Microfluidics Technology

A special issue of Microarrays (ISSN 2076-3905).

Deadline for manuscript submissions: closed (15 April 2017) | Viewed by 27090

Special Issue Editor

School of Medicine, New York Medical College, Valhalla, NY 10595, USA
Interests: biofilm development and cell dispersion; COPD exacerbation; anti-microbial agent discovery; oral and systemic health linkage

Special Issue Information

Dear Colleagues

This Special Issue focuses on studies utilizing novel microfluidic, micro-fabrication, systems integration and advanced informatics technology, which enables rapid and comprehensive investigations of broad-based biological systems.

Professor Zvi Loewy
Guest Editor

Manuscript Submission Information

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Keywords

  • microfluidics
  • nucleic acid amplification
  • gene expression
  • massively parallel analyses
  • quantitative determinations

Published Papers (4 papers)

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Research

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2429 KiB  
Article
Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB
by Ahsan Munir, Hassan Waseem, Maggie R. Williams, Robert D. Stedtfeld, Erdogan Gulari, James M. Tiedje and Syed A. Hashsham
Microarrays 2017, 6(2), 9; https://doi.org/10.3390/microarrays6020009 - 29 May 2017
Cited by 7 | Viewed by 6433
Abstract
Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface [...] Read more.
Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131). Full article
(This article belongs to the Special Issue Microfluidics Technology)
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3760 KiB  
Article
Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis
by Michael Januszyk, Robert C. Rennert, Michael Sorkin, Zeshaan N. Maan, Lisa K. Wong, Alexander J. Whittam, Arnetha Whitmore, Dominik Duscher and Geoffrey C. Gurtner
Microarrays 2015, 4(4), 540-550; https://doi.org/10.3390/microarrays4040540 - 04 Nov 2015
Cited by 29 | Viewed by 6222
Abstract
Significant transcriptional heterogeneity is an inherent property of complex tissues such as tumors and healing wounds. Traditional methods of high-throughput analysis rely on pooling gene expression data from hundreds of thousands of cells and reporting a population-wide average that is unable to capture [...] Read more.
Significant transcriptional heterogeneity is an inherent property of complex tissues such as tumors and healing wounds. Traditional methods of high-throughput analysis rely on pooling gene expression data from hundreds of thousands of cells and reporting a population-wide average that is unable to capture differences within distinct cell subsets. Recent advances in microfluidic technology have permitted the development of large-scale single cell analytic methods that overcome this limitation. The increased granularity afforded by such approaches allows us to answer the critical question of whether expansion in cell culture significantly alters the transcriptional characteristics of cells isolated from primary tissue. Here we examine an established population of human adipose-derived stem cells (ASCs) using a novel, microfluidic-based method for high-throughput transcriptional interrogation, coupled with advanced bioinformatic analysis, to evaluate the dynamics of single cell gene expression among primary, passage 0, and passage 1 stem cells. We find significant differences in the transcriptional profiles of cells from each group, as well as a considerable shift in subpopulation dynamics as those subgroups better able to adhere and proliferate under these culture conditions gradually emerge as dominant. Taken together, these findings reinforce the importance of using primary or very early passage cells in future studies. Full article
(This article belongs to the Special Issue Microfluidics Technology)
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Review

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619 KiB  
Review
Microarray-Based Comparative Genomic and Transcriptome Analysis of Borrelia burgdorferi
by Radha Iyer and Ira Schwartz
Microarrays 2016, 5(2), 9; https://doi.org/10.3390/microarrays5020009 - 16 Apr 2016
Cited by 14 | Viewed by 4980
Abstract
Borrelia burgdorferi, the spirochetal agent of Lyme disease, is maintained in nature in a cycle involving a tick vector and a mammalian host. Adaptation to the diverse conditions of temperature, pH, oxygen tension and nutrient availability in these two environments requires the [...] Read more.
Borrelia burgdorferi, the spirochetal agent of Lyme disease, is maintained in nature in a cycle involving a tick vector and a mammalian host. Adaptation to the diverse conditions of temperature, pH, oxygen tension and nutrient availability in these two environments requires the precise orchestration of gene expression. Over 25 microarray analyses relating to B. burgdorferi genomics and transcriptomics have been published. The majority of these studies has explored the global transcriptome under a variety of conditions and has contributed substantially to the current understanding of B. burgdorferi transcriptional regulation. In this review, we present a summary of these studies with particular focus on those that helped define the roles of transcriptional regulators in modulating gene expression in the tick and mammalian milieus. By performing comparative analysis of results derived from the published microarray expression profiling studies, we identified composite gene lists comprising differentially expressed genes in these two environments. Further, we explored the overlap between the regulatory circuits that function during the tick and mammalian phases of the enzootic cycle. Taken together, the data indicate that there is interplay among the distinct signaling pathways that function in feeding ticks and during adaptation to growth in the mammal. Full article
(This article belongs to the Special Issue Microfluidics Technology)
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3869 KiB  
Review
Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification
by Michael G. Mauk, Changchun Liu, Jinzhao Song and Haim H. Bau
Microarrays 2015, 4(4), 474-489; https://doi.org/10.3390/microarrays4040474 - 20 Oct 2015
Cited by 11 | Viewed by 8900
Abstract
Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the [...] Read more.
Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 103 virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed. Full article
(This article belongs to the Special Issue Microfluidics Technology)
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