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Mar 2012

Volume 6, Issue 1 (partial)

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Resolution limit for DNA barcodes in the Odijk regime

Yanwei Wang, Wes F. Reinhart, Douglas R. Tree, and Kevin D. Dorfman

Biomicrofluidics 6, 014101 (2012); http://dx.doi.org/10.1063/1.3672691 (9 pages)

Online Publication Date: 3 January 2012

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We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of the DNA, simulations indicate that the theoretical predictions are reasonably accurate for channel widths up to two-thirds of the persistence length. Our results quantify the conjecture that DNA barcoding has kilobase pair resolution—provided the nanochannel lies in the Odijk regime.
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87.15.ak Monte Carlo simulations
87.14.gk DNA
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Electrotaxis of lung cancer cells in ordered three-dimensional scaffolds

Yung-Shin Sun, Shih-Wei Peng, Keng-Hui Lin, and Ji-Yen Cheng

Biomicrofluidics 6, 014102 (2012); http://dx.doi.org/10.1063/1.3671399 (14 pages)

Online Publication Date: 4 January 2012

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In this paper, we report a new method to incorporate 3D scaffold with electrotaxis measurement in the microfluidic device. The electrotactic response of lung cancer cells in the 3D foam scaffolds which resemble the in vivo pulmonary alveoli may give more insight on cellular behaviors in vivo. The 3D scaffold consists of ordered arrays of uniform spherical pores in gelatin. We found that cell morphology in the 3D scaffold was different from that in 2D substrate. Next, we applied a direct current electric field (EF) of 338 mV/mm through the scaffold for the study of cells’ migration within. We measured the migration directedness and speed of different lung cancer cell lines, CL1-0, CL1-5, and A549, and compared with those examined in 2D gelatin-coated and bare substrates. The migration direction is the same for all conditions but there are clear differences in cell morphology, directedness, and migration speed under EF. Our results demonstrate cell migration under EF is different in 2D and 3D environments and possibly due to different cell morphology and/or substrate stiffness.
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87.17.Jj Cell locomotion, chemotaxis
87.50.cf Biophysical mechanisms of interaction
47.61.-k Micro- and nano- scale flow phenomena
85.85.+j Micro- and nano-electromechanical systems (MEMS/NEMS) and devices
87.80.Ek Mechanical and micromechanical techniques

Resistive pulse sensing of magnetic beads and supraparticle structures using tunable pores

Geoff R. Willmott, Mark Platt, and Gil U. Lee

Biomicrofluidics 6, 014103 (2012); http://dx.doi.org/10.1063/1.3673596 (15 pages)

Online Publication Date: 12 January 2012

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Tunable pores (TPs) have been used for resistive pulse sensing of 1 μm superparamagnetic beads, both dispersed and within a magnetic field. Upon application of this field, magnetic supraparticle structures (SPSs) were observed. Onset of aggregation was most effectively indicated by an increase in the mean event magnitude, with data collected using an automated thresholding method. Simulations enabled discrimination between resistive pulses caused by dimers and individual particles. Distinct but time-correlated peaks were often observed, suggesting that SPSs became separated in pressure-driven flow focused at the pore constriction. The distinct properties of magnetophoretic and pressure-driven transport mechanisms can explain variations in the event rate when particles move through an asymmetric pore in either direction, with or without a magnetic field applied. Use of TPs for resistive pulse sensing holds potential for efficient, versatile analysis and measurement of nano- and microparticles, while magnetic beads and particle aggregation play important roles in many prospective biosensing applications.
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87.85.J- Biomaterials
87.80.-y Biophysical techniques (research methods)

Microfluidic carbon-blackened polydimethylsiloxane device with reduced ultra violet background fluorescence for simultaneous two-color ultra violet/visible-laser induced fluorescence detection in single cell analysis

Lukas Galla, Dominik Greif, Jan Regtmeier, and Dario Anselmetti

Biomicrofluidics 6, 014104 (2012); http://dx.doi.org/10.1063/1.3675608 (10 pages)

Online Publication Date: 12 January 2012

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In single cell analysis (SCA), individual cell-specific properties and inhomogeneous cellular responses are being investigated that is not subjected to ensemble-averaging or heterogeneous cell population effects. For proteomic single cell analysis, ultra-sensitive and reproducible separation and detection techniques are essential. Microfluidic devices combined with UV laser induced fluorescence (UV-LIF) detection have been proposed to fulfill these requirements. Here, we report on a novel microfluidic chip fabrication procedure that combines straightforward production of polydimethylsiloxane (PDMS) chips with a reduced UV fluorescence background (83%-reduction) by using PDMS droplets with carbon black pigments (CBP) as additives. The CBP-droplet is placed at the point of detection, whereas the rest of the chip remains transparent, ensuring full optical control of the chip. We systematically studied the relation of the UV background fluorescence at CBP to PDMS ratios (varying from 1:10 to 1:1000) for different UV laser powers. Using a CBP/PDMS ratio of 1:20, detection of a 100 nM tryptophan solution (S/N = 3.5) was possible, providing a theoretical limit of detection of 86 nM (with S/N = 3). Via simultaneous two color UV/VIS-LIF detection, we were able to demonstrate the electrophoretic separation of an analyte mixture of 500 nM tryptophan (UV) and 5 nM fluorescein (VIS) within 30 s. As an application, two color LIF detection was also used for the electrophoretic separation of the protein content from a GFP-labeled single Spodoptera frugiperda (Sf9) insect cell. Thereby just one single peak could be measured in the visible spectral range that could be correlated with one single peak among others in the ultraviolet spectra. This indicates an identification of the labeled protein γ-PKC and envisions a further feasible identification of more than one single protein in the future.
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87.80.Ek Mechanical and micromechanical techniques
87.80.Qk Biochemical separation processes
47.85.-g Applied fluid mechanics
82.45.-h Electrochemistry and electrophoresis
85.85.+j Micro- and nano-electromechanical systems (MEMS/NEMS) and devices
87.17.-d Cell processes
87.15.R- Reactions and kinetics
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A nanoporous optofluidic microsystem for highly sensitive and repeatable surface enhanced Raman spectroscopy detection

Soroush H. Yazdi and Ian M. White

Biomicrofluidics 6, 014105 (2012); http://dx.doi.org/10.1063/1.3677369 (9 pages)

Online Publication Date: 13 January 2012

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We report the demonstration of an optofluidic surface enhanced Raman spectroscopy (SERS) device that leverages a nanoporous microfluidic matrix to improve the SERS detection performance by more than two orders of magnitude as compared to a typical open microfluidic channel. Although it is a growing trend to integrate optical biosensors into microfluidic channels, this basic combination has been detrimental to the sensing performance when applied to SERS. Recently, however, synergistic combinations between microfluidic functions and photonics (i.e., optofluidics) have been implemented that improve the detection performance of SERS. Conceptually, the simplest optofluidic SERS techniques reported to date utilize a single nanofluidic channel to trap nanoparticle-analyte conjugates as a method of preconcentration before detection. In this work, we leverage this paradigm while improving upon the simplicity by forming a 3D nanofluidic network with packed nanoporous silica microspheres in a microfluidic channel; this creates a concentration matrix that traps silver nanoclusters and adsorbed analytes into the SERS detection volume. With this approach, we are able to achieve a detection limit of 400 attomoles of Rhodamine 6G after only 2 min of sample loading with high chip-to-chip repeatability. Due to the high number of fluidic paths in the nanoporous channel, this approach is less prone to clogging than single nanofluidic inlets, and the loading time is decreased compared to previous reports. In addition, fabrication of this microsystem is quite simple, as nanoscale fabrication is not necessary. Finally, integrated multimode fiber optic cables eliminate the need for optical alignment, and thus the device is relevant for portable and automated applications in the field, including point-of-sample and point-of-care detection. To illustrate a relevant field-based application, we demonstrate the detection of 12 ppb of the organophosphate malathion in water using the nanofluidic SERS microsystem.
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87.85.Rs Nanotechnologies-applications
47.85.Np Fluidics
85.85.+j Micro- and nano-electromechanical systems (MEMS/NEMS) and devices
42.81.Pa Sensors, gyros

Fluid flow due to collective non-reciprocal motion of symmetrically-beating artificial cilia

S. N. Khaderi, J. M. J. den Toonder, and P. R. Onck

Biomicrofluidics 6, 014106 (2012); http://dx.doi.org/10.1063/1.3676068 (14 pages)

Online Publication Date: 20 January 2012

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Using a magneto-mechanical solid-fluid numerical model for permanently magnetic artificial cilia, we show that the metachronal motion of symmetrically beating cilia establishes a net pressure gradient in the direction of the metachronal wave, which creates a unidirectional flow. The flow generated is characterised as a function of the cilia spacing, the length of the metachronal wave, and a dimensionless parameter that characterises the relative importance of the viscous forces over the elastic forces in the cilia.
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87.85.gf Fluid mechanics and rheology
47.63.Jd Microcirculation and flow through tissues

A tapered channel microfluidic device for comprehensive cell adhesion analysis, using measurements of detachment kinetics and shear stress-dependent motion

Peter Rupprecht, Laurent Golé, Jean-Paul Rieu, Cyrille Vézy, Rosaria Ferrigno, Hichem C. Mertani, and Charlotte Rivière

Biomicrofluidics 6, 014107 (2012); http://dx.doi.org/10.1063/1.3673802 (12 pages)

Online Publication Date: 31 January 2012

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We have developed a method for studying cellular adhesion by using a custom-designed microfluidic device with parallel non-connected tapered channels. The design enables investigation of cellular responses to a large range of shear stress (ratio of 25) with a single input flow-rate. For each shear stress, a large number of cells are analyzed (500–1500 cells), providing statistically relevant data within a single experiment. Besides adhesion strength measurements, the microsystem presented in this paper enables in-depth analysis of cell detachment kinetics by real-time videomicroscopy. It offers the possibility to analyze adhesion-associated processes, such as migration or cell shape change, within the same experiment. To show the versatility of our device, we examined quantitatively cell adhesion by analyzing kinetics, adhesive strength and migration behaviour or cell shape modifications of the unicellular model cell organism Dictyostelium discoideum at 21 °C and of the human breast cancer cell line MDA-MB-231 at 37 °C. For both cell types, we found that the threshold stresses, which are necessary to detach the cells, follow lognormal distributions, and that the detachment process follows first order kinetics. In addition, for particular conditions’ cells are found to exhibit similar adhesion threshold stresses, but very different detachment kinetics, revealing the importance of dynamics analysis to fully describe cell adhesion. With its rapid implementation and potential for parallel sample processing, such microsystem offers a highly controllable platform for exploring cell adhesion characteristics in a large set of environmental conditions and cell types, and could have wide applications across cell biology, tissue engineering, and cell screening.
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87.80.Ek Mechanical and micromechanical techniques
85.85.+j Micro- and nano-electromechanical systems (MEMS/NEMS) and devices
07.10.Cm Micromechanical devices and systems
87.17.Uv Biotechnology of cell processes
87.17.Rt Cell adhesion and cell mechanics

Michaelis-Menten kinetics in shear flow: Similarity solutions for multi-step reactions

W. D. Ristenpart and H. A. Stone

Biomicrofluidics 6, 014108 (2012); http://dx.doi.org/10.1063/1.3679950 (9 pages)

Online Publication Date: 31 January 2012

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Models for chemical reaction kinetics typically assume well-mixed conditions, in which chemical compositions change in time but are uniform in space. In contrast, many biological and microfluidic systems of interest involve non-uniform flows where gradients in flow velocity dynamically alter the effective reaction volume. Here, we present a theoretical framework for characterizing multi-step reactions that occur when an enzyme or enzymatic substrate is released from a flat solid surface into a linear shear flow. Similarity solutions are developed for situations where the reactions are sufficiently slow compared to a convective time scale, allowing a regular perturbation approach to be employed. For the specific case of Michaelis-Menten reactions, we establish that the transversally averaged concentration of product scales with the distance x downstream as x5/3. We generalize the analysis to n-step reactions, and we discuss the implications for designing new microfluidic kinetic assays to probe the effect of flow on biochemical processes.
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82.39.Fk Enzyme kinetics
47.85.Np Fluidics
47.70.Fw Chemically reactive flows
47.63.-b Biological fluid dynamics
87.14.ej Enzymes
82.40.-g Chemical kinetics and reactions: special regimes and techniques

High-throughput study of alpha-synuclein expression in yeast using microfluidics for control of local cellular microenvironment

Patrícia Rosa, Sandra Tenreiro, Virginia Chu, Tiago F. Outeiro, and João Pedro Conde

Biomicrofluidics 6, 014109 (2012); http://dx.doi.org/10.1063/1.3683161 (9 pages)

Online Publication Date: 9 February 2012

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Microfluidics is an emerging technology which allows the miniaturization, integration, and automation of fluid handling processes. Microfluidic systems offer low sample consumption, significantly reduced processing time, and the prospect of massive parallelization. A microfluidic platform was developed for the control of the soluble cellular microenvironment of Saccharomyces cerevisiae cells, which enabled high-throughput monitoring of the controlled expression of alpha-synuclein (aSyn), a protein involved in Parkinson’s disease. Y-shaped structures were fabricated using particle desorption mass spectrometry-based soft-lithography techniques to generate biomolecular gradients along a microchannel. Cell traps integrated along the microchannel allowed the positioning and monitoring of cells in precise locations, where different, well-controlled chemical environments were established. S. cerevisiae cells genetically engineered to encode the fusion protein aSyn-GFP (green fluorescent protein) under the control of GAL1, a galactose inducible promoter, were loaded in the microfluidic structure. A galactose concentration gradient was established in the channel and a time-dependent aSyn-GFP expression was obtained as a function of the positioning of cells along the galactose gradient. Our results demonstrate the applicability of this microfluidic platform to the spatiotemporal control of cellular microenvironment and open a range of possibilities for the study of cellular processes based on single-cell analysis.
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87.85.Ox Biomedical instrumentation and transducers, including micro-electro-mechanical systems (MEMS)
47.85.Np Fluidics
87.19.X- Diseases
87.16.-b Subcellular structure and processes
87.15.B- Structure of biomolecules
87.14.E- Proteins
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Oxygen and nitrogen plasma hydrophilization and hydrophobic recovery of polymers

Ville Jokinen, Pia Suvanto, and Sami Franssila

Biomicrofluidics 6, 016501 (2012); http://dx.doi.org/10.1063/1.3673251 (10 pages)

Online Publication Date: 3 January 2012

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Plasma hydrophilization and subsequent hydrophobic recovery are studied for ten different polymers of microfabrication interest: polydimethylsiloxane (PDMS), polymethylmethacrylate, polycarbonate, polyethylene, polypropylene, polystyrene, epoxy polymer SU-8, hybrid polymer ORMOCOMP, polycaprolactone, and polycaprolactone/D,L-lactide (P(CL/DLLA)). All polymers are treated identically with oxygen and nitrogen plasmas, in order to make comparisons between polymers as easy as possible. The primary measured parameter is the contact angle, which was measured on all polymers for more than 100 days in order to determine the kinetics of the hydrophobic recovery for both dry stored and rewashed samples. Clear differences and trends are observed both between different polymers and between different plasma parameters.
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52.77.-j Plasma applications
61.41.+e Polymers, elastomers, and plastics
68.03.Cd Surface tension and related phenomena

Wafer-scale fabrication of high-aspect ratio nanochannels based on edge-lithography technique

Quan Xie, Qing Zhou, Fei Xie, Jianming Sang, Wei Wang, Haixia Alice Zhang, Wengang Wu, and Zhihong Li

Biomicrofluidics 6, 016502 (2012); http://dx.doi.org/10.1063/1.3683164 (8 pages)

Online Publication Date: 9 February 2012

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This paper introduced a wafer-scale fabrication approach for the preparation of nanochannels with high-aspect ratio (the ratio of the channel depth to its width). Edge lithography was used to pattern nanogaps in an aluminum film, which was functioned as deep reactive ion etching mask thereafter to form the nanochannel. Nanochannels with aspect ratio up to 172 and width down to 44 nm were successfully fabricated on a 4-inch Si wafer with width nonuniformity less than 13.6%. A microfluidic chip integrated with nanometer-sized filters was successfully fabricated by utilizing the present method for geometric-controllable nanoparticle packing.
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87.80.Ek Mechanical and micromechanical techniques

A new fabrication technique to form complex polymethylmethacrylate microchannel for bioseparation

Talukder Z. Jubery, Mohammad R. Hossan, Danny R. Bottenus, Cornelius F. Ivory, Wenji Dong, and Prashanta Dutta

Biomicrofluidics 6, 016503 (2012); http://dx.doi.org/10.1063/1.3683163 (13 pages)

Online Publication Date: 10 February 2012

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Recent studies show that reduction in cross-sectional area can be used to improve the concentration factor in microscale bioseparations. Due to simplicity in fabrication process, a step reduction in cross-sectional area is generally implemented in microchip to increase the concentration factor. But the sudden change in cross-sectional area can introduce significant band dispersion and distortion. This paper reports a new fabrication technique to form a gradual reduction in cross-sectional area in polymethylmethacrylate (PMMA) microchannel for both anionic and cationic isotachophoresis (ITP). The fabrication technique is based on hot embossing and surface modification assisted bonding method. Both one-dimensional and two-dimensional gradual reduction in cross-sectional area microchannels were formed on PMMA with high fidelity using proposed techniques. ITP experiments were conducted to separate and preconcentrate fluorescent proteins in these microchips. Thousand fold and ten thousand fold increase in concentrations were obtained when 10 × and 100 × gradual reduction in cross-sectional area microchannels were used for ITP.
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87.80.Qk Biochemical separation processes
87.15.Tt Electrophoresis
07.10.Cm Micromechanical devices and systems
85.85.+j Micro- and nano-electromechanical systems (MEMS/NEMS) and devices
87.80.Ek Mechanical and micromechanical techniques
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