October 12, 2009 - Article in Press: "Volume reduction solid phase extraction of DNA from dilute, large volume biological samples" - Carmen - FSI: Genetics - doi:10.1016/j.fsigen.2009.09.005

October 7, 2009 - Article in Press: "An integrated microfluidic device for DNA purification and PCR amplification of STR fragments" - Joan and Lindsay - FSI: Genetics - doi:10.1016/j.fsigen.2009.02.010

October 7, 2009 - Carmen presented her poster entitled "Solid Phase Extraction of Biological Samples in a High Surface Area PMMA Microdevice" at the National Cancer Institute's (NCI) Tenth Principal Investigators Meeting for the Innovative Molecular Analysis Technologies (IMAT) program in Bethesda, MD.





September 7, 2009 - Carol and Dan L.'s review entitled "Nucleic acid extraction techniques and application to the microchip" is published in this week's issue of Lab on a Chip.
    Abstract: "As recently as the early 1990s, DNA purification was time-consuming, requiring the use of toxic, hazardous reagents. The advent of solid phase extraction techniques and the availability of commercial kits for quick and reliable DNA extraction has relegated those early techniques largely to the history books. High quality DNA can now be extracted from whole blood, serum, saliva, urine, stool, cerebral spinal fluid, tissues, and cells in less time without sacrificing recovery. Having achieved such a radical change in the methodology of DNA extraction, focus has shifted to adapting these methods to a miniaturized system, or lab-on-a-chip (A. Manz, N. Graber and H. M. Widmer, Sens. Actuators, B, 1990, 1, 244–248). Manz et al.'s concept of a miniaturized total chemical analysis system (µTAS) involved a silicon chip that incorporated sample pretreatment, separation and detection. This review will focus on the first of these steps, sample pretreatment in the form of DNA purification. The intention of this review is to provide an overview of the fundamentals of nucleic acid purification and solid phase extraction (SPE) and to discuss specific microchip DNA extraction successes and challenges. In order to fully appreciate the advances in DNA purification, a brief review of the history of DNA extraction is provided so that the reader has an understanding of the impact that the development of SPE techniques have had. This review will highlight the different methods of nucleic acid extraction, including relevant citations, but without an exhaustive summary of the literature. A recent review by Wen et al. (J. Wen, L. A. Legendre, J. M. Bienvenue and J. P. Landers, Anal. Chem., 2008, 80, 6472–6479) covers solid phase extraction methods with a greater focus on their incorporation into integrated microfluidic systems."

August 25, 2009 - Welcome to Natalie Coult and Josh Higginson, international student researchers from the University of Huddersfield (UK)!

August 1, 2009 - Jess' article entitled "Acoustic Differential Extraction for Forensic Analysis of Sexual Assault Evidence" is published and featured in "Research Highlights" in this week's issue of Analytical Chemistry.
    Abstract: "Forensic DNA analysis of samples obtained from sexual assault evidence relies on separation of male and female components of the recovered genetic material. The conventional separation method used by crime laboratories, differential extraction (DE), is one of the most time-consuming sample preparation steps, requires extensive sample handling, is difficult to automate, and often results in inefficient separation of female DNA from the male sample components. To circumvent conventional DE, acoustic differential extraction (ADE) analysis was developed on a microfluidic device. The ADE method relies on acoustic trapping of sperm cells in the presence of epithelial cell lysate (which is unretained), and laminar flow valving to direct the male and female fractions to separate outlets. Following the separation of sperm from epithelial cell lysate, DNA extraction, quantitation, amplification, and separation were performed using conventional laboratory methods. The results show that highly purified male and female fractions can be obtained with the ADE microdevice from mock sexual assault samples in 14 min. ADE analysis provides the potential to significantly alter the means by which sexual assault evidence is processed in crime laboratories."

July 27, 2009 - Ling Huang sucessfully defended his PhD - Dissertation titile: "PDMS-based Chemo-mechanical Sensors and Microfluidic Devices" Congrats Dr. Huang!

July 1, 2009 - Kristin's article entitled "Chitosan-coated Silica as a Solid Phase for RNA Purification in a Microfluidic Device" is published in this week's issue of  Analytical Chemistry.
    Abstract: "Chitosan-coated silica particles and chitosan-coated microchannels have been explored as an alternative to a standard silica phase for DNA extraction in a microdevice (Cao, W.; Easley, C. J.; Ferrance, J. P.; Landers, J. P. Anal. Chem. 2006, 78 (20), 7222−7228). A method that exploits the use of aqueous buffers for nucleic acid binding to and release from a solid phase is advantageous, avoiding the reagents used for conventional extraction (isopropanol and guanadinium hydrochloride), which are potent PCR inhibitors. The pH-controlled approach, which promotes nucleic acid binding to and release to the chitosan phase based on a change in buffer pH, is exploited here for RNA purification in a microfluidic device. The chitosan phase reproducibly allowed for higher RNA extraction efficiencies under aqueous conditions (71%) compared to that with a silica phase under chaotropic conditions (53%). The effectiveness of the chitosan phase was demonstrated with the successful purification of RNA from the alveolar rhabdomyosarcoma (ARMS) cancer cell line, with 3.5-fold greater extraction efficiencies than obtained when the same sample was purified using a silica phase: the resulting RNA was found to be amplifiable in reverse-transcription PCR. Low-molecular weight chitosan is also a proven inhibitor of RNases, further demonstrating the advantages of chitosan as a solid phase for RNA purification compared to silica. The chitosan phase is, therefore, a superior choice for extraction and purification of RNA in a microfluidic device and is compatible with biological samples found in a clinical or forensic setting."

May 7, 2009 - Dan Marchiarullo sucessfully defended his PhD - Dissertation title: "Development of Microfluidic Technologies for On-site Clinical and Forensic Analysis" Congrats Dr. Marchiarullo!

April 7, 2009 - Dan L.'s article published in Nature Physics is featured in "Research Highlights" in this week's issue of Lab on a Chip.
    Text: "The control of fluids is a central issue in the design of microfluidic devices. For most applications, in which continuous liquid supply is required, hydrodynamic flow is induced by the use of syringe pumps. For a temporal flow control, e.g., to stop and meter the fluidic sample, different solutions have been developed including the integration of switching solenoids in the tubing system, or the pinching of microchannels made of flexible polymers. These additional components, however, require external hardware, which naturally reduces the portability of the entire system. A simple strategy for fully on-chip flow control has recently been presented by researchers from the University of Virginia. They designed fluidic analogues to electronic capacitors and diodes composed of deformable elastomer features embedded in a microchannel. A single pressure source creates a time-modulated pressure function, while the design and material of the embedded components determines the response in the channel, i.e., the flow pattern. Two examples are shown: (i) a fluidic capacitor is created by placing a thin deformable film over reservoirs that are part of a microfluidic network. As the pressure increases inside the network, fluid is stored in the deformed bulge, much like an electrical capacitor stores charge; (ii) a diode that permits flow in the forward direction only is created by bonding deformable films around weirs that separate two channels in the network. The authors analysed the relation of pressure-input and flow-output, and demonstrate thereby the potential of this approach, in which flow control is achieved by passive fluidic circuits."

April 2, 2009 - Carmen presented her poster entitlted "Dual-domain Microchip-based Process for Volume Reduction Solid Phase Extraction of Dilute, Large Volume Biological Samples " at the 3rd Year poster session.

March 20, 2009 - Dan L.'s article published in Nature Physics is featured as an Editor's Choice in this weeks issue of Science.
    Text: "A nagging problem in microfluidic reactor design is the need for bulky external apparatus to control the pumping and directing of the fluid flows. To circumvent this issue, Leslie et al. tried to mimic passive electrical circuits--resistors, capacitors, and diodes. Capacitors store electrical charge, a function mimicked by bonding a deformable elastomeric film to a fluid microchannel, so that the film bulged to allow more fluid storage as the overall pressure increased. Diodes, which permit flow in only one direction, were fabricated by bonding a deformable film on top of a weir, thus allowing flow only when the pressure was above a critical value. Through a combination of these circuit elements, fluid flow could be predicted and controlled by modulating a pressure source with time through a selection of resistive channels and capacitors. More complex flows were achieved by creating branched streams that merged at the output channel. The flow from each branch was regulated by the frequency of the pressure oscillations, effectively rendering the device a bandpass filter. Diodes, with their nonlinear response to pressure, were used to convert oscillatory flow to steady flow, similar to the conversion of electrical current from ac to dc."

March 1, 2009 - Dan L.'s article entitled "Frequency-specific flow control in microfluidic circuits with passive elastomeric features" is published and featured in "News & Views" in this month's issue of Nature Physics.
    Abstract: "A fundamental challenge in the design of microfluidic devices lies in the need to control the transport of fluid according to complex patterns in space and time, and with sufficient accuracy. Although strategies based on externally actuated valves have enabled marked breakthroughs in chip-based analysis, this requires significant off-chip hardware, such as vacuum pumps and switching solenoids, which strongly tethers such devices to laboratory environments. Severing the microfluidic chip from this off-chip hardware would enable a new generation of devices that place the power of microfluidics in a broader range of disciplines. For example, complete on-chip flow control would empower highly portable microfluidic tools for diagnostics, forensics, environmental analysis and food safety, and be particularly useful in field settings where infrastructure is limited. Here, we demonstrate an elegantly simple strategy for flow control: fluidic networks with embedded deformable features are shown to transport fluid selectively in response to the frequency of a time-modulated pressure source. Distinct fluidic flow patterns are activated through the dynamic control of a single pressure input, akin to the analog responses of passive electrical circuits composed of resistors, capacitors and diodes."

February  17-20, 2009 - Jenny presented her poster entitled "Development of a One-Step Cell Elution and Preferential Lysis Method for Analysis of Sexual Assault Samples" and Kristin presented her poster entitled "Towards a Microfluidic Device for Integrated Purification and Amplification of RNA" at  the American Academy of Forensic Sciences Annual Scientific Meeting in Denver, CO.




February 11-13, 2009 - Congrats to Jenny and Brian for successfully passing their candidacy exams!

December 2008 - Welcome to Jingyi Li, the newest lab member.

November 15, 2008 - Kristin's article entitled "Microchip-Based Solid-Phase Purification of RNA from Biological Samples" is published in this week's issue of Analytical Chemistry.
    Abstract: "Having previously detailed a method for chip-based extraction of DNA (Anal. Chem. 2003, 75, 1880−1886.), we describe here a microchip-based solid-phase extraction method for purification of RNA from biological samples is demonstrated. The method involves the use of silica beads as a solid phase, and the capacity of the device containing silica beads for RNA, RNA in the presence of protein, and DNA was determined. The capacity of the device for RNA binding in the presence of protein is 360 ng, which demonstrates sufficient capacity of the device for complete genetic analysis. An extraction of RNA can be performed on the device in as few as 9 min (analytical time), a time comparable to that of a commercial extraction method, but with less reagent consumption. The microchip-based extraction is also performed in a closed system, unlike the commercial extraction method, which provides the advantage of decreased opportunity for the introduction of RNases and contaminants essential for the sensitive RNA-based analyses presented in this work. RNA purified using the device was shown to be amplifiable using reverse transcription PCR (RT-PCR), allowing for translation of the method to the purification and subsequent amplification of biological samples. RNA was purified using the microchip-based method from neat semen, a mock semen stain, and cultured cells from a common pediatric cancer, alveolar rhabdomyosarcoma."

September 5, 2008 - Jessica Norris successfully defended her PhD - Dissertation title "Advances in Forensic Science: Improving Sexual Assault Evidence Analysis" Congrats Dr. Norris!

September 1, 2008 - Jian and Lindsay's article entitled "Purifcation of Nucleic Acids in a Microdevice" is published in and featured on the cover of  this week's issue of Analytical Chemistry.
    Introduction: "In many ways, polynucleic acids are to biological systems what the microprocessor chip is to electronics the hardware that governs the storage and transfer of information that is vital to the viability of the system. DNA provides the physical architecture (chromosomes and plasmids) that houses the core information of the cell; the various forms of RNA function as part of the reproduction machinery of the cell that translates the core information into structural or enzymatic protein form. Table 1 provides information about the various masses of DNA, mRNA, ribosomal RNA (rRNA), and low-molecular-weight polyribonucleic acids (transfer and microRNA) found in a single diploid cell relative to the protein component. In many ways, this table encapsulates the challenge associated with extracting nucleic acids (NAs) from biological samples the NA component of the cell is dwarfed by orders of magnitude by the protein mass of the cell. In simple terms, the efficient extraction of NAs from a single microliter of whole blood requires the removal of tens of nanograms of DNA from tens of micrograms of protein."

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