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Abstract: "This work describes the performance of poly(methyl methacrylate) (PMMA) microfluidic DNA purification devices with embedded microfabricated posts, functionalized with chitosan. PMMA is attractive as a substrate for creating high surface area (SA) posts for DNA capture because X-ray lithography can be exploited for extremely reproducible fabrication of high SA structures. However, this advantage is offset by the delicate nature of the posts when attempting bonding to create a closed system, and by the challenge of functionalizing the PMMA surface with a group that invokes DNA binding. Methods are described for covalent functionalization of the post surfaces with chitosan that binds DNA in a pH-dependent manner, as well as for bonding methods that avoid damaging the underlying post structure. A number of geometric posts designs are explored, with the goal of identifying post structures that provide the requisite surface area without a concurrent rise in fluidic resistance that promotes device failure. Initial proof-of-principle is shown by recovery of prepurified human genomic DNA (hgDNA), with real-world utility illustrated by purifying hgDNA from whole blood and demonstrating it to be PCR-amplifiable."

March 21, 2011 - Kristin's article entitled "A valveless microfluidic device for integrated solid phase extraction and polymerase chain reaction for short tandem repeat (STR) anaylsis" is published in this week's issue of Analyst.                        
  Abstract: "A valveless microdevice has been developed for the integration of solid phase extraction (SPE) and polymerase chain reaction (PCR) on a single chip for the short tandem repeat (STR) analysis of DNA from a biological sample. The device consists of two domains--a SPE domain filled with silica beads as a solid phase and a PCR domain with an ~500 nL reaction chamber. DNA from buccal swabs was purified and amplified using the integrated device and a full STR profile (16 loci) resulted. The 16 loci Identifiler® multiplex amplification was performed using a non-contact infrared (IR)-mediated PCR system built in-house, after syringe-driven SPE, providing an ~80-fold and 2.2-fold reduction in sample and reagent volumes consumed, respectively, as well as an ~5-fold reduction in the overall analysis time in comparison to conventional analysis. Results indicate that the SPE-PCR system can be used for many applications requiring genetic analysis, and the future addition of microchip electrophoresis (ME) to the system would allow for the complete processing of biological samples for forensic STR analysis on a single microdevice."

March 13-18, 2011 - Jenny presented her posters entitled "Amplification of short tandem repeat (STR) regions of the genome for forensic DNA analysis in a plastic microfluidic device" and "The use of polyimide filters for improving infrared-based PCR amplification in microfluidic devices", Jingyi presented his poster entitled "A microscale method for visual and label-free quantitation of DNA, bacterial detection, nucleated cell counting, and more", Yiwen presented her posters entitled "Multiplexed DNA extraction and infrared temperature controlled polymerase chain reaction in disposable polyester-toner chip", and Brian gave a talk entitled "Integrated acoustic cell trapping and polymerase chain reaction: a novel method to detect food-born pathogens" repectively at the PITTCON 2011 in Atlanta, GA.

March 7, 2011 - Kristin's article entitled "An integrated, valveless system for microfluidic purification and reverse transcription-PCR amplification of RNA for detection of infectious agents" is published in this week's issue of Lab on a Chip.
  Abstract: "We describe the first miniaturized device capable of the front-end sample preparation essential for detecting RNA-based infectious agents. The microfluidic device integrates sample purification and reverse transcription PCR (RT-PCR) amplification for the identification and detection of influenza A. The device incorporates a chitosan-based RNA binding phase for the completely aqueous isolation of nucleic acids, avoiding the PCR inhibitory effects of guanidine and isopropanol used in silica-based extraction methods. The purified nucleic acids and the reagents needed for single-step RT-PCR amplification are fluidically mobilized simultaneously to a PCR chamber. Utilizing infrared (IR)-mediated heating allowed for a > 5-fold decrease in RT-PCR analysis time compared to a standard thermal cycling protocol used in a conventional thermal cycler. Influenza A virus [A/PR/8/34 (H1N1)] was used as a simulant in this study for virus-based infectious and biowarfare agents with RNA genomes, and was successfully detected in a mock nasal swab sample at clinically relevant concentrations. Following on-chip purification, a fragment specific to the influenza A nucleoprotein gene was first amplified via RT-PCR amplification using IR-mediated heating to achieve more rapid heating and cooling rates. This was initially accomplished on a two-chip system to optimize the SPE and RT-PCR, and then translated to an integrated SPE-RT-PCR device. "

March 4, 2011 - Article in Press: "Solid phase extraction of DNA from biological samples in a post-based, high surface area poly(methyl methacrylate) (PMMA) microdevice" - Carmen - Lab on a Chip - doi: 10.1039/C0LC00597E

February 23-26, 2010 - Jenny presented her posters entitled "Expedited enzyme-based preparation of PCR-ready DNA from forensic biological samples on glass and PMMA microdevices" and gave 2 talks "Enzyme-based preparation of PCR-ready DNA from neat semen and semen stains" and "Towards a plastic microdevice for integrated enzyme-based DNA preparation and PCR focusedon forensic STR analysis" at the 63nd American Academy of Forensic Sciences Annual Scientific Meeting in Chicago, IL.




Feb 22, 2011 - Carmen's article entitled "A modular microfluidic system for deoxyribonucleic acid identification by short tandem repeat analysis" is published in this week's issue of Analytica Chimica Acta.

  Abstract: "Microfluidic technology has been utilized in the development of a modular system for DNA identification through STR (short tandem repeat) analysis, reducing the total analysis time from the ∼6 h required with conventional approaches to less than 3h. Results demonstrate the utilization of microfluidic devices for the purification, amplification, separation and detection of 9 loci associated with a commercially-available miniSTR amplification kit commonly used in the forensic community. First, DNA from buccal swabs purified in a microdevice was proven amplifiable for the 9 miniSTR loci via infrared (IR)-mediated PCR (polymerase chain reaction) on a microdevice. Microchip electrophoresis (ME) was then demonstrated as an effective method for the separation and detection of the chip-purified and chip-amplified DNA with results equivalent to those obtained using conventional separation methods on an ABI 310 Genetic Analyzer. The 3-chip system presented here demonstrates development of a modular, microfluidic system for STR analysis, allowing for user-discretion as to how to proceed after each process during the analysis of forensic casework samples."

February 14, 2011 - Congrats to Kerui, Briony, and Yiwen for successfully passing their candidacy exams!

January 2011 - Happy New Year!

December 16, 2010 - Article in Press: "A modular microfluidic system for deoxyrbonucleic acid identification by short tandem repeat analysis" - Carmen and Kristin - Analytica Chimica Acta:doi:10.1016/j.aca.2010.12.016

December 8, 2010 - Advance Article: "An integrated, valveless system for microfluidic purification and reverse transcription-PCR amplification of RNA for detection of infectious agents" - Kristin - Lab on a Chip - doi:10.1039/c0lc00136h.

December 2010 - Welcome to Qian Liu, Dan Nelson and Kyudam Oh, our newest lab members!

November 19, 2010 - Dr. Utz and Dr. Landers have an article entitled "Magnetic Resonance and Microfluidics" published in the "Perspectives" section in this week's issue of Science.

  Introduction: "Magnetic resonance imaging (MRI) is a well-established clinical tool that is routinely used to locate cartilage or ligament damage, cancerous lesions, and blood vessel occlusions; when combined with magnetic resonance spectroscopy (MRS), it can even map brain function. The image contrast in MRI instruments comes from the change in orientation of the rotational axis (precession) of atomic nuclei in a magnetic field, and can be adjusted to selectively image tissues on the basis of oxygen content, diffusivity, flow velocity, and other properties. Microfluidic “lab-on-a-chip” (LOC) devices represent an emerging technology with potential applications in medical diagnostics. These devices flow samples (which often consist of suspensions of cells) and reagents through miniaturized chemical reactors, and are typically fabricated via lithographic methods similar to those used in microelectronics. Although in principle, MRI should be the ideal tool for monitoring reactions on LOC devices, in practice this turns out to be notoriously difficult because of limitations in sensitivity and resolution. On page 1078 of this issue, Bajaj et al. (1) present an ingenious method that allows sensitive MRI measurements on an LOC device by recording magnetic resonance signals from the spent fluid that exits the device."

October 26, 2010 - Carmen Reedy sucessfully defended her Ph.D. - Dissertation title "DNA Purification on Microfluidic Devices with a Focus on Large Volume, Forensic Biological Samples" Congrats Dr. Reedy!

October 11-13, 2010 - Jenny had her posters entitled "Towards an Integrated, Valveless, Plastic Microdevice for Enzyme-Based DNA Preparation and PCR for Forensic STR Analysis" and "Preparation of High Quality, PCR-Ready DNA from Semen Using an Enzymatic Preparation Method" presented at  the 21st International Symposium on Human Identification in San Antonio, TX.

October 3-7, 2010 - Brian presented his poster entitled "Developments Towards Integrated Acoustic Cell Trapping and PCR", and Carmen and Jenny had their posters entitled "Microfluidic Volume Reduction Solid Phase Extraction of Compromsed and Low DNA Template Forensic Samples" and "Towards an Integrated Microdevice for Enzyme-Based DNA Preparation and PCR Applicable to Forensic DNA Analysis", repectively, presented at the 14th International Micro Total Analysis Systems (uTAS) conference in Groningen, Netherlands.



July 20, 2010 - Kristin Hagan sucessfully defended her Ph.D. - Dissertation titile: "Microfluidic Systems for Sample Preparation with a Focus on RNA Analysis" Congrats Dr. Hagan!

July 15, 2010 - Dan's article entitled "A simple method for the evaluation of microfluidic architecture using flow quantitation via a multiplexed fluidic resisitance measurement" is published in this week's issue of Lab on a Chip.

  Abstract: "Quality control of microdevices adds significant costs, in time and money, to any fabrication process. A simple, rapid quantitative method for the post-fabrication characterization of microchannel architecture using the measurement of flow with volumes relevant to microfluidics is presented. By measuring the mass of a dye solution passed through the device, it circumvents traditional gravimetric and interface-tracking methods that suffer from variable evaporation rates and the increased error associated with smaller volumes. The multiplexed fluidic resistance (MFR) measurement method measures flow via stable visible-wavelength dyes, a standard spectrophotometer and common laboratory glassware. Individual dyes are used as molecular markers of flow for individual channels, and in channel architectures where multiple channels terminate at a common reservoir, spectral deconvolution reveals the individual flow contributions. On-chip, this method was found to maintain accurate flow measurement at lower flow rates than the gravimetric approach. Multiple dyes are shown to allow for independent measurement of multiple flows on the same device simultaneously. We demonstrate that this technique is applicable for measuring the fluidic resistance, which is dependent on channel dimensions, in four fluidically connected channels simultaneously, ultimately determining that one chip was partially collapsed and, therefore, unusable for its intended purpose. This method is thus shown to be widely useful in troubleshooting microfluidic flow characteristics."

July 1, 2010 - Carmen's article entitled "Dual Domain Microchip-Based Process for Volume Reduction Solid Phase Extraction of Nucleic Acids from Dilute, Large Volume Biological Samples" is published in this week's issue of Analytical Chemstry.

  Abstract: "A microfluidic device was developed to carry out integrated volume reduction and purification of nucleic acids from dilute, large volume biological samples commonly encountered in forensic genetic analysis. The dual-phase device seamlessly integrates two orthogonal solid-phase extraction (SPE) processes, a silica solid phase using chaotrope-driven binding and an ion exchange phase using totally aqueous chemistry (chitosan phase), providing the unique capability of removing polymerase chain reaction (PCR) inhibitors used in silica-based extractions (guanidine and isopropanol). Nucleic acids from a large volume sample are shown to undergo a substantial volume reduction on the silica phase, followed by a more stringent extraction on the chitosan phase. The key to interfacing the two steps is mixing of the eluted nucleic acids from the first phase with loading buffer which is facilitated by flow-mediated mixing over a herringbone mixing region in the device. The complete aqueous chemistry associated with the second purification step yields a highly concentrated PCR-ready eluate of nucleic acids devoid of PCR inhibitors that are reagent-based (isopropanol) and sample-based (indigo dye), both of which are shown to be successfully removed using the dual-phase device but not by the traditional microfluidic SPE (μSPE). The utility of the device for purifying DNA was demonstrated with dilute whole blood, dilute semen, a semen stain, and a blood sample inhibited with indigo dye, with the resultant DNA from all shown to be PCR amplifiable. The same samples purified using μSPE were not all PCR amplifiable due to a smaller concentration of the DNA and the lack of PCR-compatible aqueous chemistry in the extraction method. The utility of the device for the purification of RNA was also demonstrated, by the extraction of RNA from a dilute semen sample, with the resulting RNA amplified using reverse transcription (RT)-PCR. The vrSPE-SPE device reliably yields a volume reduction for DNA and RNA purification on the order of 50- and 14-fold, respectively, both compatible with downstream PCR analysis. In addition, purification of all samples consumed less reagents (2.6-fold) than traditional purification methods, with the added advantage of being a “closed system” that eliminates sample transfer steps, thereby reducing the possible entrance points for contaminants."

July 1, 2010 - Ling's article entitled "Molecular Interactions in Surface-Assembled Monolayers of Short Double-Stranded DNA" is published in this week's issue of Langmuir.
 
 Abstract: "We present an experimental study of the energetics of repulsion between end-grafted fragments of double-stranded DNA. The absorption isotherm of thiolated DNA fragments has been measured as a function of DNA chain length as well as the salinity of the surrounding solution. The results are consistent with a simple excluded-volume model of the interaction between neighboring DNA strands."