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Biomedical subjects

James P Landers

Publications and source records attributed to James P Landers.

At least 19 recordsLinked to original sources
PubMed2006

A fully integrated microfluidic genetic analysis system with sample-in-answer-out capability.

We describe a microfluidic genetic analysis system that represents a previously undescribed integrated microfluidic device capable of accepting whole blood as a crude biological sample with the endpoint generation of a genetic profile. Upon loading the sample, the glass microfluidic genetic analysis system device carries out on-chip DNA purification and PCR-based amplification, followed by separation and detection in a manner that allows for microliter samples to be screened for infectious pathogens with sample-in-answer-out results in < 30 min. A single syringe pump delivers sample/reagents to the chip for nucleic acid purification from a biological sample. Elastomeric membrane valving isolates each distinct functional region of the device and, together with resistive flow, directs purified DNA and PCR reagents from the extraction domain into a 550-nl chamber for rapid target sequence PCR amplification. Repeated pressure-based injections of nanoliter aliquots of amplicon (along with the DNA sizing standard) allow electrophoretic separation and detection to provide DNA fragment size information. The presence of Bacillus anthracis (anthrax) in 750 nl of whole blood from living asymptomatic infected mice and of Bordetella pertussis in 1 microl of nasal aspirate from a patient suspected of having whooping cough are confirmed by the resultant genetic profile.

DNA↗
PubMed2006

On-chip pumping for pressure mobilization of the focused zones following microchip isoelectric focusing.

Isoelectric focusing (IEF), traditionally accomplished in slab or tube gels, has also been performed extensively in capillary and, more recently, in microchip formats. IEF separations performed in microchips typically use electroosmotic flow (EOF) or chemical treatment to mobilize the focused zones past the detection point. This report describes the development and optimization of a microchip IEF method in a hybrid PDMS-glass device capable of controlling the mobilization of the focused zones past the detector using on-chip diaphragm pumping. The microchip design consisted of a glass fluid layer (separation channels), a PDMS layer and a glass valve layer (pressure connections and valve seats). Pressure mobilization was achieved on-chip using a diaphragm pump consisting of a series of reversible elastomeric valves, where a central diaphragm valve determined the volume of solution displaced while the gate valves on either side imparted directionality. The pumping rate could be adjusted to control the mobilization flow rate by varying the actuation times and pressure applied to the PDMS to actuate the valves. In order to compare the separation obtained using the chip with that obtained in a capillary, a serpentine channel design was used to match the separation length of the capillary, thereby evaluating the effect of diaphragm pumping itself on the overall separation quality. The optimized mIEF method was applied to the separation of labeled amino acids.

Amino Acids↗
PubMed2006

Chitosan as a polymer for pH-induced DNA capture in a totally aqueous system.

A novel DNA solid-phase extraction protocol based on the pH-dependent charge of chitosan was developed specifically for low-volume DNA extraction on microchips. The method uses chitosan-coated beads to extract DNA at pH 5 and release it from the chitosan at pH 9. DNA extraction efficiency as high as 92% could be attained, even from complex samples such as human blood containing significant amounts of protein. Using this method, PCR inhibitors that are typically used in DNA extraction procedures (e.g., chaotropic salts, 2-propanol) can be avoided, making the method more conducive to downstream sample processing using PCR. A high-density multichannel microchip device was then fabricated and the microchannels coated with chitosan for DNA extraction in an open channel configuration without the need for an additional stationary phase. This design provided a relatively high surface area-to-volume ratio for extraction, while retaining the low flow resistance commensurate with open channels. With a flow rate of approximately 1 microL/min during the extraction, the total extraction time was less than 10 min, with most of the DNA recovered in the first 2 microL of elution buffer. Using the microchip device, extraction efficiencies for lambda-phage DNA and human genomic DNA were as high as 67 and 63%, respectively. Human genomic DNA from whole blood samples could be extracted in 10 min with an extraction efficiency of 75 +/- 4% (n = 3), and the purified DNA was suitable for PCR amplification of a fragment of the gelsolin gene. The combination of an entirely aqueous DNA extraction method with a high-density, low-flow resistance microchannel pattern sets the stage for future integration into microfluidic genomic analysis devices.

Chitosan↗
PubMed2006

Microchip-based macroporous silica sol-gel monolith for efficient isolation of DNA from clinical samples.

Effective microchip extraction of deoxyribonucleic acid (DNA) from crude biological matrixes has been demonstrated using silica beads or hybrid phases composed of beads and sol-gel. However, the use of monolithic sol-gels alone for extraction of human genomic DNA has been more difficult to define. Here we describe, for the first time, the successful use of monolithic tetramethyl orthosilicate-based sol-gels for effective micro-solid-phase extraction (muSPE) of DNA in a glass microchip format. A functional monolithic silica phase with micrometer-scale pores in the silica matrix resulted from addition of poly(ethylene glycol), a poragen, to the precursor mixture. This allowed a monolithic sol-gel bed to be established in a microchip channel that provided large surface area for DNA extraction with little flow-induced back pressure. DNA extraction efficiencies for simple systems (lambda-phage DNA) were approximately 85%, while efficiencies for the reproducible extraction of human genomic DNA from complex biological matrixes (human blood) were approximately 70%. Blockage of the sol-gel pores by components in the lysed blood was observed in repeat extraction on a single device as a decrease in the extraction efficiency. The developed muSPE protocol was further evaluated to show applicability to clinical samples and bacterial cultures, through extraction of PCR-amplifiable DNA.

DNA↗
PubMed2006

Multicolor fluorescence detection on an electrophoretic microdevice using an acoustooptic tunable filter.

An acoustooptic tunable filter (AOTF) is used to detect multiple fluorescent signals on a fluidic microdevice. A confocal laser-induced fluorescence detection setup is used to excite fluorescent dyes in glass microchannels, presenting a streamlined and robust detection system consisting of the narrow-bandwidth AO filter and a single photodetector. The flexibility of the filter is demonstrated by alternating between wavelengths for precise microchannel alignment and sweeping through a range of wavelengths for preliminary spectral characterization of subnanoliter probe volumes of target analytes. The AOTF is also coupled with an electrophoretic separation for the multicolor detection of PCR-amplified DNA against a labeled sizing standard, the discrimination of multiple amplicons overlapped in time, and the identification of amplified biowarfare agents in a fluorescent spiking experiment. Finally, to demonstrate the multicolor capability of the system, 19-wavelength detection is performed during the separation of a three-dye sample mixture.

Acoustics↗
PubMed2006

Quenching of the electrochemiluminescence of tris(2,2'-bipyridine)ruthenium(II) by ferrocene and its potential application to quantitative DNA detection.

Efficient and stable quenching of electrochemiluminescence (ECL) of tris(2,2'-bipyridine)ruthenium(II) by oxidizing ferrocene methanol (FcMeOH) at the electrode is reported. Bimolecular energy or electron transfer between Ru(bpy)(3)(2+*) and ferrocenium (Fc(+)), the oxidized species of Fc, along with suppression of radical reactions is suggested as the mechanism for quenching ECL. Fc shows more efficient quenching of ECL compared with the known quenchers phenol and 1,1-dimethyl-4,4'-bipyridine dication (MV(2+)). The ECL quenching rate constant was 5.6 x 10(10) M(-)(1) s(-)(1). Using Fc as a quencher label on a complementary DNA sequence, an intramolecular ECL quenching in hybridized oligonucleotide strands has been realized. With essentially complete quenching efficiency, this system has the potential for application to sequence-specific DNA detection.

2,2'-Dipyridyl↗
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

A simple, valveless microfluidic sample preparation device for extraction and amplification of DNA from nanoliter-volume samples.

A glass microdevice has been constructed for the on-line integration of solid-phase extraction (SPE) of DNA and polymerase chain reaction (PCR) on a single chip. The chromatography required for SPE in the microfluidic sample preparation device (muSPD) was carried out in a silica bead/sol-gel SPE bed, where the purified DNA was eluted directly into a downstream chamber where conventional thermocycling allowed for PCR amplification of specific DNA target sequences. Through rapid, simple passivation of the PCR chamber with a silanizing reagent, reproducible DNA extraction and amplification was demonstrated from complex biological matrixes in a manner amenable to any research laboratory, using only a syringe pump and a conventional thermocycler. The muSPD allowed for SPE concentration of DNA from 600 nL of blood coupled to subsequent on-chip amplification that yielded a detectable amplicon; this simple device can be applied to a variety of routine genetic analyses without the need for sophisticated instrumentation. In addition, the applicability of these developments to nonconventional thermocycling was demonstrated through the use of noncontact, IR-mediated heating. This was exemplified with the isolation of DNA from an anthrax spore-spiked nasal swab and the subsequent on-chip amplification of target DNA sequences in a total processing time of only 25 min.

DNA↗
PubMed2006

DNA extraction using a tetramethyl orthosilicate-grafted photopolymerized monolithic solid phase.

A novel high-capacity, high-efficiency DNA extraction method is described using a photopolymerized silica-based monolithic column in a fused-silica capillary. Development involved investigation of the composition of the sol-gel monomer, fabrication conditions, and surface modifications in order to optimize the binding capacity. Extraction capacity and efficiency with the 3-(trimethoxysilyl)propyl methacrylate (TMSPM) monolith formulations fabricated in capillaries were investigated using a simple three-step procedure consisting of sample loading, washing of the solid phase, and elution of the DNA using a low ionic strength Tris buffer at pH 8. Once the TMSPM monomer concentration was optimized to yield a monolith with maximum test stability (robustness) and minimum back pressure, the monolith surface was modified by the grafting of tetramethyl orthosilicate (TMOS) for increased DNA binding capacity. After the examination of a variety of TMOS concentrations, 85% v/v TMOS was found to be optimal for DNA extraction without any obvious changes to the monolith structure. The reduction of time allowed for TMSPM hydrolysis prior to UV polymerization from 20 to 5 min led to a lower back pressure of the monolith, enabling better TMOS derivatization and therefore higher binding capacity. Minimal buffer volume (as low as 1 muL) was required to elute DNA from the solid phase, providing a DNA concentrating effect potentially important for downstream processes. While experimentation employed monolithic columns that were 12 cm in length, reduction of the length to 2 cm still allowed for a DNA binding capacity of at least 100 ng of prepurified human genomic DNA and extraction efficiencies greater than 85%. Extraction of low sample volumes (submicroliter) of human whole blood were successfully performed, with extraction efficiencies from the 2-cm monolithic column higher than those obtained from a commercial DNA extraction kit. These results position this novel matrix as an attractive alternative for solid-phase extraction of DNA and other biologically active molecules in microscale devices.

Blood↗
PubMed2006

Use of a capillary electrophoresis instrument with laser-induced fluorescence detection for DNA quantitation. Comparison of YO-PRO-1 and PicoGreen assays.

Highly selective and sensitive assays are required for detection and quantitation of the small masses of DNA typically encountered in clinical and forensic settings. High detection sensitivity is achieved using fluorescent labeling dyes and detection techniques such as spectrofluorometers, microplate readers and cytometers. This work describes the use of a laser-induced fluorescence (LIF) detector in conjunction with a commercial capillary electrophoresis instrument for DNA quantitation. PicoGreen and YO-PRO-1, two fluorescent DNA labeling dyes, were used to assess the potential of the system for routine DNA analysis. Linearity, reproducibility, sensitivity, limits of detection and quantitation, and sample stability were examined for the two assays. The LIF detector response was found to be linear (R2 > 0.999) and reproducible (RSD < 9%) in both cases. The PicoGreen assay displayed lower limits of detection and quantitation (20 pg and 60 pg, respectively) than the YO-PRO-1 assay (60 pg and 260 pg, respectively). Although a small variation in fluorescence was observed for the DNA/dye complexes over time, quantitation was not significantly affected and the solutions were found to be relatively stable for 80 min. The advantages of the technique include a 4- to 40-fold reduction in the volume of sample required compared to traditional assays, a 2- to 20-fold reduction in the volume of reagents consumed, fast and automated analysis, and low cost (no specific instrumentation required).

Benzoxazoles↗
PubMed2006

Unconventional detection methods for microfluidic devices.

The direction of modern analytical techniques is to push for lower detection limits, improved selectivity and sensitivity, faster analysis time, higher throughput, and more inexpensive analysis systems with ever-decreasing sample volumes. These very ambitious goals are exacerbated by the need to reduce the overall size of the device and the instrumentation - the quest for functional micrototal analysis systems epitomizes this. Microfluidic devices fabricated in glass, and more recently, in a variety of polymers, brings us a step closer to being able to achieve these stringent goals and to realize the economical fabrication of sophisticated instrumentation. However, this places a significant burden on the detection systems associated with microchip-based analysis systems. There is a need for a universal detector that can efficiently detect sample analytes in real time and with minimal sample manipulation steps, such as lengthy labeling protocols. This review highlights the advances in uncommon or less frequently used detection methods associated with microfluidic devices. As a result, the three most common methods - LIF, electrochemical, and mass spectrometric techniques - are omitted in order to focus on the more esoteric detection methods reported in the literature over the last 2 years.

Electrophoresis, Capillary↗
PubMed2006

Method for determining intracapillary solution temperatures: application to sample zone heating for enhanced fluorescent labeling of proteins.

A fundamental premise in CE relies heavily on the assumption that temperature within the capillary is accurately known and controlled. Theoretical calculations for sample zone and BGE temperature during voltage application are presented. We propose that transient elevation of the sample zone temperature allowed for denaturing and renaturing of proteins in the presence of a fluorescent dynamic labeling reagent. Comparison with the extent of labeling possible with standard on-column dynamic labeling in the absence of elevated temperatures showed order-of-magnitude increases in the fluorescence detection sensitivity of proteins with low surface hydrophobicity. As a result, this represents an example where excess heating in the sample zone during electrophoresis can be exploited advantageously.

Electrophoresis, Capillary↗
PubMed2006

Microchip-based cell lysis and DNA extraction from sperm cells for application to forensic analysis.

The current backlog of casework is among the most significant challenges facing crime laboratories at this time. While the development of next-generation microchip-based technology for expedited forensic casework analysis offers one solution to this problem, this will require the adaptation of manual, large-volume, benchtop chemistry to small volume microfluidic devices. Analysis of evidentiary materials from rape kits where semen or sperm cells are commonly found represents a unique set of challenges for on-chip cell lysis and DNA extraction that must be addressed for successful application. The work presented here details the development of a microdevice capable of DNA extraction directly from sperm cells for application to the analysis of sexual assault evidence. A variety of chemical lysing agents are assessed for inclusion in the extraction protocol and a method for DNA purification from sperm cells is described. Suitability of the extracted DNA for short tandem repeat (STR) analysis is assessed and genetic profiles shown. Finally, on-chip cell lysis methods are evaluated, with results from fluorescence visualization of cell rupture and DNA extraction from an integrated cell lysis and purification with subsequent STR amplification presented. A method for on-chip cell lysis and DNA purification is described, with considerations toward inclusion in an integrated microdevice capable of both differential cell sorting and DNA extraction. The results of this work demonstrate the feasibility of incorporating microchip-based cell lysis and DNA extraction into forensic casework analysis.

Buffers↗
PubMed2006

Enhanced elution of sperm from cotton swabs via enzymatic digestion for rape kit analysis.

This report describes development of a method for enhanced cell elution from cotton swabs. The method exploits an enzyme mixture for digestion of the cotton to remove intact cells, and can be utilized in conjunction with or to circumvent conventional differential extraction (DE). Samples digested with Aspergillus niger cellulase yielded sperm cell recoveries (18+/-3.5%) similar to conventional DE buffer (23+/-7.8%) while providing intact epithelial cells. Storage time affected the concentration of enzyme required for optimal sperm cell recovery, with longer times requiring increased cellulase concentrations. Cellulase from A. niger yielded a twofold enhancement in sperm cell elution over buffer alone, and preliminary testing of higher activity cellulases from Trichoderma reesei and Trichoderma viride showed even greater enhancement. These results indicate that cellulose-digesting enzymes enhance the release of sperm and epithelial cells from a cotton swab over buffer alone, providing for efficient DNA analysis.

Aspergillus niger↗
PubMed2006

Development of a human-specific real-time PCR assay for the simultaneous quantitation of total genomic and male DNA.

A duplex real-time quantitative PCR assay was developed for forensic DNA analysis, which provides simultaneous quantitation of total genomic human DNA and human male DNA. The assay utilizes two spectrally resolved fluorogenic probes in a 5' nuclease (TaqMantrade mark) assay. Within the range of organisms empirically tested and based upon theoretical specificity using National Center for Biotechnology Information GenBank sequences, primer and probe sequences were shown to be human specific, and the Y-chromosome probe, male-specific. A mixture-challenge study resulted in accurate quantitation of 25 pg male DNA in a mixture of up to 1:5000 (male:female DNA). Additional experimental results include comparisons with the slot blot method and commercial real-time PCR kits. The assay developed addresses the shortcomings of the traditional slot blot method as well as the commercial real-time PCR kits. This method is shown to be specific, relatively simple, rapid, has low limits of detection, and consumes limited sample in addition to reporting both the male and total genomic DNA concentrations present.

Chromosomes, Human, Y↗
PubMed2006

Rapid DNA amplification in glass microdevices.

The polymerase chain reaction (PCR) for amplification of DNA has become a very useful tool in scientific research and analytical laboratories, yet conventional techniques are time-consuming, and the reagents are expensive. Miniaturization of this technique has the potential to drastically reduce amplification time and reagent consumption while simultaneously improving the efficiency of the reaction. Increasing the surface area-to-volume ratio using microfluidic reaction chambers allows homogeneous solution temperatures to be achieved much more rapidly than in conventional heating blocks. Employing infrared radiation to selectively heat the reaction solution can additionally reduce the time and energy needed for thermocycling; the reaction container is not heated and can even serve as a heat sink for enhancement of cooling. Microchip systems also provide the potential for fabrication of structures for additional processing steps directly in line with the PCR chamber. Not only can amplification be integrated with product separation and analysis, but sample preparation steps can also be incorporated prior to amplification. The ultimate goal is a miniature total-analysis-system with seamlessly coupled sample-in/answer-out capabilities that consumes very low volumes of reagents and drastically reduces the time for analysis. This chapter will focus on the materials and methods involved in simple straight-channel microchip PCR on glass substrates using non-contact thermocycling.

Bacterial Proteins↗
PubMed2005

Pressure injection on a valved microdevice for electrophoretic analysis of submicroliter samples.

A recent report describes a reversible valve that can be used in series to achieve diaphragm pumping on chip (Grover, W. H.; Skelley, A. M.; Liu, C. N.; Lagally, E. T.; and Mathies, R. A. Sens. Actuators, B 2003, 89, 315-323). Here, the functionality of an integrated diaphragm pump on a hybrid PDMS-glass microchip to perform pressure injections for electrophoretic separations is demonstrated. A chip design that can perform both pressure and electrokinetic (EK) injection is described, and a mixture of fluorescein and ROX dyes in borate buffer is utilized as a model sample system. Multiple electrophoretic separations of sample injected with pressure and voltage are compared. Over multiple EK injections, an electrophoretic bias is observed and the injected analytes are not representative of the sample, with the peak area ratio changing 20% after 20 runs. Over multiple pressure injections, however, the sample composition is maintained, with a 3.6% CV over 20 runs. The data presented show the ability to alternate between injection types and pressure-inject a representative sample volume after a bias has already been observed with multiple EK injections. Multiple pressure injections have been performed on sample volumes as low as 500 nL while maintaining sample composition, supporting its use in integrated systems for small-volume sampling.

Electrochemistry↗