.13 microm(-1)) SiO2 microchannels and observed the reaction yield and uniformity. The concentrations of the enzyme, magnesium chloride, and reaction template were varied in the reaction mix, and PCR amplification was performed in devices of various surface-to-volume ratios. We found that microchannels with higher surface-to-volume ratios required higher enzyme concentrations to achieve the same amplification efficiency. We investigated the possibility that the observed reaction nonuniformity was related to the specific adsorption of magnesium ions to the negatively charged SiO2 surface. The effect of several modifications to the reaction chemistry, the addition of the caged-magnesium dye DM-Nitrophen, the replacement of human DNA template with PCR product, and the coating of the microchannel surface with Teflon were all studied. These modifications resulted in improved reaction uniformity in the microchannels and present opportunities for further studies on enhancing the efficiency and uniformity of PCR in high surface-to-volume ratio SiO2 microchannels.

Base Sequence↗

PubMed2004

Reactions and fluidics in miniaturized natural convection systems.

Buoyancy-driven convection offers a novel and greatly simplified mechanism for generating continuous nonpulsatile flow fields and performing thermally activated biochemical reactions. In this paper, we build on our previous work by constructing a multiwell device incorporating an array of 35-microL cylindrical cavities to perform polymerase chain reaction (PCR) amplification of a 191-base pair fragment associated with membrane channel proteins M1 and M2 of the influenza-A virus in as little as 15 min with performance comparable to conventional thermocyclers. We also describe entirely new adaptations of convective flows by conducting a series of coordinated flow visualization and computational studies to explore the design of closed-loop systems to execute tunable thermocycling, pumping, and mixing operations in a format suitable for integration into miniaturized biochemical analysis systems. Using 15-microL convective flow loops, we are able to perform PCR amplification of the same 191-base pair fragment associated with the influenza-A virus, as well as a 295-base pair segment of the human beta-actin gene in a format offering an enhanced degree of control and tunability. These convective flow devices can be further scaled down to nanoliter volumes and are ideally suited as a platform for a new generation of low-power, portable microfluidic DNA analysis systems.

Actins↗

PubMed2004

Phase change microvalve for integrated devices.

An active microvalve that uses a meltable piston in place of a conventional solid material to obstruct fluid flow in a microfluidic channel has been developed. This phase change valve is simple to operate and requires no additional fabrication steps. The valve is inherently latched, reusable, and leak-proof (to at least 250 psi) and can be electronically addressed using resistive heaters. The valve has been characterized for a range of operational parameters that will serve as a design guide. For the designs tested, piston displacements of 5 mm or more in 1 s have been achieved. Valves 1.4 mm in length in a 50 microm x 200 microm channel have been integrated on a biochemical reaction device, and successful DNA amplification using PCR has been achieved. The phase change valve can be easily implemented in an array format that can be used to realize complex microfluidic circuits.

Glass↗

PubMed2004

Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions.

Many routine genomic-analysis assays rely on gel electrophoresis to perform size-selective fractionation of DNA fragments in the size range below 1 kb in length. Over the past decade, impressive progress has been made towards the development of microfabricated electrophoresis systems to conduct these assays in a microfluidic lab-on-a-chip format. Since these devices are inexpensive, require only nanolitre sample volumes, and do not rely on the availability of a pre-existing laboratory infrastructure, they are readily deployable in remote field locations for use in a variety of medical and biosensing applications. The design and construction of microfabricated electrophoresis devices poses a variety of challenges, including the need to achieve high-resolution separations over distances of a few centimetres or less, and the need to easily interface with additional microfluidic components to produce self-contained integrated DNA-analysis systems. In this paper, we review recent efforts to develop devices to satisfy these requirements and live up to the promise of fulfilling the growing need for inexpensive portable genomic-analysis equipment.

DNA↗

PubMed2004

Integrated microsystems for controlled drug delivery.

Efficient drug delivery and administration are needed to realize the full potential of molecular therapeutics. Integrated microsystems that incorporate extremely fast sensory and actuation capabilities can fulfill this need for efficient drug delivery tools. Photolithographic technologies borrowed from the semiconductor industry enable mass production of such microsystems. Rapid prototyping allows for the quick development of customized devices that would accommodate for diverse therapeutic requirements. This paper reviews the capabilities of existing microfabrication and their applications in controlled drug delivery microsystems. The next generation of drug delivery systems--fully integrated and self-regulating--would not only improve drug administration, but also revolutionize the health-care industry.

Chemical Engineering↗

PubMed2003

Selective extraction of size-fractioned DNA samples in microfabricated electrophoresis devices.

We have designed and constructed a microfabricated device for separation of double-stranded DNA fragments using a crosslinked sieving medium and spatially selective extraction of the desired fraction. Based on measuring the width and spacing of migrating bands, a narrow side channel is constructed perpendicular to the separation channel to collect the DNA fragments of interest. This selective collection technique was tested using a 100 base pair double-stranded DNA ladder. We successfully demonstrate selective extraction of the desired fragment with minimal interference from the adjacent bands in an electric field of 31 V/cm. We also achieve extraction of multiple DNA fragments using an array of microelectrodes in this side channel. The device uses cross-linked polyacrylamide gel matrix, allowing the separation to be performed in a distance of 1 cm or less and at a low electric field strength. Together with on-chip electrode, this design is amenable to integration with reaction chambers into a single device for portable genetic-based analysis.

DNA↗

PubMed2003

Light-induced molecular cutting: localized reaction on a single DNA molecule.

A short focused pulse of light was used to selectively cut lambda-phage DNA molecules at specific restriction sites. Lambda DNA (48.5 kbp) was stretched and placed in a solution containing a restriction enzyme (Sma 1), caged magnesium ions (using a DM-Nitrophen complex), and a chelating agent (EDTA). When a pulse of UV light was directed at a particular location on the stretched DNA molecule, magnesium ions were released into solution. A series of binding reactions then occur in which the enzyme and the chelating agent compete for free Mg2+ ions. Since Sma 1 functions only in the presence of Mg2+, as is true of most endonucleases, the site(s) in the vicinity of the pulse (typically approximately 6 microm) were cut while other sites (three total for this DNA/enzyme pair) were not. The ratio of the concentration of the chelating agent to that of the magnesium ions was used to control the radius of this reaction zone with higher ratios leading to smaller, localized reaction areas. This optically based reaction mechanism could be useful to understand single molecule enzymatic kinetics, and when coupled with other DNA analysis techniques, this could be used to construct complex genotyping and sequencing devices that would analyze parts of single DNA molecules.

Bacteriophage lambda↗

PubMed2003

Cell affinity separations using magnetically stabilized fluidized beds: erythrocyte subpopulation fractionation utilizing a lectin-magnetite support.

A magnetically stabilized fluidized bed is used to separate erythrocyte subpopulations. Binding specificity was obtained by immobilizing the lectin Helix pomatia Agglutinin (HpA) or Griffonia simplicifolia I (GSI) onto a magnetite-containing support. Separation of type A and type O erythrocytes with the lectin HpA was particularly effective, leading to a 94% purity of retained type A erythrocytes. A 3.1 +/- 0.6 log removal of type A erythrocytes was also accomplished leading to a 99.7% +/- 0.4% purity and 95% +/- 7% yield of type O erythrocytes in the collected effluent. Elution of the purified cells was accomplished using fluidization in the presence of a sugar competing for the lectin-erythrocyte binding site. A mathematical model based on the depth filtration model of Putnam and Burns (Chem Eng Sci 1997;52(1):93-105) was extended to include multicomponent cell adhesion. This filtration model is the first to take into account the finite binding capacity of the chromatographic support and is used to characterize the cell binding behavior and to determine optimal parameters and conditions that lead to high capacities and selectivities. Model parameter values and observations from in situ adsorption studies suggest that the non-spherical shape of the magnetite-based support allows for a more efficient utilization of the support surface area than the spherical shape. Using a 1.5-cm diameter laboratory column and realistic parameter values, the processing rates of the system are predicted to be at least an order of magnitude greater than the 10(8)/h cells that can typically be processed in packed bed cell affinity chromatography (CAC) systems.

ABO Blood-Group System↗