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Sample records for microfluidic protein patterning

  1. Rapid photochemical surface patterning of proteins in thiol-ene based microfluidic devices

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Kwapiszewski, Radoslaw; Jensen, Thomas Glasdam;

    2013-01-01

    The suitable optical properties of thiol–ene polymers combined with the ease of modifying their surface for the attachment of recognition molecules make them ideal candidates in many biochip applications. This paper reports the rapid one-step photochemical surface patterning of biomolecules...... in microfluidic thiol–ene chips. This work focuses on thiol–ene substrates featuring an excess of thiol groups at their surface. The thiol–ene stoichiometric composition can be varied to precisely control the number of surface thiol groups available for surface modification up to an average surface density of 136...... ! 17 SH nm"2. Biotin alkyne was patterned directly inside thiol–ene microchannels prior to conjugation with fluorescently labelled streptavidin. The surface bound conjugates were detected by evanescent waveinduced fluorescence (EWIF), demonstrating the success of the grafting procedure and its...

  2. Rapid photochemical surface patterning of proteins in thiol-ene based microfluidic devices

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Kwapiszewski, Radoslaw; Jensen, Thomas Glasdam;

    2012-01-01

    ” and “ene” monomers present in the microfluidic chip bulk material provides a simple and efficient way of tuning the chip’s surface chemistry. Here, thiol-ene chips displaying an excess of functional thiol groups at their surfaces are functionalized with biotin and streptavidin in a controlled fashion using...

  3. Microfluidic Tools for Protein Crystallography

    Science.gov (United States)

    Abdallah, Bahige G.

    X-ray crystallography is the most widely used method to determine the structure of proteins, providing an understanding of their functions in all aspects of life to advance applications in fields such as drug development and renewable energy. New techniques, namely serial femtosecond crystallography (SFX), have unlocked the ability to unravel the structures of complex proteins with vital biological functions. A key step and major bottleneck of structure determination is protein crystallization, which is very arduous due to the complexity of proteins and their natural environments. Furthermore, crystal characteristics govern data quality, thus need to be optimized to attain the most accurate reconstruction of the protein structure. Crystal size is one such characteristic in which narrowed distributions with a small modal size can significantly reduce the amount of protein needed for SFX. A novel microfluidic sorting platform was developed to isolate viable ~200 nm -- ~600 nm photosystem I (PSI) membrane protein crystals from ~200 nm -- ~20 ?m crystal samples using dielectrophoresis, as confirmed by fluorescence microscopy, second-order nonlinear imaging of chiral crystals (SONICC), and dynamic light scattering. The platform was scaled-up to rapidly provide 100s of microliters of sorted crystals necessary for SFX, in which similar crystal size distributions were attained. Transmission electron microscopy was used to view the PSI crystal lattice, which remained well-ordered postsorting, and SFX diffraction data was obtained, confirming a high-quality, viable crystal sample. Simulations indicated sorted samples provided accurate, complete SFX datasets with 3500-fold less protein than unsorted samples. Microfluidic devices were also developed for versatile, rapid protein crystallization screening using nanovolumes of sample. Concentration gradients of protein and precipitant were generated to crystallize PSI, phycocyanin, and lysozyme using modified counterdiffusion

  4. Integrated Microfluidics for Protein Modification Discovery*

    Science.gov (United States)

    Noach-Hirsh, Meirav; Nevenzal, Hadas; Glick, Yair; Chorni, Evelin; Avrahami, Dorit; Barbiro-Michaely, Efrat; Gerber, Doron; Tzur, Amit

    2015-01-01

    Protein post-translational modifications mediate dynamic cellular processes with broad implications in human disease pathogenesis. There is a large demand for high-throughput technologies supporting post-translational modifications research, and both mass spectrometry and protein arrays have been successfully utilized for this purpose. Protein arrays override the major limitation of target protein abundance inherently associated with MS analysis. This technology, however, is typically restricted to pre-purified proteins spotted in a fixed composition on chips with limited life-time and functionality. In addition, the chips are expensive and designed for a single use, making complex experiments cost-prohibitive. Combining microfluidics with in situ protein expression from a cDNA microarray addressed these limitations. Based on this approach, we introduce a modular integrated microfluidic platform for multiple post-translational modifications analysis of freshly synthesized protein arrays (IMPA). The system's potency, specificity and flexibility are demonstrated for tyrosine phosphorylation and ubiquitination in quasicellular environments. Unlimited by design and protein composition, and relying on minute amounts of biological material and cost-effective technology, this unique approach is applicable for a broad range of basic, biomedical and biomarker research. PMID:26276765

  5. Integrated Microfluidics for Protein Modification Discovery.

    Science.gov (United States)

    Noach-Hirsh, Meirav; Nevenzal, Hadas; Glick, Yair; Chorni, Evelin; Avrahami, Dorit; Barbiro-Michaely, Efrat; Gerber, Doron; Tzur, Amit

    2015-10-01

    Protein post-translational modifications mediate dynamic cellular processes with broad implications in human disease pathogenesis. There is a large demand for high-throughput technologies supporting post-translational modifications research, and both mass spectrometry and protein arrays have been successfully utilized for this purpose. Protein arrays override the major limitation of target protein abundance inherently associated with MS analysis. This technology, however, is typically restricted to pre-purified proteins spotted in a fixed composition on chips with limited life-time and functionality. In addition, the chips are expensive and designed for a single use, making complex experiments cost-prohibitive. Combining microfluidics with in situ protein expression from a cDNA microarray addressed these limitations. Based on this approach, we introduce a modular integrated microfluidic platform for multiple post-translational modifications analysis of freshly synthesized protein arrays (IMPA). The system's potency, specificity and flexibility are demonstrated for tyrosine phosphorylation and ubiquitination in quasicellular environments. Unlimited by design and protein composition, and relying on minute amounts of biological material and cost-effective technology, this unique approach is applicable for a broad range of basic, biomedical and biomarker research.

  6. A microfluidic device with groove patterns for studying cellular behavior.

    Science.gov (United States)

    Chung, Bong Geun; Manbachi, Amir; Khademhosseini, Ali

    2007-01-01

    We describe a microfluidic device with microgrooved patterns for studying cellular behavior. This microfluidic platform consists of a top fluidic channel and a bottom microgrooved substrate. To fabricate the microgrooved channels, a top poly(dimethylsiloxane) (PDMS) mold containing the impression of the microfluidic channels was aligned and bonded to a microgrooved substrate. Using this device, mouse fibroblast cells were immobilized and patterned within microgrooved substrates (25, 50, 75, and 100 microm wide). To study apoptosis in a microfluidic device, media containing hydrogen peroxide, Annexin V, and propidium iodide was perfused into the fluidic channel for 2 hours. We found that cells exposed to the oxidative stress became apoptotic. These apoptotic cells were confirmed by Annexin V that bound to phosphatidylserine at the outer leaflet of the plasma membrane during the apoptosis process. Using this microfluidic device with microgrooved patterns, the apoptosis process was observed in real-time and analyzed by using an inverted microscope containing an incubation chamber (37 degrees C, 5% CO(2)). Therefore, this microfluidic device incorporated with microgrooved substrates could be useful for studying the cellular behavior and performing high-throughput drug screening.

  7. Microfluidic chips for protein differential expression profiling.

    Science.gov (United States)

    Armenta, Jenny M; Dawoud, Abdulilah A; Lazar, Iulia M

    2009-04-01

    Biomarker discovery and screening using novel proteomic technologies is an area that is attracting increased attention in the biomedical community. Early detection of abnormal physiological conditions will be highly beneficial for diagnosing various diseases and increasing survivability rates. Clearly, progress in this area will depend on the development of fast, reliable, and highly sensitive and specific sample bioanalysis methods. Microfluidics has emerged as a technology that could become essential in proteomics research as it enables the integration of all sample preparation, separation, and detection steps, with the added benefit of enhanced sample throughput. The combination of these advantages with the sensitivity and capability of MS detection to deliver precise structural information makes microfluidics-MS a very competitive technology for biomarker discovery. The integration of LC microchip devices with MS detection, and specifically their applicability to biomarker screening applications in MCF-7 breast cancer cellular extracts is reported in this manuscript. Loading approximately 0.1-1 microg of crude protein extract tryptic digest on the chip has typically resulted in the reliable identification of approximately 40-100 proteins. The potential of an LC-ESI-MS chip for comparative proteomic analysis of isotopically labeled MCF-7 breast cancer cell extracts is explored for the first time.

  8. Chemoselective ligand patterning of electroactive surfaces using microfluidics.

    Science.gov (United States)

    Westcott, Nathan P; Yousaf, Muhammad N

    2009-10-01

    To generate model substrates for cell adhesion, we have developed two different biocompatible strategies based on self-assembled monolayers (SAMs) of alkanethiolates on gold terminated with latent ketones and aldehydes. Under spatial control, the hydroquinone and alcohol-terminated SAMs can be oxidized to allow for oxyamine ligand patterning on the surface with microfluidic cassettes. These immobilization strategies were characterized by electrochemistry, fluorescence, and utilizing a cell adhesive peptide, cell patterns were generated.

  9. Microfluidic mixers for studying protein folding.

    Science.gov (United States)

    Waldauer, Steven A; Wu, Ling; Yao, Shuhuai; Bakajin, Olgica; Lapidus, Lisa J

    2012-04-10

    The process by which a protein folds into its native conformation is highly relevant to biology and human health yet still poorly understood. One reason for this is that folding takes place over a wide range of timescales, from nanoseconds to seconds or longer, depending on the protein. Conventional stopped-flow mixers have allowed measurement of folding kinetics starting at about 1 ms. We have recently developed a microfluidic mixer that dilutes denaturant ~100-fold in ~8 μs. Unlike a stopped-flow mixer, this mixer operates in the laminar flow regime in which turbulence does not occur. The absence of turbulence allows precise numeric simulation of all flows within the mixer with excellent agreement to experiment. Laminar flow is achieved for Reynolds numbers Re ≤100. For aqueous solutions, this requires micron scale geometries. We use a hard substrate, such as silicon or fused silica, to make channels 5-10 μm wide and 10 μm deep (See Figure 1). The smallest dimensions, at the entrance to the mixing region, are on the order of 1 μm in size. The chip is sealed with a thin glass or fused silica coverslip for optical access. Typical total linear flow rates are ~1 m/s, yielding Re~10, but the protein consumption is only ~0.5 nL/s or 1.8 μL/hr. Protein concentration depends on the detection method: For tryptophan fluorescence the typical concentration is 100 μM (for 1 Trp/protein) and for FRET the typical concentration is ~100 nM. The folding process is initiated by rapid dilution of denaturant from 6 M to 0.06 M guanidine hydrochloride. The protein in high denaturant flows down a central channel and is met on either side at the mixing region by buffer without denaturant moving ~100 times faster (see Figure 2). This geometry causes rapid constriction of the protein flow into a narrow jet ~100 nm wide. Diffusion of the light denaturant molecules is very rapid, while diffusion of the heavy protein molecules is much slower, diffusing less than 1 μm in 1 ms. The

  10. Multiplexed microfluidic quantification of proteins in serum

    Science.gov (United States)

    Rajan, Nitin; Rajauria, Sukumar; Cleland, Andrew

    2015-03-01

    Rapid and low cost immunoassays targeting proteins in blood or other bodily fluids are highly sought after for point-of-care devices and early screening of patients. Immunoturbidimetric assays utilize latex particles functionalized with antibodies, with particle aggregation in the presence of the analyte detected by a change in absorbance. Using a high throughput micro-fluidic particle analyzer based solely on electrical signals (resistive pulse sensing), we are able to accurately quantify the degree of aggregation by analyzing the changes in the particle size distribution. Thus we study the aggregation of streptavidin (SAv) coated beads in the presence of biotinylated bovine serum albumin as a proof-of-principle assay and extract the binding capacity of the SAv beads from the dose-response curve. We also use our aggregation measurement platform to characterize a commercial C-reactive protein (CRP) immunoturbidimetric assay (hsCRP, Diazyme Inc.). We obtain a linear calibration curve as well as a better limit of detection of CRP than that obtained by absorbance measurements. By using different bead sizes functionalized with different antibodies, multiplexed analyte detection is also possible. We demonstrate this by combining the commercial anti-CRP functionalized beads (0.4 microns) with biotin coated beads (1.0 microns), and carry out the simultaneous detection of SAv and CRP in a single sample.

  11. Using Adhesive Patterning to Construct 3D Paper Microfluidic Devices.

    Science.gov (United States)

    Kalish, Brent; Tsutsui, Hideaki

    2016-04-01

    We demonstrate the use of patterned aerosol adhesives to construct both planar and nonplanar 3D paper microfluidic devices. By spraying an aerosol adhesive through a metal stencil, the overall amount of adhesive used in assembling paper microfluidic devices can be significantly reduced. We show on a simple 4-layer planar paper microfluidic device that the optimal adhesive application technique and device construction style depends heavily on desired performance characteristics. By moderately increasing the overall area of a device, it is possible to dramatically decrease the wicking time and increase device success rates while also reducing the amount of adhesive required to keep the device together. Such adhesive application also causes the adhesive to form semi-permanent bonds instead of permanent bonds between paper layers, enabling single-use devices to be non-destructively disassembled after use. Nonplanar 3D origami devices also benefit from the semi-permanent bonds during folding, as it reduces the likelihood that unrelated faces may accidently stick together. Like planar devices, nonplanar structures see reduced wicking times with patterned adhesive application vs uniformly applied adhesive.

  12. High throughput and multiplex localization of proteins and cells for in situ micropatterning using pneumatic microfluidics.

    Science.gov (United States)

    Wang, Jian-Chun; Liu, Wenming; Tu, Qin; Ma, Chao; Zhao, Lei; Wang, Yaolei; Ouyang, Jia; Pang, Long; Wang, Jinyi

    2015-02-07

    Micropatterning technologies are emerging as an enabling tool for various microfluidic-based applications in life sciences. However, the high throughput and multiplex localization of multiple bio-components in a microfluidic device has not yet been well established. In this paper, we describe a simple and in situ micropatterning method using an integrated microfluidic device with pneumatic microstructures (PμSs) for highly controllable immobilization of both proteins and cells in a high throughput, geometry-dynamic, and multi-patterning way. The precise Pluronic F127 passivation of a microchamber surface except the PμS-blocked regions was performed and characterized, and the spatial dynamics and consistency of both the PμSs and protein/cell micropatterning were optically evaluated and quantitatively demonstrated too. Furthermore, a systematic investigation of PμS-assisted micropatterning in microfluidics was carried out. The feature of high throughput and spatial control of micropatterning can be simply realized by using the well-designed PμS arrays. Meanwhile, the co-micropatterning of different proteins (bovine serum albumin and chicken egg albumin) and cells (human umbilical vein endothelial cells and human hepatocellular carcinoma cells) in a microfluidic device was successfully accomplished with the orderly serial manipulation of PμS groups. We demonstrate that PμS-assisted micropatterning can be applied as a convenient microfluidic component for large-scale and diversified protein/cell patterning and manipulation, which could be useful for cell-based tissue organization, high-throughput imaging, protein-related interactions and immunoassays.

  13. RNA-protein binding kinetics in an automated microfluidic reactor.

    Science.gov (United States)

    Ridgeway, William K; Seitaridou, Effrosyni; Phillips, Rob; Williamson, James R

    2009-11-01

    Microfluidic chips can automate biochemical assays on the nanoliter scale, which is of considerable utility for RNA-protein binding reactions that would otherwise require large quantities of proteins. Unfortunately, complex reactions involving multiple reactants cannot be prepared in current microfluidic mixer designs, nor is investigation of long-time scale reactions possible. Here, a microfluidic 'Riboreactor' has been designed and constructed to facilitate the study of kinetics of RNA-protein complex formation over long time scales. With computer automation, the reactor can prepare binding reactions from any combination of eight reagents, and is optimized to monitor long reaction times. By integrating a two-photon microscope into the microfluidic platform, 5-nl reactions can be observed for longer than 1000 s with single-molecule sensitivity and negligible photobleaching. Using the Riboreactor, RNA-protein binding reactions with a fragment of the bacterial 30S ribosome were prepared in a fully automated fashion and binding rates were consistent with rates obtained from conventional assays. The microfluidic chip successfully combines automation, low sample consumption, ultra-sensitive fluorescence detection and a high degree of reproducibility. The chip should be able to probe complex reaction networks describing the assembly of large multicomponent RNPs such as the ribosome.

  14. Patterning electrohydrodynamic flows with conductive obstacles in microfluidic channels.

    Energy Technology Data Exchange (ETDEWEB)

    Hill, Tyrone F.; Simmons, Blake Alexander; Barrett, Louis C.; Cummings, Eric B.; Fiechtner, Gregory J.; Harnett, Cindy K.; Skulan, Andrew J.

    2005-03-01

    Flow patterns with both recirculating and unidirectional characteristics are useful for controlled mixing and pumping within microfluidic devices. We have developed a fabrication process that converts injection-molded polymer chips into devices that demonstrate induced-charge electroosmosis (ICEO) effects (1,2) in AC fields. Polymeric insulating posts are coated with metal to produce a nonuniform zeta potential under an applied electric field. Induced flows are analyzed by particle image velocimetry. Stable, recirculating flow patterns are discussed, along with their potential to produce well-characterized and reversible streamlines for on-chip mixing in chemical separation and synthesis devices. Asymmetric conductive features can bias the flow direction, generating unidirectional pumping in an AC field. This pumping approach will be discussed in comparison with DC electrokinetic pumps we have studied.

  15. Microfluidic-based patterning of embryonic stem cells for in vitro development studies.

    Science.gov (United States)

    Suri, Shalu; Singh, Ankur; Nguyen, Anh H; Bratt-Leal, Andres M; McDevitt, Todd C; Lu, Hang

    2013-12-07

    In vitro recapitulation of mammalian embryogenesis and examination of the emerging behaviours of embryonic structures require both the means to engineer complexity and accurately assess phenotypes of multicellular aggregates. Current approaches to study multicellular populations in 3D configurations are limited by the inability to create complex (i.e. spatially heterogeneous) environments in a reproducible manner with high fidelity thus impeding the ability to engineer microenvironments and combinations of cells with similar complexity to that found during morphogenic processes such as development, remodelling and wound healing. Here, we develop a multicellular embryoid body (EB) fusion technique as a higher-throughput in vitro tool, compared to a manual assembly, to generate developmentally relevant embryonic patterns. We describe the physical principles of the EB fusion microfluidic device design; we demonstrate that >60 conjoined EBs can be generated overnight and emulate a development process analogous to mouse gastrulation during early embryogenesis. Using temporal delivery of bone morphogenic protein 4 (BMP4) to embryoid bodies, we recapitulate embryonic day 6.5 (E6.5) during mouse embryo development with induced mesoderm differentiation in murine embryonic stem cells leading to expression of Brachyury-T-green fluorescent protein (T-GFP), an indicator of primitive streak development and mesoderm differentiation during gastrulation. The proposed microfluidic approach could be used to manipulate hundreds or more of individual embryonic cell aggregates in a rapid fashion, thereby allowing controlled differentiation patterns in fused multicellular assemblies to generate complex yet spatially controlled microenvironments.

  16. Using Microfluidics to Decouple Nucleation and Growth of Protein Crystals.

    Science.gov (United States)

    Shim, Jung-Uk; Cristobal, Galder; Link, Darren R; Thorsen, Todd; Fraden, Seth

    2007-01-01

    A high throughput, low volume microfluidic device has been designed to decouple the physical processes of protein crystal nucleation and growth. This device, called the Phase Chip, is constructed out of poly(dimethylsiloxane) (PDMS) elastomer. One of the Phase Chip's innovations is to exploit surface tension forces to guide each drop to a storage chamber. We demonstrate that nanoliter water-in-oil drops of protein solutions can be rapidly stored in individual wells thereby allowing the screening of 1000 conditions while consuming a total of only 10 mug protein on a 20 cm(2) chip. Another significant advance over current microfluidic devices is that each well is in contact with a reservoir via a dialysis membrane through which only water and other low molecular weight organic solvents can pass, but not salt, polymer, or protein. This enables the concentration of all solutes in a solution to be reversibly, rapidly, and precisely varied in contrast to current methods, such as the free interface diffusion or sitting drop methods, which are irreversible. The Phase Chip operates by first optimizing conditions for nucleation by using dialysis to supersaturate the protein solution, which leads to nucleation of many small crystals. Next, conditions are optimized for crystal growth by using dialysis to reduce the protein and precipitant concentrations, which leads small crystals to dissolve while simultaneously causing only the largest ones to grow, ultimately resulting in the transformation of many small, unusable crystals into a few large ones.

  17. Microfluidic Immunoassays Based on Self-Assembled Magnetic Bead Patterns and Time-Resolved Luminescence Detection

    OpenAIRE

    Sivagnanam, Venkataragavalu

    2010-01-01

    Microfluidic bio-assays have emerged as the most privileged solutions and provide the basis for the realization of miniaturized bio-analytical systems and clinical diagnostic devices that are portable, user-friendly and cost-effective (Lab-on-a-chip). Two important steps that are implemented in a microfluidic bio-assay are: (a) the immobilization and/or patterning of target-specific bio-molecules on the surface of a microfluidic channel, for selectively capturing bio-targets like antigens or ...

  18. Patterned Fibers Embedded Microfluidic Chips Based on PLA and PDMS for Ag Nanoparticle Safety Testing

    Directory of Open Access Journals (Sweden)

    Yaowen Liu

    2016-11-01

    Full Text Available A new method to integrate poly-dl-lactide (PLA patterned electrospun fibers with a polydimethylsiloxane (PDMS microfluidic chip was successfully developed via lithography. Hepatocyte behavior under static and dynamic conditions was investigated. Immunohistochemical analyses indicated good hepatocyte survival under the dynamic culture system with effective hepatocyte spheroid formation in the patterned microfluidic chip vs. static culture conditions and tissue culture plate (TCP. In particular, hepatocytes seeded in this microfluidic chip under a flow rate of 10 μL/min could re-establish hepatocyte polarity to support biliary excretion and were able to maintain high levels of albumin and urea secretion over 15 days. Furthermore, the optimized system could produce sensitive and consistent responses to nano-Ag-induced hepatotoxicity during culture. Thus, this microfluidic chip device provides a new means of fabricating complex liver tissue-engineered scaffolds, and may be of considerable utility in the toxicity screening of nanoparticles.

  19. Effect of microfluidized and stearic acid modified soy protein in natural rubber

    Science.gov (United States)

    Microfluidized and stearic acid modified soy protein aggregates were used to reinforced natural rubber. The size of soy protein particles was reduced with a microfluidizing and ball milling process. Filler size reduction with longer ball milling time tends to increase tensile strength of the rubber ...

  20. Three-dimensional paper-based microfluidic device for assays of protein and glucose in urine.

    Science.gov (United States)

    Sechi, Deidre; Greer, Brady; Johnson, Jesse; Hashemi, Nastaran

    2013-11-19

    The first step in curing a disease is being able to detect the disease effectively. Paper-based microfluidic devices are biodegradable and can make diagnosing diseases cost-effective and easy in almost all environments. We created a three-dimesnional (3D) paper device using wax printing fabrication technique and basic principles of origami. This design allows for a versatile fabrication technique over previously reported patterning of SU-8 photoresist on chromatography paper by employing a readily available wax printer. The design also utilizes multiple colorimetric assays that can accommodate one or more analytes including urine, blood, and saliva. In this case to demonstrate the functionality of the 3D paper-based microfluidic system, a urinalysis of protein and glucose assays is conducted. The amounts of glucose and protein introduced to the device are found to be proportional to the color change of each assay. This color change was quantified by use of Adobe Photoshop. Urine samples from participants with no pre-existing health conditions and one person with diabetes were collected and compared against synthetic urine samples with predetermined glucose and protein levels. Utilizing this method, we were able to confirm that both protein and glucose levels were in fact within healthy ranges for healthy participants. For the participant with diabetes, glucose was found to be above the healthy range while the protein level was in the healthy range.

  1. Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization

    Science.gov (United States)

    Fan, Beiyuan; Li, Xiufeng; Chen, Deyong; Peng, Hongshang; Wang, Junbo; Chen, Jian

    2016-01-01

    This article reviews recent developments in microfluidic systems enabling high-throughput characterization of single-cell proteins. Four key perspectives of microfluidic platforms are included in this review: (1) microfluidic fluorescent flow cytometry; (2) droplet based microfluidic flow cytometry; (3) large-array micro wells (microengraving); and (4) large-array micro chambers (barcode microchips). We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on three key performance parameters (absolute quantification, sensitivity, and throughput). PMID:26891303

  2. Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization

    Directory of Open Access Journals (Sweden)

    Beiyuan Fan

    2016-02-01

    Full Text Available This article reviews recent developments in microfluidic systems enabling high-throughput characterization of single-cell proteins. Four key perspectives of microfluidic platforms are included in this review: (1 microfluidic fluorescent flow cytometry; (2 droplet based microfluidic flow cytometry; (3 large-array micro wells (microengraving; and (4 large-array micro chambers (barcode microchips. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on three key performance parameters (absolute quantification, sensitivity, and throughput.

  3. Light-sheet based lithography technique for patterning an array of microfluidic channels.

    Science.gov (United States)

    Mohan, Kavya; Mondal, Partha Pratim

    2017-02-08

    We propose a Light-sheet laser interference lithography technique for fabricating periodic microfluidic channels. This technique uses multiple light-sheet illumination pattern that is generated using a spatial filter at the back-aperture of the cylindrical lens. Specially designed spatial filter is used that give rise to a periodic pattern at the focal plane which is essentially a 1D Fourier transform of the spatial filter transfer function. One-dimensional focusing property of the cylindrical lens result in the generation of line shaped channel geometry. To design microfluidic channels, the illumination pattern is exposed to the glass substrate coated with a photopolymer sensitized to 532 nm and subsequently developed using standard chemical protocols. Experimentally, the 1D periodic channel structure has an approximate width and periodicity of approximately 11.25 microns. Light-sheets based lithography technique offer a fast and single-shot process to generate microfluidic channels. © 2016 Wiley Periodicals, Inc.

  4. 3D-printed microfluidic chips with patterned, cell-laden hydrogel constructs.

    Science.gov (United States)

    Knowlton, Stephanie; Yu, Chu Hsiang; Ersoy, Fulya; Emadi, Sharareh; Khademhosseini, Ali; Tasoglu, Savas

    2016-06-20

    Three-dimensional (3D) printing offers potential to fabricate high-throughput and low-cost fabrication of microfluidic devices as a promising alternative to traditional techniques which enables efficient design iterations in the development stage. In this study, we demonstrate a single-step fabrication of a 3D transparent microfluidic chip using two alternative techniques: a stereolithography-based desktop 3D printer and a two-step fabrication using an industrial 3D printer based on polyjet technology. This method, compared to conventional fabrication using relatively expensive materials and labor-intensive processes, presents a low-cost, rapid prototyping technique to print functional 3D microfluidic chips. We enhance the capabilities of 3D-printed microfluidic devices by coupling 3D cell encapsulation and spatial patterning within photocrosslinkable gelatin methacryloyl (GelMA). The platform presented here serves as a 3D culture environment for long-term cell culture and growth. Furthermore, we have demonstrated the ability to print complex 3D microfluidic channels to create predictable and controllable fluid flow regimes. Here, we demonstrate the novel use of 3D-printed microfluidic chips as controllable 3D cell culture environments, advancing the applicability of 3D printing to engineering physiological systems for future applications in bioengineering.

  5. Development of a multiplexed microfluidic proteomic reactor and its application for studying protein-protein interactions.

    Science.gov (United States)

    Tian, Ruijun; Hoa, Xuyen Dai; Lambert, Jean-Philippe; Pezacki, John Paul; Veres, Teodor; Figeys, Daniel

    2011-06-01

    Mass spectrometry-based proteomics techniques have been very successful for the identification and study of protein-protein interactions. Typically, immunopurification of protein complexes is conducted, followed by protein separation by gel electrophoresis and in-gel protein digestion, and finally, mass spectrometry is performed to identify the interacting partners. However, the manual processing of the samples is time-consuming and error-prone. Here, we developed a polymer-based microfluidic proteomic reactor aimed at the parallel analysis of minute amounts of protein samples obtained from immunoprecipitation. The design of the proteomic reactor allows for the simultaneous processing of multiple samples on the same devices. Each proteomic reactor on the device consists of SCX beads packed and restricted into a 1 cm microchannel by two integrated pillar frits. The device is fabricated using a combination of low-cost hard cyclic olefin copolymer thermoplastic and elastomeric thermoplastic materials (styrene/(ethylene/butylenes)/styrene) using rapid hot-embossing replication techniques with a polymer-based stamp. Three immunopurified protein samples are simultaneously captured, reduced, alkylated, and digested on the device within 2-3 h instead of the days required for the conventional protein-protein interaction studies. The limit of detection of the microfluidic proteomic reactor was shown to be lower than 2 ng of protein. Furthermore, the application of the microfluidic proteomic reactor was demonstrated for the simultaneous processing of the interactome of the histone variant Htz1 in wild-type yeast and in a swr1Δ yeast strain compared to an untagged control using a novel three-channel microfluidic proteomic reactor.

  6. Direct optical patterning of poly(dimethylsiloxane) microstructures for microfluidic chips

    Science.gov (United States)

    Gao, Shaorui; Tung, Wing-Tai; Wong, Dexter S.; Bian, Liming; Zhang, A. Ping

    2016-10-01

    In this paper, we present an optical maskless exposure approach for direct patterning of large-area high resolution microfluidic chips using photosensitive poly(dimethylsiloxane) (PDMS) materials. Both positive- and negative-tone photosensitive PDMS (photoPDMS) were successfully patterned into various microfluidic devices with complex geometries by using an optical maskless lithography process. The positive-tone PDMS is used for patterning of largearea chips, while the negative-tone PDMS is demonstrated to fabricate high-resolution microstructures and on-chip devices. With the seamless pattern-stitching technique, a large-area microfluidic chip with size of 5.5 × 2.8 cm2 with complex three-dimensional (3D) staggered herringbone mixers (SHMs) for micro-flow gradient generation has been directly fabricated within 125 minutes by using the positive-tone PDMS. A small microfluidic chip with feature size as small as 5 μm is demonstrated by using the negative-tone PDMS. The experimental results reveal that the optical maskless lithography technology enables to rapidly pattern high-resolution microstructures and is very promising for development of lab-on-a-chip devices.

  7. Pathogen receptor discovery with a microfluidic human membrane protein array

    Science.gov (United States)

    Glick, Yair; Ben-Ari, Ya’ara; Drayman, Nir; Pellach, Michal; Neveu, Gregory; Boonyaratanakornkit, Jim; Avrahami, Dorit; Einav, Shirit; Oppenheim, Ariella

    2016-01-01

    The discovery of how a pathogen invades a cell requires one to determine which host cell receptors are exploited. This determination is a challenging problem because the receptor is invariably a membrane protein, which represents an Achilles heel in proteomics. We have developed a universal platform for high-throughput expression and interaction studies of membrane proteins by creating a microfluidic-based comprehensive human membrane protein array (MPA). The MPA is, to our knowledge, the first of its kind and offers a powerful alternative to conventional proteomics by enabling the simultaneous study of 2,100 membrane proteins. We characterized direct interactions of a whole nonenveloped virus (simian virus 40), as well as those of the hepatitis delta enveloped virus large form antigen, with candidate host receptors expressed on the MPA. Selected newly discovered membrane protein–pathogen interactions were validated by conventional methods, demonstrating that the MPA is an important tool for cellular receptor discovery and for understanding pathogen tropism. PMID:27044079

  8. Microfluidic Patterning of Metal Structures for Flexible Conductors by In Situ Polymer-Assisted Electroless Deposition.

    Science.gov (United States)

    Liang, Suqing; Li, Yaoyao; Zhou, Tingjiao; Yang, Jinbin; Zhou, Xiaohu; Zhu, Taipeng; Huang, Junqiao; Zhu, Julie; Zhu, Deyong; Liu, Yizhen; He, Chuanxin; Zhang, Junmin; Zhou, Xuechang

    2017-02-01

    A low-cost, solution-processed, versatile, microfluidic approach is developed for patterning structures of highly conductive metals (e.g., copper, silver, and nickel) on chemically modified flexible polyethylene terephthalate thin films by in situ polymer-assisted electroless metal deposition. This method has significantly lowered the consumption of catalyst as well as the metal plating solution.

  9. Regioselective patterning of multiple SAMs and applications in surface-guided smart microfluidics.

    Science.gov (United States)

    Chen, Chuanzhao; Xu, Pengcheng; Li, Xinxin

    2014-12-24

    A top-down nanofabrication technology is developed to integrate multiple SAMs (self-assembled monolayers) into regioselective patterns. With ultraviolet light exposure through regioselectively hollowed hard mask, an existing SAM at designated microregions can be removed and a dissimilar kind of SAM can be regrown there. By repeating the photolithography-like process cycle, diverse kinds of SAM building blocks can be laid out as a desired pattern in one microfluidic channel. In order to ensure high quality of the surface modifications, the SAMs are vapor-phase deposited before the channel is closed by a bonding process. For the first time the technique makes it possible to integrate three or more kinds of SAMs in one microchannel. The technique is very useful for multiplex surface functionalization of microfluidic chips where different segments of a microfluidic channel need to be individually modified with different SAMs or into arrayed pattern for surface-guided fluidic properties like hydrophobicity/philicity and/or oleophobicity/philicity, etc. The technique has been well validated by experimental demonstration of various surface-directed flow-guiding functions. By modifying a microchannel surface into an arrayed pattern of multi-SAM "two-tone" stripe array, surface-guiding-induced 3D swirling flow is generated in a microfluidic channel that experimentally exhibits quick oil/water mixing and high-efficiency oil-to-water chemical extraction.

  10. "Print-n-Shrink" technology for the rapid production of microfluidic chips and protein microarrays.

    Science.gov (United States)

    Sollier, Kevin; Mandon, Céline A; Heyries, Kevin A; Blum, Loïc J; Marquette, Christophe A

    2009-12-21

    An innovative method for the production of microfluidic chips integrating protein spots is described. The technology, called "Print-n-Shrink", is based on the screen-printing of a microfluidic design (using a dielectric ink) onto Polyshrink polystyrene sheets. The initial print which has a minimum size of 15 microm (height) x 230 microm (width) is thermally treated (30 seconds, 163 degrees C) to shrink and generate features of 85 microm (height) x 100 microm (width). Concomitantly, proteins such as monoclonal antibodies or cellular adhesion proteins are spotted onto the Polyshrink sheets and shrunk together with the microfluidic design, creating a complete biochip integrating both complex microfluidic designs and protein spots for bioanalytical applications.

  11. Identification of microfluidic two-phase flow patterns in lab-on-chip devices.

    Science.gov (United States)

    Yang, Zhaochu; Dong, Tao; Halvorsen, Einar

    2014-01-01

    This work describes a capacitive sensor for identification of microfluidic two-phase flow in lab-on-chip devices. With interdigital electrodes and thin insulation layer utilized, this sensor is capable of being integrated with the microsystems easily. Transducing principle and design considerations are presented with respect to the microfluidic gas/liquid flow patterns. Numerical simulation results verify the operational principle. And the factors affecting the performance of the sensor are discussed. Besides, a feasible process flow for the fabrication is also proposed.

  12. Proteolysis in microfluidic droplets: an approach to interface protein separation and peptide mass spectrometry

    OpenAIRE

    Ji, Ji; Nie, Lei; Qiao, Liang; Li, Yixin; Guo, Liping; Liu, Baohong; Yang, Pengyuan; Girault, Hubert H.

    2012-01-01

    A versatile microreactor protocol based on microfluidic droplets has been developed for on-line protein digestion. Proteins separated by liquid chromatography are fractionated in water-in-oil droplets and digested in sequence. The microfluidic reactor acts also as an electrospray ionization emitter for mass spectrometry analysis of the peptides produced in the individual droplets. Each droplet is an enzymatic micro-reaction unit with efficient proteolysis due to rapid mixing, enhanced mass tr...

  13. An optimized resistor pattern for temperature gradient control in microfluidics

    Science.gov (United States)

    Selva, Bertrand; Marchalot, Julien; Jullien, Marie-Caroline

    2009-06-01

    In this paper, we demonstrate the possibility of generating high-temperature gradients with a linear temperature profile when heating is provided in situ. Thanks to improved optimization algorithms, the shape of resistors, which constitute the heating source, is optimized by applying the genetic algorithm NSGA-II (acronym for the non-dominated sorting genetic algorithm) (Deb et al 2002 IEEE Trans. Evol. Comput. 6 2). Experimental validation of the linear temperature profile within the cavity is carried out using a thermally sensitive fluorophore, called Rhodamine B (Ross et al 2001 Anal. Chem. 73 4117-23, Erickson et al 2003 Lab Chip 3 141-9). The high level of agreement obtained between experimental and numerical results serves to validate the accuracy of this method for generating highly controlled temperature profiles. In the field of actuation, such a device is of potential interest since it allows for controlling bubbles or droplets moving by means of thermocapillary effects (Baroud et al 2007 Phys. Rev. E 75 046302). Digital microfluidics is a critical area in the field of microfluidics (Dreyfus et al 2003 Phys. Rev. Lett. 90 14) as well as in the so-called lab-on-a-chip technology. Through an example, the large application potential of such a technique is demonstrated, which entails handling a single bubble driven along a cavity using simple and tunable embedded resistors.

  14. A microfluidic, high throughput protein crystal growth method for microgravity.

    Directory of Open Access Journals (Sweden)

    Carl W Carruthers

    Full Text Available The attenuation of sedimentation and convection in microgravity can sometimes decrease irregularities formed during macromolecular crystal growth. Current terrestrial protein crystal growth (PCG capabilities are very different than those used during the Shuttle era and that are currently on the International Space Station (ISS. The focus of this experiment was to demonstrate the use of a commercial off-the-shelf, high throughput, PCG method in microgravity. Using Protein BioSolutions' microfluidic Plug Maker™/CrystalCard™ system, we tested the ability to grow crystals of the regulator of glucose metabolism and adipogenesis: peroxisome proliferator-activated receptor gamma (apo-hPPAR-γ LBD, as well as several PCG standards. Overall, we sent 25 CrystalCards™ to the ISS, containing ~10,000 individual microgravity PCG experiments in a 3U NanoRacks NanoLab (1U = 10(3 cm.. After 70 days on the ISS, our samples were returned with 16 of 25 (64% microgravity cards having crystals, compared to 12 of 25 (48% of the ground controls. Encouragingly, there were more apo-hPPAR-γ LBD crystals in the microgravity PCG cards than the 1g controls. These positive results hope to introduce the use of the PCG standard of low sample volume and large experimental density to the microgravity environment and provide new opportunities for macromolecular samples that may crystallize poorly in standard laboratories.

  15. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion

    Science.gov (United States)

    Hansen, Carl L.; Skordalakes, Emmanuel; Berger, James M.; Quake, Stephen R.

    2002-12-01

    Producing robust and scalable fluid metering in a microfluidic device is a challenging problem. We developed a scheme for metering fluids on the picoliter scale that is scalable to highly integrated parallel architectures and is independent of the properties of the working fluid. We demonstrated the power of this method by fabricating and testing a microfluidic chip for rapid screening of protein crystallization conditions, a major hurdle in structural biology efforts. The chip has 480 active valves and performs 144 parallel reactions, each of which uses only 10 nl of protein sample. The properties of microfluidic mixing allow an efficient kinetic trajectory for crystallization, and the microfluidic device outperforms conventional techniques by detecting more crystallization conditions while using 2 orders of magnitude less protein sample. We demonstrate that diffraction-quality crystals may be grown and harvested from such nanoliter-volume reactions.

  16. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion

    Science.gov (United States)

    Hansen, Carl L.; Skordalakes, Emmanuel; Berger, James M.; Quake, Stephen R.

    2002-01-01

    Producing robust and scalable fluid metering in a microfluidic device is a challenging problem. We developed a scheme for metering fluids on the picoliter scale that is scalable to highly integrated parallel architectures and is independent of the properties of the working fluid. We demonstrated the power of this method by fabricating and testing a microfluidic chip for rapid screening of protein crystallization conditions, a major hurdle in structural biology efforts. The chip has 480 active valves and performs 144 parallel reactions, each of which uses only 10 nl of protein sample. The properties of microfluidic mixing allow an efficient kinetic trajectory for crystallization, and the microfluidic device outperforms conventional techniques by detecting more crystallization conditions while using 2 orders of magnitude less protein sample. We demonstrate that diffraction-quality crystals may be grown and harvested from such nanoliter-volume reactions. PMID:12486223

  17. A robotics platform for automated batch fabrication of high density, microfluidics-based DNA microarrays, with applications to single cell, multiplex assays of secreted proteins.

    Science.gov (United States)

    Ahmad, Habib; Sutherland, Alex; Shin, Young Shik; Hwang, Kiwook; Qin, Lidong; Krom, Russell-John; Heath, James R

    2011-09-01

    Microfluidics flow-patterning has been utilized for the construction of chip-scale miniaturized DNA and protein barcode arrays. Such arrays have been used for specific clinical and fundamental investigations in which many proteins are assayed from single cells or other small sample sizes. However, flow-patterned arrays are hand-prepared, and so are impractical for broad applications. We describe an integrated robotics/microfluidics platform for the automated preparation of such arrays, and we apply it to the batch fabrication of up to eighteen chips of flow-patterned DNA barcodes. The resulting substrates are comparable in quality with hand-made arrays and exhibit excellent substrate-to-substrate consistency. We demonstrate the utility and reproducibility of robotics-patterned barcodes by utilizing two flow-patterned chips for highly parallel assays of a panel of secreted proteins from single macrophage cells.

  18. Integration of protein processing steps on a droplet microfluidics platform for MALDI-MS analysis.

    Science.gov (United States)

    Chatterjee, Debalina; Ytterberg, A Jimmy; Son, Sang Uk; Loo, Joseph A; Garrell, Robin L

    2010-03-01

    A droplet-based (digital) microfluidics platform has been developed to prepare and purify protein samples for measurement by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Liquid droplets are moved in air by sequentially applying an electric potential to an array of electrodes patterned beneath a hydrophobic dielectric layer. We show that a complete integrated sequence of protein processing steps can be performed on this platform, including disulfide reduction, alkylation, and enzymatic digestion, followed by cocrystallization with a MALDI matrix and analysis of the sample in situ by MALDI-MS. Proteins carbonic anhydrase, cytochrome c, and ubiquitin were used to demonstrate the digestion and postdigestion steps; insulin, serum albumin, and lysozyme were used to illustrate the complete sequence of protein processing steps available with the platform. Several functional improvements in the platform are reported, notably, the incorporation of acetonitrile in the protein droplets to facilitate movement, and patterning the device surfaces to optimize sample crystallization. The method is fast, simple, repeatable, and results in lower reagent consumption and sample loss than conventional techniques for proteomics sample preparation.

  19. A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion

    OpenAIRE

    Hansen, Carl L.; Skordalakes, Emmanuel; Berger, James M.; Quake, Stephen R.

    2002-01-01

    Producing robust and scalable fluid metering in a microfluidic device is a challenging problem. We developed a scheme for metering fluids on the picoliter scale that is scalable to highly integrated parallel architectures and is independent of the properties of the working fluid. We demonstrated the power of this method by fabricating and testing a microfluidic chip for rapid screening of protein crystallization conditions, a major hurdle in structural biology efforts. The chip has 480 active...

  20. A novel approach to determine the efficacy of patterned surfaces for biofouling control in relation to its microfluidic environment.

    Science.gov (United States)

    Halder, Partha; Nasabi, Mahyar; Lopez, Francisco Javier Tovar; Jayasuriya, Niranjali; Bhattacharya, Satinath; Deighton, Margaret; Mitchell, Arnan; Bhuiyan, Muhammed Ali

    2013-01-01

    Biofouling, the unwanted growth of sessile microorganisms on submerged surfaces, presents a serious problem for underwater structures. While biofouling can be controlled to various degrees with different microstructure-based patterned surfaces, understanding of the underlying mechanism is still imprecise. Researchers have long speculated that microtopographies might influence near-surface microfluidic conditions, thus microhydrodynamically preventing the settlement of microorganisms. It is therefore very important to identify the microfluidic environment developed on patterned surfaces and its relation with the antifouling behaviour of those surfaces. This study considered the wall shear stress distribution pattern as a significant aspect of this microfluidic environment. In this study, patterned surfaces with microwell arrays were assessed experimentally with a real-time biofilm development monitoring system using a novel microchannel-based flow cell reactor. Finally, computational fluid dynamics simulations were carried out to show how the microfluidic conditions were affecting the initial settlement of microorganisms.

  1. Tape transfer atomization patterning of liquid alloys for microfluidic stretchable wireless power transfer.

    Science.gov (United States)

    Jeong, Seung Hee; Hjort, Klas; Wu, Zhigang

    2015-02-12

    Stretchable electronics offers unsurpassed mechanical compliance on complex or soft surfaces like the human skin and organs. To fully exploit this great advantage, an autonomous system with a self-powered energy source has been sought for. Here, we present a new technology to pattern liquid alloys on soft substrates, targeting at fabrication of a hybrid-integrated power source in microfluidic stretchable electronics. By atomized spraying of a liquid alloy onto a soft surface with a tape transferred adhesive mask, a universal fabrication process is provided for high quality patterns of liquid conductors in a meter scale. With the developed multilayer fabrication technique, a microfluidic stretchable wireless power transfer device with an integrated LED was demonstrated, which could survive cycling between 0% and 25% strain over 1,000 times.

  2. Controlling Nonspecific Protein Adsorption in a Plug-Based Microfluidic System by Controlling Interfacial Chemistry Using Fluorous-Phase Surfactants

    OpenAIRE

    Roach, L. Spencer; Song, Helen; Ismagilov, Rustem F.

    2005-01-01

    Control of surface chemistry and protein adsorption is important for using microfluidic devices for biochemical analysis and high-throughput screening assays. This paper describes the control of protein adsorption at the liquid-liquid interface in a plug-based microfluidic system. The microfluidic system uses multiphase flows of immiscible fluorous and aqueous fluids to form plugs, which are aqueous droplets that are completely surrounded by fluorocarbon oil and do not come into direct contac...

  3. Protein crystallization using microfluidic technologies based on valves, droplets, and SlipChip.

    Science.gov (United States)

    Li, Liang; Ismagilov, Rustem F

    2010-01-01

    To obtain protein crystals, researchers must search for conditions in multidimensional chemical space. Empirically, thousands of crystallization experiments are carried out to screen various precipitants at multiple concentrations. Microfluidics can manipulate fluids on a nanoliter scale, and it affects crystallization twofold. First, it miniaturizes the experiments that can currently be done on a larger scale and enables crystallization of proteins that are available only in small amounts. Second, it offers unique experimental approaches that are difficult or impossible to implement on a larger scale. Ongoing development of microfluidic techniques and their integration with protein production, characterization, and in situ diffraction promises to accelerate the progress of structural biology.

  4. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

    Energy Technology Data Exchange (ETDEWEB)

    Lyubimov, Artem Y. [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Murray, Thomas D. [University of California, Berkeley, CA 94720 (United States); Johns Hopkins University School of Medicine, Baltimore, MD 21205 (United States); Koehl, Antoine [Stanford University, Stanford, CA 94305 (United States); Araci, Ismail Emre [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Uervirojnangkoorn, Monarin; Zeldin, Oliver B. [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Cohen, Aina E.; Soltis, S. Michael; Baxter, Elizabeth L. [SLAC National Accelerator Laboratory, Stanford, CA 94305 (United States); Brewster, Aaron S.; Sauter, Nicholas K. [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Brunger, Axel T., E-mail: brunger@stanford.edu [Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Stanford University, Stanford, CA 94305 (United States); Berger, James M., E-mail: brunger@stanford.edu [Johns Hopkins University School of Medicine, Baltimore, MD 21205 (United States); Stanford University, Stanford, CA 94305 (United States)

    2015-04-01

    A microfluidic platform has been developed for the capture and X-ray analysis of protein microcrystals, affording a means to improve the efficiency of XFEL and synchrotron experiments. X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.

  5. Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast

    DEFF Research Database (Denmark)

    Huang, Mingtao; Bai, Yunpeng; Sjostrom, Staffan L.

    2015-01-01

    interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by UV...... to construct efficient cell factories for protein secretion. The combined use of microfluidics screening and whole-genome sequencing to map the mutations associated with the improved phenotype can easily be adapted for other products and cell types to identify novel engineering targets, and this approach could...

  6. Controlling the magnetic field distribution on the micrometer scale and generation of magnetic bead patterns for microfluidic applications.

    Science.gov (United States)

    Yu, Xu; Feng, Xuan; Hu, Jun; Zhang, Zhi-Ling; Pang, Dai-Wen

    2011-04-19

    As is well known, controlling the local magnetic field distribution on the micrometer scale in a microfluidic chip is significant and has many applications in bioanalysis based on magnetic beads. However, it is a challenge to tailor the magnetic field introduced by external permanent magnets or electromagnets on the micrometer scale. Here, we demonstrated a simple approach to controlling the local magnetic field distribution on the micrometer scale in a microfluidic chip by nickel patterns encapsulated in a thin poly(dimethylsiloxane) (PDMS) film under the fluid channel. With the precisely controlled magnetic field, magnetic bead patterns were convenient to generate. Moreover, two kinds of fluorescent magnetic beads were patterned in the microfluidic channel, which demonstrated that it was possible to generate different functional magnetic bead patterns in situ, and could be used for the detection of multiple targets. In addition, this method was applied to generate cancer cell patterns.

  7. Fabrication of thermo-responsive microfluidic membrane using photopolymerization patterning

    Science.gov (United States)

    Kim, Hyejeong; Lee, Sang Joon

    2015-11-01

    The programmed manipulation of responsive functional hydrogels is receiving large attention because of its unique functions and wide range of engineering applications. In this study, we developed an innovative stomata-inspired membrane (SIM) by fabricating a temperature-responsive hydrogel with a simple, cost effective, and high-throughput photopolymerization patterning process. Polymerization-induced diffusion on the macro-scale surface gives rise to form a multi-parted polymer membrane with fine pores by simple UV irradiation. After heating the SIM, the less deformable thick frame supports the whole structure, and the highly deformable thin base regulates the size of pores. The morphological configuration of the SIM can be easily changed by varying the solution composition or selecting a suitable photomask with different pattern. The developed SIM has the special sensing-to-actuation functions of stimuli-responsive hydrogels. This membrane with temperature-responsive pores would be potentially utilized in numerous practical applications, such as filter membranes with self-adjustable pores, membrane-based sensors, membrane-based actuators, and multi-functional membranes etc. This study was supported by the National Research Foundation of Korea (NRF) and funded by the Korean government (MSIP) (Grant No. 2008-0061991).

  8. Understanding wax screen-printing: a novel patterning process for microfluidic cloth-based analytical devices.

    Science.gov (United States)

    Liu, Min; Zhang, Chunsun; Liu, Feifei

    2015-09-01

    In this work, we first introduce the fabrication of microfluidic cloth-based analytical devices (μCADs) using a wax screen-printing approach that is suitable for simple, inexpensive, rapid, low-energy-consumption and high-throughput preparation of cloth-based analytical devices. We have carried out a detailed study on the wax screen-printing of μCADs and have obtained some interesting results. Firstly, an analytical model is established for the spreading of molten wax in cloth. Secondly, a new wax screen-printing process has been proposed for fabricating μCADs, where the melting of wax into the cloth is much faster (∼5 s) and the heating temperature is much lower (75 °C). Thirdly, the experimental results show that the patterning effects of the proposed wax screen-printing method depend to a certain extent on types of screens, wax melting temperatures and melting time. Under optimized conditions, the minimum printing width of hydrophobic wax barrier and hydrophilic channel is 100 μm and 1.9 mm, respectively. Importantly, the developed analytical model is also well validated by these experiments. Fourthly, the μCADs fabricated by the presented wax screen-printing method are used to perform a proof-of-concept assay of glucose or protein in artificial urine with rapid high-throughput detection taking place on a 48-chamber cloth-based device and being performed by a visual readout. Overall, the developed cloth-based wax screen-printing and arrayed μCADs should provide a new research direction in the development of advanced sensor arrays for detection of a series of analytes relevant to many diverse applications.

  9. Fluorescence enhancement and multiple protein detection in ZnO nanostructure microfluidic devices.

    Science.gov (United States)

    Sang, Chen-Hsiang; Chou, Shu-Jen; Pan, F M; Sheu, Jeng-Tzong

    2016-01-15

    In this study, different morphological ZnO nanostructures, those of sharp nanowires (NWs), rod NWs, and hexahedral-puncheon nanostructures, were grown in microfluidic channels on the same glass substrate. Characterizations of correspondent biomolecule binding properties were simulated and demonstrated. The surface was modified using 3-ammineopropyl-triethoxysilane (3-APTES) and biotin-N-hydroxysuccinimide ester (NHS-biotin). Different concentrations (4.17pM to 41.7nM) of dye-conjugated streptavidin were simultaneously infused through the second microfluidic channels, which lie 90° from the first microfluidic channels. The florescent intensity at the crossover areas showed good agreement with simulations, with sharp ZnO NWs exhibiting the largest dynamic range and the highest fluorescent intensity. We further characterize correspondent protein detection using sharp ZnO NWs. The surfaces of these ZnO NWs were modified with mouse immunoglobulin G (IgG), infused through the second microfluidic channels with dye-conjugated (Alexa 546) anti-mouse IgG in different concentrations. Concentrations ranging from 417fM to 41.7nM can be resolved using sharp ZnO NWs. Finally, multiple protein detection was demonstrated using a five-by-eight microfluidic channel array. Fluorescence images present clear multiple detections at the crossover areas when using the sharp ZnO NWs for simultaneous dye-conjugated anti-mouse IgG and dye-conjugated anti-rabbit IgG (Alexa 647) detection.

  10. Paramagnetic Structures within a Microfluidic Channel for Enhanced Immunomagnetic Isolation and Surface Patterning of Cells

    Science.gov (United States)

    Sun, Chen; Hassanisaber, Hamid; Yu, Richard; Ma, Sai; Verbridge, Scott S.; Lu, Chang

    2016-07-01

    In this report, we demonstrate a unique method for embedding magnetic structures inside a microfluidic channel for cell isolation. We used a molding process to fabricate these structures out of a ferrofluid of cobalt ferrite nanoparticles. We show that the embedded magnetic structures significantly increased the magnetic field in the channel, resulting in up to 4-fold enhancement in immunomagnetic capture as compared with a channel without these embedded magnetic structures. We also studied the spatial distribution of trapped cells both experimentally and computationally. We determined that the surface pattern of these trapped cells was determined by both location of the magnet and layout of the in-channel magnetic structures. Our magnetic structure embedded microfluidic device achieved over 90% capture efficiency at a flow velocity of 4 mm/s, a speed that was roughly two orders of magnitude faster than previous microfluidic systems used for a similar purpose. We envision that our technology will provide a powerful tool for detection and enrichment of rare cells from biological samples.

  11. Nucleic acid and protein extraction from electropermeabilized E. coli cells on a microfluidic chip

    DEFF Research Database (Denmark)

    Matos, T.; Senkbeil, Silja; Mendonça, A.

    2013-01-01

    technique has been developed which is based on exposing E. coli cells to low voltages to allow extraction of nucleic acids and proteins. The flow-through electropermeability chip used consists of a microfluidic channel with integrated gold electrodes that promote cell envelope channel formation at low...

  12. A Novel Impedimetric Microfluidic Analysis System for Transgenic Protein Cry1Ab Detection

    Science.gov (United States)

    Jin, Shunru; Ye, Zunzhong; Wang, Yixian; Ying, Yibin

    2017-01-01

    Impedimetric analysis method is an important tool for food safety detection. In this work, a novel impedimetric microfluidic analysis system consisted of a printed gold electrode chip and a microfluidic flow cell was developed for sensitive and selective detection of transgenic protein Cry1Ab. Anti-Cry1Ab aptamer coated magnetic beads were used to recognize transgenic protein Cry1Ab and form Cry1Ab-aptamer modified magnetic beads. After separation, the obtained Cry1Ab-aptamer modified magnetic beads were dissolved in 0.01 M mannitol and followed by injection into the microfluidic flow cell for impedimetric measurement. At the frequency of 358.3 Hz, the impedance signal shows a good linearity with the concentrations of Cry1Ab protein at a range from 0 to 0.2 nM, and the detection limit is 0.015 nM. The results demonstrate that the impedimetric microfluidic analysis system provides an alternative way to enable sensitive, rapid and specific detection of transgenic protein Cry1Ab. PMID:28251986

  13. Electrochemical Protein Cleavage in a Microfluidic Cell with Integrated Boron Doped Diamond Electrodes

    NARCIS (Netherlands)

    van den Brink, Floris T G; Zhang, Tao; Ma, Liwei; Bomer, Johan; Odijk, Mathieu; Olthuis, Wouter; Permentier, Hjalmar P; Bischoff, Rainer; van den Berg, Albert

    2016-01-01

    Specific electrochemical cleavage of peptide bonds at the C-terminal side of tyrosine and tryptophan generates peptides amenable to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis for protein identification. To this end we developed a microfluidic electrochemical cell of 160 nL vo

  14. Fabrication of anti-protein-fouling poly(ethylene glycol) microfluidic chip electrophoresis by sandwich photolithography.

    Science.gov (United States)

    Cong, Hailin; Xu, Xiaodan; Yu, Bing; Liu, Huwei; Yuan, Hua

    2016-07-01

    Microfluidic chip electrophoresis (MCE) is a powerful separation tool for biomacromolecule analysis. However, adsorption of biomacromolecules, particularly proteins onto microfluidic channels severely degrades the separation performance of MCE. In this paper, an anti-protein-fouling MCE was fabricated using a novel sandwich photolithography of poly(ethylene glycol) (PEG) prepolymers. Photopatterned microchannel with a minimum resolution of 10 μm was achieved. After equipped with a conventional online electrochemical detector, the device enabled baseline separation of bovine serum albumin, lysozyme (Lys), and cytochrome c (Cyt-c) in 53 s under a voltage of 200 V. Compared with a traditional polydimethylsiloxane MCE made by soft lithography, the PEG MCE made by the sandwich photolithography not only eliminated the need of a master mold and the additional modification process of the microchannel but also showed excellent anti-protein-fouling properties for protein separation.

  15. Protein-protein interaction analysis in single microfluidic droplets using FRET and fluorescence lifetime detection.

    Science.gov (United States)

    Benz, Christian; Retzbach, Heiko; Nagl, Stefan; Belder, Detlev

    2013-07-21

    Herein, we demonstrate the feasibility of a protein-protein interaction analysis and reaction progress monitoring in microfluidic droplets using FRET and microscopic fluorescence lifetime measurements. The fabrication of microdroplet chips using soft- and photolithographic techniques is demonstrated and the resulting chips reliably generate microdroplets of 630 pL and 6.71 nL at frequencies of 7.9 and 0.75 Hz, respectively. They were used for detection of protein-protein interactions in microdroplets using a model system of Alexa Fluor 488 labelled biotinylated BSA, Alexa Fluor 594 labelled streptavidin and unlabelled chicken egg white avidin. These microchips could be used for quantitative detection of avidin and streptavidin in microdroplets in direct and competitive assay formats with nanomolar detection limits, corresponding to attomole protein amounts. Four droplets were found to be sufficient for analytical determination. Fluorescence intensity ratio and fluorescence lifetime measurements were performed and compared for microdroplet FRET determination. A competitive on-chip binding assay for determination of unlabelled avidin using fluorescence lifetime detection could be performed within 135 s only.

  16. Proteolysis in microfluidic droplets: an approach to interface protein separation and peptide mass spectrometry.

    Science.gov (United States)

    Ji, Ji; Nie, Lei; Qiao, Liang; Li, Yixin; Guo, Liping; Liu, Baohong; Yang, Pengyuan; Girault, Hubert H

    2012-08-07

    A versatile microreactor protocol based on microfluidic droplets has been developed for on-line protein digestion. Proteins separated by liquid chromatography are fractionated in water-in-oil droplets and digested in sequence. The microfluidic reactor acts also as an electrospray ionization emitter for mass spectrometry analysis of the peptides produced in the individual droplets. Each droplet is an enzymatic micro-reaction unit with efficient proteolysis due to rapid mixing, enhanced mass transfer and automated handling. This droplet approach eliminates sample loss, cross-contamination, non-specific absorption and memory effect. A protein mixture was successfully identified using the droplet-based micro-reactor as interface between reverse phase liquid chromatography and mass spectrometry.

  17. Specific transport of target molecules by motor proteins in microfluidic channels.

    Science.gov (United States)

    Tarhan, Mehmet C; Yokokawa, Ryuji; Morin, Fabrice O; Fujita, Hiroyuki

    2013-06-03

    Direct transport powered by motor proteins can alleviate the challenges presented by miniaturization of microfluidic systems. There have been several recent attempts to build motor-protein-driven transport systems based on simple capturing or transport mechanisms. However, to achieve a multifunctional device for practical applications, a more complex sorting/transport system should be realized. Herein, the proof of concept of a sorting device employing selective capture of distinct target molecules and transport of the sorted molecules to different predefined directions is presented. By combining the bottom-up functionality of biological systems with the top-down handling capabilities of micro-electromechanical systems technology, highly selective molecular recognition and motor-protein-based transport is integrated in a microfluidic channel network.

  18. A microfluidic linear node array for the study of protein-ligand interactions.

    Science.gov (United States)

    Li, Cheuk-Wing; Yu, Guodong; Jiang, Jingyun; Lee, Simon Ming-Yuen; Yi, Changqing; Yue, Wanqing; Yang, Mengsu

    2014-10-21

    We have developed a microfluidic device for the continuous separation of small molecules from a protein mixture and demonstrated its practical use in the study of protein-ligand binding, a crucial aspect in drug discovery. Our results demonstrated dose-dependent binding between bovine serum albumin (BSA) and its small-molecule site marker, Eosin Y (EY), and found that the binding reached a plateau when the BSA : EY ratio was above 1, which agreed with the eosin binding capacity of BSA reported in literature. By streamline control using a combination of two fundamental building blocks (R and L nodes) with a microdevice operated at a high flow rate (up to 1300 μL h(-1)), a solution barrier was created to "filter" off protein/protein-ligand complexes such that the small unbound molecules were isolated and quantified easily. The percentage decrease of small molecules with increasing protein concentration indicated the presence of binding events. Several fluorophores with different molecular weights were used to test the performance of the microfluidic "filter", which was tunable by 1) the total flow rate, and/or 2) the flow distribution ratio between the two device inlets; both were easily controllable by changing the syringe pump settings. Since the microdevice was operated at a relatively high flow rate, aliquots were easily recovered from the device outlets to facilitate off-chip detection. This microfluidic design is a novel and promising tool for preliminary drug screening.

  19. Rapid cell-patterning and microfluidic chip fabrication by crack-free CO2 laser ablation on glass

    Science.gov (United States)

    Yen, Meng-Hua; Cheng, Ji-Yen; Wei, Cheng-Wey; Chuang, Yung-Chuan; Young, Tai-Horng

    2006-07-01

    This paper uses a widely available CO2 laser scriber (λ = 10.6 µm) to perform the direct-writing ablation of quartz, borofloat and pyrex substrates for the development of microfluidic chips and cell chips. The surface quality of the ablated microchannels and the presence of debris and distortion are examined by scanning electron microscopy, atomic force microscopy and surface profile measurement techniques. The developed laser ablation system provides a versatile and economic approach for the fabrication of glass microfluidic chips with crack-free structures. In the laser writing process, the desired microfluidic patterns are designed using commercial computer software and are then transferred to the laser scriber to ablate the trenches. This process eliminates the requirement for corrosive chemicals and photomasks, and hence the overall microchip development time is limited to less than 24 h. Additionally, since the laser writing process is not limited by the dimensions of a photomask, the microchannels can be written over a large substrate area. The machining capability and versatility of the laser writing system are demonstrated through its application to the fabrication of a borofloat microfluidic chip and the writing of a series of asymmetric trenches in a microwell array. It is shown that the minimum attainable trench width is 95 µm and that the maximum trench depth is 225 µm. The system provides an economic and powerful means of rapid glass microfluidic chip development. A rapid cell-patterning method based on this method is also demonstrated.

  20. Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies.

    Science.gov (United States)

    Yamaguchi, Hiroshi; Miyazaki, Masaya

    2015-01-01

    Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies.

  1. Microfluidics-assisted engineering of polymeric microcapsules with high encapsulation efficiency for protein drug delivery.

    Science.gov (United States)

    Pessi, Jenni; Santos, Hélder A; Miroshnyk, Inna; JoukoYliruusi; Weitz, David A; Mirza, Sabiruddin

    2014-09-10

    In this study, microfluidic technology was employed to develop protein formulations. The microcapsules were produced with a biphasic flow to create water-oil-water (W/O/W) double emulsion droplets with ultrathin shells. Optimized microcapsule formulations containing 1% (w/w) bovine serum albumin (BSA) in the inner phase were prepared with poly(vinyl alcohol), polycaprolactone and polyethylene glycol. All the particles were found to be intact and with a particle size of 23-47 μm. Furthermore, the particles were monodisperse, non-porous and stable up to 4 weeks. The encapsulation efficiency of BSA in the microcapsules was 84%. The microcapsules released 30% of their content within 168 h. This study demonstrates that microfluidics is a powerful technique for engineering formulations for therapeutic proteins.

  2. Nanoliter-Scale Protein Crystallization and Screening with a Microfluidic Droplet Robot

    OpenAIRE

    Ying Zhu; Li-Na Zhu; Rui Guo; Heng-Jun Cui; Sheng Ye; Qun Fang

    2014-01-01

    Large-scale screening of hundreds or even thousands of crystallization conditions while with low sample consumption is in urgent need, in current structural biology research. Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening and the droplet-based microfluidic technique. A semi-contact dispensing method was developed to achieve flexible, programma...

  3. Electrostatic protein immobilization using charged polyacrylamide gels and cationic detergent microfluidic Western blotting.

    Science.gov (United States)

    Kim, Dohyun; Karns, Kelly; Tia, Samuel Q; He, Mei; Herr, Amy E

    2012-03-06

    We report a novel protein immobilization matrix for fully integrated microfluidic Western blotting (WB). The electrostatic immobilization gel (EIG) enables immobilization of all proteins sized using cetyl trimethylammonium bromide polyacrylamide gel electrophoresis (CTAB-PAGE), for subsequent electrophoretic probing with detection affinity reagents (e.g., labeled antibodies). The "pan-analyte" capture strategy introduced here uses polyacrylamide gel grafted with concentrated point charges (zwitterionic macromolecules), in contrast to existing microfluidic WB strategies that rely on a sandwich immunoassay format for analyte immobilization and detection. Sandwich approaches limit analyte immobilization to capture of only a priori known targets. A charge interaction mechanism study supports the hypothesis that electrostatic interaction plays a major role in analyte immobilization on the EIG. We note that protein capture efficiency depends on both the concentration of copolymerized charges and ionic strength of the gel buffer. We demonstrate pan-analyte immobilization of sized CTAB-laden model proteins (protein G, ovalbumin, bovine serum albumin, β-galactosidase, lactoferrin) on the EIG with initial capture efficiencies ranging from 21 to 100%. Target proteins fixed on the EIG (protein G, lactoferrin) are detected using antibody probes with signal-to-noise ratios of 34 to 275. The approach advances protein immunoblotting performance through 200× reduction on sample consumption, 12× reduction in assay duration, and automated assay operation, compared to slab-gel WB. Using the microfluidic WB assay, assessment of lactoferrin in human tear fluid is demonstrated with a goal of advancing toward nonbiopsy-based diagnosis of Sjögren's Syndrome, an autoimmune disease.

  4. Nanoliter-scale protein crystallization and screening with a microfluidic droplet robot.

    Science.gov (United States)

    Zhu, Ying; Zhu, Li-Na; Guo, Rui; Cui, Heng-Jun; Ye, Sheng; Fang, Qun

    2014-05-23

    Large-scale screening of hundreds or even thousands of crystallization conditions while with low sample consumption is in urgent need, in current structural biology research. Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening and the droplet-based microfluidic technique. A semi-contact dispensing method was developed to achieve flexible, programmable and reliable liquid-handling operations for nanoliter-scale protein crystallization experiments. We applied the droplet robot in large-scale screening of crystallization conditions of five soluble proteins and one membrane protein with 35-96 different crystallization conditions, study of volume effects on protein crystallization, and determination of phase diagrams of two proteins. The volume for each droplet reactor is only ca. 4-8 nL. The protein consumption significantly reduces 50-500 fold compared with current crystallization stations.

  5. Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

    Science.gov (United States)

    Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

    2017-03-01

    Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

  6. A Versatile Method of Patterning Proteins and Cells.

    Science.gov (United States)

    Shrirao, Anil B; Kung, Frank H; Yip, Derek; Firestein, Bonnie L; Cho, Cheul H; Townes-Anderson, Ellen

    2017-02-26

    Substrate and cell patterning techniques are widely used in cell biology to study cell-to-cell and cell-to-substrate interactions. Conventional patterning techniques work well only with simple shapes, small areas and selected bio-materials. This article describes a method to distribute cell suspensions as well as substrate solutions into complex, long, closed (dead-end) polydimethylsiloxane (PDMS) microchannels using negative pressure. This method enables researchers to pattern multiple substrates including fibronectin, collagen, antibodies (Sal-1), poly-D-lysine (PDL), and laminin. Patterning of substrates allows one to indirectly pattern a variety of cells. We have tested C2C12 myoblasts, the PC12 neuronal cell line, embryonic rat cortical neurons, and amphibian retinal neurons. In addition, we demonstrate that this technique can directly pattern fibroblasts in microfluidic channels via brief application of a low vacuum on cell suspensions. The low vacuum does not significantly decrease cell viability as shown by cell viability assays. Modifications are discussed for application of the method to different cell and substrate types. This technique allows researchers to pattern cells and proteins in specific patterns without the need for exotic materials or equipment and can be done in any laboratory with a vacuum.

  7. Microfluidic devices for label-free separation of cells through transient interaction with asymmetric receptor patterns

    Science.gov (United States)

    Bose, S.; Singh, R.; Hollatz, M. H.; Lee, C.-H.; Karp, J.; Karnik, R.

    2012-02-01

    Cell sorting serves an important role in clinical diagnosis and biological research. Most of the existing microscale sorting techniques are either non-specific to antigen type or rely on capturing cells making sample recovery difficult. We demonstrate a simple; yet effective technique for isolating cells in an antigen specific manner by using transient interactions of the cell surface antigens with asymmetric receptor patterned surface. Using microfluidic devices incorporating P-selectin patterns we demonstrate separation of HL60 cells from K562 cells. We achieved a sorting purity above 90% and efficiency greater than 85% with this system. We also present a mathematical model incorporating flow mediated and adhesion mediated transport of cells in the microchannel that can be used to predict the performance of these devices. Lastly, we demonstrate the clinical significance of the method by demonstrating single step separation of neutrophils from whole blood. When whole blood is introduced in the device, the granulocyte population gets separated exclusively yielding neutrophils of high purity (<10% RBC contamination). To our knowledge, this is the first ever demonstration of continuous label free sorting of neutrophils from whole blood. We believe this technology will be useful in developing point-of-care diagnostic devices and also for a host of cell sorting applications.

  8. Wettability patterning for high-rate, pumpless fluid transport on open, non-planar microfluidic platforms.

    Science.gov (United States)

    Ghosh, Aritra; Ganguly, Ranjan; Schutzius, Thomas M; Megaridis, Constantine M

    2014-05-07

    Surface tension driven transport of liquids on open substrates offers an enabling tool for open micro total analysis systems that are becoming increasingly popular for low-cost biomedical diagnostic devices. The present study uses a facile wettability patterning method to produce open microfluidic tracks that - due to their shape, surface texture and chemistry - are capable of transporting a wide range of liquid volumes (~1-500 μL) on-chip, overcoming viscous and other opposing forces (e.g., gravity) at the pertinent length scales. Small volumes are handled as individual droplets, while larger volumes require repeated droplet transport. The concept is developed and demonstrated with coatings based on TiO2 filler particles, which, when present in adequate (~80 wt.%) quantities within a hydrophobic fluoroacrylic polymer matrix, form composites that are intrinsically superhydrophobic. Such composite coatings become superhydrophilic upon exposure to UV light (390 nm). A commercial laser printer-based photo-masking approach is used on the coating for spatially selective wettability conversion from superhydrophobic to superhydrophilic. Carefully designed wedge-patterned surface tension confined tracks on the open-air devices move liquid on them without power input, even when acting against gravity. Simple designs of wettability patterning are used on versatile substrates (e.g., metals, polymers, paper) to demonstrate complex droplet handling tasks, e.g., merging, splitting and metered dispensing, some of which occur in 3-D geometries. Fluid transport rates of up to 350 μL s(-1) are attained. Applicability of the design on metal substrates allows these devices to be used also for other microscale engineering applications, e.g., water management in fuel cells.

  9. Inkjet patterned superhydrophobic paper for open-air surface microfluidic devices.

    Science.gov (United States)

    Elsharkawy, Mohamed; Schutzius, Thomas M; Megaridis, Constantine M

    2014-03-21

    We present a facile approach for the fabrication of low-cost surface biomicrofluidic devices on superhydrophobic paper created by drop-casting a fluoroacrylic copolymer onto microtextured paper. Wettability patterning is performed with a common household printer, which produces regions of varying wettability by simply controlling the intensity of ink deposited over prespecified domains. The procedure produces surfaces that are capable of selective droplet sliding and adhesion, when inclined. Using this methodology, we demonstrate the ability to tune the sliding angles of 10 μL water droplets in the range from 13° to 40° by printing lines of constant ink intensity and varied width from 0.1 mm to 2 mm. We also formulate a simple model to predict the onset of droplet sliding on printed lines of known width and wettability. Experiments demonstrate open-air surface microfluidic devices that are capable of pumpless transport, mixing and rapid droplet sampling (~0.6 μL at 50 Hz). Lastly, post treatment of printed areas with pH indicator solutions exemplifies the utility of these substrates in point-of-care diagnostics, which are needed at geographical locations where access to sophisticated testing equipment is limited or non-existent.

  10. Development-on-chip: in vitro neural tube patterning with a microfluidic device

    Science.gov (United States)

    Soundararajan, Prabakaran; Chennampally, Phaneendra; Cox, Gregory A.

    2016-01-01

    Embryogenesis is a highly regulated process in which the precise spatial and temporal release of soluble cues directs differentiation of multipotent stem cells into discrete populations of specialized adult cell types. In the spinal cord, neural progenitor cells are directed to differentiate into adult neurons through the action of mediators released from nearby organizing centers, such as the floor plate and paraxial mesoderm. These signals combine to create spatiotemporal diffusional landscapes that precisely regulate the development of the central nervous system (CNS). Currently, in vivo and ex vivo studies of these signaling factors present some inherent ambiguity. In vitro methods are preferred for their enhanced experimental clarity but often lack the technical sophistication required for biological realism. In this article, we present a versatile microfluidic platform capable of mimicking the spatial and temporal chemical environments found in vivo during neural tube development. Simultaneous opposing and/or orthogonal gradients of developmental morphogens can be maintained, resulting in neural tube patterning analogous to that observed in vivo. PMID:27246712

  11. Mass Spectrometry-Based Monitoring of Millisecond Protein-Ligand Binding Dynamics Using an Automated Microfluidic Platform

    Energy Technology Data Exchange (ETDEWEB)

    Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.; Orton, Daniel J.; Geng, Tao; Baker, Erin Shammel; Kelly, Ryan T.

    2016-03-24

    Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

  12. Theoretical microfluidics

    DEFF Research Database (Denmark)

    Bruus, Henrik

    , complex flow patterns and acousto-fluidics, as well as the new fields of opto- and nano-fluidics. Throughout the book simple models with analytical solutions are presented to provide the student with a thorough physical understanding of order of magnitudes and various selected microfluidic phenomena...

  13. Functionalized poly(ethylene glycol) diacrylate microgels by microfluidics: In situ peptide encapsulation for in serum selective protein detection.

    Science.gov (United States)

    Celetti, Giorgia; Natale, Concetta Di; Causa, Filippo; Battista, Edmondo; Netti, Paolo A

    2016-09-01

    Polymeric microparticles represent a robustly platform for the detection of clinically relevant analytes in biological samples; they can be functionalized encapsulating a multiple types of biologics entities, enhancing their applications as a new class of colloid materials. Microfluidic offers a versatile platform for the synthesis of monodisperse and engineered microparticles. In this work, we report microfluidic synthesis of novel polymeric microparticles endowed with specific peptide due to its superior specificity for target binding in complex media. A peptide sequence was efficiently encapsulated into the polymeric network and protein binding occurred with high affinity (KD 0.1-0.4μM). Fluidic dynamics simulation was performed to optimize the production conditions for monodisperse and stable functionalized microgels. The results demonstrate the easy and fast realization, in a single step, of functionalized monodisperse microgels using droplet-microfluidic technique, and how the inclusion of the peptide within polymeric network improve both the affinity and the specificity of protein capture.

  14. Protein patterning by a DNA origami framework.

    Science.gov (United States)

    Aslan, Hüsnü; Krissanaprasit, Abhichart; Besenbacher, Flemming; Gothelf, Kurt V; Dong, Mingdong

    2016-08-18

    A spatial arrangement of proteins provides structural and functional advantages in vast technological applications as well as fundamental research. Most protein patterning procedures employ complicated, time consuming and very costly nanofabrication techniques. As an alternative route, we developed a fully biomolecular self-assembly method using DNA Origami Frames (DOF) as a template for both small and large scale protein patterning. We employed a triangular DOF (tDOF) to arrange the Bovine Serum Albumin (BSA) protein. Our in situ protein patterning strategy provides a novel, fully organic platform using a fast and low-cost surface approach with possible utilization in fundamental science and technological applications.

  15. A smart surface in a microfluidic chip for controlled protein separation.

    Science.gov (United States)

    Mu, Li; Liu, Ying; Cai, Shaoyu; Kong, Jilie

    2007-01-01

    The smart surface created in a microfluidic chip has shown the capability of adsorbing and releasing proteins under electrical control. The inner surface of the chip channel was first coated by a thin layer of Au through sputtering and was subsequently modified with loosely packed self-assembled monolayers (SAMs) of thiols with terminal carboxylic or amino groups. Upon application of an external electric potential to the gold substrate, reversible conformational transformation between "bent" and "straight" states for the anchored mercapto chains could be modulated, through the electrostatic effect between the ionized terminal groups and the charged gold substrate. Thus, a hydrophobic or hydrophilic channel surface was established and could be reversibly switched electrochemically. Accordingly, the microchips prepared in this way can reversibly and selectively adsorb and release differently charged proteins under electrical control. Two model proteins, avidin and streptavidin, were demonstrated to be readily adsorbed by the smart chips under negative and positive potential, respectively. Also, more than 90 % of the adsorbed proteins could be released upon an electrical command. Furthermore, these chips were applied to the controlled separation of avidin and streptavidin mixtures with 1:1 and 1:1000 molar ratios. Under specific applied potentials, the chips adsorbed a certain protein from the mixture whereas the other protein was allowed to flow out, after which the adsorbed protein could be released by switching the applied potential. Thus, two eluted protein fractions were obtained and the separation of the two proteins was achieved. For the former mixture, each eluted fraction contained up to approximately 80-90 % avidin or streptavidin. For the latter mixture, the resulting separation efficiency indicated that the molar ratio of avidin and streptavidin could be increased from 1:1000 to about 32:1 after five run separations.

  16. Use of PLL-g-PEG in micro-fluidic devices for localizing selective and specific protein binding.

    Science.gov (United States)

    Marie, Rodolphe; Beech, Jason P; Vörös, Janos; Tegenfeldt, Jonas O; Höök, Fredrik

    2006-11-21

    By utilizing flow-controlled PLL-g-PEG and PLL-g-PEGbiotin modification of predefined regions of a poly(dimethylsiloxane) (PDMS) micro-fluidic device, with an intentionally chosen large (approximately 1 cm2) internal surface area, we report rapid (10 min), highly localized (6 x 10(-6) cm2), and specific surface-based protein capture from a sample volume (100 microL) containing a low amount of protein (160 attomol in pure buffer and 400 attomol in serum). The design criteria for this surface modification were achieved using QCM-D (quartz crystal microbalance with energy dissipation monitoring) of serum protein adsorption onto PLL-g-PEG-modified oxidized PDMS. Equally good, or almost as good, results were obtained for oxidized SU-8, Topas, and poly(methyl metacrylate) (PMMA), demonstrating the generic potential of PLL-g-PEG for surface modification in various micro-fluidic applications.

  17. Microfluidic flow cytometer for quantifying photobleaching of fluorescent proteins in cells.

    Science.gov (United States)

    Lubbeck, Jennifer L; Dean, Kevin M; Ma, Hairong; Palmer, Amy E; Jimenez, Ralph

    2012-05-01

    Traditional flow cytometers are capable of rapid cellular assays on the basis of fluorescence intensity and light scatter. Microfluidic flow cytometers have largely followed the same path of technological development as their traditional counterparts; however, the significantly smaller transport distance and resulting lower cell speeds in microchannels provides for the opportunity to detect novel spectroscopic signatures based on multiple, nontemporally coincident excitation beams. Here, we characterize the design and operation of a cytometer with a three-beam, probe/bleach/probe geometry, employing HeLa suspension cells expressing fluorescent proteins. The data collection rate exceeds 20 cells/s under a range of beam intensities (5 kW to 179 kW/cm(2)). The measured percent photobleaching (ratio of fluorescence intensities excited by the first and third beams: S(beam3)/S(beam1)) partially resolves a mixture of four red fluorescent proteins in mixed samples. Photokinetic simulations are presented and demonstrate that the percent photobleaching reflects a combination of the reversible and irreversible photobleaching kinetics. By introducing a photobleaching optical signature, which complements traditional fluorescence intensity-based detection, this method adds another dimension to multichannel fluorescence cytometry and provides a means for flow-cytometry-based screening of directed libraries of fluorescent protein photobleaching.

  18. Novel approach to protein crystallizations: Control of the phase behavior of aqueous solutions using microfluidics

    Science.gov (United States)

    Shim, Jung Uk

    A microfluidic device denoted the Phase Chip has been developed to exploit the permeation of water through poly(dimethylsiloxane) (PDMS) in order to vary the concentration of aqueous nanoliter volume microdrops stored in wells. The permeation of water in the Phase Chip is modeled using the diffusion equation and good agreement between experiment and theory is obtained. The phase diagram of a polymer/salt mixture is measured employing the Phase Chip and agrees well with the phase diagram obtained off-chip. The Phase Chip first creates drops of the polymer/salt mixture whose composition varies sequentially. Subsequently the drops are docked in storage wells and the concentration of each stored drop is controlled by varying the water activity of a reservoir that is separated from the drops by a thin layer of PDMS through which water, but not the solutes, permeates. The Phase Chip, incorporating a dialysis membrane on-chip, presents several advantages for protein crystallizations. First, protein crystallization is a non-equilibrium process so it makes sense to have dynamic control over the key thermodynamic variable; concentration. The Phase Chip, with its ability to reversibly control protein and precipitant concentrations, renders varying concentration as convenient as varying temperature. Second, by varying the water content of each drop we can explore many different crystallization conditions in the same drop. Finally, we have demonstrated that we can first formulate stable protein solutions, next induce nucleation and then grow large protein crystals. For these reasons, the Phase Chip promises to be a faster, better, and cheaper method for protein crystallization.

  19. One-step patterning of hollow microstructures in paper by laser cutting to create microfluidic analytical devices.

    Science.gov (United States)

    Nie, Jinfang; Liang, Yuanzhi; Zhang, Yun; Le, Shangwang; Li, Dunnan; Zhang, Songbai

    2013-01-21

    In this paper, we report a simple, low-cost method for rapid, highly reproductive fabrication of paper-based microfluidics by using a commercially available, minitype CO(2) laser cutting/engraving machine. This method involves only one operation of cutting a piece of paper by laser according to a predesigned pattern. The hollow microstructures formed in the paper are used as the 'hydrophobic barriers' to define the hydrophilic flowing paths. A typical paper device on a 4 cm × 4 cm piece of paper can be fabricated within ∼7-20 s; it is ready for use once the cutting process is finished. The main fabrication parameters such as the applied current and cutting rate of the laser were optimized. The fabrication resolution and multiplexed analytical capability of the hollow microstructure-patterned paper were also characterized.

  20. Fabrication of a polystyrene microfluidic chip coupled to electrospray ionization mass spectrometry for protein analysis.

    Science.gov (United States)

    Hu, Xianqiao; Dong, Yuanyuan; He, Qiaohong; Chen, Hengwu; Zhu, Zhiwei

    2015-05-15

    A highly integrated polystyrene (PS) microfluidic chip coupled to electrospray ionization mass spectrometry for on-chip protein digestion and online analysis was developed. The immobilized enzymatic microreactor for on-chip protein digestion was integrated onto microchip via the novel method of region-selective UV-modification combined with glutaraldehyde-based immobilization. The micro film electric contact for applying high voltage was prepared on chips by using UV-directed electroless plating technique. A micro-tip was machined at the end of main channel, serving as the interface between microchip and mass spectrometric detector. On-chip digestion and online detection of protein was carried out by coupling the microchip with mass spectrometry (MS). The influences of methanol flow rate in side channel on the stability of spray and intensity of signals were investigated systematically. Also the influence of sample flow rate on the performance of immobilized enzymatic reactor were investigated. Stable spray was obtained at the spray voltage of 2.8-3.0kV and the methanol flow rate of 500-700nLmin(-1) with the relative standard deviation (RSD) of total ion current (TIC) less than 10%. The influence of sample flow rate on the performance of immobilized enzymatic reactor was also studied. The sequence coverage of protein identification decreased with the increase of flow rate of the sample solution. A sequence coverage of 96% was obtained with immobilized enzymatic reactor at the sample flow rate of 100nLmin(-1) with the reaction time of 8.4min. It could detect cytochrome c as low as 10μgmL(-1) with the developed system. No obvious decrease in protein digestion efficiency was observed after the chip continuously performed for 4h and stored for 15d.

  1. Geometry-induced protein pattern formation.

    Science.gov (United States)

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-19

    Protein patterns are known to adapt to cell shape and serve as spatial templates that choreograph downstream processes like cell polarity or cell division. However, how can pattern-forming proteins sense and respond to the geometry of a cell, and what mechanistic principles underlie pattern formation? Current models invoke mechanisms based on dynamic instabilities arising from nonlinear interactions between proteins but neglect the influence of the spatial geometry itself. Here, we show that patterns can emerge as a direct result of adaptation to cell geometry, in the absence of dynamical instability. We present a generic reaction module that allows protein densities robustly to adapt to the symmetry of the spatial geometry. The key component is an NTPase protein that cycles between nucleotide-dependent membrane-bound and cytosolic states. For elongated cells, we find that the protein dynamics generically leads to a bipolar pattern, which vanishes as the geometry becomes spherically symmetrical. We show that such a reaction module facilitates universal adaptation to cell geometry by sensing the local ratio of membrane area to cytosolic volume. This sensing mechanism is controlled by the membrane affinities of the different states. We apply the theory to explain AtMinD bipolar patterns in [Formula: see text] EcMinDE Escherichia coli. Due to its generic nature, the mechanism could also serve as a hitherto-unrecognized spatial template in many other bacterial systems. Moreover, the robustness of the mechanism enables self-organized optimization of protein patterns by evolutionary processes. Finally, the proposed module can be used to establish geometry-sensitive protein gradients in synthetic biological systems.

  2. Microfluidic sorting of protein nanocrystals by size for X-ray free-electron laser diffraction

    Directory of Open Access Journals (Sweden)

    Bahige G. Abdallah

    2015-07-01

    Full Text Available The advent and application of the X-ray free-electron laser (XFEL has uncovered the structures of proteins that could not previously be solved using traditional crystallography. While this new technology is powerful, optimization of the process is still needed to improve data quality and analysis efficiency. One area is sample heterogeneity, where variations in crystal size (among other factors lead to the requirement of large data sets (and thus 10–100 mg of protein for determining accurate structure factors. To decrease sample dispersity, we developed a high-throughput microfluidic sorter operating on the principle of dielectrophoresis, whereby polydisperse particles can be transported into various fluid streams for size fractionation. Using this microsorter, we isolated several milliliters of photosystem I nanocrystal fractions ranging from 200 to 600 nm in size as characterized by dynamic light scattering, nanoparticle tracking, and electron microscopy. Sorted nanocrystals were delivered in a liquid jet via the gas dynamic virtual nozzle into the path of the XFEL at the Linac Coherent Light Source. We obtained diffraction to ∼4 Å resolution, indicating that the small crystals were not damaged by the sorting process. We also observed the shape transforms of photosystem I nanocrystals, demonstrating that our device can optimize data collection for the shape transform-based phasing method. Using simulations, we show that narrow crystal size distributions can significantly improve merged data quality in serial crystallography. From this proof-of-concept work, we expect that the automated size-sorting of protein crystals will become an important step for sample production by reducing the amount of protein needed for a high quality final structure and the development of novel phasing methods that exploit inter-Bragg reflection intensities or use variations in beam intensity for radiation damage-induced phasing. This method will also

  3. Pattern Recognition of Adsorbing HP Lattice Proteins

    Science.gov (United States)

    Wilson, Matthew S.; Shi, Guangjie; Wüst, Thomas; Landau, David P.; Schmid, Friederike

    2015-03-01

    Protein adsorption is relevant in fields ranging from medicine to industry, and the qualitative behavior exhibited by course-grained models could shed insight for further research in such fields. Our study on the selective adsorption of lattice proteins utilizes the Wang-Landau algorithm to simulate the Hydrophobic-Polar (H-P) model with an efficient set of Monte Carlo moves. Each substrate is modeled as a square pattern of 9 lattice sites which attract either H or P monomers, and are located on an otherwise neutral surface. The fully enumerated set of 102 unique surfaces is simulated with each protein sequence. A collection of 27-monomer sequences is used- each of which is non-degenerate and protein-like. Thermodynamic quantities such as the specific heat and free energy are calculated from the density of states, and are used to investigate the adsorption of lattice proteins on patterned substrates. Research supported by NSF.

  4. Different migration patterns of sea urchin and mouse sperm revealed by a microfluidic chemotaxis device.

    Directory of Open Access Journals (Sweden)

    Haixin Chang

    Full Text Available Chemotaxis refers to a process whereby cells move up or down a chemical gradient. Sperm chemotaxis is known to be a strategy exploited by marine invertebrates such as sea urchins to reach eggs efficiently in moving water. Less is understood about how or whether chemotaxis is used by mammalian sperm to reach eggs, where fertilization takes place within the confinement of a reproductive tract. In this report, we quantitatively assessed sea urchin and mouse sperm chemotaxis using a recently developed microfluidic model and high-speed imaging. Results demonstrated that sea urchin Arbacia punctulata sperm were chemotactic toward the peptide resact with high chemotactic sensitivity, with an average velocity Vx up the chemical gradient as high as 20% of its average speed (238 μm/s, while mouse sperm displayed no statistically significant chemotactic behavior in progesterone gradients, which had been proposed to guide mammalian sperm toward eggs. This work demonstrates the validity of a microfluidic model for quantitative sperm chemotaxis studies, and reveals a biological insight that chemotaxis up a progesterone gradient may not be a universal strategy for mammalian sperm to reach eggs.

  5. High-performance fluorescence-encoded magnetic microbeads as microfluidic protein chip supports for AFP detection.

    Science.gov (United States)

    Gong, Xiaoqun; Yan, Huan; Yang, Jiumin; Wu, Yudong; Zhang, Jian; Yao, Yingyi; Liu, Ping; Wang, Huiquan; Hu, Zhidong; Chang, Jin

    2016-10-01

    Fluorescence-encoded magnetic microbeads (FEMMs), with the fluorescence encoding ability of quantum dots (QDs) and magnetic enrichment and separation functions of Fe3O4 nanoparticles, have been widely used for multiple biomolecular detection as microfluidic protein chip supports. However, the preparation of FEMMs with long-term fluorescent encoding and immunodetection stability is still a challenge. In this work, we designed a novel high-temperature chemical swelling strategy. The QDs and Fe3O4 nanoparticles were effectively packaged into microbeads via the thermal motion of the polymer chains and the hydrophobic interaction between the nanoparticles and microbeads. The FEMMs obtained a highly uniform fluorescent property and long-term encoding and immunodetection stability and could be quickly magnetically separated and enriched. Then, the QD-encoded magnetic microbeads were applied to alpha fetoprotein (AFP) detection via sandwich immunoreaction. The properties of the encoded microspheres were characterized using a self-designed detecting apparatus, and the target molecular concentration in the sample was also quantified. The results suggested that the high-performance FEMMs have great potential in the field of biomolecular detection.

  6. A simple microfluidic platform to study age-dependent protein abundance and localization changes in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Margarita Cabrera

    2017-04-01

    Full Text Available The budding yeast Saccharomyces cerevisiae divides asymmetrically, with a smaller daughter cell emerging from its larger mother cell. While the daughter lineage is immortal, mother cells age with each cell division and have a finite lifespan. The replicative ageing of the yeast mother cell has been used as a model to study the ageing of mitotically active human cells. Several microfluidic platforms, which use fluid flow to selectively remove daughter cells, have recently been developed that can monitor cell physiology as mother cells age. However, these platforms are not trivial to set up and users often require many hours of training. In this study, we have developed a simple system, which combines a commercially available microfluidic platform (the CellASIC ONIX Microfluidic Platform and a genetic tool to prevent the proliferation of daughter cells (the Mother Enrichment Program, to monitor protein abundance and localization changes during approximately the first half of the yeast replicative lifespan. We validated our system by observing known age-dependent changes, such as decreased Sir2 abundance, and have identified a protein with a previously unknown age-dependent change in localization.

  7. Laser micromachined wax-covered plastic paper as both sputter deposition shadow masks and deep-ultraviolet patterning masks for polymethylmethacrylate-based microfluidic systems

    Science.gov (United States)

    Fan, Yiqiang; Li, Huawei; Yi, Ying; Foulds, Ian G.

    2013-10-01

    We report a technically innovative method of fabricating masks for both deep-ultraviolet (UV) patterning and metal sputtering on polymethylmethacrylate (PMMA) for microfluidic systems. We used a CO laser system to cut the required patterns on wax-covered plastic paper; the laser-patterned wax paper will either work as a mask for deep-UV patterning or as a mask for metal sputtering. A microfluidic device was also fabricated to demonstrate the feasibility of this method. The device has two layers: the first layer is a 1-mm thick PMMA substrate that was patterned by deep-UV exposure to create microchannels. The mask used in this process was the laser-cut wax paper. The second layer, also a 1-mm thick PMMA layer, was gold sputtered with patterned wax paper as the shadow mask. These two pieces of PMMA were then bonded to form microchannels with exposed electrodes. This process is a simple and rapid method for creating integrated microfluidic systems that do not require cleanroom facilities.

  8. Laser micromachined wax-covered plastic paper as both sputter deposition shadow masks and deep-ultraviolet patterning masks for polymethylmethacrylate-based microfluidic systems

    KAUST Repository

    Fan, Yiqiang

    2013-12-16

    We report a technically innovative method of fabricating masks for both deep-ultraviolet (UV) patterning and metal sputtering on polymethylmethacrylate (PMMA) for microfluidic systems. We used a CO2 laser system to cut the required patterns on wax-covered plastic paper; the laser-patterned wax paper will either work as a mask for deep-UV patterning or as a mask for metal sputtering. A microfluidic device was also fabricated to demonstrate the feasibility of this method. The device has two layers: the first layer is a 1-mm thick PMMA substrate that was patterned by deep-UV exposure to create microchannels. The mask used in this process was the laser-cut wax paper. The second layer, also a 1-mm thick PMMA layer, was gold sputtered with patterned wax paper as the shadow mask. These two pieces of PMMA were then bonded to form microchannels with exposed electrodes. This process is a simple and rapid method for creating integrated microfluidic systems that do not require cleanroom facilities.

  9. Discovering functional interaction patterns in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Can Tolga

    2008-06-01

    Full Text Available Abstract Background In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution of PPI networks and identification of conserved subnetworks across different species, discovery of modules of interaction, use of PPI networks for functional annotation of uncharacterized proteins, and improvement of the accuracy of currently available networks. Results In this article, we map known functional annotations of proteins onto a PPI network in order to identify frequently occurring interaction patterns in the functional space. We propose a new frequent pattern identification technique, PPISpan, adapted specifically for PPI networks from a well-known frequent subgraph identification method, gSpan. Existing module discovery techniques either look for specific clique-like highly interacting protein clusters or linear paths of interaction. However, our goal is different; instead of single clusters or pathways, we look for recurring functional interaction patterns in arbitrary topologies. We have applied PPISpan on PPI networks of Saccharomyces cerevisiae and identified a number of frequently occurring functional interaction patterns. Conclusion With the help of PPISpan, recurring functional interaction patterns in an organism's PPI network can be identified. Such an analysis offers a new perspective on the modular organization of PPI networks. The complete list of identified functional interaction patterns is available at http://bioserver.ceng.metu.edu.tr/PPISpan/.

  10. Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering.

    Science.gov (United States)

    Blackburn, Matthew C; Petrova, Ekaterina; Correia, Bruno E; Maerkl, Sebastian J

    2016-04-20

    The capability to rapidly design proteins with novel functions will have a significant impact on medicine, biotechnology and synthetic biology. Synthetic genes are becoming a commodity, but integrated approaches have yet to be developed that take full advantage of gene synthesis. We developed a solid-phase gene synthesis method based on asymmetric primer extension (APE) and coupled this process directly to high-throughput, on-chip protein expression, purification and characterization (via mechanically induced trapping of molecular interactions, MITOMI). By completely circumventing molecular cloning and cell-based steps, APE-MITOMI reduces the time between protein design and quantitative characterization to 3-4 days. With APE-MITOMI we synthesized and characterized over 400 zinc-finger (ZF) transcription factors (TF), showing that although ZF TFs can be readily engineered to recognize a particular DNA sequence, engineering the precise binding energy landscape remains challenging. We also found that it is possible to engineer ZF-DNA affinity precisely and independently of sequence specificity and that in silico modeling can explain some of the observed affinity differences. APE-MITOMI is a generic approach that should facilitate fundamental studies in protein biophysics, and protein design/engineering.

  11. Design and Testing of Digital Microfluidic Biochips

    CERN Document Server

    Zhao, Yang

    2013-01-01

    This book provides a comprehensive methodology for automated design, test and diagnosis, and use of robust, low-cost, and manufacturable digital microfluidic systems. It focuses on the development of a comprehensive CAD optimization framework for digital microfluidic biochips that unifies different design problems. With the increase in system complexity and integration levels, biochip designers can utilize the design methods described in this book to evaluate different design alternatives, and carry out design-space exploration to obtain the best design point. Describes practical design automation tools that address different design problems (e.g., synthesis, droplet routing, control-pin mapping, testing and diagnosis, and error recovery) in a unified manner; Applies test pattern generation and error-recovery techniques for digital microfluidics-based biochips; Uses real bioassays as evaluation examples, e.g., multiplexed in vitro human physiological fluids diagnostics, PCR, protein crystallization.  

  12. An in-line spectrophotometer on a centrifugal microfluidic platform for real-time protein determination and calibration.

    Science.gov (United States)

    Ding, Zhaoxiong; Zhang, Dongying; Wang, Guanghui; Tang, Minghui; Dong, Yumin; Zhang, Yixin; Ho, Ho-Pui; Zhang, Xuping

    2016-09-21

    In this paper, an in-line, low-cost, miniature and portable spectrophotometric detection system is presented and used for fast protein determination and calibration in centrifugal microfluidics. Our portable detection system is configured with paired emitter and detector diodes (PEDD), where the light beam between both LEDs is collimated with enhanced system tolerance. It is the first time that a physical model of PEDD is clearly presented, which could be modelled as a photosensitive RC oscillator. A portable centrifugal microfluidic system that contains a wireless port in real-time communication with a smartphone has been built to show that PEDD is an effective strategy for conducting rapid protein bioassays with detection performance comparable to that of a UV-vis spectrophotometer. The choice of centrifugal microfluidics offers the unique benefits of highly parallel fluidic actuation at high accuracy while there is no need for a pump, as inertial forces are present within the entire spinning disc and accurately controlled by varying the spinning speed. As a demonstration experiment, we have conducted the Bradford assay for bovine serum albumin (BSA) concentration calibration from 0 to 2 mg mL(-1). Moreover, a novel centrifugal disc with a spiral microchannel is proposed for automatic distribution and metering of the sample to all the parallel reactions at one time. The reported lab-on-a-disc scheme with PEDD detection may offer a solution for high-throughput assays, such as protein density calibration, drug screening and drug solubility measurement that require the handling of a large number of reactions in parallel.

  13. Design of Smart Polymer-Protein Conjugates and Smart Magnetic Nanoparticles for Use in Microfluidic Diagnostic Assays

    Institute of Scientific and Technical Information of China (English)

    Allan; S.Hoffman

    2007-01-01

    1 Results In this talk,I will describe the design,synthesis and application of smart polymers for use in microfluidic diagnostic devices.We are synthesizing a variety of temperature- and pH-responsive polymers using RAFT living free radical polymerization techniques.This allows us to control molecular weight and to achieve a narrow MW distribution of the polymers. Furthermore,RAFT polymers have reactive end groups that are used to conjugate the polymers to proteins.We are also using those groups to bind...

  14. Monitoring the differentiation and migration patterns of neural cells derived from human embryonic stem cells using a microfluidic culture system.

    Science.gov (United States)

    Lee, Nayeon; Park, Jae Woo; Kim, Hyung Joon; Yeon, Ju Hun; Kwon, Jihye; Ko, Jung Jae; Oh, Seung-Hun; Kim, Hyun Sook; Kim, Aeri; Han, Baek Soo; Lee, Sang Chul; Jeon, Noo Li; Song, Jihwan

    2014-06-01

    Microfluidics can provide unique experimental tools to visualize the development of neural structures within a microscale device, which is followed by guidance of neurite growth in the axonal isolation compartment. We utilized microfluidics technology to monitor the differentiation and migration of neural cells derived from human embryonic stem cells (hESCs). We co-cultured hESCs with PA6 stromal cells, and isolated neural rosette-like structures, which subsequently formed neurospheres in suspension culture. Tuj1-positive neural cells, but not nestin-positive neural precursor cells (NPCs), were able to enter the microfluidics grooves (microchannels), suggesting that neural cell-migratory capacity was dependent upon neuronal differentiation stage. We also showed that bundles of axons formed and extended into the microchannels. Taken together, these results demonstrated that microfluidics technology can provide useful tools to study neurite outgrowth and axon guidance of neural cells, which are derived from human embryonic stem cells.

  15. Microfluidic networks embedded in a printed circuit board

    Science.gov (United States)

    Dong, Liangwei; Hu, Yueli

    2017-07-01

    In order to improve the robustness of microfluidic networks in printed circuit board (PCB)-based microfluidic platforms, a new method was presented. A pattern in a PCB was formed using hollowed-out technology. Polydimethylsiloxane was partly filled in the hollowed-out fields after mounting an adhesive tape on the bottom of the PCB, and solidified in an oven. Then, microfluidic networks were built using soft lithography technology. Microfluidic transportation and dilution operations were demonstrated using the fabricated microfluidic platform. Results show that this method can embed microfluidic networks into a PCB, and microfluidic operations can be implemented in the microfluidic networks embedded into the PCB.

  16. A simple and cost-effective method for fabrication of integrated electronic-microfluidic devices using a laser-patterned PDMS layer

    KAUST Repository

    Li, Ming

    2011-12-03

    We report a simple and cost-effective method for fabricating integrated electronic-microfluidic devices with multilayer configurations. A CO 2 laser plotter was employed to directly write patterns on a transferred polydimethylsiloxane (PDMS) layer, which served as both a bonding and a working layer. The integration of electronics in microfluidic devices was achieved by an alignment bonding of top and bottom electrode-patterned substrates fabricated with conventional lithography, sputtering and lift-off techniques. Processes of the developed fabrication method were illustrated. Major issues associated with this method as PDMS surface treatment and characterization, thickness-control of the transferred PDMS layer, and laser parameters optimization were discussed, along with the examination and testing of bonding with two representative materials (glass and silicon). The capability of this method was further demonstrated by fabricating a microfluidic chip with sputter-coated electrodes on the top and bottom substrates. The device functioning as a microparticle focusing and trapping chip was experimentally verified. It is confirmed that the proposed method has many advantages, including simple and fast fabrication process, low cost, easy integration of electronics, strong bonding strength, chemical and biological compatibility, etc. © Springer-Verlag 2011.

  17. A critical insight into the development pipeline of microfluidic immunoassay devices for the sensitive quantitation of protein biomarkers at the point of care.

    Science.gov (United States)

    Barbosa, Ana I; Reis, Nuno M

    2017-03-13

    The latest clinical procedures for the timely and cost-effective diagnosis of chronic and acute clinical conditions, such as cardiovascular diseases, cancer, chronic respiratory diseases, diabetes or sepsis (i.e. the biggest causes of death worldwide), involve the quantitation of specific protein biomarkers released into the blood stream or other physiological fluids (e.g. urine or saliva). The clinical thresholds are usually in the femtomolar to picolomar range, and consequently the measurement of these protein biomarkers heavily relies on highly sophisticated, bulky and automated equipment in centralised pathology laboratories. The first microfluidic devices capable of measuring protein biomarkers in miniaturised immunoassays were presented nearly two decades ago and promised to revolutionise point-of-care (POC) testing by offering unmatched sensitivity and automation in a compact POC format; however, the development and adoption of microfluidic protein biomarker tests has fallen behind expectations. This review presents a detailed critical overview into the pipeline of microfluidic devices developed in the period 2005-2016 capable of measuring protein biomarkers from the pM to fM range in formats compatible with POC testing, with a particular focus on the use of affordable microfluidic materials and compact low-cost signal interrogation. The integration of these two important features (essential unique selling points for the successful microfluidic diagnostic products) has been missed in previous review articles and explain the poor adoption of microfluidic technologies in this field. Most current miniaturised devices compromise either on the affordability, compactness and/or performance of the test, making current tests unsuitable for the POC measurement of protein biomarkers. Seven core technical areas, including (i) the selected strategy for antibody immobilisation, (ii) the surface area and surface-area-to-volume ratio, (iii) surface passivation, (iv) the

  18. Microfluidic electronics.

    Science.gov (United States)

    Cheng, Shi; Wu, Zhigang

    2012-08-21

    Microfluidics, a field that has been well-established for several decades, has seen extensive applications in the areas of biology, chemistry, and medicine. However, it might be very hard to imagine how such soft microfluidic devices would be used in other areas, such as electronics, in which stiff, solid metals, insulators, and semiconductors have previously dominated. Very recently, things have radically changed. Taking advantage of native properties of microfluidics, advances in microfluidics-based electronics have shown great potential in numerous new appealing applications, e.g. bio-inspired devices, body-worn healthcare and medical sensing systems, and ergonomic units, in which conventional rigid, bulky electronics are facing insurmountable obstacles to fulfil the demand on comfortable user experience. Not only would the birth of microfluidic electronics contribute to both the microfluidics and electronics fields, but it may also shape the future of our daily life. Nevertheless, microfluidic electronics are still at a very early stage, and significant efforts in research and development are needed to advance this emerging field. The intention of this article is to review recent research outcomes in the field of microfluidic electronics, and address current technical challenges and issues. The outlook of future development in microfluidic electronic devices and systems, as well as new fabrication techniques, is also discussed. Moreover, the authors would like to inspire both the microfluidics and electronics communities to further exploit this newly-established field.

  19. A cyclic-olefin-copolymer microfluidic immobilized-enzyme reactor for rapid digestion of proteins from dried blood spots.

    Science.gov (United States)

    Wouters, Bert; Dapic, Irena; Valkenburg, Thalassa S E; Wouters, Sam; Niezen, Leon; Eeltink, Sebastiaan; Corthals, Garry L; Schoenmakers, Peter J

    2017-03-31

    A critical step in the bottom-up characterization of proteomes is the conversion of proteins to peptides, by means of endoprotease digestion. Nowadays this method typically uses overnight digestion and as such represents a considerable bottleneck for high-throughput analysis. This report describes protein digestion using an immobilized-enzyme reactor (IMER), which enables accelerated digestion times that are completed within seconds to minutes. For rapid digestion to occur, a cyclic-olefin-copolymer microfluidic reactor was constructed containing trypsin immobilized on a polymer monolithic material through a 2-vinyl-4,4-dimethylazlactone linker. The IMER was applied for the rapid offline digestion of both singular protein standards and a complex protein mixture prior to liquid chromatography-electrospray ionisation-tandem mass spectrometry (LC-ESI-MS/MS) analysis. The effects of protein concentration and residence time in the IMER were assessed for protein standards of varying molecular weight between 11 and 240kDa. Compared to traditional in-solution digestion, IMER-facilitated protein digestion at room temperature for 5min yielded similar results in terms of sequence coverage and number of identified peptides. Good repeatability was demonstrated with a relative standard deviation of 6% for protein-sequence coverage. The potential of the IMER was also demonstrated for a complex protein mixture in the analysis of dried blood spots. Compared to a traditional workflow a similar number of proteins could be identified, while reducing the total analysis time from 22.5h to 4h and importantly omitting the sample-pre-treatment steps (denaturation, reduction, and alkylation). The identified proteins from two workflows showed similar distributions in terms of molecular weight and hydrophobic character.

  20. 3D imaging of flow patterns in an internally-pumped microfluidic device: redox magnetohydrodynamics and electrochemically-generated density gradients.

    Science.gov (United States)

    Gao, Feng; Kreidermacher, Adam; Fritsch, Ingrid; Heyes, Colin D

    2013-05-07

    Redox magnetohydrodynamics (MHD) is a promising technique for developing new electrochemical-based microfluidic flow devices with unique capabilities, such as easily switching flow direction and adjusting flow speeds and flow patterns as well as avoiding bubble formation. However, a detailed description of all the forces involved and predicting flow patterns in confined geometries is lacking. In addition to redox-MHD, density gradients caused by the redox reactions also play important roles. Flow in these devices with small fluid volumes has mainly been characterized by following microbead motion by optical microscopy either by particle tracking velocimetry (PTV) or by processing the microbead images by particle image velocimetry (PIV) software. This approach has limitations in spatial resolution and dimensionality. Here we use fluorescence correlation spectroscopy (FCS) to quantitatively and accurately measure flow speeds and patterns in the ~5-50 μm/s range in redox-MHD-based microfluidic devices, from which 3D flow maps are obtained with a spatial resolution down to 2 μm. The 2 μm spatial resolution flow speeds map revealed detailed flow profiles during redox-MHD in which the velocity increases linearly from above the electrode and reaches a plateau across the center of the cell. By combining FCS and video-microscopy (with PTV and PIV processing approaches), we are able to quantify a vertical flow of ~10 μm/s above the electrodes as a result of density gradients caused by the redox reactions and follow convection flow patterns. Overall, combining FCS, PIV, and PTV analysis of redox-MHD is a powerful combination to more thoroughly characterize the underlying forces in these promising microfluidic devices.

  1. A computational study of enzyme patterning on microfluidic biofuel cell electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Kjeang, E.; Sinton, D.; Harrington, D.; Djilali, N. [Victoria Univ., BC (Canada). Inst. for Integrated Energy Systems

    2005-07-01

    In an enzymatic fuel cell, chemical reactions are catalyzed by biological redox enzymes that can be separated and purified from suitable organisms. Enzyme catalysts are specific to particular substances and the presence of other substances does not usually impact the rate of catalysis. Enzyme catalysis enables the combination of fuel and oxidant streams in a single manifold, with many benefits regarding fuel cell design and operation. This study examined ways to produce biofuel cell systems through experiments that modeled species transfer associated with heterogenous chemical reactions and enzyme kinetics based on a microchannel geometry. An electrically conducting material was deposited on the interior surfaces to form the anode and cathode, and the enzymes were tethered directly to the layers. The intent was to determine whether the process was diffusion limited or reaction rate limited. Various enzyme-electrode patterns coupled with coherent bulk velocities were investigated in order to realize efficient fuel cell operation. A microstructured multi-step enzymatic biofuel cell structure was proposed. Species transport coupled with laminar flow and Michaelis-Menten kinetics was examined using a 2-dimensional numerical solution. Biofuel cell performance was shown to be limited by the reactions rates associated with enzyme kinetics. Turnover rates for individual enzymes were key parameters throughout the analysis and directly determined the realizable current densities. The pumping power required for the microchannel flow was determined to be negligible compared to the output power of the unit cell. It was concluded that methanol is the better fuel in terms of energy density. Four separated and mixed electrode enzyme strategies were presented and tested with bulk velocities to optimize overall current density and fuel consumption. It was suggested that the mixed transport regime is particularly attractive for biofuel cell operation, with superior characteristics

  2. Surface acoustic wave microfluidics.

    Science.gov (United States)

    Ding, Xiaoyun; Li, Peng; Lin, Sz-Chin Steven; Stratton, Zackary S; Nama, Nitesh; Guo, Feng; Slotcavage, Daniel; Mao, Xiaole; Shi, Jinjie; Costanzo, Francesco; Huang, Tony Jun

    2013-09-21

    The recent introduction of surface acoustic wave (SAW) technology onto lab-on-a-chip platforms has opened a new frontier in microfluidics. The advantages provided by such SAW microfluidics are numerous: simple fabrication, high biocompatibility, fast fluid actuation, versatility, compact and inexpensive devices and accessories, contact-free particle manipulation, and compatibility with other microfluidic components. We believe that these advantages enable SAW microfluidics to play a significant role in a variety of applications in biology, chemistry, engineering and medicine. In this review article, we discuss the theory underpinning SAWs and their interactions with particles and the contacting fluids in which they are suspended. We then review the SAW-enabled microfluidic devices demonstrated to date, starting with devices that accomplish fluid mixing and transport through the use of travelling SAW; we follow that by reviewing the more recent innovations achieved with standing SAW that enable such actions as particle/cell focusing, sorting and patterning. Finally, we look forward and appraise where the discipline of SAW microfluidics could go next.

  3. DETECTION OF TOPOLOGICAL PATTERNS IN PROTEIN NETWORKS.

    Energy Technology Data Exchange (ETDEWEB)

    MASLOV,S.SNEPPEN,K.

    2003-11-17

    interesting property of many biological networks that was recently brought to attention of the scientific community [3, 4, 5] is an extremely broad distribution of node connectivities defined as the number of immediate neighbors of a given node in the network. While the majority of nodes have just a few edges connecting them to other nodes in the network, there exist some nodes, that we will refer to as ''hubs'', with an unusually large number of neighbors. The connectivity of the most connected hub in such a network is typically several orders of magnitude larger than the average connectivity in the network. Often the distribution of connectivities of individual nodes can be approximated by a scale-free power law form [3] in which case the network is referred to as scale-free. Among biological networks distributions of node connectivities in metabolic [4], protein interaction [5], and brain functional [6] networks can be reasonably approximated by a power law extending for several orders of magnitude. The set of connectivities of individual nodes is an example of a low-level (single-node) topological property of a network. While it answers the question about how many neighbors a given node has, it gives no information about the identity of those neighbors. It is clear that most functional properties of networks are defined at a higher topological level in the exact pattern of connections of nodes to each other. However, such multi-node connectivity patterns are rather difficult to quantify and compare between networks. In this work we concentrate on multi-node topological properties of protein networks. These networks (as any other biological networks) lack the top-down design. Instead, selective forces of biological evolution shape them from raw material provided by random events such as mutations within individual genes, and gene duplications. As a result their connections are characterized by a large degree of randomness. One may wonder which

  4. Protein surface patterning using nanoscale PEG hydrogels.

    Science.gov (United States)

    Hong, Ye; Krsko, Peter; Libera, Matthew

    2004-12-01

    We have used focused electron-beam cross-linking to create nanosized hydrogels and thus present a new method with which to bring the attractive biocompatibility associated with macroscopic hydrogels into the submicron length-scale regime. Using amine-terminated poly(ethylene glycol) thin films on silicon substrates, we generate nanohydrogels with lateral dimensions of order 200 nm which can swell by a factor of at least five, depending on the radiative dose. With the focused electron beam, high-density arrays of such nanohydrogels can be flexibly patterned onto silicon surfaces. Significantly, the amine groups remain functional after e-beam exposure, and we show that they can be used to covalently bind proteins and other molecules. We use bovine serum albumin to amplify the number of amine groups, and we further demonstrate that different proteins can be covalently bound to different hydrogel pads on the same substrate to create multifunctional surfaces useful in emerging bio/proteomic and sensor technologies.

  5. Wax-bonding 3D microfluidic chips

    KAUST Repository

    Gong, Xiuqing

    2013-10-10

    We report a simple, low-cost and detachable microfluidic chip incorporating easily accessible paper, glass slides or other polymer films as the chip materials along with adhesive wax as the recycling bonding material. We use a laser to cut through the paper or film to form patterns and then sandwich the paper and film between glass sheets or polymer membranes . The hot-melt adhesive wax can realize bridge bonding between various materials, for example, paper, polymethylmethacrylate (PMMA) film, glass sheets, or metal plate. The bonding process is reversible and the wax is reusable through a melting and cooling process. With this process, a three-dimensional (3D) microfluidic chip is achievable by vacuating and venting the chip in a hot-water bath. To study the biocompatibility and applicability of the wax-based microfluidic chip, we tested the PCR compatibility with the chip materials first. Then we applied the wax-paper based microfluidic chip to HeLa cell electroporation (EP ). Subsequently, a prototype of a 5-layer 3D chip was fabricated by multilayer wax bonding. To check the sealing ability and the durability of the chip, green fluorescence protein (GFP) recombinant Escherichia coli (E. coli) bacteria were cultured, with which the chemotaxis of E. coli was studied in order to determine the influence of antibiotic ciprofloxacin concentration on the E. coli migration.

  6. PDMS bonding to a bio-friendly photoresist via self-polymerized poly(dopamine) adhesive for complex protein micropatterning inside microfluidic channels.

    Science.gov (United States)

    Kim, Miju; Song, Kwang Hoon; Doh, Junsang

    2013-12-01

    Protein micropatterned surfaces integrated with microfluidics are useful in numerous bioanalytical and biological applications. In this study, we demonstrated the fabrication of complex protein micropatterned surfaces within poly(dimethylsiloxane) (PDMS) microfluidic channels by attaching the PDMS channels to bio-friendly photoresist films and subsequently performing microscope projection photolithography (MPP). A muscle-inspired poly(dopamine) (PDA) coating was employed to mediate the bonding between the PDMS and the bio-friendly photoresist poly(2,2-dimethoxy nitrobenzyl methacrylate-r-methyl methacrylate-r-poly(ethylene glycol) methacrylate) (PDMP). By adjusting the dip-coating time for the PDA coating, we could successfully introduce sufficient amounts of functional groups on the PDMP surfaces to mediate strong bonding between the PDMS channels and the PDA-coated PDMP thin films with minimal alteration of the surface properties of the PDMP thin films that are critical for protein micropatterning. Using this novel bonding strategy, we successfully fabricated multiple protein micropatterns and gradient micropatterns of proteins within microfluidic channels. The technique developed in this study will be useful for the fabrication of complex biochips for multiplex bioassays and fundamental cell biological studies.

  7. Liquid metal enabled microfluidics.

    Science.gov (United States)

    Khoshmanesh, Khashayar; Tang, Shi-Yang; Zhu, Jiu Yang; Schaefer, Samira; Mitchell, Arnan; Kalantar-Zadeh, Kourosh; Dickey, Michael D

    2017-03-14

    Several gallium-based liquid metal alloys are liquid at room temperature. As 'liquid', such alloys have a low viscosity and a high surface tension while as 'metal', they have high thermal and electrical conductivities, similar to mercury. However, unlike mercury, these liquid metal alloys have low toxicity and a negligible vapor pressure, rendering them much safer. In comparison to mercury, the distinguishing feature of these alloys is the rapid formation of a self-limiting atomically thin layer of gallium oxide over their surface when exposed to oxygen. This oxide layer changes many physical and chemical properties of gallium alloys, including their interfacial and rheological properties, which can be employed and modulated for various applications in microfluidics. Injecting liquid metal into microfluidic structures has been extensively used to pattern and encapsulate highly deformable and reconfigurable electronic devices including electrodes, sensors, antennas, and interconnects. Likewise, the unique features of liquid metals have been employed for fabricating miniaturized microfluidic components including pumps, valves, heaters, and electrodes. In this review, we discuss liquid metal enabled microfluidic components, and highlight their desirable attributes including simple fabrication, facile integration, stretchability, reconfigurability, and low power consumption, with promising applications for highly integrated microfluidic systems.

  8. A novel microfluidic mixer based on dual-hydrodynamic focusing for interrogating the kinetics of DNA-protein interaction.

    Science.gov (United States)

    Li, Ying; Xu, Fei; Liu, Chao; Xu, Youzhi; Feng, Xiaojun; Liu, Bi-Feng

    2013-08-21

    Kinetic measurement of biomacromolecular interaction plays a significant role in revealing the underlying mechanisms of cellular activities. Due to the small diffusion coefficient of biomacromolecules, it is difficult to resolve the rapid kinetic process with traditional analytical methods such as stopped-flow or laminar mixers. Here, we demonstrated a unique continuous-flow laminar mixer based on microfluidic dual-hydrodynamic focusing to characterize the kinetics of DNA-protein interactions. The time window of this mixer for kinetics observation could cover from sub-milliseconds to seconds, which made it possible to capture the folding process with a wide dynamic range. Moreover, the sample consumption was remarkably reduced to <0.55 μL min⁻¹, over 1000-fold saving in comparison to those reported previously. We further interrogated the interaction kinetics of G-quadruplex and the single-stranded DNA binding protein, indicating that this novel micromixer would be a useful approach for analyzing the interaction kinetics of biomacromolecules.

  9. Measuring dynamics in weakly structured regions of proteins using microfluidics-enabled subsecond H/D exchange mass spectrometry.

    Science.gov (United States)

    Rob, Tamanna; Liuni, Peter; Gill, Preet Kamal; Zhu, Shaolong; Balachandran, Naresh; Berti, Paul J; Wilson, Derek J

    2012-04-17

    This work introduces an integrated microfluidic device for measuring rapid H/D exchange (HDX) in proteins. By monitoring backbone amide HDX on the millisecond to low second time scale, we are able to characterize conformational dynamics in weakly structured regions, such as loops and molten globule-like domains that are inaccessible in conventional HDX experiments. The device accommodates the entire MS-based HDX workflow on a single chip with residence times sufficiently small (ca. 8 s) that back-exchange is negligible (≤5%), even without cooling. Components include an adjustable position capillary mixer providing a variable-time labeling pulse, a static mixer for HDX quenching, a proteolytic microreactor for rapid protein digestion, and on-chip electrospray ionization (ESI). In the present work, we characterize device performance using three model systems, each illustrating a different application of 'time-resolved' HDX. Ubiquitin is used to illustrate a crude, high throughput structural analysis based on a single subsecond HDX time-point. In experiments using cytochrome c, we distinguish dynamic behavior in loops, establishing a link between flexibility and interactions with the heme prosthetic group. Finally, we localize an unusually high 'burst-phase' of HDX in the large tetrameric enzyme DAHP synthase to a 'molten globule-like' region surrounding the active site.

  10. Network based approaches reveal clustering in protein point patterns

    Science.gov (United States)

    Parker, Joshua; Barr, Valarie; Aldridge, Joshua; Samelson, Lawrence E.; Losert, Wolfgang

    2014-03-01

    Recent advances in super-resolution imaging have allowed for the sub-diffraction measurement of the spatial location of proteins on the surfaces of T-cells. The challenge is to connect these complex point patterns to the internal processes and interactions, both protein-protein and protein-membrane. We begin analyzing these patterns by forming a geometric network amongst the proteins and looking at network measures, such the degree distribution. This allows us to compare experimentally observed patterns to models. Specifically, we find that the experimental patterns differ from heterogeneous Poisson processes, highlighting an internal clustering structure. Further work will be to compare our results to simulated protein-protein interactions to determine clustering mechanisms.

  11. Chromosome driven spatial patterning of proteins in bacteria.

    Directory of Open Access Journals (Sweden)

    Saeed Saberi

    Full Text Available The spatial patterning of proteins in bacteria plays an important role in many processes, from cell division to chemotaxis. In the asymmetrically dividing bacteria Caulobacter crescentus, a scaffolding protein, PopZ, localizes to both poles and aids the differential patterning of proteins between mother and daughter cells during division. Polar patterning of misfolded proteins in Escherichia coli has also been shown, and likely plays an important role in cellular ageing. Recent experiments on both of the above systems suggest that the presence of chromosome free regions along with protein multimerization may be a mechanism for driving the polar localization of proteins. We have developed a simple physical model for protein localization using only these two driving mechanisms. Our model reproduces all the observed patterns of PopZ and misfolded protein localization--from diffuse, unipolar, and bipolar patterns and can also account for the observed patterns in a variety of mutants. The model also suggests new experiments to further test the role of the chromosome in driving protein patterning, and whether such a mechanism is responsible for helping to drive the differentiation of the cell poles.

  12. Cu2+ Detection with Gold Nanoparticles by Patterning Colorimetric Strips on a Filter Membrane Assembled in a Microfluidic Chip%Cu2+ Detection with Gold Nanoparticles by Patterning Colorimetric Strips on a Filter Membrane Assembled in a Microfluidic Chip

    Institute of Scientific and Technical Information of China (English)

    刘颖昳; 虞洁; 陈雯雯; 刘定斌; 王卓; 蒋兴宇

    2012-01-01

    We have developed a microfluidic chip for colorimetric CH2+ detection. In this chip, it is facile to do colorimet- ric Cu2+ detection based on gold nanoparticles. This method has a dynamic detection range from 0.75 to 50 lamol/L with only 20μL solution including detection reagents and sample. The result can be readout by naked eye and pho-tographed by digital cameras. With the help of image processing software, we could measure the RGB value and calculate the Blue/Red ratio for more accurate quantification. Tap water could be detected in this portable chip.

  13. Photolithography-free laser-patterned HF acid-resistant chromium-polyimide mask for rapid fabrication of microfluidic systems in glass

    Science.gov (United States)

    Zamuruyev, Konstantin O.; Zrodnikov, Yuriy; Davis, Cristina E.

    2017-01-01

    Excellent chemical and physical properties of glass, over a range of operating conditions, make it a preferred material for chemical detection systems in analytical chemistry, biology, and the environmental sciences. However, it is often compromised with SU8, PDMS, or Parylene materials due to the sophisticated mask preparation requirements for wet etching of glass. Here, we report our efforts toward developing a photolithography-free laser-patterned hydrofluoric acid-resistant chromium-polyimide tape mask for rapid prototyping of microfluidic systems in glass. The patterns are defined in masking layer with a diode-pumped solid-state laser. Minimum feature size is limited to the diameter of the laser beam, 30 µm minimum spacing between features is limited by the thermal shrinkage and adhesive contact of the polyimide tape to 40 µm. The patterned glass substrates are etched in 49% hydrofluoric acid at ambient temperature with soft agitation (in time increments, up to 60 min duration). In spite of the simplicity, our method demonstrates comparable results to the other current more sophisticated masking methods in terms of the etched depth (up to 300 µm in borosilicate glass), feature under etch ratio in isotropic etch (~1.36), and low mask hole density. The method demonstrates high yield and reliability. To our knowledge, this method is the first proposed technique for rapid prototyping of microfluidic systems in glass with such high performance parameters. The proposed method of fabrication can potentially be implemented in research institutions without access to a standard clean-room facility.

  14. Direct-writing colloidal photonic crystal microfluidic chips by inkjet printing for label-free protein detection.

    Science.gov (United States)

    Shen, Weizhi; Li, Mingzhu; Ye, Changqing; Jiang, Lei; Song, Yanlin

    2012-09-07

    Integrating photonic crystals (PC) into microfluidic systems has attracted immense interest for its novel functions. However, it is still a great challenge to fabricate PC microfluidic chips rapidly with complex functions. In this work, a direct-writing colloidal PC microchannel was firstly achieved by inkjet printing and was used for the surface-tension-confined microfluidic immune assay. PC channels with different structure colors have been successfully integrated on one chip. The fabricated chip has the advantages of rapid fabrication, quick fluidic transport and can monitor the fluidic fluxion using the naked eye. Utilizing this PC microfluidic chip, a colorimetric label-free immune assay was realized without nonspecific adsorption interference of the target.

  15. Nanoliter-scale protein crystallization and screening with a microfluidic droplet robot

    National Research Council Canada - National Science Library

    Zhu, Ying; Zhu, Li-Na; Guo, Rui; Cui, Heng-Jun; Ye, Sheng; Fang, Qun

    2014-01-01

    .... Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening...

  16. Advanced fluidic handling and use of two-phase flow for high throughput structural investigation of proteins on a microfluidic sample preparation platform

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Snakenborg, Detlef; Møller, M.

    2010-01-01

    Research on the structure of proteins can bring forth a wealth of information about biological function and can be used to better understand the processes in living cells. This paper reports a new microfluidic sample preparation system for the structural investigation of proteins by Small Angle X......-ray Scattering (SAXS). The system includes hardware and software features for precise fluidic control, synchrotron beamline control, UV absorbance measurements and automated data analysis. The precise fluidic handling capabilities are used to transport and precisely position samples as small as 500 n...

  17. Adsorption of HP Lattice Proteins on Patterned Surfaces

    Science.gov (United States)

    Wilson, Matthew; Shi, Guangjie; Landau, David P.; Li, Ying Wai; Wuest, Thomas

    2014-03-01

    The HP lattice model[2] is a course-grained, yet useful tool for modeling protein sequences where amino acids are treated as either hydrophobic (H) or polar (P) monomers. With the use of Wang-Landau sampling and an efficient set of Monte-Carlo moves[3], HP lattice proteins adsorbed on patterned surfaces are studied. Each substrate is modeled as a periodically bounded pattern of lattice sites that interact with either H or P monomers in the lattice protein, where the energy contributions of the surface are determined by assigned coupling strengths. By analyzing energy degeneracies, along with the thermodynamic and structural quantities of the protein, both the protein folding and surface adsorption can be observed. The adsorption behavior of the lattice proteins on patterned surfaces will be compared to those interacting with uniform surfaces. Research supported by NSF.

  18. Prototyping chips in minutes: Direct Laser Plotting (DLP) of functional microfluidic structures

    KAUST Repository

    Wang, Limu

    2013-10-10

    We report a fast and simple prototyping method to fabricate polymer-based microfluidic chips using Direct Laser Plotting (DLP) technique, by which various functional micro-structures can be realized within minutes, in a mask-free and out-of-cleanroom fashion. A 2D Computer-Aid-Design (CAD) software was employed to layout the required micro-structures and micro-channels, a CO2 laser plotter was then used to construct the microstructures. The desired patterns can be plotted directly on PDMS substrates and bio-compatible polymer films by manipulating the strength and density of laser pulses. With the DLP technique, chip-embedded micro-electrodes, micro-mixers and 3D microfluidic chips with 5 layers, which normally require several days of work in a cleanroom facility, can be fabricated in minutes in common laboratory. This novel method can produce microfluidic channels with average feature size of 100 μm, while feature size of 50 μm or smaller is achievable by making use of the interference effect from laser impulsion. In this report, we present the optimized parameters for successful fabrication of 3D microchannels, micro-mixers and microfluidic chips for protein concentration measurements (Bovine Serum Albumine (BSA) test), and a novel procedure to pattern flexible embedding electrodes on PDMS-based microfluidic chips. DLP offers a convenient and low cost alternative to conventional microfluidic channel fabrication technique which relies on complicated and hazardous soft lithography process.

  19. Stereomask lithography for multi-protein patterning.

    Science.gov (United States)

    Zhao, Siwei; Chen, Arnold; Revzin, Alexander; Pan, Tingrui

    2014-01-01

    The advances of biologically-friendly micropatterning technologies have benefited many areas of biological and medical research, including quantitative biochemical assay, point-of-care devices, biosensing and regenerative medicine. Conventional micropatterning techniques, for example, photolithography and soft lithography, have seen encouraging adaptation to creating biological micropatterns in the last decades. However, they still have not completely addressed the major needs of constructing multi-object biological microarrays with single-cell resolution without requiring cleanroom access. In this chapter, we present a novel versatile biological lithography technique to achieve integrated multi-object patterning with high feature resolution and high adaptability to various biomaterials, referred to as stereomask lithography (SML). A novel three-dimensional stereomask has been developed for successive patterning of multiple objects. The stereomask consists of both patterned through holes, which layout new micropatterns and non-through recesses, which protect pre-existing features on the substrate. Furthermore, high-precision reversible alignment among multiple bio-objects is achieved by adopting a peg-in-hole design between the substrate and stereomasks. As demonstration, we have successfully used the SML technique to construct complex biological microenvironment with various bio-functional components at single-cell resolution. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Control and automation of multilayered integrated microfluidic device fabrication.

    Science.gov (United States)

    Kipper, Sarit; Frolov, Ludmila; Guy, Ortal; Pellach, Michal; Glick, Yair; Malichi, Asaf; Knisbacher, Binyamin A; Barbiro-Michaely, Efrat; Avrahami, Dorit; Yavets-Chen, Yehuda; Levanon, Erez Y; Gerber, Doron

    2017-01-31

    Integrated microfluidics is a sophisticated three-dimensional (multi layer) solution for high complexity serial or parallel processes. Fabrication of integrated microfluidic devices requires soft lithography and the stacking of thin-patterned PDMS layers. Precise layer alignment and bonding is crucial. There are no previously reported standards for alignment of the layers, which is mostly performed using uncontrolled processes with very low alignment success. As a result, integrated microfluidics is mostly used in academia rather than in the many potential industrial applications. We have designed and manufactured a semiautomatic Microfluidic Device Assembly System (μDAS) for full device production. μDAS comprises an electrooptic mechanical system consisting of four main parts: optical system, smart media holder (for PDMS), a micropositioning xyzθ system and a macropositioning XY mechanism. The use of the μDAS yielded valuable information regarding PDMS as the material for device fabrication, revealed previously unidentified errors, and enabled optimization of a robust fabrication process. In addition, we have demonstrated the utilization of the μDAS technology for fabrication of a complex 3 layered device with over 12 000 micromechanical valves and an array of 64 × 64 DNA spots on a glass substrate with high yield and high accuracy. We increased fabrication yield from 25% to about 85% with an average layer alignment error of just ∼4 μm. It also increased our protein expression yields from 80% to over 90%, allowing us to investigate more proteins per experiment. The μDAS has great potential to become a valuable tool for both advancing integrated microfluidics in academia and producing and applying microfluidic devices in the industry.

  1. Improving sensitivity and linear dynamic range of intact protein analysis using a robust and easy to use microfluidic device.

    Science.gov (United States)

    Roman, Gregory T; Murphy, James P

    2017-03-27

    We demonstrate an integrated microfluidic LC device coupled to a QTOF capable of improving sensitivity and linearity for intact protein analysis while also tuning the charge state distributions (CSD) of whole antibodies. The mechanism for sensitivity improvement using microflow ESI is demonstrated by shifting of the CSD to higher charge state, and narrowing of the overall CSD. Both of these aspects serve to improve ion current of the most abundant charge state of antibodies and lead to improvement in sensitivity over high flow ESI by a factor of 15×. Current limits of detection are 0.1 ng (on-column) (n = 100, %RSD = 17.5) using IgG glycosylated antibody, as compared to 5 ng (on-column) (n = 10, %RSD = 15) for high flow LC-ESI-MS. In addition to improvements in sensitivity we also observe improvements in linear dynamic range for microflow ESI that results from a combination of lower limits of detection and narrower CSD. An improvement of linear dynamic range of 1.5 orders of magnitude was observed over conventional high flow LC-MS. In cases where the complexity of the antibody limited both sensitivity and spectral charge state resolution, we employed supercharging and decharging mechanisms to further improve sensitivity and charge state spacing resolution. We demonstrate an 89% increase in sensitivity using glycerol that was added post column, with retention of the glycoform resolution. Since large proteins reside in a relatively low noise region of the mass spectra it is possible to realize effects of supercharging for intact proteins, specifically antibodies of 150 kDa, that are less pronounced for peptide supercharging. We also demonstrate a 51% increase in charge state resolution as imidazole was used to generate lower charge states for high-mass ions. The increase in charge state resolution enables more complex antibodies, or antibody mixtures that coelute in the LC, to be deconvoluted more efficiently. In summary, we demonstrate an analytical technique that

  2. Elastohydrodynamics and kinetics of protein patterning in the immunological synapse

    CERN Document Server

    Carlson, Andreas

    2015-01-01

    The cellular basis for the adaptive immune response during antigen recognition relies on a specialized protein interface known as the immunological synapse (IS). Understanding the biophysical basis for protein patterning by deciphering the quantitative rules for their formation and motion is an important aspect of characterizing immune cell recognition and thence the rules for immune system activation. We propose a minimal mathematical model for the physical basis of membrane protein patterning in the IS, which encompass membrane mechanics, protein binding kinetics and motion, and fluid flow in the synaptic cleft. Our theory leads to simple predictions for the spatial and temporal scales of protein cluster formation, growth and arrest as a function of membrane stiffness, rigidity and kinetics of the adhesive proteins, and the fluid in the synaptic cleft. Numerical simulations complement these scaling laws by quantifying the nucleation, growth and stabilization of proteins domains on the size of the cell. Dire...

  3. Pattern of occurrence and occupancy of carbonylation sites in proteins

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Møller, Ian Max

    2011-01-01

    Proteins are targets for modification by reactive oxygen species, and carbonylation is an important irreversible modification that increases during oxidative stress. While information on protein carbonylation is accumulating, its pattern is not yet understood. We have made a meta-analysis of the ......Proteins are targets for modification by reactive oxygen species, and carbonylation is an important irreversible modification that increases during oxidative stress. While information on protein carbonylation is accumulating, its pattern is not yet understood. We have made a meta...... sites. Comparison of metal-catalyzed oxidation of two closely related proteins indicates that this type of carbonylation might not be very specific in proteins. Interestingly, carbonylated sites show a very strong tendency to cluster together in the protein primary sequence hinting at some sort...

  4. A Microfluidic Bioreactor with in Situ SERS Imaging for the Study of Controlled Flow Patterns of Biofilm Precursor Materials

    Directory of Open Access Journals (Sweden)

    Jesse Greener

    2013-10-01

    Full Text Available A microfluidic bioreactor with an easy to fabricate nano-plasmonic surface is demonstrated for studies of biofilms and their precursor materials via Surface Enhanced Raman Spectroscopy (SERS. The system uses a novel design to induce sheath flow confinement of a sodium citrate biofilm precursor stream against the SERS imaging surface to measure spatial variations in the concentration profile. The unoptimised SERS enhancement was approximately 2.5 × 104, thereby improving data acquisition time, reducing laser power requirements and enabling a citrate detection limit of 0.1 mM, which was well below the concentrations used in biofilm nutrient solutions. The flow confinement was observed by both optical microscopy and SERS imaging with good complementarity. We demonstrate the new bioreactor by growing flow-templated biofilms on the microchannel wall. This work opens the way for in situ spectral imaging of biofilms and their biochemical environment under dynamic flow conditions.

  5. Abnormal erythrocyte membrane protein pattern in severe megaloblastic anemia.

    Science.gov (United States)

    Ballas, S K

    1978-01-01

    The erythrocyte membrane protein pattern of patients with megaloblastic anemia was determined by polyacrylamide gel electrophoresis in sodium dodecyl sulfate. In severe megaloblastic anemia, secondary either to folic acid or vitamin B12 deficiency, the erythrocyte membrane protein pattern was grossly abnormal, lacking bands 1, 2 (spectrin), and 3 and having several diffuse, faster migrating bands. After adequate vitamin replacement therapy, the erythrocyte membrane protein pattern returned to normal. In mild megaloblastic anemia, secondary either to folic acid of vitamin B12 deficiency, and in severe iron deficiency anemia, the erythrocyte membrane protein pattern was normal. Erythrocyte membrane protein pattern of normal membranes did not change after mixing with abnormal membranes before polyacrylamide gel electrophoresis in sodium dodecyl sulfate. Protease activity extracted from membranes of megalocytes was not different from normal. These findings indicate that the erythrocyte membrane protein pattern is abnormal in severe megaloblastic anemia and that this abnormality is not secondary to increased activity of the endogenous erythrocyte membrane proteinase. Images PMID:659579

  6. Label-free protein detection using a microfluidic Coulter-counter device

    DEFF Research Database (Denmark)

    Rodriguez-Trujíllo, Romén; Ajine, Mohammad Akram; Orzan, A.;

    2014-01-01

    A new method for measuring specific protein concentrations in solutions has been developed. The technique makes use of the Coulter effect for detecting and sizing of micro-scaled objects suspended in a buffer fluid. The method is completely label-free as it is only based on the electrical readout...

  7. Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

    KAUST Repository

    Simone, Giuseppina

    2013-02-11

    Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction\\'s strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Quantitative analysis of four protein biomarkers: An automated microfluidic cartridge-based method and its comparison to colorimetric ELISA.

    Science.gov (United States)

    Dysinger, Mark; Marusov, Greg; Fraser, Stephanie

    2017-09-13

    Biomarker quantitation with ligand binding assays has matured greatly in recent years. This maturation has been partly in response to demands for more data points from fewer samples or less available sample volume. Multiplexing offers opportunities to acquire data for multiple analytes from single sample assay iterations, but has its own unique challenges and limitations. ProteinSimple has developed Simple Plex™, an automated immunoassay platform consisting of microfluidic cartridge-based assays run on the Ella instrument. Ella subverts traditional multiplexing challenges by rapidly performing triplicate measurements of up to four different analytes simultaneously, each in their own respective assay vessels and all from a single sample. Here we describe a comparison of the Simple Plex platform versus colorimetric ELISA and their respective abilities to quantitate four common biomarkers (MCP-1/CCL2, VEGF-A, TNF-α, and IL-6) from twenty-eight healthy individual donor plasma samples. Each biomarker was tested on the two platforms on each of two days. Ella analysis required significantly reduced sample volume, manual steps, and total time. Overall, Ella was able to quantify results for all twenty-eight samples for each of the four biomarkers. In contrast, ELISA was able to measure quantifiable results within respective calibration curve ranges for MCP-1/CCL2 (96% of samples) and VEGFA (7% of samples). For TNF-α and IL-6, ELISA was not sensitive enough to quantify any samples in the assay ranges. This stark difference in quantitative results underscores Ella's ability to multiplex without compromising sensitivity, and has far reaching potential for biomarker panel measurement in support of diagnosis, prognosis, and monitoring of disease. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Characterization of oligopeptide patterns in large protein sets

    Directory of Open Access Journals (Sweden)

    Persson Bengt

    2007-10-01

    Full Text Available Abstract Background Recent sequencing projects and the growth of sequence data banks enable oligopeptide patterns to be characterized on a genome or kingdom level. Several studies have focused on kingdom or habitat classifications based on the abundance of short peptide patterns. There have also been efforts at local structural prediction based on short sequence motifs. Oligopeptide patterns undoubtedly carry valuable information content. Therefore, it is important to characterize these informational peptide patterns to shed light on possible new applications and the pitfalls implicit in neglecting bias in peptide patterns. Results We have studied four classes of pentapeptide patterns (designated POP, NEP, ORP and URP in the kingdoms archaea, bacteria and eukaryotes. POP are highly abundant patterns statistically not expected to exist; NEP are patterns that do not exist but are statistically expected to; ORP are patterns unique to a kingdom; and URP are patterns excluded from a kingdom. We used two data sources: the de facto standard of protein knowledge Swiss-Prot, and a set of 386 completely sequenced genomes. For each class of peptides we looked at the 100 most extreme and found both known and unknown sequence features. Most of the known sequence motifs can be explained on the basis of the protein families from which they originate. Conclusion We find an inherent bias of certain oligopeptide patterns in naturally occurring proteins that cannot be explained solely on the basis of residue distribution in single proteins, kingdoms or databases. We see three predominant categories of patterns: (i patterns widespread in a kingdom such as those originating from respiratory chain-associated proteins and translation machinery; (ii proteins with structurally and/or functionally favored patterns, which have not yet been ascribed this role; (iii multicopy species-specific retrotransposons, only found in the genome set. These categories will affect the

  10. Elastohydrodynamics and Kinetics of Protein Patterning in the Immunological Synapse.

    Directory of Open Access Journals (Sweden)

    Andreas Carlson

    2015-12-01

    Full Text Available We propose a minimal mathematical model for the physical basis of membrane protein patterning in the immunological synapse (IS, which encompass membrane mechanics, protein binding kinetics and motion, and fluid flow in the synaptic cleft. Our theory leads to simple predictions for the spatial and temporal scales of protein cluster formation, growth and arrest as a function of membrane stiffness, rigidity and kinetics of the adhesive proteins, and the fluid flow in the synaptic cleft. Numerical simulations complement these scaling laws by quantifying the nucleation, growth and stabilization of proteins domains on the size of the cell. Direct comparison with experiment shows that passive elastohydrodynamics and kinetics of protein binding in the synaptic cleft can describe the short-time formation and organization of protein clusters, without evoking any active processes in the cytoskeleton. Despite the apparent complexity of the process, our analysis shows that just two dimensionless parameters characterize the spatial and temporal evolution of the protein pattern: a ratio of membrane elasticity to protein stiffness, and the ratio of a hydrodynamic time scale for fluid flow relative to the protein binding rate. A simple phase diagram encompasses the variety of patterns that can arise.

  11. Micro- and Nanostructured Microfluidic Devices for Localized Protein Immobilization and Other Biomedical Applications

    OpenAIRE

    Steidle, Nicole E.

    2014-01-01

    A new immobilization method for the localized adsorption of proteins on thermoplastic surfaces is introduced. Artificial three-phase interfaces were realized by surface structuring to control the wetting behavior which lead to a preferred adsorption in these modified areas. Additionally, different fabrication methods were analyzed to determine mass fabrication capabilities. These fabrication methods also allowed the production of fully structured microchannels to tune the fluids behavior within.

  12. Theoretical microfluidics

    DEFF Research Database (Denmark)

    Bruus, Henrik

    in complexity, a proper theoretical understanding becomes increasingly important. The basic idea of the book is to provide a self-contained formulation of the theoretical framework of microfluidics, and at the same time give physical motivation and examples from lab-on-a-chip technology. After three chapters...

  13. Integrated microfluidic platforms for investigating neuronal networks

    Science.gov (United States)

    Kim, Hyung Joon

    This dissertation describes the development and application of integrated microfluidics-based assay platforms to study neuronal activities in the nervous system in-vitro. The assay platforms were fabricated using soft lithography and micro/nano fabrication including microfluidics, surface patterning, and nanomaterial synthesis. The use of integrated microfluidics-based assay platform allows culturing and manipulating many types of neuronal tissues in precisely controlled microenvironment. Furthermore, they provide organized multi-cellular in-vitro model, long-term monitoring with live cell imaging, and compatibility with molecular biology techniques and electrophysiology experiment. In this dissertation, the integrated microfluidics-based assay platforms are developed for investigation of neuronal activities such as local protein synthesis, impairment of axonal transport by chemical/physical variants, growth cone path finding under chemical/physical cues, and synaptic transmission in neuronal circuit. Chapter 1 describes the motivation, objectives, and scope for developing in-vitro platform to study various neuronal activities. Chapter 2 introduces microfluidic culture platform for biochemical assay with large-scale neuronal tissues that are utilized as model system in neuroscience research. Chapter 3 focuses on the investigation of impaired axonal transport by beta-Amyloid and oxidative stress. The platform allows to control neuronal processes and to quantify mitochondrial movement in various regions of axons away from applied drugs. Chapter 4 demonstrates the development of microfluidics-based growth cone turning assay to elucidate the mechanism underlying axon guidance under soluble factors and shear flow. Using this platform, the behaviors of growth cone of mammalian neurons are verified under the gradient of inhibitory molecules and also shear flow in well-controlled manner. In Chapter 5, I combine in-vitro multicellular model with microfabricated MEA

  14. Rapid, highly efficient extraction and purification of membrane proteins using a microfluidic continuous-flow based aqueous two-phase system.

    Science.gov (United States)

    Hu, Rui; Feng, Xiaojun; Chen, Pu; Fu, Meng; Chen, Hong; Guo, Lin; Liu, Bi-Feng

    2011-01-07

    Membrane proteins play essential roles in regulating various fundamental cellular functions. To investigate membrane proteins, extraction and purification are usually prerequisite steps. Here, we demonstrated a microfluidic aqueous PEG/detergent two-phase system for the purification of membrane proteins from crude cell extract, which replaced the conventional discontinuous agitation method with continuous extraction in laminar flows, resulting in significantly increased extraction speed and efficiency. To evaluate this system, different separation and detection methods were used to identify the purified proteins, such as capillary electrophoresis, SDS-PAGE and nano-HPLC-MS/MS. Swiss-Prot database with Mascot search engine was used to search for membrane proteins from random selected bands of SDS-PAGE. Results indicated that efficient purification of membrane proteins can be achieved within 5-7s and approximately 90% of the purified proteins were membrane proteins (the highest extraction efficiency reported up to date), including membrane-associated proteins and integral membrane proteins with multiple transmembrane domains. Compared to conventional approaches, this new method had advantages of greater specific surface area, minimal emulsification, reduced sample consumption and analysis time. We expect the developed method to be potentially useful in membrane protein purifications, facilitating the investigation of membrane proteomics.

  15. Development of Plate Reader and On-Line Microfluidic Screening to Identify Ligands of the 5-Hydroxytryptamine Binding Protein in Venoms

    Directory of Open Access Journals (Sweden)

    Reka A. Otvos

    2015-06-01

    Full Text Available The 5-HT3 receptor is a ligand-gated ion channel, which is expressed in the nervous system. Its antagonists are used clinically for treatment of postoperative- and radiotherapy-induced emesis and irritable bowel syndrome. In order to better understand the structure and function of the 5-HT3 receptor, and to allow for compound screening at this receptor, recently a serotonin binding protein (5HTBP was engineered with the Acetylcholine Binding Protein as template. In this study, a fluorescence enhancement assay for 5HTBP ligands was developed in plate-reader format and subsequently used in an on-line microfluidic format. Both assay types were validated using an existing radioligand binding assay. The on-line microfluidic assay was coupled to HPLC via a post-column split which allowed parallel coupling to a mass spectrometer to collect MS data. This high-resolution screening (HRS system is well suitable for compound mixture analysis. As a proof of principle, the venoms of Dendroapsis polylepis, Pseudonaja affinis and Pseudonaja inframacula snakes were screened and the accurate masses of the found bioactives were established. To demonstrate the subsequent workflow towards structural identification of bioactive proteins and peptides, the partial amino acid sequence of one of the bioactives from the Pseudonaja affinis venom was determined using a bottom-up proteomics approach.

  16. Patterns of fluorescent protein expression in Scleractinian corals.

    Science.gov (United States)

    Gruber, David F; Kao, Hung-Teh; Janoschka, Stephen; Tsai, Julia; Pieribone, Vincent A

    2008-10-01

    Biofluorescence exists in only a few classes of organisms, with Anthozoa possessing the majority of species known to express fluorescent proteins. Most species within the Anthozoan subgroup Scleractinia (reef-building corals) not only express green fluorescent proteins, they also localize the proteins in distinct anatomical patterns.We examined the distribution of biofluorescence in 33 coral species, representing 8 families, from study sites on Australia's Great Barrier Reef. For 28 of these species, we report the presence of biofluorescence for the first time. The dominant fluorescent emissions observed were green (480-520 nm) and red (580-600 nm). Fluorescent proteins were expressed in three distinct patterns (highlighted, uniform, and complementary) among specific anatomical structures of corals across a variety of families. We report no significant overlap between the distribution of fluorescent proteins and the distribution of zooxanthellae. Analysis of the patterns of fluorescent protein distribution provides evidence that the scheme in which fluorescent proteins are distributed among the anatomical structures of corals is nonrandom. This targeted expression of fluorescent proteins in corals produces contrast and may function as a signaling mechanism to organisms with sensitivity to specific wavelengths of light.

  17. The Microfluidic Jukebox

    Science.gov (United States)

    Tan, Say Hwa; Maes, Florine; Semin, Benoît; Vrignon, Jérémy; Baret, Jean-Christophe

    2014-04-01

    Music is a form of art interweaving people of all walks of life. Through subtle changes in frequencies, a succession of musical notes forms a melody which is capable of mesmerizing the minds of people. With the advances in technology, we are now able to generate music electronically without relying solely on physical instruments. Here, we demonstrate a musical interpretation of droplet-based microfluidics as a form of novel electronic musical instruments. Using the interplay of electric field and hydrodynamics in microfluidic devices, well controlled frequency patterns corresponding to musical tracks are generated in real time. This high-speed modulation of droplet frequency (and therefore of droplet sizes) may also provide solutions that reconciles high-throughput droplet production and the control of individual droplet at production which is needed for many biochemical or material synthesis applications.

  18. Automated microfluidic sample-preparation platform for high-throughput structural investigation of proteins by small-angle X-ray scattering

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Snakenborg, Detlef; Nielsen, Søren Skou

    2011-01-01

    A new microfluidic sample-preparation system is presented for the structural investigation of proteins using small-angle X-ray scattering (SAXS) at synchrotrons. The system includes hardware and software features for precise fluidic control, sample mixing by diffusion, automated X-ray exposure...... control, UV absorbance measurements and automated data analysis. As little as 15 l of sample is required to perform a complete analysis cycle, including sample mixing, SAXS measurement, continuous UV absorbance measurements, and cleaning of the channels and X-ray cell with buffer. The complete analysis...... cycle can be performed in less than 3 min. Bovine serum albumin was used as a model protein to characterize the mixing efficiency and sample consumption of the system. The N2 fragment of an adaptor protein (p120-RasGAP) was used to demonstrate how the device can be used to survey the structural space...

  19. Multistability and dynamic transitions of intracellular Min protein patterns.

    Science.gov (United States)

    Wu, Fabai; Halatek, Jacob; Reiter, Matthias; Kingma, Enzo; Frey, Erwin; Dekker, Cees

    2016-06-08

    Cells owe their internal organization to self-organized protein patterns, which originate and adapt to growth and external stimuli via a process that is as complex as it is little understood. Here, we study the emergence, stability, and state transitions of multistable Min protein oscillation patterns in live Escherichia coli bacteria during growth up to defined large dimensions. De novo formation of patterns from homogenous starting conditions is observed and studied both experimentally and in simulations. A new theoretical approach is developed for probing pattern stability under perturbations. Quantitative experiments and simulations show that, once established, Min oscillations tolerate a large degree of intracellular heterogeneity, allowing distinctly different patterns to persist in different cells with the same geometry. Min patterns maintain their axes for hours in experiments, despite imperfections, expansion, and changes in cell shape during continuous cell growth. Transitions between multistable Min patterns are found to be rare events induced by strong intracellular perturbations. The instances of multistability studied here are the combined outcome of boundary growth and strongly nonlinear kinetics, which are characteristic of the reaction-diffusion patterns that pervade biology at many scales.

  20. Microfluidic Device

    Science.gov (United States)

    Tai, Yu-Chong (Inventor); Zheng, Siyang (Inventor); Lin, Jeffrey Chun-Hui (Inventor); Kasdan, Harvey L. (Inventor)

    2017-01-01

    Described herein are particular embodiments relating to a microfluidic device that may be utilized for cell sensing, counting, and/or sorting. Particular aspects relate to a microfabricated device that is capable of differentiating single cell types from dense cell populations. One particular embodiment relates a device and methods of using the same for sensing, counting, and/or sorting leukocytes from whole, undiluted blood samples.

  1. Modeling associated protein-DNA pattern discovery with unified scores.

    Science.gov (United States)

    Chan, Tak-Ming; Lo, Leung-Yau; Sze-To, Ho-Yin; Leung, Kwong-Sak; Xiao, Xinshu; Wong, Man-Hon

    2013-01-01

    Understanding protein-DNA interactions, specifically transcription factor (TF) and transcription factor binding site (TFBS) bindings, is crucial in deciphering gene regulation. The recent associated TF-TFBS pattern discovery combines one-sided motif discovery on both the TF and the TFBS sides. Using sequences only, it identifies the short protein-DNA binding cores available only in high-resolution 3D structures. The discovered patterns lead to promising subtype and disease analysis applications. While the related studies use either association rule mining or existing TFBS annotations, none has proposed any formal unified (both-sided) model to prioritize the top verifiable associated patterns. We propose the unified scores and develop an effective pipeline for associated TF-TFBS pattern discovery. Our stringent instance-level evaluations show that the patterns with the top unified scores match with the binding cores in 3D structures considerably better than the previous works, where up to 90 percent of the top 20 scored patterns are verified. We also introduce extended verification from literature surveys, where the high unified scores correspond to even higher verification percentage. The top scored patterns are confirmed to match the known WRKY binding cores with no available 3D structures and agree well with the top binding affinities of in vivo experiments.

  2. Solid-phase extraction and purification of membrane proteins using a UV-modified PMMA microfluidic bioaffinity μSPE device.

    Science.gov (United States)

    Battle, Katrina N; Jackson, Joshua M; Witek, Małgorzata A; Hupert, Mateusz L; Hunsucker, Sally A; Armistead, Paul M; Soper, Steven A

    2014-03-21

    We present a novel microfluidic solid-phase extraction (μSPE) device for the affinity enrichment of biotinylated membrane proteins from whole cell lysates. The device offers features that address challenges currently associated with the extraction and purification of membrane proteins from whole cell lysates, including the ability to release the enriched membrane protein fraction from the extraction surface so that they are available for downstream processing. The extraction bed was fabricated in PMMA using hot embossing and was comprised of 3600 micropillars. Activation of the PMMA micropillars by UV/O3 treatment permitted generation of surface-confined carboxylic acid groups and the covalent attachment of NeutrAvidin onto the μSPE device surfaces, which was used to affinity select biotinylated MCF-7 membrane proteins directly from whole cell lysates. The inclusion of a disulfide linker within the biotin moiety permitted release of the isolated membrane proteins via DTT incubation. Very low levels (∼20 fmol) of membrane proteins could be isolated and recovered with ∼89% efficiency with a bed capacity of 1.7 pmol. Western blotting indicated no traces of cytosolic proteins in the membrane protein fraction as compared to significant contamination using a commercial detergent-based method. We highlight future avenues for enhanced extraction efficiency and increased dynamic range of the μSPE device using computational simulations of different micropillar geometries to guide future device designs.

  3. Isozyme patterns and protein profiles in neuromuscular disorders.

    Science.gov (United States)

    Edwards, Y H; Tipler, T D; Morgan-Hughes, J A; Neerunjun, J S; Hopkinson, D A

    1982-06-01

    The isozyme patterns of six different enzymes and the polypeptide profiles of soluble proteins have been examined in muscle biopsy specimens from 74 patients with a wide variety of neuromuscular disorders. About half of the samples showed unusual features in at least one, and often several, of the enzymes and proteins tested. The extent of the biochemical abnormalities was roughly proportional to the severity of the disorders. In all cases the unusual isozymes and polypeptide profiles seemed to reflect a reversion to the fetal pattern of gene expression. However, this change appeared to occur in extant muscle and was not dependent on the appearance of new muscle fibres. Among the enzymes, phosphoglycerate mutase followed by creatine kinase appeared to be the most sensitive index of muscle disorder. The extent of the change in the muscle creatine kinase isozyme pattern was not correlated with the levels of serum creatine kinase activity.

  4. Multivariate analysis of 2-DE protein patterns - Practical approaches

    DEFF Research Database (Denmark)

    Jacobsen, Charlotte; Jacobsen, Susanne; Grove, H.

    2007-01-01

    Practical approaches to the use of multivariate data analysis of 2-DE protein patterns are demonstrated by three independent strategies for the image analysis and the multivariate analysis on the same set of 2-DE data. Four wheat varieties were selected on the basis of their baking quality. Two...... of the varieties were of strong baking quality and hard wheat kernel and two were of weak baking quality and soft kernel. Gliadins at different stages of grain development were analyzed by the application of multivariate data analysis on images of 2-DEs. Patterns related to the wheat varieties, harvest times...... and quality were detected on images of 2-DE protein patterns for all the three strategies. The use of the multivariate methods was evaluated in the alignment and matching procedures of 2-DE gels. All the three strategies were able to discriminate the samples according to quality, harvest time and variety...

  5. Droplet based microfluidics.

    Science.gov (United States)

    Seemann, Ralf; Brinkmann, Martin; Pfohl, Thomas; Herminghaus, Stephan

    2012-01-01

    Droplet based microfluidics is a rapidly growing interdisciplinary field of research combining soft matter physics, biochemistry and microsystems engineering. Its applications range from fast analytical systems or the synthesis of advanced materials to protein crystallization and biological assays for living cells. Precise control of droplet volumes and reliable manipulation of individual droplets such as coalescence, mixing of their contents, and sorting in combination with fast analysis tools allow us to perform chemical reactions inside the droplets under defined conditions. In this paper, we will review available drop generation and manipulation techniques. The main focus of this review is not to be comprehensive and explain all techniques in great detail but to identify and shed light on similarities and underlying physical principles. Since geometry and wetting properties of the microfluidic channels are crucial factors for droplet generation, we also briefly describe typical device fabrication methods in droplet based microfluidics. Examples of applications and reaction schemes which rely on the discussed manipulation techniques are also presented, such as the fabrication of special materials and biophysical experiments.

  6. Droplet based microfluidics

    Science.gov (United States)

    Seemann, Ralf; Brinkmann, Martin; Pfohl, Thomas; Herminghaus, Stephan

    2012-01-01

    Droplet based microfluidics is a rapidly growing interdisciplinary field of research combining soft matter physics, biochemistry and microsystems engineering. Its applications range from fast analytical systems or the synthesis of advanced materials to protein crystallization and biological assays for living cells. Precise control of droplet volumes and reliable manipulation of individual droplets such as coalescence, mixing of their contents, and sorting in combination with fast analysis tools allow us to perform chemical reactions inside the droplets under defined conditions. In this paper, we will review available drop generation and manipulation techniques. The main focus of this review is not to be comprehensive and explain all techniques in great detail but to identify and shed light on similarities and underlying physical principles. Since geometry and wetting properties of the microfluidic channels are crucial factors for droplet generation, we also briefly describe typical device fabrication methods in droplet based microfluidics. Examples of applications and reaction schemes which rely on the discussed manipulation techniques are also presented, such as the fabrication of special materials and biophysical experiments.

  7. Microfluidic Analytical Separator for Proteomics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SHOT proposes an innovative microfluidic device designed to effect a 2-dimensional resolution of a mixture of proteins based on isoelectric point (pI) and molecular...

  8. Microfluidic Analytical Separator for Proteomics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation is a microfluidic device designed to effect a 2-dimensional resolution of a mixture of proteins based on isoelectric point (pI) and molecular...

  9. A simple method of fabricating mask-free microfluidic devices for biological analysis.

    KAUST Repository

    Yi, Xin

    2010-09-07

    We report a simple, low-cost, rapid, and mask-free method to fabricate two-dimensional (2D) and three-dimensional (3D) microfluidic chip for biological analysis researches. In this fabrication process, a laser system is used to cut through paper to form intricate patterns and differently configured channels for specific purposes. Bonded with cyanoacrylate-based resin, the prepared paper sheet is sandwiched between glass slides (hydrophilic) or polymer-based plates (hydrophobic) to obtain a multilayer structure. In order to examine the chip\\'s biocompatibility and applicability, protein concentration was measured while DNA capillary electrophoresis was carried out, and both of them show positive results. With the utilization of direct laser cutting and one-step gas-sacrificing techniques, the whole fabrication processes for complicated 2D and 3D microfluidic devices are shorten into several minutes which make it a good alternative of poly(dimethylsiloxane) microfluidic chips used in biological analysis researches.

  10. Protein pattern of Xenopus laevis embryos grown in simulated microgravity.

    Science.gov (United States)

    Tedeschi, Gabriella; Pagliato, Lara; Negroni, Manuela; Montorfano, Gigliola; Corsetto, Paola; Nonnis, Simona; Negri, Armando; Rizzo, Angela Maria

    2011-03-01

    Numerous studies indicate that microgravity affects cell growth and differentiation in many living organisms, and various processes are modified when cells are placed under conditions of weightlessness. However, until now, there is no coherent explanation for these observations, and little information is available concerning the biomolecules involved. Our aim has been to investigate the protein pattern of Xenopus laevis embryos exposed to simulated microgravity during the first 6 days of development. A proteomic approach was applied to compare the protein profiles of Xenopus embryos developed in simulated microgravity and in normal conditions. Attention was focused on embryos that do not present visible malformations in order to investigate if weightlessness has effects at protein level in the absence of macroscopic alterations. The data presented strongly suggest that some of the major components of the cytoskeleton vary in such conditions. Three major findings are described for the first time: (i) the expression of important factors involved in the organization and stabilization of the cytoskeleton, such as Arp (actin-related protein) 3 and stathmin, is heavily affected by microgravity; (ii) the amount of the two major cytoskeletal proteins, actin and tubulin, do not change in such conditions; however, (iii) an increase in the tyrosine nitration of these two proteins can be detected. The data suggest that, in the absence of morphological alterations, simulated microgravity affects the intracellular movement system of cells by altering cytoskeletal proteins heavily involved in the regulation of cytoskeleton remodelling.

  11. Room-temperature serial crystallography using a kinetically optimized microfluidic device for protein crystallization and on-chip X-ray diffraction

    Directory of Open Access Journals (Sweden)

    Michael Heymann

    2014-09-01

    Full Text Available An emulsion-based serial crystallographic technology has been developed, in which nanolitre-sized droplets of protein solution are encapsulated in oil and stabilized by surfactant. Once the first crystal in a drop is nucleated, the small volume generates a negative feedback mechanism that lowers the supersaturation. This mechanism is exploited to produce one crystal per drop. Diffraction data are measured, one crystal at a time, from a series of room-temperature crystals stored on an X-ray semi-transparent microfluidic chip, and a 93% complete data set is obtained by merging single diffraction frames taken from different unoriented crystals. As proof of concept, the structure of glucose isomerase was solved to 2.1 Å, demonstrating the feasibility of high-throughput serial X-ray crystallography using synchrotron radiation.

  12. Fractal flow patterns in hydrophobic microfluidic pore networks: experimental modeling of two-phase flow in porous electrodes

    CERN Document Server

    Berejnov, Viatcheslav; Sinton, David; Djilali, Ned

    2009-01-01

    Experimental two-phase invasion percolation flow patterns were observed in hydrophobic micro-porous networks designed to model fuel cell specific porous media. In order to mimic the operational conditions encountered in the porous electrodes of polymer electrolyte membrane fuel cells (PEMFCs), micro-porous networks were fabricated with corresponding microchannel size distributions. The inlet channels were invaded homogeneously with flow rates corresponding to fuel cell current densities of 1.0 to 0.1 A/cm2 (Ca 10e-7-10e-8). A variety of fractal breakthrough patterns were observed and analyzed to quantify flooding density and geometrical diversity in terms of the total saturation, St, local saturations, s, and fractal dimension, D. It was found that St increases monotonically during the invasion process until the breakthrough point is reached, and s profiles indicate the dynamic distribution of the liquid phase during the process. Fractal analysis confirmed that the experiments fall within the flow regime of i...

  13. Using macromolecular-crystallography beamline and microfluidic platform for small-angle diffraction studies of lipidic matrices for membrane-protein crystallization

    Science.gov (United States)

    Kondrashkina, E.; Khvostichenko, D. S.; Perry, S. L.; Von Osinski, J.; Kenis, P. J. A.; Brister, K.

    2013-03-01

    Macromolecular-crystallography (MX) beamlines routinely provide a possibility to change X-ray beam energy, focus the beam to a size of tens of microns, align a sample on a microdiffractometer using on-axis video microscope, and collect data with an area-detector positioned in three dimensions. These capabilities allow for running complementary measurements of small-angle X-ray scattering and diffraction (SAXS) at the same beamline with such additions to the standard MX setup as a vacuum path between the sample and the detector, a modified beam stop, and a custom sample cell. On the 21-ID-D MX beamline at the Advanced Photon Source we attach a vacuum flight tube to the area detector support and use the support motion for aligning a beam stop built into the rear end of the flight tube. At 8 KeV energy and 1 m sample-to-detector distance we can achieve a small-angle resolution of 0.01A-1 in the reciprocal space. Measuring SAXS with this setup, we have studied phase diagrams of lipidic mesophases used as matrices for membrane-protein crystallization. The outcome of crystallization trials is significantly affected by the structure of the lipidic mesophases, which is determined by the composition of the crystallization mixture. We use a microfluidic chip for the mesophase formulation and in situ SAXS data collection. Using the MX beamline and the microfluidic platform we have demonstrated the viability of the high-throughput SAXS studies facilitating screening of lipidic matrices for membrane-protein crystallization.

  14. Microfluidic electrochemical reactors

    Science.gov (United States)

    Nuzzo, Ralph G [Champaign, IL; Mitrovski, Svetlana M [Urbana, IL

    2011-03-22

    A microfluidic electrochemical reactor includes an electrode and one or more microfluidic channels on the electrode, where the microfluidic channels are covered with a membrane containing a gas permeable polymer. The distance between the electrode and the membrane is less than 500 micrometers. The microfluidic electrochemical reactor can provide for increased reaction rates in electrochemical reactions using a gaseous reactant, as compared to conventional electrochemical cells. Microfluidic electrochemical reactors can be incorporated into devices for applications such as fuel cells, electrochemical analysis, microfluidic actuation, pH gradient formation.

  15. Pbx homeodomain proteins pattern both the zebrafish retina and tectum

    Directory of Open Access Journals (Sweden)

    Stout Jennifer

    2007-07-01

    Full Text Available Abstract Background Pbx genes encode TALE class homeodomain transcription factors that pattern the developing neural tube, pancreas, and blood. Within the hindbrain, Pbx cooperates with Hox proteins to regulate rhombomere segment identity. Pbx cooperates with Eng to regulate midbrain-hindbrain boundary maintenance, and with MyoD to control fast muscle cell differentiation. Although previous results have demonstrated that Pbx is required for proper eye size, functions in regulating retinal cell identity and patterning have not yet been examined. Results Analysis of retinal ganglion cell axon pathfinding and outgrowth in pbx2/4 null embryos demonstrated a key role for pbx genes in regulating neural cell behavior. To identify Pbx-dependent genes involved in regulating retino-tectal pathfinding, we conducted a microarray screen for Pbx-dependent transcripts in zebrafish, and detected genes that are specifically expressed in the eye and tectum. A subset of Pbx-dependent retinal transcripts delineate specific domains in the dorso-temporal lobe of the developing retina. Furthermore, we determined that some Pbx-dependent transcripts also require Meis1 and Gdf6a function. Since gdf6a expression is also dependent on Pbx, we propose a model in which Pbx proteins regulate expression of the growth factor gdf6a, which in turn regulates patterning of the dorso-temporal lobe of the retina. This, in concert with aberrant tectal patterning in pbx2/4 null embryos, may lead to the observed defects in RGC outgrowth. Conclusion These data define a novel role for Pbx in patterning the vertebrate retina and tectum in a manner required for proper retinal ganglion cell axon outgrowth.

  16. Paper based microfluidic devices for environmental diagnostics

    CSIR Research Space (South Africa)

    Govindasamy, K

    2012-09-01

    Full Text Available such as elevated temperatures and mechanical stresses. Paper based microfluidic chips are patterned with micron sized hydrophobic barriers which penetrate the paper?s cross section. These barriers guide the capillary movement of fluids through the cellulose... visual or electrochemical signal, indicating whether the analyte is present in the sample. Although based on a similar operational principal as lateral flow technologies (such as home pregnancy tests), paper based microfluidics seeks to offer a more...

  17. Semiconductor sensor embedded microfluidic chip for protein biomarker detection using a bead-based immunoassay combined with deoxyribonucleic acid strand labeling.

    Science.gov (United States)

    Lin, Yen-Heng; Peng, Po-Yu

    2015-04-15

    Two major issues need to be addressed in applying semiconductor biosensors to detecting proteins in immunoassays. First, the length of the antibody on the sensor surface surpasses the Debye lengths (approximately 1 nm, in normal ionic strength solution), preventing certain specifically bound proteins from being tightly attached to the sensor surface. Therefore, these proteins do not contribute to the sensor's surface potential change. Second, these proteins carry a small charge and can be easily affected by the pH of the surrounding solution. This study proposes a magnetic bead-based immunoassay using a secondary antibody to label negatively charged DNA fragments for signal amplification. An externally imposed magnetic force attaches the analyte tightly to the sensor surface, thereby effectively solving the problem of the analyte protein's distance to the sensor surface surpassing the Debye lengths. In addition, a normal ion intensity buffer can be used without dilution for the proposed method. Experiments revealed that the sensitivity can be improved by using a longer DNA fragment for labeling and smaller magnetic beads as solid support for the antibody. By using a 90 base pair DNA label, the signal was 15 times greater than that without labeling. In addition, by using a 120 nm magnetic bead, a minimum detection limit of 12.5 ng mL(-1) apolipoprotein A1 can be measured. Furthermore, this study integrates a semiconductor sensor with a microfluidic chip. With the help of microvalves and micromixers in the chip, the length of the mixing step for each immunoassay has been reduced from 1h to 20 min, and the sample volume has been reduced from 80 μL to 10 μL. In practice, a protein biomarker in a urinary bladder cancer patient's urine was successfully measured using this technique. This study provides a convenient and effective method to measure protein using a semiconductor sensor.

  18. Surface modification of poly(dimethylsiloxane) for microfluidic assay applications

    Energy Technology Data Exchange (ETDEWEB)

    Seguin, Christine; McLachlan, Jessica M.; Norton, Peter R. [Department of Chemistry, University of Western Ontario, 1151 Richmond St., London, ON, N6A 5B7 (Canada); Lagugne-Labarthet, Francois, E-mail: flagugne@uwo.ca [Department of Chemistry, University of Western Ontario, 1151 Richmond St., London, ON, N6A 5B7 (Canada)

    2010-02-01

    The surface of a poly(dimethylsiloxane) (PDMS) film was imparted with patterned functionalities at the micron-scale level. Arrays of circles with diameters of 180 and 230 {mu}m were functionalized using plasma oxidation coupled with aluminum deposition, followed by silanization with solutions of 3-aminopropyltrimethoxy silane (3-APTMS) and 3-mercaptopropyltrimethoxy silane (3-MPTMS), to obtain patterned amine and thiol functionalities, respectively. The modification of the samples was confirmed using X-ray photoelectron spectroscopy (XPS), gold nanoparticle adhesion coupled with optical microscopy, as well as by derivatization with fluorescent dyes. To further exploit the novel surface chemistry of the modified PDMS, samples with surface amine functionalities were used to develop a protein assay as well as an array capable of cellular capture and patterning. The modified substrate was shown to successfully selectively immobilize fluorescently labeled immunoglobulin G (IgG) by tethering Protein A to the surface, and, for the cellular arrays, C2C12 rat endothelial cells were captured. Finally, this novel method of patterning chemical functionalities onto PDMS has been incorporated into microfluidic channels. Finally, we demonstrate the in situ chemical modification of the protected PDMS oxidized surface within a microfluidic device. This emphasizes the potential of our method for applications involving micron-scale assays since the aluminum protective layer permits to functionalize the oxidized PDMS surface several weeks after plasma treatment simply after etching away the metallic thin film.

  19. Fabrication of universal serial bus flash disk type microfluidic chip electrophoresis and application for protein analysis under ultra low voltage.

    Science.gov (United States)

    Cong, Hailin; Xu, Xiaodan; Yu, Bing; Liu, Huwei; Yuan, Hua

    2016-03-01

    A simple and effective universal serial bus (USB) flash disk type microfluidic chip electrophoresis (MCE) was developed by using poly(dimethylsiloxane) based soft lithography and dry film based printed circuit board etching techniques in this paper. The MCE had a microchannel diameter of 375 μm and an effective length of 25 mm. Equipped with a conventional online electrochemical detector, the device enabled effectively separation of bovine serum albumin, lysozyme, and cytochrome c in 80 s under the ultra low voltage from a computer USB interface. Compared with traditional capillary electrophoresis, the USB flash disk type MCE is not only portable and inexpensive but also fast with high separation efficiency.

  20. Recognition of higher order patterns in proteins: immunologic kernels.

    Directory of Open Access Journals (Sweden)

    Robert D Bremel

    Full Text Available By applying analysis of the principal components of amino acid physical properties we predicted cathepsin cleavage sites, MHC binding affinity, and probability of B-cell epitope binding of peptides in tetanus toxin and in ten diverse additional proteins. Cross-correlation of these metrics, for peptides of all possible amino acid index positions, each evaluated in the context of a ±25 amino acid flanking region, indicated that there is a strongly repetitive pattern of short peptides of approximately thirty amino acids each bounded by cathepsin cleavage sites and each comprising B-cell linear epitopes, MHC-I and MHC-II binding peptides. Such "immunologic kernel" peptides comprise all signals necessary for adaptive immunologic cognition, response and recall. The patterns described indicate a higher order spatial integration that forms a symbolic logic coordinating the adaptive immune system.

  1. Pattern Formation by Electrostatic Self-Organization of Membrane Proteins

    Science.gov (United States)

    Boedec, G.; Jaeger, M.; Homble, F.; Leonetti, M.

    2012-07-01

    The electric activity of biological cells and organs such as heart for example is at the origin of various phenomena of pattern formation. The electric membrane potential appears as the order parameter to characterize these spatiotemporal dynamics. A kind of patterns is characterized by a stationary spatial modulation of membrane potential along the cell, breaking a symmetry of the system. They are associated to transcellular currents. A mechanism proposed in literature is based on the coupling of the electric current produced by membrane proteins and their electrophoretic mobilities. Beyond its classical linear stability analysis, the numerical and theoretical analysis of this model offers a variety of spatiotemporal dynamics. Firstly, the background in the modelization of electric phenomena is recalled. Secondly, the analysis is focused on two nonlinear dynamics.

  2. Microfluidics' great promise for Biology - Microfluidics as a new engine for the molecular sciences

    KAUST Repository

    Kodzius, Rimantas

    2010-06-04

    History of the Life Sciences Origins of life Discoveries and instrumentation The power of genetic variation Diagnostics based on DNA/ protein variation Genomic scanning providers DNA sequencing companies Microfluidics story Commercial products available P

  3. PREFACE: Nano- and microfluidics Nano- and microfluidics

    Science.gov (United States)

    Jacobs, Karin

    2011-05-01

    The field of nano- and microfluidics emerged at the end of the 1990s parallel to the demand for smaller and smaller containers and channels for chemical, biochemical and medical applications such as blood and DNS analysis [1], gene sequencing or proteomics [2, 3]. Since then, new journals and conferences have been launched and meanwhile, about two decades later, a variety of microfluidic applications are on the market. Briefly, 'the small flow becomes mainstream' [4]. Nevertheless, research in nano- and microfluidics is more than downsizing the spatial dimensions. For liquids on the nanoscale, surface and interface phenomena grow in importance and may even dominate the behavior in some systems. The studies collected in this special issue all concentrate on these type of systems and were part ot the priority programme SPP1164 'Nano- and Microfluidics' of the German Science Foundation (Deutsche Forschungsgemeinschaft, DFG). The priority programme was initiated in 2002 by Hendrik Kuhlmann and myself and was launched in 2004. Friction between a moving liquid and a solid wall may, for instance, play an important role so that the usual assumption of a no-slip boundary condition is no longer valid. Likewise, the dynamic deformations of soft objects like polymers, vesicles or capsules in flow arise from the subtle interplay between the (visco-)elasticity of the object and the viscous stresses in the surrounding fluid and, potentially, the presence of structures confining the flow like channels. Consequently, new theories were developed ( see articles in this issue by Münch and Wagner, Falk and Mecke, Bonthuis et al, Finken et al, Almenar and Rauscher, Straube) and experiments were set up to unambiguously demonstrate deviations from bulk, or 'macro', behavior (see articles in this issue by Wolff et al, Vinogradova and Belyaev, Hahn et al, Seemann et al, Grüner and Huber, Müller-Buschbaum et al, Gutsche et al, Braunmüller et al, Laube et al, Brücker, Nottebrock et al

  4. Novel technique sheds new light on protein colocalization patterns

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ The potential of MELC, a brand-new and highly efficient technique for studying the temporal and spatial distribution of proteins in living tissue,has been explored jointly over the last years by Walter Schubert, its inventor from the Molecular Pattern-Recognition Research Group at the Institute of Medical Neurobiology, Otto-von-Guericke University (Magdeburg, Germany),and his collaborators including Andreas Dress from the CAS-MPG Partner Institute for Computational Biology (PICB), the Shanghai Institutes for Biological Sciences (SIBS).

  5. Microfluidic Dye Lasers

    DEFF Research Database (Denmark)

    Kristensen, Anders; Balslev, Søren; Gersborg-Hansen, Morten

    2006-01-01

    A technology for miniaturized, polymer based lasers, suitable for integration with planar waveguides and microfluidic networks is presented. The microfluidic dye laser device consists of a microfluidic channel with an embedded optical resonator. The devices are fabricated in a thin polymer film...

  6. Microfluidic sieve valves

    Science.gov (United States)

    Quake, Stephen R; Marcus, Joshua S; Hansen, Carl L

    2015-01-13

    Sieve valves for use in microfluidic device are provided. The valves are useful for impeding the flow of particles, such as chromatography beads or cells, in a microfluidic channel while allowing liquid solution to pass through the valve. The valves find particular use in making microfluidic chromatography modules.

  7. Microfluidic single sperm analysis

    NARCIS (Netherlands)

    Wagenaar, de Bjorn

    2016-01-01

    Microfluidic technology has been occasionally used for in vitro analysis and separation of cells. The small dimensions of microfluidic chips are very suitable to study cells on the single cell level rather than in whole populations. Also sperm cells have been studied and manipulated using microfluid

  8. Morphology and protein patterns of honey bee drone accessory glands.

    Science.gov (United States)

    Cruz-Landim, Carminda da; Dallacqua, Rodrigo Pires

    2005-09-30

    We used light and transmission electron microscopy to examine the morphology of the accessory glands of immature and mature adult males of Apis mellifera L. We also made an electrophoretic analysis of the protein content of the mature gland. The glands of the immature male actively secrete a mucous substance that can be seen in the lumen of the gland of the mature male. This secretion stains with mercury bromophenol blue and with periodic acid-Schiff reaction, which stain glyconjugates. The protein content was higher in the lumen secretion than in the gland wall extracts. The electrophoresis patterns of the wall extracts were different from those of the secretion found in the gland lumen.

  9. In search of low cost biological analysis: Wax or acrylic glue bonded paper microfluidic devices

    KAUST Repository

    Kodzius, Rimantas

    2011-01-22

    In this body of work we have been developing and characterizing paper based microfluidic fabrication technologies to produce low cost biological analysis. Specifically we investigated the performance of paper microfluidics that had been bonded using wax or acrylic glue, and characterized the affect of these and other microfluidic materials on the polymerase chain reaction (PCR). We report a simple, low-cost and detachable microfluidic chip incorporating easily accessible paper, glass slides or other polymer films as the chip materials along with adhesive wax or cyanoacrylate-based resin as the recycling bonding material. We use a laser to cut through the paper or film to form patterns and then sandwich the paper and film between glass sheets or polymer membranes. The hot-melt adhesive wax or simple cyanoacrylate-based resin can realize bridge bonding between various materials, for example, paper, polymethylmethacrylate film, glass sheets, or metal plate. The wax bonding process is reversible and the wax is reusable through a melting and cooling process. With this process, a three-dimensional (3D) microfluidic chip is achievable by evacuating the channels of adhesive material in a hot-water. We applied the wax-paper based microfluidic chip to HeLa cell electroporation. Subsequently, a prototype of a 5-layer 3D chip was fabricated by multilayer wax bonding. To check the sealing ability and the durability of the chip, green fluorescence protein recombinant E. coli bacteria were cultured, with which the chemotaxis of E. coli was studied in order to determine the influence of antibiotic ciprofloxacin concentration on the E. coli migration. The chip bonded with cyanoacrylate-based resin was tested by measuring protein concentration and carrying out DNA capillary electrophoresis. To study the biocompatibility and applicability of our microfluidic chip fabrication technology, we tested the PCR compatibility of our chip materials along with various other common materials

  10. Electro-Microfluidic Packaging

    Science.gov (United States)

    Benavides, G. L.; Galambos, P. C.

    2002-06-01

    There are many examples of electro-microfluidic products that require cost effective packaging solutions. Industry has responded to a demand for products such as drop ejectors, chemical sensors, and biological sensors. Drop ejectors have consumer applications such as ink jet printing and scientific applications such as patterning self-assembled monolayers or ejecting picoliters of expensive analytes/reagents for chemical analysis. Drop ejectors can be used to perform chemical analysis, combinatorial chemistry, drug manufacture, drug discovery, drug delivery, and DNA sequencing. Chemical and biological micro-sensors can sniff the ambient environment for traces of dangerous materials such as explosives, toxins, or pathogens. Other biological sensors can be used to improve world health by providing timely diagnostics and applying corrective measures to the human body. Electro-microfluidic packaging can easily represent over fifty percent of the product cost and, as with Integrated Circuits (IC), the industry should evolve to standard packaging solutions. Standard packaging schemes will minimize cost and bring products to market sooner.

  11. The E4 protein; structure, function and patterns of expression

    Energy Technology Data Exchange (ETDEWEB)

    Doorbar, John, E-mail: jdoorba@nimr.mrc.ac.uk

    2013-10-15

    }E4, these kinases regulate one of the E1{sup ∧}E4 proteins main functions, the association with the cellular keratin network, and eventually also its cleavage by the protease calpain which allows assembly into amyloid-like fibres and reorganisation of the keratin network. Although the E4 proteins of different HPV types appear divergent at the level of their primary amino acid sequence, they share a recognisable modular organisation and pattern of expression, which may underlie conserved functions and regulation. Assembly into higher-order multimers and suppression of cell proliferation are common to all E4 proteins examined. Although not yet formally demonstrated, a role in virus release and transmission remains a likely function for E4. - Highlights: • E4 gene products have a modular structure, and are expressed from the E1{sup ∧}E4 spliced mRNA. • E4 proteins are modified during epithelial differentiation by phosphorylation and proteolysis. • The E4 proteins contribute to genome amplification-efficiency and virus synthesis. • E4 proteins are abundantly expressed and may facilitate efficient virus release and transmission. • High-risk E4 proteins are deposited as amyloid fibres and can be used as infection biomarkers.

  12. Fragile X mental retardation protein (FMRP) interacting proteins exhibit different expression patterns during development.

    Science.gov (United States)

    Bonaccorso, C M; Spatuzza, M; Di Marco, B; Gloria, A; Barrancotto, G; Cupo, A; Musumeci, S A; D'Antoni, S; Bardoni, B; Catania, M V

    2015-05-01

    Fragile X syndrome is caused by the lack of expression of fragile X mental retardation protein (FMRP), an RNA-binding protein involved in mRNA transport and translation. FMRP is a component of mRNA ribonucleoprotein complexes and it can interact with a range of proteins either directly or indirectly, as demonstrated by two-hybrid selection and co-immunoprecipitation, respectively. Most of FMRP-interacting proteins are RNA-binding proteins such as FXR1P, FXR2P and 82-FIP. Interestingly, FMRP can also interact directly with the cytoplasmic proteins CYFIP1 and CYFIP2, which do not bind RNA and link FMRP to the RhoGTPase pathway. The interaction with these different proteins may modulate the functions of FMRP by influencing its affinity to RNA and by affecting the FMRP ability of cytoskeleton remodeling through Rho/Rac GTPases. To better define the relationship of FMRP with its interacting proteins during brain development, we have analyzed the expression pattern of FMRP and its interacting proteins in the cortex, striatum, hippocampus and cerebellum at different ages in wild type (WT) mice. FMRP and FXR2P were strongly expressed during the first week and gradually decreased thereafter, more rapidly in the cerebellum than in the cortex. FXR1P was also expressed early and showed a reduction at later stages of development with a similar developmental pattern in these two regions. CYFIP1 was expressed at all ages and peaked in the third post-natal week. In contrast, CYFIP2 and 82-FIP (only in forebrain regions) were moderately expressed at P3 and gradually increased after P7. In general, the expression pattern of each protein was similar in the regions examined, except for 82-FIP, which exhibited a strong expression at P3 and low levels at later developmental stages in the cerebellum. Our data indicate that FMRP and its interacting proteins have distinct developmental patterns of expression and suggest that FMRP may be preferentially associated to certain proteins in

  13. Concentration Dependent Ion-Protein Interaction Patterns Underlying Protein Oligomerization Behaviours

    Science.gov (United States)

    Batoulis, Helena; Schmidt, Thomas H.; Weber, Pascal; Schloetel, Jan-Gero; Kandt, Christian; Lang, Thorsten

    2016-04-01

    Salts and proteins comprise two of the basic molecular components of biological materials. Kosmotropic/chaotropic co-solvation and matching ion water affinities explain basic ionic effects on protein aggregation observed in simple solutions. However, it is unclear how these theories apply to proteins in complex biological environments and what the underlying ionic binding patterns are. Using the positive ion Ca2+ and the negatively charged membrane protein SNAP25, we studied ion effects on protein oligomerization in solution, in native membranes and in molecular dynamics (MD) simulations. We find that concentration-dependent ion-induced protein oligomerization is a fundamental chemico-physical principle applying not only to soluble but also to membrane-anchored proteins in their native environment. Oligomerization is driven by the interaction of Ca2+ ions with the carboxylate groups of aspartate and glutamate. From low up to middle concentrations, salt bridges between Ca2+ ions and two or more protein residues lead to increasingly larger oligomers, while at high concentrations oligomers disperse due to overcharging effects. The insights provide a conceptual framework at the interface of physics, chemistry and biology to explain binding of ions to charged protein surfaces on an atomistic scale, as occurring during protein solubilisation, aggregation and oligomerization both in simple solutions and membrane systems.

  14. Recent Progress of Microfluidic Techniques for Protein Crystallization and Screening%基于微流控技术的蛋白质结晶及其筛选方法的研究进展

    Institute of Scientific and Technical Information of China (English)

    朱丽娜; 祝莹; 方群

    2014-01-01

    微流控技术以其高通量、低消耗和集成化等优点成为蛋白质结晶微型化研究的重要手段。本文综述了基于微流控技术的蛋白质结晶技术和方法,主要包括微泵微阀、液滴( Droplet)、滑动芯片( SlipChip)以及液滴实验室( DropLab)等技术。此外,还针对当前膜蛋白在结构生物学研究中的重要地位,综述了应用于膜蛋白结晶的微流控技术的研究进展。%With the advantages of high throughput, low consumption and large-scale integration, microfluidics has proven to be a promising technique for protein crystallization and screening. This article reviews the recent progress of various microfluidic techniques successfully applied in protein crystallization, including PDMS-based valve and pump, droplet, SlipChip and DropLab. In addition, due to the high importance and great challenges of membrane proteins in structural biology, we further introduce the microfluidic techniques for crystallization of membrane proteins.

  15. Microfluidic System for Solution Array Based Bioassays

    Energy Technology Data Exchange (ETDEWEB)

    Dougherty, G M; Tok, J B; Pannu, S S; Rose, K A

    2006-02-10

    The objective of this project is to demonstrate new enabling technology for multiplex biodetection systems that are flexible, miniaturizable, highly automated, low cost, and high performance. It builds on prior successes at LLNL with particle-based solution arrays, such as those used in the Autonomous Pathogen Detection System (APDS) successfully field deployed to multiple locations nationwide. We report the development of a multiplex solution array immunoassay based upon engineered metallic nanorod particles. Nanobarcodes{reg_sign} particles are fabricated by sequential electrodeposition of dissimilar metals within porous alumina templates, yielding optically encoded striping patterns that can be read using standard laboratory microscope optics and PC-based image processing software. The addition of self-assembled monolayer (SAM) coatings and target-specific antibodies allows each encoded class of nanorod particles to be directed against a different antigen target. A prototype assay panel directed against bacterial, viral, and soluble protein targets demonstrates simultaneous detection at sensitivities comparable to state of the art immunoassays, with minimal cross-reactivity. Studies have been performed to characterize the colloidal properties (zeta potential) of the suspended nanorod particles as a function of pH, the ionic strength of the suspending solution, and surface functionalization state. Additional studies have produced means for the non-contact manipulation of the particles, including the insertion of magnetic nickel stripes within the encoding pattern, and control via externally applied electromagnetic fields. Using the results of these studies, the novel Nanobarcodes{reg_sign} based assay was implemented in a prototype automated system with the sample processing functions and optical readout performed on a microfluidic card. The unique physical properties of the nanorod particles enable the development of integrated microfluidic systems for

  16. Dynamic expression pattern of kinesin accessory protein in Drosophila

    Indian Academy of Sciences (India)

    Ritu Sarpal; Krishanu Ray

    2002-09-01

    We have identified the Drosophila homologue of the non-motor accessory subunit of kinesin-II motor complex. It is homologous to the SpKAP115 of the sea urchin, KAP3A and KAP3B of the mouse, and SMAP protein in humans. In situ hybridization using a DmKAP specific cRNA probe has revealed a dynamic pattern of expression in the developing nervous system. The staining first appears in a subset of cells in the embryonic central nervous system at stage 13 and continues till the first instar larva stage. At the third instar larva stage the staining gets restricted to a few cells in the optic lobe and in the ventral ganglion region. It has also stained a subset of sensory neurons from late stage 13 and till the first instar larva stage. The DmKAP expression pattern in the nervous system corresponds well with that of Klp64D and Klp68D as reported earlier. In addition, we have found that the DmKAP gene is constitutively expressed in the germline cells and in follicle cells during oogenesis. These cells are also stained using an antibody to KLP68D protein, but mRNA in situ hybridization using KLP64D specific probe has not stained these cells. Together these results proved a basis for further analysis of tissue specific function of DmKAP in future.

  17. Microfluidic technology for PET radiochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Gillies, J.M. [Cancer Research-UK/University of Manchester Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester, M20 4BX (United Kingdom)]. E-mail: jgillies@picr.man.ac.uk; Prenant, C. [Cancer Research-UK/University of Manchester Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester, M20 4BX (United Kingdom); School of Chemical Engineering and Analytical Sciences, University of Manchester, P.O. Box 88, Manchester, M60 1QD (United Kingdom); Chimon, G.N. [Cancer Research-UK/University of Manchester Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester, M20 4BX (United Kingdom); School of Chemical Engineering and Analytical Sciences, University of Manchester, P.O. Box 88, Manchester, M60 1QD (United Kingdom); Smethurst, G.J. [Cancer Research-UK/University of Manchester Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester, M20 4BX (United Kingdom); Dekker, B.A. [Cancer Research-UK/University of Manchester Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester, M20 4BX (United Kingdom); Zweit, J. [Cancer Research-UK/University of Manchester Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester, M20 4BX (United Kingdom); School of Chemical Engineering and Analytical Sciences, University of Manchester, P.O. Box 88, Manchester, M60 1QD (United Kingdom)

    2006-03-15

    This paper describes the first application of a microfabricated reaction system to positron emission tomography (PET) radiochemistry. We have applied microfluidic technology to synthesise PET radiopharmaceuticals using {sup 18}F and {sup 124}I as labels for fluorodeoxyglucose (FDG) and Annexin-V, respectively. These reactions involved established methods of nucleophilic substitution on a mannose triflate precursor and direct iodination of the protein using iodogen as an oxidant. This has demonstrated a proof of principle of using microfluidic technology to radiochemical reactions involving low and high molecular weight compounds. Using microfluidic reactions, [{sup 18}F]FDG was synthesised with a 50% incorporation of the available F-18 radioactivity in a very short time of 4 s. The radiolabelling efficiency of {sup 124}I Annexin-V was 40% after 1 min reaction time. Chromatographic analysis showed that such reaction yields are comparable to conventional methods, but in a much shorter time. The yields can be further improved with more optimisation of the microfluidic device itself and its fluid mixing profiles. This demonstrates the potential for this technology to have an impact on rapid and simpler radiopharmaceutical synthesis using short and medium half-life radionuclides.

  18. The E4 protein; structure, function and patterns of expression.

    Science.gov (United States)

    Doorbar, John

    2013-10-01

    the E1^E4 proteins main functions, the association with the cellular keratin network, and eventually also its cleavage by the protease calpain which allows assembly into amyloid-like fibres and reorganisation of the keratin network. Although the E4 proteins of different HPV types appear divergent at the level of their primary amino acid sequence, they share a recognisable modular organisation and pattern of expression, which may underlie conserved functions and regulation. Assembly into higher-order multimers and suppression of cell proliferation are common to all E4 proteins examined. Although not yet formally demonstrated, a role in virus release and transmission remains a likely function for E4. © 2013 The Author. Published by Elsevier Inc. All rights reserved.

  19. Design of hydrodynamically confined microfluidics: controlling flow envelope and pressure.

    Science.gov (United States)

    Christ, Kevin V; Turner, Kevin T

    2011-04-21

    Closed-channel microfluidic devices are widely used in a number of chemical and biological applications; however, it is often difficult to interact with samples, such as cells, that are enclosed inside them. Hydrodynamically confined microflows (HCMs) allow microfluidic-type flows to be generated in open liquid environments, such as Petri dishes, thus greatly increasing the flexibility of microfluidic approaches. HCMs have previously been used for protein patterning and selective cell treatment applications, but the underlying fluid mechanics is not fully understood. Here, we examine the effect of device geometry and flow parameters on the properties of the flow envelope and pressure drop of several two-port HCM devices using a combination of experiments and modeling. A three-port device, which allows for different flow envelope shapes to be generated, is also analyzed. The experimental results agree well with the 3-D computational fluid dynamics simulations, with the majority of the measurements within 10% of the simulations. The results presented provide a framework for understanding the fluid mechanics of HCMs and will aid in the design of HCM devices for a broad range of applications.

  20. Microfluidic White Organic Light-Emitting Diode Based on Integrated Patterns of Greenish-Blue and Yellow Solvent-Free Liquid Emitters

    Science.gov (United States)

    Kobayashi, Naofumi; Kasahara, Takashi; Edura, Tomohiko; Oshima, Juro; Ishimatsu, Ryoichi; Tsuwaki, Miho; Imato, Toshihiko; Shoji, Shuichi; Mizuno, Jun

    2015-01-01

    We demonstrated a novel microfluidic white organic light-emitting diode (microfluidic WOLED) based on integrated sub-100-μm-wide microchannels. Single-μm-thick SU-8-based microchannels, which were sandwiched between indium tin oxide (ITO) anode and cathode pairs, were fabricated by photolithography and heterogeneous bonding technologies. 1-Pyrenebutyric acid 2-ethylhexyl ester (PLQ) was used as a solvent-free greenish-blue liquid emitter, while 2,8-di-tert-butyl-5,11-bis(4-tert-butylphenyl)-6,12-diphenyltetracene (TBRb)-doped PLQ was applied as a yellow liquid emitter. In order to form the liquid white light-emitting layer, the greenish-blue and yellow liquid emitters were alternately injected into the integrated microchannels. The fabricated electro-microfluidic device successfully exhibited white electroluminescence (EL) emission via simultaneous greenish-blue and yellow emissions under an applied voltage of 100 V. A white emission with Commission Internationale de l’Declairage (CIE) color coordinates of (0.40, 0.42) was also obtained; the emission corresponds to warm-white light. The proposed device has potential applications in subpixels of liquid-based microdisplays and for lighting. PMID:26439164

  1. Manufacturing methods and applications of membranes in microfluidics.

    Science.gov (United States)

    Chen, Xueye; Shen, Jienan; Hu, Zengliang; Huo, Xuyao

    2016-12-01

    Applications of membranes in microfluidics solved many thorny problems for analytical chemistry and bioscience, so that the use of membranes in microfluidics has been a topic of growing interest. Many different examples have been reported, demonstrating the versatile use of membranes. This work reviews a lot of applications of membranes in microfluidics. Membranes in microfluidics for applications including chemical reagents detection, gas detection, drug screening, cell, protein, microreactor, electrokinetical fluid, pump and valve and fluid transport control and so on, have been analyzed and discussed. In addition, the definition and basic concepts of membranes are summed up. And the methods of manufacturing membranes in microfluidics are discussed. This paper will provide a helpful reference to researchers who want to study applications of membranes in microfluidics.

  2. Digital Microfluidics Sample Analyzer

    Science.gov (United States)

    Pollack, Michael G.; Srinivasan, Vijay; Eckhardt, Allen; Paik, Philip Y.; Sudarsan, Arjun; Shenderov, Alex; Hua, Zhishan; Pamula, Vamsee K.

    2010-01-01

    Three innovations address the needs of the medical world with regard to microfluidic manipulation and testing of physiological samples in ways that can benefit point-of-care needs for patients such as premature infants, for which drawing of blood for continuous tests can be life-threatening in their own right, and for expedited results. A chip with sample injection elements, reservoirs (and waste), droplet formation structures, fluidic pathways, mixing areas, and optical detection sites, was fabricated to test the various components of the microfluidic platform, both individually and in integrated fashion. The droplet control system permits a user to control droplet microactuator system functions, such as droplet operations and detector operations. Also, the programming system allows a user to develop software routines for controlling droplet microactuator system functions, such as droplet operations and detector operations. A chip is incorporated into the system with a controller, a detector, input and output devices, and software. A novel filler fluid formulation is used for the transport of droplets with high protein concentrations. Novel assemblies for detection of photons from an on-chip droplet are present, as well as novel systems for conducting various assays, such as immunoassays and PCR (polymerase chain reaction). The lab-on-a-chip (a.k.a., lab-on-a-printed-circuit board) processes physiological samples and comprises a system for automated, multi-analyte measurements using sub-microliter samples of human serum. The invention also relates to a diagnostic chip and system including the chip that performs many of the routine operations of a central labbased chemistry analyzer, integrating, for example, colorimetric assays (e.g., for proteins), chemiluminescence/fluorescence assays (e.g., for enzymes, electrolytes, and gases), and/or conductometric assays (e.g., for hematocrit on plasma and whole blood) on a single chip platform.

  3. A microfluidic platform with a flow-balanced fluidic network for osteoarthritis diagnosis

    Science.gov (United States)

    Kim, Kangil; Park, Yoo Min; Yoon, Hyun C.; Yang, Sang Sik

    2013-05-01

    Osteoarthritis (OA) is one of the most common human diseases, and the occurrence of OA is likely to increase with the increase of population ages. The diagnosis of OA is based on patientrelevant measures, structural measures, and measurement of biomarkers that are released through joint metabolism. Traditionally, radiography or magnetic resonance imaging (MRI) is used to diagnose OA and predict its course. However, diagnostic imaging in OA provides only indirect information on pathology and treatment response. A sensing of OA based on the detection of biomarkers insignificantly improves the accuracy and sensitivity of diagnosis and reduces the cost compared with that of radiography or MRI. In our former study, we proposed microfluidic platform to detect biomarker of OA. But the platform can detect only one biomarker because it has one microfluidic channel. In this report, we proposes microfluidic platform that can detect several biomarkers. The proposed platform has three layers. The bottom layer has gold patterns on a Si substrate for optical sensing. The middle layer and top layer were fabricated by polydimethysiloxane (PDMS) using soft-lithography. The middle layer has four channels connecting top layer to bottom layer. The top layer consists of one sample injection inlet, and four antibody injection inlets. To this end, we designed a flow-balanced microfluidic network using analogy between electric and hydraulic systems. Also, the designed microfluidic network was confirmed by finite element model (FEM) analysis using COMSOL FEMLAB. To verify the efficiency of fabricated platform, the optical sensing test was performed to detect biomarker of OA using fluorescence microscope. We used cartilage oligomeric matrix protein (COMP) as biomarker because it reflects specific changes in joint tissues. The platform successfully detected various concentration of COMP (0, 100, 500, 1000 ng/ml) at each chamber. The effectiveness of the microfluidic platform was verified

  4. Rapid wasted-free microfluidic fabrication based on ink-jet approach for microfluidic sensing applications

    Science.gov (United States)

    Jarujareet, Ungkarn; Amarit, Rattasart; Sumriddetchkajorn, Sarun

    2016-11-01

    Realizing that current microfluidic chip fabrication techniques are time consuming and labor intensive as well as always have material leftover after chip fabrication, this research work proposes an innovative approach for rapid microfluidic chip production. The key idea relies on a combination of a widely-used inkjet printing method and a heat-based polymer curing technique with an electronic-mechanical control, thus eliminating the need of masking and molds compared to typical microfluidic fabrication processes. In addition, as the appropriate amount of polymer is utilized during printing, there is much less amount of material wasted. Our inkjet-based microfluidic printer can print out the desired microfluidic chip pattern directly onto a heated glass surface, where the printed polymer is suddenly cured. Our proof-of-concept demonstration for widely-used single-flow channel, Y-junction, and T-junction microfluidic chips shows that the whole microfluidic chip fabrication process requires only 3 steps with a fabrication time of 6 minutes.

  5. Integrated Microfluidic Reactors.

    Science.gov (United States)

    Lin, Wei-Yu; Wang, Yanju; Wang, Shutao; Tseng, Hsian-Rong

    2009-12-01

    Microfluidic reactors exhibit intrinsic advantages of reduced chemical consumption, safety, high surface-area-to-volume ratios, and improved control over mass and heat transfer superior to the macroscopic reaction setting. In contract to a continuous-flow microfluidic system composed of only a microchannel network, an integrated microfluidic system represents a scalable integration of a microchannel network with functional microfluidic modules, thus enabling the execution and automation of complicated chemical reactions in a single device. In this review, we summarize recent progresses on the development of integrated microfluidics-based chemical reactors for (i) parallel screening of in situ click chemistry libraries, (ii) multistep synthesis of radiolabeled imaging probes for positron emission tomography (PET), (iii) sequential preparation of individually addressable conducting polymer nanowire (CPNW), and (iv) solid-phase synthesis of DNA oligonucleotides. These proof-of-principle demonstrations validate the feasibility and set a solid foundation for exploring a broad application of the integrated microfluidic system.

  6. Commercialization of microfluidic devices.

    Science.gov (United States)

    Volpatti, Lisa R; Yetisen, Ali K

    2014-07-01

    Microfluidic devices offer automation and high-throughput screening, and operate at low volumes of consumables. Although microfluidics has the potential to reduce turnaround times and costs for analytical devices, particularly in medical, veterinary, and environmental sciences, this enabling technology has had limited diffusion into consumer products. This article analyzes the microfluidics market, identifies issues, and highlights successful commercialization strategies. Addressing niche markets and establishing compatibility with existing workflows will accelerate market penetration. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Two-dimensional isoelectric focusing OFFGEL and microfluidic lab-on-chip electrophoresis for assessing dissolved proteins in seawater.

    Science.gov (United States)

    García-Otero, Natalia; Peña-Vázquez, Elena; Barciela-Alonso, María Carmen; Bermejo-Barrera, Pilar; Moreda-Piñeiro, Antonio

    2013-06-18

    Dissolved proteins were assessed in surface and deep seawater by two-dimensional isoelectric focusing (IEF) OFFGEL-lab-on-chip (LOC) electrophoresis after tangential flow ultrafiltration followed by centrifugal ultrafiltration (preconcentration factor of 3000). Dissolved protein isolation was performed by treating the ultrafiltrated retentate with cold acetone and also with chloroform as precipitating reagents. The best electrophoretic behavior of the isolated proteins was obtained after protein precipitation with chloroform before different rinsing stages for removing methanol and water interferences. Metals bound to proteins in the different OFFGEL fractions were assessed by inductively coupled plasma-optical emission spectrometry and electrothermal atomic absorption spectrometry, under optimized operating conditions. Experiments regarding stability of the metal-binding proteins [superoxide dismutase (SOD) and alcohol dehydrogenase (ADH) as protein models] showed the integrity of the Zn-binding SOD/ADH under the OFFGEL electrophoretic conditions. However, stability of Cu bound to SOD is not guaranteed. The first electrophoretic dimension (IEF OFFGEL) showed that dissolved proteins in surface seawater exhibit alkaline isoelectric points (pIs of 8.10 and 8.37) and also acid Ips (4.82, 5.13, 5.43, and 5.73), while LOC showed that the isolated proteins exhibit a spread molecular weight range (within 15 - 63 kDa); although, high molecular weights were the most commonly found. Regarding deep seawater, isolated proteins were of acid Ips (from 3.30 to 4.22) and low molecular weight (within the 21-24 kDa range). Elements such as Cd, Cu, Mn, and Ni were mainly associated with dissolved proteins of alkaline pIs in surface seawater, while Zn was mainly associated to proteins of acid pIs. However, only Cu and Mn were found to be bound to dissolved proteins of higher Ips in deep seawater, and the amount of Mn (from 68 to 84 μg L(-1)) was higher than that found in dissolved

  8. Predicting Droplet Formation on Centrifugal Microfluidic Platforms

    Science.gov (United States)

    Moebius, Jacob Alfred

    Centrifugal microfluidics is a widely known research tool for biological sample and water quality analysis. Currently, the standard equipment used for such diagnostic applications include slow, bulky machines controlled by multiple operators. These machines can be condensed into a smaller, faster benchtop sample-to-answer system. Sample processing is an important step taken to extract, isolate, and convert biological factors, such as nucleic acids or proteins, from a raw sample to an analyzable solution. Volume definition is one such step. The focus of this thesis is the development of a model predicting monodispersed droplet formation and the application of droplets as a technique for volume definition. First, a background of droplet microfluidic platforms is presented, along with current biological analysis technologies and the advantages of integrating such technologies onto microfluidic platforms. Second, background and theories of centrifugal microfluidics is given, followed by theories relevant to droplet emulsions. Third, fabrication techniques for centrifugal microfluidic designs are discussed. Finally, the development of a model for predicting droplet formation on the centrifugal microfluidic platform are presented for the rest of the thesis. Predicting droplet formation analytically based on the volumetric flow rates of the continuous and dispersed phases, the ratios of these two flow rates, and the interfacial tension between the continuous and dispersed phases presented many challenges, which will be discussed in this work. Experimental validation was completed using continuous phase solutions of different interfacial tensions. To conclude, prospective applications are discussed with expected challenges.

  9. Tunable Microfluidic Dye Laser

    DEFF Research Database (Denmark)

    Olsen, Brian Bilenberg; Helbo, Bjarne; Kutter, Jörg Peter

    2003-01-01

    We present a tunable microfluidic dye laser fabricated in SU-8. The tunability is enabled by integrating a microfluidic diffusion mixer with an existing microfluidic dye laser design by Helbo et al. By controlling the relative flows in the mixer between a dye solution and a solvent......, the concentration of dye in the laser cavity can be adjusted, allowing the wavelength to be tuned. Wavelength tuning controlled by the dye concentration was demonstrated with macroscopic dye lasers already in 1971, but this principle only becomes practically applicable by the use of microfluidic mixing...

  10. The use of protein patterns in genetic diversity analysis in some Brassica napus cultivars

    Directory of Open Access Journals (Sweden)

    Roya Razavizadeh

    2013-11-01

    Full Text Available In this study, protein variations of seeds and five-day old cotyledonal leaves of four selected Brassica napus cultivars including Elite, Ocapy, Tasilo and Zarfam were analyzed by SDS-PAGE to identify protein markers. The amount of total soluble protein of seed storage proteins did not show significant differences in all cultivars whereas it was different in cotyledonal leaves. Protein patterns of seeds and cotyledonal leaves showed significant differences using SDS-PAGE and consequence analysis of bands by ImageJ program. Relative expression of six protein bands in seeds and five-day old cotyledonal leaves were significantly different. Three protein markers were identified by protein patterns of seed and cotyledonal leaves. The results of relationship analysis based on presence and absence of the specific protein bands in protein pattern of seed storage proteins showed that Tasilo and Elite cultivars had the highest similarities.

  11. Parallel imaging microfluidic cytometer.

    Science.gov (United States)

    Ehrlich, Daniel J; McKenna, Brian K; Evans, James G; Belkina, Anna C; Denis, Gerald V; Sherr, David H; Cheung, Man Ching

    2011-01-01

    By adding an additional degree of freedom from multichannel flow, the parallel microfluidic cytometer (PMC) combines some of the best features of fluorescence-activated flow cytometry (FCM) and microscope-based high-content screening (HCS). The PMC (i) lends itself to fast processing of large numbers of samples, (ii) adds a 1D imaging capability for intracellular localization assays (HCS), (iii) has a high rare-cell sensitivity, and (iv) has an unusual capability for time-synchronized sampling. An inability to practically handle large sample numbers has restricted applications of conventional flow cytometers and microscopes in combinatorial cell assays, network biology, and drug discovery. The PMC promises to relieve a bottleneck in these previously constrained applications. The PMC may also be a powerful tool for finding rare primary cells in the clinic. The multichannel architecture of current PMC prototypes allows 384 unique samples for a cell-based screen to be read out in ∼6-10 min, about 30 times the speed of most current FCM systems. In 1D intracellular imaging, the PMC can obtain protein localization using HCS marker strategies at many times for the sample throughput of charge-coupled device (CCD)-based microscopes or CCD-based single-channel flow cytometers. The PMC also permits the signal integration time to be varied over a larger range than is practical in conventional flow cytometers. The signal-to-noise advantages are useful, for example, in counting rare positive cells in the most difficult early stages of genome-wide screening. We review the status of parallel microfluidic cytometry and discuss some of the directions the new technology may take.

  12. Microfluidic Devices for Blood Fractionation

    Directory of Open Access Journals (Sweden)

    Chwee Teck Lim

    2011-07-01

    Full Text Available Blood, a complex biological fluid, comprises 45% cellular components suspended in protein rich plasma. These different hematologic components perform distinct functions in vivo and thus the ability to efficiently fractionate blood into its individual components has innumerable applications in both clinical diagnosis and biological research. Yet, processing blood is not trivial. In the past decade, a flurry of new microfluidic based technologies has emerged to address this compelling problem. Microfluidics is an attractive solution for this application leveraging its numerous advantages to process clinical blood samples. This paper reviews the various microfluidic approaches realized to successfully fractionate one or more blood components. Techniques to separate plasma from hematologic cellular components as well as isolating blood cells of interest including certain rare cells are discussed. Comparisons based on common separation metrics including efficiency (sensitivity, purity (selectivity, and throughput will be presented. Finally, we will provide insights into the challenges associated with blood-based separation systems towards realizing true point-of-care (POC devices and provide future perspectives.

  13. Fabrication and characterization of mesoscale protein patterns using atomic force microscopy (AFM)

    Science.gov (United States)

    Gao, Pei

    2011-07-01

    A versatile AFM local oxidation lithography was developed for fabricating clean protein patterns ranging from nanometer to sub-millimeter scale on octadecyltrichlorosilane (OTS) layer of Si (100) wafer. This protein patterning method can generate bio-active protein pattern with a clean background without the need of the anti-fouling the surface or repetitive rinsing. As a model system, lysozyme protein patterns were investigated through their binding reactions with antibodies and aptamers by AFM. Polyclonal anti-lysozyme antibodies and anti-lysozyme aptamer are found to preferentially bind to the lysozyme molecules on the edge of a protein pattern before their binding to the interior ones. It was also demonstrated that the topography of the immobilized protein pattern affects the antibody binding direction. We found that the anti-lysozyme antibodies binding to the edge lysozyme molecules on the half-buried pattern started from the top but the binding on the extruded pattern started from the side because of their different spatial accessibility. In addition, after incubating lysozyme pattern with anti-lysozyme aptamer in buffer solution for enough long time, some fractal-shaped aptamer fibers with 1-6nm high and up to tens of micrometers long were formed by the self-assembling of aptamer molecules on the surface. The aptamer fibers anchor specifically on the edge of protein patterns, which originates from the biospecific recognition between the aptamer and its target protein. Once these edge-bound fibers have formed, they can serve as scaffolds for further assembly processes. We used these aptamer fibers as templates to fabricate palladium and streptavidin nanowires, which anchored on the pattern edges and never cross over or collapse over each other. The aptamer fiber scaffold potentially can lead to an effective means to fabricate and interface nanowires to existing surface patterns. KEYWORDS: Atomic Force Microscopy (AFM), Protein Patterns, Lysozyme, Aptamer

  14. Unconventional microfluidics: expanding the discipline.

    Science.gov (United States)

    Nawaz, Ahmad Ahsan; Mao, Xiaole; Stratton, Zackary S; Huang, Tony Jun

    2013-04-21

    Since its inception, the discipline of microfluidics has been harnessed for innovations in the biomedicine/chemistry fields-and to great effect. This success has had the natural side-effect of stereotyping microfluidics as a platform for medical diagnostics and miniaturized lab processes. But microfluidics has more to offer. And very recently, some researchers have successfully applied microfluidics to fields outside its traditional domains. In this Focus article, we highlight notable examples of such "unconventional" microfluidics applications (e.g., robotics, electronics). It is our hope that these early successes in unconventional microfluidics prompt further creativity, and inspire readers to expand the microfluidics discipline.

  15. Trehalose glycopolymer resists allow direct writing of protein patterns by electron-beam lithography

    Science.gov (United States)

    Bat, Erhan; Lee, Juneyoung; Lau, Uland Y.; Maynard, Heather D.

    2015-03-01

    Direct-write patterning of multiple proteins on surfaces is of tremendous interest for a myriad of applications. Precise arrangement of different proteins at increasingly smaller dimensions is a fundamental challenge to apply the materials in tissue engineering, diagnostics, proteomics and biosensors. Herein, we present a new resist that protects proteins during electron-beam exposure and its application in direct-write patterning of multiple proteins. Polymers with pendant trehalose units are shown to effectively crosslink to surfaces as negative resists, while at the same time providing stabilization to proteins during the vacuum and electron-beam irradiation steps. In this manner, arbitrary patterns of several different classes of proteins such as enzymes, growth factors and immunoglobulins are realized. Utilizing the high-precision alignment capability of electron-beam lithography, surfaces with complex patterns of multiple proteins are successfully generated at the micrometre and nanometre scale without requiring cleanroom conditions.

  16. Microfluidic PDMS on paper (POP) devices.

    Science.gov (United States)

    Shangguan, Jin-Wen; Liu, Yu; Pan, Jian-Bin; Xu, Bi-Yi; Xu, Jing-Juan; Chen, Hong-Yuan

    2016-12-20

    In this paper, we propose a generalized concept of microfluidic polydimethylsiloxane (PDMS) on paper (POP) devices, which combines well the merits of paper chips and PDMS chips. First, we optimized the conditions for accurate PDMS spatial patterning on paper, based on screen printing and a high temperature enabled superfast curing technique, which enables PDMS patterning to an accuracy of tens of microns in less than ten seconds. This, in turn, makes it available for seamless, reversible and reliable integration of the resulting paper layer with other PDMS channel structures. The integrated POP devices allow for both porous paper and smooth channels to be spatially defined on the devices, greatly extending the flexibility for designers to be able to construct powerful functional structures. To demonstrate the versatility of this design, a prototype POP device for the colorimetric analysis of liver function markers, serum protein, alkaline phosphatase (ALP) and aspartate aminotransferase (AST), was constructed. On this POP device, quantitative sample loading, mixing and multiplex analysis have all been realized.

  17. Easy fabrication of thin membranes with through holes. Application to protein patterning.

    Directory of Open Access Journals (Sweden)

    Thomas Masters

    Full Text Available Since protein patterning on 2D surfaces has emerged as an important tool in cell biology, the development of easy patterning methods has gained importance in biology labs. In this paper we present a simple, rapid and reliable technique to fabricate thin layers of UV curable polymer with through holes. These membranes are as easy to fabricate as microcontact printing stamps and can be readily used for stencil patterning. We show how this microfabrication scheme allows highly reproducible and highly homogeneous protein patterning with micron sized resolution on surfaces as large as 10 cm(2. Using these stencils, fragile proteins were patterned without loss of function in a fully hydrated state. We further demonstrate how intricate patterns of multiple proteins can be achieved by stacking the stencil membranes. We termed this approach microserigraphy.

  18. Microfluidics and microbial engineering.

    Science.gov (United States)

    Kou, Songzi; Cheng, Danhui; Sun, Fei; Hsing, I-Ming

    2016-02-01

    The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.

  19. Microfluidic Diffusion Viscometer for Rapid Analysis of Complex Solutions.

    Science.gov (United States)

    Arosio, Paolo; Hu, Kevin; Aprile, Francesco A; Müller, Thomas; Knowles, Tuomas P J

    2016-04-05

    The viscosity of complex solutions is a physical property of central relevance for a large number of applications in material, biological, and biotechnological sciences. Here we demonstrate a microfluidic technology to measure the viscosity of solutions by following the advection and diffusion of tracer particles under steady-state flow. We validate our method with standard water-glycerol mixtures, and then we apply this microfluidic diffusion viscometer to measure the viscosity of protein solutions at high concentrations as well as of a crude cell lysate. Our approach exhibits a series of attractive features, including analysis time on the order of seconds and the consumption of a few μL of sample, as well as the possibility to readily integrate the microfluidic viscometer in other instrument platforms or modular microfluidic devices. These characteristics make microfluidic diffusion viscometry an attractive approach in automated processes in biotechnology and health-care sciences where fast measurements with limited amount of sample consumption are required.

  20. Integrated multifunctional microfluidics for automated proteome analyses.

    Science.gov (United States)

    Osiri, John K; Shadpour, Hamed; Witek, Małgorzata A; Soper, Steven A

    2011-01-01

    Proteomics is a challenging field for realizing totally integrated microfluidic systems for complete proteome processing due to several considerations, including the sheer number of different protein types that exist within most proteomes, the large dynamic range associated with these various protein types, and the diverse chemical nature of the proteins comprising a typical proteome. For example, the human proteome is estimated to have >10(6) different components with a dynamic range of >10(10). The typical processing pipeline for proteomics involves the following steps: (1) selection and/or extraction of the particular proteins to be analyzed; (2) multidimensional separation; (3) proteolytic digestion of the protein sample; and (4) mass spectral identification of either intact proteins (top-down proteomics) or peptide fragments generated from proteolytic digestions (bottom-up proteomics). Although a number of intriguing microfluidic devices have been designed, fabricated and evaluated for carrying out the individual processing steps listed above, work toward building fully integrated microfluidic systems for protein analysis has yet to be realized. In this chapter, information will be provided on the nature of proteomic analysis in terms of the challenges associated with the sample type and the microfluidic devices that have been tested to carry out individual processing steps. These include devices such as those for multidimensional electrophoretic separations, solid-phase enzymatic digestions, and solid-phase extractions, all of which have used microfluidics as the functional platform for their implementation. This will be followed by an in-depth review of microfluidic systems, which are defined as units possessing two or more devices assembled into autonomous systems for proteome processing. In addition, information will be provided on the challenges involved in integrating processing steps into a functional system and the approaches adopted for device

  1. Nanomaterials meet microfluidics.

    Science.gov (United States)

    Pumera, Martin

    2011-05-28

    Nanomaterials and lab-on-a-chip platforms have undergone enormous development during the past decade. Here, we present an overview of how microfluidics benefited from the use of nanomaterials for the enhanced separation and detection of analytes. We also discuss how nanomaterials benefit from microfluidics in terms of synthesis and in terms of the simulation of environments for nanomotors and nanorobots. In our opinion, the "marriage" of nanomaterials and microfluidics is highly beneficial and is expected to solve vital challenges in related fields.

  2. Integration of agglutination assay for protein detection in microfluidic disc using Blu-ray optical pickup unit and optical fluid scanning

    DEFF Research Database (Denmark)

    Uddin, Rokon; Burger, Robert; Donolato, Marco;

    2015-01-01

    We present a novel strategy for thrombin detection by combining a magnetic bead based agglutination assay and low-cost microfluidic disc. The detection method is based on an optomagnetic readout system implemented using a Blu-ray optical pickup unit (OPU) as main optoelectronic component. The assay...

  3. Integration of agglutination assay for protein detection in microfluidic disc using Blu-ray optical pickup unit and optical fluid scanning

    DEFF Research Database (Denmark)

    Uddin, Rokon; Burger, Robert; Donolato, Marco;

    2015-01-01

    We present a novel strategy for thrombin detection by combining a magnetic bead based agglutination assay and low-cost microfluidic disc. The detection method is based on an optomagnetic readout system implemented using a Blu-ray optical pickup unit (OPU) as main optoelectronic component. The ass...

  4. Electroporation of cells in microfluidic droplets.

    Science.gov (United States)

    Zhan, Yihong; Wang, Jun; Bao, Ning; Lu, Chang

    2009-03-01

    Droplet-based microfluidics has raised a lot of interest recently due to its wide applications to screening biological/chemical assays with high throughput. Despite the advances on droplet-based assays involving cells, gene delivery methods that are compatible with the droplet platform have been lacking. In this report, we demonstrate a simple microfluidic device that encapsulates cells into aqueous droplets and then electroporates the encapsulated cells. The electroporation occurs when the cell-containing droplets (in oil) flow through a pair of microelectrodes with a constant voltage established in between. We investigate the parameters and characteristics of the electroporation. We demonstrate delivering enhanced green fluorescent protein (EGFP) plasmid into Chinese hamster ovary (CHO) cells. We envision the application of this technique to high-throughput functional genomics studies based on droplet microfluidics.

  5. Characterization of white grub (Melolonthidae; Coleoptera in salak plantation based on morphology and protein banding pattern

    Directory of Open Access Journals (Sweden)

    SUGIYARTO

    2009-07-01

    Full Text Available Maryati KT, Sugiyarto. 2010. Characterization of white grub (Melolonthidae; Coleoptera in salak plantation based on morphology and protein banding pattern. Nusantara Bioscience 1: 72-77. This research aims to find out the white grub (Melolonthidae; Coleoptera variability based on the morphological characteristic and protein banding pattern found in ”salak pondoh” farm in Regencies of Sleman, Yogyakarta and Magelang, Central Java. Each area has five sampling points. Morphological analysis on white grub was conducted using descriptive method and analysis on protein banding pattern was conducted using qualitative analysis based on the presence or absent of band pattern on the gel, and qualitatively based on the relative mobility value (Rf of protein. The result indicated that the white grub in Sleman and Magelang, based on morphology characteristic is only one species, namely Holothricia sp. Based on the protein banding pattern, the white grub sample have differences of protein band number and protein molecular weight. Key words: Salacca zalacca, white grub, morphology, protein banding pattern.Abstrak. Maryati KT, Sugiyarto. 2010. Karakterisasi lundi putih (Melolonthidae: Coleoptera pada pertanaman salak berdasarkan ciri morfologi dan pola pita protein. Nusantara Bioscience 1: 72-77. Penelitian ini bertujuan untuk mengetahui keanekaragaman lundi putih (Melolonthidae; Coleoptera berdasarkan ciri morfologi dan pola pita protein yang ditemukan di lahan pertanaman salak pondoh di Kabupaten Sleman, Yogyakarta dan Kabupaten Magelang, Jawa Tengah. Pada masing-masing wilayah diambil lima titik sampling. Analisis morfologi lundi putih digunakan metode deskriptif, dan analisis pola pita protein digunakan analisis kualitatif berdasarkan muncul tidaknya pola pita pada gel, dan secara kuantitatif berdasarkan nilai mobilitas relatif protein (RF. Hasil penelitian menunjukkan bahwa sampel lundi putih di Kabupaten Sleman dan Magelang, berdasar karakter

  6. Punch Card Programmable Microfluidics

    CERN Document Server

    Korir, George

    2014-01-01

    Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes a series of operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series ...

  7. Cell manipulation in microfluidics.

    Science.gov (United States)

    Yun, Hoyoung; Kim, Kisoo; Lee, Won Gu

    2013-06-01

    Recent advances in the lab-on-a-chip field in association with nano/microfluidics have been made for new applications and functionalities to the fields of molecular biology, genetic analysis and proteomics, enabling the expansion of the cell biology field. Specifically, microfluidics has provided promising tools for enhancing cell biological research, since it has the ability to precisely control the cellular environment, to easily mimic heterogeneous cellular environment by multiplexing, and to analyze sub-cellular information by high-contents screening assays at the single-cell level. Various cell manipulation techniques in microfluidics have been developed in accordance with specific objectives and applications. In this review, we examine the latest achievements of cell manipulation techniques in microfluidics by categorizing externally applied forces for manipulation: (i) optical, (ii) magnetic, (iii) electrical, (iv) mechanical and (v) other manipulations. We furthermore focus on history where the manipulation techniques originate and also discuss future perspectives with key examples where available.

  8. Microfluidics in inorganic chemistry.

    Science.gov (United States)

    Abou-Hassan, Ali; Sandre, Olivier; Cabuil, Valérie

    2010-08-23

    The application of microfluidics in chemistry has gained significant importance in the recent years. Miniaturized chemistry platforms provide controlled fluid transport, rapid chemical reactions, and cost-saving advantages over conventional reactors. The advantages of microfluidics have been clearly established in the field of analytical and bioanalytical sciences and in the field of organic synthesis. It is less true in the field of inorganic chemistry and materials science; however in inorganic chemistry it has mostly been used for the separation and selective extraction of metal ions. Microfluidics has been used in materials science mainly for the improvement of nanoparticle synthesis, namely metal, metal oxide, and semiconductor nanoparticles. Microfluidic devices can also be used for the formulation of more advanced and sophisticated inorganic materials or hybrids.

  9. Microfluidic chemical reaction circuits

    Science.gov (United States)

    Lee, Chung-cheng; Sui, Guodong; Elizarov, Arkadij; Kolb, Hartmuth C.; Huang, Jiang; Heath, James R.; Phelps, Michael E.; Quake, Stephen R.; Tseng, Hsian-rong; Wyatt, Paul; Daridon, Antoine

    2012-06-26

    New microfluidic devices, useful for carrying out chemical reactions, are provided. The devices are adapted for on-chip solvent exchange, chemical processes requiring multiple chemical reactions, and rapid concentration of reagents.

  10. Microfluidic Bead Suspension Hopper

    OpenAIRE

    Price, Alexander K.; MacConnell, Andrew B.; Paegel, Brian M.

    2014-01-01

    Many high-throughput analytical platforms, from next-generation DNA sequencing to drug discovery, rely on beads as carriers of molecular diversity. Microfluidic systems are ideally suited to handle and analyze such bead libraries with high precision and at minute volume scales; however, the challenge of introducing bead suspensions into devices before they sediment usually confounds microfluidic handling and analysis. We developed a bead suspension hopper that exploits sedimentation to load b...

  11. Punch Card Programmable Microfluidics

    OpenAIRE

    George Korir; Manu Prakash

    2014-01-01

    Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external component...

  12. 微射流均质预处理提高大豆分离蛋白酶解效率及酶解产物乳化性能%Microfluidization pretreatment improving enzymatic hydrolysis of soy isolated protein and emulsifying properties of hydrolysates

    Institute of Scientific and Technical Information of China (English)

    陈林; 吴克刚; 柴向华; 余林

    2015-01-01

    structure of globular proteins and break up protein aggregates, which may cause the exposure of more cleavage sites. However, limited information is available concerning the effects of microfluidization pretreatment on the enzymatic hydrolysis pattern of soy proteins or on the emulsifying properties of its hydrolysates. Hence, the objective of this work was to study the effects of combining microfluidization pretreatment and controlled enzymatic hydrolysis using Papain on the emulsifying properties of soy protein isolates (SPI). Microfluidizaiton pretreated SPI (MSPI) was prepared using a microfluidizer at a specific pressure level of 120 MPa. Papain was used as protease for the preparation of SPI hydrolysates (SPIH) and MSPI hydrolysates (MSPIH). Oil-in-water emulsions (20% v/v sunflower oil, 20 g/L protein sample, pH=7.0) were formed by SPIH and MSPIH with various DH (degree of hydrolysis). And the analysis of mean droplet sizes and microstructures of these emulsions showed that emulsions formed by control SPI and SPIH were unstable to bridging flocculation, suggesting their poor emulsifying capability. This findings may be explained by the fact that there were insufficient soluble protein with high surface activity existed in control SPI and SPIH. In contrast, some MSPIH (DH was 1.3%-1.7%) showed that the emulsifying capability and emulsions stabilization against bridging flocculation were markedly improved. Compared with control SPI and SPIH (0.6% DH), MSPIH (1.7% DH) was capable of producing a stable fine emulsion (d43≈1.6μm) at a lower concentration (30 g/L), suggesting its better emulsifying capability. Composition of subunits, protein solubility (NSI), surface hydrophobicity (H0) and molecular weight distribution of SPIH and MSPIH have been measured in order to study the underpinning mechanisms of improving emulsifying capability for SPIH and MSPIH. The analysis of sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of different hydrolysates showed

  13. Microfluidic parallel circuit for measurement of hydraulic resistance.

    Science.gov (United States)

    Choi, Sungyoung; Lee, Myung Gwon; Park, Je-Kyun

    2010-08-31

    We present a microfluidic parallel circuit that directly compares the test channel of an unknown hydraulic resistance with the reference channel with a known resistance, thereby measuring the unknown resistance without any measurement setup, such as standard pressure gauges. Many of microfluidic applications require the precise transport of fluid along a channel network with complex patterns. Therefore, it is important to accurately characterize and measure the hydraulic resistance of each channel segment, and determines whether the device principle works well. However, there is no fluidic device that includes features, such as the ability to diagnose microfluidic problems by measuring the hydraulic resistance of a microfluidic component in microscales. To address the above need, we demonstrate a simple strategy to measure an unknown hydraulic resistance, by characterizing the hydraulic resistance of microchannels with different widths and defining an equivalent linear channel of a microchannel with repeated patterns of a sudden contraction and expansion.

  14. MEMS in microfluidic channels.

    Energy Technology Data Exchange (ETDEWEB)

    Ashby, Carol Iris Hill; Okandan, Murat; Michalske, Terry A.; Sounart, Thomas L.; Matzke, Carolyn M.

    2004-03-01

    Microelectromechanical systems (MEMS) comprise a new class of devices that include various forms of sensors and actuators. Recent studies have shown that microscale cantilever structures are able to detect a wide range of chemicals, biomolecules or even single bacterial cells. In this approach, cantilever deflection replaces optical fluorescence detection thereby eliminating complex chemical tagging steps that are difficult to achieve with chip-based architectures. A key challenge to utilizing this new detection scheme is the incorporation of functionalized MEMS structures within complex microfluidic channel architectures. The ability to accomplish this integration is currently limited by the processing approaches used to seal lids on pre-etched microfluidic channels. This report describes Sandia's first construction of MEMS instrumented microfluidic chips, which were fabricated by combining our leading capabilities in MEMS processing with our low-temperature photolithographic method for fabricating microfluidic channels. We have explored in-situ cantilevers and other similar passive MEMS devices as a new approach to directly sense fluid transport, and have successfully monitored local flow rates and viscosities within microfluidic channels. Actuated MEMS structures have also been incorporated into microfluidic channels, and the electrical requirements for actuation in liquids have been quantified with an elegant theory. Electrostatic actuation in water has been accomplished, and a novel technique for monitoring local electrical conductivities has been invented.

  15. Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks.

    Science.gov (United States)

    Ramakrishnan, Saminathan; Subramaniam, Sivaraman; Stewart, A Francis; Grundmeier, Guido; Keller, Adrian

    2016-11-16

    DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.

  16. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    Energy Technology Data Exchange (ETDEWEB)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist invariants across lattices related to fundamental properties of the protein folding process. This paper considers whether performance-guaranteed approximability is such an invariant for HP lattice models. The authors define a master approximation algorithm that has provable performance guarantees provided that a specific sublattice exists within a given lattice. They describe a broad class of crystal lattices that are approximable, which further suggests that approximability is a general property of HP lattice models.

  17. Patterns of molecular evolution in pathogenesis-related proteins

    OpenAIRE

    Scherer,Nicole M.; Thompson,Claudia E.; Freitas,Loreta B.; Bonatto, Sandro L.; Salzano,Francisco M.

    2005-01-01

    The genes encoding 13 classes of pathogenesis-related (PR) proteins were examined for positive selection using maximum-likelihood (ML) models of codon substitution. The study involved 194 sequences from 54 species belonging to 37 genera. Although the sizes of the sequences examined varied from 237 bp for PR12 to 1,110 bp for PR7, most classes (9 out of 13) contained sequences made up of more than 400 nucleotides. Signs of positive selection were obtained for sites in PR proteins 4, 6, 8, 9 an...

  18. Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site

    Energy Technology Data Exchange (ETDEWEB)

    Valley, Cary T.; Porter, Douglas F.; Qiu, Chen; Campbell, Zachary T.; Tanaka Hall, Traci M.; Wickens, Marvin (NIEHS); (UW)

    2012-06-28

    mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even closely related noncognate sites. In the PUF [Pumilio and fem-3 binding factor (FBF)] family of RNA binding proteins, individual proteins discriminate differences in the length and sequence of binding sites, allowing each PUF to bind a distinct battery of mRNAs. Here, we show that despite these differences, the pattern of RNA interactions is conserved among PUF proteins: the two ends of the PUF protein make critical contacts with the two ends of the RNA sites. Despite this conserved 'two-handed' pattern of recognition, the RNA sequence is flexible. Among the binding sites of yeast Puf4p, RNA sequence dictates the pattern in which RNA bases are flipped away from the binding surface of the protein. Small differences in RNA sequence allow new modes of control, recruiting Puf5p in addition to Puf4p to a single site. This embedded information adds a new layer of biological meaning to the connections between RNA targets and PUF proteins.

  19. Highly efficient and selective isolation of rare tumor cells using a microfluidic chip with wavy-herringbone micro-patterned surfaces.

    Science.gov (United States)

    Wang, Shunqiang; Thomas, Antony; Lee, Elaine; Yang, Shu; Cheng, Xuanhong; Liu, Yaling

    2016-04-07

    Circulating tumor cells (CTCs) in peripheral blood have been recognized as a general biomarker for diagnosing cancer and providing guidance for personalized treatments. Yet due to their rarity, the challenge for their clinical utility lies in the efficient isolation while avoiding the capture of other non-targeted white blood cells (WBCs). In this paper, a wavy-herringbone (HB) microfluidic chip coated with antibody directly against epithelial cell adhesion molecule (anti-EpCAM) was developed for highly efficient and selective isolation of tumor cells from tumor cell-spiked whole blood samples. By extending the concept of the hallmark HB-Chip in the literature, the wavy-HB chip not only achieves high capture efficiency (up to 85.0%) by micro-vortexes induced by HB structures, but also achieves high purity (up to 39.4%) due to the smooth wavy microstructures. These smooth wavy-HB structures eliminate the ultra-low shear rate regions in the traditional grooved-HB structures that lead to non-specific trapping of cells. Compared with the grooved-HB chip with sharp corners, the wavy-HB chip shows significantly higher purity while maintaining similarly high capture efficiency. Furthermore, the wavy-HB chip has up to 11% higher captured cell viability over the grooved-HB chip. The distributions of tumor cells and WBCs along the grooves and waves are investigated to help understand the mechanisms behind the better performance of the wavy-HB chip. The wavy-HB chip may serve as a promising platform for CTC capture and cancer diagnosis.

  20. Punch card programmable microfluidics.

    Science.gov (United States)

    Korir, George; Prakash, Manu

    2015-01-01

    Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of 15 on-chip pumps with enhanced mixing, normally-closed valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word "PUNCHCARD MICROFLUIDICS" using the droplet generator. Multiplexing is demonstrated by implementing an example colorimetric water quality assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world.

  1. Punch card programmable microfluidics.

    Directory of Open Access Journals (Sweden)

    George Korir

    Full Text Available Small volume fluid handling in single and multiphase microfluidics provides a promising strategy for efficient bio-chemical assays, low-cost point-of-care diagnostics and new approaches to scientific discoveries. However multiple barriers exist towards low-cost field deployment of programmable microfluidics. Incorporating multiple pumps, mixers and discrete valve based control of nanoliter fluids and droplets in an integrated, programmable manner without additional required external components has remained elusive. Combining the idea of punch card programming with arbitrary fluid control, here we describe a self-contained, hand-crank powered, multiplex and robust programmable microfluidic platform. A paper tape encodes information as a series of punched holes. A mechanical reader/actuator reads these paper tapes and correspondingly executes operations onto a microfluidic chip coupled to the platform in a plug-and-play fashion. Enabled by the complexity of codes that can be represented by a series of holes in punched paper tapes, we demonstrate independent control of 15 on-chip pumps with enhanced mixing, normally-closed valves and a novel on-demand impact-based droplet generator. We demonstrate robustness of operation by encoding a string of characters representing the word "PUNCHCARD MICROFLUIDICS" using the droplet generator. Multiplexing is demonstrated by implementing an example colorimetric water quality assays for pH, ammonia, nitrite and nitrate content in different water samples. With its portable and robust design, low cost and ease-of-use, we envision punch card programmable microfluidics will bring complex control of microfluidic chips into field-based applications in low-resource settings and in the hands of children around the world.

  2. Topographic patterns of vascular disease: HOX proteins as determining factors?

    Institute of Scientific and Technical Information of China (English)

    Richard; P; Visconti; Alexander; Awgulewitsch

    2015-01-01

    Steadily increasing evidence supports the idea that genetic diversities in the vascular bed are, in addition to hemodynamic influences, a major contributing factor in determining region-specific cardiovascular disease susceptibility. Members of the phylogenetically highly conserved Hox gene family of developmental regulators have to be viewed as prime candidates for determining these regional genetic differences in the vasculature. During embryonic patterning, the regionally distinct and precisely choreographed expression patterns of HOX transcription factors are essential for the correct specification of positional identities. Apparently, these topographic patterns are to some degree retained in certain adult tissues, including the circulatory system. While an understanding of the functional significance of these localized Hox activities in adult blood vessels is only beginning to emerge, an argument can be made for a role of Hox genes in the maintenance of vessel wall homeostasis and functional integrity on the one hand, and in regulating the development and progression of regionally restricted vascular pathologies, on the other. Initial functional studies in animal models, as well as data from clinical studies provide some level of support for this view. The data suggest that putative genetic regulatory networks of Hox-dependent cardiovascular disease processes include genes of diverse functional categories(extracellular matrix remodeling, transmembrane signaling, cell cycle control, inflammatory response, transcriptional control, etc.), as potential targets in both vascular smooth muscle and endothelial cells, as well as cell populations residing in the adventitia.

  3. Protein patterns of black fungi under simulated Mars-like conditions

    Science.gov (United States)

    Zakharova, Kristina; Marzban, Gorji; de Vera, Jean-Pierre; Lorek, Andreas; Sterflinger, Katja

    2014-05-01

    Two species of microcolonial fungi - Cryomyces antarcticus and Knufia perforans - and a species of black yeasts-Exophiala jeanselmei - were exposed to thermo-physical Mars-like conditions in the simulation chamber of the German Aerospace Center. In this study the alterations at the protein expression level from various fungi species under Mars-like conditions were analyzed for the first time using 2D gel electrophoresis. Despite of the expectations, the fungi did not express any additional proteins under Mars simulation that could be interpreted as stress induced HSPs. However, up-regulation of some proteins and significant decreasing of protein number were detected within the first 24 hours of the treatment. After 4 and 7 days of the experiment protein spot number was increased again and the protein patterns resemble the protein patterns of biomass from normal conditions. It indicates the recovery of the metabolic activity under Martian environmental conditions after one week of exposure.

  4. Interaction of Hepatitis C virus proteins with pattern recognition receptors

    Directory of Open Access Journals (Sweden)

    Imran Muhammad

    2012-06-01

    Full Text Available Abstract Hepatitis C virus (HCV is an important human pathogen that causes acute and chronic hepatitis, cirrhosis and hepatocellular carcinoma worldwide. This positive stranded RNA virus is extremely efficient in establishing persistent infection by escaping immune detection or hindering the host immune responses. Recent studies have discovered two important signaling pathways that activate the host innate immunity against viral infection. One of these pathways utilizes members of Toll-like receptor (TLR family and the other uses the RNA helicase retinoic acid inducible gene I (RIG-I as the receptors for intracellular viral double stranded RNA (dsRNA, and activation of transcription factors. In this review article, we summarize the interaction of HCV proteins with various host receptors/sensors through one of these two pathways or both, and how they exploit these interactions to escape from host defense mechanisms. For this purpose, we searched data from Pubmed and Google Scholar. We found that three HCV proteins; Core (C, non structural 3/4 A (NS3/4A and non structural 5A (NS5A have direct interactions with these two pathways. Core protein only in the monomeric form stimulates TLR2 pathway assisting the virus to evade from the innate immune system. NS3/4A disrupts TLR3 and RIG-1 signaling pathways by cleaving Toll/IL-1 receptor domain-containing adapter inducing IFN-beta (TRIF and Cardif, the two important adapter proteins of these signaling cascades respectively, thus halting the defense against HCV. NS5A downmodulates the expressions of NKG2D on natural killer cells (NK cells via TLR4 pathway and impairs the functional ability of these cells. TLRs and RIG-1 pathways have a central role in innate immunity and despite their opposing natures to HCV proteins, when exploited together, HCV as an ever developing virus against host immunity is able to accumulate these mechanisms for near unbeatable survival.

  5. Research highlights: microfluidics meets big data.

    Science.gov (United States)

    Tseng, Peter; Weaver, Westbrook M; Masaeli, Mahdokht; Owsley, Keegan; Di Carlo, Dino

    2014-03-07

    In this issue we highlight a collection of recent work in which microfluidic parallelization and automation have been employed to address the increasing need for large amounts of quantitative data concerning cellular function--from correlating microRNA levels to protein expression, increasing the throughput and reducing the noise when studying protein dynamics in single-cells, and understanding how signal dynamics encodes information. The painstaking dissection of cellular pathways one protein at a time appears to be coming to an end, leading to more rapid discoveries which will inevitably translate to better cellular control--in producing useful gene products and treating disease at the individual cell level. From these studies it is also clear that development of large scale mutant or fusion libraries, automation of microscopy, image analysis, and data extraction will be key components as microfluidics contributes its strengths to aid systems biology moving forward.

  6. Quantity of dietary protein intake, but not pattern of intake, affects net protein balance primarily through differences in protein synthesis in older adults.

    Science.gov (United States)

    Kim, Il-Young; Schutzler, Scott; Schrader, Amy; Spencer, Horace; Kortebein, Patrick; Deutz, Nicolaas E P; Wolfe, Robert R; Ferrando, Arny A

    2015-01-01

    To examine whole body protein turnover and muscle protein fractional synthesis rate (MPS) following ingestions of protein in mixed meals at two doses of protein and two intake patterns, 20 healthy older adult subjects (52-75 yr) participated in one of four groups in a randomized clinical trial: a level of protein intake of 0.8 g (1RDA) or 1.5 g·kg(-1)·day(-1) (∼2RDA) with uneven (U: 15/20/65%) or even distribution (E: 33/33/33%) patterns of intake for breakfast, lunch, and dinner over the day (1RDA-U, 1RDA-E, 2RDA-U, or 2RDA-E). Subjects were studied with primed continuous infusions of L-[(2)H5]phenylalanine and L-[(2)H2]tyrosine on day 4 following 3 days of diet habituation. Whole body protein kinetics [protein synthesis (PS), breakdown, and net balance (NB)] were expressed as changes from the fasted to the fed states. Positive NB was achieved at both protein levels, but NB was greater in 2RDA vs. 1RDA (94.8 ± 6.0 vs. 58.9 ± 4.9 g protein/750 min; P = 0.0001), without effects of distribution on NB. The greater NB was due to the higher PS with 2RDA vs. 1RDA (15.4 ± 4.8 vs. -18.0 ± 8.4 g protein/750 min; P = 0.0018). Consistent with PS, MPS was greater with 2RDA vs. 1RDA, regardless of distribution patterns. In conclusion, whole body net protein balance was greater with protein intake above recommended dietary allowance (0.8 g protein·kg(-1)·day(-1)) in the context of mixed meals, without demonstrated effects of protein intake pattern, primarily through higher rates of protein synthesis at whole body and muscle levels.

  7. A microfluidic dialysis device for complex biological mixture SERS analysis

    KAUST Repository

    Perozziello, Gerardo

    2015-08-01

    In this paper, we present a microfluidic device fabricated with a simple and inexpensive process allowing rapid filtering of peptides from a complex mixture. The polymer microfluidic device can be used for sample preparation in biological applications. The device is fabricated by micromilling and solvent assisted bonding, in which a microdialysis membrane (cut-off of 12-14 kDa) is sandwiched in between an upper and a bottom microfluidic chamber. An external frame connects the microfluidic device to external tubes, microvalves and syringe pumps. Bonding strength and interface sealing are pneumatically tested. Microfluidic protocols are also described by using the presented device to filter a sample composed of specific peptides (MW 1553.73 Da, at a concentration of 1.0 ng/μl) derived from the BRCA1 protein, a tumor-suppressor molecule which plays a pivotal role in the development of breast cancer, and albumin (MW 66.5 kDa, at a concentration of 35 μg/μl), the most represented protein in human plasma. The filtered samples coming out from the microfluidic device were subsequently deposited on a SERS (surface enhanced Raman scattering) substrate for further analysis by Raman spectroscopy. By using this approach, we were able to sort the small peptides from the bigger and highly concentrated protein albumin and to detect them by using a label-free technique at a resolution down to 1.0 ng/μl.

  8. Fluorescent Biotin Analogues for Microstructure Patterning and Selective Protein Immobilization.

    Science.gov (United States)

    Krishna, K Vijaya; Ghosh, Subhadip; Sharma, Bikramjit; Singh, Leeju; Mukherjee, Saptarshi; Verma, Sandeep

    2015-11-24

    Benzyl substitution on ureido nitrogens of biotin led to manifestation of aggregation-induced emission, which was studied by steady-state fluorescence, microscopy, and TD-DFT, providing a rationale into the observed photophysical behavior. Besides exhibiting solvatochromism, the biotin derivatives revealed emission peaks centered at ∼430 and 545 nm, which has been attributed to the π-π stacking interactions. Our TD-DFT results also correlate the spectroscopic data and quantify the nature of transitions involved. The isothermal titration calorimetry data substantiates that the binding of the biotin derivatives with avidin are pretty strong. These derivatives on lithographic patterning present a platform for site specific strept(avidin) immobilization, thus opening avenues for potential applications exploiting these interactions. The fluorescent biotin derivatives can thus find applications in cellular biology and imaging.

  9. Collective waves in dense and confined microfluidic droplet arrays

    Science.gov (United States)

    Schiller, Ulf D.; Fleury, Jean-Baptiste; Seemann, Ralf; Gompper, Gerhard

    Excitation mechanisms for collective waves in confined dense one-dimensional microfluidic droplet arrays are investigated by experiments and computer simulations. We demonstrate that distinct modes can be excited by creating specific `defect' patterns in flowing droplet trains. Excited longitudinal modes exhibit a short-lived cascade of pairs of laterally displacing droplets. Transversely excited modes obey the dispersion relation of microfluidic phonons and induce a coupling between longitudinal and transverse modes, whose origin is the hydrodynamic interaction of the droplets with the confining walls. Moreover, we investigate the long-time behaviour of the oscillations and discuss possible mechanisms for the onset of instabilities. Our findings demonstrate that the collective dynamics of microfluidic droplet ensembles can be studied particularly well in dense and confined systems. Experimentally, the ability to control microfluidic droplets may allow to modulate the refractive index of optofluidic crystals which is a promising approach for the production of dynamically programmable metamaterials.

  10. Microfluidic Flame Barrier

    Science.gov (United States)

    Mungas, Gregory S. (Inventor); Fisher, David J. (Inventor); Mungas, Christopher (Inventor)

    2013-01-01

    Propellants flow through specialized mechanical hardware that is designed for effective and safe ignition and sustained combustion of the propellants. By integrating a micro-fluidic porous media element between a propellant feed source and the combustion chamber, an effective and reliable propellant injector head may be implemented that is capable of withstanding transient combustion and detonation waves that commonly occur during an ignition event. The micro-fluidic porous media element is of specified porosity or porosity gradient selected to be appropriate for a given propellant. Additionally the propellant injector head design integrates a spark ignition mechanism that withstands extremely hot running conditions without noticeable spark mechanism degradation.

  11. Development & Characterization of Multifunctional Microfluidic Materials

    Science.gov (United States)

    Ucar, Ahmet Burak

    developing 'smart' windows and heat management. To better design new color changing elastomers, we investigated the role of the network geometry on liquid replacement efficiency with the aid of a multiphysics modeling and simulation software package, COMSOL. We simulated the liquid flow in various network geometries. Serpentine, parallel channel and lattice networks, as well as their tapered versions were compared. The comparison criteria were based on rapid and uniform liquid replacement with the least amount of dye/liquid required, for which we set multiple constraints such as constant inlet pressure or total channel area. We demonstrated that the tapered lattice type network provided the most rapid and uniform replacement with minimal liquid waste. Next, we designed a simple and inexpensive liquid dispensing microfluidic material which does not require complex micromachining techniques or automated actuators. It consisted of only a PDMS matrix with embedded chambers and channels. 'Pores/slits' were made on the surface and the liquid was released by contact on the dispensing surface of the material. We varied the network design, geometry, dimension, slit shape and length, and tested the material's liquid release performance. Promising preliminary results were obtained but for an end product with repeatable and reproducible performance, both material fabrication and characterization need to be improved further. Finally, we describe an alternative material/method for the fabrication of microfluidic materials. We aimed to replace the conventional fabrication material PDMS with Polyethylene (PE) sheets. The sheets were as transparent and flexible as PDMS, and also thinner. Channel patterns were drawn with a polymer solution of PolyVinylAlcohol (PVA), which is immiscible with PE, and captured in between the two PE sheets. After fusing the PE sheets on a hot press, PVA was washed off with water, so that the 'microfluidic channels' were successfully created. The produced channel

  12. Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

    Science.gov (United States)

    Handfield, Louis-François; Chong, Yolanda T.; Simmons, Jibril; Andrews, Brenda J.; Moses, Alan M.

    2013-01-01

    Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images. PMID:23785265

  13. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    Directory of Open Access Journals (Sweden)

    Louis-François Handfield

    Full Text Available Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  14. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    Directory of Open Access Journals (Sweden)

    Louis-François Handfield

    Full Text Available Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  15. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    Science.gov (United States)

    Handfield, Louis-François; Chong, Yolanda T; Simmons, Jibril; Andrews, Brenda J; Moses, Alan M

    2013-01-01

    Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  16. Expression patterns of protein kinase D 3 during mouse development

    Directory of Open Access Journals (Sweden)

    Lutz Sylke

    2008-04-01

    Full Text Available Abstract Background The PKD family of serine/threonine kinases comprises a single member in Drosophila (dPKD, two isoforms in C. elegans (DKF-1 and 2 and three members, PKD1, PKD2 and PKD3 in mammals. PKD1 and PKD2 have been the focus of most studies up to date, which implicate these enzymes in very diverse cellular functions, including Golgi organization and plasma membrane directed transport, immune responses, apoptosis and cell proliferation. Concerning PKD3, a role in the formation of vesicular transport carriers at the trans-Golgi network (TGN and in basal glucose transport has been inferred from in vitro studies. So far, however, the physiological functions of the kinase during development remain unknown. Results We have examined the expression pattern of PKD3 during the development of mouse embryos by immunohistochemistry. Using a PKD3 specific antibody we demonstrate that the kinase is differentially expressed during organogenesis. In the developing heart a strong PKD3 expression is constantly detected from E10 to E16.5. From E12.5 on PKD3 is increasingly expressed in neuronal as well as in the supporting connective tissue and in skeletal muscles. Conclusion The data presented support an important role for PKD3 during development of these tissues.

  17. Isolation of cancer cells by "in situ" microfluidic biofunctionalization protocols

    DEFF Research Database (Denmark)

    De Vitis, Stefania; Matarise, Giuseppina; Pardeo, Francesca

    2014-01-01

    The aim of this work is the development of a microfluidic immunosensor for the immobilization of cancer cells and their separation from healthy cells by using "in situ" microfluidic biofunctionalization protocols. These protocols allow to link antibodies on microfluidic device surfaces and can...... for the isolation of cancer cells in heterogeneous blood samples by exploiting the binding of specific antibody to an adhesion protein (EpCAM), overexpressed on the tumor cell membranes. The presented biofunctionalization protocols can be performed right before running the experiment: this allows to have a flexible...... be used to study the interaction between cell membrane and biomolecules. Moreover they allow to perform analysis with high processing speed, small quantity of reagents and samples, short reaction times and low production costs. In this work the developed protocols were used in microfluidic devices...

  18. Microfabrication and microfluidics for tissue engineering: state of the art and future opportunities

    NARCIS (Netherlands)

    Andersson, Helene; van den Berg, Albert

    2004-01-01

    An introductory overview of the use of microfluidic devices for tissue engineering is presented. After a brief description of the background of tissue engineering, different application areas of microfluidic devices are examined. Among these are methods for patterning cells, topographical control

  19. Microfabrication and microfluidics for tissue engineering: state of the art and future opportunities

    NARCIS (Netherlands)

    Andersson, Helene; Berg, van den Albert

    2004-01-01

    An introductory overview of the use of microfluidic devices for tissue engineering is presented. After a brief description of the background of tissue engineering, different application areas of microfluidic devices are examined. Among these are methods for patterning cells, topographical control ov

  20. Inkjet printing of UV-curable adhesive and dielectric inks for microfluidic devices.

    Science.gov (United States)

    Hamad, E M; Bilatto, S E R; Adly, N Y; Correa, D S; Wolfrum, B; Schöning, M J; Offenhäusser, A; Yakushenko, A

    2016-01-01

    Bonding of polymer-based microfluidics to polymer substrates still poses a challenge for Lab-On-a-Chip applications. Especially, when sensing elements are incorporated, patterned deposition of adhesives with curing at ambient conditions is required. Here, we demonstrate a fabrication method for fully printed microfluidic systems with sensing elements using inkjet and stereolithographic 3D-printing.

  1. Expression Patterns of Extracellular Matrix Proteins during Posterior Commissure Development

    Science.gov (United States)

    Stanic, Karen; Saldivia, Natalia; Förstera, Benjamín; Torrejón, Marcela; Montecinos, Hernán; Caprile, Teresa

    2016-01-01

    Extracellular matrix (ECM) molecules are pivotal for central nervous system (CNS) development, facilitating cell migration, axonal growth, myelination, dendritic spine formation, and synaptic plasticity, among other processes. During axon guidance, the ECM not only acts as a permissive or non-permissive substrate for navigating axons, but also modulates the effects of classical guidance cues, such as netrin or Eph/ephrin family members. Despite being highly important, little is known about the expression of ECM molecules during CNS development. Therefore, this study assessed the molecular expression patterns of tenascin, HNK-1, laminin, fibronectin, perlecan, decorin, and osteopontin along chick embryo prosomere 1 during posterior commissure development. The posterior commissure is the first transversal axonal tract of the embryonic vertebrate brain. Located in the dorso-caudal portion of prosomere 1, posterior commissure axons primarily arise from the neurons of basal pretectal nuclei that run dorsally to the roof plate midline, where some turn toward the ipsilateral side. Expressional analysis of ECM molecules in this area these revealed to be highly arranged, and molecule interactions with axon fascicles suggested involvement in processes other than structural support. In particular, tenascin and the HNK-1 epitope extended in ventro-dorsal columns and enclosed axons during navigation to the roof plate. Laminin and osteopontin were expressed in the midline, very close to axons that at this point must decide between extending to the contralateral side or turning to the ipsilateral side. Finally, fibronectin, decorin, and perlecan appeared unrelated to axonal pathfinding in this region and were instead restricted to the external limiting membrane. In summary, the present report provides evidence for an intricate expression of different extracellular molecules that may cooperate in guiding posterior commissure axons. PMID:27733818

  2. Expression Patterns of Extracellular Matrix Proteins during Posterior Commissure Development

    Directory of Open Access Journals (Sweden)

    Karen Stanic

    2016-09-01

    Full Text Available Extracellular matrix (ECM molecules are pivotal for central nervous system development, facilitating cell migration, axonal growth, myelination, dendritic spine formation, and synaptic plasticity, among other processes. During axonal guidance, the ECM not only acts as a permissive or non-permissive substrate for navigating axons, but also modulates the effects of classical guidance cues, such as netrin or Eph/ephrin family members. Despite being highly important, little is known about the expression of ECM molecules during central nervous system development. Therefore, this study assessed the molecular expression patterns of tenascin, HNK-1, laminin, fibronectin, perlecan, decorin, and osteopontin along chick embryo prosomere 1 during posterior commissure development. The posterior commissure is the first transversal axonal tract of the embryonic vertebrate brain. Located in the dorso-caudal portion of prosomere 1, posterior commissure axons primarily arise from the neurons of basal pretectal nuclei that run dorsally to the roof plate midline, where some turn towards the ipsilateral side. Expressional analysis of ECM molecules in this area these revealed to be highly arranged, and molecule interactions with axon fascicles suggested involvement in processes other than structural support. In particular, tenascin and the HNK-1 epitope extended in ventro-dorsal columns and enclosed axons during navigation to the roof plate. Laminin and osteopontin were expressed in the midline, very close to axons that at this point must decide between extending to the contralateral side or turning to the ipsilateral side. Finally, fibronectin, decorin, and perlecan appeared unrelated to axonal pathfinding in this region and were instead restricted to the external limiting membrane. In summary, the present report provides evidence for an intricate expression of different extracellular molecules that may cooperate in guiding posterior commissure axons.

  3. Expression pattern of protein kinase C δ during mouse embryogenesis

    Directory of Open Access Journals (Sweden)

    Carracedo Sergio

    2013-01-01

    Full Text Available Abstract Background The members of the protein kinase C (PKC family consist of serine/threonine kinases classified according to their regulatory domain. Those that belong to the novel PKC subfamily, such as PKCδ, are dependent on diacylglycerol but not Calcium when considering their catalytic activity. Although several studies have shown the importance of PKCδ in different cellular events in health and disease, the overall in vivo distribution of this PKC isoform during development is still lacking. Through Lac Z and antibody staining procedures, we show here the in vivo expression of PKCδ during mouse embryogenesis. Results Ganglia were the domains with most prominent expression of PKCδ in most of the stages analysed, although PKCδ could also be detected in heart and somites at earlier stages, and cartilage primordium and skin among other sites in older embryos. Conclusions The strong expression of PKCδ in ganglia during murine development shown in this study suggests a significant role of this isoform as well as redundancy with other PKCs within the nervous system, since PKCδ deficient mice develop normally.

  4. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Buffalo, Cosmo Z.; Bahn-Suh, Adrian J.; Hirakis, Sophia P.; Biswas, Tapan; Amaro, Rommie E.; Nizet, Victor; Ghosh, Partho

    2016-09-05

    No vaccine exists against group A Streptococcus (GAS), a leading cause of worldwide morbidity and mortality. A severe hurdle is the hypervariability of its major antigen, the M protein, with >200 different M types known. Neutralizing antibodies typically recognize M protein hypervariable regions (HVRs) and confer narrow protection. In stark contrast, human C4b-binding protein (C4BP), which is recruited to the GAS surface to block phagocytic killing, interacts with a remarkably large number of M protein HVRs (apparently ∼90%). Such broad recognition is rare, and we discovered a unique mechanism for this through the structure determination of four sequence-diverse M proteins in complexes with C4BP. The structures revealed a uniform and tolerant ‘reading head’ in C4BP, which detected conserved sequence patterns hidden within hypervariability. Our results open up possibilities for rational therapies that target the M–C4BP interaction, and also inform a path towards vaccine design.

  5. Predicting Droplet Formation on Centrifugal Microfluidic Platforms

    OpenAIRE

    Moebius, Jacob Alfred

    2015-01-01

    Centrifugal microfluidics is a widely known research tool for biological sample and water quality analysis. Currently, the standard equipment used for such diagnostic applications include slow, bulky machines controlled by multiple operators. These machines can be condensed into a smaller, faster benchtop sample-to-answer system.Sample processing is an important step taken to extract, isolate, and convert biological factors, such as nucleic acids or proteins, from a raw sample to an analyzabl...

  6. Surfactants in microfluidics

    NARCIS (Netherlands)

    Michler, D.

    2015-01-01

    The rapid development of microfluidic techniques in the last two decades has revolutionized chemical and biological research. This technology has enabled scientists in a manifold of research fields to analyze and synthesize specimens with hither to unreached speed and precision. The number of applic

  7. Basic Microfluidics Theory

    DEFF Research Database (Denmark)

    Svendsen, Winnie Edith

    2015-01-01

    ,000 m−1, which is a huge difference and has a large impact on flow behavior. In this chapter the basic microfluidic theory will be presented, enabling the reader to gain a comprehensive understanding of how liquids behave at the microscale, enough to be able to engage in design of micro systems...

  8. Microfluidics for medical applications

    NARCIS (Netherlands)

    van den Berg, Albert; van den Berg, A.; Segerink, L.I.; Segerink, Loes Irene; Unknown, [Unknown

    2015-01-01

    Lab-on-a-chip devices for point of care diagnostics have been present in clinics for several years now. Alongside their continual development, research is underway to bring the organs and tissue on-a-chip to the patient, amongst other medical applications of microfluidics. This book provides the

  9. Enzyme detection by microfluidics

    DEFF Research Database (Denmark)

    2013-01-01

    Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted...

  10. Chemistry in Microfluidic Channels

    Science.gov (United States)

    Chia, Matthew C.; Sweeney, Christina M.; Odom, Teri W.

    2011-01-01

    General chemistry introduces principles such as acid-base chemistry, mixing, and precipitation that are usually demonstrated in bulk solutions. In this laboratory experiment, we describe how chemical reactions can be performed in a microfluidic channel to show advanced concepts such as laminar fluid flow and controlled precipitation. Three sets of…

  11. Enzyme detection by microfluidics

    DEFF Research Database (Denmark)

    2013-01-01

    Microfluidic-implemented methods of detecting an enzyme, in particular a DNA-modifying enzyme, are provided, as well as methods for detecting a cell, or a microorganism expressing said enzyme. The enzyme is detected by providing a nucleic acid substrate, which is specifically targeted...... by that enzyme...

  12. Magnetic digital microfluidics - a review.

    Science.gov (United States)

    Zhang, Yi; Nguyen, Nam-Trung

    2017-03-14

    A digital microfluidic platform manipulates droplets on an open surface. Magnetic digital microfluidics utilizes magnetic forces for actuation and offers unique advantages compared to other digital microfluidic platforms. First, the magnetic particles used in magnetic digital microfluidics have multiple functions. In addition to serving as actuators, they also provide a functional solid substrate for molecule binding, which enables a wide range of applications in molecular diagnostics and immunodiagnostics. Second, magnetic digital microfluidics can be manually operated in a "power-free" manner, which allows for operation in low-resource environments for point-of-care diagnostics where even batteries are considered a luxury item. This review covers research areas related to magnetic digital microfluidics. This paper first summarizes the current development of magnetic digital microfluidics. Various methods of droplet manipulation using magnetic forces are discussed, ranging from conventional magnetic particle-based actuation to the recent development of ferrofluids and magnetic liquid marbles. This paper also discusses several new approaches that use magnetically controlled flexible substrates for droplet manipulation. In addition, we emphasize applications of magnetic digital microfluidics in biosensing and medical diagnostics, and identify the current limitations of magnetic digital microfluidics. We provide a perspective on possible solutions to close these gaps. Finally, the paper discusses the future improvement of magnetic digital microfluidics to explore potential new research directions.

  13. Microfluidic Sample Preparation for Immunoassays

    Energy Technology Data Exchange (ETDEWEB)

    Visuri, S; Benett, W; Bettencourt, K; Chang, J; Fisher, K; Hamilton, J; Krulevitch, P; Park, C; Stockton, C; Tarte, L; Wang, A; Wilson, T

    2001-08-09

    Researchers at Lawrence Livermore National Laboratory are developing means to collect and identify fluid-based biological pathogens in the forms of proteins, viruses, and bacteria. to support detection instruments, they are developing a flexible fluidic sample preparation unit. The overall goal of this Microfluidic Module is to input a fluid sample, containing background particulates and potentially target compounds, and deliver a processed sample for detection. They are developing techniques for sample purification, mixing, and filtration that would be useful to many applications including immunologic and nucleic acid assays. Many of these fluidic functions are accomplished with acoustic radiation pressure or dielectrophoresis. They are integrating these technologies into packaged systems with pumps and valves to control fluid flow through the fluidic circuit.

  14. Reversible Dialysis in a Microfluidic Formulator.

    Science.gov (United States)

    Selimovic, Seila; Shim, Jung-Uk; Fraden, Seth

    2006-03-01

    In order to facilitate the screening of conditions for protein crystallization, we have been using the Microfluidic Formulator chip (Stephen Quake, PNAS Vol. 101, 40 ). This PDMS device allows us to mix up to 40 different reagents and protein solutions. We use this combinatorial approach along with a ``drop-on-demand'' method whereby we employ on-chip positive displacement pumps to form aqueous droplets containing protein and separate them by plugs of oil. Subsequently, the aqueous drops containing protein are guided by surface tension forces into storage chambers. To control the chemical potential of these sub-nanoliter protein samples, we fabricate reservoirs underneath the storage compartments. A thin PDMS membrane that is permeable to water, but not to protein or salt, separates the reservoirs from the storage chambers. Water can permeate into or out of the stored samples until the chemical potentials of the reservoir and the protein solution are equal leading to protein crystallization in some chambers.

  15. Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes.

    Directory of Open Access Journals (Sweden)

    Michail Yu Lobanov

    Full Text Available We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/. We have compiled the largest database of disordered patterns (141 from the clustered PDB where identity between chains inside of a cluster is larger or equal to 75% (version of 28 June 2010 by using simple rules of selection. The results of these analyses would help to further our understanding of the physicochemical and structural determinants of intrinsically disordered regions that serve as molecular recognition elements. We have analyzed the occurrence of the selected patterns in 97 eukaryotic and in 26 bacterial proteomes. The disordered patterns appear more often in eukaryotic than in bacterial proteomes. The matrix of correlation coefficients between numbers of proteins where a disordered pattern from the library of 141 disordered patterns appears at least once in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside of the considered kingdom than between them. The patterns with the frequent occurrence in proteomes have low complexity (PPPPP, GGGGG, EEEED, HHHH, KKKKK, SSTSS, QQQQQP, and the type of patterns vary across different proteomes, http://bioinfo.protres.ru/fp/search_new_pattern.html.

  16. Proteomic analysis of cow, yak, buffalo, goat and camel milk whey proteins: quantitative differential expression patterns.

    Science.gov (United States)

    Yang, Yongxin; Bu, Dengpan; Zhao, Xiaowei; Sun, Peng; Wang, Jiaqi; Zhou, Lingyun

    2013-04-05

    To aid in unraveling diverse genetic and biological unknowns, a proteomic approach was used to analyze the whey proteome in cow, yak, buffalo, goat, and camel milk based on the isobaric tag for relative and absolute quantification (iTRAQ) techniques. This analysis is the first to produce proteomic data for the milk from the above-mentioned animal species: 211 proteins have been identified and 113 proteins have been categorized according to molecular function, cellular components, and biological processes based on gene ontology annotation. The results of principal component analysis showed significant differences in proteomic patterns among goat, camel, cow, buffalo, and yak milk. Furthermore, 177 differentially expressed proteins were submitted to advanced hierarchical clustering. The resulting clustering pattern included three major sample clusters: (1) cow, buffalo, and yak milk; (2) goat, cow, buffalo, and yak milk; and (3) camel milk. Certain proteins were chosen as characterization traits for a given species: whey acidic protein and quinone oxidoreductase for camel milk, biglycan for goat milk, uncharacterized protein (Accession Number: F1MK50 ) for yak milk, clusterin for buffalo milk, and primary amine oxidase for cow milk. These results help reveal the quantitative milk whey proteome pattern for analyzed species. This provides information for evaluating adulteration of specific specie milk and may provide potential directions for application of specific milk protein production based on physiological differences among animal species.

  17. Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Buus, Ole Thomsen; Wollenweber, Bernd

    2010-01-01

    Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underly......Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins...... and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average......-against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly...

  18. Regular patterns for proteome-wide distribution of protein abundance across species.

    Directory of Open Access Journals (Sweden)

    Fan Zhong

    Full Text Available A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category are more abundant than those that act on information modulation (information category. Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function.

  19. Inference of Hopfield-Potts patterns from covariation in protein families: calculation and statistical error bars

    Science.gov (United States)

    Cocco, Simona; Monasson, Rémi; Weigt, Martin

    2013-12-01

    We consider the Hopfield-Potts model for the covariation between residues in protein families recently introduced in Cocco, Monasson, Weigt (2013). The patterns of the model are inferred from the data within a new gauge, more symmetric in the residues. We compute the statistical error bars on the pattern components. Results are illustrated on real data for a response regulator receiver domain (Pfam ID PF00072) family.

  20. Authentication of Whey Protein Powders by Portable Mid-Infrared Spectrometers Combined with Pattern Recognition Analysis.

    Science.gov (United States)

    Wang, Ting; Tan, Siow Ying; Mutilangi, William; Aykas, Didem P; Rodriguez-Saona, Luis E

    2015-10-01

    The objective of this study was to develop a simple and rapid method to differentiate whey protein types (WPC, WPI, and WPH) used for beverage manufacturing by combining the spectral signature collected from portable mid-infrared spectrometers and pattern recognition analysis. Whey protein powders from different suppliers are produced using a large number of processing and compositional variables, resulting in variation in composition, concentration, protein structure, and thus functionality. Whey protein powders including whey protein isolates, whey protein concentrates and whey protein hydrolysates were obtained from different suppliers and their spectra collected using portable mid-infrared spectrometers (single and triple reflection) by pressing the powder onto an Attenuated Total Reflectance (ATR) diamond crystal with a pressure clamp. Spectra were analyzed by soft independent modeling of class analogy (SIMCA) generating a classification model showing the ability to differentiate whey protein types by forming tight clusters with interclass distance values of >3, considered to be significantly different from each other. The major bands centered at 1640 and 1580 cm(-1) were responsible for separation and were associated with differences in amide I and amide II vibrations of proteins, respectively. Another important band in whey protein clustering was associated with carboxylate vibrations of acidic amino acids (∼1570 cm(-1)). The use of a portable mid-IR spectrometer combined with pattern recognition analysis showed potential for discriminating whey protein ingredients that can help to streamline the analytical procedure so that it is more applicable for field-based screening of ingredients. A rapid, simple and accurate method was developed to authenticate commercial whey protein products by using portable mid-infrared spectrometers combined with chemometrics, which could help ensure the functionality of whey protein ingredients in food applications. © 2015

  1. [Protein expression patterns identify morphological variability of ascomatal hairs in two species of genus Chaetomium].

    Science.gov (United States)

    Sun, Qin; Liu, Xiaoyong; Wang, Qian; Luo, Yuanming; Wang, Xuewei

    2012-10-04

    Morphology of ascomatal hairs was traditionally used as a primary character in the classification of the fungal genus Chaetomium. However, the taxonomic value of ascomatal hair morphology is questioned in modern taxonomy of Chaetomium. Chaetomium indicum and C. funicola are two species proposed only by their differences in ascomatal hairs. The aim of this study is to understand the difference between these two species and their variability in the morphology of ascomatal hairs at the level of protein expression patterns, as well as to ressess the taxonomic value of the ascomatal hairs. We performed microscopic examination to obtain the morphological characters of the typical and variable strains in both C. indicum and C. funicola. Then we used two-dimensional gel electrophoresis (2DE) to compare the protein expression patterns of the two species, including their typical and variable strains. The comparison of the obtained 2DE maps indicated that C. indicum and C. funicola exhibited species-specific protein expression patterns. The phylogenetic tree derived from the distance matrix of expression patterns with Neighbor-joining algorithm also revealed that the tested strains of C. indicum and C. funicola fell into two distinct clades, among which the variant strains were grouped together with the typical strains of the same species. The consistency of species delimitation between C. indicum and C. funicola based on morphological characters of ascomatal hairs and species-specific protein expression patterns demonstrates that ascomatal hairs can be still used as potential morphological parameters in taxonomy of Chaetomium.

  2. Variation of morphology, karyotype and protein band pattern of adenium (Adenium obesum varieties

    Directory of Open Access Journals (Sweden)

    PRABANG SETYONO

    2009-07-01

    Full Text Available Hastuti D, Suranto, Setyono P. 2009. Variation of morphology, karyotype and protein band pattern of adenium (Adenium obesum varieties. Nusantara Bioscience 1: 78-83. The aim of this research to find out the Adenium obesum variation from six varieties, namely: obesum, cery, red lucas, red fanta , white bigben and harry potter based on morphology, karyotype, as well as protein banding pattern. The chromosome preparation was made using semi-permanent squash method from the tip of root plant; while protein banding pattern was made using SDS-PAGE method. Qualitative data included shape and color of the leave and flower described from each variety. Data were presented in morphometry and analyzed using ANOVA and then followed by DMRT with 5% of confidence levels, indicated significance difference. Protein banding pattern, the root, stem, leave and all organs were analyzed using Hierarchical Cluster Analysis method with Average Linkage (between Groups using SPSS 10.0. The result of research shows that the six A. obesum varieties have morphological character with no variation of light green to dark green leave, not hairy, smooth leave bone, meanwhile for light red to dark red flower crown color although some of them are white and the same funnel color, yellow. All varieties of A. obesum have same number of chromosome, 2n = 22 and shows the difference ranging from 2.56 to 5.13 um. In the banding pattern formed qualitatively, there is variation among the six varieties.

  3. Collective oscillations and coupled modes in confined microfluidic droplet arrays

    Science.gov (United States)

    Schiller, Ulf D.; Fleury, Jean-Baptiste; Seemann, Ralf; Gompper, Gerhard

    Microfluidic droplets have a wide range of applications ranging from analytic assays in cellular biology to controlled mixing in chemical engineering. Ensembles of microfluidic droplets are interesting model systems for non-equilibrium many-body phenomena. When flowing in a microchannel, trains of droplets can form microfluidic crystals whose dynamics are governed by long-range hydrodynamic interactions and boundary effects. In this contribution, excitation mechanisms for collective waves in dense and confined microfluidic droplet arrays are investigated by experiments and computer simulations. We demonstrate that distinct modes can be excited by creating specific `defect' patterns in flowing droplet trains. While longitudinal modes exhibit a short-lived cascade of pairs of laterally displacing droplets, transversely excited modes form propagating waves that behave like microfluidic phonons. We show that the confinement induces a coupling between longitudinal and transverse modes. We also investigate the life time of the collective oscillations and discuss possible mechanisms for the onset of instabilities. Our results demonstrate that microfluidic phonons can exhibit effects beyond the linear theory, which can be studied particularly well in dense and confined systems. This work was supported by Deutsche Forschungsgemeinschaft under Grant No. SE 1118/4.

  4. Cell-based bioassays in microfluidic systems

    Science.gov (United States)

    Itle, Laura J.; Zguris, Jeanna C.; Pishko, Michael V.

    2004-12-01

    The development of cell-based bioassays for high throughput drug screening or the sensing of biotoxins is contingent on the development of whole cell sensors for specific changes in intracellular conditions and the integration of those systems into sample delivery devices. Here we show the feasibility of using a 5-(and-6)-carboxy SNARF-1, acetoxymethyl ester, acetate, a fluorescent dye capable of responding to changes in intracellular pH, as a detection method for the bacterial endotoxin, lipopolysaccharide. We used photolithography to entrap cells with this dye within poly(ethylene) glyocol diacrylate hydrogels in microfluidic channels. After 18 hours of exposure to lipopolysaccharide, we were able to see visible changes in the fluorescent pattern. This work shows the feasibility of using whole cell based biosensors within microfluidic networks to detect cellular changes in response to exogenous agents.

  5. Bonding PMMA microfluidics using commercial microwave ovens

    Science.gov (United States)

    Toossi, A.; Moghadas, H.; Daneshmand, M.; Sameoto, D.

    2015-08-01

    In this paper, a novel low-cost, rapid substrate-bonding technique is successfully applied to polymethyl methacrylate (PMMA) microfluidics bonding for the first time. This technique uses a thin intermediate metallic microwave susceptor layer at the interface of the bonding site (microchannels) which produces localized heating required for bonding during microwave irradiation. The metallic susceptor pattern is designed using a multiphysics simulation model developed in ANSYS Multiphysics software (high-frequency structural simulation (HFSS) coupled with ANSYS-Thermal). In our experiments, the required microwave energy for bonding is delivered using a relatively inexpensive, widely accessible commercial microwave oven. Using this technique, simple PMMA microfluidics prototypes are successfully bonded and sealed in less than 35 seconds with a minimum measured bond strength of 1.375 MPa.

  6. Microfluidic technologies for studying synthetic circuits.

    Science.gov (United States)

    Lin, Benjamin; Levchenko, Andre

    2012-08-01

    Advances in synthetic biology have augmented the available toolkit of biomolecular modules, allowing engineering and manipulation of signaling in a variety of organisms, ranging in complexity from single bacteria and eukaryotic cells to multi-cellular systems. The richness of synthetic circuit outputs can be dramatically enhanced by sophisticated environmental control systems designed to precisely pattern spatial-temporally heterogeneous environmental stimuli controlling these circuits. Moreover, the performance of the synthetic modules and 'blocks' needed to assemble more complicated networks requires more complete characterization as a function of arbitrarily complex environmental inputs. Microfluidic technologies are poised to meet these needs through a variety of innovative designs capitalizing on the unique benefits of manipulating fluids on the micro-scales and nano-scales. This review discusses the utility of microfluidics for the study of synthetic circuits and highlights recent work in the area.

  7. Simulation of Droplet Trains in Microfluidic Networks

    CERN Document Server

    Behzad, Mehran Djalali; Ejtehadi, Mohammad Reza

    2009-01-01

    In this work we show that in a microfluidic network and in low Reynolds numbers a system can be irreversible because of hysteresis effects.The network, which is employed in our simulations, is taken from recent experiments. The network consists of one loop connected to input and output pipes. A train of droplets enter the system at a uniform rate, but they may leave it in different patterns, e.g. periodic or even chaotic. The out put pattern depends on the time interval among the incoming droplets as well as the network geometry and for some parameters the system is not reversible.

  8. Direct digital manufacturing of autonomous centrifugal microfluidic device

    Science.gov (United States)

    Ukita, Yoshiaki; Takamura, Yuzuru; Utsumi, Yuichi

    2016-06-01

    This paper presents strategies that attempt to solve two key problems facing the commercialization of microfluidics: cost reduction in microfluidic chip manufacturing and microfluidic device driver development. To reduce the cost of microfluidic chip manufacturing, we propose to use of three-dimensional (3D) printers for direct digital manufacturing (DDM). An evaluation of 3D micro-scale structure printing using several 3D printers is reported, and some of the technical issues to be addressed in the future are suggested. To evaluate micro-scale printing, three types of 3D printers, with the ability to print structures on the scale of several hundred meters, were selected by first screening six 3D printers. Line and space patterns with line widths of 100-500 µm and an aspect ratio of one were printed and evaluated. The estimated critical dimension was around 200 µm. The manufacturing of a monolithic microfluidic chip with embedded channels was also demonstrated. Monolithic microfluidic chips with embedded microchannels having 500 × 500 and 250 × 250 µm2 cross sections and 2-20 mm lengths were printed, and the fidelity of the channel shape, residual supporting material, and flow of liquid water were evaluated. The liquid flow evaluation showed that liquid water could flow through all of the microchannels with the 500 × 500 µm2 cross section, whereas this was not possible through some of the channels with the 250 × 250 µm2 cross section because of the residual resin or supporting material. To reduce the device-driver cost, we propose to use of the centrifugal microfluidic concept. An autonomous microfluidic device that could implement sequential flow control under a steadily rotating condition was printed. Four-step flow injection under a steadily rotating condition at 1500 rpm was successfully demonstrated without any external triggering such as changing the rotational speed.

  9. Droplet microfluidics based microseparation systems.

    Science.gov (United States)

    Xiao, Zhiliang; Niu, Menglei; Zhang, Bo

    2012-06-01

    Lab on a chip (LOC) technology is a promising miniaturization approach. The feature that it significantly reduced sample consumption makes great sense in analytical and bioanalytical chemistry. Since the start of LOC technology, much attention has been focused on continuous flow microfluidic systems. At the turn of the century, droplet microfluidics, which was also termed segmented flow microfluidics, was introduced. Droplet microfluidics employs two immiscible phases to form discrete droplets, which are ideal vessels with confined volume, restricted dispersion, limited cross-contamination, and high surface area. Due to these unique features, droplet microfluidics proves to be a versatile tool in microscale sample handling. This article reviews the utility of droplet microfluidics in microanalytical systems with an emphasize on separation science, including sample encapsulation at ultra-small volume, compartmentalization of separation bands, isolation of droplet contents, and related detection techniques.

  10. Protein patterns and chemical constituents of Ailanthus altissima (Miller) Swingle and Ailanthus excelsa Roxb.

    OpenAIRE

    Bayçu, Gülriz; Said, Ataa; Farag, Ahmed; Rashed, Khaled

    2010-01-01

     There is a growing interest in correlating biochemical constituents of plants with their taxonomic properties. Generally the genus Ailanthus is noted for the presence of quassinoids, alkaloids, lipids, fatty acids, terpenoids and some proteins. In this study, we aimed to investigate the similarities and/or differences in the chemical constituents and protein patterns of different Ailanthus species. We assume that our parameters may be used as an additional tool for chemotaxonomic st...

  11. The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis.

    Science.gov (United States)

    Slabodnick, Mark M; Ruby, J Graham; Dunn, Joshua G; Feldman, Jessica L; DeRisi, Joseph L; Marshall, Wallace F

    2014-05-01

    Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular. But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown. Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus. Here we show that the RNA interference (RNAi) machinery is conserved in Stentor. Using RNAi, we identify the kinase coactivator Mob1--with conserved functions in cell division and morphogenesis from plants to humans-as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor. Our studies reopen the door for Stentor as a model regeneration system.

  12. The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis.

    Directory of Open Access Journals (Sweden)

    Mark M Slabodnick

    2014-05-01

    Full Text Available Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular. But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown. Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus. Here we show that the RNA interference (RNAi machinery is conserved in Stentor. Using RNAi, we identify the kinase coactivator Mob1--with conserved functions in cell division and morphogenesis from plants to humans-as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor. Our studies reopen the door for Stentor as a model regeneration system.

  13. The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor Morphogenesis

    Science.gov (United States)

    Slabodnick, Mark M.; Ruby, J. Graham; Dunn, Joshua G.; Feldman, Jessica L.; DeRisi, Joseph L.; Marshall, Wallace F.

    2014-01-01

    Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular. But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown. Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus. Here we show that the RNA interference (RNAi) machinery is conserved in Stentor. Using RNAi, we identify the kinase coactivator Mob1—with conserved functions in cell division and morphogenesis from plants to humans—as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor. Our studies reopen the door for Stentor as a model regeneration system. PMID:24823688

  14. Characterization of a nanoscale S-layer protein based template for biomolecular patterning.

    Science.gov (United States)

    Wong, Wing Sze; Yung, Pun To

    2014-01-01

    Well organized template for biomolecular conjugation is the foundation for biosensing. Most of the current devices are fabricated using lithographic patterning processes and self-assembly monolayer (SAM) methods. However, the research toward developing a sub-10 nm patterned, self-regenerated template on various types of substrates is limited, mainly due to the limited functional groups of the building material. Bacterial surface layer proteins (S-layer proteins) can self-assemble into ordered lattice with regular pore sizes of 2-8 nm on different material supports and interfaces. The ordered structure can regenerate after extreme variations of solvent conditions. In this work, we developed a nanoscale biomolecular template based on S-layer proteins on gold surface for fabrication of sensing layer in biosensors. S-layer proteins were isolated from Bacillus cereus, Lysinibacillus sphaericus and Geobacillus stearothermophilus. Protein concentrations were measured by Bradford assay. The protein purities were verified by SDS-PAGE, showing molecular weights ranging from 97-135 kDa. The hydrophilicity of the substrate surface was measured after surface treatments of protein recrystallization. Atomic force microscopic (AFM) measurement was performed on substrate surface, indicating a successful immobilization of a monolayer of S-layer protein with 8-9 nm height on gold surface. The template can be applied on various material supports and acts as a self-regenerated sensing layer of biosensors in the future.

  15. Protein and cell patterning in closed polymer channels by photoimmobilizing proteins on photografted poly(ethylene glycol) diacrylate

    DEFF Research Database (Denmark)

    Larsen, Esben Kjær Unmack; Mikkelsen, Morten Bo Lindholm; Larsen, Niels Bent

    2014-01-01

    present a one-step photochemical process to coat the inner surfaces of closed microfluidic channels with a nanometer thick layer of poly(ethylene glycol) (PEG), well known to strongly reduce non-specific adsorption, using only commercially available reagents in an aqueous environment. The coating consists...

  16. Centrifugal microfluidic platforms: advanced unit operations and applications.

    Science.gov (United States)

    Strohmeier, O; Keller, M; Schwemmer, F; Zehnle, S; Mark, D; von Stetten, F; Zengerle, R; Paust, N

    2015-10-01

    Centrifugal microfluidics has evolved into a mature technology. Several major diagnostic companies either have products on the market or are currently evaluating centrifugal microfluidics for product development. The fields of application are widespread and include clinical chemistry, immunodiagnostics and protein analysis, cell handling, molecular diagnostics, as well as food, water, and soil analysis. Nevertheless, new fluidic functions and applications that expand the possibilities of centrifugal microfluidics are being introduced at a high pace. In this review, we first present an up-to-date comprehensive overview of centrifugal microfluidic unit operations. Then, we introduce the term "process chain" to review how these unit operations can be combined for the automation of laboratory workflows. Such aggregation of basic functionalities enables efficient fluidic design at a higher level of integration. Furthermore, we analyze how novel, ground-breaking unit operations may foster the integration of more complex applications. Among these are the storage of pneumatic energy to realize complex switching sequences or to pump liquids radially inward, as well as the complete pre-storage and release of reagents. In this context, centrifugal microfluidics provides major advantages over other microfluidic actuation principles: the pulse-free inertial liquid propulsion provided by centrifugal microfluidics allows for closed fluidic systems that are free of any interfaces to external pumps. Processed volumes are easily scalable from nanoliters to milliliters. Volume forces can be adjusted by rotation and thus, even for very small volumes, surface forces may easily be overcome in the centrifugal gravity field which enables the efficient separation of nanoliter volumes from channels, chambers or sensor matrixes as well as the removal of any disturbing bubbles. In summary, centrifugal microfluidics takes advantage of a comprehensive set of fluidic unit operations such as

  17. Microfluidic microwell and microcapillary biochips

    Science.gov (United States)

    Minot, Michael J.; Stowe, David W.; Detarando, Michael A.; Krans, Joseph A.; Kass, Jason L.

    2006-02-01

    Utilizing nanotechnology, proprietary chemistry, and microfluidics, innovative firms are developing biochips and instrument systems that enable high-speed automated biomedical sequencing. Incom Inc. presents development results on five novel biochip technologies based on FiberOptic MicroSlide and microcapillary technology. FiberOptic MicroSlides are fiber optic interrogated (FOI) biochips made up of millions of fused optical fibers, and are uniquely suited as a platform for microarray applications. FiberOptic MicroSlides (henceforth referred to as "MicroSlides" or "slides" in this paper) act as a 'zero thickness substrate' transmitting optical signals from top to bottom without spreading, so that fluorescent or luminescent activity on the surface or within a well can be directly coupled to a CCD device without additional optics. In contrast to bulk optics, the slides are compact and have excellent light-gathering power. They are an alternative to conventional microscope slides for applications involving moderate-resolution bottom viewing (inverted microscopy). The surface of the MicroSlides can be etched or patterned with a permanent polymer to form microwell arrays, or microfluidic structures suitable for genomic and proteomic analysis, cell migration studies and other applications. Low-cost microcapillary array plates have also been developed. These plates act as microscopic test tubes, which enable picoliter reactions to be detected, counted and analyzed. Progress in developing large area (300 mm X 300 mm) arrays with up to 100 million capillaries, and diameter / length aspect ratios up to 10,000: 1 is presented. Results demonstrate negligible optical cross talk between capillaries, resulting in improved signal-to-noise ratios while minimizing false hits.

  18. Microfluidic Production of Multiple Emulsions

    Directory of Open Access Journals (Sweden)

    Goran T. Vladisavljević

    2017-03-01

    Full Text Available Microfluidic devices are promising tools for the production of monodispersed tuneable complex emulsions. This review highlights the advantages of microfluidics for the fabrication of emulsions and presents an overview of the microfluidic emulsification methods including two-step and single-step methods for the fabrication of high-order multiple emulsions (double, triple, quadruple and quintuple and emulsions with multiple and/or multi-distinct inner cores. The microfluidic methods for the formation of multiple emulsion drops with ultra-thin middle phase, multi-compartment jets, and Janus and ternary drops composed of two or three distinct surface regions are also presented. Different configurations of microfluidic drop makers are covered, such as co-flow, T-junctions and flow focusing (both planar and three-dimensional (3D. Furthermore, surface modifications of microfluidic channels and different modes of droplet generation are summarized. Non-confined microfluidic geometries used for buoyancy-driven drop generation and membrane integrated microfluidics are also discussed. The review includes parallelization and drop splitting strategies for scaling up microfluidic emulsification. The productivity of a single drop maker is typically <1 mL/h; thus, more than 1000 drop makers are needed to achieve commercially relevant droplet throughputs of >1 L/h, which requires combining drop makers into twodimensional (2D and 3D assemblies fed from a single set of inlet ports through a network of distribution and collection channels.

  19. Methods of making microfluidic devices

    KAUST Repository

    Buttner, Ulrich

    2017-06-01

    Microfluidics has advanced in terms of designs and structures, however, fabrication methods are either time consuming or expensive to produce, in terms of the facilities and equipment needed. A fast and economically viable method is provided to allow, for example, research groups to have access to microfluidic fabrication. Unlike most fabrication methods, a method is provided to fabricate a microfluidic device in one step. In an embodiment, a resolution of 50 micrometers was achieved by using maskless high-resolution digital light projection (MDLP). Bonding and channel fabrication of complex or simple structures can be rapidly incorporated to fabricate the microfluidic devices.

  20. Pattern of protein retention in growing boars of different breeds, and estimation of maximum protein retention

    DEFF Research Database (Denmark)

    Tauson, A H; Chwalibog, André; Jakobsen, K

    1998-01-01

    Protein and energy metabolism in boars of different breeds, 10 each of Hampshire, Duroc and Danish Landrace was measured in balance and respiration experiments by means of indirect calorimetry in an open-air circulation system. Measurements were performed in four periods (Period I-IV) covering...... the body weight range from 25 to 100 kg. In order to achieve maximum protein retention (RP) a daily intake of digestible protein > 12 g/kg0.75 and metabolisable energy > 1100 kJ/kg0.75 was assumed to be necessary. Protein retention of Danish Landrace boars was inferior to that of Hampshire and Duroc boars...... in Periods III and IV, and therefore, 55 measurements on Hampshire and Duroc boars fulfilling the chosen criteria for digested protein and ME intake were used for calculation of maximum protein retention, giving the following significant quadratic relationship: RP [g/d] = 11.43.W0.75-0.144.W1.50 (n = 55, RSD...

  1. Dry-Mass Sensing for Microfluidics

    CERN Document Server

    Müller, T; Knowles, T P J

    2014-01-01

    We present an approach for interfacing an electromechanical sensor with a microfluidic device for the accurate quantification of the dry mass of analytes within microchannels. We show that depositing solutes onto the active surface of a quartz crystal microbalance by means of an on-chip microfluidic spray nozzle and subsequent solvent removal provides the basis for the real-time determination of dry solute mass. Moreover, this detection scheme does not suffer from the decrease in the sensor quality factor and the viscous drag present if the measurement is performed in a liquid environment, yet allows solutions to be analysed. We demonstrate the sensitivity and reliability of our approach by controlled deposition of nanogram levels of salt and protein from a micrometer-sized channel.

  2. Microfluidic electroporation for cellular analysis and delivery.

    Science.gov (United States)

    Geng, Tao; Lu, Chang

    2013-10-01

    Electroporation is a simple yet powerful technique for breaching the cell membrane barrier. The applications of electroporation can be generally divided into two categories: the release of intracellular proteins, nucleic acids and other metabolites for analysis and the delivery of exogenous reagents such as genes, drugs and nanoparticles with therapeutic purposes or for cellular manipulation. In this review, we go over the basic physics associated with cell electroporation and highlight recent technological advances on microfluidic platforms for conducting electroporation. Within the context of its working mechanism, we summarize the accumulated knowledge on how the parameters of electroporation affect its performance for various tasks. We discuss various strategies and designs for conducting electroporation at the microscale and then focus on analysis of intracellular contents and delivery of exogenous agents as two major applications of the technique. Finally, an outlook for future applications of microfluidic electroporation in increasingly diverse utilities is presented.

  3. Microfluidic bubble logic.

    Science.gov (United States)

    Prakash, Manu; Gershenfeld, Neil

    2007-02-09

    We demonstrate universal computation in an all-fluidic two-phase microfluidic system. Nonlinearity is introduced into an otherwise linear, reversible, low-Reynolds number flow via bubble-to-bubble hydrodynamic interactions. A bubble traveling in a channel represents a bit, providing us with the capability to simultaneously transport materials and perform logical control operations. We demonstrate bubble logic AND/OR/NOT gates, a toggle flip-flop, a ripple counter, timing restoration, a ring oscillator, and an electro-bubble modulator. These show the nonlinearity, gain, bistability, synchronization, cascadability, feedback, and programmability required for scalable universal computation. With increasing complexity in large-scale microfluidic processors, bubble logic provides an on-chip process control mechanism integrating chemistry and computation.

  4. Microfluidic colloid filtration

    Science.gov (United States)

    Linkhorst, John; Beckmann, Torsten; Go, Dennis; Kuehne, Alexander J. C.; Wessling, Matthias

    2016-03-01

    Filtration of natural and colloidal matter is an essential process in today’s water treatment processes. The colloidal matter is retained with the help of micro- and nanoporous synthetic membranes. Colloids are retained in a “cake layer” – often coined fouling layer. Membrane fouling is the most substantial problem in membrane filtration: colloidal and natural matter build-up leads to an increasing resistance and thus decreasing water transport rate through the membrane. Theoretical models exist to describe macroscopically the hydrodynamic resistance of such transport and rejection phenomena; however, visualization of the various phenomena occurring during colloid retention is extremely demanding. Here we present a microfluidics based methodology to follow filter cake build up as well as transport phenomena occuring inside of the fouling layer. The microfluidic colloidal filtration methodology enables the study of complex colloidal jamming, crystallization and melting processes as well as translocation at the single particle level.

  5. Microfluidic redox battery.

    Science.gov (United States)

    Lee, Jin Wook; Goulet, Marc-Antoni; Kjeang, Erik

    2013-07-01

    A miniaturized microfluidic battery is proposed, which is the first membraneless redox battery demonstrated to date. This unique concept capitalizes on dual-pass flow-through porous electrodes combined with stratified, co-laminar flow to generate electrical power on-chip. The fluidic design is symmetric to allow for both charging and discharging operations in forward, reverse, and recirculation modes. The proof-of-concept device fabricated using low-cost materials integrated in a microfluidic chip is shown to produce competitive power levels when operated on a vanadium redox electrolyte. A complete charge/discharge cycle is performed to demonstrate its operation as a rechargeable battery, which is an important step towards providing sustainable power to lab-on-a-chip and microelectronic applications.

  6. Versatile functional microstructured polystyrene-based platforms for protein patterning and recognition.

    Science.gov (United States)

    Palacios-Cuesta, Marta; Cortajarena, Aitziber L; García, Olga; Rodríguez-Hernández, Juan

    2013-09-09

    We report the preparation of different functional surface patterns based on the optimization of the photo-cross-linking/degradation kinetics of polystyrene (PS) upon exposure to UV-light. We employed a PS-b-PGA (polystyrene-block-poly(l-glutamic acid)) block copolymer that will, in addition to the surface pattern, provide functionality. By using short irradiation times, PS can be initially cross-linked, whereas an excess of the exposure time provokes the degradation of the material. As a result of the optimization of time of exposure, the use of an appropriate cover, or the incorporation of an appropriate amount of absorbing active species (photoinitiator), different tailor-made surface patterns can be obtained, from boxes to needles. Moreover, in addition to the surface pattern, we introduced changes on the chemical composition of the polystyrene using an amphiphilic block copolymer (for instance, we employ PS-b-PGA) that will provide functional surfaces with major advantages. In particular, the presence of carboxylic functional groups provides a unique opportunity to anchor, for instance polypeptide sequences. We describe the immobilization of polypeptide sequences in precise surface positions that allows the use of the surfaces for protein recognition purposes. The immobilization of the proteins evidence the success of the recognition and opens a new alternative for protein patterning on surfaces for many biotechnological and biomedical applications.

  7. Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study

    Indian Academy of Sciences (India)

    Piyali Ganguli; Saikat Chowdhury; Rupa Bhowmick; Ram Rup Sarkar

    2015-10-01

    Various T-cell co-receptor molecules and calcium channel CRAC play a pivotal role in the maintenance of cell’s functional responses by regulating the production of effector molecules (mostly cytokines) that aids in immune clearance and also maintaining the cell in a functionally active state. Any defect in these co-receptor signalling pathways may lead to an altered expression pattern of the effector molecules. To study the propagation of such defects with time and their effect on the intracellular protein expression patterns, a comprehensive and largest pathway map of T-cell activation network is reconstructed manually. The entire pathway reactions are then translated using logical equations and simulated using the published time series microarray expression data as inputs. After validating the model, the effect of in silico knock down of co-receptor molecules on the expression patterns of their downstream proteins is studied and simultaneously the changes in the phenotypic behaviours of the T-cell population are predicted, which shows significant variations among the proteins expression and the signalling routes through which the response is propagated in the cytoplasm. This integrative computational approach serves as a valuable technique to study the changes in protein expression patterns and helps to predict variations in the cellular behaviour.

  8. Protein Adsorption Patterns and Analysis on IV Nanoemulsions—The Key Factor Determining the Organ Distribution

    Directory of Open Access Journals (Sweden)

    Mirko Jansch

    2012-12-01

    Full Text Available Intravenous nanoemulsions have been on the market for parenteral nutrition since the 1950s; meanwhile, they have also been used successfully for IV drug delivery. To be well tolerable, the emulsions should avoid uptake by the MPS cells of the body; for drug delivery, they should be target-specific. The organ distribution is determined by the proteins adsorbing them after injection from the blood (protein adsorption pattern, typically analyzed by two-dimensional polyacrylamide gel electrophoresis, 2-D PAGE. The article reviews the 2-D PAGE method, the analytical problems to be faced and the knowledge available on how the composition of emulsions affects the protein adsorption patterns, e.g., the composition of the oil phase, stabilizer layer and drug incorporation into the interface or oil core. Data were re-evaluated and compared, and the implications for the in vivo distribution are discussed. Major results are that the interfacial composition of the stabilizer layer is the main determining factor and that this composition can be modulated by simple processes. Drug incorporation affects the pattern depending on the localization of the drug (oil core versus interface. The data situation regarding in vivo effects is very limited; mainly, it has to be referred to in the in vivo data of polymeric nanoparticles. As a conclusion, determination of the protein adsorption patterns can accelerate IV nanoemulsion formulation development regarding optimized organ distribution and related pharmacokinetics.

  9. Development of a fast thermal response microfluidic system using liquid metal

    Science.gov (United States)

    Gao, Meng; Gui, Lin

    2016-07-01

    Room temperature liquid metal gallium alloy has been widely used in many micro-electromechanical systems applications, such as on-chip electrical microheaters, micro temperature sensors, micro pumps and so on. Injecting liquid metal into microchannels can provide a simple, rapid, low-cost but efficient way to integrate these elements in microfluidic chips with high accuracy. The liquid metal-filled microstructures can be designed in any shape and easily integrated into microfluidic chips. In this paper, an on-chip liquid metal-based thermal microfluidic system is proposed for quick temperature control at the microscale. The micro system utilizes just one microfluidic chip as a basic working platform, which has liquid metal-based on-chip heaters, temperature sensors and electroosmotic flow pumps. Under the comprehensive control of these elements, the micro system can quickly change the temperature of a target fluid in the microfluidic chip. These liquid metal-based on-chip elements are very helpful for the fabrication and miniaturization of the microfluidic chip. In this paper, deionized water is used to test the temperature control performance of the thermal microfluidic system. According to the experimental results, the micro system can efficiently control the temperature of water ranging from 28 °C to 90 °C. The thermal microfluidic system has great potential for use in many microfluidic applications, such as on-chip polymerase chain reaction, temperature gradient focusing, protein crystallization and chemical synthesis.

  10. Compare local pocket and global protein structure models by small structure patterns

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns; and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11; 669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://www.cbrc.kaust.edu.sa/prosta/

  11. Protein synthesis patterns of Paracoccidiodes brasiliensis isolates in stage-specific forms and during cellular differentiation.

    Science.gov (United States)

    Salem-Izacc, S M; Jesuino, R S; Brito, W A; Pereira, M; Felipe, M S; Soares, C M

    1997-01-01

    In this paper we compared the protein synthesis patterns of Paracoccidioides brasiliensis isolates. The protein profiles were compared for both yeast and mycelial forms and similarity analysis among them was performed by calculating similarity matrices and grouping the isolates in dendrograms. The examined isolates exhibited highly variable cellular morphology at 36 degrees C, when typical yeast cells were expected. On the other hand, at 26 degrees C all the isolates showed mycelial morphology. The analysis of protein synthesis profiles made it possible to cluster the P. brasiliensis isolates into groups that correlated with the morphological data. Interestingly, growth at 36 degrees C strongly decreased the heterogeneity of protein synthesis patterns seen in mycelial isolates. It was possible to cluster the isolates grown at 36 degrees C in three groups based on their two-dimensional protein synthesis analysis. The similarity index observed among the mycelial isolates was lower than that obtained with yeast cells, suggesting a more homogenous gene expression pattern in the host-adapted form than in the saprobic phase.

  12. Laser Direct Writing of Thick Hybrid Polymers for Microfluidic Chips

    OpenAIRE

    Akanksha Singh; Gianmario Scotti; Tiina Sikanen; Ville Jokinen; Sami Franssila

    2014-01-01

    This work presents patterning of thick (10–50 µm) hybrid polymer structures of ORMOCER® by laser direct writing. ORMOCER® combine polymer-like fabrication processes with glass-like surface chemistry that is beneficial for many bio-microfluidic applications. ORMOCER® is liquid before exposure, so patterning is done by contact-free lithography, such as proximity exposure. With laser direct writing, we obtained higher resolution patterns, with smaller radius of curvature (~2–4 µm), compared to p...

  13. Microfluidic desalination. Capacitive deionization on chip for microfluidic sample preparation

    NARCIS (Netherlands)

    Roelofs, Susan Helena

    2015-01-01

    The main aim of the work described in this thesis is to implement the desalination technique capacitive deionization (CDI) on a microfluidic chip to improve the reproducibility in the analysis of biological samples for drug development. Secondly, microfluidic CDI allows for the in situ study of ion

  14. Tyrosine Phosphorylation Pattern in Sperm Proteins Isolated from Normospermic and Teratospermic Men

    Science.gov (United States)

    Jabbari, Sepideh; Sadeghi, Mohammad Reza; Akhondi, Mohammad Mahdi; Ebrahim Habibi, Azadeh; Amirjanati, Naser; Lakpour, Niknam; Asgharpour, Lima; Ardekani, Ali M.

    2009-01-01

    Introduction In mammalian system, spermatozoa are not able to fertilize the oocyte immediately upon ejaculation, thus they undergo a series of biochemical and molecular changes which is termed capacitation. During sperm capacitation, signal transduction pathways are activated which lead to protein tyrosine phosphorylation. Tyrosine phosphorylated proteins have an important role in sperm capacitation such as hyperactive motility, interaction with zona pellucida and acrosome reaction. Evaluation of tyrosine phosphorylation pattern is important for further understanding of molecular mechanisms of fertilization and the etiology of sperm dysfunctions and abnormalities such as teratospermia. The goal of this study is to characterize tyrosine phosphorylation pattern in sperm proteins isolated from normospermic and teratospermic infertile men attending Avicenna Infertility Clinic in Tehran. Materials and Methods Semen samples were collected and the spermatozoa were isolated using Percoll gradient centrifugation. Then the spermatozoa were incubated up to 6h at 37°C with 5% CO2 in 3% Bovine Serum Albumin-supplemented Ham's F-10 for capacitation to take place. The total proteins from spermatozoa were extracted and were subjected to SDS-PAGE before and after capacitation. To evaluate protein tyrosine phosphorylation pattern, western blotting with specific antibody against phosphorylated tyrosines was performed. Results The results upon western blotting showed: 1) at least six protein bands were detected before capacitation in the spermatozoa from normospermic samples. However, comparable levels of tyrosine phosphorylation was not observed in the spermatozoa from teratospermic samples. 2) The intensity of protein tyrosine phosphorylation appears to have been increased during capacitation in the normospermic relative to the teratospermic group. Conclusion For the first time, these findings demonstrate and suggest that the differences in the types of proteins and diminished

  15. Association between dietary pattern and serum C-reactive protein in Japanese men and women.

    Science.gov (United States)

    Nanri, Hinako; Nakamura, Kazuyo; Hara, Megumi; Higaki, Yasuki; Imaizumi, Takeshi; Taguchi, Naoto; Sakamoto, Tatsuhiko; Horita, Mikako; Shinchi, Koichi; Tanaka, Keitaro

    2011-01-01

    Dietary pattern may influence the risks of cardiovascular disease, atherosclerosis, type 2 diabetes, and metabolic syndrome through its effects on inflammation. We evaluated the association between dietary pattern and serum high-sensitivity C-reactive protein (hs-CRP) in a Japanese population. In this cross-sectional analysis, we used baseline data from 3905 men and 5640 women (age 40-69 years) who participated in a population-based cohort study between November 2005 and December 2007. Participants with possible inflammation-related diseases, current analgesic use, high hs-CRP levels (≥3000 ng/mL) or extreme dietary energy intake were excluded. We used 46 items from a validated short food frequency questionnaire and examined major dietary patterns by factor analysis. We identified 5 dietary patterns: healthy (high in vegetables and fruit), Western (high in meat and fried foods), seafood (high in shellfish, squid, fish, etc.), bread (high in bread and low in rice), and dessert (high in confections and fruit). After adjustment for age, alcohol use, smoking, physical activity, and body mass index, hs-CRP levels in men were inversely associated with the healthy, bread, and dessert patterns (P-trend: 0.01, 0.06, and <0.01, respectively) and positively associated with the seafood pattern (P-trend = 0.02). In women, hs-CRP levels were inversely associated with the healthy pattern (P-trend = 0.06) and positively associated with the Western pattern (P-trend = 0.06). The healthy dietary pattern may be associated with suppressed inflammation in Japanese men and women, independently of body mass index and other factors. The sex-specific associations of hs-CRP with other dietary patterns (eg, the seafood pattern) require further study.

  16. Distinct expression patterns of ICK/MAK/MOK protein kinases in the intestine implicate functional diversity.

    Directory of Open Access Journals (Sweden)

    Tufeng Chen

    Full Text Available ICK/MRK (intestinal cell kinase/MAK-related kinase, MAK (male germ cell-associated kinase, and MOK (MAPK/MAK/MRK-overlapping kinase are closely related serine/threonine protein kinases in the protein kinome. The biological functions and regulatory mechanisms of the ICK/MAK/MOK family are still largely elusive. Despite significant similarities in their catalytic domains, they diverge markedly in the sequence and structural organization of their C-terminal non-catalytic domains, raising the question as to whether they have distinct, overlapping, or redundant biological functions. In order to gain insights into their biological activities and lay a fundamental groundwork for functional studies, we investigated the spatio-temporal distribution patterns and the expression dynamics of ICK/MAK/MOK protein kinases in the intestine. We found that ICK/MAK/MOK proteins display divergent expression patterns along the duodenum-to-colon axis and during postnatal murine development. Furthermore, they are differentially partitioned between intestinal epithelium and mesenchyme. A significant increase in the protein level of ICK, but not MAK, was induced in human primary colon cancer specimens. ICK protein level was up-regulated whereas MOK protein level was down-regulated in mouse intestinal adenomas as compared with their adjacent normal intestinal mucosa. These data suggest distinct roles for ICK/MAK/MOK protein kinases in the regulation of intestinal neoplasia. Taken together, our findings demonstrate that the expressions of ICK/MAK/MOK proteins in the intestinal tract can be differentially and dynamically regulated, implicating a significant functional diversity within this group of protein kinases.

  17. Microfluidic liquid chromatography system for proteomic applications and biomarker screening.

    Science.gov (United States)

    Lazar, Iulia M; Trisiripisal, Phichet; Sarvaiya, Hetal A

    2006-08-01

    A microfluidic liquid chromatography (LC) system for proteomic investigations that integrates all the necessary components for stand-alone operation, i.e., pump, valve, separation column, and electrospray interface, is described in this paper. The overall size of the LC device is small enough to enable the integration of two fully functional separation systems on a 3 in. x 1 in. glass microchip. A multichannel architecture that uses electroosmotic pumping principles provides the necessary functionality for eluent propulsion and sample valving. The flow rates generated within these chips are fully consistent with the requirements of nano-LC platforms that are routinely used in proteomic applications. The microfluidic device was evaluated for the analysis of a protein digest obtained from the MCF7 breast cancer cell line. The cytosolic protein extract was processed according to a shotgun protocol, and after tryptic digestion and prefractionation using strong cation exchange chromatography (SCX), selected sample subfractions were analyzed with conventional and microfluidic LC platforms. Using similar experimental conditions, the performance of the microchip LC was comparable to that obtained with benchtop instrumentation, providing an overlap of 75% in proteins that were identified by more than two unique peptides. The microfluidic LC analysis of a protein-rich SCX fraction enabled the confident identification of 77 proteins by using conventional data filtering parameters, of 39 proteins with p screening applications.

  18. Protein coverage on polymer nanolayers leading to mesenchymal stem cell patterning.

    Science.gov (United States)

    You, Jungmok; Yoshida, Akihito; Heo, June Seok; Kim, Han-Soo; Kim, Hyun Ok; Tamada, Kaoru; Kim, Eunkyoung

    2011-10-21

    Interactions of gelatin and albumin with a photo-reactive diphenylamino-s-triazine bridged p-phenylene vinylene polymer (DTOPV) were examined by using surface plasmon resonance (SPR) spectroscopy to explore the effect of the polymer structure on protein coverage of DTOPV nanofilms. The SPR data revealed a significant increase of gelatin adsorption on UV-DTOPV nanofilms, while the adsorption of albumin was decreased by UV exposure in the time frame of the experiment. We also found that the selective adsorption of these proteins was highly dependent on the protein concentration; the highest selectivity of protein adsorption was obtained at the lowest concentration (3.5 μg ml(-1)), while no selective adsorption was confirmed at high concentrations (350 and 1000 μg ml(-1)). The selective attachment of mesenchymal stem cells (MSCs) was directly correlated with the selective adsorption of these proteins onto DTOPV nanofilms. The MSCs attachment onto UV-DTOPV films was promoted with only small mass coverage of gelatin, which led to MSC patterning onto the patterned DTOPV nanofilms successfully. The role of cell adhesion proteins that we found in this study will be a clue to elucidate the complex response of biomolecules on functional polymer nanolayers, and contribute to build up biocompatible surfaces on various advanced materials for the sake of cell engineering and medical implants.

  19. Path to Low Cost Microfluidics

    CERN Document Server

    Govyadinov, Alexander N; Kornilovitch, Pavel; Markel, David

    2016-01-01

    The paper describes a novel concept for a low cost microfluidic platform utilizing materials and processes used in low cost thermal inkjet printing. The concept re-purposes the jetting elements to create pumps, mixers, and valves all necessary components for the transport of fluids in a broad range of microfluidic applications.

  20. Microfluidic devices for biological applications

    CSIR Research Space (South Africa)

    Potgieter, S

    2010-01-01

    Full Text Available , faster reaction times and process-specific designs. A microfluidic system typically consists of a series of channels with components like pumps, valves and actuators to control the flow of fluids. One of the applications being worked on is a microfluidic...

  1. Centrifugal microfluidics for biomedical applications.

    Science.gov (United States)

    Gorkin, Robert; Park, Jiwoon; Siegrist, Jonathan; Amasia, Mary; Lee, Beom Seok; Park, Jong-Myeon; Kim, Jintae; Kim, Hanshin; Madou, Marc; Cho, Yoon-Kyoung

    2010-07-21

    The centrifugal microfluidic platform has been a focus of academic and industrial research efforts for almost 40 years. Primarily targeting biomedical applications, a range of assays have been adapted on the system; however, the platform has found limited commercial success as a research or clinical tool. Nonetheless, new developments in centrifugal microfluidic technologies have the potential to establish wide-spread utilization of the platform. This paper presents an in-depth review of the centrifugal microfluidic platform, while highlighting recent progress in the field and outlining the potential for future applications. An overview of centrifugal microfluidic technologies is presented, including descriptions of advantages of the platform as a microfluidic handling system and the principles behind centrifugal fluidic manipulation. The paper also discusses a history of significant centrifugal microfluidic platform developments with an explanation of the evolution of the platform as it pertains to academia and industry. Lastly, we review the few centrifugal microfluidic-based sample-to-answer analysis systems shown to date and examine the challenges to be tackled before the centrifugal platform can be more broadly accepted as a new diagnostic platform. In particular, fully integrated, easy to operate, inexpensive and accurate microfluidic tools in the area of in vitro nucleic acid diagnostics are discussed.

  2. Ultrathin coatings from isocyanate terminated star PEG prepolymers: patterning of proteins on the layers.

    Science.gov (United States)

    Groll, Juergen; Haubensak, Wulf; Ameringer, Thomas; Moeller, Martin

    2005-03-29

    This study presents the easy and fast patterning of low molecular weight molecules that act as binding partners for proteins on Star PEG coatings. These coatings are prepared from isocyanate terminated star shaped prepolymers and form a highly cross-linked network on the substrate in which the stars are connected via urea groups and free amino groups are present. Streptavidin has been patterned on these layers by microcontact printing (muCP) of an amino reactive biotin derivative and consecutive binding of streptavidin to the biotin. Patterns of Ni(2+)-nitriltriacetic acid (NTA) receptors have been prepared by printing amino functional NTA molecules in freshly prepared Star PEG layers that still contain amino reactive isocyanate groups. Complexation of the NTA groups with Ni(II) ions enabled the binding of His-tag enhanced green fluorescent protein (EGFP) in the desired pattern on the substrates. Since the unmodified Star PEG layers prevent unspecific protein adsorption, His-EGFP could selectively be bound to the sample by immersion into crude, nonpurified His-tag EGFP containing cell lysate.

  3. Acoustofluidics 1: Governing equations in microfluidics

    DEFF Research Database (Denmark)

    Bruus, Henrik

    2011-01-01

    Governing equations for microfluidics and basic flow solutions are presented. Equivalent circuit modeling for determining flow rates in microfluidic networks is introduced.......Governing equations for microfluidics and basic flow solutions are presented. Equivalent circuit modeling for determining flow rates in microfluidic networks is introduced....

  4. Protein patterning on polycrystalline silicon-germanium via standard UV lithography for bioMEMS applications

    Energy Technology Data Exchange (ETDEWEB)

    Lenci, S., E-mail: silvia.lenci@gmail.com [Dipartimento di Ingegneria dell' Informazione, University of Pisa, Via G. Caruso 16, I-56122 Pisa (Italy); imec, Kapeldreef 75, Leuven B-3001 (Belgium); Tedeschi, L.; Domenici, C.; Lande, C. [Istituto di Fisiologia Clinica, CNR, via G. Moruzzi 1, Pisa I-56124 (Italy); Nannini, A.; Pennelli, G.; Pieri, F. [Dipartimento di Ingegneria dell' Informazione, University of Pisa, Via G. Caruso 16, I-56122 Pisa (Italy); Severi, S. [imec, Kapeldreef 75, Leuven B-3001 (Belgium)

    2010-10-12

    Polycrystalline silicon-germanium (poly-SiGe) is a promising structural material for the post-processing of micro electro-mechanical systems (MEMS) on top of complementary metal-oxide-semiconductor (CMOS) substrates. Combining MEMS and CMOS allows for the development of high-performance devices. We present for the first time selective protein immobilization on top of poly-SiGe surfaces, an enabling technique for the development of novel poly-SiGe based MEMS biosensors. Active regions made of 3-aminopropyl-triethoxysilane (APTES) were defined using silane deposition onto photoresist patterns followed by lift-off in organic solvents. Subsequently, proteins were covalently bound on the created APTES patterns. Fluorescein-labeled human serum albumin (HSA) was used to verify the immobilization procedure while the binding capability of the protein layer was tested by an antigen-labeled antibody pair. Inspection by fluorescence microscopy showed protein immobilization inside the desired bioactive areas and low non-specific adsorption outside the APTES pattern. Furthermore, the quality of the silane patches was investigated by treatment with 30 nm-diameter gold nanoparticles and scanning electron microscope observation. The developed technique is therefore a promising first step towards the realization of poly-SiGe based biosensors.

  5. Characterizing genes with distinct methylation patterns in the context of protein-protein interaction network: application to human brain tissues.

    Science.gov (United States)

    Li, Yongsheng; Xu, Juan; Chen, Hong; Zhao, Zheng; Li, Shengli; Bai, Jing; Wu, Aiwei; Jiang, Chunjie; Wang, Yuan; Su, Bin; Li, Xia

    2013-01-01

    DNA methylation is an essential epigenetic mechanism involved in transcriptional control. However, how genes with different methylation patterns are assembled in the protein-protein interaction network (PPIN) remains a mystery. In the present study, we systematically dissected the characterization of genes with different methylation patterns in the PPIN. A negative association was detected between the methylation levels in the brain tissues and topological centralities. By focusing on two classes of genes with considerably different methylation levels in the brain tissues, namely the low methylated genes (LMGs) and high methylated genes (HMGs), we found that their organizing principles in the PPIN are distinct. The LMGs tend to be the center of the PPIN, and attacking them causes a more deleterious effect on the network integrity. Furthermore, the LMGs express their functions in a modular pattern and substantial differences in functions are observed between the two types of genes. The LMGs are enriched in the basic biological functions, such as binding activity and regulation of transcription. More importantly, cancer genes, especially recessive cancer genes, essential genes, and aging-related genes were all found more often in the LMGs. Additionally, our analysis presented that the intra-classes communications are enhanced, but inter-classes communications are repressed. Finally, a functional complementation was revealed between methylation and miRNA regulation in the human genome. We have elucidated the assembling principles of genes with different methylation levels in the context of the PPIN, providing key insights into the complex epigenetic regulation mechanisms.

  6. Finite cell-size effects on protein variability in Turing patterned tissues.

    Science.gov (United States)

    Buceta, Javier

    2017-08-01

    Herein we present a framework to characterize different sources of protein expression variability in Turing patterned tissues. In this context, we introduce the concept of granular noise to account for the unavoidable fluctuations due to finite cell-size effects and show that the nearest-neighbours autocorrelation function provides the means to measure it. To test our findings, we perform in silico experiments of growing tissues driven by a generic activator-inhibitor dynamics. Our results show that the relative importance of different sources of noise depends on the ratio between the characteristic size of cells and that of the pattern domains and on the ratio between the pattern amplitude and the effective intensity of the biochemical fluctuations. Importantly, our framework provides the tools to measure and distinguish different stochastic contributions during patterning: granularity versus biochemical noise. In addition, our analysis identifies the protein species that buffer the stochasticity the best and, consequently, it can help to determine key instructive signals in systems driven by a Turing instability. Altogether, we expect our study to be relevant in developmental processes leading to the formation of periodic patterns in tissues. © 2017 The Author(s).

  7. Biased inheritance of the protein PatN frees vegetative cells to initiate patterned heterocyst differentiation.

    Science.gov (United States)

    Risser, Douglas D; Wong, Francis C Y; Meeks, John C

    2012-09-18

    Heterocysts, cells specialized for nitrogen fixation in certain filamentous cyanobacteria, appear singly in a nonrandom spacing pattern along the chain of vegetative cells. A two-stage, biased initiation and competitive resolution model has been proposed to explain the establishment of this spacing pattern. There is substantial evidence that competitive resolution of a subset of cells initiating differentiation occurs by interactions between a self-enhancing activator protein, HetR, and a diffusible pentapeptide inhibitor PatS-5 (RGSGR). Results presented here show that the absence of a unique membrane protein, PatN, in Nostoc punctiforme strain ATCC 29133 leads to a threefold increase in heterocyst frequency and a fourfold decrease in the vegetative cell interval between heterocysts. A PatN-GFP translational fusion shows a pattern of biased inheritance in daughter vegetative cells of ammonium-grown cultures. Inactivation of another heterocyst patterning gene, patA, is epistatic to inactivation of patN, and transcription of patA increases in a patN-deletion strain, implying that patN may function by modulating levels of patA. The presence of PatN is hypothesized to decrease the competency of a vegetative cell to initiate heterocyst differentiation, and the cellular concentration of PatN is dependent on cell division that results in cells transiently depleted of PatN. We suggest that biased inheritance of cell-fate determinants is a phylogenetic domain-spanning paradigm in the development of biological patterns.

  8. Electrophoretic separation of purified myelin: a method to improve the protein pattern resolving.

    Science.gov (United States)

    Ravera, Silvia; Bartolucci, Martina; Barbarito, Giulia; Calzia, Daniela; Panfoli, Isabella

    2013-01-01

    Myelin sheath is a lipid-rich membrane, consisting of 70% lipid and 30% proteins, that is involved in physiological and pathological processes. For this reason its protein composition has been often investigated, principally by two-dimensional electrophoresis; however, the consistent lipid content makes it difficult to obtain good proteins separation. To improve the resolution of myelin proteins in a denaturing monodimensional gel electrophoresis, we examined several mixtures for the denaturation of the sample, utilizing different detergents and reducing agents. The definition of the protein pattern was analyzed by both "Blue Silver" Coomassie staining and Western Blot analysis against myelin basic protein, one of the most represented myelin proteins. The best resolution is observed when the sample was incubated with a mixture containing 1.25% dithiothreitol, 4 M urea, and 1% dodecyl maltoside or 1 % 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate, prior to addition of denaturing agents. In conclusion, this work describes a novel method to improve the separation of myelin proteins in a monodimensional gel electrophoresis. It may be also useful for investigating other lipid-rich samples.

  9. Automated classification of immunostaining patterns in breast tissue from the human protein Atlas

    Directory of Open Access Journals (Sweden)

    Issac Niwas Swamidoss

    2013-01-01

    Full Text Available Background: The Human Protein Atlas (HPA is an effort to map the location of all human proteins (http://www.proteinatlas.org/. It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples. Materials and Methods: The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM features, complex wavelet co-occurrence matrix (CWCM features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM and linear discriminant analysis (LDA classifier. Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue. Results: We present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert. Conclusions: Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for

  10. Analysis of surface protein expression reveals the growth pattern of the gram-negative outer membrane.

    Directory of Open Access Journals (Sweden)

    Tristan S Ursell

    Full Text Available The outer membrane (OM of Gram-negative bacteria is a complex bilayer composed of proteins, phospholipids, lipoproteins, and lipopolysaccharides. Despite recent advances revealing the molecular pathways underlying protein and lipopolysaccharide incorporation into the OM, the spatial distribution and dynamic regulation of these processes remain poorly understood. Here, we used sequence-specific fluorescent labeling to map the incorporation patterns of an OM-porin protein, LamB, by labeling proteins only after epitope exposure on the cell surface. Newly synthesized LamB appeared in discrete puncta, rather than evenly distributed over the cell surface. Further growth of bacteria after labeling resulted in divergence of labeled LamB puncta, consistent with a spatial pattern of OM growth in which new, unlabeled material was also inserted in patches. At the poles, puncta remained relatively stationary through several rounds of division, a salient characteristic of the OM protein population as a whole. We propose a biophysical model of growth in which patches of new OM material are added in discrete bursts that evolve in time according to Stokes flow and are randomly distributed over the cell surface. Simulations based on this model demonstrate that our experimental observations are consistent with a bursty insertion pattern without spatial bias across the cylindrical cell surface, with approximately one burst of ≈ 10(-2 µm(2 of OM material per two minutes per µm(2. Growth by insertion of discrete patches suggests that stochasticity plays a major role in patterning and material organization in the OM.

  11. MICROFLUIDIC COMPONENT CAPABLE OF SELF-SEALING

    DEFF Research Database (Denmark)

    2009-01-01

    A microfluidic component (100) for building a microfluidic system is provided. The microfluidic component (100) can be mounted on a microf luidic breadboard (202) in a manner that allows it to be connected to other microfluidic components (204, 206) without the requirement of additional devices....... The microfluidic component (100) comprises at least one flexible tube piece (102) for transporting a fluid. The microfluidic component (100) also comprises means for applying and maintaining pressure (104) between the flexible tube piece (102) and a tube piece (208, 210) housed in another microfluidic component...

  12. Micro patterning of cell and protein non-adhesive plasma polymerized coatings for biochip applications

    DEFF Research Database (Denmark)

    Bouaidat, Salim; Berendsen, C.; Thomsen, P.;

    2004-01-01

    Micro scale patterning of bioactive surfaces is desirable for numerous biochip applications. Polyethyleneoxide-like (PEO-like) coating with non-fouling functionality has been deposited using low frequency AC plasma polymerization. The non-fouling properties of the coating were tested with human...... cells ( HeLa) and fluorescence labeled proteins (isothiocyanate-labeled bovine serum albumin, i.e. FITC-BSA). The PEO-like coatings were fabricated by plasma polymerization of 12-crown-4 (ppCrown) with plasma polymerized hexene (ppHexene) as adhesion layer. The coatings were micro patterned using...

  13. Protein micro patterned lattices to probe a fundamental lengthscale involved in cell adhesion

    CERN Document Server

    Guillou, Herve; Chaussy, Jacques; Block, Marc R

    2009-01-01

    Cell adhesion, a fundamental process of cell biology is involved in the embryo development and in numerous pathologies especially those related to cancers. We constrained cells to adhere on extracellular matrix proteins patterned in a micro lattices. The actin cytoskeleton is particularly sensitive to this constraint and reproducibly self organizes in simple geometrical patterns. Such highly organized cells are functional and proliferate. We performed statistical analysis of spread cells morphologies and discuss the existence of a fundamental lengthscale associated with active processes required for spreading.

  14. Microfluidic Device for Automated High-Throughput Protein Crystallization Screening by Osmotic Dewatering%基于渗透脱水的自动化蛋白质结晶高通量筛选芯片

    Institute of Scientific and Technical Information of China (English)

    罗娅慧; 李刚; 陈强; 赵建龙

    2012-01-01

    构建了一种基于渗透脱水模式的自动进样微流控结晶芯片.该芯片通过真空预脱气将包含蛋白质和结晶剂的液滴自动分配至结晶微腔阵列中,然后利用集成的一排包含不同浓度盐溶液的透析管道,通过渗透脱水方式经一层聚二甲基硅氧烷(PDMS)膜实现液滴的逐渐浓缩,使之趋于过饱和状态,进而形成结晶.此芯片可一次筛选较宽范围的过饱和状态,实现蛋白质结晶的快速优化.利用模式蛋白溶菌酶的结晶实验验证了该芯片的性能.%A self-dispensing and osmosis-based microfluidic crystallization device was reported. This device automatically dispenses droplets containing protein and precipitant into an array of crystallization chambers by pre-degassing, and then gradually concentrates these droplets at different rates by osmotic dewatering through a polydimethylsiboxane(PDMS) membrane using a row of integrated dialysis channels filled with different concentration of salt solution. This concentration process drives the protein/precipitant mixture into supersaturated , thus tending toward the crystallization state. This device allows for screening a wide range of supersatura-tion in one trial for rapid optimization of protein crystallization. The feasibility of this crystallization device is demonstrated using the model proteins of lysozyme.

  15. Reconfigurable microfluidic pump enabled by opto-electrical-thermal transduction

    Science.gov (United States)

    Takeuchi, Masaru; Hagiwara, Masaya; Haulot, Gauvain; Ho, Chih-Ming

    2013-10-01

    Flexible integration of a microfluidic system comprising pumps, valves, and microchannels was realized by an optoelectronic reconfigurable microchannels (OERM) technique. Projecting a low light fluidic device pattern—e.g., pumps, valves, and channels—onto an OERM platform generates Joule heating and melts the substrate in the bright area on the platform; thus, the fluidic system can be reconfigured by changing the projected light pattern. Hexadecane was used as the substrate of the microfluidic system. The volume change of hexadecane during the liquid-solid phase transition was utilized to generate pumping pressure. The system can pump nanoliters of water within several seconds.

  16. Microfluidic vascular channels in gels using commercial 3D printers

    Science.gov (United States)

    Selvaganapathy, P. Ravi; Attalla, Rana

    2016-03-01

    This paper details the development of a three dimensional (3D) printing system with a modified microfluidic printhead used for the generation of complex vascular tissue scaffolds. The print-head features an integrated coaxial nozzle that allows the fabrication of hollow, calcium-polymerized alginate tubes that can easily be patterned using 3Dbioprinting techniques. This microfluidic design allows the incorporation of a wide range of scaffold materials as well as biological constituents such as cells, growth factors, and ECM material. With this setup, gel constructs with embedded arrays of hollow channels can be created and used as a potential substitute for blood vessel networks.

  17. Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

    DEFF Research Database (Denmark)

    Jensen, Kristina Nedenskov; Jessen, Flemming; Jørgensen, Bo

    2008-01-01

    One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only...... on single spot differences, but on the covariance structure between proteins. However, their outcome is dependent on data scaling, and they may fail in producing valid multivariate models due to the much higher number of "irrelevant" spots present in the gels. The case where only few gels are available...

  18. Rapid, low-cost prototyping of centrifugal microfluidic devices for effective implementation of various microfluidic operations

    CSIR Research Space (South Africa)

    Hugo, S

    2013-10-01

    Full Text Available The work presented here details the implementation of a centrifugal microfluidic platform – the first of its kind in South Africa – as a foundation for the development of various microfluidic operations. Microfluidic systems enable the precise...

  19. Microfluidic Scintillation Detectors

    CERN Multimedia

    Microfluidic scintillation detectors are devices of recent introduction for the detection of high energy particles, developed within the EP-DT group at CERN. Most of the interest for such technology comes from the use of liquid scintillators, which entails the possibility of changing the active material in the detector, leading to an increased radiation resistance. This feature, together with the high spatial resolution and low thickness deriving from the microfabrication techniques used to manufacture such devices, is desirable not only in instrumentation for high energy physics experiments but also in medical detectors such as beam monitors for hadron therapy.

  20. Rapid manufacturing for microfluidics

    CSIR Research Space (South Africa)

    Land, K

    2012-10-01

    Full Text Available . Microfluidics is at the forefront of developing solutions for drug discovery, diagnostics (from glucose tests to malaria and TB testing) and environmental diagnostics (E-coli monitoring of drinking water). In order to quickly implement new designs, a rapid... stream_source_info Land_2012.pdf.txt stream_content_type text/plain stream_size 2089 Content-Encoding ISO-8859-1 stream_name Land_2012.pdf.txt Content-Type text/plain; charset=ISO-8859-1 Rapid manufacturing...

  1. Microfluidic Cell Culture Device

    Science.gov (United States)

    Takayama, Shuichi (Inventor); Cabrera, Lourdes Marcella (Inventor); Heo, Yun Seok (Inventor); Smith, Gary Daniel (Inventor)

    2014-01-01

    Microfluidic devices for cell culturing and methods for using the same are disclosed. One device includes a substrate and membrane. The substrate includes a reservoir in fluid communication with a passage. A bio-compatible fluid may be added to the reservoir and passage. The reservoir is configured to receive and retain at least a portion of a cell mass. The membrane acts as a barrier to evaporation of the bio-compatible fluid from the passage. A cover fluid may be added to cover the bio-compatible fluid to prevent evaporation of the bio-compatible fluid.

  2. Spatial manipulation with microfluidics

    Directory of Open Access Journals (Sweden)

    Benjamin eLin

    2015-04-01

    Full Text Available Biochemical gradients convey information through space, time, and concentration, and are ultimately capable of spatially resolving distinct cellular phenotypes, such as differentiation, proliferation, and migration. How these gradients develop, evolve, and function during development, homeostasis, and various disease states is a subject of intense interest across a variety of disciplines. Microfluidic technologies have become essential tools for investigating gradient sensing in vitro due to their ability to precisely manipulate fluids on demand in well controlled environments at cellular length scales. This minireview will highlight their utility for studying gradient sensing along with relevant applications to biology.

  3. A light writable microfluidic "flash memory": optically addressed actuator array with latched operation for microfluidic applications.

    Science.gov (United States)

    Hua, Zhishan; Pal, Rohit; Srivannavit, Onnop; Burns, Mark A; Gulari, Erdogan

    2008-03-01

    This paper presents a novel optically addressed microactuator array (microfluidic "flash memory") with latched operation. Analogous to the address-data bus mediated memory address protocol in electronics, the microactuator array consists of individual phase-change based actuators addressed by localized heating through focused light patterns (address bus), which can be provided by a modified projector or high power laser pointer. A common pressure manifold (data bus) for the entire array is used to generate large deflections of the phase change actuators in the molten phase. The use of phase change material as the working media enables latched operation of the actuator array. After the initial light "writing" during which the phase is temporarily changed to molten, the actuated status is self-maintained by the solid phase of the actuator without power and pressure inputs. The microfluidic flash memory can be re-configured by a new light illumination pattern and common pressure signal. The proposed approach can achieve actuation of arbitrary units in a large-scale array without the need for complex external equipment such as solenoid valves and electrical modules, which leads to significantly simplified system implementation and compact system size. The proposed work therefore provides a flexible, energy-efficient, and low cost multiplexing solution for microfluidic applications based on physical displacements. As an example, the use of the latched microactuator array as "normally closed" or "normally open" microvalves is demonstrated. The phase-change wax is fully encapsulated and thus immune from contamination issues in fluidic environments.

  4. Microfluidic paper-based biomolecule preconcentrator based on ion concentration polarization.

    Science.gov (United States)

    Han, Sung Il; Hwang, Kyo Seon; Kwak, Rhokyun; Lee, Jeong Hoon

    2016-06-21

    Microfluidic paper-based analytical devices (μPADs) for molecular detection have great potential in the field of point-of-care diagnostics. Currently, a critical problem being faced by μPADs is improving their detection sensitivity. Various preconcentration processes have been developed, but they still have complicated structures and fabrication processes to integrate into μPADs. To address this issue, we have developed a novel paper-based preconcentrator utilizing ion concentration polarization (ICP) with minimal addition on lateral-flow paper. The cation selective membrane (i.e., Nafion) is patterned on adhesive tape, and this tape is then attached to paper-based channels. When an electric field is applied across the Nafion, ICP is initiated to preconcentrate the biomolecules in the paper channel. Departing from previous paper-based preconcentrators, we maintain steady lateral fluid flow with the separated Nafion layer; as a result, fluorescent dyes and proteins (FITC-albumin and bovine serum albumin) are continuously delivered to the preconcentration zone, achieving high preconcentration performance up to 1000-fold. In addition, we demonstrate that the Nafion-patterned tape can be integrated with various geometries (multiplexed preconcentrator) and platforms (string and polymer microfluidic channel). This work would facilitate integration of various ICP devices, including preconcentrators, pH/concentration modulators, and micro mixers, with steady lateral flows in paper-based platforms.

  5. Protein and Glycoprotein Patterns Related to Morphogenesis in Mammillaria gracillis Pfeiff. Tissue Culture

    Directory of Open Access Journals (Sweden)

    Biljana Balen

    2002-01-01

    Full Text Available As plants with Crassulacean Acid Metabolism (CAM, cacti are highly affected by artificial environmental conditions in tissue culture. Plants of Mammillaria gracillis Pfeiff. (Cactaceae propagated in vitro produced callus spontaneously. This habituated callus regenerated normal and hyperhydric shoots without the addition of growth regulators. In order to compare habituated callus with the tumorous one, cactus cells were transformed with two strains of Agrobacterium tumefaciens: the wild strain B6S3 (tumour line TW and the rooty mutant GV3101 (tumour line TR. Gene expression in cactus plants, habituated callus, regenerated shoots and two tumour lines was analysed at the level of cellular and extracellular protein and glycoprotein profiles. Proteins were separated by SDS-polyacrylamide gel electrophoresis and 2-D PAGE electrophoresis and silver stained. Concavalin A-peroxidase staining detected glycoproteins with D-manose in their glycan component on protein blots. Developmentally specific protein patterns of Mammillaria gracillis tissue lines were detected. The 2-D PAGE electrophoresis revealed some tissue specific protein groups. The cellular glycoprotein of 42 kDa detected by ConA was highly expressed in undifferentiated tissues (habituated callus, TW and TR tumours and in hyperhydric regenerants. Tumours produced extracellular proteins of 33, 23 and 22 kDa. The N glycosylation of cellular and extracellular proteins was related to specific developmental stage of cactus tissue.

  6. Automatic classification and pattern discovery in high-throughput protein crystallization trials.

    Science.gov (United States)

    Cumbaa, Christian; Jurisica, Igor

    2005-01-01

    Conceptually, protein crystallization can be divided into two phases search and optimization. Robotic protein crystallization screening can speed up the search phase, and has a potential to increase process quality. Automated image classification helps to increase throughput and consistently generate objective results. Although the classification accuracy can always be improved, our image analysis system can classify images from 1,536-well plates with high classification accuracy (85%) and ROC score (0.87), as evaluated on 127 human-classified protein screens containing 5,600 crystal images and 189,472 non-crystal images. Data mining can integrate results from high-throughput screens with information about crystallizing conditions, intrinsic protein properties, and results from crystallization optimization. We apply association mining, a data mining approach that identifies frequently occurring patterns among variables and their values. This approach segregates proteins into groups based on how they react in a broad range of conditions, and clusters cocktails to reflect their potential to achieve crystallization. These results may lead to crystallization screen optimization, and reveal associations between protein properties and crystallization conditions. We also postulate that past experience may lead us to the identification of initial conditions favorable to crystallization for novel proteins.

  7. Influence of protein source on amino acid uptake patterns and protein utilization in rainbow trout Oncorhynchus mykiss

    DEFF Research Database (Denmark)

    Rolland, Marine; Holm, Jørgen; Dalsgaard, Anne Johanne Tang

    acids to the fishmeal diet level (see Table 1). Amino acid uptake patterns were assessed by the appearance of amino acids in the blood stream following the ingestion of a meal, while dietary protein utilization was evaluated by examining the metabolic response to digestion and ammonium and urea...... described time sampling. Fish were killed by a blow in the head and blood was collected from the caudal vein with heparinized syringes. Plasma and red blood cells content were stored separately at -80 for amino acid content analysis. The ammonium excretion profiles (Figure 1) will be correlated...... with the amino acid profile in the blood and oxygen consumption during digestion to investigate the effect on protein utilization for each treatment...

  8. EXPERIMENTAL STUDY ON THE HOT EMBOSSING POLYMER MICROFLUIDIC CHIP

    Institute of Scientific and Technical Information of China (English)

    HE Yong; FU Jianzhong; CHEN Zichen

    2008-01-01

    Experiments are used to study the fabrication of polymer microfluidic chip with hot embossing method. The pattern fidelity with respect to the process parameters is analyzed. Experiment results show that the relationship between the imprint temperature and the microchannel width is approximately exponential. However, the depth of micro channel isn't sensitive to the imprint temperature. When the imprint pressure is larger than 1 MPa and the imprint time is longer than 2 min, the increasing of imprint pressure and holding time has little impact on the microchannel width. So over long holding time is not needed in hot embossing. Based on the experiment analysis, a series of optimization process parameters is obtained and a fine microfluidic chip is fabricated. The electrophoresis separation experiment are used to verify the microfluidic chip performance after bonding. The results show that 100bp-ladder DNA sample can be separated in less than 5 min successfully.

  9. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants.

    Science.gov (United States)

    Klimmek, Frank; Sjödin, Andreas; Noutsos, Christos; Leister, Dario; Jansson, Stefan

    2006-03-01

    We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

  10. Fabrication of polyimide based microfluidic channels for biosensor devices

    Science.gov (United States)

    Zulfiqar, Azeem; Pfreundt, Andrea; Svendsen, Winnie Edith; Dimaki, Maria

    2015-03-01

    The ever-increasing complexity of the fabrication process of Point-of-care (POC) devices, due to high demand of functional versatility, compact size and ease-of-use, emphasizes the need of multifunctional materials that can be used to simplify this process. Polymers, currently in use for the fabrication of the often needed microfluidic channels, have limitations in terms of their physicochemical properties. Therefore, the use of a multipurpose biocompatible material with better resistance to the chemical, thermal and electrical environment, along with capability of forming closed channel microfluidics is inevitable. This paper demonstrates a novel technique of fabricating microfluidic devices using polyimide (PI) which fulfills the aforementioned properties criteria. A fabrication process to pattern microfluidic channels, using partially cured PI, has been developed by using a dry etching method. The etching parameters are optimized and compared to those used for fully cured PI. Moreover, the formation of closed microfluidic channel on wafer level by bonding two partially cured PI layers or a partially cured PI to glass with high bond strength has been demonstrated. The reproducibility in uniformity of PI is also compared to the most commonly used SU8 polymer, which is a near UV sensitive epoxy resin. The potential applications of PI processing are POC and biosensor devices integrated with microelectronics.

  11. Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids

    Science.gov (United States)

    Choudhury, Pabitra Pal; Jana, Siddhartha Sankar

    2016-01-01

    Comparison of amino acid sequence similarity is the fundamental concept behind the protein phylogenetic tree formation. By virtue of this method, we can explain the evolutionary relationships, but further explanations are not possible unless sequences are studied through the chemical nature of individual amino acids. Here we develop a new methodology to characterize the protein sequences on the basis of the chemical nature of the amino acids. We design various algorithms for studying the variation of chemical group transitions and various chemical group combinations as patterns in the protein sequences. The amino acid sequence of conventional myosin II head domain of 14 family members are taken to illustrate this new approach. We find two blocks of maximum length 6 aa as ‘FPKATD’ and ‘Y/FTNEKL’ without repeating the same chemical nature and one block of maximum length 20 aa with the repetition of chemical nature which are common among all 14 members. We also check commonality with another motor protein sub-family kinesin, KIF1A. Based on our analysis we find a common block of length 8 aa both in myosin II and KIF1A. This motif is located in the neck linker region which could be responsible for the generation of mechanical force, enabling us to find the unique blocks which remain chemically conserved across the family. We also validate our methodology with different protein families such as MYOI, Myosin light chain kinase (MLCK) and Rho-associated protein kinase (ROCK), Na+/K+-ATPase and Ca2+-ATPase. Altogether, our studies provide a new methodology for investigating the conserved amino acids’ pattern in different proteins. PMID:27930687

  12. Expression Pattern of Fatty Acid Binding Proteins in Celiac Disease Enteropathy

    Directory of Open Access Journals (Sweden)

    Natalia M. Bottasso Arias

    2015-01-01

    Full Text Available Celiac disease (CD is an immune-mediated enteropathy that develops in genetically susceptible individuals following exposure to dietary gluten. Severe changes at the intestinal mucosa observed in untreated CD patients are linked to changes in the level and in the pattern of expression of different genes. Fully differentiated epithelial cells express two isoforms of fatty acid binding proteins (FABPs: intestinal and liver, IFABP and LFABP, respectively. These proteins bind and transport long chain fatty acids and also have other important biological roles in signaling pathways, particularly those related to PPARγ and inflammatory processes. Herein, we analyze the serum levels of IFABP and characterize the expression of both FABPs at protein and mRNA level in small intestinal mucosa in severe enteropathy and normal tissue. As a result, we observed higher levels of circulating IFABP in untreated CD patients compared with controls and patients on gluten-free diet. In duodenal mucosa a differential FABPs expression pattern was observed with a reduction in mRNA levels compared to controls explained by the epithelium loss in severe enteropathy. In conclusion, we report changes in FABPs’ expression pattern in severe enteropathy. Consequently, there might be alterations in lipid metabolism and the inflammatory process in the small intestinal mucosa.

  13. Fabrication of a Paper-Based Microfluidic Device to Readily Determine Nitrite Ion Concentration by Simple Colorimetric Assay

    Science.gov (United States)

    Wang, Bo; Lin, Zhiqiang; Wang, Min

    2015-01-01

    Paper-based microfluidic devices (µPAD) are a burgeoning platform of microfluidic analysis technology. The method described herein is for use in undergraduate and high school chemistry laboratories. A simple and convenient µPAD was fabricated by easy patterning of filter paper using a permanent marker pen. The usefulness of the device was…

  14. Nanoscale programmable sequence-specific patterning of DNA scaffolds using RecA protein

    Science.gov (United States)

    Sharma, R.; Davies, A. G.; Wälti, C.

    2012-09-01

    Molecular self-assembly inherent to many biological molecules, in conjunction with suitable molecular scaffolds to facilitate programmable positioning of nanoscale objects, offers a promising approach for the integration of functional nanoscale complexes into macroscopic host devices. Here, we report the use of the protein RecA as a means of highly efficient programmable patterning of double-stranded (ds)DNA molecules with molecular-scale precision at specific locations along the DNA strand. RecA proteins form nucleoprotein filaments with single-stranded (ss)DNA molecules, which are chosen to be of sequence homologous to the desired binding region on the dsDNA scaffold. We show that the patterning yield can be in excess of 85% and we demonstrate that concurrent patterning of multiple locations on the same dsDNA scaffold can be achieved with separation between the assembled nucleoprotein filaments of less than 4 nm. This is an important prerequisite for this programmable and flexible DNA scaffold patterning technique to be employed in molecular- and nanoscale assembly applications.

  15. Recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices.

    Science.gov (United States)

    Sasaki, Naoki

    2012-01-01

    AC electrokinetics is a generic term that refers to an induced motion of particles and fluids under nonuniform AC electric fields. The AC electric fields are formed by application of AC voltages to microelectrodes, which can be easily integrated into microfluidic devices by standard microfabrication techniques. Moreover, the magnitude of the motion is large enough to control the mass transfer on the devices. These advantages are attractive for biomolecular analysis on the microfluidic devices, in which the characteristics of small space and microfluidics have been mainly employed. In this review, I describe recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. The applications include fluid pumping and mixing by AC electrokinetic flow, and manipulation of biomolecules such as DNA and proteins by various AC electrokinetic techniques. Future prospects for highly functional biomolecular analysis on microfluidic devices with the aid of AC electrokinetics are also discussed.

  16. Microcontact printing-based fabrication of digital microfluidic devices.

    Science.gov (United States)

    Watson, Michael W L; Abdelgawad, Mohamed; Ye, George; Yonson, Neal; Trottier, Justin; Wheeler, Aaron R

    2006-11-15

    Digital microfluidics is a fluid manipulation technique in which discrete droplets are actuated on patterned arrays of electrodes. Although there is great enthusiasm for the application of this technique to chemical and biological assays, development has been hindered by the requirement of clean room fabrication facilities. Here, we present a new fabrication scheme, relying on microcontact printing (microCP), an inexpensive technique that does not require clean room facilities. In microCP, an elastomeric poly(dimethylsiloxane) stamp is used to deposit patterns of self-assembled monolayers onto a substrate. We report three different microCP-based fabrication techniques: (1) selective etching of gold-on-glass substrates; (2) direct printing of a suspension of palladium colloids; and (3) indirect trapping of gold colloids from suspension. In method 1, etched gold electrodes are used for droplet actuation; in methods 2 and 3, colloid patterns are used to seed electroless deposition of copper. We demonstrate, for the first time, that digital microfluidic devices can be formed by microCP and are capable of the full range of digital microfluidics operations: dispensing, merging, motion, and splitting. Devices formed by the most robust of the new techniques were comparable in performance to devices formed by conventional methods, at a fraction of the fabrication time. These new techniques for digital microfluidics device fabrication have the potential to facilitate expansion of this technology to any research group, even those without access to conventional microfabrication tools and facilities.

  17. Fabricating PFPE Membranes for Microfluidic Valves and Pumps

    Science.gov (United States)

    Greer, Frank; White, Victor E.; Lee, Michael C.; Willis, Peter A.; Grunthaner, Frank J.; Rolland, Jason; Rolland, Jason

    2009-01-01

    A process has been developed for fabricating membranes of a perfluoropolyether (PFPE) and integrating them into valves and pumps in laboratory-on-achip microfluidic devices. Membranes of poly(tetrafluoroethylene) [PTFE] and poly(dimethylsilane) [PDMS] have been considered for this purpose and found wanting. By making it possible to use PFPE instead of PTFE or PDMS, the present process expands the array of options for further development of microfluidic devices for diverse applications that could include detection of biochemicals of interest, detection of toxins and biowarfare agents, synthesis and analysis of proteins, medical diagnosis, and synthesis of fuels.

  18. Cancer-associated fibroblasts promote non-small cell lung cancer cell invasion by upregulation of glucose-regulated protein 78 (GRP78) expression in an integrated bionic microfluidic device.

    Science.gov (United States)

    Yu, Ting; Guo, Zhe; Fan, Hui; Song, Jing; Liu, Yuanbin; Gao, Zhancheng; Wang, Qi

    2016-05-01

    The tumor microenvironment is comprised of cancer cells and various stromal cells and their respective cellular components. Cancer-associated fibroblasts (CAFs), a major part of the stromal cells, are a key determinant in tumor progression, while glucose-regulated protein (GRP)78 is overexpressed in many human cancers and is involved in tumor invasion and metastasis. This study developed a microfluidic-based three dimension (3D) co-culture device to mimic an in vitro tumor microenvironment in order to investigate tumor cell invasion in real-time. This bionic chip provided significant information regarding the role of GRP78, which may be stimulated by CAFs, to promote non-small cell lung cancer cell invasion in vitro. The data showed that CAF induced migration of NSCLC A549 and SPCA-1 cells in this three-dimensional invasion microdevice, which is confirmed by using the traditional Transwell system. Furthermore, CAF induced GRP78 expression in A549 and SPCA-1 cells to facilitate NSCLC cell migration and invasion, whereas knockdown of GRP78 expression blocked A549 and SPCA-1 cell migration and invasion capacity. In conclusion, these data indicated that CAFs might promote NSCLC cell invasion by up-regulation of GRP78 expression and this bionic chip microdevice is a robust platform to assess the interaction of cancer and stromal cells in tumor environment study.

  19. Microfluidic fuel cells and batteries

    CERN Document Server

    Kjeang, Erik

    2014-01-01

    Microfluidic fuel cells and batteries represent a special type of electrochemical power generators that can be miniaturized and integrated in a microfluidic chip. Summarizing the initial ten years of research and development in this emerging field, this SpringerBrief is the first book dedicated to microfluidic fuel cell and battery technology for electrochemical energy conversion and storage. Written at a critical juncture, where strategically applied research is urgently required to seize impending technology opportunities for commercial, analytical, and educational utility, the intention is

  20. Microfluidic reactor for the radiosynthesis of PET radiotracers

    Energy Technology Data Exchange (ETDEWEB)

    Gillies, J.M. [Cancer Research-UK/UMIST Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom)]. E-mail: jgillies@picr.man.ac.uk; Prenant, C. [Cancer Research-UK/UMIST Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); School of Chemical Engineering and Analytical Sciences, University of Manchester, PO Box 88, Manchester M60 1QD (United Kingdom); Chimon, G.N. [Cancer Research-UK/UMIST Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); School of Chemical Engineering and Analytical Sciences, University of Manchester, PO Box 88, Manchester M60 1QD (United Kingdom); Smethurst, G.J. [Cancer Research-UK/UMIST Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); Perrie, W. [Department of Engineering, University of Liverpool, Liverpool L69 3GH (United Kingdom); Hamblett, I. [Cancer Research-UK/UMIST Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); Dekker, B. [Cancer Research-UK/UMIST Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); Zweit, J. [Cancer Research-UK/UMIST Radiochemical Targeting and Imaging Group, Paterson Institute for Cancer Research, Manchester M20 4BX (United Kingdom); School of Chemical Engineering and Analytical Sciences, University of Manchester, PO Box 88, Manchester M60 1QD (United Kingdom)

    2006-03-15

    Here we show the first application of a microfabricated reaction system to PET radiochemistry, we term 'microfluidic PET'. The short half-life of the positron emitting isotopes and the trace chemical quantities used in radiolabelling make PET radiochemistry amenable to miniaturisation. Microfluidic technologies are capable of controlling and transferring tiny quantities of liquids which allow chemical and biochemical assays to be integrated and carried out on a small scale. Such technologies provide distinct advantages over current methods of PET radiochemical synthesis. To demonstrate 'proof of principle' we have investigated the radiohalogenation of small and large molecular weight molecules using the microfluidic device. These reactions involved the direct radioiodination of the apoptosis marker Annexin V using iodine-124, the indirect radioiodination of the anti-cancer drug doxorubicin from a tin-butyl precursor and the radiosynthesis of 2-[{sup 18}F]FDG from a mannose triflate precursor and fluorine-18 and hence provide a test bed for microfluidic reactions. We demonstrate the rapid radioiodination of the protein Annexin V (40% radiochemical yield within 1 min) and the rapid radiofluorination of 2-[{sup 18}F]FDG (60% radiochemical yield within 4 s) using a polymer microreactor chip. Chromatographic analysis showed that the labelling efficiency of the unoptimised microfluidic chip is comparable to conventional PET radiolabelling reactions.

  1. Protein and alkaloid patterns of the floral nectar in some solanaceous species.

    Science.gov (United States)

    Kerchner, András; Darók, Judit; Bacskay, Ivett; Felinger, Attila; Jakab, Gábor; Farkas, Ágnes

    2015-09-01

    The family Solanaceae includes several melliferous plants, which tend to produce copious amounts of nectar. Floral nectar is a chemically complex aqueous solution, dominated by sugars, but minor components such as amino acids, proteins, flavonoids and alkaloids are present as well. This study aimed at analysing the protein and alkaloid profile of the nectar in seven solanaceous species. Proteins were examined with SDS-PAGE and alkaloids were analyzed with HPLC. The investigation of protein profile revealed significant differences in nectar-protein patterns not only between different plant genera, but also between the three Nicotiana species investigated. SDS-PAGE suggested the presence of several Nectarin proteins with antimicrobial activity in Nicotiana species. The nectar of all tobacco species contained the alkaloid nicotine, N. tabacum having the highest nicotine content. The nectar of Brugmansia suaveolens, Datura stramonium, Hyoscyamus niger and Lycium barbarum contained scopolamine, the highest content of which was measured in B. suaveolens. The alkaloid concentrations in the nectars of most solanaceous species investigated can cause deterrence in honeybees, and the nectar of N. rustica and N. tabacum can be considered toxic for honeybees.

  2. Regulation of gene expression in prediapausing embryos of the silkworm, Bombyx mori: pattern of protein synthesis.

    Science.gov (United States)

    Dorel, C; Coulon, M

    1988-03-01

    Specific qualitative and quantitative changes in protein synthesis occur from the fertilization to the onset of diapause in the silkworm. We have used two-dimensional gel electrophoresis to analyse the patterns of proteins synthesized in prediapausing eggs of Bombyx. This analysis has been carried out with in vivo labelled polypeptides and with proteins synthesized in vitro by RNA isolated at different stages. The oocyte contains an abundant supply of diverse mRNA which are translatable in vitro. A set of proteins with molecular weight range of 68,000 to 74,000 and isoelectric points of 5.85-5.95 (hereafter referred to as No. 30) is specific of the germ-anlage stage. Transcripts encoding the No. 30 proteins are not detectable in oocytes, and inhibition of transcription by actinomycin D indicates that No. 30 mRNA are synthesized de novo. Treating eggs at the germ-anlage stage with 4 N HCl at 46 degrees C prevents diapause and is accompanied by overproduction of No. 30 protein. The induction of No. 30 synthesis is also the main event of the heat shock response. The implications of these findings in relation to early embryonic development and prevention of diapause are discussed.

  3. Biocatalytic process development using microfluidic miniaturized systems

    DEFF Research Database (Denmark)

    Krühne, Ulrich; Heintz, Søren; Ringborg, Rolf Hoffmeyer

    2014-01-01

    The increasing interest in biocatalytic processes means there is a clear need for a new systematic development paradigm which encompasses both protein engineering and process engineering. This paper argues that through the use of a new microfluidic platform, data can be collected more rapidly...... and integrated with process modeling, can provide the basis for validating a reduced number of potential processes. The miniaturized platform should use a smaller reagent inventory and make better use of precious biocatalysts. The EC funded BIOINTENSE project will use ω-transaminase based synthesis of chiral...

  4. Active micromachines: Microfluidics powered by mesoscale turbulence

    CERN Document Server

    Thampi, Sumesh P; Shendruk, Tyler N; Golestanian, Ramin; Yeomans, Julia M

    2016-01-01

    Dense active matter, from bacterial suspensions and microtubule bundles driven by motor proteins to cellular monolayers and synthetic Janus particles, is characterised by mesoscale turbulence, the emergence of chaotic flow structures. By immersing an ordered array of symmetric rotors in an active fluid, we introduce a microfluidic system that exploits spontaneous symmetry breaking in mesoscale turbulence to generate work. The lattice of rotors self-organises into a spin-state where neighbouring discs continuously rotate in permanent alternating directions due to combined hydrodynamic and elastic effects. Our virtual prototype demonstrates a new research direction for the design of micromachines powered by the nematohydrodynamic properties of active turbulence.

  5. Evolutionarily Conserved Pattern of Interactions in a Protein Revealed by Local Thermal Expansion Properties.

    Science.gov (United States)

    Dellarole, Mariano; Caro, Jose A; Roche, Julien; Fossat, Martin; Barthe, Philippe; García-Moreno E, Bertrand; Royer, Catherine A; Roumestand, Christian

    2015-07-29

    The way in which the network of intramolecular interactions determines the cooperative folding and conformational dynamics of a protein remains poorly understood. High-pressure NMR spectroscopy is uniquely suited to examine this problem because it combines the site-specific resolution of the NMR experiments with the local character of pressure perturbations. Here we report on the temperature dependence of the site-specific volumetric properties of various forms of staphylococcal nuclease (SNase), including three variants with engineered internal cavities, as measured with high-pressure NMR spectroscopy. The strong temperature dependence of pressure-induced unfolding arises from poorly understood differences in thermal expansion between the folded and unfolded states. A significant inverse correlation was observed between the global thermal expansion of the folded proteins and the number of strong intramolecular hydrogen bonds, as determined by the temperature coefficient of the backbone amide chemical shifts. Comparison of the identity of these strong H-bonds with the co-evolution of pairs of residues in the SNase protein family suggests that the architecture of the interactions detected in the NMR experiments could be linked to a functional aspect of the protein. Moreover, the temperature dependence of the residue-specific volume changes of unfolding yielded residue-specific differences in expansivity and revealed how mutations impact intramolecular interaction patterns. These results show that intramolecular interactions in the folded states of proteins impose constraints against thermal expansion and that, hence, knowledge of site-specific thermal expansivity offers insight into the patterns of strong intramolecular interactions and other local determinants of protein stability, cooperativity, and potentially also of function.

  6. Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns.

    Science.gov (United States)

    Park, Yungki; Helms, Volkhard

    2006-09-01

    The transmembrane (TM) domains of most membrane proteins consist of helix bundles. The seemingly simple task of TM helix bundle assembly has turned out to be extremely difficult. This is true even for simple TM helix bundle proteins, i.e., those that have the simple form of compact TM helix bundles. Herein, we present a computational method that is capable of generating native-like structural models for simple TM helix bundle proteins having modest numbers of TM helices based on sequence conservation patterns. Thus, the only requirement for our method is the presence of more than 30 homologous sequences for an accurate extraction of sequence conservation patterns. The prediction method first computes a number of representative well-packed conformations for each pair of contacting TM helices, and then a library of tertiary folds is generated by overlaying overlapping TM helices of the representative conformations. This library is scored using sequence conservation patterns, and a subsequent clustering analysis yields five final models. Assuming that neighboring TM helices in the sequence contact each other (but not that TM helices A and G contact each other), the method produced structural models of Calpha atom root-mean-square deviation (CA RMSD) of 3-5 A from corresponding crystal structures for bacteriorhodopsin, halorhodopsin, sensory rhodopsin II, and rhodopsin. In blind predictions, this type of contact knowledge is not available. Mimicking this, predictions were made for the rotor of the V-type Na(+)-adenosine triphosphatase without such knowledge. The CA RMSD between the best model and its crystal structure is only 3.4 A, and its contact accuracy reaches 55%. Furthermore, the model correctly identifies the binding pocket for sodium ion. These results demonstrate that the method can be readily applied to ab initio structure prediction of simple TM helix bundle proteins having modest numbers of TM helices.

  7. Diurnal patterns of soluble amyloid precursor protein metabolites in the human central nervous system.

    Directory of Open Access Journals (Sweden)

    Justyna A Dobrowolska

    Full Text Available The amyloid-β (Aβ protein is diurnally regulated in both the cerebrospinal fluid and blood in healthy adults; circadian amplitudes decrease with aging and the presence of cerebral Aβ deposits. The cause of the Aβ diurnal pattern is poorly understood. One hypothesis is that the Amyloid Precursor Protein (APP is diurnally regulated, leading to APP product diurnal patterns. APP in the central nervous system is processed either via the β-pathway (amyloidogenic, generating soluble APP-β (sAPPβ and Aβ, or the α-pathway (non-amyloidogenic, releasing soluble APP-α (sAPPα. To elucidate the potential contributions of APP to the Aβ diurnal pattern and the balance of the α- and β- pathways in APP processing, we measured APP proteolytic products over 36 hours in human cerebrospinal fluid from cognitively normal and Alzheimer's disease participants. We found diurnal patterns in sAPPα, sAPPβ, Aβ40, and Aβ42, which diminish with increased age, that support the hypothesis that APP is diurnally regulated in the human central nervous system and thus results in Aβ diurnal patterns. We also found that the four APP metabolites were positively correlated in all participants without cerebral Aβ deposits. This positive correlation suggests that the α- and β- APP pathways are non-competitive under normal physiologic conditions where APP availability may be the limiting factor that determines sAPPα and sAPPβ production. However, in participants with cerebral Aβ deposits, there was no correlation of Aβ to sAPP metabolites, suggesting that normal physiologic regulation of cerebrospinal fluid Aβ is impaired in the presence of amyloidosis. Lastly, we found that the ratio of sAPPβ to sAPPα was significantly higher in participants with cerebral Aβ deposits versus those without deposits. Therefore, the sAPPβ to sAPPα ratio may be a useful biomarker for cerebral amyloidosis.

  8. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors.

    Science.gov (United States)

    Lakkaraju, Sirish Kaushik; Yu, Wenbo; Raman, E Prabhu; Hershfeld, Alena V; Fang, Lei; Deshpande, Deepak A; MacKerell, Alexander D

    2015-03-23

    Occluded ligand-binding pockets (LBP) such as those found in nuclear receptors (NR) and G-protein coupled receptors (GPCR) represent a significant opportunity and challenge for computer-aided drug design. To determine free energies maps of functional groups of these LBPs, a Grand-Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) strategy is combined with the Site Identification by Ligand Competitive Saturation (SILCS) methodology. SILCS-GCMC/MD is shown to map functional group affinity patterns that recapitulate locations of functional groups across diverse classes of ligands in the LBPs of the androgen (AR) and peroxisome proliferator-activated-γ (PPARγ) NRs and the metabotropic glutamate (mGluR) and β2-adreneric (β2AR) GPCRs. Inclusion of protein flexibility identifies regions of the binding pockets not accessible in crystal conformations and allows for better quantitative estimates of relative ligand binding affinities in all the proteins tested. Differences in functional group requirements of the active and inactive states of the β2AR LBP were used in virtual screening to identify high efficacy agonists targeting β2AR in Airway Smooth Muscle (ASM) cells. Seven of the 15 selected ligands were found to effect ASM relaxation representing a 46% hit rate. Hence, the method will be of use for the rational design of ligands in the context of chemical biology and the development of therapeutic agents.

  9. Site-selective adsorption of protein induced by a metal pattern on a poly(ethylene terephthalate) surface.

    Science.gov (United States)

    Cao, Jiali; Wu, Zhongkui; Li, Shaoying; Tang, Hongxiao; Mei, Qilin

    2013-11-01

    A novel technique for inducing site-selective adsorption of protein through constructing metal patterns on flexible poly(ethylene terephthalate) surfaces is presented. The substrates were first modified by vacuum ultraviolet (VUV) irradiation through a photomask to introduce regions with different functional groups. Then the designed metal patterns were constructed on the surfaces of VUV-treated substrates. The surface rearrangement was effectively prevented by constructing silver patterns on poly(ethylene terephthalate) surfaces, thus significantly improving the stability and selectivity of protein adsorption on the surfaces. Moreover, the protein-repulsive layer further reinforced the effect. Finally, protein patterns were successfully obtained. As confirmed by fluorescence microscope, field emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS), and static water contact angle measurement, the protein patterns possess both excellent selectivity and high fidelity. Feature size of the protein patterns surrounded by a protein-repulsive layer was exactly the same as that of the photomask. And the grain sizes of silver particles were approximately 50 nm. This work could potentially be used in various fields such as biomedicine, bioelectronic components, and tissue repair and replacement, where selective adsorption of protein is desired.

  10. Development of an enzymatic reactor applying spontaneously adsorbed trypsin on the surface of a PDMS microfluidic device.

    Science.gov (United States)

    Kecskemeti, Adam; Bako, Jozsef; Csarnovics, Istvan; Csosz, Eva; Gaspar, Attila

    2017-03-15

    Herein, a microfluidic device (MD) containing immobilized trypsin for rapid and efficient proteolysis was described. Trypsin was immobilized via non-specific protein adsorption onto the hydrophobic poly(dimethylsiloxane) (PDMS) channel wall of the MD. Peptide mapping of bovine serum albumin (BSA) samples was carried out to estimate the stability of trypsin adsorbed on PDMS surface. Peptide maps of BSA samples were obtained by capillary zone electrophoresis (CZE), the RSD% for migration times were under 1%. Several proteins (hemoglobin, myoglobin, lysozyme, and BSA) in a wide molecular size range (15-70 kDa) were digested efficiently with ∼50 s contact time. The number of separated peaks correlated well with the expected number of peptides formed in the complete tryptic digestion of the proteins. Peptide mass fingerprinting of BSA and human serum was carried out. Trypsin retained its activity for 2 h; within this period, the MD can be used for multiple digestions. The main properties of this device are simple channel pattern, simple immobilization procedure, regenerability, and disposability; all these features make this MD one of the simplest yet applicable enzymatic microreactors. Graphical abstract Development of microfluidic device including a serpentine channel as an enzyme reactor for protein digestion.

  11. A Droplet Microfluidic Platform for Automating Genetic Engineering.

    Science.gov (United States)

    Gach, Philip C; Shih, Steve C C; Sustarich, Jess; Keasling, Jay D; Hillson, Nathan J; Adams, Paul D; Singh, Anup K

    2016-05-20

    We present a water-in-oil droplet microfluidic platform for transformation, culture and expression of recombinant proteins in multiple host organisms including bacteria, yeast and fungi. The platform consists of a hybrid digital microfluidic/channel-based droplet chip with integrated temperature control to allow complete automation and integration of plasmid addition, heat-shock transformation, addition of selection medium, culture, and protein expression. The microfluidic format permitted significant reduction in consumption (100-fold) of expensive reagents such as DNA and enzymes compared to the benchtop method. The chip contains a channel to continuously replenish oil to the culture chamber to provide a fresh supply of oxygen to the cells for long-term (∼5 days) cell culture. The flow channel also replenished oil lost to evaporation and increased the number of droplets that could be processed and cultured. The platform was validated by transforming several plasmids into Escherichia coli including plasmids containing genes for fluorescent proteins GFP, BFP and RFP; plasmids with selectable markers for ampicillin or kanamycin resistance; and a Golden Gate DNA assembly reaction. We also demonstrate the applicability of this platform for transformation in widely used eukaryotic organisms such as Saccharomyces cerevisiae and Aspergillus niger. Duration and temperatures of the microfluidic heat-shock procedures were optimized to yield transformation efficiencies comparable to those obtained by benchtop methods with a throughput up to 6 droplets/min. The proposed platform offers potential for automation of molecular biology experiments significantly reducing cost, time and variability while improving throughput.

  12. Microfluidic Multichannel Flow Cytometer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation is a "Microfluidic Multichannel Flow Cytometer." Several novel concepts are integrated to produce the final design, which is compatible with...

  13. Whole-Teflon microfluidic chips

    National Research Council Canada - National Science Library

    Kangning Ren; Wen Dai; Jianhua Zhou; Jing Su; Hongkai Wu

    2011-01-01

    .... In this work, we present a convenient strategy for fabricating whole-Teflon microfluidic chips with integrated valves that show outstanding inertness to various chemicals and extreme resistance against all solvents...

  14. Overlapping functions of argonaute proteins in patterning and morphogenesis of Drosophila embryos.

    Directory of Open Access Journals (Sweden)

    Wibke J Meyer

    2006-08-01

    Full Text Available Argonaute proteins are essential components of the molecular machinery that drives RNA silencing. In Drosophila, different members of the Argonaute family of proteins have been assigned to distinct RNA silencing pathways. While Ago1 is required for microRNA function, Ago2 is a crucial component of the RNA-induced silencing complex in siRNA-triggered RNA interference. Drosophila Ago2 contains an unusual amino-terminus with two types of imperfect glutamine-rich repeats (GRRs of unknown function. Here we show that the GRRs of Ago2 are essential for the normal function of the protein. Alleles with reduced numbers of GRRs cause specific disruptions in two morphogenetic processes associated with the midblastula transition: membrane growth and microtubule-based organelle transport. These defects do not appear to result from disruption of siRNA-dependent processes but rather suggest an interference of the mutant Ago2 proteins in an Ago1-dependent pathway. Using loss-of-function alleles, we further demonstrate that Ago1 and Ago2 act in a partially redundant manner to control the expression of the segment-polarity gene wingless in the early embryo. Our findings argue against a strict separation of Ago1 and Ago2 functions and suggest that these proteins act in concert to control key steps of the midblastula transition and of segmental patterning.

  15. Perspective: microfluidic applications in microbiology.

    Science.gov (United States)

    Saleh-Lakha, Saleema; Trevors, Jack T

    2010-07-01

    The application of microfluidics technology to microbiology research is an excellent platform for the analysis of microorganisms and their nucleic acids. This technology combines engineering, physics, chemistry, biology and computing to control the devices. In this perspective we discuss how microfluidics can be applied to microbiological research and used in diagnostic applications. We also summarize advantages and limitations of this technology, as well as highlight some recent microbiological applications.

  16. Microfluidics - Sorting particles with light

    DEFF Research Database (Denmark)

    Glückstad, J.

    2004-01-01

    Microfluidic systems have great potential to perform complex chemical and biological processing and analysis on a single disposable chip. That goal is now a step closer with the demonstration of an efficient all-optical particle sorter.......Microfluidic systems have great potential to perform complex chemical and biological processing and analysis on a single disposable chip. That goal is now a step closer with the demonstration of an efficient all-optical particle sorter....

  17. Passive microfluidic array card and reader

    Science.gov (United States)

    Dugan, Lawrence Christopher [Modesto, CA; Coleman, Matthew A [Oakland, CA

    2011-08-09

    A microfluidic array card and reader system for analyzing a sample. The microfluidic array card includes a sample loading section for loading the sample onto the microfluidic array card, a multiplicity of array windows, and a transport section or sections for transporting the sample from the sample loading section to the array windows. The microfluidic array card reader includes a housing, a receiving section for receiving the microfluidic array card, a viewing section, and a light source that directs light to the array window of the microfluidic array card and to the viewing section.

  18. Microfluidic Mechanics and Applications: a Review

    Directory of Open Access Journals (Sweden)

    Sandeep Arya

    2014-01-01

    Full Text Available Microfluidics involves the transportation, splitting and mixing of minute fluids to perform several chemical and biological reactions including drug screening, heating, cooling or dissolution of reagents. Efforts have been made to develop different microfluidic devices, droplets and valves that can stop and resume flow of liquids inside a microchannel. This paper provides the review related to the theory and mechanics of microfluidic devices and fluid flow. Different materials and techniques for fabricating microfluidic devices are discussed. Subsequently, the microfluidic components that are responsible for successful micrfluidic device formation are presented. Finally, recent applications related to the microfluidics are highlighted.

  19. Dewetting of polystyrene thin films on poly(ethylene glycol)-modified surfaces as a simple approach for patterning proteins.

    Science.gov (United States)

    Cai, Yangjun; Newby, Bi-min Zhang

    2008-05-20

    A simple technique for patterning proteins utilizing dewetted polystyrene (PS) droplets is demonstrated. A polystyrene thin film was spin coated on a poly(ethylene glycol) (PEG) silane-modified surface. As the PS film dewets from the surface, upon annealing, to form droplets, the PEG-silane-modified surface is exposed, which retains its capability to resist protein adsorption, and the PS droplets allow the selective adsorption of proteins. In contrast to the undewetted flat PS film, the droplet surface had a greater amount of adsorbed proteins. Atomic force microscopy scans reveal that the roughness of the droplet surface is higher, and a multilayer of proteins results on the droplet surface. Moreover, micro- and nanoscale droplet patterns can easily be achieved by tuning the thickness of PS thin films. Because dewetting approaches for generating ordered dewetting droplets have been successfully generated by others, those approaches could be easily combined with this technique to fabricate ordered protein patterns.

  20. Early, nonciliary role for microtubule proteins in left-right patterning is conserved across kingdoms.

    Science.gov (United States)

    Lobikin, Maria; Wang, Gang; Xu, Jingsong; Hsieh, Yi-Wen; Chuang, Chiou-Fen; Lemire, Joan M; Levin, Michael

    2012-07-31

    Many types of embryos' bodyplans exhibit consistently oriented laterality of the heart, viscera, and brain. Errors of left-right patterning present an important class of human birth defects, and considerable controversy exists about the nature and evolutionary conservation of the molecular mechanisms that allow embryos to reliably orient the left-right axis. Here we show that the same mutations in the cytoskeletal protein tubulin that alter asymmetry in plants also affect very early steps of left-right patterning in nematode and frog embryos, as well as chirality of human cells in culture. In the frog embryo, tubulin α and tubulin γ-associated proteins are required for the differential distribution of maternal proteins to the left or right blastomere at the first cell division. Our data reveal a remarkable molecular conservation of mechanisms initiating left-right asymmetry. The origin of laterality is cytoplasmic, ancient, and highly conserved across kingdoms, a fundamental feature of the cytoskeleton that underlies chirality in cells and multicellular organisms.

  1. Symmetry and scale orient Min protein patterns in shaped bacterial sculptures

    Science.gov (United States)

    Wu, Fabai; van Schie, Bas G. C.; Keymer, Juan E.; Dekker, Cees

    2015-08-01

    The boundary of a cell defines the shape and scale of its subcellular organization. However, the effects of the cell's spatial boundaries as well as the geometry sensing and scale adaptation of intracellular molecular networks remain largely unexplored. Here, we show that living bacterial cells can be ‘sculpted’ into defined shapes, such as squares and rectangles, which are used to explore the spatial adaptation of Min proteins that oscillate pole-to-pole in rod-shaped Escherichia coli to assist cell division. In a wide geometric parameter space, ranging from 2 × 1 × 1 to 11 × 6 × 1 μm3, Min proteins exhibit versatile oscillation patterns, sustaining rotational, longitudinal, diagonal, stripe and even transversal modes. These patterns are found to directly capture the symmetry and scale of the cell boundary, and the Min concentration gradients scale with the cell size within a characteristic length range of 3-6 μm. Numerical simulations reveal that local microscopic Turing kinetics of Min proteins can yield global symmetry selection, gradient scaling and an adaptive range, when and only when facilitated by the three-dimensional confinement of the cell boundary. These findings cannot be explained by previous geometry-sensing models based on the longest distance, membrane area or curvature, and reveal that spatial boundaries can facilitate simple molecular interactions to result in far more versatile functions than previously understood.

  2. Spiral microfluidic nanoparticle separators

    Science.gov (United States)

    Bhagat, Ali Asgar S.; Kuntaegowdanahalli, Sathyakumar S.; Dionysiou, Dionysios D.; Papautsky, Ian

    2008-02-01

    Nanoparticles have potential applications in many areas such as consumer products, health care, electronics, energy and other industries. As the use of nanoparticles in manufacturing increases, we anticipate a growing need to detect and measure particles of nanometer scale dimensions in fluids to control emissions of possible toxic nanoparticles. At present most particle separation techniques are based on membrane assisted filtering schemes. Unfortunately their efficiency is limited by the membrane pore size, making them inefficient for separating a wide range of sizes. In this paper, we propose a passive spiral microfluidic geometry for momentum-based particle separations. The proposed design is versatile and is capable of separating particulate mixtures over a wide dynamic range and we expect it will enable a variety of environmental, medical, or manufacturing applications that involve rapid separation of nanoparticles in real-world samples with a wide range of particle components.

  3. Interplay between materials and microfluidics

    Science.gov (United States)

    Hou, Xu; Zhang, Yu Shrike; Santiago, Grissel Trujillo-De; Alvarez, Mario Moisés; Ribas, João; Jonas, Steven J.; Weiss, Paul S.; Andrews, Anne M.; Aizenberg, Joanna; Khademhosseini, Ali

    2017-04-01

    Developments in the field of microfluidics have triggered technological revolutions in many disciplines, including chemical synthesis, electronics, diagnostics, single-cell analysis, micro- and nanofabrication, and pharmaceutics. In many of these areas, rapid growth is driven by the increasing synergy between fundamental materials development and new microfluidic capabilities. In this Review, we critically evaluate both how recent advances in materials fabrication have expanded the frontiers of microfluidic platforms and how the improved microfluidic capabilities are, in turn, furthering materials design. We discuss how various inorganic and organic materials enable the fabrication of systems with advanced mechanical, optical, chemical, electrical and biointerfacial properties — in particular, when these materials are combined into new hybrids and modular configurations. The increasing sophistication of microfluidic techniques has also expanded the range of resources available for the fabrication of new materials, including particles and fibres with specific functionalities, 3D (bio)printed composites and organoids. Together, these advances lead to complex, multifunctional systems, which have many interesting potential applications, especially in the biomedical and bioengineering domains. Future exploration of the interactions between materials science and microfluidics will continue to enrich the diversity of applications across engineering as well as the physical and biomedical sciences.

  4. An LRR-only protein representing a new type of pattern recognition receptor in Chlamys farreri.

    Science.gov (United States)

    Wang, Mengqiang; Wang, Lingling; Guo, Ying; Yi, Qilin; Song, Linsheng

    2016-01-01

    Accumulating evidence has demonstrated that leucine-rich repeat (LRR)-only proteins could mediate protein-ligand and protein-protein interactions and were involved in the immune response. In the present study, an LRR-only protein (designed as CfLRRop-1) was cloned from Zhikong scallop Chlamys farreri. The complete cDNA sequence of CfLRRop-1 contained an open reading frame (ORF) of 1377 bp, which encoded a protein of 458 amino acids. An LRRNT motif, an LRR_7 motif and seven LRR motifs were found in the deduced amino acid sequence of CfLRRop-1. And these seven LRR motifs contained a conserved signature sequence LxxLxLxxNxL. The mRNA transcripts of CfLRRop-1 were constitutively expressed in all the tested tissues, including haemocytes, muscle, mantle, gill, hepatopancreas and gonad, with the highest expression level in hepatopancreas. After the stimulation of lipopolysaccharide (LPS), peptidoglycan (PGN), glucan (GLU) and polyinosinic-polycytidylic acid (poly I:C), the mRNA transcripts of CfLRRop-1 in haemocytes all increased firstly within the first 6 h and secondly during 12-24 h post stimulation. The mRNA expression level of CfLRRop-1 was continuously up-regulated, after the expression of CfTLR (previously identified Toll-like receptor in C. farreri) was suppressed via RNA interference (RNAi). The recombinant CfLRRop-1 protein could directly bind LPS, PGN, GLU and poly I:C, and induce the release of TNF-α in mixed primary cultured scallop haemocytes. These results collectively indicated that CfLRRop-1 would function as a powerful pattern recognition receptor (PRR) and play a pivotal role in the immune response of scallops.

  5. Direct Write Protein Patterns for Multiplexed Cytokine Detection From Live Cells Using Electron Beam Lithography

    Science.gov (United States)

    Lau, Uland Y.; Saxer, Sina S.; Lee, Juneyoung; Bat, Erhan; Maynard, Heather D.

    2016-01-01

    Simultaneous detection of multiple biomarkers, such as extracellular signaling molecules, is a critical aspect in disease profiling and diagnostics. Precise positioning of antibodies on surfaces, especially at the micro- and nano- scale, is important for the improvement of assays, biosensors, and diagnostics on the molecular level, and therefore, the pursuit of device miniaturization for parallel, fast, low-volume assays is a continuing challenge. Here, we describe a multiplexed cytokine immunoassay utilizing electron beam lithography and a trehalose glycopolymer as a resist for the direct writing of antibodies on silicon substrates allowing for micro- and nano-scale precision of protein immobilization. Specifically, anti-interleukin 6 (IL-6) and anti-tumor necrosis factor alpha (TNFα) antibodies were directly patterned. Retention of the specific binding properties of the patterned antibodies was shown by the capture of secreted cytokines from stimulated RAW 264.7 macrophages. A sandwich immunoassay was employed using gold nanoparticles and enhancement with silver for the detection and visualization of bound cytokines to the patterns by localized surface plasmon resonance detected with dark field microscopy. Multiplexing with both IL-6 and TNFα on a single chip was also successfully demonstrated with high specificity and in relevant cell culture conditions and at different times after cell stimulation. The direct fabrication of capture antibody patterns for cytokine detection described here could be useful for biosensing applications. PMID:26679368

  6. Direct Write Protein Patterns for Multiplexed Cytokine Detection from Live Cells Using Electron Beam Lithography.

    Science.gov (United States)

    Lau, Uland Y; Saxer, Sina S; Lee, Juneyoung; Bat, Erhan; Maynard, Heather D

    2016-01-26

    Simultaneous detection of multiple biomarkers, such as extracellular signaling molecules, is a critical aspect in disease profiling and diagnostics. Precise positioning of antibodies on surfaces, especially at the micro- and nanoscale, is important for the improvement of assays, biosensors, and diagnostics on the molecular level, and therefore, the pursuit of device miniaturization for parallel, fast, low-volume assays is a continuing challenge. Here, we describe a multiplexed cytokine immunoassay utilizing electron beam lithography and a trehalose glycopolymer as a resist for the direct writing of antibodies on silicon substrates, allowing for micro- and nanoscale precision of protein immobilization. Specifically, anti-interleukin 6 (IL-6) and antitumor necrosis factor alpha (TNFα) antibodies were directly patterned. Retention of the specific binding properties of the patterned antibodies was shown by the capture of secreted cytokines from stimulated RAW 264.7 macrophages. A sandwich immunoassay was employed using gold nanoparticles and enhancement with silver for the detection and visualization of bound cytokines to the patterns by localized surface plasmon resonance detected with dark-field microscopy. Multiplexing with both IL-6 and TNFα on a single chip was also successfully demonstrated with high specificity and in relevant cell culture conditions and at different times after cell stimulation. The direct fabrication of capture antibody patterns for cytokine detection described here could be useful for biosensing applications.

  7. Developmentally regulated epitopes of cell surface arabinogalactan proteins and their relation to root tissue pattern formation.

    Science.gov (United States)

    Knox, J P; Linstead, P J; Peart, J; Cooper, C; Roberts, K

    1991-11-01

    Two polymorphic forms of an extracellular arabinogalactan protein (AGP1 and AGP2), obtained from the conditioned media of two carrot suspension-cultured cell lines, have been identified in terms of binding of the anti-plasma membrane antibodies JIM4 and MAC207. AGP1 and AGP2 have been used as immunogens to generate further anti-AGP monoclonal antibodies. JIM14 identified an epitope carried by AGP2 and also by glycoproteins of low molecular weight localized to the plant cell wall. In addition, further antibodies (JIM13 and JIM15) identified carbohydrate epitopes of the AGPs that also occur on plasma membrane glycoproteins and are expressed by patterns of cells that reflect cell position at the carrot root apex. Indirect immunofluorescence microscopy indicated that JIM13 recognized the surface of cells forming the epidermis and cells marking the region and axis of the future xylem. JIM15 recognized a pattern of cells directly complementary to the JIM13 pattern. The panel of anti-AGP monoclonal antibodies now available indicates groups of cells within the root meristem that may reflect an early pre-pattern of the tissues of the mature root structure and suggests extensive modulation of cell surface AGPs during cell development and the positioning of cells within the apex.

  8. Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves.

    Science.gov (United States)

    Guo, Feng; Zhou, Weijie; Li, Peng; Mao, Zhangming; Yennawar, Neela H; French, Jarrod B; Huang, Tony Jun

    2015-06-01

    Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable.

  9. Light at night alters daily patterns of cortisol and clock proteins in female Siberian hamsters.

    Science.gov (United States)

    Bedrosian, T A; Galan, A; Vaughn, C A; Weil, Z M; Nelson, R J

    2013-06-01

    Humans and other organisms have adapted to a 24-h solar cycle in response to life on Earth. The rotation of the planet on its axis and its revolution around the sun cause predictable daily and seasonal patterns in day length. To successfully anticipate and adapt to these patterns in the environment, a variety of biological processes oscillate with a daily rhythm of approximately 24 h in length. These rhythms arise from hierarchally-coupled cellular clocks generated by positive and negative transcription factors of core circadian clock gene expression. From these endogenous cellular clocks, overt rhythms in activity and patterns in hormone secretion and other homeostatic processes emerge. These circadian rhythms in physiology and behaviour can be organised by a variety of cues, although they are most potently entrained by light. In recent history, there has been a major change from naturally-occurring light cycles set by the sun, to artificial and sometimes erratic light cycles determined by the use of electric lighting. Virtually every individual living in an industrialised country experiences light at night (LAN) but, despite its prevalence, the biological effects of such unnatural lighting have not been fully considered. Using female Siberian hamsters (Phodopus sungorus), we investigated the effects of chronic nightly exposure to dim light on daily rhythms in locomotor activity, serum cortisol concentrations and brain expression of circadian clock proteins (i.e. PER1, PER2, BMAL1). Although locomotor activity remained entrained to the light cycle, the diurnal fluctuation of cortisol concentrations was blunted and the expression patterns of clock proteins in the suprachiasmatic nucleus and hippocampus were altered. These results demonstrate that chronic exposure to dim LAN can dramatically affect fundamental cellular function and emergent physiology.

  10. Microfluidic large scale integration of viral-host interaction analysis.

    Science.gov (United States)

    Ben-Ari, Ya'ara; Glick, Yair; Kipper, Sarit; Schwartz, Nika; Avrahami, Dorit; Barbiro-Michaely, Efrat; Gerber, Doron

    2013-06-21

    Viral-host interactions represent potential drug targets for novel antiviral strategies (Flisiak et al., Hepatology, 2008, 47, 817-26). Hence, it is important to establish an adequate platform for identifying and analyzing such interactions. In this review, we discuss bottlenecks in conventional protein-protein interaction methodologies and present the contribution of innovative microfluidic-based technologies towards a solution to these problems with respect to viral-host proteomics.

  11. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations

    DEFF Research Database (Denmark)

    Kirk, Isa Kristina; Weinhold, Nils; Belling, Kirstine González-Izarzugaza

    2017-01-01

    Gene copy-number changes influence phenotypes through gene-dosage alteration and subsequent changes of protein complex stoichiometry. Human trisomies where gene copy numbers are increased uniformly over entire chromosomes provide generic cases for studying these relationships. In most trisomies......, gene and protein level alterations have fatal consequences. We used genome-wide protein-protein interaction data to identify chromosome-specific patterns of protein interactions. We found that some chromosomes encode proteins that interact infrequently with each other, chromosome 21 in particular. We...

  12. Distinct protein domains and expression patterns confer divergent axon guidance functions for Drosophila Robo receptors.

    Science.gov (United States)

    Spitzweck, Bettina; Brankatschk, Marko; Dickson, Barry J

    2010-02-05

    The orthogonal array of axon pathways in the Drosophila CNS is constructed in part under the control of three Robo family axon guidance receptors: Robo1, Robo2 and Robo3. Each of these receptors is responsible for a distinct set of guidance decisions. To determine the molecular basis for these functional specializations, we used homologous recombination to create a series of 9 "robo swap" alleles: expressing each of the three Robo receptors from each of the three robo loci. We demonstrate that the lateral positioning of longitudinal axon pathways relies primarily on differences in gene regulation, not distinct combinations of Robo proteins as previously thought. In contrast, specific features of the Robo1 and Robo2 proteins contribute to their distinct functions in commissure formation. These specializations allow Robo1 to prevent crossing and Robo2 to promote crossing. These data demonstrate how diversification of expression and structure within a single family of guidance receptors can shape complex patterns of neuronal wiring.

  13. Accelerating Yeast Prion Biology using Droplet Microfluidics

    Science.gov (United States)

    Ung, Lloyd; Rotem, Assaf; Jarosz, Daniel; Datta, Manoshi; Lindquist, Susan; Weitz, David

    2012-02-01

    Prions are infectious proteins in a misfolded form, that can induce normal proteins to take the misfolded state. Yeast prions are relevant, as a model of human prion diseases, and interesting from an evolutionary standpoint. Prions may also be a form of epigenetic inheritance, which allow yeast to adapt to stressful conditions at rates exceeding those of random mutations and propagate that adaptation to their offspring. Encapsulation of yeast in droplet microfluidic devices enables high-throughput measurements with single cell resolution, which would not be feasible using bulk methods. Millions of populations of yeast can be screened to obtain reliable measurements of prion induction and loss rates. The population dynamics of clonal yeast, when a fraction of the cells are prion expressing, can be elucidated. Furthermore, the mechanism by which certain strains of bacteria induce yeast to express prions in the wild can be deduced. Integrating the disparate fields of prion biology and droplet microfluidics reveals a more complete picture of how prions may be more than just diseases and play a functional role in yeast.

  14. Differential expression patterns of arabinogalactan proteins in Arabidopsis thaliana reproductive tissues

    Science.gov (United States)

    Pereira, Ana Marta; Masiero, Simona; Nobre, Margarida Sofia; Costa, Mário Luís; Solís, María-Teresa; Testillano, Pilar S.; Sprunck, Stefanie; Coimbra, Sílvia

    2014-01-01

    Arabinogalactan proteins (AGPs) are heavily glycosylated proteins existing in all members of the plant kingdom and are differentially distributed through distinctive developmental stages. Here, we showed the individual distributions of specific Arabidopsis AGPs: AGP1, AGP9, AGP12, AGP15, and AGP23, throughout reproductive tissues and indicated their possible roles in several reproductive processes. AGP genes specifically expressed in female tissues were identified using available microarray data. This selection was confirmed by promoter analysis using multiple green fluorescent protein fusions to a nuclear localization signal, β-glucuronidase fusions, and in situ hybridization as approaches to confirm the expression patterns of the AGPs. Promoter analysis allowed the detection of a specific and differential presence of these proteins along the pathway followed by the pollen tube during its journey to reach the egg and the central cell inside the embryo sac. AGP1 was expressed in the stigma, style, transmitting tract, and the chalazal and funiculus tissues of the ovules. AGP9 was present along the vasculature of the reproductive tissues and AGP12 was expressed in the stigmatic cells, chalazal and funiculus cells of the ovules, and in the septum. AGP15 was expressed in all pistil tissues, except in the transmitting tract, while AGP23 was specific to the pollen grain and pollen tube. The expression pattern of these AGPs provides new evidence for the detection of a subset of specific AGPs involved in plant reproductive processes, being of significance for this field of study. AGPs are prominent candidates for male–female communication during reproduction. PMID:25053647

  15. Droplet Microfluidics for Chip-Based Diagnostics

    Directory of Open Access Journals (Sweden)

    Karan V. I. S. Kaler

    2014-12-01

    Full Text Available Droplet microfluidics (DMF is a fluidic handling technology that enables precision control over dispensing and subsequent manipulation of droplets in the volume range of microliters to picoliters, on a micro-fabricated device. There are several different droplet actuation methods, all of which can generate external stimuli, to either actively or passively control the shape and positioning of fluidic droplets over patterned substrates. In this review article, we focus on the operation and utility of electro-actuation-based DMF devices, which utilize one or more micro-/nano-patterned substrates to facilitate electric field-based handling of chemical and/or biological samples. The underlying theory of DMF actuations, device fabrication methods and integration of optical and opto-electronic detectors is discussed in this review. Example applications of such electro-actuation-based DMF devices have also been included, illustrating the various actuation methods and their utility in conducting chip-based laboratory and clinical diagnostic assays.

  16. Microfluidic Flow of Cholesteric Liquid Crystals

    CERN Document Server

    Wiese, Oliver; Henrich, Oliver

    2016-01-01

    We explore the rheology and flow-induced morphological changes of cholesteric liquid crystal patterns subject to Poiseuille flow within a slab geometry, and under different anchoring conditions at the wall. Our focus is particularly on the behaviour of Cholesteric Fingers of the first kind and of Blue Phase II. Depending on the applied pressure gradient, we observe a number of dynamic regimes with different rheological properties. Our results provide the first insight into the flow response of cholesteric phases with fully two- or three-dimensional director field patterns and normal and planar degenerate anchoring conditions as commonly realised in experiments. They are also of high relevance for a fundamental understanding of complex liquid crystals in confinement and an important step towards future microfluidic applications that are based on cholesteric liquid crystals.

  17. Microfluidic flow of cholesteric liquid crystals.

    Science.gov (United States)

    Wiese, Oliver; Marenduzzo, Davide; Henrich, Oliver

    2016-11-16

    We explore the rheology and flow-induced morphological changes of cholesteric liquid crystal patterns subject to Poiseuille flow within a slab geometry, and under different anchoring conditions at the wall. Our focus is particularly on the behaviour of "Cholesteric Fingers of the first kind" and of Blue Phase II. Depending on the applied pressure gradient, we observe a number of dynamic regimes with different rheological properties. Our results provide the first insight into the flow response of cholesteric phases with fully two- or three-dimensional director field patterns and normal and planar degenerate anchoring conditions as commonly realised in experiments. They are also of high relevance for a fundamental understanding of complex liquid crystals in confinement and an important step towards future microfluidic applications that are based on cholesteric liquid crystals.

  18. Interfacial microfluidic transport on micropatterned superhydrophobic textile.

    Science.gov (United States)

    Xing, Siyuan; Jiang, Jia; Pan, Tingrui

    2013-05-21

    Textile-enabled interfacial microfluidics, utilizing fibrous hydrophilic yarns (e.g., cotton) to guide biological reagent flows, has been extended to various biochemical analyses recently. The restricted capillary-driving mechanism, however, persists as a major challenge for continuous and facilitated biofluidic transport. In this paper, we have first introduced a novel interfacial microfluidic transport principle to drive three-dimensional liquid flows on a micropatterned superhydrophobic textile (MST) platform in a more autonomous and controllable manner. Specifically, the MST system utilizes the surface tension-induced Laplace pressure to facilitate the liquid motion along the hydrophilic yarn, in addition to the capillarity present in the fibrous structure. The fabrication of MST is simply accomplished by stitching hydrophilic cotton yarn into a superhydrophobic fabric substrate (contact angle 140 ± 3°), from which well-controlled wetting patterns are established for interfacial microfluidic operations. The geometric configurations of the stitched micropatterns, e.g., the lengths and diameters of the yarn and bundled arrangement, can all influence the transport process, which is investigated both experimentally and theoretically. Two operation modes, discrete and continuous transport, are also presented in detail. In addition, the gravitational effect as well as the droplet removal process have been also considered and quantitatively analysed during the transport process. As a demonstration, an MST design has been implemented on an artificial skin surface to collect and remove sweat in a highly efficient and facilitated means. The results have illustrated that the novel interfacial transport on the textile platform can be potentially extended to a variety of biofluidic collection and removal applications.

  19. Aligning protein sequence and analysing substitution pattern using a class-specific matrix

    Indian Academy of Sciences (India)

    Hai Song Xu; Wen Ke Ren; Xiao Hui Liu; Xiao Qin Li

    2010-06-01

    Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in the ‘twilight zone’ remains an open issue. It is feasible and necessary to construct a new score matrix as more protein structures are resolved. Three structural class-specific score matrices (all-alpha, all-beta and alpha/beta) were constructed based on the structure alignment of low identity proteins of the corresponding structural classes. The class-specific score matrices were significantly better than a structure-derived matrix (HSDM) and three other generalized matrices (BLOSUM30, BLOSUM60 and Gonnet250) in alignment performance tests. The optimized gap penalties presented here also promote alignment performance. The results indicate that different protein classes have distinct amino acid substitution patterns, and an amino acid score matrix should be constructed based on different structural classes. The class-specific score matrices could also be used in profile construction to improve homology detection.

  20. Sex hormones and expression pattern of cytoskeletal proteins in the rat brain throughout pregnancy.

    Science.gov (United States)

    González-Arenas, Aliesha; Piña-Medina, Ana Gabriela; González-Flores, Oscar; Galván-Rosas, Agustín; Porfirio Gómora-Arrati; Camacho-Arroyo, Ignacio

    2014-01-01

    Pregnancy involves diverse changes in brain function that implicate a re-organization in neuronal cytoskeleton. In this physiological state, the brain is in contact with several hormones that it has never been exposed, as well as with very high levels of hormones that the brain has been in touch throughout life. Among the latter hormones are progesterone and estradiol which regulate several brain functions, including learning, memory, neuroprotection, and the display of sexual and maternal behavior. These functions involve changes in the structure and organization of neurons and glial cells that require the participation of cytoskeletal proteins whose expression and activity is regulated by estradiol and progesterone. We have found that the expression pattern of Microtubule Associated Protein 2, Tau, and Glial Fibrillary Acidic Protein changes in a tissue-specific manner in the brain of the rat throughout gestation and the start of lactation, suggesting that these proteins participate in the plastic changes observed in the brain during pregnancy. This article is part of a Special Issue entitled 'Pregnancy and Steroids'.

  1. Studying the expression patterns of OCT4 and SOX2 proteins in regenerating rabbit ear tissue

    Directory of Open Access Journals (Sweden)

    A. S. Javanmard

    2016-06-01

    Full Text Available Epimorphic regeneration in New Zealand rabbit ear is an interesting example of mammalian wound healing in which blastema formation is involved in replacement of injured tissues. It has been suggested that isolated cells from regenerating rabbit ear possess stem-like properties. In this study, we aimed to determine the expression of stemness markers, OCT4 and SOX2 proteins, in regenerating rabbit tissues by immunohistochemistry. Results indicated that both proteins could be detected in epithelial cells, hair follicle cells and perichondrium cells. Expression pattern analysis of OCT4 and SOX2 proteins showed no clear differences between regenerative and non-regenerative control tissues. According to several reports of OCT4 and SOX2 proteins expression in adult stem cells, it could be proposed that OCT4 and SOX2 expressing cells in regenerating rabbit ear tissues are progenitor/adult stem cells which are resident in these tissues, and other markers should be used for detection of blastema cells.

  2. Simple approach to study biomolecule adsorption in polymeric microfluidic channels.

    Science.gov (United States)

    Gubala, Vladimir; Siegrist, Jonathan; Monaghan, Ruairi; O'Reilly, Brian; Gandhiraman, Ram Prasad; Daniels, Stephen; Williams, David E; Ducrée, Jens

    2013-01-14

    Herein a simple analytical method is presented for the characterization of biomolecule adsorption on cyclo olefin polymer (COP, trade name: Zeonor(®)) substrates which are widely used in microfluidic lab-on-a-chip devices. These Zeonor(®) substrates do not possess native functional groups for specific reactions with biomolecules. Therefore, depending on the application, such substrates must be functionalized by surface chemistry methods to either enhance or suppress biomolecular adsorption. This work demonstrates a microfluidic method for evaluating the adsorption of antibodies and oligonucleotides surfaces. The method uses centrifugal microfluidic flow-through chips and can easily be implemented using common equipment such as a spin coater. The working principle is very simple. The user adds 40 L of the solution containing the sample to the starting side of a microfluidic channel, where it is moved through by centrifugal force. Some molecules are adsorbed in the channel. The sample is then collected at the other end in a small reservoir and the biomolecule concentration is measured. As a pilot application, we characterized the adsorption of goat anti-human IgG and a 20-mer DNA on Zeonor(®), and on three types of functionalized Zeonor: 3-aminopropyltriethoxysilane (APTES) modified surface with mainly positive charge, negatively charged surface with immobilized bovine serum albumin (BSA), and neutral, hydrogel-like film with polyethylene glycol (PEG) characteristics. This simple analytical approach adds to the fundamental understanding of the interaction forces in real, microfluidic systems. This method provides a straightforward and rapid way to screen surface compositions and chemistry, and relate these to their effects on the sensitivity and resistance to non-specific binding of bioassays using them. In an additional set of experiments, the surface area of the channels in this universal microfluidic chip was increased by precision milling of microscale

  3. A microfluidic multiplex proteomic immunoassay device for translational research.

    Science.gov (United States)

    Cao, Jing; Seegmiller, Jesse; Hanson, Naomi Q; Zaun, Christopher; Li, Danni

    2015-01-01

    Microfluidic technology has the potential to miniaturize and automate complex laboratory procedures. The objective of this study was to assess a microfluidic immunoassay device, Simple Plex, which simultaneously measured IL-1β, TNF-α, IL-6, and IL-10 in serum samples. This assessment is important to understanding the potentials of this microfluidic device as a valuable tool in translational research efforts. We studied the operational characteristics of Simple Plex, and compared to other immunoassay systems including bead-based (i.e., Bio-Plex(®) from Bio-Rad) and planar micro-spot based (i.e., Multi-Array from Meso Scale Discovery) multiplex assays. We determined imprecisions for each of the Simple Plex assays and evaluated the ability of Simple Plex to detect IL-1β, TNF-α, IL-6, and IL-10 in serum samples. Simple Plex assays required 25 µL serum, and 1.5 h to run 16 samples per cartridge per instrument. Assay imprecisions, evaluated by measurement of 6 replicates in duplicate from a serum pool using three different cartridges, were less than 10 % for all 4 cytokine protein biomarkers, comparable to the imprecisions of traditional ELISAs. The Simple Plex assays were able to detect 32, 95, 97, and 100 % [i.e., percentages of the results within the respective analytical measurement ranges (AMRs)] of IL-1β, TNF-α, IL-6, and IL-10, respectively, in 66 serum samples. Simple Plex is a microfluidic multiplex immunoassay device that offers miniaturized, and automated analysis of protein biomarkers. Microfluidic devices such as Simple Plex represent a promising platform to be used in translational research to measure protein biomarkers in real clinical samples.

  4. Electrorheological fluid-actuated microfluidic pump

    Science.gov (United States)

    Liu, Liyu; Chen, Xiaoqing; Niu, Xize; Wen, Weijia; Sheng, Ping

    2006-08-01

    The authors report the design and implementation of an electrorheological (ER) fluid-actuated microfluidic pump, with programmable digital control. Our microfluidic pump has a multilayered structure fabricated on polydimethylsiloxane by soft-lithographic technique. The ER microfluidic pump exhibits good performance at high pumping frequencies and uniform liquid flow characteristics. It can be easily integrated with other microfluidic components. The programmable control also gives the device flexibility in its operations.

  5. Functional properties of whey proteins affected by heat treatment and hydrodynamic high-pressure shearing.

    Science.gov (United States)

    Dissanayake, M; Vasiljevic, T

    2009-04-01

    Two batches of native whey proteins (WP) were subjected to microfluidization or heat denaturation accompanied by microfluidization, followed by spray drying. Powders were assessed for their solubility, heat stability, coagulation time, and emulsifying and foaming properties. Effects of denaturation and shearing were examined by particle size analysis, differential scanning calorimetry, reducing and nonreducing sodium dodecyl sulfate-PAGE, and size exclusion-HPLC. Heat treatment significantly decreased solubility, whereas the number of microfluidization passes markedly improved solubility. The combined effect of heat and pressure significantly increased heat coagulation time. Emulsifying activity index substantially increased upon heat denaturation and was further enhanced by microfluidization. Emulsion stability appeared unaffected by the combined treatment, but the concentration of adsorbed protein on fat droplets was significantly increased. Foaming properties were diminished by heating. Particle size distribution patterns, sodium dodecyl sulfate-PAGE, and size exclusion-HPLC revealed disappearance of major WP and creation of relatively higher, as well as smaller, molecular weight aggregates as a result of the 2 treatments. The use of heat and microfluidization in combination could be used to stabilize WP against heat by producing microparticulated species that have different surface and colloidal properties compared with native WP. These results have implications for the use of WP as an additive in heat-processed foods.

  6. Genome-wide expression patterns of calcium-dependent protein kinases in Toxoplasma gondii.

    Science.gov (United States)

    Wang, Jin-Lei; Huang, Si-Yang; Zhang, Nian-Zhang; Chen, Jia; Zhu, Xing-Quan

    2015-06-04

    Calcium-dependent protein kinases (CDPKs) are found in plants and some Apicomplexan parasites but not in animals or fungi. CDPKs have been shown to play important roles in various calcium-signaling pathways such as host cell invasion, egress and protein secretion in Toxoplasma gondii. The objectives of the present study were to examine the T. gondii CDPK genes expression patterns during different development stages and stress responses. We carried out a comprehensive expression analysis of CDPK genes based on previously published microarray datasets, and we also used real time quantitative RT-PCR to study ten T. gondii CDPK genes expression patterns under acid, alkali, high temperature and low temperature conditions. Microarrays analysis indicated that some TgCDPK genes exhibited different expression levels in IFN-γ stimuli conditions or at different developmental stages, suggesting that CDPK genes may play different roles in these processes. Expression profiles under low temperature, high temperature, acid and alkaline indicated that most CDPK may be involved in regulating high temperature, acid and alkaline signaling pathways. We present a genome-wide expression analysis of CDPK genes in T. gondii for the first time, and the mRNA levels change with abiotic and biotic stresses, suggesting their functional roles in these processes. These results will provide a solid basis for future functional studies of the CDPK gene family in T. gondii.

  7. Pattern of distribution and cycling of SLOB, Slowpoke channel binding protein, in Drosophila

    Directory of Open Access Journals (Sweden)

    Sheldon Amanda

    2004-01-01

    Full Text Available Abstract Background SLOB binds to and modulates the activity of the Drosophila Slowpoke (dSlo calcium activated potassium channel. Recent microarray analyses demonstrated circadian cycling of slob mRNA. Results We report the mRNA and protein expression pattern of slob in Drosophila heads. slob transcript is present in the photoreceptors, optic lobe, pars intercerebralis (PI neurons and surrounding brain cortex. SLOB protein exhibits a similar distribution pattern, and we show that it cycles in Drosophila heads, in photoreceptor cells and in neurosecretory cells of the PI. The cycling of SLOB is altered in various clock gene mutants, and SLOB is expressed in ectopic locations in tim01 flies. We also demonstrate that SLOB no longer cycles in the PI neurons of Clkjrk flies, and that SLOB expression is reduced in the PI neurons of flies that lack pigment dispersing factor (PDF, a neuropeptide secreted by clock cells. Conclusions These data are consistent with the idea that SLOB may participate in one or more circadian pathways in Drosophila.

  8. Rapid prototyping of microfluidic systems using a PDMS/polymer tape composite.

    Science.gov (United States)

    Kim, Jungkyu; Surapaneni, Rajesh; Gale, Bruce K

    2009-05-01

    Rapid prototyping of microfluidic systems using a combination of double-sided tape and PDMS (polydimethylsiloxane) is introduced. PDMS is typically difficult to bond using adhesive tapes due to its hydrophobic nature and low surface energy. For this reason, PDMS is not compatible with the xurography method, which uses a knife plotter and various adhesive coated polymer tapes. To solve these problems, a PDMS/tape composite was developed and demonstrated in microfluidic applications. The PDMS/tape composite was created by spinning it to make a thin layer of PDMS over double-sided tape. Then the PDMS/tape composite was patterned to create channels using xurography, and bonded to a PDMS slab. After removing the backing paper from the tape, a complete microfluidic system could be created by placing the construct onto nearly any substrate; including glass, plastic or metal-coated glass/silicon substrates. The bond strength was shown to be sufficient for the pressures that occur in typical microfluidic channels used for chemical or biological analysis. This method was demonstrated in three applications: standard microfluidic channels and reactors, a microfluidic system with an integrated membrane, and an electrochemical biosensor. The PDMS/tape composite rapid prototyping technique provides a fast and cost effective fabrication method and can provide easy integration of microfluidic channels with sensors and other components without the need for a cleanroom facility.

  9. Honeycomb-patterned films of polystyrene/poly(ethylene glycol): Preparation, surface aggregation and protein adsorption

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Highly ordered honeycomb-patterned polystyrene (PS)/poly(ethylene glycol) (PEG) films were prepared by a water-assisted method using an improved setup, which facilitated the formation of films with higher regularity, better reproducibility, and larger area of honeycomb structures. Surface aggregation of hydrophilic PEG and adsorption of bovine serum albumin (BSA) on the honeycomb-patterned films were investigated. Field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM) were used to observe the surface morphologies of the films before and after being rinsed with water. As confirmed by the FESEM images and the AFM phase images, PEG was enriched in the pores and could be gradually removed by water. The adsorption of fluorescence-labeled BSA on the films was studied in visual form using laser scanning confocal microscopy. Results clearly demonstrated that the protein-resistant PEG was selectively enriched in the pores. This water-assisted method may be a latent tool to prepare honeycomb-patterned biofunctional surfaces.

  10. Lead exposure in pheochromocytoma cells induces persistent changes in amyloid precursor protein gene methylation patterns.

    Science.gov (United States)

    Li, Yuan-Yuan; Chen, Tian; Wan, Yanjian; Xu, Shun-qing

    2012-08-01

    It has been suggested that lead (Pb) exposure in early life may increase amyloid precursor protein (APP) expression and promote the pathogenesis of Alzheimer's disease in old age. The current study examined whether the DNA methylation patterns of APP gene in rat pheochromocytoma (PC12) cells changed after Pb acetate exposure. Undifferentiated PC12 cells were exposed to three doses of Pb acetate (50, 250, and 500 nM) and one control for 2 days or 1 week. The methylation patterns of APP promoter and global DNA methylation were analyzed. The DNA methyltransferase 1 (DNMT1) expression and the level of amyloid β peptide (Aβ) were also investigated. The results showed that the exposure of the three concentrations of Pb acetate could make the APP promoter hypomethylated. The global DNA methylation level and the expression of DNMT1 were changed in the 500 nM group after 2 days exposure and in the 250 and 500 nM group after 7 days exposure. Thus, Pb may exert neurotoxic effects through mechanisms that alter the global and promoter methylation patterns of APP gene. © 2010 Wiley Periodicals, Inc. Environ Toxicol, 2012. Copyright © 2010 Wiley Periodicals, Inc.

  11. Rapid patterning of 1-D collagenous topography as an ECM protein fibril platform for image cytometry.

    Directory of Open Access Journals (Sweden)

    Niannan Xue

    Full Text Available Cellular behavior is strongly influenced by the architecture and pattern of its interfacing extracellular matrix (ECM. For an artificial culture system which could eventually benefit the translation of scientific findings into therapeutic development, the system should capture the key characteristics of a physiological microenvironment. At the same time, it should also enable standardized, high throughput data acquisition. Since an ECM is composed of different fibrous proteins, studying cellular interaction with individual fibrils will be of physiological relevance. In this study, we employ near-field electrospinning to create ordered patterns of collagenous fibrils of gelatin, based on an acetic acid and ethyl acetate aqueous co-solvent system. Tunable conformations of micro-fibrils were directly deposited onto soft polymeric substrates in a single step. We observe that global topographical features of straight lines, beads-on-strings, and curls are dictated by solution conductivity; whereas the finer details such as the fiber cross-sectional profile are tuned by solution viscosity. Using these fibril constructs as cellular assays, we study EA.hy926 endothelial cells' response to ROCK inhibition, because of ROCK's key role in the regulation of cell shape. The fibril array was shown to modulate the cellular morphology towards a pre-capillary cord-like phenotype, which was otherwise not observed on a flat 2-D substrate. Further facilitated by quantitative analysis of morphological parameters, the fibril platform also provides better dissection in the cells' response to a H1152 ROCK inhibitor. In conclusion, the near-field electrospun fibril constructs provide a more physiologically-relevant platform compared to a featureless 2-D surface, and simultaneously permit statistical single-cell image cytometry using conventional microscopy systems. The patterning approach described here is also expected to form the basics for depositing other protein

  12. Microfluidic devices for cell cultivation and proliferation

    OpenAIRE

    Tehranirokh, Masoomeh; Kouzani, Abbas Z.; Francis, Paul S.; Kanwar, Jagat R.

    2013-01-01

    Microfluidic technology provides precise, controlled-environment, cost-effective, compact, integrated, and high-throughput microsystems that are promising substitutes for conventional biological laboratory methods. In recent years, microfluidic cell culture devices have been used for applications such as tissue engineering, diagnostics, drug screening, immunology, cancer studies, stem cell proliferation and differentiation, and neurite guidance. Microfluidic technology allows dynamic cell cul...

  13. Using a microfluidic device for high-content analysis of cell signaling.

    Science.gov (United States)

    Cheong, Raymond; Wang, Chiaochun Joanne; Levchenko, Andre

    2009-06-16

    Quantitative analysis and understanding of signaling networks require measurements of the location and activities of key proteins over time, at the level of single cells, in response to various perturbations. Microfluidic devices enable such analyses to be conducted in a high-throughput and in a highly controlled manner. We describe in detail how to design and use a microfluidic device to perform such information-rich experiments.

  14. Discovering approximate-associated sequence patterns for protein-DNA interactions

    KAUST Repository

    Chan, Tak Ming

    2010-12-30

    Motivation: The bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental protein-DNA interactions in transcriptional regulation. Extensive efforts have been made to better understand the protein-DNA interactions. Recent mining on exact TF-TFBS-associated sequence patterns (rules) has shown great potentials and achieved very promising results. However, exact rules cannot handle variations in real data, resulting in limited informative rules. In this article, we generalize the exact rules to approximate ones for both TFs and TFBSs, which are essential for biological variations. Results: A progressive approach is proposed to address the approximation to alleviate the computational requirements. Firstly, similar TFBSs are grouped from the available TF-TFBS data (TRANSFAC database). Secondly, approximate and highly conserved binding cores are discovered from TF sequences corresponding to each TFBS group. A customized algorithm is developed for the specific objective. We discover the approximate TF-TFBS rules by associating the grouped TFBS consensuses and TF cores. The rules discovered are evaluated by matching (verifying with) the actual protein-DNA binding pairs from Protein Data Bank (PDB) 3D structures. The approximate results exhibit many more verified rules and up to 300% better verification ratios than the exact ones. The customized algorithm achieves over 73% better verification ratios than traditional methods. Approximate rules (64-79%) are shown statistically significant. Detailed variation analysis and conservation verification on NCBI records demonstrate that the approximate rules reveal both the flexible and specific protein-DNA interactions accurately. The approximate TF-TFBS rules discovered show great generalized capability of exploring more informative binding rules. © The Author 2010. Published by Oxford University Press. All rights reserved.

  15. Douglas Weibel: using microfluidics for microbiology.

    Science.gov (United States)

    Brownlee, Christen

    2010-07-16

    The ubiquity of microorganisms is unparalleled in any other known organism. These creatures surround our outsides and colonize our insides, a fact that has been known for centuries. However, despite their prevalence and long study, many of their characteristics still remain largely unexplained, including how proteins organize within microbial cells and how microbes interact with each other and with their environments. Many of the techniques used to study microorganisms are nearly as old as the knowledge of microorganisms themselves. Seeking new ways to look at microbiology, Douglas Weibel, Ph.D., an assistant professor of biochemistry at the University of Wisconsin-Madison, turned to chemistry. He and his colleagues are using novel microfluidic methods to develop new ways to culture bacteria and small molecules to control the function of proteins in vivo. By combining chemistry with microbiology, Weibel and his team hope to shine new light on this old field.

  16. Expression Pattern Analysis of Zinc Finger Protein Genes in Wheat (Triticum aestivum L.) Under Phosphorus Deprivation

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-juan; GUO Cheng-jin; LU Wen-jing; DUAN Wei-wei; ZHAO Miao; MA Chun-ying; GU Jun-tao; XIAO Kai

    2014-01-01

    Zinc ifnger protein (ZFP) genes comprise a large and diverse gene family, and are involved in biotic and abiotic stress responses in plants. In this study, a total of 126 ZFP genes classiifed into various types in wheat were characterized and subjected to expression pattern analysis under inorganic phosphate (Pi) deprivation. The wheat ZFP genes and their corresponding GenBank numbers were obtained from the information of a 4×44K wheat gene expression microarray chip. They were conifrmed by sequence similarity analysis and named based on their homologs in Brachypodium distachyon or Oriza sativa. Expression analysis based on the microarray chip revealed that these ZFP genes are categorized into 11 classes according to their gene expression patterns in a 24-h of Pi deprivation regime. Among them, ten genes were differentially up-regulated, ten genes differentially down-regulated, and two genes both differentially up-and down-regulated by Pi deprivation. The differentially up-or down-regulated genes exhibited signiifcantly more or less transcripts at one, two, or all of the checking time points (1, 6, and 24 h) of Pi stress in comparison with those of normal growth, respectively. The both differentially up-and down-regulated genes exhibited contrasting expression patterns, of these, TaWRKY70;5 showed significantly up-regulated at 1 and 6 h and down-regulated at 24 h whereas TaAN1AN20-8;2 displayed signiifcantly upregulated at 1 h and downregulated at 6 h under deprivation Pi condition. Real time PCR analysis conifrmed the expression patterns of the differentially expressed genes obtained by the microarray chip. Our results indicate that numerous ZFP genes in wheat respond to Pi deprivation and have provided further insight into the molecular basis that plants respond to Pi deprivation mediated by the ZFP gene family.

  17. Zebrafish Thsd7a is a neural protein required for angiogenic patterning during development.

    Science.gov (United States)

    Wang, Chieh-Huei; Chen, I-Hui; Kuo, Meng-Wei; Su, Pei-Tsu; Lai, Zih-Yin; Wang, Chian-Huei; Huang, Wei-Chang; Hoffman, Jana; Kuo, Calvin J; You, May-Su; Chuang, Yung-Jen

    2011-06-01

    Angiogenesis is a highly organized process under the control of guidance cues that direct endothelial cell (EC) migration. Recently, many molecules that were initially described as regulators of neural guidance were subsequently shown to also direct EC migration. Here, we report a novel protein, thrombospondin type I domain containing 7A (Thsd7a), that is a neural molecule required for directed EC migration during embryonic angiogenesis in zebrafish. Thsd7a is a vertebrate conserved protein. Zebrafish thsd7a transcript was detected along the ventral edge of the neural tube in the developing zebrafish embryos, correlating with the growth path of angiogenic intersegmental vessels (ISVs). Morpholino-knockdown of Thsd7a caused a lateral deviation of angiogenic ECs below the thsd7a-expressing sites, resulting in aberrant ISV patterning. Collectively, our study shows that zebrafish Thsd7a is a neural protein required for ISV angiogenesis, and suggests an important role of Thsd7a in the neurovascular interaction during zebrafish development.

  18. Conservation and divergence of plant LHP1 protein sequences and expression patterns in angiosperms and gymnosperms.

    Science.gov (United States)

    Guan, Hexin; Zheng, Zhengui; Grey, Paris H; Li, Yuhua; Oppenheimer, David G

    2011-05-01

    Floral transition is a critical and strictly regulated developmental process in plants. Mutations in Arabidopsis LIKE HETEROCHROMATIN PROTEIN 1 (AtLHP1)/TERMINAL FLOWER 2 (TFL2) result in early and terminal flowers. Little is known about the gene expression, function and evolution of plant LHP1 homologs, except for Arabidopsis LHP1. In this study, the conservation and divergence of plant LHP1 protein sequences was analyzed by sequence alignments and phylogeny. LHP1 expression patterns were compared among taxa that occupy pivotal phylogenetic positions. Several relatively conserved new motifs/regions were identified among LHP1 homologs. Phylogeny of plant LHP1 proteins agreed with established angiosperm relationships. In situ hybridization unveiled conserved expression of plant LHP1 in the axillary bud/tiller, vascular bundles, developing stamens, and carpels. Unlike AtLHP1, cucumber CsLHP1-2, sugarcane SoLHP1 and maize ZmLHP1, rice OsLHP1 is not expressed in the shoot apical meristem (SAM) and the OsLHP1 transcript level is consistently low in shoots. "Unequal crossover" might have contributed to the divergence in the N-terminal and hinge region lengths of LHP1 homologs. We propose an "insertion-deletion" model for soybean (Glycine max L.) GmLHP1s evolution. Plant LHP1 homologs are more conserved than previously expected, and may favor vegetative meristem identity and primordia formation. OsLHP1 may not function in rice SAM during floral induction.

  19. Binding patterns of seminal plasma plasma proteins on bovine epididymal and ejaculated sperm membrane

    Directory of Open Access Journals (Sweden)

    C.E.A. Souza

    2011-06-01

    Full Text Available The present study was designed to investigate the topographical distribution of seminal plasma (SP proteins on epididymal and ejaculated bovine sperm. Using immunocytochemistry and confocal microscopy the binding patterns of bovine SP proteins BSP-A3, albumin, transferrin, prostaglandin D-synthase (PGDS and nucleobindin in ejaculated and cauda epididymal sperm from adult bulls were evaluated. Experiments were performed using sperm from 5 males. Data showed a positive signal, only detected for anti-PGDS, in the acrosomal cap of epididymal and ejaculated sperm. In ejaculated sperm, a very weak signal for nucleobindin 2 in the midpiece and equatorial regions was detected, using the anti-rat nucleobindin. BSP-A3 was detected on all sperm regions studied, with a more evidenced signal in acrosome and midpiece. However, no binding was detected for albumin or transferrin in neither epididymal nor ejaculated sperm. In conclusion, PGDS, BSP-A3 and nucleobindin interact directly with bovine sperm, with specific topographic distribution. These findings may add to the knowledge of how these proteins modulate sperm functions, thus providing fundamental support for studies designed to evaluate how they influence sperm functions.

  20. Inhibitory effect of common microfluidic materials on PCR outcome

    KAUST Repository

    Kodzius, Rimantas

    2012-02-20

    Microfluidic chips have a variety of applications in the biological sciences and medicine. In contrast with traditional experimental approaches, microfluidics entails lower sample and reagent consumption, allows faster reactions and enables efficient separation. Additionally microfluidics offers other advantages accruing from the fluids’ various distinct behaviors, such as energy dissipation, fluidic resistance, laminar flow, and surface tension. Biological molecules suspended in fluid and transported through microfluidics channels interact with the channel-wall material. This interaction is even stronger in high surface-area-to-volume ratio (SAVR) microfluidic channels. Adsorption and inhibition of biomolecules occur when these materials come in contact with biomolecular reaction components. Polymerase chain reaction (PCR) is a thermal cycling procedure for amplifying target DNA. The PCR compatibility of silicon, silicon dioxide (SiO2) and other surfaces have been studied; however the results are inconclusive. Usually for protein-surface interaction measurements, bulky and expensive equipment is used, such as Atomic Force Microscopy (AFM), Scanning or Transmission Electron Microscopy (SEM, TEM), spectrophotometric protein concentration measurement, Fourier transform infrared spectroscopy (FTIR) or X-Ray photoelectron spectroscopy (XPS). \\tThe PCR reaction components include the DNA template, primers, DNA polymerase (the main component), dNTPs, a buffer, divalent ions (MgCl2), and KCl. \\tWe designed a simple, relatively quick measurement that only requires a PCR cycler; thus it mimics actual conditions in PCR cycling. In our study, we evaluated the inhibitory affect of different materials on PCR, which is one of the most frequently used enzymatic reactions in microfluidics. PCR reaction optimization through choice of surface materials is of the upmost importance, as it enables and improves enzymatic reaction in microfluidics. Our assessment of the PCR

  1. Microfluidic stretchable RF electronics.

    Science.gov (United States)

    Cheng, Shi; Wu, Zhigang

    2010-12-07

    Stretchable electronics is a revolutionary technology that will potentially create a world of radically different electronic devices and systems that open up an entirely new spectrum of possibilities. This article proposes a microfluidic based solution for stretchable radio frequency (RF) electronics, using hybrid integration of active circuits assembled on flex foils and liquid alloy passive structures embedded in elastic substrates, e.g. polydimethylsiloxane (PDMS). This concept was employed to implement a 900 MHz stretchable RF radiation sensor, consisting of a large area elastic antenna and a cluster of conventional rigid components for RF power detection. The integrated radiation sensor except the power supply was fully embedded in a thin elastomeric substrate. Good electrical performance of the standalone stretchable antenna as well as the RF power detection sub-module was verified by experiments. The sensor successfully detected the RF radiation over 5 m distance in the system demonstration. Experiments on two-dimensional (2D) stretching up to 15%, folding and twisting of the demonstrated sensor were also carried out. Despite the integrated device was severely deformed, no failure in RF radiation sensing was observed in the tests. This technique illuminates a promising route of realizing stretchable and foldable large area integrated RF electronics that are of great interest to a variety of applications like wearable computing, health monitoring, medical diagnostics, and curvilinear electronics.

  2. Vibration Induced Microfluidic Atomization

    Science.gov (United States)

    Yeo, Leslie; Qi, Aisha; Friend, James

    2008-11-01

    We demonstrate rapid generation of micron aerosol droplets in a microfluidic device in which a fluid drop is exposed to surface vibration as it sits atop a piezoelectric substrate. Little, however, is understood about the processes by which these droplets form due to the complex hydrodynamic processes that occur across widely varying length and time scales. Through experiments, scaling theory and numerical modelling, we elucidate the interfacial destabilization mechanisms that lead to droplet formation. Droplets form due to the axisymmetric break-up of cylindrical liquid jets ejected as a consequence of interfacial destabilization. Their 10 μm size correlates with the jet radius and the instability wavelength, both determined from a viscous-capillary dominant force balance and confirmed through a numerical solution. With the exception of drops that spread into thin films with thicknesses on the order of the boundary layer dimension, the free surface is always observed to vibrate at the capillary-viscous resonance frequency despite the surface vibration frequency being several orders larger. This is contrary to common assumptions used in deriving subharmonic models resulting in a Mathieu equation, which has commonly led to spurious predictions in the droplet size.

  3. Microfluidic structures for LOC devices designed by laser lithography

    Science.gov (United States)

    Figurova, M.; Pudis, D.; Gaso, P.

    2016-12-01

    Nowadays, lab on a chip (LOC) applications are very popular in the field of biomedicine. LOC device works with biological materials and enables to arrange conventional laboratory operations on a small chip. Philosophy of LOC applications stands on quick and precise diagnostics process and technology, which uses cheap materials with possibility of rapid prototyping. LOC, as a time saving application, works with small volume of samples and reagents and enables better control over the sample. We present fabrication method of functional LOC chip for different biomedical microfluidic applications based on direct laser writing (DLW) lithography. We present fabrication of few types of microfluidic and micro-optic structures with different capabilities created by DLW system. The combination of DLW lithography in photoresist layer deposited on glass substrate and polydimethylsiloxane (PDMS) replica molding process were used for patterning of designed microstructures. Prepared microfluidic and micro-optic structures were observed by confocal microscope and microfluidic flow observations were investigated by conventional optical microscope and CCD camera.

  4. Expression patterns of protein kinases correlate with gene architecture and evolutionary rates.

    Directory of Open Access Journals (Sweden)

    Aleksey Y Ogurtsov

    Full Text Available BACKGROUND: Protein kinase (PK genes comprise the third largest superfamily that occupy approximately 2% of the human genome. They encode regulatory enzymes that control a vast variety of cellular processes through phosphorylation of their protein substrates. Expression of PK genes is subject to complex transcriptional regulation which is not fully understood. PRINCIPAL FINDINGS: Our comparative analysis demonstrates that genomic organization of regulatory PK genes differs from organization of other protein coding genes. PK genes occupy larger genomic loci, have longer introns, spacer regions, and encode larger proteins. The primary transcript length of PK genes, similar to other protein coding genes, inversely correlates with gene expression level and expression breadth, which is likely due to the necessity to reduce metabolic costs of transcription for abundant messages. On average, PK genes evolve slower than other protein coding genes. Breadth of PK expression negatively correlates with rate of non-synonymous substitutions in protein coding regions. This rate is lower for high expression and ubiquitous PKs, relative to low expression PKs, and correlates with divergence in untranslated regions. Conversely, rate of silent mutations is uniform in different PK groups, indicating that differing rates of non-synonymous substitutions reflect variations in selective pressure. Brain and testis employ a considerable number of tissue-specific PKs, indicating high complexity of phosphorylation-dependent regulatory network in these organs. There are considerable differences in genomic organization between PKs up-regulated in the testis and brain. PK genes up-regulated in the highly proliferative testicular tissue are fast evolving and small, with short introns and transcribed regions. In contrast, genes up-regulated in the minimally proliferative nervous tissue carry long introns, extended transcribed regions, and evolve slowly. CONCLUSIONS

  5. Two different immunostaining patterns of beta-amyloid precursor protein (APP) may distinguish traumatic from nontraumatic axonal injury.

    Science.gov (United States)

    Hayashi, Takahito; Ago, Kazutoshi; Nakamae, Takuma; Higo, Eri; Ogata, Mamoru

    2015-09-01

    Immunostaining for beta-amyloid precursor protein (APP) is recognized as an effective tool for detecting traumatic axonal injury, but it also detects axonal injury due to ischemic or other metabolic causes. Previously, we reported two different patterns of APP staining: labeled axons oriented along with white matter bundles (pattern 1) and labeled axons scattered irregularly (pattern 2) (Hayashi et al. (Leg Med (Tokyo) 11:S171-173, 2009). In this study, we investigated whether these two patterns are consistent with patterns of trauma and hypoxic brain damage, respectively. Sections of the corpus callosum from 44 cases of blunt head injury and equivalent control tissue were immunostained for APP. APP was detected in injured axons such as axonal bulbs and varicose axons in 24 of the 44 cases of head injuries that also survived for three or more hours after injury. In 21 of the 24 APP-positive cases, pattern 1 alone was observed in 14 cases, pattern 2 alone was not observed in any cases, and both patterns 1 and 2 were detected in 7 cases. APP-labeled injured axons were detected in 3 of the 44 control cases, all of which were pattern 2. These results suggest that pattern 1 indicates traumatic axonal injury, while pattern 2 results from hypoxic insult. These patterns may be useful to differentiate between traumatic and nontraumatic axonal injuries.

  6. Microfluidic tools toward industrial biotechnology.

    Science.gov (United States)

    Oliveira, Aline F; Pessoa, Amanda C S N; Bastos, Reinaldo G; de la Torre, Lucimara G

    2016-11-01

    Microfluidics is a technology that operates with small amounts of fluids and makes possible the investigation of cells, enzymes, and biomolecules and encapsulation of biocatalysts in a greater variety of conditions than permitted using conventional methods. This review discusses technological possibilities that can be applied in the field of industrial biotechnology, presenting the principal definitions and fundamental aspects of microfluidic parameters to better understand advanced approaches. Specifically, concentration gradient generators, droplet-based microfluidics, and microbioreactors are explored as useful tools that can contribute to industrial biotechnology. These tools present potential applications, inclusive as commercial platforms to optimizing in bioprocesses development as screening cells, encapsulating biocatalysts, and determining critical kinetic parameters. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1372-1389, 2016. © 2016 American Institute of Chemical Engineers.

  7. Magnetic separation in microfluidic systems

    DEFF Research Database (Denmark)

    Smistrup, Kristian

    2007-01-01

    This Ph.D. thesis presents theory, modeling, design, fabrication, experiments and results for microfluidic magnetic separators. A model for magnetic bead movement in a microfluidic channel is presented, and the limits of the model are discussed. The effective magnetic field gradient is defined...... for fabrication of silicon based systems. This fabrication scheme is explained, and it is shown how, it is applied with variations for several designs of magnetic separators. An experimental setup for magnetic separation experiments has been developed. It has been coupled with an image analysis program....... It is shown conceptually how such a system can be applied for parallel biochemical processing in a microfluidic system. ’Passive’ magnetic separators are presented, where on-chip soft magnetic elements are magnetized by an external magnetic field and create strong magnetic fields and gradients inside...

  8. Microfluidic Technologies for Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Sung Kuk Lee

    2011-06-01

    Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

  9. Microfluidic lithography of SAMs on gold to create dynamic surfaces for directed cell migration and contiguous cell cocultures.

    Science.gov (United States)

    Lamb, Brian M; Barrett, Devin G; Westcott, Nathan P; Yousaf, Muhammad N

    2008-08-19

    A straightforward, flexible, and inexpensive method to create patterned self-assembled monolayers (SAMs) on gold using microfluidics-microfluidic lithography-has been developed. Using a microfluidic cassette, alkanethiols were rapidly patterned on gold surfaces to generate monolayers and mixed monolayers. The patterning methodology is flexible and, by controlling the solvent conditions and thiol concentration, permeation of alkanethiols into the surrounding PDMS microfluidic cassette can be advantageously used to create different patterned feature sizes and to generate well-defined SAM surface gradients with a single microfluidic chip. To demonstrate the utility of microfluidic lithography, multiple cell experiments were conducted. By patterning cell adhesive regions in an inert background, a combination of selective masking of the surface and centrifugation achieved spatial and temporal control of patterned cells, enabling the design of both dynamic surfaces for directed cell migration and contiguous cocultures. Cellular division and motility resulted in directed, dynamic migration, while the centrifugation-aided seeding of a second cell line produced contiguous cocultures with multiple sites for heterogeneous cell-cell interactions.

  10. Capillary-driven multiparametric microfluidic chips for one-step immunoassays.

    Science.gov (United States)

    Gervais, Luc; Hitzbleck, Martina; Delamarche, Emmanuel

    2011-09-15

    Here we present a capillary-driven microfluidic chip for "one-step" immunoassays. The chip allows for easy modification of several assay parameters such as the flow rates of sample, the volumes of samples for tests, and the type of reagents and receptors for detecting analytes. We therefore term such a chip a multiparametric chip and illustrate this concept with the integration and release of anti-C-reactive protein (CRP) detection antibodies (dAbs) together with splitting flow of samples containing CRP across lines of anti-CRP capture antibodies (cAbs). The microfluidic chip is fabricated in Si and is sealed with polydimethylsiloxane (PDMS) patterned with cAbs. The microfluidic chip is ∼1.7×3.4 cm(2) and is capable of analyzing 20 μL of human serum in 6 parallel flow paths with a range of flow rates from 3.3 nL s(-1) to 0.46 nL s(-1). An inkjet spotter was used to deposit 10.6 nL of dAb solution in a structure vicinal to the main flow path of the chip. The consequent asymmetric release of dAbs in a stream of human serum is compensated by a Dean flow mixer having 9 mixing loops and a footprint of 2.8 mm × 0.78 mm. The quantity of dAb present in the half of the flow path close to the spotting region decreases from 83% at the entrance of the mixer to 52% in the region after the mixer. The sample is then equally split into 6 reaction chambers and proceeds via connecting channels to 2 μL capillary pumps. The hydraulic resistance of the connecting channels is designed to vary flow rates, and therefore the kinetics of capture of CRP-dAb complexes, from 10 min to 72 min. The increased incubation time leads to a fourfold increase in detection signal in the reaction chamber with the longer incubation time. The concept presented here is flexible and suited for implementing various surface fluorescence immunoassays on a capillary-driven microfluidic chip.

  11. Applications of microfluidics in quantitative biology.

    Science.gov (United States)

    Bai, Yang; Gao, Meng; Wen, Lingling; He, Caiyun; Chen, Yuan; Liu, Chenli; Fu, Xiongfei; Huang, Shuqiang

    2017-10-04

    Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, we present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future. This article is protected by copyright. All rights reserved.

  12. Integration of plasma-assisted surface chemical modification, soft lithography, and protein surface activation for single-cell patterning

    Science.gov (United States)

    Cheng, Q.; Komvopoulos, K.

    2010-07-01

    Surface patterning for single-cell culture was accomplished by combining plasma-assisted surface chemical modification, soft lithography, and protein-induced surface activation. Hydrophilic patterns were produced on Parylene C films deposited on glass substrates by oxygen plasma treatment through the windows of polydimethylsiloxane shadow masks. After incubation first with Pluronic F108 solution and then serum medium overnight, surface seeding with mesenchymal stem cells in serum medium resulted in single-cell patterning. The present method provides a means of surface patterning with direct implications in single-cell culture.

  13. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules.

    Directory of Open Access Journals (Sweden)

    Gregory R Johnson

    2015-12-01

    Full Text Available Characterizing the spatial distribution of proteins directly from microscopy images is a difficult problem with numerous applications in cell biology (e.g. identifying motor-related proteins and clinical research (e.g. identification of cancer biomarkers. Here we describe the design of a system that provides automated analysis of punctate protein patterns in microscope images, including quantification of their relationships to microtubules. We constructed the system using confocal immunofluorescence microscopy images from the Human Protein Atlas project for 11 punctate proteins in three cultured cell lines. These proteins have previously been characterized as being primarily located in punctate structures, but their images had all been annotated by visual examination as being simply "vesicular". We were able to show that these patterns could be distinguished from each other with high accuracy, and we were able to assign to one of these subclasses hundreds of proteins whose subcellular localization had not previously been well defined. In addition to providing these novel annotations, we built a generative approach to modeling of punctate distributions that captures the essential characteristics of the distinct patterns. Such models are expected to be valuable for representing and summarizing each pattern and for constructing systems biology simulations of cell behaviors.

  14. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules.

    Science.gov (United States)

    Johnson, Gregory R; Li, Jieyue; Shariff, Aabid; Rohde, Gustavo K; Murphy, Robert F

    2015-12-01

    Characterizing the spatial distribution of proteins directly from microscopy images is a difficult problem with numerous applications in cell biology (e.g. identifying motor-related proteins) and clinical research (e.g. identification of cancer biomarkers). Here we describe the design of a system that provides automated analysis of punctate protein patterns in microscope images, including quantification of their relationships to microtubules. We constructed the system using confocal immunofluorescence microscopy images from the Human Protein Atlas project for 11 punctate proteins in three cultured cell lines. These proteins have previously been characterized as being primarily located in punctate structures, but their images had all been annotated by visual examination as being simply "vesicular". We were able to show that these patterns could be distinguished from each other with high accuracy, and we were able to assign to one of these subclasses hundreds of proteins whose subcellular localization had not previously been well defined. In addition to providing these novel annotations, we built a generative approach to modeling of punctate distributions that captures the essential characteristics of the distinct patterns. Such models are expected to be valuable for representing and summarizing each pattern and for constructing systems biology simulations of cell behaviors.

  15. Microfluidic Screening of Electric Fields for Electroporation

    Science.gov (United States)

    Garcia, Paulo A.; Ge, Zhifei; Moran, Jeffrey L.; Buie, Cullen R.

    2016-02-01

    Electroporation is commonly used to deliver molecules such as drugs, proteins, and/or DNA into cells, but the mechanism remains poorly understood. In this work a rapid microfluidic assay was developed to determine the critical electric field threshold required for inducing bacterial electroporation. The microfluidic device was designed to have a bilaterally converging channel to amplify the electric field to magnitudes sufficient to induce electroporation. The bacterial cells are introduced into the channel in the presence of SYTOX®, which fluorescently labels cells with compromised membranes. Upon delivery of an electric pulse, the cells fluoresce due to transmembrane influx of SYTOX® after disruption of the cell membranes. We calculate the critical electric field by capturing the location within the channel of the increase in fluorescence intensity after electroporation. Bacterial strains with industrial and therapeutic relevance such as Escherichia coli BL21 (3.65 ± 0.09 kV/cm), Corynebacterium glutamicum (5.20 ± 0.20 kV/cm), and Mycobacterium smegmatis (5.56 ± 0.08 kV/cm) have been successfully characterized. Determining the critical electric field for electroporation facilitates the development of electroporation protocols that minimize Joule heating and maximize cell viability. This assay will ultimately enable the genetic transformation of bacteria and archaea considered intractable and difficult-to-transfect, while facilitating fundamental genetic studies on numerous diverse microbes.

  16. Fabrication of freestanding, microperforated membranes and their applications in microfluidics.

    Science.gov (United States)

    Zheng, Yizhe; Dai, Wen; Ryan, Declan; Wu, Hongkai

    2010-09-27

    This manuscript describes a convenient method for the fabrication of freestanding, microperforated membranes in photocurable polymers using only one step of photolithography. We used photosensitive prepolymers to make the membranes and photolithography to define the micropatterns. We demonstrated the fabrication of single- and multilayer microperforated membranes in SU-8 photoresist and Norland Optical Adhesive prepolymer. These membranes can be used to pattern surfaces in various materials and to fabricate complex three-dimensional microfluidic channel structures.

  17. Microfluidic 3D Helix Mixers

    Directory of Open Access Journals (Sweden)

    Georgette B. Salieb-Beugelaar

    2016-10-01

    Full Text Available Polymeric microfluidic systems are well suited for miniaturized devices with complex functionality, and rapid prototyping methods for 3D microfluidic structures are increasingly used. Mixing at the microscale and performing chemical reactions at the microscale are important applications of such systems and we therefore explored feasibility, mixing characteristics and the ability to control a chemical reaction in helical 3D channels produced by the emerging thread template method. Mixing at the microscale is challenging because channel size reduction for improving solute diffusion comes at the price of a reduced Reynolds number that induces a strictly laminar flow regime and abolishes turbulence that would be desired for improved mixing. Microfluidic 3D helix mixers were rapidly prototyped in polydimethylsiloxane (PDMS using low-surface energy polymeric threads, twisted to form 2-channel and 3-channel helices. Structure and flow characteristics were assessed experimentally by microscopy, hydraulic measurements and chromogenic reaction, and were modeled by computational fluid dynamics. We found that helical 3D microfluidic systems produced by thread templating allow rapid prototyping, can be used for mixing and for controlled chemical reaction with two or three reaction partners at the microscale. Compared to the conventional T-shaped microfluidic system used as a control device, enhanced mixing and faster chemical reaction was found to occur due to the combination of diffusive mixing in small channels and flow folding due to the 3D helix shape. Thus, microfluidic 3D helix mixers can be rapidly prototyped using the thread template method and are an attractive and competitive method for fluid mixing and chemical reactions at the microscale.

  18. Electrofluidics fabricated by space-selective metallization in glass microfluidic structures using femtosecond laser direct writing.

    Science.gov (United States)

    Xu, Jian; Wu, Dong; Hanada, Yasutaka; Chen, Chi; Wu, Sizhu; Cheng, Ya; Sugioka, Koji; Midorikawa, Katsumi

    2013-12-07

    Space-selective metallization of the inside of glass microfluidic structures using femtosecond laser direct-write ablation followed by electroless plating is demonstrated. Femtosecond laser direct writing followed by thermal treatment and successive chemical etching allows us to fabricate three-dimensional microfluidic structures inside photosensitive glass. Then, femtosecond laser ablation followed by electroless metal plating enables flexible deposition of patterned metal films on desired locations of not only the top and bottom walls but also the sidewalls of fabricated microfluidic structures. A volume writing scheme for femtosecond laser irradiation inducing homogeneous ablation on the sidewalls of microfluidic structures is proposed for sidewall metallization. The developed technique is used to fabricate electrofluidics in which microelectric components are integrated into glass microchannels. The fabricated electrofluidics are applied to control the temperature of liquid samples in the microchannels for the enhancement of chemical reactions and to manipulate the movement of biological samples in the microscale space.

  19. Digital microfluidics-enabled single-molecule detection by printing and sealing single magnetic beads in femtoliter droplets.

    Science.gov (United States)

    Witters, Daan; Knez, Karel; Ceyssens, Frederik; Puers, Robert; Lammertyn, Jeroen

    2013-06-07

    Digital microfluidics is introduced as a novel platform with unique advantages for performing single-molecule detection. We demonstrate how superparamagnetic beads, used for capturing single protein molecules, can be printed with unprecedentedly high loading efficiency and single bead resolution on an electrowetting-on-dielectric-based digital microfluidic chip by micropatterning the Teflon-AF surface of the device. By transporting droplets containing suspended superparamagnetic beads over a hydrophilic-in-hydrophobic micropatterned Teflon-AF surface, single beads are trapped inside the hydrophilic microwells due to their selective wettability and tailored dimensions. Digital microfluidics presents the following advantages for printing and sealing magnetic beads for single-molecule detection: (i) droplets containing suspended beads can be transported back and forth over the array of hydrophilic microwells to obtain high loading efficiencies of microwells with single beads, (ii) the use of hydrophilic-in-hydrophobic patterns permits the use of a magnet to speed up the bead transfer process to the wells, while the receding droplet meniscus removes excess beads off the chip surface and thereby shortens the bead patterning time, and (iii) reagents can be transported over the printed beads multiple times, while capillary forces and a magnet hold the printed beads in place. High loading efficiencies (98% with a CV of 0.9%) of single beads in microwells were obtained by transporting droplets of suspended beads over the array 10 times in less than 1 min, which is much higher than previously reported methods (40-60%), while the total surface area needed for performing single-molecule detection can be decreased. The performance of the device was demonstrated by fluorescent detection of the presence of the biotinylated enzyme β-galactosidase on streptavidin-coated beads with a linear dynamic range of 4 orders of magnitude ranging from 10 aM to 90 fM.

  20. Fluid control in microfluidic devices using a fluid conveyance extension and an absorbent microfluidic flow modulator.

    Science.gov (United States)

    Yuen, Po Ki

    2013-05-07

    This article presents a simple method for controlling fluid in microfluidic devices without the need for valves or pumps. A fluid conveyance extension is fluidly coupled to the enclosed outlet chamber of a microfluidic device. After a fluid is introduced into the microfluidic device and saturates the fluid conveyance extension, a fluid flow in the microfluidic device is generated by contacting an absorbent microfluidic flow modulator with the fluid conveyance extension to absorb the fluid from the fluid conveyance extension through capillary action. Since the fluid in the microfluidic device is fluidly coupled with the fluid conveyance extension and the fluid conveyance extension is fluidly coupled with the absorbent microfluidic flow modulator, the absorption rate of the absorbent microfluidic flow modulator, which is the rate at which the absorbent microfluidic flow modulator absorbs fluid, matches the fluid flow rate in the microfluidic device. Thus, the fluid flow rate in the microfluidic device is set by the absorption rate of the absorbent microfluidic flow modulator. Sheath flow and fluid switching applications are demonstrated using this simple fluid control method without the need for valves or pumps. Also, the ability to control the fluid flow rate in the microfluidic device is demonstrated using absorbent microfluidic flow modulators with various absorbent characteristics and dimensions.

  1. Microfluidic device for drug delivery

    Science.gov (United States)

    Beebe, David J. (Inventor); MacDonald, Michael J. (Inventor); Eddington, David T. (Inventor); Mensing, Glennys A. (Inventor)

    2010-01-01

    A microfluidic device is provided for delivering a drug to an individual. The microfluidic device includes a body that defines a reservoir for receiving the drug therein. A valve interconnects the reservoir to an output needle that is insertable into the skin of an individual. A pressure source urges the drug from the reservoir toward the needle. The valve is movable between a closed position preventing the flow of the drug from the reservoir to the output needle and an open position allowing for the flow of the drug from the reservoir to the output needle in response to a predetermined condition in the physiological fluids of the individual.

  2. Microfluidic devices for droplet injection

    Science.gov (United States)

    Aubrecht, Donald; Akartuna, Ilke; Weitz, David

    2012-02-01

    As picoliter-scale reaction vessels, microfluidic water-in-oil emulsions have found application for high-throughput, large-sample number analyses. Often, the biological or chemical system under investigation needs to be encapsulated into droplets to prevent cross contamination prior to the introduction of reaction reagents. Previous techniques of picoinjection or droplet synchronization and merging enable the addition of reagents to individual droplets, but present limitations on what can be added to each droplet. We present microfluidic devices that couple the strengths of picoinjection and droplet merging, allowing us to selectively add precise volume to our droplet reactions.

  3. Isolation of cancer cells by "in situ" microfluidic biofunctionalization protocols

    KAUST Repository

    De Vitis, Stefania

    2014-07-01

    The aim of this work is the development of a microfluidic immunosensor for the immobilization of cancer cells and their separation from healthy cells by using "in situ" microfluidic biofunctionalization protocols. These protocols allow to link antibodies on microfluidic device surfaces and can be used to study the interaction between cell membrane and biomolecules. Moreover they allow to perform analysis with high processing speed, small quantity of reagents and samples, short reaction times and low production costs. In this work the developed protocols were used in microfluidic devices for the isolation of cancer cells in heterogeneous blood samples by exploiting the binding of specific antibody to an adhesion protein (EpCAM), overexpressed on the tumor cell membranes. The presented biofunctionalization protocols can be performed right before running the experiment: this allows to have a flexible platform where biomolecules of interest can be linked on the device surface according to the user\\'s needs. © 2014 Elsevier B.V. All rights reserved.

  4. Spinal cord injury markedly altered protein expression patterns in the affected rat urinary bladder during healing stages.

    Science.gov (United States)

    Lee, Ji-Young; Kim, Bong Jo; Sim, Gyujin; Kim, Gyu-Tae; Kang, Dawon; Jung, Jae Hun; Hwa, Jeong Seok; Kwak, Yeon Ju; Choi, Yeon Jin; Park, Young Sook; Han, Jaehee; Lee, Cheol Soon; Kang, Kee Ryeon

    2011-06-01

    The influence of spinal cord injury (SCI) on protein expression in the rat urinary bladder was assessed by proteomic analysis at different time intervals post-injury. After contusion SCI between T9 and T10, bladder tissues were processed by 2-DE and MALDI-TOF/MS at 6 hr to 28 days after SCI to identify proteins involved in the healing process of SCI-induced neurogenic bladder. Approximately 1,000 spots from the bladder of SCI and sham groups were visualized and identified. At one day after SCI, the expression levels of three protein were increased, and seven spots were down-regulated, including heat shock protein 27 (Hsp27) and heat shock protein 20 (Hsp20). Fifteen spots such as S100-A11 were differentially expressed seven days post-injury, and seven proteins including transgelin had altered expression patterns 28 days after injury. Of the proteins with altered expression levels, transgelin, S100-A11, Hsp27 and Hsp20 were continuously and variably expressed throughout the entire post-SCI recovery of the bladder. The identified proteins at each time point belong to eight functional categories. The altered expression patterns identified by 2-DE of transgelin and S100-A11 were verified by Western blot. Transgelin and protein S100-A11 may be candidates for protein biomarkers in the bladder healing process after SCI.

  5. Single cell microfluidics for systems oncology

    Science.gov (United States)

    Fan, Rong

    2012-02-01

    The singular term ``cancer'' is never one kind of disease, but deceivingly encompasses a large number of heterogeneous disease states, which makes it impossible to completely treat cancer using a generic approach. Rather systems approaches are urgently required to assess cancer heterogeneity, stratify patients and enable the most effective, individualized treatment. The heterogeneity of tumors at the single cell level is reflected by the hierarchical complexity of the tumor microenvironment. To identify all the cellular components, including both tumor and infiltrating immune cells, and to delineate the associated cell-to-cell signaling network that dictates tumor initiation, progression and metastasis, we developed a single cell microfluidics chip that can analyze a panel of proteins that are potentially associated inter-cellular signaling network in tumor microenvironment from hundreds of single cells in parallel. This platform integrates two advanced technologies -- microfluidic single cell handling and ultra-high density protein array. This device was first tested for highly multiplexed profiling of secreted proteins including tumor-immune signaling molecules from monocytic leukemia cells. We observed profound cellular heterogeneity with all functional phenotypes quantitatively identified. Correlation analysis further indicated the existence of an intercellular cytokine network in which TNFα-induced secondary signaling cascades further increased functional cellular diversity. It was also exploited to evaluate polyfunctionality of tumor antigen-specific T cells from melanoma patients being treated with adoptive T cell transfer immunotherapy. This platform could be further extended to analyze both solid tumor cells (e.g. human lung carcinoma cells) and infiltrating immune cells (e.g. macrophages) so as to enable systems analysis of the complex tumor microenvironment from small amounts of clinical specimens, e.g. skinny needle biopsies. Thus, it could potentially

  6. A prototypic microfluidic platform generating stepwise concentration gradients for real-time study of cell apoptosis.

    Science.gov (United States)

    Dai, Wen; Zheng, Yizhe; Luo, Kathy Qian; Wu, Hongkai

    2010-04-16

    This work describes the development of a prototypic microfluidic platform for the generation of stepwise concentration gradients of drugs. A sensitive apoptotic analysis method is integrated into this microfluidic system for studying apoptosis of HeLa cells under the influence of anticancer drug, etoposide, with various concentrations in parallel; it measures the yellow fluorescent proteincyan fluorescent protein fluorescence resonance energy transfer (FRET) signal that responds to the activation of caspase-3, an indicator of cell apoptosis. Sets of microfluidic valves on the chip generate stepwise concentration gradient of etoposide in various cell-culture microchambers. The FRET signals from multiple chambers are simultaneously monitored under a fluorescent microscope for long-time observation and the on-chip results are compared with those from 96-well plate study and the methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay. The microfluidic platform shows several advantages including high-throughput capacity, low drug consumption, and high sensitivity.

  7. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.

    Science.gov (United States)

    Cibrián-Jaramillo, Angélica; De la Torre-Bárcena, Jose E; Lee, Ernest K; Katari, Manpreet S; Little, Damon P; Stevenson, Dennis W; Martienssen, Rob; Coruzzi, Gloria M; DeSalle, Rob

    2010-07-12

    We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.

  8. Stem fasciation in cacti and succulent species--tissue anatomy, protein pattern and RAPD polymorphisms.

    Science.gov (United States)

    El-Banna, A N; El-Nady, M F; Dewir, Y H; El-Mahrouk, M E

    2013-09-01

    Fasciated and normal stem segments of Opuntia microdasys, Opuntia cylindrica, Huernia primulina and Euphorbia lactea were collected from the same plant and compared for their anatomy, water relations and genetic variations. Anatomical differences in terms of thickness of cuticle, vascular bundle, xylem and phloem were analyzed in both normal and fasciated stems. The mucilage cells were higher in the fasciated form of Opuntia microdasys than that in the normal form. Water status in terms of total water content (TWC), water deficit and relative water content (RWC) was influenced by fasciation. Genetic variations were tested in normal and fasciated stems using randomly amplified polymorphic DNA (RAPD) fingerprints and SDS-PAGE of soluble protein extracts. SDS-PAGE protein and RAPD analysis confirmed that normal and fasciated tissues were genetically different. Polymerase chain reaction (PCR) yielded different polymorphic banding patterns that were unique to each primer and distinguishable over all samples. The PCR results of normal and fasciated samples were significantly different in cases of primers P1, P2 and P3. These results indicate that occurrence of fasciation in Opuntia microdasys, Opuntia cylindrica, Huernia primulina and Euphorbia lactea is an epigenetic mutation of tissues.

  9. 以微流体技术构建纹状体神经元流道图案的形态学研究%A Morphological Study on Creation of Neural Flow Patterns with Cultured Striatal Neurons in Vitro Using A Microfluidic Technique

    Institute of Scientific and Technical Information of China (English)

    罗亚黎; 高侃; 徐群渊

    2011-01-01

    To make a designed neurochip practical, the adhesion and neurite growth of patterned striatal neurons were investigated by a microfluidic technique on the surface of mixture of polyethyleneimine (PEI) and laminin (LN) in vitro. Four different substrates, including LN, poly-L-lysine (PLL), PEI and mixture of PEI with LN (PEI+LN), characterized with strong positive surface charges were micropatterned on the silicon slide using a microfluidic technique. The striatal neurons from the forebrain of pastnatal SD rats were cultured in vitro on these materials, respedively. The survival, adhesion and neurite growth of the cultured neurons, as well as their flow pattems on different substrates were evaluated, especially by immunofluorescent staining.Different effects of the neural flow patterns on different designs of the pattem (different spaces between the flow lines) fabricated on PEI+LN material were also compared using same method. The quantity of neuronal growth on the pattems of PEI, PLL and PEI+LN was apparently larger than that on LN. Moreover, the coated pattern of neurons on the PEI+LN was more integrated than on the others, and its morphology was more completely when the cells grew on the pattern with flow line spaces ranged between 150 and 200 μm.The substrate of PEI and LN mixture is in favor of creation of neural flow patterns. by using the microfluidic technology, when a suitable design of the pattern is selected. The observation in present study may help creation of some practical neurochips in the future times.%在以微流体技术加工的聚乙烯亚胺(polyethyleneimine,PEI)及层粘连蛋白(laminin,LN)混合物材料上,培养纹状体神经元图案式黏附、生长,为制备神经芯片打好基础.以微流体印刷方法在硅片上微加工四种不同的黏附底物:LN、带正电荷的多聚赖氨酸(poly-L-lysine,PLL)、PEI和PEI+LN混合物.体外分离培养新生乳鼠纹状体神经元,评价神经元在不同图案化黏附底物上的

  10. Multiplex protein pattern unmixing using a non-linear variable-weighted support vector machine as optimized by a particle swarm optimization algorithm.

    Science.gov (United States)

    Yang, Qin; Zou, Hong-Yan; Zhang, Yan; Tang, Li-Juan; Shen, Guo-Li; Jiang, Jian-Hui; Yu, Ru-Qin

    2016-01-15

    Most of the proteins locate more than one organelle in a cell. Unmixing the localization patterns of proteins is critical for understanding the protein functions and other vital cellular processes. Herein, non-linear machine learning technique is proposed for the first time upon protein pattern unmixing. Variable-weighted support vector machine (VW-SVM) is a demonstrated robust modeling technique with flexible and rational variable selection. As optimized by a global stochastic optimization technique, particle swarm optimization (PSO) algorithm, it makes VW-SVM to be an adaptive parameter-free method for automated unmixing of protein subcellular patterns. Results obtained by pattern unmixing of a set of fluorescence microscope images of cells indicate VW-SVM as optimized by PSO is able to extract useful pattern features by optimally rescaling each variable for non-linear SVM modeling, consequently leading to improved performances in multiplex protein pattern unmixing compared with conventional SVM and other exiting pattern unmixing methods.

  11. Controlled Cavitation in Microfluidic Systems

    NARCIS (Netherlands)

    Zwaan, Ed; le Gac, Severine; Tsuji, Kinko; Ohl, C.D.

    2007-01-01

    We report on cavitation in confined microscopic environments which are commonly called microfluidic or lab-on-a-chip systems. The cavitation bubble is created by focusing a pulsed laser into these structures filled with a lght-absorbing liquid. At hte center of a 20 mu m thick and 1 mm wide channel,

  12. Membranes and microfluidics: a review

    NARCIS (Netherlands)

    de Jong, J.; Lammertink, Rob G.H.; Wessling, Matthias

    2006-01-01

    The integration of mass transport control by means of membrane functionality into microfluidic devices has shown substantial growth over the last 10 years. Many different examples of mass transport control have been reported, demonstrating the versatile use of membranes. This review provides an

  13. Microfluidic fabrication of plasmonic microcapsules

    NARCIS (Netherlands)

    Wang, J.; Jin, M.L.; Eijkel, J.C.T.; Berg, van den A.; Zhou, G.F.; Shui, L.L.

    2016-01-01

    This paper presents the plasmonic microcapsules with well-ordered nanoparticles embedded in polymer network fabricated by using a microfluidic device. The well-ordered nanoparticle arrays on the microcapsule form high-density uniform “hot-spots” with a deposited metal film, on which the localized su

  14. Microfluidic Liquid-Liquid Contactors

    Energy Technology Data Exchange (ETDEWEB)

    Mcculloch, Quinn [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-07-25

    This report describes progress made on the microfluidic contactor. A model was developed to predict its failure, a surrogate chemical system was selected to demonstrate mass transfer, and an all-optical system has been invented and implemented to monitor carryover and flowrates.

  15. Mixing in a Microfluid Device

    DEFF Research Database (Denmark)

    Hjorth, Poul G.; Deryabin, Mikhail

    Mixing of fluids in microchannels cannot rely on turbulence since the flow takes place at extremly low Reynolds numbers. Various active and passive devices have been developed to induce mixing in microfluid flow devices. We describe here a model of an active mixer where a transverse periodic flow...

  16. Topology optimization of microfluidic mixers

    DEFF Research Database (Denmark)

    Andreasen, Casper Schousboe; Gersborg, Allan Roulund; Sigmund, Ole

    2009-01-01

    This paper demonstrates the application of the topology optimization method as a general and systematic approach for microfluidic mixer design. The mixing process is modeled as convection dominated transport in low Reynolds number incompressible flow. The mixer performance is maximized by altering...

  17. Complement activating soluble pattern recognition molecules with collagen-like regions, mannan-binding lectin, ficolins and associated proteins

    DEFF Research Database (Denmark)

    Thiel, Steffen

    2007-01-01

    Mannan-binding lectin (MBL), L-ficolin, M-ficolin and H-ficolin are all complement activating soluble pattern recognition molecules with recognition domains linked to collagen-like regions. All four may form complexes with four structurally related proteins, the three MBL-associated serine...... proteases (MASPs), MASP-1, MASP-2 and MASP-3, and a smaller MBL-associated protein (MAp19). The four recognition molecules recognize patterns of carbohydrate or acetyl-group containing ligands. After binding to the relevant targets all four are able to activate the complement system. We thus have a system...... where four different and/or overlapping patterns of microbial origin or patterns of altered-self may be recognized, but in all cases the signalling molecules, the MASPs, are shared. MASP-1 and MASP-3 are formed from one gene, MASP1/3, by alternative splicing generating two different mRNAs from a single...

  18. Terminal sequence importance of de novo proteins from binary-patterned library: stable artificial proteins with 11- or 12-amino acid alphabet.

    Science.gov (United States)

    Okura, Hiromichi; Takahashi, Tsuyoshi; Mihara, Hisakazu

    2012-06-01

    Successful approaches of de novo protein design suggest a great potential to create novel structural folds and to understand natural rules of protein folding. For these purposes, smaller and simpler de novo proteins have been developed. Here, we constructed smaller proteins by removing the terminal sequences from stable de novo vTAJ proteins and compared stabilities between mutant and original proteins. vTAJ proteins were screened from an α3β3 binary-patterned library which was designed with polar/ nonpolar periodicities of α-helix and β-sheet. vTAJ proteins have the additional terminal sequences due to the method of constructing the genetically repeated library sequences. By removing the parts of the sequences, we successfully obtained the stable smaller de novo protein mutants with fewer amino acid alphabets than the originals. However, these mutants showed the differences on ANS binding properties and stabilities against denaturant and pH change. The terminal sequences, which were designed just as flexible linkers not as secondary structure units, sufficiently affected these physicochemical details. This study showed implications for adjusting protein stabilities by designing N- and C-terminal sequences.

  19. Tunable-angle wedge transducer for improved acoustophoretic control in a microfluidic chip

    DEFF Research Database (Denmark)

    Iranmanesh, I.; Barnkob, Rune; Bruus, Henrik;

    2012-01-01

    coupling angle, and transducer actuation method (single-frequency actuation or frequency-modulation actuation). The energy-density analysis is based on measuring the transmitted light intensity through a microfluidic channel filled with a suspension of 5-μm-diameter beads and the results with the tunable...... particle patterns with average acoustic energy densities comparable to those obtained using single-frequency actuation.......We present a tunable-angle wedge ultrasound transducer for improved control of microparticle acoustophoresis in a microfluidic chip. The transducer is investigated by analyzing the pattern of aligned particles and induced acoustic energy density while varying the system geometry, transducer...

  20. Tunable-angle wedge transducer for improved acoustophoretic control in a microfluidic chip

    DEFF Research Database (Denmark)

    Iranmanesh, I.; Barnkob, Rune; Bruus, Henrik;

    2013-01-01

    coupling angle, and transducer actuation method (single-frequency actuation or frequency-modulation actuation). The energy-density analysis is based on measuring the transmitted light intensity through a microfluidic channel filled with a suspension of 5 µm diameter beads and the results with the tunable...... uniform particle patterns with average acoustic energy densities comparable to those obtained using single-frequency actuation.......We present a tunable-angle wedge ultrasound transducer for improved control of microparticle acoustophoresis in a microfluidic chip. The transducer is investigated by analyzing the pattern of aligned particles and induced acoustic energy density while varying the transducer geometry, transducer...

  1. An enzyme reactor based on aptamer modified microfluidic chip for protein analysis%基于核酸适配体的微流控芯片酶反应器用于蛋白质的分析

    Institute of Scientific and Technical Information of China (English)

    肖鹏; 李大雷; 满燕; 耿利娜; 吕雪飞; 邓玉林

    2012-01-01

    As a kind of recognition molecule, aptamer has been studied and applied widely in numerous science fields in recent years. Immobilized enzymatic reactor has drawn much attention because of its striking advantages, such as high digestion efficiency and ease in coupling with the separation and detection systems. In this study, a novel microfluidic enzymatic chip, which immobilized trypsin based on aptamer, was prepared and proposed. An online analysis platform, which consisted of an aptamer-based chip and high performance liquid chromatogra-phy tandem mass spectrometry, was established by using a 6-port valve and applied to protein analysis. The enzymatic capacity and stability performance of chip reactor were characterized by using mixed protein sample, which consisted of bovine serum albumin (BSA), myoglobin ( Mb) and cytochrome c (Cyt. c). The sample digestion time of the chip reactor was about 5. 76 s while 1 fi,L/min of flow rate was adopted; and moreover, 5 ng of Mb was identified successfully with the sequence coverage of 37%. Furthermore, the sequence coverages and the relative standard deviations were 44.3% and 6.5% for BSA, 65.0% and 2.7% for Mb, 62.0% and 5. 6% for Cyt. c respectively when 500 ng digest of mixed proteins were analyzed in three runs. According to experimental results, the online analysis platform possesses the ability of high sensitivity and good stability, which can provide a promising tool for rapid and high-throughput proteomics study in the near future.%将核酸适配体作为胰蛋白酶固定化介质,制备了一种新型的微流控芯片酶反应器,并与高效液相色谱-串联质谱联用,搭建了在线分析平台;分别使用标准蛋白及混合蛋白样品对芯片的酶解效率及联用平台的分析能力进行了初步评价.结果表明,5 ng肌红蛋白经该平台分析后肽段覆盖率可达到37%;对500 ng混合蛋白进行3次平行分析,肽段覆盖率及相对标准偏差分别为44.3%、6.5

  2. Assessment of Carbon- and Metal-Based Nanoparticle DNA Damage with Microfluidic Electrophoretic Separation Technology.

    Science.gov (United States)

    Schrand, Amanda M; Powell, Thomas; Robertson, Tiffany; Hussain, Saber M

    2015-02-01

    In this study, we examined the feasibility of extracting DNA from whole cell lysates exposed to nanoparticles using two different methodologies for evaluation of fragmentation with microfluidic electrophoretic separation. Human lung macrophages were exposed to five different carbon- and metal-based nanoparticles at two different time points (2 h, 24 h) and two different doses (5 µg/ml, 100 µg/ml). The primary difference in the banding patterns after 2 h of nanoparticle exposure is more DNA fragmentation at the higher NP concentration when examining cells exposed to nanoparticles of the same composition. However, higher doses of carbon and silver nanoparticles at both short and long dosing periods can contribute to erroneous or incomplete data with this technique. Also comparing DNA isolation methodologies, we recommend the centrifugation extraction technique, which provides more consistent banding patterns in the control samples compared to the spooling technique. Here we demonstrate that multi-walled carbon nanotubes, 15 nm silver nanoparticles and the positive control cadmium oxide cause similar DNA fragmentation at the short time point of 2 h with the centrifugation extraction technique. Therefore, the results of these studies contribute to elucidating the relationship between nanoparticle physicochemical properties and DNA fragmentation results while providing the pros and cons of altering the DNA isolation methodology. Overall, this technique provides a high throughput way to analyze subcellular alterations in DNA profiles of cells exposed to nanomaterials to aid in understanding the consequences of exposure and mechanistic effects. Future studies in microfluidic electrophoretic separation technologies should be investigated to determine the utility of protein or other assays applicable to cellular systems exposed to nanoparticles.

  3. Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida.

    Science.gov (United States)

    Young, Monica R; Hebert, Paul D N

    2015-01-01

    Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625). It examines divergences at three taxonomic levels-among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10-0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07-0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is 'locked down' in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in 'locked down' taxa.

  4. Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI from the Class Arachnida.

    Directory of Open Access Journals (Sweden)

    Monica R Young

    Full Text Available Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625. It examines divergences at three taxonomic levels-among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10-0.39, while the mean of the Family Distances for the ten orders ranges fivefold (0.07-0.35. BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is 'locked down' in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in 'locked down' taxa.

  5. Proline content and protein patterns in Eucalyptus grandis shoots submitted to high and low temperature shocks

    Directory of Open Access Journals (Sweden)

    Gustavo M. Souza

    2004-07-01

    Full Text Available Proline content and protein patterns changes in response to temperature shocks of both acclimated and non acclimated E. grandis shoots cultivated in vitro were investigated. Analysis of soluble proteins through SDS-PAGE and proline were carried out after 12h at 12ºC (cold acclimation or 33ºC (heat acclimation, and immediately after temperature shocks at 41ºC and 0ºC. Analyses were also performed 24h after the temperature shocks (recovery period. Temperature treatment at 0ºC did not change soluble protein patterns both in acclimatized and non acclimatized plants, whereas cold temperature induced high proline levels, which kept relatively high after recovery period. Three novel, probably HSPs, proteins (90.5, 75 and 39 kDa were observed in both acclimated and non acclimated plants submitted to high temperatures. Plants exposed at 41ºC were able to recover from heat shocks after 24h, whereas they did not recover completely from cold shocks. The effect of the acclimation period on the recovering (homeostasis varied depending on the parameter evaluated, and type and duration of the temperature shock.As respostas às mudanças de temperatura de plantas aclimatadas e não aclimatadas de E. grandis cultivadas in vitro foram avaliadas considerando alterações dos níveis de prolina e proteínas solúveis totais. Análises de proteínas solúveis através de SDS-PAGE e prolina foram realizadas após 12h a 12ºC (aclimatação ao frio ou a 33ºC (aclimatação ao calor, e imediatamente depois dos choques térmicos a 41ºC e 0ºC. Análises também foram realizadas após um período de 24h depois dos choques térmicos (período de recuperação. O tratamento de temperatura a 0ºC não alterou o padrão de proteínas nas plantas aclimatadas e não aclimatadas, entretanto a temperatura baixa induziu altos níveis de prolina, que se mantiveram relativamente altos após o período de recuperação. Três novas proteínas (90,5, 75 e 39 kDa, provavelmente

  6. Influence of protein source on amino acid uptake patterns and protein utilization in rainbow trout Oncorhynchus mykiss

    DEFF Research Database (Denmark)

    Rolland, Marine; Holm, Jørgen; Dalsgaard, Anne Johanne Tang

    Matrixes of different protein sources (fish and plant products) combined with the use of crystalline amino acids allow for formulation of diets that meet fish requirements with little or no effect on protein digestibility and/or feed intake. Despite this, a total or partial replacement of fish meal...... induces reduced growth performances that remain partly unexplained. The aim of the current study was to investigate the effect of exchanging the protein source on protein utilization. Marine (fish meal) and vegetable (pea protein) sources were used with or without supplementation of crystalline amino...

  7. Phenols content and 2-D electrophoresis protein pattern: a promising tool to monitor Posidonia meadows health state

    Directory of Open Access Journals (Sweden)

    Randazzo Davide

    2007-07-01

    Full Text Available Abstract Background The endemic seagrass Posidonia oceanica (L. Delile colonizes soft bottoms producing highly productive meadows that play a crucial role in coastal ecosystems dynamics. Human activities and natural events are responsible for a widespread meadows regression; to date the identification of "diagnostic" tools to monitor conservation status is a critical issue. In this study the feasibility of a novel tool to evaluate ecological impacts on Posidonia meadows has been tested. Quantification of a putative stress indicator, i.e. phenols content, has been coupled to 2-D electrophoretic protein analysis of rhizome samples. Results The overall expression pattern from Posidonia rhizome was determined using a preliminary proteomic approach, 437 protein spots were characterized by pI and molecular weight. We found that protein expression differs in samples belonging to sites with high or low phenols: 22 unique protein spots are peculiar of "low phenols" and 27 other spots characterize "high phenols" samples. Conclusion Posidonia showed phenols variations within the meadow, that probably reflect the heterogeneity of environmental pressures. In addition, comparison of the 2-D electrophoresis patterns allowed to highlight qualitative protein expression differences in response to these pressures. These differences may account for changes in metabolic/physiological pathways as adaptation to stress. A combined approach, based on phenols content determination and 2-D electrophoresis protein pattern, seems a promising tool to monitor Posidonia meadows health state.

  8. Photothermal generation of microbubbles on plasmonic nanostructures inside microfluidic channels

    Science.gov (United States)

    Li, Jingting; Li, Ming; Santos, Greggy M.; Zhao, Fusheng; Shih, Wei-Chuan

    2016-03-01

    Microbubbles have been utilized as micro-pumps, micro-mixers, micro-valves, micro-robots and surface cleaners. Various generation techniques can be found in the literature, including resistive heating, hydrodynamic methods, illuminating patterned metal films and noble metal nanoparticles of Au or Ag. We present photothermal microbubble generation by irradiating nanoporous gold disk covered microfluidic channels. The size of the microbubble can be controlled by adjusting the laser power. The dynamics of both bubble growth and shrinkage are studied. The advantages of this technique are flexible bubble generation locations, long bubble lifetimes, no need for light-adsorbing dyes, high controllability over bubble size, low power consumption, etc. This technique has the potential to provide new flow control functions in microfluidic devices.

  9. pH-Sensitive Hydrogel for Micro-Fluidic Valve

    Directory of Open Access Journals (Sweden)

    Zhengzhi Yang

    2012-07-01

    Full Text Available The deformation behavior of a pH-sensitive hydrogel micro-fluidic valve system is investigated using inhomogeneous gel deformation theory, in which the fluid-structure interaction (FSI of the gel solid and fluid flow in the pipe is considered. We use a finite element method with a well adopted hydrogel constitutive equation, which is coded in commercial software, ABAQUS, to simulate the hydrogel valve swelling deformation, while FLUENT is adopted to model the fluid flow in the pipe of the hydrogel valve system. The study demonstrates that FSI significantly affects the gel swelling deformed shapes, fluid flow pressure and velocity patterns. FSI has to be considered in the study on fluid flow regulated by hydrogel microfluidic valve. The study provides a more accurate and adoptable model for future design of new pH-sensitive hydrogel valves, and also gives a useful guideline for further studies on hydrogel fluidic applications.

  10. Paper-based inkjet-printed microfluidic analytical devices.

    Science.gov (United States)

    Yamada, Kentaro; Henares, Terence G; Suzuki, Koji; Citterio, Daniel

    2015-04-27

    Rapid, precise, and reproducible deposition of a broad variety of functional materials, including analytical assay reagents and biomolecules, has made inkjet printing an effective tool for the fabrication of microanalytical devices. A ubiquitous office device as simple as a standard desktop printer with its multiple ink cartridges can be used for this purpose. This Review discusses the combination of inkjet printing technology with paper as a printing substrate for the fabrication of microfluidic paper-based analytical devices (μPADs), which have developed into a fast-growing new field in analytical chemistry. After introducing the fundamentals of μPADs and inkjet printing, it touches on topics such as the microfluidic patterning of paper, tailored arrangement of materials, and functionalities achievable exclusively by the inkjet deposition of analytical assay components, before concluding with an outlook on future perspectives.

  11. Fluoropolymer surface coatings to control droplets in microfluidic devices.

    Science.gov (United States)

    Riche, Carson T; Zhang, Chuchu; Gupta, Malancha; Malmstadt, Noah

    2014-06-07

    We have demonstrated the application of low surface energy fluoropolymer coatings onto poly(dimethylsiloxane) (PDMS) microfluidic devices for droplet formation and extraction-induced merger of droplets. Initiated chemical vapor deposition (iCVD) was used to pattern fluoropolymer coatings within microchannels based on geometrical constraints. In a two-phase flow system, the range of accessible flow rates for droplet formation was greatly enhanced in the coated devices. The ability to controllably apply the coating only at the inlet facilitated a method for merging droplets. An organic spacer droplet was extracted from between a pair of aqueous droplets. The size of the organic droplet and the flow rate controlled the time to merge the aqueous droplets; the process of merging was independent of the droplet sizes. Extraction-induced droplet merging is a robust method for manipulating droplets that could be applied in translating multi-step reactions to microfluidic platforms.

  12. Multiligand Specificity of Pathogen-associated Molecular Pattern-binding Site in Peptidoglycan Recognition Protein*

    Science.gov (United States)

    Sharma, Pradeep; Dube, Divya; Sinha, Mau; Mishra, Biswajit; Dey, Sharmistha; Mal, Gorakh; Pathak, Krishan M. L.; Kaur, Punit; Sharma, Sujata; Singh, Tej P.

    2011-01-01

    The peptidoglycan recognition protein PGRP-S is an innate immunity molecule that specifically interacts with microbial peptidoglycans and other pathogen-associated molecular patterns. We report here two structures of the unique tetrameric camel PGRP-S (CPGRP-S) complexed with (i) muramyl dipeptide (MDP) at 2.5 Å resolution and (ii) GlcNAc and β-maltose at 1.7Å resolution. The binding studies carried out using surface plasmon resonance indicated that CPGRP-S binds to MDP with a dissociation constant of 10−7 m, whereas the binding affinities for GlcNAc and β-maltose separately are in the range of 10−4 m to 10−5 m, whereas the dissociation constant for the mixture of GlcNAc and maltose was estimated to be 10−6 m. The data from bacterial suspension culture experiments showed a significant inhibition of the growth of Staphylococcus aureus cells when CPGRP-S was added to culture medium. The ELISA experiment showed that the amount of MDP-induced production of TNF-α and IL-6 decreased considerably after the introduction of CPGRP-S. The crystal structure determinations of (i) a binary complex with MDP and (ii) a ternary complex with GlcNAc and β-maltose revealed that MDP, GlcNAc, and β-maltose bound to CPGRP-S in the ligand binding cleft, which is situated at the interface of molecules C and D of the homotetramer formed by four protein molecules A, B, C, and D. In the binary complex, the muramyl moiety of MDP is observed at the C-D interface, whereas the peptide chain protrudes into the center of tetramer. In the ternary complex, GlcNAc and β-maltose occupy distinct non-overlapping positions belonging to different subsites. PMID:21784863

  13. Development of a paper-based carbon nanotube sensing microfluidic device for biological detection.

    Science.gov (United States)

    Yang, Shih-I; Lei, Kin Fong; Tsai, Shiao-Wen; Hsu, Hsiao-Ting

    2013-01-01

    Carbon nanotube (CNT) has been utilized for the biological detection due to its extremely sensitive to biological molecules. A paper-based CNT sensing microfluidic device has been developed for the detection of protein, i.e., biotin-avidin, binding. We have developed a fabrication method that allows controlled deposition of bundled CNTs with well-defined dimensions to form sensors on paper. Then, polydimethyl siloxane (PDMS) was used to pattern the hydrophobic boundary on paper to form the reaction sites. The proposed fabrication method is based on vacuum filtration process with a metal mask covering on a filter paper for the definition of the dimension of sensor. The length, width, and thickness of the CNT-based sensors are readily controlled by the metal mask and the weight of the CNT powder used during the filtration process, respectively. Homogeneous deposition of CNTs with well-defined dimensions can be achieved. The CNT-based sensor on paper has been demonstrated on the detection of the protein binding. Biotin was first immobilized on the CNT's sidewall and avidin suspended solution was applied to the site. The result of the biotin-avidin binding was measured by the resistance change of the sensor, which is a label-free detection method. It showed the CNT is sensitive to the biological molecules and the proposed paper-based CNT sensing device is a possible candidate for point-of-care biosensors. Thus, electrical bio-assays on paper-based microfluidics can be realized to develop low cost, sensitive, and specific diagnostic devices.

  14. A microfluidic D-subminiature connector.

    Science.gov (United States)

    Scott, Adina; Au, Anthony K; Vinckenbosch, Elise; Folch, Albert

    2013-06-07

    Standardized, affordable, user-friendly world-to-chip interfaces represent one of the major barriers to the adoption of microfluidics. We present a connector system for plug-and-play interfacing of microfluidic devices to multiple input and output lines. The male connectors are based on existing standardized housings from electronics that are inexpensive and widely available. The female connectors are fabricated using familiar replica molding techniques that can easily be adopted by microfluidic developers.

  15. [Recent development of microfluidic diagnostic technologies].

    Science.gov (United States)

    Li, Haifang; Zhang, Qianyun; Lin, Jin-Ming

    2011-04-01

    Microfluidic devices exhibit a great promising development in clinical diagnosis and disease screening due to their advantages of precise controlling of fluid flow, requirement of miniamount sample, rapid reaction speed and convenient integration. In this paper, the improvements of microfluidic diagnostic technologies in recent years are reviewed. The applications and developments of on-chip disease marker detection, microfluidic cell selection and cell drug metabolism, and diagnostic micro-devices are discussed.

  16. Dynamics of Microvalve Operations in Integrated Microfluidics

    OpenAIRE

    Alan T. H. Lau; Hon Ming Yip; Kathy C. C. Ng; Xin Cui; Lam, Raymond H. W.

    2014-01-01

    Pneumatic microvalves are widely used key components for automating liquid manipulation and flow control in microfluidics for more than one decade. Due to their robust operations and the ease of fabrication, tremendous microfluidic systems have been developed with the multiple microvalves for higher throughput and extended functionalities. Therefore, operation performance of the microvalves in the integrated microfluidic devices is crucial to the related applications, in fields such as micro-...

  17. Bio-microfluidics: biomaterials and biomimetic designs.

    Science.gov (United States)

    Domachuk, Peter; Tsioris, Konstantinos; Omenetto, Fiorenzo G; Kaplan, David L

    2010-01-12

    Bio-microfluidics applies biomaterials and biologically inspired structural designs (biomimetics) to microfluidic devices. Microfluidics, the techniques for constraining fluids on the micrometer and sub-micrometer scale, offer applications ranging from lab-on-a-chip to optofluidics. Despite this wealth of applications, the design of typical microfluidic devices imparts relatively simple, laminar behavior on fluids and is realized using materials and techniques from silicon planar fabrication. On the other hand, highly complex microfluidic behavior is commonplace in nature, where fluids with nonlinear rheology flow through chaotic vasculature composed from a range of biopolymers. In this Review, the current state of bio-microfluidic materials, designs and applications are examined. Biopolymers enable bio-microfluidic devices with versatile functionalization chemistries, flexibility in fabrication, and biocompatibility in vitro and in vivo. Polymeric materials such as alginate, collagen, chitosan, and silk are being explored as bulk and film materials for bio-microfluidics. Hydrogels offer options for mechanically functional devices for microfluidic systems such as self-regulating valves, microlens arrays and drug release systems, vital for integrated bio-microfluidic devices. These devices including growth factor gradients to study cell responses, blood analysis, biomimetic capillary designs, and blood vessel tissue culture systems, as some recent examples of inroads in the field that should lead the way in a new generation of microfluidic devices for bio-related needs and applications. Perhaps one of the most intriguing directions for the future will be fully implantable microfluidic devices that will also integrate with existing vasculature and slowly degrade to fully recapitulate native tissue structure and function, yet serve critical interim functions, such as tissue maintenance, drug release, mechanical support, and cell delivery.

  18. Microfluidics for optics and quantitative cell biology

    OpenAIRE

    Campbell, James Kyle

    2008-01-01

    Microfluidics is a quickly expanding field with numerous applications. The advent of rapid-prototyping and soft- lithography allow for easy and inexpensive fabrication of microfluidic devices. Fluid manipulation on the microscale allows for new functionalities of devices and components not available on the macroscale. Fluid flows on the microscale are laminar with chemical mixing defined strictly by diffusion allowing us to design microfluidic devices with precise control of fluid flow and ch...

  19. Changing pattern of the subcellular distribution of erythroblast macrophage protein (Emp) during macrophage differentiation.

    Science.gov (United States)

    Soni, Shivani; Bala, Shashi; Kumar, Ajay; Hanspal, Manjit

    2007-01-01

    Erythroblast macrophage protein (Emp) mediates the attachment of erythroid cells to macrophages and is required for normal differentiation of both cell lineages. In erythroid cells, Emp is believed to be involved in nuclear extrusion, however, its role in macrophage differentiation is unknown. Information on the changes in the expression level and subcellular distribution of Emp in differentiating macrophages is essential for understanding the function of Emp. Macrophages of varying maturity were examined by immunofluorescence microscopy and biochemical methods. Our data show that Emp is expressed in all stages of maturation, but its localization pattern changes dramatically during maturation: in immature macrophages, a substantial fraction of Emp is associated with the nuclear matrix, whereas in more mature cells, Emp is expressed largely at cell surface. Pulse-chase experiments show that nascent Emp migrates intracellularly from the cytoplasm to the plasma membrane more efficiently in mature macrophages than in immature cells. Incubation of erythroid cells with macrophages in culture shows that erythroid cells attach to mature macrophages but not to immature macrophage precursors. Together, our data show that the temporal and spatial expression of Emp correlates with its role in erythroblastic island formation and suggest that Emp may be involved in multiple cellular functions.

  20. Alterations in the protein pattern of subcellular fractions isolated from Paramecium cells suppressed in phagocytosis.

    Science.gov (United States)

    Surmacz, L; Wiejak, J; Wyroba, E

    2001-01-01

    SDS-PAGE and quantitative densitometric analysis revealed alterations in the protein pattern of subcellular fractions (100,000 x g) isolated from Paramecium aurelia (299s axenic) cells suppressed in phagocytosis as compared with the control. Two different agents were used to block phagocytosis: the beta-adrenergic antagonist-1-propranolol (200 microM) and inhibitor of calmodulin-dependent processes--trifluoperazine (20 microM). More than 40 polypeptides were identified in the cytosolic (soluble) fractions S1 and S2. A considerable decrease in band intensity was found for three polypeptides: by 60% for 87 kDa band, 52% for 75 kDa and 37% for 42 kDa in comparison to the control, when S2 fractions from propranolol-treated cells of equal load were quantified. TFP treatment evoked only a small decrease in the intensity of the same bands: 9%, 10% and 6%, respectively. The 42 kDa band was identified by Western blot analysis and chemiluminiscent detection to be actin. This result suggests that actin may be a primary target of pharmacological agents used in this study to inhibit Paramecium phagocytic activity.

  1. Expression pattern of the CsPK3 auxin-responsive protein kinase gene.

    Science.gov (United States)

    Chono, M; Suzuki, Y; Nemoto, K; Yamane, H; Murofushi, N; Yamaguchi, I

    2001-03-01

    We have previously cloned a cDNA of a putative serine/threonine protein kinase gene named CsPK3 from cucumber, the mRNA level of which was up-regulated by auxin and down-regulated by light irradiation. To examine the CsPK3 gene expression in detail, we cloned a genomic DNA of CsPK3 gene and made transgenic tobacco (Nicotiana tabacum L. cv. Petit Havana SR1) plants containing the fused CsPK3 promoter-beta-glucuronidase gene. The beta-glucuronidase expression was detected in the shoot apex, vascular tissues, and the outermost layer of cortex. The histological distribution of CsPK3 mRNA in cucumber seedlings was supported by in situ hybridization, where the positive signals were observed in similar tissues as those observed by beta-glucuronidase staining. The responsiveness of the CsPK3 gene to auxin and light was also confirmed for beta-glucuronidase activity. The pattern of beta-glucuronidase staining changed during the development of the tobacco seedlings. The results of our experiment showed that CsPK3 was expressed in a wide variety of tissues and cells in which the developmental and growth controls by auxin are suggested.

  2. Simple approach to study biomolecule adsorption in polymeric microfluidic channels

    Energy Technology Data Exchange (ETDEWEB)

    Gubala, Vladimir, E-mail: V.Gubala@kent.ac.uk [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); Medway School of Pharmacy, University of Kent, Central Avenue, Anson 120, Chatham Maritime, Kent ME4 4TB (United Kingdom); Siegrist, Jonathan; Monaghan, Ruairi; O' Reilly, Brian; Gandhiraman, Ram Prasad [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); Daniels, Stephen [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); National Centre for Plasma Science and Technology (NCPST), Dublin City University, Dublin 9 (Ireland); Williams, David E. [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical Sciences, University of Auckland, Auckland 1142 (New Zealand); Ducree, Jens [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland)

    2013-01-14

    Highlights: Black-Right-Pointing-Pointer A simple tool to assess biomolecule adsorption onto the surfaces of microchannels. Black-Right-Pointing-Pointer Development for dilution by surface-adsorption based depletion of protein samples. Black-Right-Pointing-Pointer It can easily be done using a readily available apparatus like a spin-coater. Black-Right-Pointing-Pointer The assessment tool is facile and quantitative. Black-Right-Pointing-Pointer Straightforward comparison of different surface chemistries. - Abstract: Herein a simple analytical method is presented for the characterization of biomolecule adsorption on cyclo olefin polymer (COP, trade name: Zeonor{sup Registered-Sign }) substrates which are widely used in microfluidic lab-on-a-chip devices. These Zeonor{sup Registered-Sign} substrates do not possess native functional groups for specific reactions with biomolecules. Therefore, depending on the application, such substrates must be functionalized by surface chemistry methods to either enhance or suppress biomolecular adsorption. This work demonstrates a microfluidic method for evaluating the adsorption of antibodies and oligonucleotides surfaces. The method uses centrifugal microfluidic flow-through chips and can easily be implemented using common equipment such as a spin coater. The working principle is very simple. The user adds 40 L of the solution containing the sample to the starting side of a microfluidic channel, where it is moved through by centrifugal force. Some molecules are adsorbed in the channel. The sample is then collected at the other end in a small reservoir and the biomolecule concentration is measured. As a pilot application, we characterized the adsorption of goat anti-human IgG and a 20-mer DNA on Zeonor{sup Registered-Sign }, and on three types of functionalized Zeonor: 3-aminopropyltriethoxysilane (APTES) modified surface with mainly positive charge, negatively charged surface with immobilized bovine serum albumin (BSA), and

  3. A microfluidic platform with a free-standing perforated polymer membrane

    Science.gov (United States)

    Choi, Junseo; Roychowdhury, Anish; Kim, Namwon; Nikitopoulos, Dimitris E.; Lee, Wonbong; Han, Haksoo; Park, Sunggook

    2010-08-01

    A membrane architecture that facilitates access from both sides in microfluidic environments provides a flexible platform for the study of biosystems. Here, we report for the first time on a simple and low cost fabrication process via nanoimprint lithography (NIL) for a thin, fully released SU-8 membrane with perforated micro- and sub-micron pores and a modular microfluidic system integrated with the membrane. A modified NIL process which combines thermal and UV NIL was employed to define the pore structures in an SU-8 layer coated on a sacrificial layer. We have demonstrated the production of large area SU-8 membranes of as large as 4 inch diameter that are fully covered with perforated micropores. The released SU-8 membrane was easily integrated as a modular component into a microfluidic system by sandwiching the membrane between two microfluidic chips. Important aspects to reliably produce the membrane architecture such as materials selection and process conditions for fabrication are discussed. After demonstrating selective adsorption of lipid vesicles at the micropore sites of the SU-8 membrane, we have reconstituted lipid bilayers at the micropores within the microfluidic system following the method developed by Suzuki et al (2004 Lab Chip 4 502-5). This implies that the membrane architecture can potentially be used as a microfluidic platform with lipid bilayers that can sustain external mechanical stress for biophysical studies of membrane proteins.

  4. Integration of microfluidics with a four-channel integrated optical Young interferometer immunosensor.

    Science.gov (United States)

    Ymeti, A; Kanger, J S; Greve, J; Besselink, G A J; Lambeck, P V; Wijn, R; Heideman, R G

    2005-01-15

    This report describes an optical sensing hybrid system obtained by bonding a microfluidic system to an integrated optical (IO) four-channel Young interferometer (YI) chip. The microfluidic system implemented into a glass plate consists of four microchannels with cross-sectional dimensions of 200 microm x 15 microm. The microfluidic system is structured in such a way that after bonding to the IO chip, each microchannel addresses one sensing window in the four-channel YI sensor. Experimental tests show that the implementation of the microfluidics reduces the response time of the sensor from 100s, as achieved with a bulky cuvette, to 4s. Monitoring the anti-human serum albumine/human serum albumine (alpha-HSA/HSA) immunoreaction demonstrates the feasibility to use the microfluidic sensing system for immunosensing applications. In this case, a better discrimination between the bulk refractive index change and the layer formation can be made, resulting into higher accuracy and offering the prospect of being able to use the kinetics of the immunoreaction. The microfluidic sensing system shows an average phase resolution of 7 x 10(-5) x 2pi for different pairs of channels, which at the given interaction length of 4 mm corresponds to a refractive index resolution of 6 x 10(-8), being equivalent to a protein mass coverage resolution of 20 fg/mm2.

  5. A microfluidic microprocessor: controlling biomimetic containers and cells using hybrid integrated circuit/microfluidic chips.

    Science.gov (United States)

    Issadore, David; Franke, Thomas; Brown, Keith A; Westervelt, Robert M

    2010-11-07

    We present an integrated platform for performing biological and chemical experiments on a chip based on standard CMOS technology. We have developed a hybrid integrated circuit (IC)/microfluidic chip that can simultaneously control thousands of living cells and pL volumes of fluid, enabling a wide variety of chemical and biological tasks. Taking inspiration from cellular biology, phospholipid bilayer vesicles are used as robust picolitre containers for reagents on the chip. The hybrid chip can be programmed to trap, move, and porate individual living cells and vesicles and fuse and deform vesicles using electric fields. The IC spatially patterns electric fields in a microfluidic chamber using 128 × 256 (32,768) 11 × 11 μm(2) metal pixels, each of which can be individually driven with a radio frequency (RF) voltage. The chip's basic functions can be combined in series to perform complex biological and chemical tasks and can be performed in parallel on the chip's many pixels for high-throughput operations. The hybrid chip operates in two distinct modes, defined by the frequency of the RF voltage applied to the pixels: Voltages at MHz frequencies are used to trap, move, and deform objects using dielectrophoresis and voltages at frequencies below 1 kHz are used for electroporation and electrofusion. This work represents an important step towards miniaturizing the complex chemical and biological experiments used for diagnostics and research onto automated and inexpensive chips.

  6. Genetic correlation patterns between somatic cell score and protein yield in the Italian Holstein-Friesian Population

    NARCIS (Netherlands)

    Samore, A.; Groen, A.F.; Boettcher, P.; Jamrozik, J.; Canavesi, F.; Bagnato, A.

    2008-01-01

    Genetic parameters for somatic cell score (SCS) in the Italian Holstein-Friesian population were estimated addressing the pattern of genetic correlation with protein yield in different parities (first, second, and third) and on different days in milk within each parity. Three approaches for

  7. Generation of Viable Cell and Biomaterial Patterns by Laser Transfer

    Science.gov (United States)

    Ringeisen, Bradley

    2001-03-01

    In order to fabricate and interface biological systems for next generation applications such as biosensors, protein recognition microarrays, and engineered tissues, it is imperative to have a method of accurately and rapidly depositing different active biomaterials in patterns or layered structures. Ideally, the biomaterial structures would also be compatible with many different substrates including technologically relevant platforms such as electronic circuits or various detection devices. We have developed a novel laser-based technique, termed matrix assisted pulsed laser evaporation direct write (MAPLE DW), that is able to direct write patterns and three-dimensional structures of numerous biologically active species ranging from proteins and antibodies to living cells. Specifically, we have shown that MAPLE DW is capable of forming mesoscopic patterns of living prokaryotic cells (E. coli bacteria), living mammalian cells (Chinese hamster ovaries), active proteins (biotinylated bovine serum albumin, horse radish peroxidase), and antibodies specific to a variety of classes of cancer related proteins including intracellular and extracellular matrix proteins, signaling proteins, cell cycle proteins, growth factors, and growth factor receptors. In addition, patterns of viable cells and active biomolecules were deposited on different substrates including metals, semiconductors, nutrient agar, and functionalized glass slides. We will present an explanation of the laser-based transfer mechanism as well as results from our recent efforts to fabricate protein recognition microarrays and tissue-based microfluidic networks.

  8. Comparison of static and microfluidic protease assays using modified bioluminescence resonance energy transfer chemistry.

    Directory of Open Access Journals (Sweden)

    Nan Wu

    Full Text Available BACKGROUND: Fluorescence and bioluminescence resonance energy transfer (F/BRET are two forms of Förster resonance energy transfer, which can be used for optical transduction of biosensors. BRET has several advantages over fluorescence-based technologies because it does not require an external light source. There would be benefits in combining BRET transduction with microfluidics but the low luminance of BRET has made this challenging until now. METHODOLOGY: We used a thrombin bioprobe based on a form of BRET (BRET(H, which uses the BRET(1 substrate, native coelenterazine, with the typical BRET(2 donor and acceptor proteins linked by a thrombin target peptide. The microfluidic assay was carried out in a Y-shaped microfluidic network. The dependence of the BRET(H ratio on the measurement location, flow rate and bioprobe concentration was quantified. Results were compared with the same bioprobe in a static microwell plate assay. PRINCIPAL FINDINGS: The BRET(H thrombin bioprobe has a lower limit of detection (LOD than previously reported for the equivalent BRET(1-based version but it is substantially brighter than the BRET(2 version. The normalised BRET(H ratio of the bioprobe changed 32% following complete cleavage by thrombin and 31% in the microfluidic format. The LOD for thrombin in the microfluidic format was 27 pM, compared with an LOD of 310 pM, using the same bioprobe in a static microwell assay, and two orders of magnitude lower than reported for other microfluidic chip-based protease assays. CONCLUSIONS: These data demonstrate that BRET based microfluidic assays are feasible and that BRET(H provides a useful test bed for optimising BRET-based microfluidics. This approach may be convenient for a wide range of applications requiring sensitive detection and/or quantification of chemical or biological analytes.

  9. DNA-enrichment microfluidic chip for chromatin immunoprecipitation.

    Science.gov (United States)

    Oh, Hyun Jik; Park, Joong Yull; Park, Sung Eun; Lee, Bo Yun; Park, Jong Sung; Kim, Suel-Kee; Yoon, Tae Joong; Lee, Sang-Hoon

    2009-04-15

    Chromatin immunoprecipitation (ChIP) is a powerful and widely applied technique for detecting association of individual proteins with specific genomic regions; the technique requires several complex steps and is tedious. In this paper, we develop a microbead-packed microfluidic chip which eliminates most of the laborious, time-consuming, and skill-dependent processes of the ChIP procedure. A computational fluid dynamics model was established to analyze fluidic behavior in a microbead-packed microchannel. With the use of the new chip, a ChIP procedure was performed to purify the GAPDH (glyceraldehyde 3-phosphate dehydrogenase) gene from human embryonic kidney cells (cell line 293). The ChIP capability of the microfluidic chip was evaluated and compared with that of a commercial assay kit; the precipitation performance of both methods was almost identical as shown by quantitative measurement of DNA. However, our chip offers the advantage of low resin volume, and the experimental time is greatly reduced. In addition, our method is less dependent on individual technical skill. Therefore, we expect that our microfluidic chip-based ChIP method will be widely used in DNA-, gene-, and protein-related research and will improve experimental efficiency.

  10. Laser-assisted modification of polymers for microfluidic, micro-optics, and cell culture applications

    Science.gov (United States)

    Pfleging, W.; Adamietz, R.; Brückner, H. J.; Bruns, M.; Welle, A.

    2007-02-01

    Laser-assisted patterning of polymers is investigated for the direct fabrication of polymeric lab-on-a-chip devices in microsystem technology for capillary electrophoresis chips in bio-analytical applications. In many cases the laser process induces a chemical, physical and topographical change in the laser treated surface. This material modification significantly influences the lab-on-a-chip-functionalities. We will present our current research results in laser-assisted modification of polystyrene (PS) and polymethylmethacrylate (PMMA) with respect to applications in micro-optics, micro-fluidics and cell culture applications. For this purpose the refractive index change, the wettability and the adsorption of proteins and the adhesion of animal cells were investigated as function of laser- and processing parameters. The possible change of surface chemistry was characterized by X-ray photoelectron spectroscopy. The local UV-laser-assisted formation of chemical structures suitable for improved cell adhesion was realized on two- and three-dimensional PS and polycarbonate (PC) surfaces. Above and below the laser ablation threshold two different mechanisms were detected. In one case the produced debris was responsible for improved cell adhesion, while in the other case a photolytical activation of the polymer surface including a subsequent oxidization in oxygen or ambient air leads to a highly localized alteration of protein adsorption from cell culture media and increased cell adhesion. The highly localized control of wettability on polymeric surfaces was investigated for PS and PMMA. In the case of PS the dynamic advancing contact angle could be adjusted between 2° and 150°. This was possible for a suitable exposure dose and an appropriate choice of processing gas (helium or oxygen). A similar but not so significant effect was observed for PMMA below the laser ablation threshold. For PMMA the dynamic advancing contact angle could be adjusted between nearly 50° and

  11. Advances in microfluidics for environmental analysis.

    Science.gov (United States)

    Jokerst, Jana C; Emory, Jason M; Henry, Charles S

    2012-01-07

    During the past few years, a growing number of groups have recognized the utility of microfluidic devices for environmental analysis. Microfluidic devices offer a number of advantages and in many respects are ideally suited to environmental analyses. Challenges faced in environmental monitoring, including the ability to handle complex and highly variable sample matrices, lead to continued growth and research. Additionally, the need to operate for days to months in the field requires further development of robust, integrated microfluidic systems. This review examines recently published literature on the applications of microfluidic systems for environmental analysis and provides insight in the future direction of the field.

  12. Integrated lenses in polystyrene microfluidic devices

    KAUST Repository

    Fan, Yiqiang

    2013-04-01

    This paper reports a new method for integrating microlenses into microfluidic devices for improved observation. Two demonstration microfluidic devices were provided which were fabricated using this new technique. The integrated microlenses were fabricated using a free-surface thermo-compression molding method on a polystyrene (PS) sheet which was then bonded on top of microfluidic channels as a cover plate, with the convex microlenses providing a magnified image of the channel for the easier observation of the flow in the microchannels. This approach for fabricating the integrated microlens in microfluidic devices is rapid, low cost and without the requirement of cleanroom facilities. © 2013 IEEE.

  13. Combinatorial microfluidic droplet engineering for biomimetic material synthesis

    Science.gov (United States)

    Bawazer, Lukmaan A.; McNally, Ciara S.; Empson, Christopher J.; Marchant, William J.; Comyn, Tim P.; Niu, Xize; Cho, Soongwon; McPherson, Michael J.; Binks, Bernard P.; deMello, Andrew; Meldrum, Fiona C.

    2016-01-01

    Although droplet-based systems are used in a wide range of technologies, opportunities for systematically customizing their interface chemistries remain relatively unexplored. This article describes a new microfluidic strategy for rapidly tailoring emulsion droplet compositions and properties. The approach uses a simple platform for screening arrays of droplet-based microfluidic devices and couples this with combinatorial selection of the droplet compositions. Through the application of genetic algorithms over multiple screening rounds, droplets with target properties can be rapidly generated. The potential of this method is demonstrated by creating droplets with enhanced stability, where this is achieved by selecting carrier fluid chemistries that promote titanium dioxide formation at the droplet interfaces. The interface is a mixture of amorphous and crystalline phases, and the resulting composite droplets are biocompatible, supporting in vitro protein expression in their interiors. This general strategy will find widespread application in advancing emulsion properties for use in chemistry, biology, materials, and medicine.

  14. Biofabrication of Tobacco mosaic virus-nanoscaffolded supercapacitors via temporal capillary microfluidics

    Science.gov (United States)

    Zang, Faheng; Chu, Sangwook; Gerasopoulos, Konstantinos; Culver, James N.; Ghodssi, Reza

    2017-06-01

    This paper reports the implementation of temporal capillary microfluidic patterns and biological nanoscaffolds in autonomous microfabrication of nanostructured symmetric electrochemical supercapacitors. A photoresist layer was first patterned on the substrate, forming a capillary microfluidics layer with two separated interdigitated microchannels. Tobacco mosaic virus (TMV) macromolecules suspended in solution are autonomously delivered into the microfluidics, and form a dense bio-nanoscaffolds layer within an hour. This TMV layer is utilized in the electroless plating and thermal oxidation for creating nanostructured NiO supercapacitor. The galvanostatic charge/discharge cycle showed a 3.6-fold increase in areal capacitance for the nanostructured electrode compared to planar structures. The rapid creation of nanostructure-textured microdevices with only simple photolithography and bionanostructure self-assembly can completely eliminate the needs for sophisticated synthesis or deposition processes. This method will contribute to rapid prototyping of wide range of nano-/micro-devices with enhanced performance.

  15. Fabrication of All Glass Bifurcation Microfluidic Chip for Blood Plasma Separation

    Directory of Open Access Journals (Sweden)

    Hyungjun Jang

    2017-02-01

    Full Text Available An all-glass bifurcation microfluidic chip for blood plasma separation was fabricated by a cost-effective glass molding process using an amorphous carbon (AC mold, which in turn was fabricated by the carbonization of a replicated furan precursor. To compensate for the shrinkage during AC mold fabrication, an enlarged photoresist pattern master was designed, and an AC mold with a dimensional error of 2.9% was achieved; the dimensional error of the master pattern was 1.6%. In the glass molding process, a glass microchannel plate with negligible shape errors (~1.5% compared to AC mold was replicated. Finally, an all-glass bifurcation microfluidic chip was realized by micro drilling and thermal fusion bonding processes. A separation efficiency of 74% was obtained using the fabricated all-glass bifurcation microfluidic chip.

  16. The microfluidic Kelvin water dropper

    CERN Document Server

    Marin, Alvaro G; García-Sánchez, Pablo; Shui, Lingling; Xie, Yanbo; Fontelos, Marco A; Eijkel, Jan C T; Berg, Albert van den; Lohse, Detlef

    2013-01-01

    The so-called "Kelvin water dropper" is a simple experiment demonstrating the spontaneous appearance of induced free charge in droplets emitted through a tube. As Lord Kelvin explained, water droplets spontaneously acquire a net charge during detachment from a faucet due to the presence of electrical fields in their surrounding created by any metallic object. In his experiment, two streams of droplets are allowed to drip from separated nozzles into separated buckets, which are at the same time interconnected through the dripping needles. In this paper we build a microfluidic water dropper and demonstrate that the droplets get charged and break-up due to electrohydrodynamic instabilities. A comparison with recent simulations shows the dependence of the acquired charge in the droplets on different parameters of the system. The phenomenon opens a door to cheap and accessible transformation of pneumatic pressure into electrical energy and to an enhanced control in microfluidic and biophysical manipulation of caps...

  17. Protein patterns of brush-border fragments in congenital lactose malabsorption and in specific hypolactasia of the adult.

    Science.gov (United States)

    Freiburghaus, A U; Schmitz, J; Schindler, M; Rotthauwe, H W; Kuitunen, P; Launiala, K; Hadorn, B

    1976-05-06

    Brush-border membrane proteins of the small-bowel mucosa were separated on polyacrylamide gels from intestinal biopsy specimens obtained from four children with congenital lactose malabsorption and from two adults with specific hypolactasia. In three patients with the congenital type of lactase deficiency the protein band corresponding to brush-border lactase was reduced in intensity, but was never completely absent. No difference in gel patterns was detected when this pattern in congenital deficiency was compared to that obtained from the two patients with adult-type selective hypolactasia. In one patient with congenital lactose malabsorption the protein band corresponding to lactase activity was not detectable. The findings suggest that the mechanisms leading to low lactase activity in the congenital and adult forms of lactose intolerance are similar.

  18. Acoustically-driven microfluidic systems

    Energy Technology Data Exchange (ETDEWEB)

    Wang, A W; Benett, W J; Tarte, L R

    2000-06-23

    We have demonstrated a non-contact method of concentrating and mixing particles in a plastic microfluidic chamber employing acoustic radiation pressure. A flaw cell package has also been designed that integrates liquid sample interconnects, electrical contacts and a removable sample chamber. Experiments were performed on 1, 3, 6, and 10 {micro}m polystyrene beads. Increased antibody binding to a solid-phase substrate was observed in the presence of acoustic mixing due to improve mass transport.

  19. Optical detection in microfluidic systems

    DEFF Research Database (Denmark)

    Mogensen, Klaus Bo; Kutter, Jörg Peter

    2009-01-01

    Optical detection schemes continue to be favoured for measurements in microfluidic systems. A selection of the latest progress mainly within the last two years is critically reviewed. Emphasis is on integrated solutions, such as planar waveguides, coupling schemes to the outside world, evanescent...... to ease commercialisation of the devices. This work will hopefully result in more commercial products that benefit from integrated optics, because the impact on commercial devices so far has been modest....

  20. Microfluidic fabrication of plasmonic microcapsules

    OpenAIRE

    Wang, J.; Jin, M. L.; Eijkel, J.C.T.; Berg, van den, A.E.; Zhou, G.F.; Shui, L.L.

    2016-01-01

    This paper presents the plasmonic microcapsules with well-ordered nanoparticles embedded in polymer network fabricated by using a microfluidic device. The well-ordered nanoparticle arrays on the microcapsule form high-density uniform “hot-spots” with a deposited metal film, on which the localized surface plasmon resonance effect is obtained. These plasmonic microcapsules can be engineered and modified by nanoparticle size and the metal film thickness. Repeatable Surfaced-Enhanced Raman Scatte...

  1. Whole-Teflon microfluidic chips.

    Science.gov (United States)

    Ren, Kangning; Dai, Wen; Zhou, Jianhua; Su, Jing; Wu, Hongkai

    2011-05-17

    Although microfluidics has shown exciting potential, its broad applications are significantly limited by drawbacks of the materials used to make them. In this work, we present a convenient strategy for fabricating whole-Teflon microfluidic chips with integrated valves that show outstanding inertness to various chemicals and extreme resistance against all solvents. Compared with other microfluidic materials [e.g., poly(dimethylsiloxane) (PDMS)] the whole-Teflon chip has a few more advantages, such as no absorption of small molecules, little adsorption of biomolecules onto channel walls, and no leaching of residue molecules from the material bulk into the solution in the channel. Various biological cells have been cultured in the whole-Teflon channel. Adherent cells can attach to the channel bottom, spread, and proliferate well in the channels (with similar proliferation rate to the cells in PDMS channels with the same dimensions). The moderately good gas permeability of the Teflon materials makes it suitable to culture cells inside the microchannels for a long time.

  2. Probing cell mechanical properties with microfluidic devices

    Science.gov (United States)

    Rowat, Amy

    2012-02-01

    Exploiting flow on the micron-scale is emerging as a method to probe cell mechanical properties with 10-1000x advances in throughput over existing technologies. The mechanical properties of cells and the cell nucleus are implicated in a wide range of biological contexts: for example, the ability of white blood cells to deform is central to immune response; and malignant cells show decreased stiffness compared to benign cells. We recently developed a microfluidic device to probe cell and nucleus mechanical properties: cells are forced to deform through a narrow constrictions in response to an applied pressure; flowing cells through a series of constrictions enables us to probe the ability of hundreds of cells to deform and relax during flow. By tuning the constriction width so it is narrower than the width of the cell nucleus, we can specifically probe the effects of nuclear physical properties on whole cell deformability. We show that the nucleus is the rate-limiting step in cell passage: inducing a change in its shape to a multilobed structure results in cells that transit more quickly; increased levels of lamin A, a nuclear protein that is key for nuclear shape and mechanical stability, impairs the passage of cells through constrictions. We are currently developing a new class of microfluidic devices to simultaneously probe the deformability of hundreds of cell samples in parallel. Using the same soft lithography techniques, membranes are fabricated to have well-defined pore distribution, width, length, and tortuosity. We design the membranes to interface with a multiwell plate, enabling simultaneous measurement of hundreds of different samples. Given the wide spectrum of diseases where altered cell and nucleus mechanical properties are implicated, such a platform has great potential, for example, to screen cells based on their mechanical phenotype against a library of drugs.

  3. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Leffers, H;

    1991-01-01

    Analysis of cellular protein patterns by computer-aided 2-dimensional gel electrophoresis together with recent advances in protein sequence analysis have made possible the establishment of comprehensive 2-dimensional gel protein databases that may link protein and DNA information and that offer a...

  4. A parallel microfluidic flow cytometer for high-content screening.

    Science.gov (United States)

    McKenna, Brian K; Evans, James G; Cheung, Man Ching; Ehrlich, Daniel J

    2011-05-01

    A parallel microfluidic cytometer (PMC) uses a high-speed scanning photomultiplier-based detector to combine low-pixel-count, one-dimensional imaging with flow cytometry. The 384 parallel flow channels of the PMC decouple count rate from signal-to-noise ratio. Using six-pixel one-dimensional images, we investigated protein localization in a yeast model for human protein misfolding diseases and demonstrated the feasibility of a nuclear-translocation assay in Chinese hamster ovary (CHO) cells expressing an NFκB-EGFP reporter.

  5. Timing and pattern of postexercise protein ingestion affects whole-body protein balance in healthy children: a randomized trial.

    Science.gov (United States)

    Volterman, Kimberly A; Moore, Daniel R; Breithaupt, Peter; Grathwohl, Dominik; Offord, Elizabeth A; Karagounis, Leonidas G; Timmons, Brian W

    2017-07-06

    The dose and timing of postexercise protein ingestion can influence whole-body protein balance (WBPB) in adults, although comparable data from children are scarce. This study investigated how protein intake (both amount and distribution) postexercise can affect WBPB in physically active children. Thirty-five children (26 males; 9-13 years old) underwent a 5-day adaptation diet, maintaining a protein intake of 0.95 g·kg(-1)·day(-1). Participants consumed [(15)N]glycine (2 mg·kg(-1)) before performing 3 × 20 min of variable-intensity cycling, and whole-body protein kinetics were assessed over 6 and 24 h of recovery. Fifteen grams of protein was distributed across 2 isoenergetic carbohydrate-containing beverages (15 and 240 min postexercise) containing reciprocal amounts of protein (i.e., 0 + 15 g, 5 + 10 g, 10 + 5 g, and 15 + 0 g for Groups A-D, respectively). Over the 6 h that included the exercise bout and consumption of the first beverage at 15 min postexercise, WBPB (i.e., synthesis - breakdown) demonstrated a linear increase of 0.647 g·kg(-1)·day(-1) per 1 g protein intake (P parabola (P < 0.05), suggesting that a maximum in WBPB was achieved between groups B and C. In conclusion, despite a dose response early in recovery, a periodized protein intake with multiple smaller doses after physical activity may be more beneficial than a single bolus dose in promoting daily WBPB in healthy active children.

  6. Changing patterns of acute phase proteins and inflammatory mediators in experimental caprine coccidiosis.

    Science.gov (United States)

    Hashemnia, Mohammad; Khodakaram-Tafti, Azizollah; Razavi, Seyed Mostafa; Nazifi, Saeed

    2011-09-01

    This experiment was conducted to assess the changing patterns and relative values of acute phase proteins and inflammatory cytokines in experimental caprine coccidiosis. Eighteen newborn kids were allocated to 3 equal groups. Two groups, A and B, were inoculated with a single dose of 1×10(3) and1×10(5) sporulated oocysts of Eimeria arloingi, respectively. The third group, C, received distilled water as the control. Blood samples were collected from the jugular vein of each kid in both groups before inoculation and at days 7, 14, 21, 28, 35, and 42 post-inoculation (PI), and the levels of haptoglobin (Hp), serum amyloid A (SAA), TNF-α, and IFN-γ were measured. For histopathological examinations, 2 kids were selected from each group, euthanized, and necropsied on day 42 PI. Mean Hp concentrations in groups A and B (0.34 and 0.68 g/L) at day 7 PI were 3.2 and 6.3 times higher than the levels before inoculation. The mean SAA concentrations in groups A and B (25.6 and 83.5 µg/ml) at day 7 PI were 4.2 and 13.7 times higher than the levels before inoculation. The magnitude and duration of the Hp and SAA responses correlated well with the inoculation doses and the severity of the clinical signs and diarrhea in kids. These results were consistent with the histopathological features, which showed advanced widespread lesions in group B. In both groups, significant correlations were observed for TNF-α and IFN-γ with SAA and Hp, respectively. In conclusion, Hp and SAA can be useful non-specific diagnostic indicators in caprine coccidiosis.

  7. Distillation and detection of SO2 using a microfluidic chip.

    Science.gov (United States)

    Ju, Wei-Jhong; Fu, Lung-Ming; Yang, Ruey-Jen; Lee, Chia-Lun

    2012-02-07

    A miniaturized distillation system is presented for separating sulfurous acid (H(2)SO(3)) into sulfur dioxide (SO(2)) and water (H(2)O). The major components of the proposed system include a microfluidic distillation chip, a power control module, and a carrier gas pressure control module. The microfluidic chip is patterned using a commercial CO(2) laser and comprises a serpentine channel, a heating zone, a buffer zone, a cooling zone, and a collection tank. In the proposed device, the H(2)SO(3) solution is injected into the microfluidic chip and is separated into SO(2) and H(2)O via an appropriate control of the distillation time and temperature. The gaseous SO(2) is then transported into the collection chamber by the carrier gas and is mixed with DI water. Finally, the SO(2) concentration is deduced from the absorbance measurements obtained using a spectrophotometer. The experimental results show that a correlation coefficient of R(2) = 0.9981 and a distillation efficiency as high as 94.6% are obtained for H(2)SO(3) solutions with SO(2) concentrations in the range of 100-500 ppm. The SO(2) concentrations of two commercial red wines are successfully detected using the developed device. Overall, the results presented in this study show that the proposed system provides a compact and reliable tool for SO(2) concentration measurement purposes.

  8. Seamless integration of CMOS and microfluidics using flip chip bonding

    Science.gov (United States)

    Welch, David; Blain Christen, Jennifer

    2013-03-01

    We demonstrate the microassembly of PDMS (polydimethylsiloxane) microfluidics with integrated circuits made in complementary metal-oxide-semiconductor (CMOS) processes. CMOS-sized chips are flip chip bonded to a flexible polyimide printed circuit board (PCB) with commercially available solder paste patterned using a SU-8 epoxy. The average resistance of each flip chip bond is negligible and all connections are electrically isolated. PDMS is attached to the flexible polyimide PCB using a combination of oxygen plasma treatment and chemical bonding with 3-aminopropyltriethoxysilane. The total device has a burst pressure of 175 kPA which is limited by the strength of the flip chip attachment. This technique allows the sensor area of the die to act as the bottom of the microfluidic channel. The SU-8 provides a barrier between the pad ring (electrical interface) and the fluids; post-processing is not required on the CMOS die. This assembly method shows great promise for developing analytic systems which combine the strengths of microelectronics and microfluidics into one device.

  9. Materials for microfluidic chip fabrication.

    Science.gov (United States)

    Ren, Kangning; Zhou, Jianhua; Wu, Hongkai

    2013-11-19

    Through manipulating fluids using microfabricated channel and chamber structures, microfluidics is a powerful tool to realize high sensitive, high speed, high throughput, and low cost analysis. In addition, the method can establish a well-controlled microenivroment for manipulating fluids and particles. It also has rapid growing implementations in both sophisticated chemical/biological analysis and low-cost point-of-care assays. Some unique phenomena emerge at the micrometer scale. For example, reactions are completed in a shorter amount of time as the travel distances of mass and heat are relatively small; the flows are usually laminar; and the capillary effect becomes dominant owing to large surface-to-volume ratios. In the meantime, the surface properties of the device material are greatly amplified, which can lead to either unique functions or problems that we would not encounter at the macroscale. Also, each material inherently corresponds with specific microfabrication strategies and certain native properties of the device. Therefore, the material for making the device plays a dominating role in microfluidic technologies. In this Account, we address the evolution of materials used for fabricating microfluidic chips, and discuss the application-oriented pros and cons of different materials. This Account generally follows the order of the materials introduced to microfluidics. Glass and silicon, the first generation microfluidic device materials, are perfect for capillary electrophoresis and solvent-involved applications but expensive for microfabriaction. Elastomers enable low-cost rapid prototyping and high density integration of valves on chip, allowing complicated and parallel fluid manipulation and in-channel cell culture. Plastics, as competitive alternatives to elastomers, are also rapid and inexpensive to microfabricate. Their broad variety provides flexible choices for different needs. For example, some thermosets support in-situ fabrication of

  10. NMR spin relaxation in proteins: The patterns of motion that dissipate power to the bath

    Energy Technology Data Exchange (ETDEWEB)

    Shapiro, Yury E., E-mail: eva.meirovitch@biu.ac.il, E-mail: yuryeshapiro@gmail.com; Meirovitch, Eva, E-mail: eva.meirovitch@biu.ac.il, E-mail: yuryeshapiro@gmail.com [The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900-02 (Israel)

    2014-04-21

    We developed in recent years the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for the analysis of NMR relaxation in proteins. The two bodies/rotators are the protein (diffusion tensor D{sub 1}) and the spin-bearing probe, e.g., the {sup 15}N−{sup 1}H bond (diffusion tensor, D{sub 2}), coupled by a local potential (u). A Smoluchowski equation is solved to yield the generic time correlation functions (TCFs), which are sums of weighted exponentials (eigenmodes). By Fourier transformation one obtains the generic spectral density functions (SDFs) which underlie the experimental relaxation parameters. The typical paradigm is to characterize structural dynamics in terms of the best-fit values of D{sub 1}, D{sub 2}, and u. Additional approaches we pursued employ the SRLS TCFs, SDFs, or eigenmodes as descriptors. In this study we develop yet another perspective. We consider the SDF as function of the angular velocity associated with the fluctuating fields underlying NMR relaxation. A parameter called j-fraction, which represents the relative contribution of eigenmode, i, to a given value of the SDF function at a specific frequency, ω, is defined. j-fraction profiles of the dominant eigenmodes are derived for 0 ≤ ω ≤ 10{sup 12} rad/s. They reveal which patterns of motion actuate power dissipation at given ω-values, what are their rates, and what is their relative contribution. Simulations are carried out to determine the effect of timescale separation, D{sub 1}/D{sub 2}, axial potential strength, and local diffusion axiality. For D{sub 1}/D{sub 2} ≤ 0.01 and strong local potential of 15 k{sub B}T, power is dissipated by global diffusion, renormalized (by the strong potential) local diffusion, and probe diffusion on the surface of a cone (to be called cone diffusion). For D{sub 1}/D{sub 2} = 0.1, power is dissipated by mixed eigenmodes largely of a global-diffusion-type or cone-diffusion-type, and a nearly bare renormalized

  11. UV lithography-based protein patterning on silicon: Towards the integration of bioactive surfaces and CMOS electronics

    Energy Technology Data Exchange (ETDEWEB)

    Lenci, S., E-mail: silvia.lenci@iet.unipi.it [Dipartimento di Ingegneria dell' Informazione, via G.Caruso 16, Pisa I-56122 (Italy); Tedeschi, L. [Istituto di Fisiologia Clinica - CNR, via G. Moruzzi 1, Pisa I-56124 (Italy); Pieri, F. [Dipartimento di Ingegneria dell' Informazione, via G.Caruso 16, Pisa I-56122 (Italy); Domenici, C. [Istituto di Fisiologia Clinica - CNR, via G. Moruzzi 1, Pisa I-56124 (Italy)

    2011-08-01

    A simple and fast methodology for protein patterning on silicon substrates is presented, providing an insight into possible issues related to the interaction between biological and microelectronic technologies. The method makes use of standard photoresist lithography and is oriented towards the implementation of biosensors containing Complementary Metal-Oxide-Semiconductor (CMOS) conditioning circuitry. Silicon surfaces with photoresist patterns were prepared and hydroxylated by means of resist- and CMOS backend-compatible solutions. Subsequent aminosilane deposition and resist lift-off in organic solvents resulted into well-controlled amino-terminated geometries. The discussion is focused on resist- and CMOS-compatibility problems related to the used chemicals. Some samples underwent gold nanoparticle (Au NP) labeling and Scanning Electron Microscopy (SEM) observation, in order to investigate the quality of the silane layer. Antibodies were immobilized on other samples, which were subsequently exposed to a fluorescently labeled antigen. Fluorescence microscopy observation showed that this method provides spatially selective immobilization of protein layers onto APTES-patterned silicon samples, while preserving protein reactivity inside the desired areas and low non-specific adsorption elsewhere. Strong covalent biomolecule binding was achieved, giving stable protein layers, which allows stringent binding conditions and a good binding specificity, really useful for biosensing.

  12. A review on recent developments for biomolecule separation at analytical scale using microfluidic devices.

    Science.gov (United States)

    Tetala, Kishore K R; Vijayalakshmi, M A

    2016-02-04

    Microfluidic devices with their inherent advantages like the ability to handle 10(-9) to 10(-18) L volume, multiplexing of microchannels, rapid analysis and on-chip detection are proving to be efficient systems in various fields of life sciences. This review highlights articles published since 2010 that reports the use of microfluidic devices to separate biomolecules (DNA, RNA and proteins) using chromatography principles (size, charge, hydrophobicity and affinity) along with microchip capillary electrophoresis, isotachophoresis etc. A detailed overview of stationary phase materials and the approaches to incorporate them within the microchannels of microchips is provided as well as a brief overview of chemical methods to immobilize ligand(s). Furthermore, we review research articles that deal with microfluidic devices as analytical tools for biomolecule (DNA, RNA and protein) separation.

  13. Interaction of gold and silver nanoparticles with human plasma: Analysis of protein corona reveals specific binding patterns.

    Science.gov (United States)

    Lai, Wenjia; Wang, Qingsong; Li, Lumeng; Hu, Zhiyuan; Chen, Jiankui; Fang, Qiaojun

    2017-04-01

    Determining how nanomaterials interact with plasma will assist in understanding their effects on the biological system. This work presents a systematic study of the protein corona formed from human plasma on 20nm silver and gold nanoparticles with three different surface modifications, including positive and negative surface charges. The results show that all nanoparticles, even those with positive surface modifications, acquire negative charges after interacting with plasma. Approximately 300 proteins are identified on the coronas, while 99 are commonly found on each nanomaterial. The 20 most abundant proteins account for over 80% of the total proteins abundance. Remarkably, the surface charge and core of the nanoparticles, as well as the isoelectric point of the plasma proteins, are found to play significant roles in determining the nanoparticle coronas. Albumin and globulins are present at levels of less than 2% on these nanoparticle coronas. Fibrinogen, which presents in the plasma but not in the serum, preferably binds to negatively charged gold nanoparticles. These observations demonstrate the specific plasma protein binding pattern of silver and gold nanoparticles, as well as the importance of the surface charge and core in determining the protein corona compositions. The potential downstream biological impacts of the corona proteins were also investigated.

  14. Pattern recognition in pulmonary tuberculosis defined by high content peptide microarray chip analysis representing 61 proteins from M. tuberculosis.

    Directory of Open Access Journals (Sweden)

    Simani Gaseitsiwe

    Full Text Available BACKGROUND: Serum antibody-based target identification has been used to identify tumor-associated antigens (TAAs for development of anti-cancer vaccines. A similar approach can be helpful to identify biologically relevant and clinically meaningful targets in M. tuberculosis (MTB infection for diagnosis or TB vaccine development in clinically well defined populations. METHOD: We constructed a high-content peptide microarray with 61 M. tuberculosis proteins as linear 15 aa peptide stretches with 12 aa overlaps resulting in 7446 individual peptide epitopes. Antibody profiling was carried with serum from 34 individuals with active pulmonary TB and 35 healthy individuals in order to obtain an unbiased view of the MTB epitope pattern recognition pattern. Quality data extraction was performed, data sets were analyzed for significant differences and patterns predictive of TB+/-. FINDINGS: Three distinct patterns of IgG reactivity were identified: 89/7446 peptides were differentially recognized (in 34/34 TB+ patients and in 35/35 healthy individuals and are highly predictive of the division into TB+ and TB-, other targets were exclusively recognized in all patients with TB (e.g. sigmaF but not in any of the healthy individuals, and a third peptide set was recognized exclusively in healthy individuals (35/35 but no in TB+ patients. The segregation between TB+ and TB- does not cluster into specific recognition of distinct MTB proteins, but into specific peptide epitope 'hotspots' at different locations within the same protein. Antigen recognition pattern profiles in serum from TB+ patients from Armenia vs. patients recruited in Sweden showed that IgG-defined MTB epitopes are very similar in individuals with different genetic background. CONCLUSIONS: A uniform target MTB IgG-epitope recognition pattern exists in pulmonary tuberculosis. Unbiased, high-content peptide microarray chip-based testing of clinically well-defined populations allows to visualize

  15. New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases.

    Science.gov (United States)

    Pleissner, K P; Hoffmann, F; Kriegel, K; Wenk, C; Wegner, S; Sahlström, A; Oswald, H; Alt, H; Fleck, E

    1999-01-01

    Protein spot identification in two-dimensional electrophoresis gels can be supported by the comparison of gel images accessible in different World Wide Web two-dimensional electrophoresis (2-DE) gel protein databases. The comparison may be performed either by visual cross-matching between gel images or by automatic recognition of similar protein spot patterns. A prerequisite for the automatic point pattern matching approach is the detection of protein spots yielding the x(s),y(s) coordinates and integrated spot intensities i(s). For this purpose an algorithm is developed based on a combination of hierarchical watershed transformation and feature extraction methods. This approach reduces the strong over-segmentation of spot regions normally produced by watershed transformation. Measures for the ellipticity and curvature are determined as features of spot regions. The resulting spot lists containing x(s),y(s),i(s)-triplets are calculated for a source as well as for a target gel image accessible in 2-DE gel protein databases. After spot detection a matching procedure is applied. Both the matching of a local pattern vs. a full 2-DE gel image and the global matching between full images are discussed. Preset slope and length tolerances of pattern edges serve as matching criteria. The local matching algorithm relies on a data structure derived from the incremental Delaunay triangulation of a point set and a two-step hashing technique. For the incremental construction of triangles the spot intensities are considered in decreasing order. The algorithm needs neither landmarks nor an a priori image alignment. A graphical user interface for spot detection and gel matching is written in the Java programming language for the Internet. The software package called CAROL (http://gelmatching.inf.fu-berlin.de) is realized in a client-server architecture.

  16. SDS-PAGE analysis of whole cell protein and outer memr-bane protein patterns of clinical isolates of Burkholderia pseud-omallei

    Institute of Scientific and Technical Information of China (English)

    Apichart Nontprasert; Cheeraratana Cheeramakara; Sasithon Pukrittayakamee; David AB Dance; Ty L Pitt; Michael D Smith; Sirivan Vanijanonta; Nicholas J White

    2009-01-01

    Objective:To investigate the banding patterns of whole cell protein (WCP)and outer membrane protein (OMP)of Burkholderia pseudomallei (B.pseudomallei)in clinical isolates from patients with melioidosis. Methods:WCP and OMP of of B.pseudomallei in 50 clinical isolates,from 47 patients with melioidosis were prepared and separated by polyacrylamide gel electrophoresis (SDS-PAGE)using 10% gels and stained with Coomassie brilliant blue.The banding patterns were compared by using a laser densitometer and dendrogram. Results:There were 6 different banding patterns of WCP and 2 types of OMP.Type 1-5 WCP had 8 common protein bands at 19.0 -45.0 kDa with identical OMP pattern.The banding patterns of WCP in type 6 were distinct from the others and also its OMP profile.The majority of clinical isolates (37 /50,74%)were in type 1 WCP.Of the remaining isolates,8 were in type 2,2 in type 3,and one each was in type 4 to 6.There was no significant association between the WCP typing and the demographic or clinical features of the investigated patients.Conclusion:Despite the wide variation of clinical features of melioidosis,the results of this study show that B.pseudomallei had a few differences in the WCP and OMP profiles.Therefore typing of WCP and OMP,using SDS-PAGE analysis,could be an alternative method for phenotypic differentiation in clinical iso-lates of B.pseudomallei.

  17. Integrating Electronics and Microfluidics on Paper.

    Science.gov (United States)

    Hamedi, Mahiar M; Ainla, Alar; Güder, Firat; Christodouleas, Dionysios C; Fernández-Abedul, M Teresa; Whitesides, George M

    2016-07-01

    Paper microfluidics and printed electronics have developed independently, and are incompatible in many aspects. Monolithic integration of microfluidics and electronics on paper is demonstrated. This integration makes it possible to print 2D and 3D fluidic, electrofluidic, and electrical components on paper, and to fabricate devices using them.

  18. Principles, Techniques, and Applications of Tissue Microfluidics

    Science.gov (United States)

    Wade, Lawrence A.; Kartalov, Emil P.; Shibata, Darryl; Taylor, Clive

    2011-01-01

    The principle of tissue microfluidics and its resultant techniques has been applied to cell analysis. Building microfluidics to suit a particular tissue sample would allow the rapid, reliable, inexpensive, highly parallelized, selective extraction of chosen regions of tissue for purposes of further biochemical analysis. Furthermore, the applicability of the techniques ranges beyond the described pathology application. For example, they would also allow the posing and successful answering of new sets of questions in many areas of fundamental research. The proposed integration of microfluidic techniques and tissue slice samples is called "tissue microfluidics" because it molds the microfluidic architectures in accordance with each particular structure of each specific tissue sample. Thus, microfluidics can be built around the tissues, following the tissue structure, or alternatively, the microfluidics can be adapted to the specific geometry of particular tissues. By contrast, the traditional approach is that microfluidic devices are structured in accordance with engineering considerations, while the biological components in applied devices are forced to comply with these engineering presets.

  19. Cell Culture Microfluidic Biochips: Experimental Throughput Maximization

    DEFF Research Database (Denmark)

    Minhass, Wajid Hassan; Pop, Paul; Madsen, Jan

    2011-01-01

    Microfluidic biochips offer a promising alternative to a conventional biochemical laboratory, integrating all necessary functionalities on-chip in order to perform biochemical applications. Researchers have started to propose computer-aided design tools for the synthesis of such biochips. Our focus...... metaheuristic for experimental design generation for the cell culture microfluidic biochips, and we have evaluated our approach using multiple experimental setups....

  20. Modular microfluidic system for biological sample preparation

    Energy Technology Data Exchange (ETDEWEB)

    Rose, Klint A.; Mariella, Jr., Raymond P.; Bailey, Christopher G.; Ness, Kevin Dean

    2015-09-29

    A reconfigurable modular microfluidic system for preparation of a biological sample including a series of reconfigurable modules for automated sample preparation adapted to selectively include a) a microfluidic acoustic focusing filter module, b) a dielectrophoresis bacteria filter module, c) a dielectrophoresis virus filter module, d) an isotachophoresis nucleic acid filter module, e) a lyses module, and f) an isotachophoresis-based nucleic acid filter.