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Sample records for cell arrays reveal

  1. Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins

    Directory of Open Access Journals (Sweden)

    Kahlem Pascal

    2006-06-01

    Full Text Available Abstract Background Trisomy of human chromosome 21 (Chr21 results in Down's syndrome, a complex developmental and neurodegenerative disease. Molecular analysis of Down's syndrome, however, poses a particular challenge, because the aneuploid region of Chr21 contains many genes of unknown function. Subcellular localization of human Chr21 proteins may contribute to further understanding of the functions and regulatory mechanisms of the genes that code for these proteins. Following this idea, we used a transfected-cell array technique to perform a rapid and cost-effective analysis of the intracellular distribution of Chr 21 proteins. Results We chose 89 genes that were distributed over the majority of 21q, ranging from RBM11 (14.5 Mb to MCM3AP (46.6 Mb, with part of them expressed aberrantly in the Down's syndrome mouse model. Open reading frames of these genes were cloned into a mammalian expression vector with an amino-terminal His6 tag. All of the constructs were arrayed on glass slides and reverse transfected into HEK293T cells for protein expression. Co-localization detection using a set of organelle markers was carried out for each Chr21 protein. Here, we report the subcellular localization properties of 52 proteins. For 34 of these proteins, their localization is described for the first time. Furthermore, the alteration in cell morphology and growth as a result of protein over-expression for claudin-8 and claudin-14 genes has been characterized. Conclusion The cell array-based protein expression and detection approach is a cost-effective platform for large-scale functional analyses, including protein subcellular localization and cell phenotype screening. The results from this study reveal novel functional features of human Chr21 proteins, which should contribute to further understanding of the molecular pathology of Down's syndrome.

  2. Cell membrane conformation at vertical nanowire array interface revealed by fluorescence imaging

    Science.gov (United States)

    Berthing, Trine; Bonde, Sara; Rostgaard, Katrine R.; Hannibal Madsen, Morten; Sørensen, Claus B.; Nygård, Jesper; Martinez, Karen L.

    2012-10-01

    The perspectives offered by vertical arrays of nanowires for biosensing applications in living cells depend on the access of individual nanowires to the cell interior. Recent results on electrical access and molecular delivery suggest that direct access is not always obtained. Here, we present a generic approach to directly visualize the membrane conformation of living cells interfaced with nanowire arrays, with single nanowire resolution. The method combines confocal z-stack imaging with an optimized cell membrane labelling strategy which was applied to HEK293 cells interfaced with 2-11 μm long and 3-7 μm spaced nanowires with various surface coatings (bare, aminosilane-coated or polyethyleneimine-coated indium arsenide). We demonstrate that, for all commonly used nanowire lengths, spacings and surface coatings, nanowires generally remain enclosed in a membrane compartment, and are thereby not in direct contact with the cell interior.

  3. A microfluidic platform reveals differential response of regulatory T cells to micropatterned costimulation arrays.

    Science.gov (United States)

    Lee, Joung-Hyun; Dustin, Michael L; Kam, Lance C

    2015-11-01

    T cells are key mediators of adaptive immunity. However, the overall immune response is often directed by minor subpopulations of this heterogeneous family of cells, owing to specificity of activation and amplification of functional response. Knowledge of differences in signaling and function between T cell subtypes is far from complete, but is clearly needed for understanding and ultimately leveraging this branch of the adaptive immune response. This report investigates differences in cell response to micropatterned surfaces by conventional and regulatory T cells. Specifically, the ability of cells to respond to the microscale geometry of TCR/CD3 and CD28 engagement is made possible using a magnetic-microfluidic device that overcomes limitations in imaging efficiency associated with conventional microscopy equipment. This device can be readily assembled onto micropatterned surfaces while maintaining the activity of proteins and other biomolecules necessary for such studies. In operation, a target population of cells is tagged using paramagnetic beads, and then trapped in a divergent magnetic field within the chamber. Following washing, the target cells are released to interact with a designated surface. Characterization of this system with mouse CD4(+) T cells demonstrated a 50-fold increase in target-to-background cell purity, with an 80% collection efficiency. Applying this approach to CD4(+)CD25(+) regulatory T cells, it is then demonstrated that these rare cells respond less selectively to micro-scale features of anti-CD3 antibodies than CD4(+)CD25(-) conventional T cells, revealing a difference in balance between TCR/CD3 and LFA-1-based adhesion. PKC-θ localized to the distal pole of regulatory T cells, away from the cell-substrate interface, suggests a mechanism for differential regulation of TCR/LFA-1-based adhesion. Moreover, specificity of cell adhesion to anti-CD3 features was dependent on the relative position of anti-CD28 signaling within the cell

  4. Photovoltaic cell array

    Science.gov (United States)

    Eliason, J. T. (Inventor)

    1976-01-01

    A photovoltaic cell array consisting of parallel columns of silicon filaments is described. Each fiber is doped to produce an inner region of one polarity type and an outer region of an opposite polarity type to thereby form a continuous radial semi conductor junction. Spaced rows of electrical contacts alternately connect to the inner and outer regions to provide a plurality of electrical outputs which may be combined in parallel or in series.

  5. Time-dependent c-Myc transactomes mapped by Array-based nuclear run-on reveal transcriptional modules in human B cells.

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    Jinshui Fan

    Full Text Available BACKGROUND: The definition of transcriptional networks through measurements of changes in gene expression profiles and mapping of transcription factor binding sites is limited by the moderate overlap between binding and gene expression changes and the inability to directly measure global nuclear transcription (coined "transactome". METHODOLOGY/PRINCIPAL FINDINGS: We developed a method to measure nascent nuclear gene transcription with an Array-based Nuclear Run-On (ANRO assay using commercial microarray platforms. This strategy provides the missing component, the transactome, to fully map transcriptional networks. ANRO measurements in an inducible c-Myc expressing human P493-6 B cell model reveals time-dependent waves of transcription, with a transactome early after c-Myc induction that does not persist at a late, steady-state phase, when genes that are regulated by c-Myc and E2F predominate. Gene set matrix analysis further uncovers functionally related groups of genes putatively regulated by waves of transcription factor motifs following Myc induction, starting with AP1 and CREB that are followed by EGR1, NFkB and STAT, and ending with E2F, Myc and ARNT/HIF motifs. CONCLUSIONS/SIGNIFICANCE: By coupling ANRO with previous global mapping of c-Myc binding sites by chromatin immunoprecipitation (ChIP in P493-6 cells, we define a set of transcriptionally regulated direct c-Myc target genes and pave the way for the use of ANRO to comprehensively map any transcriptional network.

  6. Array-based comparative genomic hybridization analysis reveals chromosomal copy number aberrations associated with clinical outcome in canine diffuse large B-cell lymphoma.

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    Arianna Aricò

    Full Text Available Canine Diffuse Large B-cell Lymphoma (cDLBCL is an aggressive cancer with variable clinical response. Despite recent attempts by gene expression profiling to identify the dog as a potential animal model for human DLBCL, this tumor remains biologically heterogeneous with no prognostic biomarkers to predict prognosis. The aim of this work was to identify copy number aberrations (CNAs by high-resolution array comparative genomic hybridization (aCGH in 12 dogs with newly diagnosed DLBCL. In a subset of these dogs, the genetic profiles at the end of therapy and at relapse were also assessed. In primary DLBCLs, 90 different genomic imbalances were counted, consisting of 46 gains and 44 losses. Two gains in chr13 were significantly correlated with clinical stage. In addition, specific regions of gains and losses were significantly associated to duration of remission. In primary DLBCLs, individual variability was found, however 14 recurrent CNAs (>30% were identified. Losses involving IGK, IGL and IGH were always found, and gains along the length of chr13 and chr31 were often observed (>41%. In these segments, MYC, LDHB, HSF1, KIT and PDGFRα are annotated. At the end of therapy, dogs in remission showed four new CNAs, whereas three new CNAs were observed in dogs at relapse compared with the previous profiles. One ex novo CNA, involving TCR, was present in dogs in remission after therapy, possibly induced by the autologous vaccine. Overall, aCGH identified small CNAs associated with outcome, which, along with future expression studies, may reveal target genes relevant to cDLBCL.

  7. Stem cell heterogeneity revealed

    DEFF Research Database (Denmark)

    Andersen, Marianne S; Jensen, Kim B

    2016-01-01

    The skin forms a protective, water-impermeable barrier consisting of heavily crosslinked epithelial cells. However, the specific role of stem cells in sustaining this barrier remains a contentious issue. A detailed analysis of the interfollicular epidermis now proposes a model for how a composite...... of cells with different properties are involved in its maintenance....

  8. Multijunction Ultralight Solar Cells and Arrays Project

    Data.gov (United States)

    National Aeronautics and Space Administration — There is a continuing need within NASA for solar cells and arrays with very high specific power densities (1000-5000 kW/kg) for generating power in a new generation...

  9. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation

    OpenAIRE

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-01-01

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agre...

  10. Cell Proliferation Tracking Using Graphene Sensor Arrays

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    Ronan Daly

    2012-01-01

    Full Text Available The development of a novel label-free graphene sensor array is presented. Detection is based on modification of graphene FET devices and specifically monitoring the change in composition of the nutritive components in culturing medium. Micro-dispensing of Escherichia coli in medium shows feasibility of accurate positioning over each sensor while still allowing cell proliferation. Graphene FET device fabrication, sample dosing, and initial electrical characterisation have been completed and show a promising approach to reducing the sample size and lead time for diagnostic and drug development protocols through a label-free and reusable sensor array fabricated with standard and scalable microfabrication technologies.

  11. Ion-selective microelectrode arrays for cell culture monitoring

    OpenAIRE

    Generelli, Silvia; De Rooij, Nicolas-F.

    2008-01-01

    The design, microfabrication and characterization of a platform comprising an array of ion-selective microelectrodes (µISE) aimed at in vitro cellular physiology and toxicology is described. This study focusses on K+ and Ca2+ monitoring in cell culture environments. A potential promising application of such a platform is based on recent findings in molecular biology, revealing connections between certain diseases, as for example some types of cancer or parkinsonism, and a malfunction in cellu...

  12. Automated image analysis reveals the dynamic 3-dimensional organization of multi-ciliary arrays

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    Domenico F. Galati

    2016-01-01

    Full Text Available Multi-ciliated cells (MCCs use polarized fields of undulating cilia (ciliary array to produce fluid flow that is essential for many biological processes. Cilia are positioned by microtubule scaffolds called basal bodies (BBs that are arranged within a spatially complex 3-dimensional geometry (3D. Here, we develop a robust and automated computational image analysis routine to quantify 3D BB organization in the ciliate, Tetrahymena thermophila. Using this routine, we generate the first morphologically constrained 3D reconstructions of Tetrahymena cells and elucidate rules that govern the kinetics of MCC organization. We demonstrate the interplay between BB duplication and cell size expansion through the cell cycle. In mutant cells, we identify a potential BB surveillance mechanism that balances large gaps in BB spacing by increasing the frequency of closely spaced BBs in other regions of the cell. Finally, by taking advantage of a mutant predisposed to BB disorganization, we locate the spatial domains that are most prone to disorganization by environmental stimuli. Collectively, our analyses reveal the importance of quantitative image analysis to understand the principles that guide the 3D organization of MCCs.

  13. Kinome profiling using peptide arrays in eukaryotic cells.

    Science.gov (United States)

    Parikh, Kaushal; Peppelenbosch, Maikel P; Ritsema, Tita

    2009-01-01

    Over the last 10 years array and mass spectrometry technologies have enabled the determination of the transcriptome and proteome of biological and in particular eukaryotic systems. This information will likely be of significant value to our elucidation of the molecular mechanisms that govern eukaryotic physiology. However, an equally, if not more important goal, is to define those proteins that participate in signalling pathways that ultimately control cell fate. Enzymes that phosphorylate tyrosine, serine, and threonine residues on other proteins play a major role in signalling cascades that determine cell-cycle entry, and survival and differentiation fate in the tissues across the eukaryotic kingdoms. Knowing which signalling pathways are being used in these cells is of critical importance. Traditional genetic and biochemical approaches can certainly provide answers here, but for technical and practical reasons there is typically pursued one gene or pathway at a time. Thus, a more comprehensive approach is needed in order to reveal signalling pathways active in nucleated cells. Towards this end, kinome analysis techniques using peptide arrays have begun to be applied with substantial success in a variety of organisms from all major branches of eukaryotic life, generating descriptions of cellular signalling without a priori assumptions as to possibly effected pathways. The general procedure and analysis methods are very similar disregarding whether the primary source of the material is animal, plant, or fungal of nature and will be described in this chapter. These studies will help us better understand what signalling pathways are critical to controlling eukaryotic cell function.

  14. Nanotubular array solid oxide fuel cell.

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    Motoyama, Munekazu; Chao, Cheng-Chieh; An, Jihwan; Jung, Hee Joon; Gür, Turgut M; Prinz, Friedrich B

    2014-01-28

    This report presents a demonstration and characterization of a nanotubular array of solid oxide fuel cells (SOFCs) made of one-end-closed hollow tube Ni/yttria-stabilized zirconia/Pt membrane electrode assemblies (MEAs). The tubular MEAs are nominally ∼5 μm long and have up to 660 mV (vs air) and power densities up to 1.3 μW cm(-2) were measured at 550 °C using H2 as fuel. The paper also introduces a fabrication methodology primarily based on a template process involving atomic layer deposition and electrodeposition for building the nanotubular MEA architecture as an important step toward achieving high surface area ultrathin SOFCs operating in the intermediate to low-temperature regime. A fabricated nanotubular SOFC theoretically attains a 20-fold increase in the effective surface, while projections indicate the possibility of achieving up to 40-fold. PMID:24266776

  15. Cellular heterogeneity and live cell arrays.

    Science.gov (United States)

    Walling, Maureen A; Shepard, Jason R E

    2011-07-01

    In the past decade, the tendency to move from a global, one-size-fits-all treatment philosophy to personalized medicine is based, in part, on the nuanced differences and sub-classifications of disease states. Our knowledge of these varied states stems from not only the ability to diagnose, classify, and perform experiments on cell populations as a whole, but also from new technologies that allow interrogation of cell populations at the individual cell level. Such departures from conventional thinking are driven by the recognition that clonal cell populations have numerous activities that manifest as significant levels of non-genetic heterogeneity. Clonal populations by definition originate from a single genetic origin so are regarded as having a high level of homogeneity as compared to genetically distinct cell populations. However, analysis at the single cell level has revealed a different phenomenon; cells and organisms require an inherent level of non-genetic heterogeneity to function properly, and in some cases, to survive. The growing understanding of this occurrence has lead to the development of methods to monitor, analyze, and better characterize the heterogeneity in cell populations. Following the trend of DNA- and protein microarrays, platforms capable of simultaneously monitoring each cell in a population have been developed. These cellular microarray platforms and other related formats allow for continuous monitoring of single live cells and simultaneously generate individual cell and average population data that are more descriptive and information-rich than traditional bulk methods. These technological advances have helped develop a better understanding of the intricacies associated with biological processes and afforded greater insight into complex biological systems. The associated instruments, techniques, and reagents now allow for highly multiplexed analyses, which enable multiple cellular activities, processes, or pathways to be monitored

  16. Periodic nano/micro-hole array silicon solar cell

    OpenAIRE

    Lai, Guan-Yu; Kumar, Dinesh P; Pei, Zingway

    2014-01-01

    In this study, we applied a metal catalyst etching method to fabricate a nano/microhole array on a Si substrate for application in solar cells. In addition, the surface of an undesigned area was etched because of the attachment of metal nanoparticles that is dissociated in a solution. The nano/microhole array exhibited low specular reflectance (

  17. A gate array structure for the efficient project of digital circuits: The unit cell array

    Science.gov (United States)

    Geisler, Olaf

    In this study the principles for the development of a unit-cell-array-master, which shows all the advantages of gate-arrays, are presented. By taking the cabling influence on the chip surface into account, a stochastic model of cabling for sea-of-gates-structures is used, which allows establishment of the minimal dimensions of the master-components for the cabling. As regards the cell architecture, the gate isolation technique and smaller asymmetric p-n channel transistor pairs are employed. With logical structures such as Ram, Rom or PLA (programmed logic array), the Gt density increases. The analysis of gate-array cabling capacity shows that transistors with commercial gate-arrays are often of too great dimension. A greater transistor density and a lower dissipation without any performance decrease are possible by using smaller transistors and a parallel connection in circuit paths with higher cabling capacity. Apart from its initial high cost, unit cell array is interesting from an economical point of view.

  18. Cell integrated multi-junction thermocouple array for solid oxide fuel cell temperature sensing: N+1 architecture

    Science.gov (United States)

    Ranaweera, Manoj; Kim, Jung-Sik

    2016-05-01

    Understanding the cell temperature distribution of solid oxide fuel cell (SOFC) stacks during normal operation has multifaceted advantages in performance and degradation studies. Present efforts on measuring temperature from operating SOFCs measure only the gas channel temperature and do not reveal the cell level temperature distribution, which is more important for understanding a cell's performance and its temperature-related degradation. The authors propose a cell-integrated, multi-junction thermocouple array for in-situ cell surface temperature monitoring of an operational SOFC. The proposed thermocouple array requires far fewer numbers of thermoelements than that required by sets of thermocouples for the same number of temperature sensing points. Hence, the proposed array causes lower disturbance to cell performance than thermocouples. The thermoelement array was sputter deposited on the cathode of a commercial SOFC using alumel (Ni:Al:Mn:Si - 95:2:2:1 by wt.) and chromel (Ni:Cr - 90:10 by wt.). The thermocouple array was tested in a furnace over the entire operating temperature range of a typical SOFC. The individual sensing points of the array were shown to measure temperature independently from each other with equivalent accuracy to a thermocouple. Thus, the concept of multi-junction thermocouples is experimentally validated and its stability on a porous SOFC cathode is confirmed.

  19. Fingerprinting the Asterid species using subtracted diversity array reveals novel species-specific sequences.

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    Nitin Mantri

    Full Text Available BACKGROUND: Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade. METHODOLOGY/PRINCIPAL FINDINGS: Pooled genomic DNA of 104 non-asterid angiosperm and non-angiosperm species was subtracted from pooled genomic DNA of 67 asterid species. Subsequently, 283 subtracted DNA fragments were used to construct an Asterid-specific array. The validation of Asterid-specific array revealed a high (99.5% subtraction efficiency. Twenty-five Asterid species (mostly medicinal representing 20 families and 9 orders within the clade were hybridized onto the array to reveal its level of species discrimination. All these species could be successfully differentiated using their hybridization patterns. A number of species-specific probes were identified for commercially important species like tea, coffee, dandelion, yarrow, motherwort, Japanese honeysuckle, valerian, wild celery, and yerba mate. Thirty-seven polymorphic probes were characterized by sequencing. A large number of probes were novel species-specific probes whilst some of them were from chloroplast region including genes like atpB, rpoB, and ndh that have extensively been used for fingerprinting and phylogenetic analysis of plants. CONCLUSIONS/SIGNIFICANCE: Subtracted Diversity Array technique is highly efficient in fingerprinting species with little or no genomic information. The Asterid-specific array could fingerprint all 25 species assessed including three species that were not used in constructing the array. This study validates the use of chloroplast genes for bar-coding (fingerprinting plant species. In addition, this method allowed detection of several new loci that can be

  20. Performance analysis of solar cell arrays in concentrating light intensity

    International Nuclear Information System (INIS)

    Performance of concentrating photovoltaic/thermal system is researched by experiment and simulation calculation. The results show that the I-V curve of the GaAs cell array is better than that of crystal silicon solar cell arrays and the exergy produced by 9.51% electrical efficiency of the GaAs solar cell array can reach 68.93% of the photovoltaic/thermal system. So improving the efficiency of solar cell arrays can introduce more exergy and the system value can be upgraded. At the same time, affecting factors of solar cell arrays such as series resistance, temperature and solar irradiance also have been analyzed. The output performance of a solar cell array with lower series resistance is better and the working temperature has a negative impact on the voltage in concentrating light intensity. The output power has a -20 W/V coefficient and so cooling fluid must be used. Both heat energy and electrical power are then obtained with a solar trough concentrating photovoltaic/thermal system. (semiconductor devices)

  1. An addressable cell array for a platform of biosensor chips

    Science.gov (United States)

    Yang, Seungkyoung; Choi, Soo-hee; Jung, Moon Youn; Song, Kibong; Park, Jeong Won

    2013-05-01

    In order to detect interested matters in fields, various lab-on-a-chips where chemical, physical, or biological sensors are loaded have been developed. eNOSE can be a representative example among them. Because animals can sense 300~1000 different chemicals by olfactory system - smell -, the olfactory system has been spotlighted as new materials in the field of sensing. Those investigations, however, are usually focused on how to detect signals from the olfactory neurons or receptors loaded on chips and enhance sensing efficacy of chips. Therefore, almost of those chips are designed for only one material sensing. Multi-sensing using multi-channels will be needed when the olfactory systems are adopted well on chips. For multiple sensing, we developed an addressable cell array. The chip has 38 cell-chambers arranged in a circle shape and different cell types of thirty eight can be allocated with specific addresses on the chip without any complex valve system. In order to confirm the cell addressing, we loaded EGFP-transfected and empty vector-transfected HEK293a cells into inlets of the cell array in a planned address and those cells were positioned into each chamber by brief aspiration. The arrayed cells were confirmed as a specific pattern through EGFP and nuclei staining. This cell array which can generate address of sensor materials like cells with their own specification is expected to be applied to a platform for a biosensor chip at various sensing fields.

  2. Wire Array Solar Cells: Fabrication and Photoelectrochemical Studies

    Science.gov (United States)

    Spurgeon, Joshua Michael

    Despite demand for clean energy to reduce our addiction to fossil fuels, the price of these technologies relative to oil and coal has prevented their widespread implementation. Solar energy has enormous potential as a carbon-free resource but is several times the cost of coal-produced electricity, largely because photovoltaics of practical efficiency require high-quality, pure semiconductor materials. To produce current in a planar junction solar cell, an electron or hole generated deep within the material must travel all the way to the junction without recombining. Radial junction, wire array solar cells, however, have the potential to decouple the directions of light absorption and charge-carrier collection so that a semiconductor with a minority-carrier diffusion length shorter than its absorption depth (i.e., a lower quality, potentially cheaper material) can effectively produce current. The axial dimension of the wires is long enough for sufficient optical absorption while the charge-carriers are collected along the shorter radial dimension in a massively parallel array. This thesis explores the wire array solar cell design by developing potentially low-cost fabrication methods and investigating the energy-conversion properties of the arrays in photoelectrochemical cells. The concept was initially investigated with Cd(Se, Te) rod arrays; however, Si was the primary focus of wire array research because its semiconductor properties make low-quality Si an ideal candidate for improvement in a radial geometry. Fabrication routes for Si wire arrays were explored, including the vapor-liquid-solid growth of wires using SiCl4. Uniform, vertically aligned Si wires were demonstrated in a process that permits control of the wire radius, length, and spacing. A technique was developed to transfer these wire arrays into a low-cost, flexible polymer film, and grow multiple subsequent arrays using a single Si(111) substrate. Photoelectrochemical measurements on Si wire array

  3. Low-Concentration-Ratio Solar-Cell Arrays

    Science.gov (United States)

    Biss, M. S.; Reed, David A., Jr.

    1986-01-01

    Paper presents design concept for mass-producible arrays of solar electric batteries and concentrators tailored to individual requirements. Arrays intended primarily for space stations needing about 100 kW of power. However, modular, lightweight, compact, and relatively low-cost design also fulfill requirements of some terrestrial applications. Arrays built with currently available materials. Pultrusions, injectionmolded parts, and composite materials used extensively to keep weight low. For added flexibility in design and construction, silicon and gallium arsenide solar-cell panels interchangeable.

  4. Large area magnetic micropallet arrays for cell colony sorting.

    Science.gov (United States)

    Cox-Muranami, Wesley A; Nelson, Edward L; Li, G P; Bachman, Mark

    2016-01-01

    A new micropallet array platform for adherent cell colony sorting has been developed. The platform consisted of thousands of square plastic pallets, 270 μm by 270 μm on each side, large enough to hold a single colony of cells. Each pallet included a magnetic core, allowing them to be collected with a magnet after being released using a microscope mounted laser system. The micropallets were patterned from 1002F epoxy resist and were fabricated on translucent, gold coated microscope slides. The gold layer was used as seed for electroplating the ferromagnetic cores within every individual pallet. The gold layer also facilitated the release of each micropallet during laser release. This array allows for individual observation, sorting and collection of isolated cell colonies for biological cell colony research. In addition to consistent release and recovery of individual colonies, we demonstrated stable biocompatibility and minimal loss in imaging quality compared to previously developed micropallet arrays.

  5. Large area magnetic micropallet arrays for cell colony sorting.

    Science.gov (United States)

    Cox-Muranami, Wesley A; Nelson, Edward L; Li, G P; Bachman, Mark

    2016-01-01

    A new micropallet array platform for adherent cell colony sorting has been developed. The platform consisted of thousands of square plastic pallets, 270 μm by 270 μm on each side, large enough to hold a single colony of cells. Each pallet included a magnetic core, allowing them to be collected with a magnet after being released using a microscope mounted laser system. The micropallets were patterned from 1002F epoxy resist and were fabricated on translucent, gold coated microscope slides. The gold layer was used as seed for electroplating the ferromagnetic cores within every individual pallet. The gold layer also facilitated the release of each micropallet during laser release. This array allows for individual observation, sorting and collection of isolated cell colonies for biological cell colony research. In addition to consistent release and recovery of individual colonies, we demonstrated stable biocompatibility and minimal loss in imaging quality compared to previously developed micropallet arrays. PMID:26606460

  6. Collision rates for rare cell capture in periodic obstacle arrays strongly depend on density of cell suspension.

    Science.gov (United States)

    Cimrák, I

    2016-11-01

    Recently, computational modelling has been successfully used for determination of collision rates for rare cell capture in periodic obstacle arrays. The models were based on particle advection simulations where the cells were advected according to velocity field computed from two dimensional Navier-Stokes equations. This approach may be used under the assumption of very dilute cell suspensions where no mutual cell collisions occur. We use the object-in-fluid framework to demonstrate that even with low cell-to-fluid ratio, the optimal geometry of the obstacle array significantly changes. We show computational simulations for ratios of 3.5, 6.9 and 10.4% determining the optimal geometry of the periodic obstacle arrays. It was already previously demonstrated that cells in periodic obstacle arrays follow trajectories in two modes: the colliding mode and the zig-zag mode. The colliding mode maximizes the cell-obstacle collision frequency. Our simulations reveal that for dilute suspensions and for suspensions with cell-to-fluid ratio 3.5%, there is a range of column shifts for which the cells follow colliding trajectories. However we showed, that for 6.9 and 10.4%, the cells never follow colliding trajectories. PMID:27023645

  7. Plasmonic Tipless Pyramid Arrays for Cell Poration.

    Science.gov (United States)

    Courvoisier, Sébastien; Saklayen, Nabiha; Huber, Marinus; Chen, Jun; Diebold, Eric D; Bonacina, Luigi; Wolf, Jean-Pierre; Mazur, Eric

    2015-07-01

    Improving the efficiency, cell survival, and throughput of methods to modify and control the genetic expression of cells is of great benefit to biology and medicine. We investigate, both computationally and experimentally, a nanostructured substrate made of tipless pyramids for plasmonic-induced transfection. By optimizing the geometrical parameters for an excitation wavelength of 800 nm, we demonstrate a 100-fold intensity enhancement of the electric near field at the cell-substrate contact area, while the low absorption typical for gold is maintained. We demonstrate that such a substrate can induce transient poration of cells by a purely optically induced process.

  8. RoboSCell: An automated single cell arraying and analysis instrument

    KAUST Repository

    Sakaki, Kelly

    2009-09-09

    Single cell research has the potential to revolutionize experimental methods in biomedical sciences and contribute to clinical practices. Recent studies suggest analysis of single cells reveals novel features of intracellular processes, cell-to-cell interactions and cell structure. The methods of single cell analysis require mechanical resolution and accuracy that is not possible using conventional techniques. Robotic instruments and novel microdevices can achieve higher throughput and repeatability; however, the development of such instrumentation is a formidable task. A void exists in the state-of-the-art for automated analysis of single cells. With the increase in interest in single cell analyses in stem cell and cancer research the ability to facilitate higher throughput and repeatable procedures is necessary. In this paper, a high-throughput, single cell microarray-based robotic instrument, called the RoboSCell, is described. The proposed instrument employs a partially transparent single cell microarray (SCM) integrated with a robotic biomanipulator for in vitro analyses of live single cells trapped at the array sites. Cells, labeled with immunomagnetic particles, are captured at the array sites by channeling magnetic fields through encapsulated permalloy channels in the SCM. The RoboSCell is capable of systematically scanning the captured cells temporarily immobilized at the array sites and using optical methods to repeatedly measure extracellular and intracellular characteristics over time. The instrument\\'s capabilities are demonstrated by arraying human T lymphocytes and measuring the uptake dynamics of calcein acetoxymethylester-all in a fully automated fashion. © 2009 Springer Science+Business Media, LLC.

  9. Advanced Data Mining of Leukemia Cells Micro-Arrays

    Directory of Open Access Journals (Sweden)

    Ryan M. Pierce

    2009-12-01

    Full Text Available This paper provides continuation and extensions of previous research by Segall and Pierce (2009a that discussed data mining for micro-array databases of Leukemia cells for primarily self-organized maps (SOM. As Segall and Pierce (2009a and Segall and Pierce (2009b the results of applying data mining are shown and discussed for the data categories of microarray databases of HL60, Jurkat, NB4 and U937 Leukemia cells that are also described in this article. First, a background section is provided on the work of others pertaining to the applications of data mining to micro-array databases of Leukemia cells and micro-array databases in general. As noted in predecessor article by Segall and Pierce (2009a, micro-array databases are one of the most popular functional genomics tools in use today. This research in this paper is intended to use advanced data mining technologies for better interpretations and knowledge discovery as generated by the patterns of gene expressions of HL60, Jurkat, NB4 and U937 Leukemia cells. The advanced data mining performed entailed using other data mining tools such as cubic clustering criterion, variable importance rankings, decision trees, and more detailed examinations of data mining statistics and study of other self-organized maps (SOM clustering regions of workspace as generated by SAS Enterprise Miner version 4. Conclusions and future directions of the research are also presented.

  10. Microfluidic cell arrays for metabolic monitoring of stimulated cardiomyocytes.

    Science.gov (United States)

    Cheng, Wei; Klauke, Norbert; Smith, Godfrey; Cooper, Jonathan M

    2010-04-01

    An array of PDMS microchambers was aligned to an array of sensor electrodes and stimulating microelectrodes, which was used for the electrochemical monitoring of the metabolic activity of single isolated adult ventricular myocytes inside the chamber array, stimulated within a transient electric field. The effect of the accumulation of metabolic byproducts in the limited extracellular volume of the picolitre chambers was demonstrated by measuring single muscle cell contraction optically, while concomitant changes in intracellular calcium transients and pH were recorded independently using fluorescent indicator dyes. Both the amplitude of the cell shortening and the magnitude of the intracellular calcium transients decreased over time and both nearly ceased after 20 min of continuous stimulation in the limited extracellullar volume. The intracellular pH decreased gradually during 20 min of continuous stimulation after which a dramatic pH drop was observed, indicating the breakdown of the intracellular buffering capacity. After continuous stimulation, intracellular lactate was released into the microchamber through cell electroporation and was detected electrochemically at a lactate microbiosensor, within the chamber. A mitochondrial uncoupler was used to mimic ischaemia and thus to enhance the cellular content of lactate. Under these circumstances, intracellular lactate concentrations were found to have risen to approximately 15 mM. This array system has the potential of simultaneous electrochemical and optical monitoring of extracellular and intracellular metabolites from single beating heart cells at a controlled metabolic state.

  11. Cleaning of solar cell arrays; Rausgeputzt fuer die Sonne

    Energy Technology Data Exchange (ETDEWEB)

    Petzold, Katrin

    2010-07-01

    The degree of soiling of solar cell arrays depends on the installation site, which may involve, e.g., animal shelter air, bird droppings or desert sand. Heavy rain has a cleaning effect, or else professional cleaning with osmotic water will be necessary. (orig.)

  12. Development and application of a novel genome-wide SNP array reveals domestication history in soybean.

    Science.gov (United States)

    Wang, Jiao; Chu, Shanshan; Zhang, Huairen; Zhu, Ying; Cheng, Hao; Yu, Deyue

    2016-02-09

    Domestication of soybeans occurred under the intense human-directed selections aimed at developing high-yielding lines. Tracing the domestication history and identifying the genes underlying soybean domestication require further exploration. Here, we developed a high-throughput NJAU 355 K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight. Genome-wide scanning for evidence of artificial selection revealed signs of selective sweeps involving genes controlling domestication-related agronomic traits including seed weight. To further identify genomic regions related to seed weight, a genome-wide association study (GWAS) was conducted across multiple environments in wild and cultivated soybeans. As a result, a strong linkage disequilibrium region on chromosome 20 was found to be significantly correlated with seed weight in cultivated soybeans. Collectively, these findings should provide an important basis for genomic-enabled breeding and advance the study of functional genomics in soybean.

  13. Full process for integrating silicon nanowire arrays into solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Perraud, Simon; Poncet, Severine; Noel, Sebastien; Levis, Michel; Faucherand, Pascal; Rouviere, Emmanuelle [CEA, LITEN, Laboratoire des Composants pour la Recuperation d' Energie, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Thony, Philippe; Jaussaud, Claude; Delsol, Regis [CEA, LITEN, Laboratoire des Composants Solaires, INES-RDI, Savoie Technolac, 50 avenue du Lac Leman, 73377 Le-Bourget-du-Lac (France)

    2009-09-15

    A novel process was developed for integrating silicon nanowire arrays into solar cells. n-Type silicon nanowires were grown by chemical-vapour deposition via the gold-catalysed vapour-liquid-solid method, on a p-type silicon substrate. After the growth, the nanowire array was planarized, by embedding the nanowires in a spin-on glass matrix and subsequent chemical-mechanical polishing of the front surface. This planarization step allows to deposit a continuous and uniform conductive film on top of the nanowire array, and thus to form a high-quality front electrical contact. For an illumination intensity of 100 mW/cm{sup 2}, our devices exhibit an energy conversion efficiency of 1.9%. The main performance limiting factor is a high pn junction reverse current, due to contamination by the growth catalyst or to a lack of passivation of surface electronic defects. (author)

  14. High efficiency micro solar cells integrated with lens array

    Science.gov (United States)

    Fidaner, Onur; Suarez, Ferran A.; Wiemer, Michael; Sabnis, Vijit A.; Asano, Tetsuya; Itou, Akihiro; Inoue, Daijiro; Hayashi, Nobuhiko; Arase, Hidekazu; Matsushita, Akio; Nakagawa, Tohru

    2014-03-01

    We demonstrate high efficiency triple junction solar cells with submillimeter dimensions in an all-back-contact architecture. 550 × 550 μm2 cells flash at 41.3% efficiency under the air mass 1.5 direct normal spectrum at 50 W/cm2 at 25 °C. Compared to standard size production cells, the micro cells have reduced performance at 1-sun due to perimeter recombination, but the performance gap closes at higher concentrations. Micro cells integrated with lens arrays were tested on-sun with an efficiency of 34.7%. All-back-contact architecture and submillimeter dimensions are advantageous for module integration and heat dissipation, allowing for high-performance, compact, lightweight, and cost-effective concentrated photovoltaic modules.

  15. Single cell transcriptional analysis reveals novel innate immune cell types

    Directory of Open Access Journals (Sweden)

    Linda E. Kippner

    2014-06-01

    Full Text Available Single-cell analysis has the potential to provide us with a host of new knowledge about biological systems, but it comes with the challenge of correctly interpreting the biological information. While emerging techniques have made it possible to measure inter-cellular variability at the transcriptome level, no consensus yet exists on the most appropriate method of data analysis of such single cell data. Methods for analysis of transcriptional data at the population level are well established but are not well suited to single cell analysis due to their dependence on population averages. In order to address this question, we have systematically tested combinations of methods for primary data analysis on single cell transcription data generated from two types of primary immune cells, neutrophils and T lymphocytes. Cells were obtained from healthy individuals, and single cell transcript expression data was obtained by a combination of single cell sorting and nanoscale quantitative real time PCR (qRT-PCR for markers of cell type, intracellular signaling, and immune functionality. Gene expression analysis was focused on hierarchical clustering to determine the existence of cellular subgroups within the populations. Nine combinations of criteria for data exclusion and normalization were tested and evaluated. Bimodality in gene expression indicated the presence of cellular subgroups which were also revealed by data clustering. We observed evidence for two clearly defined cellular subtypes in the neutrophil populations and at least two in the T lymphocyte populations. When normalizing the data by different methods, we observed varying outcomes with corresponding interpretations of the biological characteristics of the cell populations. Normalization of the data by linear standardization taking into account technical effects such as plate effects, resulted in interpretations that most closely matched biological expectations. Single cell transcription

  16. Solar cell array design handbook - The principles and technology of photovoltaic energy conversion

    Science.gov (United States)

    Rauschenbach, H. S.

    1980-01-01

    Photovoltaic solar cell array design and technology for ground-based and space applications are discussed from the user's point of view. Solar array systems are described, with attention given to array concepts, historical development, applications and performance, and the analysis of array characteristics, circuits, components, performance and reliability is examined. Aspects of solar cell array design considered include the design process, photovoltaic system and detailed array design, and the design of array thermal, radiation shielding and electromagnetic components. Attention is then given to the characteristics and design of the separate components of solar arrays, including the solar cells, optical elements and mechanical elements, and the fabrication, testing, environmental conditions and effects and material properties of arrays and their components are discussed.

  17. TiO2 nanotube arrays and TiO2-nanotube-array based dye-sensitized solar Cell

    Institute of Scientific and Technical Information of China (English)

    LIU YanBiao; ZHOU BaoXue; XIONG BiTao; BAI Jing; LI LongHai

    2007-01-01

    To substitute the non-regular nano-crystalline semiconductor for a novel kind of ordered microstructure is a very important aspect in the domain of dye-sensitized solar cell.One of the researching hotspots is the highly-ordered TiO2 nanotube architecture.As a new type of titania nano-material,titania nanotube arrays have drawn extraordinary attention due to its distinctive morphology,notable photoelectrical and hydro-sensitive performance.At 100% sun the new kind of TiO2 nanotube arrays solar cell exhibits an overall conversion efficiency of 5.44%.This paper introduces the preparation methods of titania nanotube arrays,the existing problems and recent progress in titania nanotube arrays solar cell.

  18. Nylon Filter Arrays Reveal Differential Expression of Expressed Sequence Tags in Wheat Roots Under Aluminum Stress

    Institute of Scientific and Technical Information of China (English)

    Kai XIAO; Gui-Hua BAI; Brett F CARVER

    2005-01-01

    To enrich differentially expressed sequence tags (ESTs) for aluminum (Al) tolerance, cDNA subtraction libraries were generated from Al-stressed roots of two wheat (Triticum aestivum L.) nearisogenic lines (NILs) contrasting in Al-tolerance gene(s) from the Al-tolerant cultivar Atlas 66, using suppression subtractive hybridization (SSH). Expression patterns of the ESTs were investigated with nylon filter arrays containing 614 cDNA clones from the subtraction library. Gene expression profiles from macroarray analysis indicated that 25 ESTs were upregulated in the tolerant NIL in response to Al stress. The result from Northern analysis of selected upregulated ESTs was similar to that from macroarray analysis. These highly expressed ESTs showed high homology with genes involved in signal transduction, oxidative stress alleviation, membrane structure, Mg2+ transportation, and other functions. Under Al stress, the Al-tolerant NIL may possess altered structure or function of the cell wall, plasma membrane, and mitochondrion. The wheat response to Al stress may involve complicated defense-related signaling and metabolic pathways.The present experiment did not detect any induced or activated genes involved in the synthesis of malate and other organic acids in wheat under Al-stress.

  19. Radial microwire array solar cell with pyramidal structure

    Science.gov (United States)

    Priyadarshini, Bindu; Das, Mukul Kumar; Sen, Mrinal; Kumar, Subindu

    2016-10-01

    In this work, a theoretical model for radial p-n junction microwire array solar cell with pyramidal structures in the space between microwires has been developed. Incorporation of pyramidal structures results in reflection of light, which would otherwise be unused, and illuminates side walls of the microwires. This additional illumination enhances absorption and, hence, efficiency of the whole structure. Efficiency enhancement is analyzed by varying different device parameters e.g., radius and length of each microwire and packing fraction of the structure. Results show that the maximum fractional efficiency enhancement can be obtained as 30% by suitable choice of these parameters.

  20. Mathematical modeling of interdigitated electrode arrays in finite electrochemical cells

    CERN Document Server

    Guajardo, Cristian; Surareungchai, Werasak

    2016-01-01

    Accurate theoretical results for interdigitated array of electrodes (IDAE) in semi-infinite cells can be found in the literature. However, these results are not always applicable when using finite cells. In this study, theoretical expressions for IDAE in a finite geometry cell are presented. At known current density, transient and steady state concentration profiles were obtained as well as the response time to a current step. Concerning the diffusion limited current, a lower bound was derived from the concentration profile and an upper bound was obtained from the limiting current of the semi-infinite case. The lower bound, which is valid when Kirchhoff's current law applies to the unit cell, can be useful to ensure a minimum current level during the design of the electrochemical cell. Finally, a criterion was developed defining when the behaviors of finite and semi-infinite cells are comparable. This allows to obtain higher current levels in finite cells, approaching that of the semi-infinite case. Examples ...

  1. Inverted Silicon Nanopencil Array Solar Cells with Enhanced Contact Structures

    Science.gov (United States)

    Liang, Xiaoguang; Shu, Lei; Lin, Hao; Fang, Ming; Zhang, Heng; Dong, Guofa; Yip, SenPo; Xiu, Fei; Ho, Johnny C.

    2016-01-01

    Although three-dimensional nanostructured solar cells have attracted extensive research attention due to their superior broadband and omnidirectional light-harvesting properties, majority of them are still suffered from complicated fabrication processes as well as disappointed photovoltaic performances. Here, we employed our newly-developed, low-cost and simple wet anisotropic etching to fabricate hierarchical silicon nanostructured arrays with different solar cell contact design, followed by systematic investigations of their photovoltaic characteristics. Specifically, nano-arrays with the tapered tips (e.g. inverted nanopencils) are found to enable the more conformal top electrode deposition directly onto the nanostructures for better series and shunt conductance, but its insufficient film coverage at the basal plane would still restrict the charge carrier collection. In contrast, the low-platform contact design facilitates a substantial photovoltaic device performance enhancement of ~24%, as compared to the one of conventional top electrode design, due to the shortened current path and improved lateral conductance for the minimized carrier recombination and series resistance. This enhanced contact structure can not only maintain excellent photon-trapping behaviors of nanostructures, but also help to eliminate adverse impacts of these tapered nano-morphological features on the contact resistance, providing further insight into design consideration in optimizing the contact geometry for high-performance nanostructured photovoltaic devices. PMID:27671709

  2. The Influence of Immunization Route, Tissue Microenvironment, and Cytokine Cell Milieu on HIV-Specific CD8+ T Cells Measured Using Fluidigm Dynamic Arrays

    OpenAIRE

    Trivedi, Shubhanshi; Ranasinghe, Charani

    2015-01-01

    Thirty different genes including cytokines, chemokines, granzymes, perforin and specifically integrins were evaluated in Peyer's patch-KdGag197–205-specific CD8+ T cells (pools of 100 cells) using Fluidigm 48.48 Dynamic arrays following three different prime-boost immunization strategies. Data revealed that the route of prime or the booster immunization differentially influenced the integrin expression profile on gut KdGag197–205-specific CD8+ T cells. Specifically, elevated numbers of integr...

  3. Topographical control of cell-cell interaction in C6 glioma by nanodot arrays

    Science.gov (United States)

    Lee, Chia-Hui; Cheng, Ya-Wen; Huang, G. Steven

    2014-05-01

    Nanotopography modulates the physiological behavior of cells and cell-cell interactions, but the manner of communication remains unclear. Cell networking (syncytium) of astroglia provides the optimal microenvironment for communication of the nervous system. C6 glioma cells were seeded on nanodot arrays with dot diameters ranging from 10 to 200 nm. Cell viability, morphology, cytoskeleton, and adhesion showed optimal cell growth on 50-nm nanodots if sufficient incubation was allowed. In particular, the astrocytic syncytium level maximized at 50 nm. The gap junction protein Cx43 showed size-dependent and time-dependent transport from the nucleus to the cell membrane. The transport efficiency was greatly enhanced by incubation on 50-nm nanodots. In summary, nanotopography is capable of modulating cell behavior and influencing the cell-cell interactions of astrocytes. By fine-tuning the nanoenvironment, it may be possible to regulate cell-cell communications and optimize the biocompatibility of neural implants.

  4. Biophotofuel cell anode containing self-organized titanium dioxide nanotube array

    Energy Technology Data Exchange (ETDEWEB)

    Gan, Yong X., E-mail: yong.gan@utoledo.edu [Mechanical, Industrial and Manufacturing Engineering, College of Engineering, University of Toledo, 2801 W Bancroft Street, Toledo, OH 43606 (United States); Gan, Bo J. [Ottawa Hills High School, 2532 Evergreen Road, Toledo, OH 43606 (United States); Su Lusheng [Mechanical, Industrial and Manufacturing Engineering, College of Engineering, University of Toledo, 2801 W Bancroft Street, Toledo, OH 43606 (United States)

    2011-09-15

    Graphical abstract: Highlights: {center_dot} A photoactive anode containing highly ordered TiO{sub 2} nanotube array was made and the formation mechanism of self-organized TiO{sub 2} nanotube array on Ti was revealed. {center_dot} Effect of electrolyte concentration and voltage on the size distribution of the nanotubes was investigated. {center_dot} Self-organized TiO{sub 2} nanotube array anode possesses good photo-catalytic behavior of biomass decomposition under ultraviolet (UV) radiation. {center_dot} The fuel cell generates electricity and hydrogen via photoelectrochemical decomposition of ethanol, apple vinegar, sugar and tissue paper. - Abstract: We made a biophotofuel cell consisting of a titanium dioxide nanotube array photosensitive anode for biomass decomposition, and a low-hydrogen overpotential metal, Pt, as the cathode for hydrogen production. The titanium dioxide nanotubes (TiO{sub 2} NTs) were prepared via electrochemical oxidation of pure Ti in NaF solutions. Scanning electron microscopy was used to analyze the morphology of the nanotubes. The average diameter, wall thickness and length of the as-prepared TiO{sub 2} NTs were 88 {+-} 16 nm, 10 {+-} 2 nm and 491 {+-} 56 nm, respectively. Such dimensions are affected by the NaF concentration and the applied voltage during processing. Higher NaF concentrations result in the formation of longer and thicker nanotubes. The higher the voltage is, the thicker the nanotubes. The photosensitive anode made from the highly ordered TiO{sub 2} NTs has good photo-catalytic property, as can be seen from the test results of ethanol, apple vinegar, sugar and tissue paper decomposition under ultraviolet (UV) radiation. It is concluded that the biophotofuel cell with the TiO{sub 2} nanotube photoanode and a Pt cathode can generate electricity, hydrogen and clean water depending on the pH value and the oxygen presence in the solutions.

  5. Cell manipulation tool with combined microwell array and optical tweezers for cell isolation and deposition

    International Nuclear Information System (INIS)

    Isolation from rare cells and deposition of sorted cells with high accuracy for further study are critical to a wide range of biomedical applications. In the current paper, we report an automated cell manipulation tool with combined optical tweezers and a uniquely designed microwell array, which functions for recognition, isolation, assembly, transportation and deposition of the interesting cells. The microwell array allows the passive hydrodynamic docking of cells, while offering the opportunity to inspect the interesting cell phenotypes with high spatio-temporal resolution based on the flexible image processing technique. In addition, dynamic and parallel cell manipulation in three dimensions can realize the target cell levitation from microwell and pattern assembly with multiple optical traps. Integrated with the programmed motorized stage, the optically levitated and assembled cells can be transported and deposited to the predefined microenvironment, so the tool can facilitate the integration of other on-chip functionalities for further study without removing these isolated cells from the chip. Experiments on human embryonic stem cells and yeast cells are performed to demonstrate the effectiveness of the proposed cell manipulation tool. Besides the application to cell isolation and deposition, three other biological applications with this tool are also presented. (paper)

  6. Fabrication of gold nanodot arrays on a transparent substrate as a nanobioplatform for label-free visualization of living cells

    International Nuclear Information System (INIS)

    Two-dimensional gold (Au) nanodot arrays on a transparent substrate were fabricated for imaging of living cells. A nanoporous alumina mask with large-area coverage capability was prepared by a two-step chemical wet etching process after a second anodization. Highly ordered Au nanodot arrays were formed on indium-tin-oxide (ITO) glass using very thin nanoporous alumina of approximately 200 nm thickness as an evaporation mask. The large-area Au nanodot arrays on ITO glass were modified with RGD peptide (arginine; glycine; aspartic acid) containing a cysteine (Cys) residue and then used to immobilize human cancer HeLa cells, the morphology of which was observed by confocal microscopy. The confocal micrographs of living HeLa cells on Au nanodot arrays revealed enhanced contrast and resolution, which enabled discernment of cytoplasmic organelles more clearly. These results suggest that two-dimensional Au nanodot arrays modified with RGD peptide on ITO glass have potential as a biocompatible nanobioplatform for the label-free visualization and adhesion of living cells.

  7. Cancer Cell Analyses at the Single Cell-Level Using Electroactive Microwell Array Device.

    Directory of Open Access Journals (Sweden)

    Marina Kobayashi

    Full Text Available Circulating tumor cells (CTCs, shed from primary tumors and disseminated into peripheral blood, are playing a major role in metastasis. Even after isolation of CTCs from blood, the target cells are mixed with a population of other cell types. Here, we propose a new method for analyses of cell mixture at the single-cell level using a microfluidic device that contains arrayed electroactive microwells. Dielectrophoretic (DEP force, induced by the electrodes patterned on the bottom surface of the microwells, allows efficient trapping and stable positioning of single cells for high-throughput biochemical analyses. We demonstrated that various on-chip analyses including immunostaining, viability/apoptosis assay and fluorescent in situ hybridization (FISH at the single-cell level could be conducted just by applying specific reagents for each assay. Our simple method should greatly help discrimination and analysis of rare cancer cells among a population of blood cells.

  8. Is cell migration or proliferation dominant in the formation of linear arrays of oligodendrocytes?

    Science.gov (United States)

    Walsh, Darragh M; Röth, Philipp T; Holmes, William R; Landman, Kerry A; Merson, Tobias D; Hughes, Barry D

    2016-10-01

    Oligodendrocytes are the myelin-producing cells of the central nervous system that are responsible for electrically insulating axons to speed the propagation of electrical impulses. A striking feature of oligodendrocyte development within white matter is that the cell bodies of many oligodendrocyte progenitor cells become organised into discrete linear arrays of three or more cells before they differentiate into myelin-producing oligodendrocytes. These linear arrays align parallel to the direction of the axons within white matter tracts and are believed to play an important role in the co-ordination of myelination. Guided by experimental data on the abundance and composition of linear arrays in the corpus callosum of the postnatal mouse brain, we construct discrete and continuous models of linear array generation to specifically investigate the relative influence of cell migration, proliferation, differentiation and death of oligodendroglia upon the genesis of linear arrays during early postnatal development. We demonstrate that only models that incorporate significant cell migration can replicate all of the experimental observations on number of arrays, number of cells in arrays and total cell count of oligodendroglia within a given area of the corpus callosum. These models are also necessary to accurately reflect experimental data on the abundance of linear arrays composed of oligodendrocytes that derive from progenitors of different clonal origins. PMID:27343034

  9. Technical evaluation of Solar Cells, Inc., CdTe module and array at NREL

    Energy Technology Data Exchange (ETDEWEB)

    Kroposki, B.; Strand, T.; Hansen, R. [National Renewable Energy Lab., Golden, CO (United States); Powell, R.; Sasala, R. [Solar Cells, Inc., Toledo, OH (United States)

    1996-05-01

    The Engineering and Technology Validation Team at the National Renewable Energy Laboratory (NREL) conducts in-situ technical evaluations of polycrystalline thin-film photovoltaic (PV) modules and arrays. This paper focuses on the technical evaluation of Solar Cells, Inc., (SCI) cadmium telluride (CdTe) module and array performance by attempting to correlate individual module and array performance. This is done by examining the performance and stability of the modules and array over a period of more than one year. Temperature coefficients for module and array parameters (P{sub max}, V{sub oc}, V{sub max}, I{sub sc}, I{sub max}) are also calculated.

  10. A Nanodot Array Modulates Cell Adhesion and Induces an Apoptosis-Like Abnormality in NIH-3T3 Cells

    Directory of Open Access Journals (Sweden)

    Hung Yao-Ching

    2009-01-01

    Full Text Available Abstract Micro-structures that mimic the extracellular substratum promote cell growth and differentiation, while the cellular reaction to a nanostructure is poorly defined. To evaluate the cellular response to a nanoscaled surface, NIH 3T3 cells were grown on nanodot arrays with dot diameters ranging from 10 to 200 nm. The nanodot arrays were fabricated by AAO processing on TaN-coated wafers. A thin layer of platinum, 5 nm in thickness, was sputtered onto the structure to improve biocompatibility. The cells grew normally on the 10-nm array and on flat surfaces. However, 50-nm, 100-nm, and 200-nm nanodot arrays induced apoptosis-like events. Abnormality was triggered after as few as 24 h of incubation on a 200-nm dot array. For cells grown on the 50-nm array, the abnormality started after 72 h of incubation. The number of filopodia extended from the cell bodies was lower for the abnormal cells. Immunostaining using antibodies against vinculin and actin filament was performed. Both the number of focal adhesions and the amount of cytoskeleton were decreased in cells grown on the 100-nm and 200-nm arrays. Pre-coatings of fibronectin (FN or type I collagen promoted cellular anchorage and prevented the nanotopography-induced programed cell death. In summary, nanotopography, in the form of nanodot arrays, induced an apoptosis-like abnormality for cultured NIH 3T3 cells. The occurrence of the abnormality was mediated by the formation of focal adhesions.

  11. CAMSAP3 orients the apical-to-basal polarity of microtubule arrays in epithelial cells.

    Science.gov (United States)

    Toya, Mika; Kobayashi, Saeko; Kawasaki, Miwa; Shioi, Go; Kaneko, Mari; Ishiuchi, Takashi; Misaki, Kazuyo; Meng, Wenxiang; Takeichi, Masatoshi

    2016-01-12

    Polarized epithelial cells exhibit a characteristic array of microtubules that are oriented along the apicobasal axis of the cells. The minus-ends of these microtubules face apically, and the plus-ends face toward the basal side. The mechanisms underlying this epithelial-specific microtubule assembly remain unresolved, however. Here, using mouse intestinal cells and human Caco-2 cells, we show that the microtubule minus-end binding protein CAMSAP3 (calmodulin-regulated-spectrin-associated protein 3) plays a pivotal role in orienting the apical-to-basal polarity of microtubules in epithelial cells. In these cells, CAMSAP3 accumulated at the apical cortices, and tethered the longitudinal microtubules to these sites. Camsap3 mutation or depletion resulted in a random orientation of these microtubules; concomitantly, the stereotypic positioning of the nucleus and Golgi apparatus was perturbed. In contrast, the integrity of the plasma membrane was hardly affected, although its structural stability was decreased. Further analysis revealed that the CC1 domain of CAMSAP3 is crucial for its apical localization, and that forced mislocalization of CAMSAP3 disturbs the epithelial architecture. These findings demonstrate that apically localized CAMSAP3 determines the proper orientation of microtubules, and in turn that of organelles, in mature mammalian epithelial cells. PMID:26715742

  12. More than a feeling: incidental learning of array geometry by blindfolded adult humans revealed through touch.

    Science.gov (United States)

    Sturz, Bradley R; Green, Marshall L; Gaskin, Katherine A; Evans, Alicia C; Graves, April A; Roberts, Jonathan E

    2013-02-15

    View-based matching theories of orientation suggest that mobile organisms encode a visual memory consisting of a visual panorama from a target location and maneuver to reduce discrepancy between current visual perception and this stored visual memory to return to a location. Recent success of such theories to explain the orientation behavior of insects and birds raises questions regarding the extent to which such an explanation generalizes to other species. In the present study, we attempted to determine the extent to which such view-based matching theories may explain the orientation behavior of a mammalian species (in this case adult humans). We modified a traditional enclosure orientation task so that it involved only the use of the haptic sense. The use of a haptic orientation task to investigate the extent to which view-based matching theories may explain the orientation behavior of adult humans appeared ideal because it provided an opportunity for us to explicitly prohibit the use of vision. Specifically, we trained disoriented and blindfolded human participants to search by touch for a target object hidden in one of four locations marked by distinctive textural cues located on top of four discrete landmarks arranged in a rectangular array. Following training, we removed the distinctive textural cues and probed the extent to which participants learned the geometry of the landmark array. In the absence of vision and the trained textural cues, participants showed evidence that they learned the geometry of the landmark array. Such evidence cannot be explained by an appeal to view-based matching strategies and is consistent with explanations of spatial orientation related to the incidental learning of environmental geometry. PMID:23125340

  13. Differentiation of cancer cell type and phenotype using quantum dot-gold nanoparticle sensor arrays

    OpenAIRE

    Liu, Qian; Yeh, Yi-Cheun; Rana, Subinoy; Jiang, Ying; Guo, Lin; Rotello, Vincent M.

    2012-01-01

    We demonstrate rapid and efficient sensing of mammalian cell types and states using nanoparticle-based sensor arrays. These arrays are comprised of cationic quantum dots (QDs) and gold nanoparticles (AuNPs) that interact with cell surfaces to generate distinguishable fluorescence responses based on cell surface signatures. The use of QDs as the recognition elements as well as the signal transducers presents the potential for direct visualization of selective cell surface interactions. Notably...

  14. Genome-wide array comparative genomic hybridization analysis reveals distinct amplifications in osteosarcoma

    International Nuclear Information System (INIS)

    Osteosarcoma is a highly malignant bone neoplasm of children and young adults. It is characterized by extremely complex karyotypes and high frequency of chromosomal amplifications. Currently, only the histological response (degree of necrosis) to therapy represent gold standard for predicting the outcome in a patient with non-metastatic osteosarcoma at the time of definitive surgery. Patients with lower degree of necrosis have a higher risk of relapse and poor outcome even after chemotherapy and complete resection of the primary tumor. Therefore, a better understanding of the underlying molecular genetic events leading to tumor initiation and progression could result in the identification of potential diagnostic and therapeutic targets. We used a genome-wide screening method – array based comparative genomic hybridization (array-CGH) to identify DNA copy number changes in 48 patients with osteosarcoma. We applied fluorescence in situ hybridization (FISH) to validate some of amplified clones in this study. Clones showing gains (79%) were more frequent than losses (66%). High-level amplifications and homozygous deletions constitute 28.6% and 3.8% of tumor genome respectively. High-level amplifications were present in 238 clones, of which about 37% of them showed recurrent amplification. Most frequently amplified clones were mapped to 1p36.32 (PRDM16), 6p21.1 (CDC5L, HSPCB, NFKBIE), 8q24, 12q14.3 (IFNG), 16p13 (MGRN1), and 17p11.2 (PMP22 MYCD, SOX1,ELAC27). We validated some of the amplified clones by FISH from 6p12-p21, 8q23-q24, and 17p11.2 amplicons. Homozygous deletions were noted for 32 clones and only 7 clones showed in more than one case. These 7 clones were mapped to 1q25.1 (4 cases), 3p14.1 (4 cases), 13q12.2 (2 cases), 4p15.1 (2 cases), 6q12 (2 cases), 6q12 (2 cases) and 6q16.3 (2 cases). This study clearly demonstrates the utility of array CGH in defining high-resolution DNA copy number changes and refining amplifications. The resolution of array CGH

  15. Independent component analysis reveals new and biologically significant structures in micro array data

    Directory of Open Access Journals (Sweden)

    Veerla Srinivas

    2006-06-01

    Full Text Available Abstract Background An alternative to standard approaches to uncover biologically meaningful structures in micro array data is to treat the data as a blind source separation (BSS problem. BSS attempts to separate a mixture of signals into their different sources and refers to the problem of recovering signals from several observed linear mixtures. In the context of micro array data, "sources" may correspond to specific cellular responses or to co-regulated genes. Results We applied independent component analysis (ICA to three different microarray data sets; two tumor data sets and one time series experiment. To obtain reliable components we used iterated ICA to estimate component centrotypes. We found that many of the low ranking components indeed may show a strong biological coherence and hence be of biological significance. Generally ICA achieved a higher resolution when compared with results based on correlated expression and a larger number of gene clusters with significantly enriched for gene ontology (GO categories. In addition, components characteristic for molecular subtypes and for tumors with specific chromosomal translocations were identified. ICA also identified more than one gene clusters significant for the same GO categories and hence disclosed a higher level of biological heterogeneity, even within coherent groups of genes. Conclusion Although the ICA approach primarily detects hidden variables, these surfaced as highly correlated genes in time series data and in one instance in the tumor data. This further strengthens the biological relevance of latent variables detected by ICA.

  16. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.

    Science.gov (United States)

    Tasic, Bosiljka; Menon, Vilas; Nguyen, Thuc Nghi; Kim, Tae Kyung; Jarsky, Tim; Yao, Zizhen; Levi, Boaz; Gray, Lucas T; Sorensen, Staci A; Dolbeare, Tim; Bertagnolli, Darren; Goldy, Jeff; Shapovalova, Nadiya; Parry, Sheana; Lee, Changkyu; Smith, Kimberly; Bernard, Amy; Madisen, Linda; Sunkin, Susan M; Hawrylycz, Michael; Koch, Christof; Zeng, Hongkui

    2016-02-01

    Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type-specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed specific and differential electrophysiological and axon projection properties, thereby confirming that the single-cell transcriptomic signatures can be associated with specific cellular properties.

  17. Localized seismic deformation in the upper mantle revealed by dense seismic arrays

    Science.gov (United States)

    Inbal, Asaf; Ampuero, Jean Paul; Clayton, Robert W.

    2016-10-01

    Seismicity along continental transform faults is usually confined to the upper half of the crust, but the Newport-Inglewood fault (NIF), a major fault traversing the Los Angeles basin, is seismically active down to the upper mantle. We use seismic array analysis to illuminate the seismogenic root of the NIF beneath Long Beach, California, and identify seismicity in an actively deforming localized zone penetrating the lithospheric mantle. Deep earthquakes, which are spatially correlated with geochemical evidence of a fluid pathway from the mantle, as well as with a sharp vertical offset in the lithosphere-asthenosphere boundary, exhibit narrow size distribution and weak temporal clustering. We attribute these characteristics to a transition from strong to weak interaction regimes in a system of seismic asperities embedded in a ductile fault zone matrix.

  18. Allele-specific amplification in cancer revealed by SNP array analysis.

    Directory of Open Access Journals (Sweden)

    Thomas LaFramboise

    2005-11-01

    Full Text Available Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. Similarly, loss-of-heterozygosity events have been finely mapped using high-throughput genotyping technologies. We have developed a probe-level allele-specific quantitation procedure that extracts both copy number and allelotype information from single nucleotide polymorphism (SNP array data to arrive at allele-specific copy number across the genome. Our approach applies an expectation-maximization algorithm to a model derived from a novel classification of SNP array probes. This method is the first to our knowledge that is able to (a determine the generalized genotype of aberrant samples at each SNP site (e.g., CCCCT at an amplified site, and (b infer the copy number of each parental chromosome across the genome. With this method, we are able to determine not just where amplifications and deletions occur, but also the haplotype of the region being amplified or deleted. The merit of our model and general approach is demonstrated by very precise genotyping of normal samples, and our allele-specific copy number inferences are validated using PCR experiments. Applying our method to a collection of lung cancer samples, we are able to conclude that amplification is essentially monoallelic, as would be expected under the mechanisms currently believed responsible for gene amplification. This suggests that a specific parental chromosome may be targeted for amplification, whether because of germ line or somatic variation. An R software package containing the methods described in this paper is freely available at http://genome.dfci.harvard.edu/~tlaframb/PLASQ.

  19. The impact of solar cell technology on planar solar array performance

    Science.gov (United States)

    Mills, Michael W.; Kurland, Richard M.

    1989-01-01

    The results of a study into the potential impact of advanced solar cell technologies on the characteristics (weight, cost, area) of typical planar solar arrays designed for low, medium and geosynchronous altitude earth orbits are discussed. The study considered planar solar array substrate designs of lightweight, rigid-panel graphite epoxy and ultra-lightweight Kapton. The study proposed to answer the following questions: Do improved cell characteristics translate into array-level weight, size and cost improvements; What is the relative importance of cell efficiency, weight and cost with respect to array-level performance; How does mission orbital environment affect array-level performance. Comparisons were made at the array level including all mechanisms, hinges, booms, and harnesses. Array designs were sized to provide 5kW of array power (not spacecraft bus power, which is system dependent but can be scaled from given values). The study used important grass roots issues such as use of the GaAs radiation damage coefficients as determined by Anspaugh. Detailed costing was prepared, including cell and cover costs, and manufacturing attrition rates for the various cell types.

  20. NeuroArray: A Universal Interface for Patterning and Interrogating Neural Circuitry with Single Cell Resolution

    OpenAIRE

    Li, Wei; Xu, Zhen; Huang, Junzhe; Lin, Xudong; Luo, Rongcong; Chen, Chia-Hung; Shi, Peng

    2014-01-01

    Recreation of neural network in vitro with designed topology is a valuable tool to decipher how neurons behave when interacting in hierarchical networks. In this study, we developed a simple and effective platform to pattern primary neurons in array formats for interrogation of neural circuitry with single cell resolution. Unlike many surface-chemistry-based patterning methods, our NeuroArray technique is specially designed to accommodate neuron's polarized morphologies to make regular arrays...

  1. Equivalent circuit-based analysis of CMUT cell dynamics in arrays.

    Science.gov (United States)

    Oguz, H K; Atalar, Abdullah; Köymen, Hayrettin

    2013-05-01

    Capacitive micromachined ultrasonic transducers (CMUTs) are usually composed of large arrays of closely packed cells. In this work, we use an equivalent circuit model to analyze CMUT arrays with multiple cells. We study the effects of mutual acoustic interactions through the immersion medium caused by the pressure field generated by each cell acting upon the others. To do this, all the cells in the array are coupled through a radiation impedance matrix at their acoustic terminals. An accurate approximation for the mutual radiation impedance is defined between two circular cells, which can be used in large arrays to reduce computational complexity. Hence, a performance analysis of CMUT arrays can be accurately done with a circuit simulator. By using the proposed model, one can very rapidly obtain the linear frequency and nonlinear transient responses of arrays with an arbitrary number of CMUT cells. We performed several finite element method (FEM) simulations for arrays with small numbers of cells and showed that the results are very similar to those obtained by the equivalent circuit model.

  2. Nanoprobe arrays for multiple single cell insertion using heterogeneous nanosphere lithography (HNSL)

    Science.gov (United States)

    Seo, Yoon Ho; Kim, Lo Hyun; Kim, Young-Beom; Ryu, Wonhyoung

    2013-08-01

    Nanoprobe arrays for multiple single cell insertion were developed using heterogeneous nanosphere lithography. Using two heterogeneous nanoparticles as sacrificial and masking particles, high aspect ratio Si nanoprobes were fabricated in an array with spacing between the nanoprobes ranging from a few to tens of micrometers. For registered single cell analysis, multiple and precise insertion of nanoprobes into multiple single cells in a parallel fashion was demonstrated using micropipette suction and micromanipulators.

  3. Identification of genes differentially expressed in monocyte-deriveddendritic cells with 1α,25-dihydroxyvitamin D3 using cDNA arrays

    Institute of Scientific and Technical Information of China (English)

    沈倩云; 郑树森

    2004-01-01

    In order to study the molecular mechanism of the inhibitory effect of 1,25-dihydroxyvitamin D3 on dendritic cells, experiments were performed using Atlas cDNA expression arrays from Clonetech to identify the differentially expressed genes of dendritic cells by 1,25-dihydroxyvitamin D3. Analysis of cDNA arrays revealed changes in the expression of 9 genes, including those involved in DNA binding and transcription, extracellular cell signaling and communication, intracellular transducers, as well as cell adhesions. The results indicated that a multiple molecular network is involved in the inhibitory role of 1,25-dihydroxyvitamin D3 on dendritic cells. The Atlas Array technology may facilitate the elucidation of complex pharmacological nrocess of 1.25-dihvdroxvvitamin D3 on dondritie cells.

  4. Microlens array induced light absorption enhancement in polymer solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yuqing [Ames Laboratory; Elshobaki, Moneim [Iowa State University; Ye, Zhuo [Ames Laboratory; Park, Joong-Mok [Ames Laboratory; Noack, Max A. [Iowa State University; Ho, Kai-Ming [Ames Laboratory; Chaudhary, Sumit [Ames Laboratory

    2013-01-24

    Over the last decade, polymer solar cells (PSCs) have attracted a lot of attention and highest power conversion efficiencies (PCE) are now close to 10%. Here we employ an optical structure – the microlens array (MLA) – to increase light absorption inside the active layer, and PCE of PSCs increased even for optimized devices. Normal incident light rays are refracted at the MLA and travel longer optical paths inside the active layers. Two PSC systems – poly(3-hexylthiophene-2,5-diyl):(6,6)-phenyl C61 butyric acid methyl ester (P3HT:PCBM) and poly[[9-(1-octylnonyl)-9H-carbazole-2,7-diyl]-2,5-thiophenediyl-2,1,3-benzothiadiazole-4,7-diyl-2,5-thiophenediyl]:(6,6)-phenyl C71 butyric acid methyl ester (PCDTBT:PC70BM) – were investigated. In the P3HT:PCBM system, MLA increased the absorption, absolute external quantum efficiency, and the PCE of an optimized device by [similar]4.3%. In the PCDTBT:PC70BM system, MLA increased the absorption, absolute external quantum efficiency, and PCE by more than 10%. In addition, simulations incorporating optical parameters of all structural layers were performed and they support the enhancement of absorption in the active layer with the assistance of MLA. Our results show that utilizing MLA is an effective strategy to further increase light absorption in PSCs, in which optical losses account for [similar]40% of total losses. MLA also does not pose materials processing challenges to the active layers since it is on the other side of the transparent substrate.

  5. Differentiation of cancer cell type and phenotype using quantum dot-gold nanoparticle sensor arrays.

    Science.gov (United States)

    Liu, Qian; Yeh, Yi-Cheun; Rana, Subinoy; Jiang, Ying; Guo, Lin; Rotello, Vincent M

    2013-07-01

    We demonstrate rapid and efficient sensing of mammalian cell types and states using nanoparticle-based sensor arrays. These arrays are comprised of cationic quantum dots (QDs) and gold nanoparticles (AuNPs) that interact with cell surfaces to generate distinguishable fluorescence responses based on cell surface signatures. The use of QDs as the recognition elements as well as the signal transducers presents the potential for direct visualization of selective cell surface interactions. Notably, this sensor is unbiased, precluding the requirement of pre-knowledge of cell state biomarkers and thus providing a general approach for phenotypic profiling of cell states, with additional potential for imaging applications. PMID:23022266

  6. Patterning pallet arrays for cell selection based on high-resolution measurements of fluorescent biosensors.

    Science.gov (United States)

    Shadpour, Hamed; Zawistowski, Jon S; Herman, Annadele; Hahn, Klaus; Allbritton, Nancy L

    2011-06-24

    Pallet arrays enable cells to be separated while they remain adherent to a surface and provide a much greater range of cell selection criteria relative to that of current technologies. However there remains a need to further broaden cell selection criteria to include dynamic intracellular signaling events. To demonstrate the feasibility of measuring cellular protein behavior on the arrays using high resolution microscopy, the surfaces of individual pallets were modified to minimize the impact of scattered light at the pallet edges. The surfaces of the three-dimensional pallets on an array were patterned with a coating such as fibronectin using a customized stamping tool. Micropatterns of varying shape and size were printed in designated regions on the pallets in single or multiple steps to demonstrate the reliability and precision of patterning molecules on the pallet surface. Use of a fibronectin matrix stamped at the center of each pallet permitted the localization of H1299 and mouse embryonic fibroblast (MEF) cells to the pallet centers and away from the edges. Compared to pallet arrays with fibronectin coating the entire top surface, arrays with a central fibronectin pattern increased the percentage of cells localized to the pallet center by 3-4-fold. Localization of cells to the pallet center also enabled the physical separation of cells from optical artifacts created by the rough pallet side walls. To demonstrate the measurement of dynamic intracellular signaling on the arrays, fluorescence measurements of high spatial resolution were performed using a RhoA GTPase biosensor. This biosensor utilized fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) to measure localized RhoA activity in cellular ruffles at the cell periphery. These results demonstrated the ability to perform spatially resolved measurements of fluorescence-based sensors on the pallet arrays. Thus, the patterned pallet arrays

  7. Patterning pallet arrays for cell selection based on high-resolution measurements of fluorescent biosensors.

    Science.gov (United States)

    Shadpour, Hamed; Zawistowski, Jon S; Herman, Annadele; Hahn, Klaus; Allbritton, Nancy L

    2011-06-24

    Pallet arrays enable cells to be separated while they remain adherent to a surface and provide a much greater range of cell selection criteria relative to that of current technologies. However there remains a need to further broaden cell selection criteria to include dynamic intracellular signaling events. To demonstrate the feasibility of measuring cellular protein behavior on the arrays using high resolution microscopy, the surfaces of individual pallets were modified to minimize the impact of scattered light at the pallet edges. The surfaces of the three-dimensional pallets on an array were patterned with a coating such as fibronectin using a customized stamping tool. Micropatterns of varying shape and size were printed in designated regions on the pallets in single or multiple steps to demonstrate the reliability and precision of patterning molecules on the pallet surface. Use of a fibronectin matrix stamped at the center of each pallet permitted the localization of H1299 and mouse embryonic fibroblast (MEF) cells to the pallet centers and away from the edges. Compared to pallet arrays with fibronectin coating the entire top surface, arrays with a central fibronectin pattern increased the percentage of cells localized to the pallet center by 3-4-fold. Localization of cells to the pallet center also enabled the physical separation of cells from optical artifacts created by the rough pallet side walls. To demonstrate the measurement of dynamic intracellular signaling on the arrays, fluorescence measurements of high spatial resolution were performed using a RhoA GTPase biosensor. This biosensor utilized fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) to measure localized RhoA activity in cellular ruffles at the cell periphery. These results demonstrated the ability to perform spatially resolved measurements of fluorescence-based sensors on the pallet arrays. Thus, the patterned pallet arrays

  8. SNP array analysis reveals novel genomic abnormalities including copy neutral loss of heterozygosity in anaplastic oligodendrogliomas.

    Directory of Open Access Journals (Sweden)

    Ahmed Idbaih

    Full Text Available Anaplastic oligodendrogliomas (AOD are rare glial tumors in adults with relative homogeneous clinical, radiological and histological features at the time of diagnosis but dramatically various clinical courses. Studies have identified several molecular abnormalities with clinical or biological relevance to AOD (e.g. t(1;19(q10;p10, IDH1, IDH2, CIC and FUBP1 mutations.To better characterize the clinical and biological behavior of this tumor type, the creation of a national multicentric network, named "Prise en charge des OLigodendrogliomes Anaplasiques (POLA," has been supported by the Institut National du Cancer (InCA. Newly diagnosed and centrally validated AOD patients and their related biological material (tumor and blood samples were prospectively included in the POLA clinical database and tissue bank, respectively.At the molecular level, we have conducted a high-resolution single nucleotide polymorphism array analysis, which included 83 patients. Despite a careful central pathological review, AOD have been found to exhibit heterogeneous genomic features. A total of 82% of the tumors exhibited a 1p/19q-co-deletion, while 18% harbor a distinct chromosome pattern. Novel focal abnormalities, including homozygously deleted, amplified and disrupted regions, have been identified. Recurring copy neutral losses of heterozygosity (CNLOH inducing the modulation of gene expression have also been discovered. CNLOH in the CDKN2A locus was associated with protein silencing in 1/3 of the cases. In addition, FUBP1 homozygous deletion was detected in one case suggesting a putative tumor suppressor role of FUBP1 in AOD.Our study showed that the genomic and pathological analyses of AOD are synergistic in detecting relevant clinical and biological subgroups of AOD.

  9. Anticarbohydrate Antibody Repertoires in Patients Transplanted with Fetal Pig Islets Revealed by Glycan Arrays

    DEFF Research Database (Denmark)

    Blixt, Klas Ola; Kumagai-Braesch, A.; Tibell, A.;

    2009-01-01

    Ten patients with type I diabetes were transplanted with porcine fetal islet-like cell clusters (ICC) between 1990 and 1993. A significant rise in the anti-a-Gal antibody titers was seen posttransplant, but also non-a-Gal-specific antibodies were detected in some patients. We have reanalyzed...

  10. Multilayer nanoparticle arrays for broad spectrum absorption enhancement in thin film solar cells

    CERN Document Server

    Krishnan, Aravind; Krishna, Siva Rama; Khan, Mohammed Zafar Ali

    2013-01-01

    In this paper, we present a theoretical study on the absorption efficiency enhancement of a thin film amorphous Silicon (a-Si) photovoltaic cell over a broad spectrum of wavelengths using multiple nanoparticle arrays. The light absorption efficiency is enhanced in the lower wavelengths by a nanoparticle array on the surface and in the higher wavelengths by another nanoparticle array embedded in the active region. The efficiency at intermediate wavelengths is enhanced by the constructive interference of plasmon coupled light. We optimize this design by tuning the radius of particles in both arrays, the period of the array and the distance between the two arrays. The optimization results in 61.44% increase in total quantum efficiency for a 500 nm thick a-Si substrate.

  11. Deformable L-shaped microwell array for trapping pairs of heterogeneous cells

    Science.gov (United States)

    Lee, Gi-Hun; Kim, Sung-Hwan; Kang, AhRan; Takayama, Shuichi; Lee, Sang-Hoon; Park, Joong Yull

    2015-03-01

    To study cell-to-cell interactions, there has been a continuous demand on developing microsystems for trapping pairs of two different cells in microwell arrays. Here, we propose an L-shaped microwell (L-microwell) array that relies on the elasticity of a polydimethylsiloxane (PDMS) substrate for trapping and pairing heterogeneous cells. We designed an L-microwell suitable for trapping single cell in each branch via stretching/releasing the PDMS substrate, and also performed 3D time-dependent diffusion simulations to visualize how cell-secreted molecules diffuse in the L-microwell and communicate with the partner cell. The computational results showed that the secreted molecule first contacted the partner cell after 35 min, and the secreted molecule fully covered the partner cell in 4 h (when referenced to 10% of the secreted molecular concentration). The molecules that diffused to the outside of the L-microwell were significantly diluted by the bulk solution, which prevented unwanted cellular communication between neighboring L-microwells. We produced over 5000 cell pairs in one 2.25 cm2 array with about 30 000 L-microwells. The proposed L-microwell array offers a versatile and convenient cell pairing method to investigate cell-to-cell interactions in, for example, cell fusion, immune reactions, and cancer metastasis.

  12. Photovoltaic cell and array technology development for future unique NASA missions

    Science.gov (United States)

    Bailey, S.; Curtis, H.; Piszczor, M.; Surampudi, R.; Hamilton, T.; Rapp, D.; Stella, P.; Mardesich, N.; Mondt, J.; Bunker, R.; Nesmith, B.; Gaddy, E.; Marvin, D.; Kazmerski, L.

    2002-01-01

    A technology review committee from NASA, the U.S. Department of Energy (DOE), and the Air Force Research Lab, was formed to assess solar cell and array technologies required for future NASA science missions.

  13. An array of asymmetries in Saturn's structure revealed by its rings

    Science.gov (United States)

    Hedman, Matthew M.; Nicholson, Philip D.; El Moutamid, Maryame; Graven, Stephanie

    2016-05-01

    Previous investigations of high-resolution stellar occultation data obtained by the Cassini spacecraft have revealed that Saturn's C ring contains numerous density waves that are probably generated by structures inside the planet. In particular, five features were attributed to long-lived asymmetries in the planet's gravity field because they had pattern speeds similar to the range of rotation rates found in Saturn's winds. Using wavelet-based techniques, we have performed a more comprehensive search for similar structures, and found that the above five waves are just the most obvious members of an entire population of ring disturbances spread over several thousand kilometers of the C ring. These structures should provide new insights into the dynamics of Saturn's deep atmosphere.

  14. Process development for cell aggregate arrays encapsulated in a synthetic hydrogel using negative dielectrophoresis.

    Science.gov (United States)

    Abdallat, Rula G; Ahmad Tajuddin, Aziela S; Gould, David H; Hughes, Michael P; Fatoyinbo, Henry O; Labeed, Fatima H

    2013-04-01

    Spatial patterning of cells is of great importance in tissue engineering and biotechnology, enabling, for example the creation of bottom-up histoarchitectures of heterogeneous cells, or cell aggregates for in vitro high-throughput toxicological and therapeutic studies within 3D microenvironments. In this paper, a single-step process for creating peelable and resilient hydrogels, encapsulating arrays of biological cell aggregates formed by negative DEP has been devised. The dielectrophoretic trapping within low-energy regions of the DEP-dot array reduces cell exposure to high field stresses while creating distinguishable, evenly spaced arrays of aggregates. In addition to using an optimal combination of PEG diacrylate pre-polymer solution concentration and a novel UV exposure mechanism, total processing time was reduced. With a continuous phase medium of PEG diacrylate at 15% v/v concentration, effective dielectrophoretic cell patterned arrays and photo-polymerisation of the mixture was achieved within a 4 min period. This unique single-step process was achieved using a 30 s UV exposure time frame within a dedicated, wide exposure area DEP light box system. To demonstrate the developed process, aggregates of yeast, human leukemic (K562) and HeLa cells were immobilised in an array format within the hydrogel. Relative cell viability for both cells within the hydrogels, after maintaining them in appropriate iso-osmotic media, over a week period was greater than 90%. PMID:23436271

  15. Understanding the radiosensitivity of hematopoietic stem cells through CDNA micro-arrays profiling

    Energy Technology Data Exchange (ETDEWEB)

    Pawlik, A.; Cebo, Ch.; Vaigot, P.; Tronik-Le Roux, D. [Evry Univ., Lab. de Genomique et Radiobiologie de l' Hematopoiese, Service de Genomique Fonctionnelle, CEA, 91 (France)

    2006-07-01

    transcriptional modulations identified as early as 1 hour after IR exposure. Many of the modulated genes were never described before as playing a role in the IR response. Clustering the modulated genes using a Q.T. clustering method led to select two specific clusters of up-regulated genes in the spleen. Cluster 1 includes transcripts that are rapidly but transiently up-regulated. Cluster 2 contains genes for which the high level of transcripts persists at least for 3 hours. This cluster includes many known p-53 target genes such as p21, Ba x and Mdm2. Promoter sequence analysis revealed that the majority of gene s included in this cluster possess p-53 cis-responsive elements. This suggests that these genes might be potentially co-regulated and might constitute novel targets of the tumor suppressor gene. This hypothesis was assessed by chromatin immunoprecipitation. We next compared the behavior of stem/early progenitor cells to that of the more sensitive mature B-lymphoid cell population after whole body irradiation. The comparison of transcription profiles of both populations revealed that the elicited response was highly dependent on the stage of differentiation of the cell. In particular, the early population mobilized many more genes than the more mature population in response to IR. To give a biological significance to the micro array results, genes identified a modulated after radiation exposure were assigned to functional categories using the G.O. annotations. This tool assigns gene products to common biological processes, molecular functions and cellular components. Moreover, a rea l statistical significance to the gene list is attributed, since the % is calculated wit h respect to the total number of genes assayed. Some of the mobilized categories were as one could expect, cell death, cellular growth and proliferation, however many of the identified genes were not studied before in the context of a radiation exposure response .Modulated genes were also analyzed

  16. Synthetic protein interactions reveal a functional map of the cell

    Science.gov (United States)

    Berry, Lisa K; Ólafsson, Guðjón; Ledesma-Fernández, Elena; Thorpe, Peter H

    2016-01-01

    To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.13053.001 PMID:27098839

  17. SEMICONDUCTOR DEVICES: Performance analysis of solar cell arrays in concentrating light intensity

    Science.gov (United States)

    Yongfeng, Xu; Ming, Li; Liuling, Wang; Wenxian, Lin; Ming, Xiang; Xinghua, Zhang; Yunfeng, Wang; Shengxian, Wei

    2009-08-01

    Performance of concentrating photovoltaic/thermal system is researched by experiment and simulation calculation. The results show that the I-V curve of the GaAs cell array is better than that of crystal silicon solar cell arrays and the exergy produced by 9.51% electrical efficiency of the GaAs solar cell array can reach 68.93% of the photovoltaic/thermal system. So improving the efficiency of solar cell arrays can introduce more exergy and the system value can be upgraded. At the same time, affecting factors of solar cell arrays such as series resistance, temperature and solar irradiance also have been analyzed. The output performance of a solar cell array with lower series resistance is better and the working temperature has a negative impact on the voltage in concentrating light intensity. The output power has a -20 W/V coefficient and so cooling fluid must be used. Both heat energy and electrical power are then obtained with a solar trough concentrating photovoltaic/thermal system.

  18. Self-Assembled Wire Arrays and ITO Contacts for Silicon Nanowire Solar Cell Applications

    Institute of Scientific and Technical Information of China (English)

    YANG Cheng; ZHANG Gang; LEE Dae-Young; LI Hua-Min; LIM Young-Dae; Y00 Won Jong; PARK Young-Jun; KIM Jong-Min

    2011-01-01

    Self-assembly of silicon nanowire(SiNW)arrays is studied using SF6/02 plasma treatment. The self-assembly method can be applied to single- and poly-crystalline Si substrates. Plasma conditions can control the length and diameter of the SiNW arrays. Lower reflectance of the wire arrays over the wavelength range 200-1100nm is obtained. The conducting transparent indium-tin-oxide(ITO) electrode can be fully coated on the self-assembled SiNW arrays by sputtering. The ITO-coated SiNW solar cells show the same low surface light reflectance and a higher carrier collection efficiency than SiNW solar cells without ITO coating. An efficiency enhancement of around 3 times for ITO coated SiNW solar cells is demonstrated via experiments.

  19. Timing and Controlling Dissolution of Cell Repellent Poly(Vinyl Alcohol) Thin Films for Patterned Cell Micro-Arrays

    OpenAIRE

    Lindboe, Frederic Menard

    2014-01-01

    Recently, a novel, high-throughput, patterned cell micro-array has been developed using polydopamine and poly(vinyl alcohol) (PVA) as cell adhesive and cell repellent surfaces, respectively. The step converting the cell repellent surface to an adhesive one was shown to be toxic, so this project set out to investigate whether the cell repellent PVA surface could be dissolved instead through timed or controlled dissolution. PVA film solubility was tested in water and in cell compatible media. V...

  20. Analysis of leakage current in GaAs micro-solar cell arrays

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The output characteristics of micro-solar cell arrays are analyzed on the basis of a modified model in which the shunt resistance between cell lines results in current leakage.The modification mainly consists of adding a shunt resistor network to the traditional model.The obtained results agree well with the reported experimental results.The calculation results demonstrate that leakage current in substrate affects seriously the performance of GaAs micro-solar cell arrays.The performance of arrays can be improved by reducing the number of cells per line.In addition,at a certain level of integration,an appropriate space occupancy rate of the single cell is recommended for ensuring high open circuit voltages,and it is more appropriate to set the rates at 80%-90% through the calculation.

  1. Engineering complex tissue-like microgel arrays for evaluating stem cell differentiation

    Science.gov (United States)

    Guermani, Enrico; Shaki, Hossein; Mohanty, Soumyaranjan; Mehrali, Mehdi; Arpanaei, Ayyoob; Gaharwar, Akhilesh K.; Dolatshahi-Pirouz, Alireza

    2016-01-01

    Development of tissue engineering scaffolds with native-like biology and microarchitectures is a prerequisite for stem cell mediated generation of off-the-shelf-tissues. So far, the field of tissue engineering has not full-filled its grand potential of engineering such combinatorial scaffolds for engineering functional tissues. This is primarily due to the many challenges associated with finding the right microarchitectures and ECM compositions for optimal tissue regeneration. Here, we have developed a new microgel array to address this grand challenge through robotic printing of complex stem cell-laden microgel arrays. The developed microgel array platform consisted of various microgel environments that where composed of native-like cellular microarchitectures resembling vascularized and bone marrow tissue architectures. The feasibility of our array system was demonstrated through localized cell spreading and osteogenic differentiation of human mesenchymal stem cells (hMSCs) into complex tissue-like structures. In summary, we have developed a tissue-like microgel array for evaluating stem cell differentiation within complex and heterogeneous cell microenvironments. We anticipate that the developed platform will be used for high-throughput identification of combinatorial and native-like scaffolds for tissue engineering of functional organs. PMID:27465860

  2. Highly efficient ultrathin-film amorphous silicon solar cells on top of imprinted periodic nanodot arrays

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Wensheng, E-mail: yws118@gmail.com; Gu, Min, E-mail: mgu@swin.edu.au [Centre for Micro-Photonics, Faculty of Science, Engineering and Technology, Swinburne University of Technology, Hawthorn, Victoria 3122 (Australia); Tao, Zhikuo [College of Electronic Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210023 (China); Ong, Thiam Min Brian [Plasma Sources and Application Center, NIE, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616 (Singapore); Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology and Research), 3 Research Link, Singapore 117602 (Singapore)

    2015-03-02

    The addressing of the light absorption and conversion efficiency is critical to the ultrathin-film hydrogenated amorphous silicon (a-Si:H) solar cells. We systematically investigate ultrathin a-Si:H solar cells with a 100 nm absorber on top of imprinted hexagonal nanodot arrays. Experimental evidences are demonstrated for not only notable silver nanodot arrays but also lower-cost ITO and Al:ZnO nanodot arrays. The measured external quantum efficiency is explained by the simulation results. The J{sub sc} values are 12.1, 13.0, and 14.3 mA/cm{sup 2} and efficiencies are 6.6%, 7.5%, and 8.3% for ITO, Al:ZnO, and silver nanodot arrays, respectively. Simulated optical absorption distribution shows high light trapping within amorphous silicon layer.

  3. Periodically Aligned Si Nanopillar Arrays as Efficient Antireflection Layers for Solar Cell Applications

    Directory of Open Access Journals (Sweden)

    Li Xiaocheng

    2010-01-01

    Full Text Available Abstract Periodically aligned Si nanopillar (PASiNP arrays were fabricated on Si substrate via a silver-catalyzed chemical etching process using the diameter-reduced polystyrene spheres as mask. The typical sub-wavelength structure of PASiNP arrays had excellent antireflection property with a low reflection loss of 2.84% for incident light within the wavelength range of 200–1,000 nm. The solar cell incorporated with the PASiNP arrays exhibited a power conversion efficiency (PCE of ~9.24% with a short circuit current density (JSC of ~29.5 mA/cm2 without using any extra surface passivation technique. The high PCE of PASiNP array-based solar cell was attributed to the excellent antireflection property of the special periodical Si nanostructure.

  4. Microtubule plus-end and minus-end capture at adherens junctions is involved in the assembly of apico-basal arrays in polarised epithelial cells.

    Science.gov (United States)

    Bellett, Gemma; Carter, Jane M; Keynton, Jennifer; Goldspink, Deborah; James, Colin; Moss, David K; Mogensen, Mette M

    2009-10-01

    Apico-basal polarisation of epithelial cells involves a dramatic reorganisation of the microtubule cytoskeleton. The classic radial array of microtubules focused on a centrally located centrosome typical of many animal cells is lost or greatly reduced and a non-centrosomal apico-basal array develops. The molecules and mechanisms responsible for the assembly and positioning of these non-centrosomal microtubules have not been fully elucidated. Using a Nocodazole induced regrowth assay in invitro culture (MDCK) and in situ epithelial (cochlear Kolliker's) cell models we establish that the apico-basal array originates from the centrosome and that the non-centrosomal microtubule minus-end anchoring sites do not contribute significantly to their nucleation. Confocal and electron microscopy revealed that an extended radial array assembles with microtubule plus-ends targeting cadheren sites at adherens junctions and EB1 and CLIP-170 co-localising with beta-catenin and dynein clusters at the junction sites. The extended radial array is likely to be a vital intermediate step in the assembly process with cortical anchored dynein providing the mechanical force required for microtubule release, translocation and capture. Ultrastructural analyses of the apico-basal arrays in fully polarised MDCK and Kolliker's cells revealed microtubule minus-end association with the most apical adherens junction (Zonula adherens). We propose that a release and capture model involving both microtubule plus- and minus-end capture at adherens junctions is responsible for the generation of non-centrosomal apico-basal arrays in most centrosome containing polarised epithelial cells. PMID:19479825

  5. Copy Number Variation Analysis by Array Analysis of Single Cells Following Whole Genome Amplification.

    Science.gov (United States)

    Dimitriadou, Eftychia; Zamani Esteki, Masoud; Vermeesch, Joris Robert

    2015-01-01

    Whole genome amplification is required to ensure the availability of sufficient material for copy number variation analysis of a genome deriving from an individual cell. Here, we describe the protocols we use for copy number variation analysis of non-fixed single cells by array-based approaches following single-cell isolation and whole genome amplification. We are focusing on two alternative protocols, an isothermal and a PCR-based whole genome amplification method, followed by either comparative genome hybridization (aCGH) or SNP array analysis, respectively.

  6. On-line observation of cell growth in a three-dimensional matrix on surface-modified microelectrode arrays.

    Science.gov (United States)

    Lin, Shu-Ping; Kyriakides, Themis R; Chen, Jia-Jin J

    2009-06-01

    Despite many successful applications of microelectrode arrays (MEAs), typical two-dimensional in-vitro cultures do not project the full scale of the cell growth environment in the three-dimensional (3D) in-vivo setting. This study aims to on-line monitor in-vitro cell growth in a 3D matrix on the surface-modified MEAs with a dynamic perfusion culture system. A 3D matrix consisting of poly(ethylene glycol) hydrogel supplemented with poly-D-lysine was subsequently synthesized in situ on the self-assembled monolayer modified MEAs. FTIR spectrum analysis revealed a peak at 2100 cm(-1) due to the degradation of the structure of the 3D matrix. After 2 wks, microscopic examination revealed that the non-degraded area was around 1500 microm(2) and provided enough space for cell growth. Fluorescence microscopy revealed that the degraded 3D matrix was non-cytotoxic allowing the growth of NIH3T3 fibroblasts and cortical neurons in vitro. Time-course changes of total impedance including resistance and reactance were recorded for 8 days to evaluate the cell growth in the 3D matrix on the MEA. A consistent trend reflecting changes of reactance and total impedance was observed. These in-vitro assays demonstrate that our 3D matrix can construct a biomimetic system for cell growth and analysis of cell surface interactions. PMID:19344948

  7. Tissue matrix arrays for high-throughput screening and systems analysis of cell function.

    Science.gov (United States)

    Beachley, Vince Z; Wolf, Matthew T; Sadtler, Kaitlyn; Manda, Srikanth S; Jacobs, Heather; Blatchley, Michael R; Bader, Joel S; Pandey, Akhilesh; Pardoll, Drew; Elisseeff, Jennifer H

    2015-12-01

    Cell and protein arrays have demonstrated remarkable utility in the high-throughput evaluation of biological responses; however, they lack the complexity of native tissue and organs. Here we spotted tissue extracellular matrix (ECM) particles as two-dimensional (2D) arrays or incorporated them with cells to generate three-dimensional (3D) cell-matrix microtissue arrays. We then investigated the responses of human stem, cancer and immune cells to tissue ECM arrays originating from 11 different tissues. We validated the 2D and 3D arrays as representative of the in vivo microenvironment by means of quantitative analysis of tissue-specific cellular responses, including matrix production, adhesion and proliferation, and morphological changes after culture. The biological outputs correlated with tissue proteomics, and network analysis identified several proteins linked to cell function. Our methodology enables broad screening of ECMs to connect tissue-specific composition with biological activity, providing a new resource for biomaterials research and further understanding of regeneration and disease mechanisms. PMID:26480475

  8. Low power and reliable SRAM memory cell and array design

    CERN Document Server

    Ishibashi, Koichiro

    2011-01-01

    Success in the development of recent advanced semiconductor device technologies is due to the success of SRAM memory cells. This book addresses various issues for designing SRAM memory cells for advanced CMOS technology. To study LSI design, SRAM cell design is the best materials subject because issues about variability, leakage and reliability have to be taken into account for the design.

  9. Molecular profiling reveals primary mesothelioma cell lines recapitulate human disease.

    Science.gov (United States)

    Chernova, T; Sun, X M; Powley, I R; Galavotti, S; Grosso, S; Murphy, F A; Miles, G J; Cresswell, L; Antonov, A V; Bennett, J; Nakas, A; Dinsdale, D; Cain, K; Bushell, M; Willis, A E; MacFarlane, M

    2016-07-01

    Malignant mesothelioma (MM) is an aggressive, fatal tumor strongly associated with asbestos exposure. There is an urgent need to improve MM patient outcomes and this requires functionally validated pre-clinical models. Mesothelioma-derived cell lines provide an essential and relatively robust tool and remain among the most widely used systems for candidate drug evaluation. Although a number of cell lines are commercially available, a detailed comparison of these commercial lines with freshly derived primary tumor cells to validate their suitability as pre-clinical models is lacking. To address this, patient-derived primary mesothelioma cell lines were established and characterized using complementary multidisciplinary approaches and bioinformatic analysis. Clinical markers of mesothelioma, transcriptional and metabolic profiles, as well as the status of p53 and the tumor suppressor genes CDKN2A and NF2, were examined in primary cell lines and in two widely used commercial lines. Expression of MM-associated markers, as well as the status of CDKN2A, NF2, the 'gatekeeper' in MM development, and their products demonstrated that primary cell lines are more representative of the tumor close to its native state and show a degree of molecular diversity, thus capturing the disease heterogeneity in a patient cohort. Molecular profiling revealed a significantly different transcriptome and marked metabolic shift towards a greater glycolytic phenotype in commercial compared with primary cell lines. Our results highlight that multiple, appropriately characterised, patient-derived tumor cell lines are required to enable concurrent evaluation of molecular profiles versus drug response. Furthermore, application of this approach to other difficult-to-treat tumors would generate improved cellular models for pre-clinical evaluation of novel targeted therapies. PMID:26891694

  10. ZnO nanowire arrays as substrates for cell proliferation and differentiation

    Energy Technology Data Exchange (ETDEWEB)

    Ciofani, Gianni, E-mail: g.ciofani@sssup.it [Italian Institute of Technology, Center of MicroBioRobotics c/o Scuola Superiore Sant' Anna, Viale Rinaldo Piaggio 34, 56025 Pontedera (Pisa) (Italy); Genchi, Giada Graziana [BioRobotics Institute, Scuola Superiore Sant' Anna, Viale Rinaldo Piaggio 34, 56025 Pontedera (Pisa) (Italy); Mattoli, Virgilio [Italian Institute of Technology, Center of MicroBioRobotics c/o Scuola Superiore Sant' Anna, Viale Rinaldo Piaggio 34, 56025 Pontedera, Pisa (Italy)

    2012-02-01

    In the latest years, the use of zinc oxide (ZnO) nanostructures has been proposed in different biomedical applications, however, to date, only a few contrasting results concerning their biocompatibility can be found in the literature. In particular, the application of the extraordinary piezoelectric properties of ZnO nanostructures has poorly been explored for the culture of electrically excitable cells, and, for this reason, systematic investigations of their interactions with these living systems appear to be necessary. In this paper, we report about adhesion, proliferation and differentiation of two mammalian cell lines (PC12, as model of neuronal cells, and H9c2, as model of muscle cells) over ZnO nanowire arrays. We demonstrate suitability of these arrays in sustaining cellular functions, and their potential in applications that range from tissue engineering to minimally invasive sensing and/or stimulation. - Highlights: Black-Right-Pointing-Pointer ZnO nanowire arrays were exploited as mammalian cell substrates. Black-Right-Pointing-Pointer Two cell lines were investigated: PC12 (neuronal-like) and H9c2 (muscle-like). Black-Right-Pointing-Pointer An intimate connection between cells and nanostructured substrates was highlighted. Black-Right-Pointing-Pointer Adhesion, proliferation and differentiation was well sustained by ZnO nanowire arrays.

  11. Multisystem Langerhans Cell Histiocytosis in Adults Revealed by Skin Lesions.

    Science.gov (United States)

    Atarguine, Hanane; Hocar, Ouafa; Oussmane, Samia; Mouafik, Sara Batoul; Hamdaoui, Abderrachid; Hafiane, Hanan; Belbaraka, Rhizlane; Akhdari, Nadia; Amal, Said

    2016-01-01

    A 37-year-old woman with no remarkable medical or family history presented with papules and vesicles on an erythematous background involving the neck, sacrum, and folds (postauricular, axillary, inguinal, and under the breasts) (Figure 1). During the previous year, she was treated with local and systemic antifungals without improvement. Her history included a secondary amenorrhea, polydipsia, and polyuria (6 L/d) that started 2 years prior. Physical examination revealed chronic bilateral purulent otorrhea with thick eardrums. Histologic examination of skin biopsy revealed a highly suggestive appearance of multisystem Langerhans cell histiocytosis (LCH) with immunohistochemistry (anti-PS100 and anti-CD1a), which were positive (Figure 2A and 2B). Pituitary magnetic resonance imaging showed a thickening of the pituitary stalk in relation to a location histiocytic (Figure 3). Bone gaps were objectified on two radiographic tibial diaphyseal. Results from computed tomography (CT) scan showed a magma coelio mesenteric, axillary, and inguinal lymph nodes. PMID:27319965

  12. Cancer Stem Cell Biomarker Discovery Using Antibody Array Technology.

    Science.gov (United States)

    Burgess, Rob; Huang, Ruo-Pan

    2016-01-01

    Cancer is a complex disease involving hundreds of pathways and numerous levels of disease progression. In addition, there is a growing body of evidence that the origins and growth rates of specific types of cancer may involve "cancer stem cells," which are defined as "cells within a tumor that possess the capacity to self-renew and to cause the development of heterogeneous lineages of cancer cells that comprise the tumor.(1)" Many types of cancer are now thought to harbor cancer stem cells. These cells themselves are thought to be unique in comparison to other cells types present within the tumor and to exhibit characteristics that allow for the promotion of tumorigenesis and in some cases metastasis. In addition, it is speculated that each type of cancer stem cell exhibits a unique set of molecular and biochemical markers. These markers, alone or in combination, may act as a signature for defining not only the type of cancer but also the progressive state. These biomarkers may also double as signaling entities which act autonomously or upon neighboring cancer stem cells or other cells within the local microenvironment to promote tumorigenesis. This review describes the heterogeneic properties of cancer stem cells and outlines the identification and application of biomarkers and signaling molecules defining these cells as they relate to different forms of cancer. Other examples of biomarkers and signaling molecules expressed by neighboring cells in the local tumor microenvironment are also discussed. In addition, biochemical signatures for cancer stem cell autocrine/paracrine signaling, local site recruitment, tumorigenic potential, and conversion to a stem-like phenotype are described.

  13. Application of a Halbach magnetic array for long-range cell and particle separations in biological samples

    Science.gov (United States)

    Kang, Joo H.; Driscoll, Harry; Super, Michael; Ingber, Donald E.

    2016-05-01

    Here, we describe a versatile application of a planar Halbach permanent magnet array for an efficient long-range magnetic separation of living cells and microparticles over distances up to 30 mm. A Halbach array was constructed from rectangular bar magnets using 3D-printed holders and compared to a conventional alternating array of identical magnets. We theoretically predicted the superiority of the Halbach array for a long-range magnetic separation and then experimentally validated that the Halbach configuration outperforms the alternating array for isolating magnetic microparticles or microparticle-bound bacterial cells at longer distances. Magnetophoretic velocities (ymag) of magnetic particles (7.9 μm diameter) induced by the Halbach array in a microfluidic device were significantly higher and extended over a larger area than those induced by the alternating magnet array (ymag = 178 versus 0 μm/s at 10 mm, respectively). When applied to 50 ml tubes (˜30 mm diameter), the Halbach array removed >95% of Staphylococcus aureus bacterial cells bound with 1 μm magnetic particles compared to ˜70% removed using the alternating array. In addition, the Halbach array enabled manipulation of 1 μm magnetic beads in a deep 96-well plate for ELISA applications, which was not possible with the conventional magnet arrays. Our analysis demonstrates the utility of the Halbach array for the future design of devices for high-throughput magnetic separations of cells, molecules, and toxins.

  14. Solar Cell and Array Technology Development for NASA Solar Electric Propulsion Missions

    Science.gov (United States)

    Piszczor, Michael; McNatt, Jeremiah; Mercer, Carolyn; Kerslake, Tom; Pappa, Richard

    2012-01-01

    NASA is currently developing advanced solar cell and solar array technologies to support future exploration activities. These advanced photovoltaic technology development efforts are needed to enable very large (multi-hundred kilowatt) power systems that must be compatible with solar electric propulsion (SEP) missions. The technology being developed must address a wide variety of requirements and cover the necessary advances in solar cell, blanket integration, and large solar array structures that are needed for this class of missions. Th is paper will summarize NASA's plans for high power SEP missions, initi al mission studies and power system requirements, plans for advanced photovoltaic technology development, and the status of specific cell and array technology development and testing that have already been conducted.

  15. Electricity from photovoltaic solar cells: Flat-Plate Solar Array Project final report. Volume IV: High-efficiency solar cells

    OpenAIRE

    Leipold, M.; L. Cheng; Daud, T.; Mokashi, A; Burger, D.

    1986-01-01

    The Flat-Plate Solar Array (FSA) Project, funded by the U.S. Government and managed by the Jet Propulsion Laboratory, was formed in 1975 to develop the module/array technology needed to attain widespread terrestrial use of photovoltaics by 1985. To accomplish this, the FSA Project established and managed an Industry, University, and Federal Government Team to perform the needed research and development (R&D). The High-Efficiency Solar Cells Task was assigned the objective of understandin...

  16. Intact mammalian cell function on semi-conductor nanowire arrays: new perspectives for cell-based biosensing

    DEFF Research Database (Denmark)

    Berthing, Trine; Bonde, Sara; Sørensen, Claus Birger;

    2011-01-01

    . A selection of critical cell functions and pathways are shown not to be impaired, including cell adhesion, membrane integrity, intracellular enzyme activity, DNA uptake, cytosolic and membrane protein expression, and the neuronal maturation pathway. The results demonstrate the low invasiveness of InAs NW...... arrays, which, combined with the unique physical properties of InAs, open up their potential for cellular investigations....

  17. Reliable single cell array CGH for clinical samples.

    Directory of Open Access Journals (Sweden)

    Zbigniew T Czyż

    Full Text Available BACKGROUND: Disseminated cancer cells (DCCs and circulating tumor cells (CTCs are extremely rare, but comprise the precursors cells of distant metastases or therapy resistant cells. The detailed molecular analysis of these cells may help to identify key events of cancer cell dissemination, metastatic colony formation and systemic therapy escape. METHODOLOGY/PRINCIPAL FINDINGS: Using the Ampli1™ whole genome amplification (WGA technology and high-resolution oligonucleotide aCGH microarrays we optimized conditions for the analysis of structural copy number changes. The protocol presented here enables reliable detection of numerical genomic alterations as small as 0.1 Mb in a single cell. Analysis of single cells from well-characterized cell lines and single normal cells confirmed the stringent quantitative nature of the amplification and hybridization protocol. Importantly, fixation and staining procedures used to detect DCCs showed no significant impact on the outcome of the analysis, proving the clinical usability of our method. In a proof-of-principle study we tracked the chromosomal changes of single DCCs over a full course of high-dose chemotherapy treatment by isolating and analyzing DCCs of an individual breast cancer patient at four different time points. CONCLUSIONS/SIGNIFICANCE: The protocol enables detailed genome analysis of DCCs and thereby assessment of the clonal evolution during the natural course of the disease and under selection pressures. The results from an exemplary patient provide evidence that DCCs surviving selective therapeutic conditions may be recruited from a pool of genomically less advanced cells, which display a stable subset of specific genomic alterations.

  18. Quantifying the Traction Force of a Single Cell by Aligned Silicon Nanowire Array

    KAUST Repository

    Li, Zhou

    2009-10-14

    The physical behaviors of stationary cells, such as the morphology, motility, adhesion, anchorage, invasion and metastasis, are likely to be important for governing their biological characteristics. A change in the physical properties of mammalian cells could be an indication of disease. In this paper, we present a silicon-nanowire-array based technique for quantifying the mechanical behavior of single cells representing three distinct groups: normal mammalian cells, benign cells (L929), and malignant cells (HeLa). By culturing the cells on top of NW arrays, the maximum traction forces of two different tumor cells (HeLa, L929) have been measured by quantitatively analyzing the bending of the nanowires. The cancer cell exhibits a larger traction force than the normal cell by ∼20% for a HeLa cell and ∼50% for a L929 cell. The traction forces have been measured for the L929 cells and mechanocytes as a function of culture time. The relationship between cells extending area and their traction force has been investigated. Our study is likely important for studying the mechanical properties of single cells and their migration characteristics, possibly providing a new cellular level diagnostic technique. © 2009 American Chemical Society.

  19. Low cost, high concentration ratio solar cell array for space applications

    Science.gov (United States)

    Patterson, R. E.; Rauschenbach, H. S.; Cannady, M. D.; Whang, U. S.; Crabtree, W. L.

    1981-01-01

    A miniaturized Cassegrainian-type concentrator solar array concept for space applications is described. In-orbit cell operating temperatures near 80 C are achieved with purely passive cell cooling and a net concentration ratio of 100. A multiplicity of miniaturized, rigid solar cell concentrator subassemblies are electrically interconnected in conventional fashion and mounted into rigid frames to form concentrator solar panel assemblies approximately 14-mm thick. A plurality of such interconnected panels forms a stowable and deployable solar cell blanket. It is projected that for 20% efficient silicon cells an array of 500 kW beginning-of-life output capability, including orbiter cradle structures, can be transported by a single shuttle orbiter flight into low earth orbit. In-orbit array specific performance is calculated to be approximately 100 W/sq m and 20 W/kg, including all stowage, deployment and array figure control equipment designed for a 30-year orbital life. Higher efficiency gallium arsenide and multiple band gap solar cells will improve these performance factors correspondingly.

  20. Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays

    OpenAIRE

    Saliba, Antoine-Emmanuel; Saias, Laure; Psychari, Eleni; Minc, Nicolas; Simon, Damien; Bidard, François-Clément; Mathiot, Claire; Pierga, Jean-Yves; Fraisier, Vincent; Salamero, Jean; Saada, Véronique; Farace, Françoise; Vielh, Philippe; Malaquin, Laurent; Viovy, Jean-Louis

    2010-01-01

    We propose a unique method for cell sorting, “Ephesia,” using columns of biofunctionalized superparamagnetic beads self-assembled in a microfluidic channel onto an array of magnetic traps prepared by microcontact printing. It combines the advantages of microfluidic cell sorting, notably the application of a well controlled, flow-activated interaction between cells and beads, and those of immunomagnetic sorting, notably the use of batch-prepared, well characterized antibody-bearing beads. On c...

  1. Formation of organic crystalline nanopillar arrays and their application to organic photovoltaic cells.

    Science.gov (United States)

    Hirade, Masaya; Nakanotani, Hajime; Yahiro, Masayuki; Adachi, Chihaya

    2011-01-01

    To enhance the performance of organic photovoltaic (OPV) cells, preparation of organic nanometer-sized pillar arrays is fascinating because a significantly large area of a donor/acceptor heterointerface having continuous conduction path to both anode and cathode electrodes can be realized. In this study, we grew cupper phthalocyanine (CuPc) crystalline nanopillar arrays by conventional thermal gradient sublimation technique using a few-nanometer-sized trigger seeds composed of a CuPc and 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) stacked layer. We optimized the pillar density by tuning crystal growth condition in order to apply it to OPV cells.

  2. Formation of organic crystalline nanopillar arrays and their application to organic photovoltaic cells.

    Science.gov (United States)

    Hirade, Masaya; Nakanotani, Hajime; Yahiro, Masayuki; Adachi, Chihaya

    2011-01-01

    To enhance the performance of organic photovoltaic (OPV) cells, preparation of organic nanometer-sized pillar arrays is fascinating because a significantly large area of a donor/acceptor heterointerface having continuous conduction path to both anode and cathode electrodes can be realized. In this study, we grew cupper phthalocyanine (CuPc) crystalline nanopillar arrays by conventional thermal gradient sublimation technique using a few-nanometer-sized trigger seeds composed of a CuPc and 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) stacked layer. We optimized the pillar density by tuning crystal growth condition in order to apply it to OPV cells. PMID:21194207

  3. High resolution array-CGH analysis of single cells

    OpenAIRE

    Fiegler, Heike; Geigl, Jochen B.; Langer, Sabine; Rigler, Diane; Porter, Keith; Unger, Kristian; Carter, Nigel P; Speicher, Michael R.

    2006-01-01

    Heterogeneity in the genome copy number of tissues is of particular importance in solid tumor biology. Furthermore, many clinical applications such as pre-implantation and non-invasive prenatal diagnosis would benefit from the ability to characterize individual single cells. As the amount of DNA from single cells is so small, several PCR protocols have been developed in an attempt to achieve unbiased amplification. Many of these approaches are suitable for subsequent cytogenetic analyses usin...

  4. Engineering complex tissue-like microgel arrays for evaluating stem cell differentiation

    DEFF Research Database (Denmark)

    Guermani, Enrico; Shaki, Hossein; Mohanty, Soumyaranjan;

    2016-01-01

    Development of tissue engineering scaffolds with native-like biology and microarchitectures is a prerequisite for stem cell mediated generation of off-the-shelf-tissues. So far, the field of tissue engineering has not full-filled its grand potential of engineering such combinatorial scaffolds...... for engineering functional tissues. This is primarily due to the many challenges associated with finding the right microarchitectures and ECM compositions for optimal tissue regeneration. Here, we have developed a new microgel array to address this grand challenge through robotic printing of complex stem cell...... spreading and osteogenic differentiation of human mesenchymal stem cells (hMSCs) into complex tissue-like structures. In summary, we have developed a tissue-like microgel array for evaluating stem cell differentiation within complex and heterogeneous cell microenvironments. We anticipate that the developed...

  5. Breast Carcinoma Cells in Primary Tumors and Effusions Have Different Gene Array Profiles

    Directory of Open Access Journals (Sweden)

    Sophya Konstantinovsky

    2010-01-01

    Full Text Available The detection of breast carcinoma cells in effusions is associated with rapidly fatal outcome, but these cells are poorly characterized at the molecular level. This study compared the gene array signatures of breast carcinoma cells in primary carcinomas and effusions. The genetic signature of 10 primary tumors and 10 effusions was analyzed using the Array-Ready Oligo set for the Human Genome platform. Results for selected genes were validated using PCR, Western blotting, and immunohistochemistry. Array analysis identified 255 significantly downregulated and 96 upregulated genes in the effusion samples. The majority of differentially expressed genes were part of pathways involved in focal adhesion, extracellular matrix-cell interaction, and the regulation of the actin cytoskeleton. Genes that were upregulated in effusions included KRT8, BCAR1, CLDN4, VIL2, while DCN, CLDN19, ITGA7, and ITGA5 were downregulated at this anatomic site. PCR, Western blotting, and immunohistochemistry confirmed the array findings for BCAR1, CLDN4, VIL2, and DCN. Our data show that breast carcinoma cells in primary carcinomas and effusions have different gene expression signatures, and differentially express a large number of molecules related to adhesion, motility, and metastasis. These differences may have a critical role in designing therapy and in prognostication for patients with metastatic disease localized to the serosal cavities.

  6. Cell-Based Odorant Sensor Array for Odor Discrimination Based on Insect Odorant Receptors.

    Science.gov (United States)

    Termtanasombat, Maneerat; Mitsuno, Hidefumi; Misawa, Nobuo; Yamahira, Shinya; Sakurai, Takeshi; Yamaguchi, Satoshi; Nagamune, Teruyuki; Kanzaki, Ryohei

    2016-07-01

    The olfactory system of living organisms can accurately discriminate numerous odors by recognizing the pattern of activation of several odorant receptors (ORs). Thus, development of an odorant sensor array based on multiple ORs presents the possibility of mimicking biological odor discrimination mechanisms. Recently, we developed novel odorant sensor elements with high sensitivity and selectivity based on insect OR-expressing Sf21 cells that respond to target odorants by displaying increased fluorescence intensity. Here we introduce the development of an odorant sensor array composed of several Sf21 cell lines expressing different ORs. In this study, an array pattern of four cell lines expressing Or13a, Or56a, BmOR1, and BmOR3 was successfully created using a patterned polydimethylsiloxane film template and cell-immobilizing reagents, termed biocompatible anchor for membrane (BAM). We demonstrated that BAM could create a clear pattern of Sf21 sensor cells without impacting their odorant-sensing performance. Our sensor array showed odorant-specific response patterns toward both odorant mixtures and single odorant stimuli, allowing us to visualize the presence of 1-octen-3-ol, geosmin, bombykol, and bombykal as an increased fluorescence intensity in the region of Or13a, Or56a, BmOR1, and BmOR3 cell lines, respectively. Therefore, we successfully developed a new methodology for creating a cell-based odorant sensor array that enables us to discriminate multiple target odorants. Our method might be expanded into the development of an odorant sensor capable of detecting a large range of environmental odorants that might become a promising tool used in various applications including the study of insect semiochemicals and food contamination.

  7. Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

    Directory of Open Access Journals (Sweden)

    Iain C. Macaulay

    2016-02-01

    Full Text Available The transcriptional programs that govern hematopoiesis have been investigated primarily by population-level analysis of hematopoietic stem and progenitor cells, which cannot reveal the continuous nature of the differentiation process. Here we applied single-cell RNA-sequencing to a population of hematopoietic cells in zebrafish as they undergo thrombocyte lineage commitment. By reconstructing their developmental chronology computationally, we were able to place each cell along a continuum from stem cell to mature cell, refining the traditional lineage tree. The progression of cells along this continuum is characterized by a highly coordinated transcriptional program, displaying simultaneous suppression of genes involved in cell proliferation and ribosomal biogenesis as the expression of lineage specific genes increases. Within this program, there is substantial heterogeneity in the expression of the key lineage regulators. Overall, the total number of genes expressed, as well as the total mRNA content of the cell, decreases as the cells undergo lineage commitment.

  8. The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing.

    Science.gov (United States)

    Björklund, Åsa K; Forkel, Marianne; Picelli, Simone; Konya, Viktoria; Theorell, Jakob; Friberg, Danielle; Sandberg, Rickard; Mjösberg, Jenny

    2016-04-01

    Innate lymphoid cells (ILCs) are increasingly appreciated as important participants in homeostasis and inflammation. Substantial plasticity and heterogeneity among ILC populations have been reported. Here we have delineated the heterogeneity of human ILCs through single-cell RNA sequencing of several hundreds of individual tonsil CD127(+) ILCs and natural killer (NK) cells. Unbiased transcriptional clustering revealed four distinct populations, corresponding to ILC1 cells, ILC2 cells, ILC3 cells and NK cells, with their respective transcriptomes recapitulating known as well as unknown transcriptional profiles. The single-cell resolution additionally divulged three transcriptionally and functionally diverse subpopulations of ILC3 cells. Our systematic comparison of single-cell transcriptional variation within and between ILC populations provides new insight into ILC biology during homeostasis, with additional implications for dysregulation of the immune system.

  9. Multi-Sensor Arrays for Online Monitoring of Cell Dynamics in in vitro Studies with Choroid Plexus Epithelial Cells

    Directory of Open Access Journals (Sweden)

    Soledad García Gómez de las Heras

    2012-02-01

    Full Text Available Sensors and multi-sensor arrays are the basis of new technologies for the non-label monitoring of cell activity. In this paper we show that choroid plexus cells can be cultured on silicon chips and that sensors register in real time changes in their activity, constituting an interesting experimental paradigm for cell biology and medical research. To validate the signals recorded (metabolism = peri-cellular acidification, oxygen consumption = respiration; impedance = adhesion, cell shape and motility we performed experiments with compounds that act in a well-known way on cells, influencing these parameters. Our in vitro model demonstrates the advantages of multi-sensor arrays in assessment and experimental characterization of dynamic cellular events—in this case in choroid plexus functions, however with applicability to other cell types as well.

  10. Multi-Sensor Arrays for Online Monitoring of Cell Dynamics in in vitro Studies with Choroid Plexus Epithelial Cells

    Science.gov (United States)

    Mestres-Ventura, Pedro; Morguet, Andrea; de las Heras, Soledad García Gómez

    2012-01-01

    Sensors and multi-sensor arrays are the basis of new technologies for the non-label monitoring of cell activity. In this paper we show that choroid plexus cells can be cultured on silicon chips and that sensors register in real time changes in their activity, constituting an interesting experimental paradigm for cell biology and medical research. To validate the signals recorded (metabolism = peri-cellular acidification, oxygen consumption = respiration; impedance = adhesion, cell shape and motility) we performed experiments with compounds that act in a well-known way on cells, influencing these parameters. Our in vitro model demonstrates the advantages of multi-sensor arrays in assessment and experimental characterization of dynamic cellular events—in this case in choroid plexus functions, however with applicability to other cell types as well. PMID:22438715

  11. High Density Crossbar Arrays with Sub- 15 nm Single Cells via Liftoff Process Only

    Science.gov (United States)

    Khiat, Ali; Ayliffe, Peter; Prodromakis, Themistoklis

    2016-09-01

    Emerging nano-scale technologies are pushing the fabrication boundaries at their limits, for leveraging an even higher density of nano-devices towards reaching 4F2/cell footprint in 3D arrays. Here, we study the liftoff process limits to achieve extreme dense nanowires while ensuring preservation of thin film quality. The proposed method is optimized for attaining a multiple layer fabrication to reliably achieve 3D nano-device stacks of 32 × 32 nanowire arrays across 6-inch wafer, using electron beam lithography at 100 kV and polymethyl methacrylate (PMMA) resist at different thicknesses. The resist thickness and its geometric profile after development were identified to be the major limiting factors, and suggestions for addressing these issues are provided. Multiple layers were successfully achieved to fabricate arrays of 1 Ki cells that have sub- 15 nm nanowires distant by 28 nm across 6-inch wafer.

  12. Process development for automated solar cell and module production. Task 4. Automated array assembly. Annual report

    Energy Technology Data Exchange (ETDEWEB)

    Witham, C.R.

    1979-06-12

    MBA has been working on the automated array assembly task of the Low-Cost Solar Array project. A baseline sequence for the manufacture of solar cell modules is specified. Starting with silicon wafers, the process goes through damage etching, texture etching, junction formation, plasma edge etch, aluminum back surface field formation, and screen printed metallization to produce finished solar cells which are then series connected on a ribbon and bonded into a finished glass, PVB, tedlar module. A number of steps required additional developmental effort to verify technical and economic feasibility. These steps include texture etching, plasma edge etch, aluminum back surface field formation, array layup and interconnect, and module edge sealing and framing.

  13. Micro-electrode array recordings reveal reductions in both excitation and inhibition in cultured cortical neuron networks lacking Shank3.

    Science.gov (United States)

    Lu, C; Chen, Q; Zhou, T; Bozic, D; Fu, Z; Pan, J Q; Feng, G

    2016-02-01

    Numerous risk genes have recently been implicated in susceptibility to autism and schizophrenia. Translating such genetic findings into disease-relevant neurobiological mechanisms is challenging due to the lack of throughput assays that can be used to assess their functions on an appropriate scale. To address this issue, we explored the feasibility of using a micro-electrode array (MEA) as a potentially scalable assay to identify the electrical network phenotypes associated with risk genes. We first characterized local and global network firing in cortical neurons with MEAs, and then developed methods to analyze the alternation between the network active period (NAP) and the network inactive period (NIP), each of which lasts tens of seconds. We then evaluated the electric phenotypes of neurons derived from Shank3 knockout (KO) mice. Cortical neurons cultured on MEAs displayed a rich repertoire of spontaneous firing, and Shank3 deletion led to reduced firing activity. Enhancing excitation with CX546 rescued the deficit in the spike rate in the Shank3 KO network. In addition, the Shank3 KO network produced a shorter NIP, and this altered network firing pattern was normalized by clonazepam, a positive modulator of the GABAA receptor. MEA recordings revealed electric phenotypes that displayed altered excitation and inhibition in the network lacking Shank3. Thus, our study highlights MEAs as an experimental framework for measuring multiple robust neurobiological end points in dynamic networks and as an assay system that could be used to identify electric phenotypes in cultured neuronal networks and to analyze additional risk genes identified in psychiatric genetics. PMID:26598066

  14. Light absorption processes and optimization of ZnO/CdTe core–shell nanowire arrays for nanostructured solar cells

    International Nuclear Information System (INIS)

    The absorption processes of extremely thin absorber solar cells based on ZnO/CdTe core–shell nanowire (NW) arrays with square, hexagonal or triangular arrangements are investigated through systematic computations of the ideal short-circuit current density using three-dimensional rigorous coupled wave analysis. The geometrical dimensions are optimized for optically designing these solar cells: the optimal NW diameter, height and array period are of 200 ± 10 nm, 1–3 μm and 350–400 nm for the square arrangement with CdTe shell thickness of 40–60 nm. The effects of the CdTe shell thickness on the absorption of ZnO/CdTe NW arrays are revealed through the study of two optical key modes: the first one is confining the light into individual NWs, the second one is strongly interacting with the NW arrangement. It is also shown that the reflectivity of the substrate can improve Fabry–Perot resonances within the NWs: the ideal short-circuit current density is increased by 10% for the ZnO/fluorine-doped tin oxide (FTO)/ideal reflector as compared to the ZnO/FTO/glass substrate. Furthermore, the optimized square arrangement absorbs light more efficiently than both optimized hexagonal and triangular arrangements. Eventually, the enhancement factor of the ideal short-circuit current density is calculated as high as 1.72 with respect to planar layers, showing the high optical potentiality of ZnO/CdTe core–shell NW arrays. (paper)

  15. Light absorption processes and optimization of ZnO/CdTe core-shell nanowire arrays for nanostructured solar cells

    Science.gov (United States)

    Michallon, Jérôme; Bucci, Davide; Morand, Alain; Zanuccoli, Mauro; Consonni, Vincent; Kaminski-Cachopo, Anne

    2015-02-01

    The absorption processes of extremely thin absorber solar cells based on ZnO/CdTe core-shell nanowire (NW) arrays with square, hexagonal or triangular arrangements are investigated through systematic computations of the ideal short-circuit current density using three-dimensional rigorous coupled wave analysis. The geometrical dimensions are optimized for optically designing these solar cells: the optimal NW diameter, height and array period are of 200 ± 10 nm, 1-3 μm and 350-400 nm for the square arrangement with CdTe shell thickness of 40-60 nm. The effects of the CdTe shell thickness on the absorption of ZnO/CdTe NW arrays are revealed through the study of two optical key modes: the first one is confining the light into individual NWs, the second one is strongly interacting with the NW arrangement. It is also shown that the reflectivity of the substrate can improve Fabry-Perot resonances within the NWs: the ideal short-circuit current density is increased by 10% for the ZnO/fluorine-doped tin oxide (FTO)/ideal reflector as compared to the ZnO/FTO/glass substrate. Furthermore, the optimized square arrangement absorbs light more efficiently than both optimized hexagonal and triangular arrangements. Eventually, the enhancement factor of the ideal short-circuit current density is calculated as high as 1.72 with respect to planar layers, showing the high optical potentiality of ZnO/CdTe core-shell NW arrays.

  16. Array comparative genomic hybridization of keratoacanthomas and squamous cell carcinomas

    DEFF Research Database (Denmark)

    Li, Jian; Wang, Kai; Gao, Fei;

    2012-01-01

    Keratoacanthoma (KA) is a benign keratinocytic neoplasm that spontaneously regresses after 3-6 months and shares features with squamous cell carcinomas (SCCs). Furthermore, there are reports of KAs that have metastasized, invoking the question of whether KA is a variant of SCC (Hodak et al., 1993...

  17. A New Method of Solving Kernels in Algebraic Decomposition for the Synthesis of Logic Cell Array

    Institute of Scientific and Technical Information of China (English)

    马光胜; 张忠伟; 等

    1995-01-01

    In this paper,an improvement has been made on the algorithm of solving the kernels of new functions which are generated after a common divisor appearing in the original functions is replaced by a new intermediate variable.And an efficient method based on kernel heritage is presented.This method has been successfully used in synthesis of LCA (Logic Cell Array).

  18. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization.

    Science.gov (United States)

    Singchat, Worapong; Hitakomate, Ekarat; Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology. PMID:27501229

  19. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization

    Science.gov (United States)

    Rerkarmnuaychoke, Budsaba; Suntronpong, Aorarat; Fu, Beiyuan; Bodhisuwan, Winai; Peyachoknagul, Surin; Yang, Fengtang; Koontongkaew, Sittichai; Srikulnath, Kornsorn

    2016-01-01

    Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology. PMID:27501229

  20. Protein Arrays for Multidrug-resistance in Human Leukemia Cell Determination

    Directory of Open Access Journals (Sweden)

    Zuhong Lu

    2005-05-01

    Full Text Available A novel technique was developed, that was high throughput simultaneousscreening of multiple resistance protein expression based on a protein array system. Themethod combined the advantage of the specificity of enzyme-linked immunosorbentassays with the sensitivity and high throughput of microspot. In this system, the multipleresistance protein arrays were created by spotting the captured antibodies onto the glassslide. The arrays were then incubated with cell samples of leukemia patients. The boundproteins were recognized by biotin-conjugated antibodies and detected by CCD.Experiments demonstrated that three multiple resistance proteins, including Pgp, MRPand BCRP which are members of the ATP-binding-cassette (ABC superfamily ofmembrane transporters could be simultaneously detected using this new approach.Research work shows the result is coincident with flow cytometry (FCM (P>0.01. Itprovided a methodology to develop many high-density protein array systems to detect avariety of proteins. The protein arrays will provide a powerful tool to identify theleukemia cell protein expression and rapidly validate their MDR determination.

  1. Large Absorption Enhancement in Ultrathin Solar Cells Patterned by Metallic Nanocavity Arrays

    Science.gov (United States)

    Wang, Wei; Zhang, Jiasen; Che, Xiaozhou; Qin, Guogang

    2016-01-01

    A new type of light trapping structure utilizing ring-shaped metallic nanocavity arrays is proposed for the absorption enhancement in ultrathin solar cells with few photonic waveguide modes. Dozens of times of broadband absorption enhancement in the spectral range of 700 to 1100 nm is demonstrated in an ultrathin Si3N4/c-Si/Ag prototype solar cell by means of finite-difference time-domain (FDTD) simulation, and this dramatic absorption enhancement can be attributed to the excitation of plasmonic cavity modes in these nanocavity arrays. The cavity modes optimally compensate for the lack of resonances in the longer wavelength range for ultrathin solar cells, and eventually a maximum Jsc enhancement factor of 2.15 is achieved under AM 1.5G solar illumination. This study opens a new perspective for light management in thin film solar cells and other optoelectronic devices. PMID:27703176

  2. Gamma ray effects on flash memory cell arrays

    Directory of Open Access Journals (Sweden)

    Dolićanin Edin Ć.

    2012-01-01

    Full Text Available Information stored in flash memories is physically represented by the absence or presence of charge on electrically isolated floating gates. Interaction of gamma rays with the insulators surrounding the floating gate produces effects that degrade the properties of memory cells, possibly leading to the corruption of the stored content. The cumulative nature of these effects is expressed through the total ionizing dose deposited by the gamma rays in the insulators surrounding the floating gate. Relying on both theory and experiment, we examine how the properties of cells in commercially available flash memories affect their sensitivity to gamma rays. Memory samples from several manufacturers, currently available on the market, can be compared with respect to data retention under gamma ray exposure.

  3. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers

    DEFF Research Database (Denmark)

    Gaasenbeek, Michelle; Howarth, Kimberley; Rowan, Andrew J;

    2006-01-01

    Cancers with chromosomal instability (CIN) are held to be aneuploid/polyploid with multiple large-scale gains/deletions, but the processes underlying CIN are unclear and different types of CIN might exist. We investigated colorectal cancer cell lines using array-comparative genomic hybridization ...

  4. Multilevel Gain Cell Arrays for Fault-Tolerant VLSI Systems

    OpenAIRE

    Khalid, Muhammad Umer

    2011-01-01

    Embedded memories dominate area, power and cost of modern very large scale integrated circuits system on chips ( VLSI SoCs). Furthermore, due to process variations, it becomes challenging to design reliable energy efficient systems. Therefore, fault-tolerant designs will be area efficient, cost effective and have low power consumption. The idea of this project is to design embedded memories where reliability is intentionally compromised to increase storage density. Gain cell memories are smal...

  5. Nanowire/nanotube array tandem cells for overall solar neutral water splitting

    OpenAIRE

    Kargar, A.; Khamwannah, J; Liu, CH; Park, N.; Wang, D; Dayeh, SA; Jin, S

    2016-01-01

    © 2015. In this study, we report the fabrication and characterization of a novel PEC tandem cell, consisting of p-Si/TiO2/Fe2O3 core/shell/hierarchical nanowire (csh-NW) array photocathode and TiO2/TiO2 core/shell nanotube (cs-NT) array photoanode, for overall solar water splitting in a neutral pH water. The p-Si/n-TiO2/n-Fe2O3 csh-NWs, made mainly by solution-processed methods, offer significantly improved performance in the neutral pH water with a low (positive) onset potential and photoact...

  6. Space satellite power system. [conversion of solar energy by photovoltaic solar cell arrays

    Science.gov (United States)

    Glaser, P. E.

    1974-01-01

    The concept of a satellite solar power station was studied. It is shown that it offers the potential to meet a significant portion of future energy needs, is pollution free, and is sparing of irreplaceable earth resources. Solar energy is converted by photovoltaic solar cell arrays to dc energy which in turn is converted into microwave energy in a large active phased array. The microwave energy is beamed to earth with little attenuation and is converted back to dc energy on the earth. Economic factors are considered.

  7. A photonic crystal hydrogel suspension array for the capture of blood cells from whole blood

    Science.gov (United States)

    Zhang, Bin; Cai, Yunlang; Shang, Luoran; Wang, Huan; Cheng, Yao; Rong, Fei; Gu, Zhongze; Zhao, Yuanjin

    2016-02-01

    Diagnosing hematological disorders based on the separation and detection of cells in the patient's blood is a significant challenge. We have developed a novel barcode particle-based suspension array that can simultaneously capture and detect multiple types of blood cells. The barcode particles are polyacrylamide (PAAm) hydrogel inverse opal microcarriers with characteristic reflection peak codes that remain stable during cell capture on their surfaces. The hydrophilic PAAm hydrogel scaffolds of the barcode particles can entrap various plasma proteins to capture different cells in the blood, with little damage to captured cells.Diagnosing hematological disorders based on the separation and detection of cells in the patient's blood is a significant challenge. We have developed a novel barcode particle-based suspension array that can simultaneously capture and detect multiple types of blood cells. The barcode particles are polyacrylamide (PAAm) hydrogel inverse opal microcarriers with characteristic reflection peak codes that remain stable during cell capture on their surfaces. The hydrophilic PAAm hydrogel scaffolds of the barcode particles can entrap various plasma proteins to capture different cells in the blood, with little damage to captured cells. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06368j

  8. Genome-wide analysis in human colorectal cancer cells reveals ischemia-mediated expression of motility genes via DNA hypomethylation.

    Science.gov (United States)

    Skowronski, Karolina; Skowronki, Karolina; Andrews, Joseph; Rodenhiser, David I; Coomber, Brenda L

    2014-01-01

    DNA hypomethylation is an important epigenetic modification found to occur in many different cancer types, leading to the upregulation of previously silenced genes and loss of genomic stability. We previously demonstrated that hypoxia and hypoglycaemia (ischemia), two common micro-environmental changes in solid tumours, decrease DNA methylation through the downregulation of DNMTs in human colorectal cancer cells. Here, we utilized a genome-wide cross-platform approach to identify genes hypomethylated and upregulated by ischemia. Following exposure to hypoxia or hypoglycaemia, methylated DNA from human colorectal cancer cells (HCT116) was immunoprecipitated and analysed with an Affymetrix promoter array. Additionally, RNA was isolated and analysed in parallel with an Affymetrix expression array. Ingenuity pathway analysis software revealed that a significant proportion of the genes hypomethylated and upregulated were involved in cellular movement, including PLAUR and CYR61. A Matrigel invasion assay revealed that indeed HCT116 cells grown in hypoxic or hypoglycaemic conditions have increased mobility capabilities. Confirmation of upregulated expression of cellular movement genes was performed with qPCR. The correlation between ischemia and metastasis is well established in cancer progression, but the molecular mechanisms responsible for this common observation have not been clearly identified. Our novel data suggests that hypoxia and hypoglycaemia may be driving changes in DNA methylation through downregulation of DNMTs. This is the first report to our knowledge that provides an explanation for the increased metastatic potential seen in ischemic cells; i.e. that ischemia could be driving DNA hypomethylation and increasing expression of cellular movement genes.

  9. Submicrometer-scale ZnO Composite Aggregate Arrays Photoanodes for Dye-sensitized Solar Cells

    Institute of Scientific and Technical Information of China (English)

    Wei Jia; Suihu Dang; Hairui Liu; Zhuxia Zhang; Tianbao Li; Xuguang Liu; Bingshe Xu

    2013-01-01

    Submicrometer-scale ZnO composite aggregate arrays of nanorods and nanoparticles were prepared by simple wet-chemical route and studied as dye-sensitized solar cells (DSSCs) photoanodes.The ZnO composite aggregate arrays significantly improved the efficiency of DSSCs due to their relatively high surface area,fast electron transport,and enhanced light-scattering capability.A short current density (Jsc) of 11.7 mA/cm2 and an overall solar-to-electric energy conversion efficiency (η) of 3.17% were achieved for the ZnO composite aggregate DSSCs,which were much higher than those obtained for the monodisperse aggregate DSSCs (Jsc=6.9mA/cm2,η=1.51 %) and ZnO nanorod array DSSCs (Jsc =4.2 mA/cm2,η=0.61%).

  10. Phased array compaction cell for measurement of the transversely isotropic elastic properties of compacting sediments

    Energy Technology Data Exchange (ETDEWEB)

    Nihei, K.T.; Nakagawa, S.; Reverdy, F.; Meyer, L.R.; Duranti, L.; Ball, G.

    2010-12-15

    Sediments undergoing compaction typically exhibit transversely isotropic (TI) elastic properties. We present a new experimental apparatus, the phased array compaction cell, for measuring the TI elastic properties of clay-rich sediments during compaction. This apparatus uses matched sets of P- and S-wave ultrasonic transducers located along the sides of the sample and an ultrasonic P-wave phased array source, together with a miniature P-wave receiver on the top and bottom ends of the sample. The phased array measurements are used to form plane P-waves that provide estimates of the phase velocities over a range of angles. From these measurements, the five TI elastic constants can be recovered as the sediment is compacted, without the need for sample unloading, recoring, or reorienting. This paper provides descriptions of the apparatus, the data processing, and an application demonstrating recovery of the evolving TI properties of a compacting marine sediment sample.

  11. Flexible complementary metal oxide semiconductor microelectrode arrays with applications in single cell characterization

    Science.gov (United States)

    Pajouhi, H.; Jou, A. Y.; Jain, R.; Ziabari, A.; Shakouri, A.; Savran, C. A.; Mohammadi, S.

    2015-11-01

    A highly flexible microelectrode array with an embedded complementary metal oxide semiconductor (CMOS) instrumentation amplifier suitable for sensing surfaces of biological entities is developed. The array is based on ultrathin CMOS islands that are thermally isolated from each other and are interconnected by meandered nano-scale wires that can adapt to cellular surfaces with micro-scale curvatures. CMOS temperature sensors are placed in the islands and are optimally biased to have high temperature sensitivity. While no live cell thermometry is conducted, a measured temperature sensitivity of 0.15 °C in the temperature range of 35 to 40 °C is achieved by utilizing a low noise CMOS lock-in amplifier implemented in the same technology. The monolithic nature of CMOS sensors and amplifier circuits and their versatile flexible interconnecting wires overcome the sensitivity and yield limitations of microelectrode arrays fabricated in competing technologies.

  12. Design of coated standing nanowire array solar cell performing beyond the planar efficiency limits

    Science.gov (United States)

    Zeng, Yang; Ye, Qinghao; Shen, Wenzhong

    2016-05-01

    The single standing nanowire (SNW) solar cells have been proven to perform beyond the planar efficiency limits in both open-circuit voltage and internal quantum efficiency due to the built-in concentration and the shifting of the absorption front. However, the expandability of these nano-scale units to a macro-scale photovoltaic device remains unsolved. The main difficulty lies in the simultaneous preservation of an effective built-in concentration in each unit cell and a broadband high absorption capability of their array. Here, we have provided a detailed theoretical guideline for realizing a macro-scale solar cell that performs furthest beyond the planar limits. The key lies in a complementary design between the light-trapping of the single SNWs and that of the photonic crystal slab formed by the array. By tuning the hybrid HE modes of the SNWs through the thickness of a coaxial dielectric coating, the optimized coated SNW array can sustain an absorption rate over 97.5% for a period as large as 425 nm, which, together with the inherited carrier extraction advantage, leads to a cell efficiency increment of 30% over the planar limit. This work has demonstrated the viability of a large-size solar cell that performs beyond the planar limits.

  13. Efficient Perovskite Solar Cells Depending on TiO2 Nanorod Arrays.

    Science.gov (United States)

    Li, Xin; Dai, Si-Min; Zhu, Pei; Deng, Lin-Long; Xie, Su-Yuan; Cui, Qian; Chen, Hong; Wang, Ning; Lin, Hong

    2016-08-24

    Perovskite solar cells (PSCs) with TiO2 materials have attracted much attention due to their high photovoltaic performance. Aligned TiO2 nanorods have long been used for potential application in highly efficient perovskite solar cells, but the previously reported efficiencies of perovskite solar cells based on TiO2 nanorod arrays were underrated. Here we show a solvothermal method based on a modified ketone-HCl system with the addition of organic acids suitable for modulation of the TiO2 nanorod array films to fabricate highly efficient perovskite solar cells. Photovoltaic measurements indicated that efficient nanorod-structured perovskite solar cells can be achieved with the length of the nanorods as long as approximately 200 nm. A record efficiency of 18.22% under the reverse scan direction has been optimized by avoiding direct contact between the TiO2 nanorods and the hole transport materials, eliminating the organic residues on the nanorod surfaces using UV-ozone treatment and tuning the nanorod array morphologies through addition of different organic acids in the solvothermal process.

  14. Efficient Perovskite Solar Cells Depending on TiO2 Nanorod Arrays.

    Science.gov (United States)

    Li, Xin; Dai, Si-Min; Zhu, Pei; Deng, Lin-Long; Xie, Su-Yuan; Cui, Qian; Chen, Hong; Wang, Ning; Lin, Hong

    2016-08-24

    Perovskite solar cells (PSCs) with TiO2 materials have attracted much attention due to their high photovoltaic performance. Aligned TiO2 nanorods have long been used for potential application in highly efficient perovskite solar cells, but the previously reported efficiencies of perovskite solar cells based on TiO2 nanorod arrays were underrated. Here we show a solvothermal method based on a modified ketone-HCl system with the addition of organic acids suitable for modulation of the TiO2 nanorod array films to fabricate highly efficient perovskite solar cells. Photovoltaic measurements indicated that efficient nanorod-structured perovskite solar cells can be achieved with the length of the nanorods as long as approximately 200 nm. A record efficiency of 18.22% under the reverse scan direction has been optimized by avoiding direct contact between the TiO2 nanorods and the hole transport materials, eliminating the organic residues on the nanorod surfaces using UV-ozone treatment and tuning the nanorod array morphologies through addition of different organic acids in the solvothermal process. PMID:27480286

  15. Cell culture arrays using micron-sized ferromagnetic ring-shaped thin films

    International Nuclear Information System (INIS)

    Cell patterning has become an important technology for tissue engineering. In this research, domain walls are formed at the two ends of a ferromagnetic ring thin film after applying a strong external magnetic field, which can effectively attract magnetically labeled cells and control the position for biological cell. Magnetophoresis experiment was conducted to quantify the magnetic nanoparticle inside the cells. A ring-shaped magnetic thin films array was fabricated through photolithography. It is observed that magnetically labeled cells can be successfully attracted to the two ends of the ring-shaped magnetic thin film structure and more cells were attracted and further attached to the structures. The cells are co-cultured with the structure and kept proliferating; therefore, such ring thin film can be an important candidate for in-vitro biomedical chips or tissue engineering

  16. Cell culture arrays using micron-sized ferromagnetic ring-shaped thin films

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Chen-Yu; Wei, Zung-Hang, E-mail: wei@pme.nthu.edu.tw [Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu City 300, Taiwan (China); Lai, Mei-Feng; Ger, Tzong-Rong [Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu City 300, Taiwan (China)

    2015-05-07

    Cell patterning has become an important technology for tissue engineering. In this research, domain walls are formed at the two ends of a ferromagnetic ring thin film after applying a strong external magnetic field, which can effectively attract magnetically labeled cells and control the position for biological cell. Magnetophoresis experiment was conducted to quantify the magnetic nanoparticle inside the cells. A ring-shaped magnetic thin films array was fabricated through photolithography. It is observed that magnetically labeled cells can be successfully attracted to the two ends of the ring-shaped magnetic thin film structure and more cells were attracted and further attached to the structures. The cells are co-cultured with the structure and kept proliferating; therefore, such ring thin film can be an important candidate for in-vitro biomedical chips or tissue engineering.

  17. Cell motility regulation on a stepped micro pillar array device (SMPAD) with a discrete stiffness gradient.

    Science.gov (United States)

    Lee, Sujin; Hong, Juhee; Lee, Junghoon

    2016-02-28

    Our tissues consist of individual cells that respond to the elasticity of their environment, which varies between and within tissues. To better understand mechanically driven cell migration, it is necessary to manipulate the stiffness gradient across a substrate. Here, we have demonstrated a new variant of the microfabricated polymeric pillar array platform that can decouple the stiffness gradient from the ECM protein area. This goal is achieved via a "stepped" micro pillar array device (SMPAD) in which the contact area with the cell was kept constant while the diameter of the pillar bodies was altered to attain the proper mechanical stiffness. Using double-step SU-8 mold fabrication, the diameter of the top of every pillar was kept uniform, whereas that of the bottom was changed, to achieve the desired substrate rigidity. Fibronectin was immobilized on the pillar tops, providing a focal adhesion site for cells. C2C12, HeLa and NIH3T3 cells were cultured on the SMPAD, and the motion of the cells was observed by time-lapse microscopy. Using this simple platform, which produces a purely physical stimulus, we observed that various types of cell behavior are affected by the mechanical stimulus of the environment. We also demonstrated directed cell migration guided by a discrete rigidity gradient by varying stiffness. Interestingly, cell velocity was highest at the highest stiffness. Our approach enables the regulation of the mechanical properties of the polymeric pillar array device and eliminates the effects of the size of the contact area. This technique is a unique tool for studying cellular motion and behavior relative to various stiffness gradients in the environment. PMID:26787193

  18. Phenomic assessment of genetic buffering by kinetic analysis of cell arrays.

    Science.gov (United States)

    Rodgers, John; Guo, Jingyu; Hartman, John L

    2014-01-01

    Quantitative high-throughput cell array phenotyping (Q-HTCP) is applied to the genomic collection of yeast gene deletion mutants for systematic, comprehensive assessment of the contribution of genes and gene combinations to any phenotype of interest (phenomic analysis). Interacting gene networks influence every phenotype. Genetic buffering refers to how gene interaction networks stabilize or destabilize a phenotype. Like genomics, phenomics varies in its resolution with there being a trade-off allocating a greater number of measurements per sample to enhance quantification of the phenotype vs. increasing the number of different samples by obtaining fewer measurements per sample. The Q-HTCP protocol we describe assesses 50,000-70,000 cultures per experiment by obtaining kinetic growth curves from time series imaging of agar cell arrays. This approach was developed for the yeast gene deletion strains, but it could be applied as well to other microbial mutant arrays grown on solid agar media. The methods we describe are for creation and maintenance of frozen stocks, liquid source array preparation, agar destination plate printing, image scanning, image analysis, curve fitting, and evaluation of gene interaction. PMID:25213246

  19. A 16 × 16 CMOS Capacitive Biosensor Array Towards Detection of Single Bacterial Cell.

    Science.gov (United States)

    Couniot, Numa; Francis, Laurent A; Flandre, Denis

    2016-04-01

    We present a 16 × 16 CMOS biosensor array aiming at impedance detection of whole-cell bacteria. Each 14 μm × 16 μm pixel comprises high-sensitive passivated microelectrodes connected to an innovative readout interface based on charge sharing principle for capacitance-to-voltage conversion and subthreshold gain stage to boost the sensitivity. Fabricated in a 0.25 μm CMOS process, the capacitive array was experimentally shown to perform accurate dielectric measurements of the electrolyte up to electrical conductivities of 0.05 S/m, with maximal sensitivity of 55 mV/fF and signal-to-noise ratio (SNR) of 37 dB. As biosensing proof of concept, real-time detection of Staphylococcus epidermidis binding events was experimentally demonstrated and provides detection limit of ca. 7 bacteria per pixel and sensitivity of 2.18 mV per bacterial cell. Models and simulations show good matching with experimental results and provide a comprehensive analysis of the sensor and circuit system. Advantages, challenges and limits of the proposed capacitive biosensor array are finally described with regards to literature. With its small area and low power consumption, the present capacitive array is particularly suitable for portable point-of-care (PoC) diagnosis tools and lab-on-chip (LoC) systems. PMID:25974947

  20. Efficiency of dense-array CPVT module with front-side interconnected cells

    Science.gov (United States)

    Polonsky, G.; Shelef, G.; Flitsanov, Y.; Wiesenfarth, M.; Steiner, M.; Helmers, H.; Bett, A. W.; Kribus, A.

    2013-09-01

    Dense array concentrating photovoltaic collectors can be used as cogeneration systems, CPV and thermal (CPVT), producing both electricity and heat, leading to high overall system efficiency. Triple-junction metamorphic III-V cells with front side interconnections were developed to minimize the spacing among the cells and maximize the active area that intercepts the concentrated radiation. Modules with front interconnected cells and active cooling were fabricated and tested outdoors in a parabolic dish under a range of temperatures. Performance of the modules and the dependence on operating temperatures are reported.

  1. A Multi-Modality CMOS Sensor Array for Cell-Based Assay and Drug Screening.

    Science.gov (United States)

    Chi, Taiyun; Park, Jong Seok; Butts, Jessica C; Hookway, Tracy A; Su, Amy; Zhu, Chengjie; Styczynski, Mark P; McDevitt, Todd C; Wang, Hua

    2015-12-01

    In this paper, we present a fully integrated multi-modality CMOS cellular sensor array with four sensing modalities to characterize different cell physiological responses, including extracellular voltage recording, cellular impedance mapping, optical detection with shadow imaging and bioluminescence sensing, and thermal monitoring. The sensor array consists of nine parallel pixel groups and nine corresponding signal conditioning blocks. Each pixel group comprises one temperature sensor and 16 tri-modality sensor pixels, while each tri-modality sensor pixel can be independently configured for extracellular voltage recording, cellular impedance measurement (voltage excitation/current sensing), and optical detection. This sensor array supports multi-modality cellular sensing at the pixel level, which enables holistic cell characterization and joint-modality physiological monitoring on the same cellular sample with a pixel resolution of 80 μm × 100 μm. Comprehensive biological experiments with different living cell samples demonstrate the functionality and benefit of the proposed multi-modality sensing in cell-based assay and drug screening.

  2. Single-cell transcriptome analyses reveal signals to activate dormant neural stem cells.

    Science.gov (United States)

    Luo, Yuping; Coskun, Volkan; Liang, Aibing; Yu, Juehua; Cheng, Liming; Ge, Weihong; Shi, Zhanping; Zhang, Kunshan; Li, Chun; Cui, Yaru; Lin, Haijun; Luo, Dandan; Wang, Junbang; Lin, Connie; Dai, Zachary; Zhu, Hongwen; Zhang, Jun; Liu, Jie; Liu, Hailiang; deVellis, Jean; Horvath, Steve; Sun, Yi Eve; Li, Siguang

    2015-05-21

    The scarcity of tissue-specific stem cells and the complexity of their surrounding environment have made molecular characterization of these cells particularly challenging. Through single-cell transcriptome and weighted gene co-expression network analysis (WGCNA), we uncovered molecular properties of CD133(+)/GFAP(-) ependymal (E) cells in the adult mouse forebrain neurogenic zone. Surprisingly, prominent hub genes of the gene network unique to ependymal CD133(+)/GFAP(-) quiescent cells were enriched for immune-responsive genes, as well as genes encoding receptors for angiogenic factors. Administration of vascular endothelial growth factor (VEGF) activated CD133(+) ependymal neural stem cells (NSCs), lining not only the lateral but also the fourth ventricles and, together with basic fibroblast growth factor (bFGF), elicited subsequent neural lineage differentiation and migration. This study revealed the existence of dormant ependymal NSCs throughout the ventricular surface of the CNS, as well as signals abundant after injury for their activation. PMID:26000486

  3. Electric Cell-Substrate Impedance Sensing (ECIS with Microelectrode Arrays for Investigation of Cancer Cell - Fibroblasts Interaction.

    Directory of Open Access Journals (Sweden)

    Trong Binh Tran

    Full Text Available The tumor microenvironment, including stromal cells, surrounding blood vessels and extracellular matrix components, has been defined as a crucial factor that influences the proliferation, drug-resistance, invasion and metastasis of malignant epithelial cells. Among other factors, the communications and interaction between cancer cells and stromal cells have been reported to play pivotal roles in cancer promotion and progression. To investigate these relationships, an on-chip co-culture model was developed to study the cellular interaction between A549-human lung carcinoma cells and MRC-5-human lung epithelial cells in both normal proliferation and treatment conditions. In brief, a co-culture device consisting of 2 individual fluidic chambers in parallel, which were separated by a 100 μm fence was utilized for cell patterning. Microelectrodes arrays were installed within each chamber including electrodes at various distances away from the confrontation line for the electrochemical impedimetric sensing assessment of cell-to-cell influence. After the fence was removed and cell-to-cell contact occurred, by evaluating the impedance signal responses representing cell condition and behavior, both direct and indirect cell-to-cell interactions through conditioned media were investigated. The impact of specific distances that lead to different influences of fibroblast cells on cancer cells in the co-culture environment was also defined.

  4. Electric Cell-Substrate Impedance Sensing (ECIS) with Microelectrode Arrays for Investigation of Cancer Cell – Fibroblasts Interaction

    Science.gov (United States)

    Tran, Trong Binh; Baek, Changyoon; Min, Junhong

    2016-01-01

    The tumor microenvironment, including stromal cells, surrounding blood vessels and extracellular matrix components, has been defined as a crucial factor that influences the proliferation, drug-resistance, invasion and metastasis of malignant epithelial cells. Among other factors, the communications and interaction between cancer cells and stromal cells have been reported to play pivotal roles in cancer promotion and progression. To investigate these relationships, an on-chip co-culture model was developed to study the cellular interaction between A549—human lung carcinoma cells and MRC-5—human lung epithelial cells in both normal proliferation and treatment conditions. In brief, a co-culture device consisting of 2 individual fluidic chambers in parallel, which were separated by a 100 μm fence was utilized for cell patterning. Microelectrodes arrays were installed within each chamber including electrodes at various distances away from the confrontation line for the electrochemical impedimetric sensing assessment of cell-to-cell influence. After the fence was removed and cell-to-cell contact occurred, by evaluating the impedance signal responses representing cell condition and behavior, both direct and indirect cell-to-cell interactions through conditioned media were investigated. The impact of specific distances that lead to different influences of fibroblast cells on cancer cells in the co-culture environment was also defined. PMID:27088611

  5. Time-Resolved Study of Nanoparticle Induced Apoptosis Using Microfabricated Single Cell Arrays.

    Science.gov (United States)

    Röttgermann, Peter J F; Dawson, Kenneth A; Rädler, Joachim O

    2016-01-01

    Cell fate decisions like apoptosis are heterogeneously implemented within a cell population and, consequently, the population response is recognized as sum of many individual dynamic events. Here, we report on the use of micro-patterned single-cell arrays for real-time tracking of nanoparticle-induced (NP) cell death in sets of thousands of cells in parallel. Annexin (pSIVA) and propidium iodide (PI), two fluorescent indicators of apoptosis, are simultaneously monitored after exposure to functionalized polystyrene (PS - NH 2) nanobeads as a model system. We find that the distribution of Annexin onset times shifts to later times and broadens as a function of decreasing NP dose. We discuss the mean time-to-death as a function of dose, and show how the EC 50 value depends both on dose and time of measurement. In addition, the correlations between the early and late apoptotic markers indicate a systematic shift from apoptotic towards necrotic cell death during the course of the experiment. Thus, our work demonstrates the potential of array-based single cell cytometry for kinetic analysis of signaling cascades in a high-throughput format. PMID:27600074

  6. Analytical cell adhesion chromatography reveals impaired persistence of metastatic cell rolling adhesion to P-selectin.

    Science.gov (United States)

    Oh, Jaeho; Edwards, Erin E; McClatchey, P Mason; Thomas, Susan N

    2015-10-15

    Selectins facilitate the recruitment of circulating cells from the bloodstream by mediating rolling adhesion, which initiates the cell-cell signaling that directs extravasation into surrounding tissues. To measure the relative efficiency of cell adhesion in shear flow for in vitro drug screening, we designed and implemented a microfluidic-based analytical cell adhesion chromatography system. The juxtaposition of instantaneous rolling velocities with elution times revealed that human metastatic cancer cells, but not human leukocytes, had a reduced capacity to sustain rolling adhesion with P-selectin. We define a new parameter, termed adhesion persistence, which is conceptually similar to migration persistence in the context of chemotaxis, but instead describes the capacity of cells to resist the influence of shear flow and sustain rolling interactions with an adhesive substrate that might modulate the probability of extravasation. Among cell types assayed, adhesion persistence to P-selectin was specifically reduced in metastatic but not leukocyte-like cells in response to a low dose of heparin. In conclusion, we demonstrate this as an effective methodology to identify selectin adhesion antagonist doses that modulate homing cell adhesion and engraftment in a cell-subtype-selective manner.

  7. Cell-to-Cell Diversity in a Synchronized Chlamydomonas Culture As Revealed by Single-Cell Analyses

    OpenAIRE

    Garz, Andreas; Sandmann, Michael; Rading, Michael; Ramm, Sascha; Menzel, Ralf; Steup, Martin

    2012-01-01

    In a synchronized photoautotrophic culture of Chlamydomonas reinhardtii, cell size, cell number, and the averaged starch content were determined throughout the light-dark cycle. For single-cell analyses, the relative cellular starch was quantified by measuring the second harmonic generation (SHG). In destained cells, amylopectin essentially represents the only biophotonic structure. As revealed by various validation procedures, SHG signal intensities are a reliable relative measure of the cel...

  8. Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements.

    Energy Technology Data Exchange (ETDEWEB)

    Leem, Sun-Hee; Kouprina, Natalay; Grimwood, Jane; Kim, Jung-Hyun; Mullokandov, Michael; Yoon, Young-Ho; Chae, Ji-Youn; Morgan, Jenna; Lucas, Susan; Richardson, Paul; Detter, Chris; Glavina, Tijana; Rubin, Eddy; Barrett, J. Carl; Larionov, Vladimir

    2003-09-01

    The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to {approx} 1 percent of euchromatic regions of the human genome. Gap filling is a laborious process because it relies on analysis of random clones of numerous genomic BAC or cosmid libraries. In this work we demonstrate that closing the gaps can be accelerated by a selective recombinational capture of missing chromosomal segments in yeast. The use of both methodologies allowed us to close the four remaining gaps on the human chromosome 19. Analysis of the gap sequences revealed that they contain several abnormalities that could result in instability of the sequences in microbe hosts, including large blocks of micro- and minisatellites and a high density of Alu repeats. Sequencing of the gap regions, in both BAC and YAC forms, allowed us to generate a complete sequence of four genes, including the neuronal cell signaling gene SCK1/SLI. The SCK1/SLI gene contains a record number of minisatellites, most of which are polymorphic and transmitted through meiosis following a Mendelian inheritance. In conclusion, the use of the alternative recombinational cloning system in yeast may greatly accelerate work on closing the remaining gaps in the human genome (as well as in other complex genomes) to achieve the goal of annotation of all human genes.

  9. Water management in a planar air-breathing fuel cell array using operando neutron imaging

    Science.gov (United States)

    Coz, E.; Théry, J.; Boillat, P.; Faucheux, V.; Alincant, D.; Capron, P.; Gébel, G.

    2016-11-01

    Operando Neutron imaging is used for the investigation of a planar air-breathing array comprising multiple cells in series. The fuel cell demonstrates a stable power density level of 150 mW/cm2. Water distribution and quantification is carried out at different operating points. Drying at high current density is observed and correlated to self-heating and natural convection. Working in dead-end mode, water accumulation at lower current density is largely observed on the anode side. However, flooding mechanisms are found to begin with water condensation on the cathode side, leading to back-diffusion and anodic flooding. Specific in-plane and through-plane water distribution is observed and linked to the planar array design.

  10. An Automated High-throughput Array Microscope for Cancer Cell Mechanics

    OpenAIRE

    Cribb, Jeremy A.; Osborne, Lukas D.; Kellie Beicker; Matthew Psioda; Jian Chen; E. Timothy O’Brien; Taylor II, Russell M.; Leandra Vicci; Joe Ping-Lin Hsiao; Chong Shao; Michael Falvo; Ibrahim, Joseph G.; Wood, Kris C.; Blobe, Gerard C.; Richard Superfine

    2016-01-01

    Changes in cellular mechanical properties correlate with the progression of metastatic cancer along the epithelial-to-mesenchymal transition (EMT). Few high-throughput methodologies exist that measure cell compliance, which can be used to understand the impact of genetic alterations or to screen the efficacy of chemotherapeutic agents. We have developed a novel array high-throughput microscope (AHTM) system that combines the convenience of the standard 96-well plate with the ability to image ...

  11. Core-Shell Nanopillar Array Solar Cells using Cadmium Sulfide Coating on Indium Phosphide Nanopillars

    OpenAIRE

    Tu, Bor-An Clayton

    2013-01-01

    This thesis presents a new strategy to fabricate nanostructured indium phosphide and cadmium sulfide photovoltaics. The cells are formed by chemical bath deposition (electroless deposition) of cadmium sulfide onto indium phosphide nanopillar arrays grown by selective-area metalorganic chemical vapor deposition. Characterizations through electrical and optical measurements show that the devices consisting of p-InP core and CdS shell have a conversion efficiency, open circuit voltage, short cir...

  12. The status of lightweight photovoltaic space array technology based on amorphous silicon solar cells

    Science.gov (United States)

    Hanak, Joseph J.; Kaschmitter, Jim

    1991-01-01

    Ultralight, flexible photovoltaic (PV) array of amorphous silicon (a-Si) was identified as a potential low cost power source for small satellites. A survey was conducted of the status of the a-Si PV array technology with respect to present and future performance, availability, cost, and risks. For existing, experimental array blankets made of commercial cell material, utilizing metal foil substrates, the Beginning of Life (BOL) performance at Air Mass Zero (AM0) and 35 C includes total power up to 200 W, power per area of 64 W/sq m and power per weight of 258 W/kg. Doubling of power per weight occurs when polyimide substrates are used. Estimated End of Life (EOL) power output after 10 years in a nominal low earth orbit would be 80 pct. of BOL, the degradation being due to largely light induced effects (-10 to -15 pct.) and in part (-5 pct.) to space radiation. Predictions for the year 1995 for flexible PV arrays, made on the basis of published results for rigid a-Si modules, indicate EOL power output per area and per weight of 105 W/sq m and 400 W/kg, respectively, while predictions for the late 1990s based on existing U.S. national PV program goals indicate EOL values of 157 W/sq m and 600 W/kg. Cost estimates by vendors for 200 W ultralight arrays in volume of over 1000 units range from $100/watt to $125/watt. Identified risks include the lack of flexible, space compatible encapsulant, the lack of space qualification effort, recent partial or full acquisitions of US manufacturers of a-Si cells by foreign firms, and the absence of a national commitment for a long range development program toward developing of this important power source for space.

  13. Genomic and expression array profiling of chromosome 20q amplicon in human colon cancer cells

    Directory of Open Access Journals (Sweden)

    Carter Jennifer

    2005-01-01

    Full Text Available Background: Gain of the q arm of chromosome 20 in human colorectal cancer has been associated with poorer survival time and has been reported to increase in frequency from adenomas to metastasis. The increasing frequency of chromosome 20q amplification during colorectal cancer progression and the presence of this amplification in carcinomas of other tissue origin has lead us to hypothesize that 20q11-13 harbors one or more genes which, when over expressed promote tumor invasion and metastasis. Aims: Generate genomic and expression profiles of the 20q amplicon in human cancer cell lines in order to identify genes with increased copy number and expression. Materials and Methods: Utilizing genomic sequencing clones and amplification mapping data from our lab and other previous studies, BAC/ PAC tiling paths spanning the 20q amplicon and genomic microarrays were generated. Array-CGH on the custom array with human cancer cell line DNAs was performed to generate genomic profiles of the amplicon. Expression array analysis with RNA from these cell lines using commercial oligo microarrays generated expression profiles of the amplicon. The data were then combined in order to identify genes with increased copy number and expression. Results: Over expressed genes in regions of increased copy number were identified and a list of potential novel genetic tumor markers was assembled based on biological functions of these genes Conclusions: Performing high-resolution genomic microarray profiling in conjunction with expression analysis is an effective approach to identify potential tumor markers.

  14. Reproducible isolation of lymph node stromal cells reveals site-dependent differences in fibroblastic reticular cells

    Directory of Open Access Journals (Sweden)

    Anne L Fletcher

    2011-09-01

    Full Text Available Within lymph nodes, non-hematopoietic stromal cells organize and interact with leukocytes in an immunologically important manner. In addition to organizing T and B cell segregation and expressing lymphocyte survival factors, several recent studies have shown that lymph node stromal cells shape the naïve T cell repertoire, expressing self-antigens which delete self-reactive T cells in a unique and non-redundant fashion. A fundamental role in peripheral tolerance, in addition to an otherwise extensive functional portfolio, necessitates closer study of lymph node stromal cell subsets using modern immunological techniques; however this has not routinely been possible in the field, due to difficulties reproducibly isolating these rare subsets. Techniques were therefore developed for successful ex vivo and in vitro manipulation and characterization of lymph node stroma. Here we discuss and validate these techniques in mice and humans, and apply them to address several unanswered questions regarding lymph node composition. We explored the steady-state stromal composition of lymph nodes isolated from mice and humans, and found that marginal reticular cells and lymphatic endothelial cells required lymphocytes for their normal maturation in mice. We also report alterations in the proportion and number of fibroblastic reticular cells (FRCs between skin-draining and mesenteric lymph nodes. Similarly, transcriptional profiling of FRCs revealed changes in cytokine production from these sites. Together, these methods permit highly reproducible stromal cell isolation, sorting, and culture.

  15. Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis

    OpenAIRE

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    In a previous study origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L) on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number o...

  16. Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis

    OpenAIRE

    Amlan Kumar Patra; Zhongtang eYu

    2015-01-01

    In a previous study origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L), on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number ...

  17. A novel isoform of MAP4 organises the paraxial microtubule array required for muscle cell differentiation.

    Science.gov (United States)

    Mogessie, Binyam; Roth, Daniel; Rahil, Zainab; Straube, Anne

    2015-01-01

    The microtubule cytoskeleton is critical for muscle cell differentiation and undergoes reorganisation into an array of paraxial microtubules, which serves as template for contractile sarcomere formation. In this study, we identify a previously uncharacterised isoform of microtubule-associated protein MAP4, oMAP4, as a microtubule organising factor that is crucial for myogenesis. We show that oMAP4 is expressed upon muscle cell differentiation and is the only MAP4 isoform essential for normal progression of the myogenic differentiation programme. Depletion of oMAP4 impairs cell elongation and cell-cell fusion. Most notably, oMAP4 is required for paraxial microtubule organisation in muscle cells and prevents dynein- and kinesin-driven microtubule-microtubule sliding. Purified oMAP4 aligns dynamic microtubules into antiparallel bundles that withstand motor forces in vitro. We propose a model in which the cooperation of dynein-mediated microtubule transport and oMAP4-mediated zippering of microtubules drives formation of a paraxial microtubule array that provides critical support for the polarisation and elongation of myotubes. PMID:25898002

  18. Silicon microhole arrays architecture for stable and efficient photoelectrochemical cells using ionic liquids electrolytes

    Science.gov (United States)

    Shen, Xiaojuan; Chen, Ling; Li, Junnan; Zhao, Jie

    2016-06-01

    Silicon microhole arrays (SiMHs) structure is constructed and fabricated by a low-cost maskless anodic etching process, which is applied as the photoanode for the silicon photoelectrochemical (PEC) cells. The depths of silicon microhole arrays can be independently controlled by the etching time. The light-scattering properties are also investigated. Additionally, surface morphology analysis show that large hole diameters of SiMHs is very favourable for the full-filling of ionic liquids electrolyte. Therefore, better electrochemical contact as well as high ionic conductivity of the ionic liquids electrolyte renders the PEC SiMHs solar cells to exhibit more excellent performance. After optimization, the maximum PCE could be achieved at 4.04% for the SiMHs cell. The performance of the SiMHs cell is highly comparable to that of silicon nanowires cell. More importantly, the liquid-state electrolyte is confined in the unique microhole structure, which can obviously prevent the leakage of the ionic liquids electrolyte, resulting in much better long-term stability than the reference devices. These preliminary results validate the concept of interpenetrating networks with semiconductor structure/ILs junction to develop stable and efficient PEC cells.

  19. Cytokine-dependent and–independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling

    Directory of Open Access Journals (Sweden)

    Burleigh Barbara A

    2009-05-01

    Full Text Available Abstract Background The requirements for growth and survival of the intracellular pathogen Trypanosoma cruzi within mammalian host cells are poorly understood. Transcriptional profiling of the host cell response to infection serves as a rapid read-out for perturbation of host physiology that, in part, reflects adaptation to the infective process. Using Affymetrix oligonucleotide array analysis we identified common and disparate host cell responses triggered by T. cruzi infection of phenotypically diverse human cell types. Results We report significant changes in transcript abundance in T. cruzi-infected fibroblasts, endothelial cells and smooth muscle cells (2852, 2155 and 531 genes respectively; fold-change ≥ 2, p-value T. cruzi-infected fibroblasts and endothelial cells transwell plates were used to distinguish cytokine-dependent and -independent gene expression profiles. This approach revealed the induction of metabolic and signaling pathways involved in cell proliferation, amino acid catabolism and response to wounding as common themes in T. cruzi-infected cells. In addition, the downregulation of genes involved in mitotic cell cycle and cell division predicted that T. cruzi infection may impede host cell cycle progression. The observation of impaired cytokinesis in T. cruzi-infected cells, following nuclear replication, confirmed this prediction. Conclusion Metabolic pathways and cellular processes were identified as significantly altered at the transcriptional level in response to T. cruzi infection in a cytokine-independent manner. Several of these alterations are supported by previous studies of T. cruzi metabolic requirements or effects on the host. However, our methods also revealed a T. cruzi-dependent block in the host cell cycle, at the level of cytokinesis, previously unrecognized for this pathogen-host cell interaction.

  20. Preliminary study of the influence of solar cell degradation due to ESD on solar array power generation

    OpenAIRE

    Okumura, Teppei; Toyoda, Kazuhiro; Kawakita, Shiro; Imaizumi, Mitsuru; 奥村 哲平; 豊田 和弘; 川北 史朗; 今泉 充; Cho, Mengu

    2008-01-01

    In space, an ElectroStatic Discharge (ESD) can occur on a solar array due to the plasma interaction. One of the issues of ESD is the degradation of solar cell electric performance. To establish the power degradation estimation method due to ESD in solar arrays, light current-voltage characteristics are evaluated in the current value at maximum power. From the results of the calculation, InGaP/GaAs/Ge solar arrays potentially suffer more serious power degradation than Si solar array.

  1. Spinal cord injury reveals multilineage differentiation of ependymal cells.

    Directory of Open Access Journals (Sweden)

    Konstantinos Meletis

    2008-07-01

    Full Text Available Spinal cord injury often results in permanent functional impairment. Neural stem cells present in the adult spinal cord can be expanded in vitro and improve recovery when transplanted to the injured spinal cord, demonstrating the presence of cells that can promote regeneration but that normally fail to do so efficiently. Using genetic fate mapping, we show that close to all in vitro neural stem cell potential in the adult spinal cord resides within the population of ependymal cells lining the central canal. These cells are recruited by spinal cord injury and produce not only scar-forming glial cells, but also, to a lesser degree, oligodendrocytes. Modulating the fate of ependymal progeny after spinal cord injury may offer an alternative to cell transplantation for cell replacement therapies in spinal cord injury.

  2. A DP based scheme for real-time reconfiguration of solar cell arrays exposed to dynamic changing inhomogeneous illuminations

    DEFF Research Database (Denmark)

    Shi, Liping; Brehm, Robert

    2016-01-01

    The overall energy conversion efficiency of solar cell arrays is highly effected by partial shading effects. Especially for solar panel arrays installed in environments which are exposed to inhomogeneous dynamic changing illuminations such as on roof tops of electrical vehicles the overall system...... efficiency is drastically reduced. Dynamic real-time reconfiguration of the solar panel array can reduce effects on the output efficiency due to partial shading. This results in a maximized power output of the panel array when exposed to dynamic changing illuminations. The optimal array configuration...... with respect to shading patterns can be stated as a combinatorial optimization problem and this paper proposes a dynamic programming (DP) based algorithm which finds the optimal feasible solution to reconfigure the solar panel array for maximum efficiency in real-time with linear time complexity. It is shown...

  3. A novel stretchable micro-electrode array (SMEA) design for directional stretching of cells

    International Nuclear Information System (INIS)

    Stretchable micro-electrode arrays (SMEAs) are useful tools to study the electrophysiology of living cells seeded on the devices under mechanical stimulation. For such applications, the SMEAs are used as cell culture substrates; therefore, the surface topography and mechanical properties of the devices should be minimally affected by the embedded stretchable electrical interconnects. In this paper, a novel design and micro-fabrication technology for a pneumatically actuated SMEA are presented to achieve stretchability with minimal surface area dedicated to the electrical interconnects and a well-defined surface strain distribution combined with integrated diverse micro-patterns to enable alignment and directional stretching of cells. The special mechanical design also enables the SMEA to have a prolonged electro-mechanical fatigue life time required for long-term cyclic stretching of the cell cultures (stable resistance of electrical interconnects for more than 160 thousand cycles of 20% stretching and relaxing). The proposed fabrication method is based on the state of the art micro-fabrication techniques and materials and circumvents the processing problems associated with using unconventional methods and materials to fabricate stretchable electrode arrays. The electrochemical impedance spectroscopy characterization of the SMEA shows 4.5 MΩ impedance magnitude at 1 kHz for a TiN electrode 12 um in diameter. Cell culture experiments demonstrate the robustness of the SMEAs for long-term culturing experiments and compatibility with inverted fluorescent microscopy. (paper)

  4. Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC).

    Science.gov (United States)

    Todhunter, Michael E; Weber, Robert J; Farlow, Justin; Jee, Noel Y; Cerchiari, Alec E; Gartner, Zev J

    2016-01-01

    Tissues are the organizational units of function in metazoan organisms. Tissues comprise an assortment of cellular building blocks, soluble factors, and extracellular matrix (ECM) composed into specific three-dimensional (3-D) structures. The capacity to reconstitute tissues in vitro with the structural complexity observed in vivo is key to understanding processes such as morphogenesis, homeostasis, and disease. In this article, we describe DNA-programmed assembly of cells (DPAC), a method to fabricate viable, functional arrays of organoid-like tissues within 3-D ECM gels. In DPAC, dissociated cells are chemically functionalized with degradable oligonucleotide "Velcro," allowing rapid, specific, and reversible cell adhesion to a two-dimensional (2-D) template patterned with complementary DNA. An iterative assembly process builds up organoids, layer-by-layer, from this initial 2-D template and into the third dimension. Cleavage of the DNA releases the completed array of tissues that are captured and fully embedded in ECM gels for culture and observation. DPAC controls the size, shape, composition, and spatial heterogeneity of organoids and permits positioning of constituent cells with single-cell resolution even within cultures several centimeters long. © 2016 by John Wiley & Sons, Inc. PMID:27622567

  5. Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

    Directory of Open Access Journals (Sweden)

    Zadeh Soheila

    2010-07-01

    Full Text Available Abstract Background HER2 gene copy status, and concomitant administration of trastuzumab (Herceptin, remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC and fluorescence in situ hybridization (FISH are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods. Methods In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms. Results Array-based comparative genomic hybridization (array CGH analysis of chromosome 17 resolved HER2 gene status in [20/20] (100% of cases and revealed additional chromosome 17 copy number changes in [18/20] (90% of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to "ratio skewing" caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability. Conclusions These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17

  6. A MULTIPLEXED ASSAY FOR DETERMINATION OF NEUROTOXICANT EFFECTS ON SPONTANEOUS NETWORK ACTIVITY AND CELL VIABILITY FROM MICROELECTRODE ARRAYS

    Science.gov (United States)

    AbstractTITLE: A MULTIPLEXED ASSAY FOR DETERMINATION OF NEUROTOXICANT EFFECTS ON SPONTANEOUS NETWORK ACTIVITY AND CELL VIABILITY FROM MICROELECTRODE ARRAYSABSTRACT BODY: Microelectrode array (MEA) recordings are increasingly being used as an in vitro method to detect and characte...

  7. Backside illuminated dye-sensitized solar cells based on titania nanotube array electrodes

    Science.gov (United States)

    Paulose, Maggie; Shankar, Karthik; Varghese, Oomman K.; Mor, Gopal K.; Hardin, Brian; Grimes, Craig A.

    2006-03-01

    Backside illuminated solar cells based on 6 µm long highly-ordered nanotube-array films sensitized by a self-assembled monolayer of bis(tetrabutylammonium)-cis-(dithiocyanato)- N,N'-bis(4-carboxylato-4'-carboxylic acid-2, 2'-bipyridine)ruthenium(II) (commonly called 'N719') show a short-circuit current density of 8.79 mA cm-2, 841 mV open circuit potential and a 0.57 fill factor yielding a power conversion efficiency of 4.24% under AM 1.5 sun. The solvent used to infiltrate the dye into the nanotube arrays, made by potentiostatic anodization of a titanium foil, was found to significantly influence the electrical characteristics of the resulting solar cell. A superior photoresponse was obtained with acetonitrile as the dye solvent. This is attributed to the improved wetting characteristics of the dye solution in acetonitrile enabling self-assembled monolayers with higher surface coverage to be formed inside the nanotubes. In comparison to nanocrystalline films, the nanotube-array films consistently exhibit larger open circuit photovoltage values; the origins of this enhancement are discussed.

  8. Inorganic/organic hybrid solar cells: optimal carrier transport in vertically aligned silicon nanowire arrays

    Science.gov (United States)

    Sato, Keisuke; Dutta, Mrinal; Fukata, Naoki

    2014-05-01

    Inorganic/organic hybrid radial heterojunction solar cells that combine vertically-aligned n-type silicon nanowires (SiNWs) with poly(3,4-ethylenedioxythiophene):poly(styrene-sulfonate) (PEDOT:PSS) have great potential for replacing commercial Si solar cells. The chief advantage of such solar cells is that they exhibit higher absorbance for a given thickness than commercial Si solar cells, due to incident light-trapping within the NW arrays, thus enabling lower-cost solar cell production. We report herein on the effects of NW length, annealing and surface electrode on the device performance of SiNW/PEDOT:PSS hybrid radial heterojunction solar cells. The power conversion efficiency (PCE) of the obtained SiNW/PEDOT:PSS hybrid solar cells can be optimized by tuning the thickness of the surface electrode, and the etching conditions during NW formation and post-annealing. The PCE of 9.3% is obtained by forming efficient transport pathways for photogenerated charge carriers to electrodes. Our approach is a significant contribution to design of high-performance and low-cost inorganic/organic hybrid heterojunction solar cells.Inorganic/organic hybrid radial heterojunction solar cells that combine vertically-aligned n-type silicon nanowires (SiNWs) with poly(3,4-ethylenedioxythiophene):poly(styrene-sulfonate) (PEDOT:PSS) have great potential for replacing commercial Si solar cells. The chief advantage of such solar cells is that they exhibit higher absorbance for a given thickness than commercial Si solar cells, due to incident light-trapping within the NW arrays, thus enabling lower-cost solar cell production. We report herein on the effects of NW length, annealing and surface electrode on the device performance of SiNW/PEDOT:PSS hybrid radial heterojunction solar cells. The power conversion efficiency (PCE) of the obtained SiNW/PEDOT:PSS hybrid solar cells can be optimized by tuning the thickness of the surface electrode, and the etching conditions during NW formation and

  9. Biomimetic emulsions reveal the effect of homeostatic pressure on cell-cell adhesion

    CERN Document Server

    Pontani, Lea-Laetitia; Viasnoff, Virgile; Brujic, Jasna

    2012-01-01

    Cell-cell contacts in tissues are continuously subject to mechanical forces due to homeostatic pressure and active cytoskeleton dynamics. While much is known about the molecular pathways of adhesion, the role of mechanics is less well understood. To isolate the role of pressure we present a dense packing of functionalized emulsion droplets in which surface interactions are tuned to mimic those of real cells. By visualizing the microstructure in 3D we find that a threshold compression force is necessary to overcome electrostatic repulsion and surface elasticity and establish protein-mediated adhesion. Varying the droplet interaction potential maps out a phase diagram for adhesion as a function of force and salt concentration. Remarkably, fitting the data with our theoretical model predicts binder concentrations in the adhesion areas that are similar to those found in real cells. Moreover, we quantify the adhesion size dependence on the applied force and thus reveal adhesion strengthening with increasing homeos...

  10. Ultrastructural observations reveal the presence of channels between cork cells.

    Science.gov (United States)

    Teixeira, Rita Teresa; Pereira, Helena

    2009-12-01

    The ultrastructure of phellem cells of Quercus suber L. (cork oak) and Calotropis procera (Ait) R. Br. were analyzed using electron transmission microscopy to determine the presence or absence of plasmodesmata (PD). Different types of Q. suber cork samples were studied: one year shoots; virgin cork (first periderm), reproduction cork (traumatic periderm), and wet cork. The channel structures of PD were found in all the samples crossing adjacent cell walls through the suberin layer of the secondary wall. Calotropis phellem also showed PD crossing the cell walls of adjacent cells but in fewer numbers compared to Q. suber. In one year stems of cork oak, it was possible to follow the physiologically active PD with ribosomic accumulation next to the aperture of the channel seen in the phellogen cells to the completely obstructed channels in the dead cells that characterize the phellem tissue.

  11. Tunable fluorescence from patterned silver nano-island arrays for sensitive sub-cell imaging

    International Nuclear Information System (INIS)

    Surface-enhanced fluorescence, a burgeoning technique in biological detection, provides largely enhanced fluorescence signal by exciting localized surfaces plasmons resonance with fluorescent dyes. Nanostructure and surroundings brings great impact on the emission signal, however, insufficient physics about the process limits further improvement on the nanostructure design. In this study, optical properties of Rhodamin-6G molecules on patterned silver nano-island arrays are tailored by precisely controlling the distance between the dyes and silver arrays. The fluorescence signal depends on the distance and the largest enhancement of 10 folds is achieved when the distance is 10 nm. The results are theoretically corroborated by finite difference time domain simulation and applied to cytoskeleton fluorescence imaging using phalloidin–fluorescein isothiocyanate. Our study provides insights into the physical mechanisms associated with the fluorescence enhancement and quenching, and our experiments suggest potential applications to high-sensitivity sub-cell imaging. (paper)

  12. Vector separation of particles and cells using an array of slanted open cavities

    CERN Document Server

    Bernate, Jorge A; Lagae, Liesbet; Konstantopoulo, Konstantinos; Drazer, German

    2014-01-01

    We present a microfluidic platform for the continuous separation of suspended particles based on their size and settling velocity. The separation method takes advantage of the flow field in the vicinity and inside a parallel array of slanted open cavities. These cavities induce flow along them, which deflects the suspended particles to a different degree depending on the extent to which they penetrate into the cavities. The cumulative deflection in the periodic array ultimately leads to vector chromatography, with the different species in the sample moving in different directions. We demonstrate density and size based separation over a range of flow rates by separating polystyrene and silica particles and show that purities nearing 100% can be achieved for multicomponent mixtures. We also demonstrate the potential of the platform to separate biological cells by fractionating different blood components. We discuss the presence of two regimes, which can be distinguished depending on the ratio between the settli...

  13. Fabrication and characterization of CaP-coated nanotube arrays

    Energy Technology Data Exchange (ETDEWEB)

    Kung, Kuan-Chen; Chen, Jia-Ling [Institute of Oral Medicine, National Cheng Kung University, Tainan 701, Taiwan (China); Liu, Yen-Ting [Department of Materials Science and Engineering, National Cheng Kung University, Tainan 701, Taiwan (China); Lee, Tzer-Min, E-mail: tmlee@mail.ncku.edu.tw [Institute of Oral Medicine, National Cheng Kung University, Tainan 701, Taiwan (China); Medical Device Innovation Center, National Cheng Kung University, Tainan 701, Taiwan (China); School of Dentistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan (China)

    2015-03-01

    Modified anodization techniques have been shown to improve the biocompatibility of titanium. This study demonstrated the anodic formation of self-organized nanotube arrays on titanium from an electrolyte solution containing 1 M H{sub 3}PO{sub 4} and 1 wt% hydrofluoric acid (HF). Our aim was to investigate the effects of sputter-deposited CaP on nanotube arrays. SEM images revealed a surface with uniform morphology and an average pore diameter of 29 nm. XRD results indicated that the phase of the nanotube arrays was amorphous. Electron spectroscopy for chemical analysis (ESCA) confirmed that the nanotube arrays were coated with calcium and phosphorus. Cell culture experiments using human osteosarcoma (HOS) cells demonstrated that the CaP/nanotube arrays had a pronounced effect on initial cell attachment as well as on the number of cells at 1, 7, and 14 days. Compared to as-polished titanium, the CaP/nanotube arrays accelerated cell proliferation, attachment, and spreading. Our results demonstrate the pronounced effects of CaP/nanotube arrays on the biological responses of HOS cells. - Highlights: • Self-organized nanotube arrays were anodically formed on titanium. • Surfaces of nanotube arrays exhibited uniform morphology and pore size. • According to ESCA results, Ca and P were successfully coated on nanotube arrays. • CaP/nanotube arrays accelerated the attachment and spreading of cells. • CaP/nanotube arrays were shown to affect biological responses of cells.

  14. Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays

    Science.gov (United States)

    Saliba, Antoine-Emmanuel; Saias, Laure; Psychari, Eleni; Minc, Nicolas; Simon, Damien; Bidard, François-Clément; Mathiot, Claire; Pierga, Jean-Yves; Fraisier, Vincent; Salamero, Jean; Saada, Véronique; Farace, Françoise; Vielh, Philippe; Malaquin, Laurent; Viovy, Jean-Louis

    2010-01-01

    We propose a unique method for cell sorting, “Ephesia,” using columns of biofunctionalized superparamagnetic beads self-assembled in a microfluidic channel onto an array of magnetic traps prepared by microcontact printing. It combines the advantages of microfluidic cell sorting, notably the application of a well controlled, flow-activated interaction between cells and beads, and those of immunomagnetic sorting, notably the use of batch-prepared, well characterized antibody-bearing beads. On cell lines mixtures, we demonstrated a capture yield better than 94%, and the possibility to cultivate in situ the captured cells. A second series of experiments involved clinical samples—blood, pleural effusion, and fine needle aspirates— issued from healthy donors and patients with B-cell hematological malignant tumors (leukemia and lymphoma). The immunophenotype and morphology of B-lymphocytes were analyzed directly in the microfluidic chamber, and compared with conventional flow cytometry and visual cytology data, in a blind test. Immunophenotyping results using Ephesia were fully consistent with those obtained by flow cytometry. We obtained in situ high resolution confocal three-dimensional images of the cell nuclei, showing intranuclear details consistent with conventional cytological staining. Ephesia thus provides a powerful approach to cell capture and typing allowing fully automated high resolution and quantitative immunophenotyping and morphological analysis. It requires at least 10 times smaller sample volume and cell numbers than cytometry, potentially increasing the range of indications and the success rate of microbiopsy-based diagnosis, and reducing analysis time and cost. PMID:20679245

  15. Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays.

    Science.gov (United States)

    Saliba, Antoine-Emmanuel; Saias, Laure; Psychari, Eleni; Minc, Nicolas; Simon, Damien; Bidard, François-Clément; Mathiot, Claire; Pierga, Jean-Yves; Fraisier, Vincent; Salamero, Jean; Saada, Véronique; Farace, Françoise; Vielh, Philippe; Malaquin, Laurent; Viovy, Jean-Louis

    2010-08-17

    We propose a unique method for cell sorting, "Ephesia," using columns of biofunctionalized superparamagnetic beads self-assembled in a microfluidic channel onto an array of magnetic traps prepared by microcontact printing. It combines the advantages of microfluidic cell sorting, notably the application of a well controlled, flow-activated interaction between cells and beads, and those of immunomagnetic sorting, notably the use of batch-prepared, well characterized antibody-bearing beads. On cell lines mixtures, we demonstrated a capture yield better than 94%, and the possibility to cultivate in situ the captured cells. A second series of experiments involved clinical samples--blood, pleural effusion, and fine needle aspirates--issued from healthy donors and patients with B-cell hematological malignant tumors (leukemia and lymphoma). The immunophenotype and morphology of B-lymphocytes were analyzed directly in the microfluidic chamber, and compared with conventional flow cytometry and visual cytology data, in a blind test. Immunophenotyping results using Ephesia were fully consistent with those obtained by flow cytometry. We obtained in situ high resolution confocal three-dimensional images of the cell nuclei, showing intranuclear details consistent with conventional cytological staining. Ephesia thus provides a powerful approach to cell capture and typing allowing fully automated high resolution and quantitative immunophenotyping and morphological analysis. It requires at least 10 times smaller sample volume and cell numbers than cytometry, potentially increasing the range of indications and the success rate of microbiopsy-based diagnosis, and reducing analysis time and cost. PMID:20679245

  16. Cell-controlled and spatially arrayed gene delivery from fibrin hydrogels.

    Science.gov (United States)

    Lei, Pedro; Padmashali, Roshan M; Andreadis, Stelios T

    2009-08-01

    We investigated fibrin-mediated gene transfer by embedding pDNA within the hydrogel during polymerization and using two modes of gene transfection with cells placed either on the surface (2D transfection) or within the hydrogel (3D transfection). Using this model, we found that cell transfection depended strongly on the local cell-pDNA microenvironment as defined by the 2D vs. 3D context, target cell type and density, as well as fibrinogen and pDNA concentrations. When cells were embedded within the fibrin matrix lipofectamine-induced cell death decreased significantly, especially at low target cell density. Addition of fibrinolytic inhibitors decreased gene transfer in a dose-dependent manner, suggesting that fibrin degradation may be necessary for efficient gene transfer. We also provided proof-of-concept that fibrin-mediated gene transfer can be used for spatially localized gene delivery, which is required in cell-transfection microarrays. When lipoplex-containing hydrogels were spotted in an array format gene transfer was strictly confined to pDNA-containing fibrin spots with no cross-contamination between neighboring sites. Collectively, our data suggest that fibrin may be used as a biomaterial to deliver genes in an efficient, cell-controlled and spatially localized manner for potential applications in vitro or in vivo. PMID:19395019

  17. Physicochemical properties of peptide-coated microelectrode arrays and their in vitro effects on neuroblast cells.

    Science.gov (United States)

    Ghane-Motlagh, Bahareh; Javanbakht, Taraneh; Shoghi, Fatemeh; Wilkinson, Kevin J; Martel, Richard; Sawan, Mohamad

    2016-11-01

    Silicon micromachined neural electrode arrays, which act as an interface between bioelectronic devices and neural tissues, play an important role in chronic implants, in vivo. The biological compatibility of chronic microelectrode arrays (MEA) is an essential factor that must be taken into account in their design and fabrication. In order to improve biocompatibility of the MEAs, the surface of the electrodes was coated with polyethylene glycol (PEG) and parylene-C, which are biocompatible polymers. An in vitro study was performed to test the capacity of poly-d-lysine (PDL) to improve neural-cell adhesion and proliferation. Increased proliferation of the neuroblast cells on the microelectrodes was observed in the presence of the PDL. The presence of the peptide on the electrode surface was confirmed using Fourier transform infrared spectroscopy and scanning electron microscopy (SEM). The impedance of the electrodes was not changed significantly before and after PDL deposition. Mouse neuroblast cells were seeded and cultured on the PDL coated and uncoated neural MEAs with different tip-coatings such as platinum, molybdenum, gold, sputtered iridium oxide, and carbon nanotubes. The neuroblast cells grew preferentially on and around peptide coated-microelectrode tips, as compared to the uncoated microelectrodes. PMID:27524064

  18. The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming

    Institute of Scientific and Technical Information of China (English)

    Athanasia D Panopoulos; Margaret Lutz; W Travis Berggren; Kun Zhang; Ronald M Evans; Gary Siuzdak; Juan Carlos Izpisua Belmonte; Oscar Yanes; SergioRuiz; Yasuyuki S Kida; Dinh Diep; Ralf Tautenhahn; Aida Herrerias; Erika M Batchelder; Nongluk Plongthongkum

    2012-01-01

    Metabolism is vital to every aspect of cell function,yet the metabolome of induced pluripotent stem cells (iPSCs)remains largely unexplored.Here we report,using an untargeted metabolomics approach,that human iPSCs share a pluripotent metabolomic signature with embryonic stem cells (ESCs) that is distinct from their parental cells,and that is characterized by changes in metabolites involved in cellular respiration.Examination of cellular bioenergetics corroborated with our metabolomic analysis,and demonstrated that somatic cells convert from an oxidative state to a glycolytic state in pluripotency.Interestingly,the bioenergetics of various somatic cells correlated with their reprogramming efficiencies.We further identified metabolites that differ between iPSCs and ESCs,which revealed novel metabolic pathways that play a critical role in regulating somatic cell reprogramming.Our findings are the first to globally analyze the metabolome of iPSCs,and provide mechanistic insight into a new layer of regulation involved in inducing pluripotency,and in evaluating iPSC and ESC equivalence.

  19. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L. reveals patterns of SNP variation associated with breeding

    Directory of Open Access Journals (Sweden)

    Zhu Tong

    2009-10-01

    Full Text Available Abstract Background Cultivated tomato (Solanum lycopersicum L. has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP discovery as a high-throughput approach for marker development in cultivated tomato. Results Three varieties, FL7600 (fresh-market, OH9242 (processing, and PI114490 (cherry were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (α used to define the confidence interval (CI, and ranged from 76% for polymorphisms identified at α ≤ 10-6 to 60% for those identified at α ≤ 10-2. Validation percentage reached a plateau between α ≤ 10-4 and α ≤ 10-7, but failure to identify known SFPs (Type II error increased dramatically at α ≤ 10-6. Trough sequence validation, we identified 279 SNPs and 27 InDels in 111 loci. Sixty loci contained ≥ 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of θ (Fst suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace, and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka to synonymous substitutions (Ks for 20 loci with multiple SNPs (≥ 4 per

  20. Molecular analysis of endothelial progenitor cell (EPC subtypes reveals two distinct cell populations with different identities

    Directory of Open Access Journals (Sweden)

    Simpson David A

    2010-05-01

    Full Text Available Abstract Background The term endothelial progenitor cells (EPCs is currently used to refer to cell populations which are quite dissimilar in terms of biological properties. This study provides a detailed molecular fingerprint for two EPC subtypes: early EPCs (eEPCs and outgrowth endothelial cells (OECs. Methods Human blood-derived eEPCs and OECs were characterised by using genome-wide transcriptional profiling, 2D protein electrophoresis, and electron microscopy. Comparative analysis at the transcript and protein level included monocytes and mature endothelial cells as reference cell types. Results Our data show that eEPCs and OECs have strikingly different gene expression signatures. Many highly expressed transcripts in eEPCs are haematopoietic specific (RUNX1, WAS, LYN with links to immunity and inflammation (TLRs, CD14, HLAs, whereas many transcripts involved in vascular development and angiogenesis-related signalling pathways (Tie2, eNOS, Ephrins are highly expressed in OECs. Comparative analysis with monocytes and mature endothelial cells clusters eEPCs with monocytes, while OECs segment with endothelial cells. Similarly, proteomic analysis revealed that 90% of spots identified by 2-D gel analysis are common between OECs and endothelial cells while eEPCs share 77% with monocytes. In line with the expression pattern of caveolins and cadherins identified by microarray analysis, ultrastructural evaluation highlighted the presence of caveolae and adherens junctions only in OECs. Conclusions This study provides evidence that eEPCs are haematopoietic cells with a molecular phenotype linked to monocytes; whereas OECs exhibit commitment to the endothelial lineage. These findings indicate that OECs might be an attractive cell candidate for inducing therapeutic angiogenesis, while eEPC should be used with caution because of their monocytic nature.

  1. Metabolic profiling of hypoxic cells revealed a catabolic signature required for cell survival.

    Directory of Open Access Journals (Sweden)

    Christian Frezza

    Full Text Available Hypoxia is one of the features of poorly vascularised areas of solid tumours but cancer cells can survive in these areas despite the low oxygen tension. The adaptation to hypoxia requires both biochemical and genetic responses that culminate in a metabolic rearrangement to counter-balance the decrease in energy supply from mitochondrial respiration. The understanding of metabolic adaptations under hypoxia could reveal novel pathways that, if targeted, would lead to specific death of hypoxic regions. In this study, we developed biochemical and metabolomic analyses to assess the effects of hypoxia on cellular metabolism of HCT116 cancer cell line. We utilized an oxygen fluorescent probe in anaerobic cuvettes to study oxygen consumption rates under hypoxic conditions without the need to re-oxygenate the cells and demonstrated that hypoxic cells can maintain active, though diminished, oxidative phosphorylation even at 1% oxygen. These results were further supported by in situ microscopy analysis of mitochondrial NADH oxidation under hypoxia. We then used metabolomic methodologies, utilizing liquid chromatography-mass spectrometry (LC-MS, to determine the metabolic profile of hypoxic cells. This approach revealed the importance of synchronized and regulated catabolism as a mechanism of adaptation to bioenergetic stress. We then confirmed the presence of autophagy under hypoxic conditions and demonstrated that the inhibition of this catabolic process dramatically reduced the ATP levels in hypoxic cells and stimulated hypoxia-induced cell death. These results suggest that under hypoxia, autophagy is required to support ATP production, in addition to glycolysis, and that the inhibition of autophagy might be used to selectively target hypoxic regions of tumours, the most notoriously resistant areas of solid tumours.

  2. Recent progress in all-solid-state quantum dot-sensitized TiO{sub 2} nanotube array solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qingyao, E-mail: wangqingyao0532@163.com [Ludong University, School of Chemistry and Materials Science (China); Chen, Chao; Liu, Wei [Tongji University, School of Materials Science and Engineering (China); Gao, Shanmin [Ludong University, School of Chemistry and Materials Science (China); Yang, Xiuchun, E-mail: yangxc@tongji.edu.cn [Tongji University, School of Materials Science and Engineering (China)

    2016-01-15

    All-solid-state quantum dot-sensitized TiO{sub 2} nanotube array solar cells have been drawing great attention to solar energy conversion, which break through restrictions in traditional solar cells, such as the high recombination at interfaces of porous TiO{sub 2} films/sensitizers/hole conductors/counter electrodes, instability of dyes, and leakage of solution electrolyte, and so the novel solar cells exhibit promising applications in the future. In this Minireview article, the assembling of solar cells including the preparation of TiO{sub 2} nanotube array photoanodes, quantum dot preparation and sensitization on photoanodes, filling of hole conductors in TiO{sub 2} nanotubes, and selection of counter electrodes are overviewed, and the development course of all-solid-state quantum dot-sensitized TiO{sub 2} nanotube array solar cells in recent years are summarized in detail. Moreover, the influences of TiO{sub 2} nanotube array photoanodes, quantum dots, solid electrolyte, and counter electrodes on photon-to-current efficiencies of solar cells are summarized. In addition, current problems of solid-state quantum dot-sensitized TiO{sub 2} nanotube array solar cells are analyzed, and the corresponding improvements, such as multisensitizers and passivation layers, are proposed to improve the photoelectric conversion efficiency. Finally, this Minireview provides a perspective for the future development of this novel solar cell.

  3. Recent progress in all-solid-state quantum dot-sensitized TiO2 nanotube array solar cells

    International Nuclear Information System (INIS)

    All-solid-state quantum dot-sensitized TiO2 nanotube array solar cells have been drawing great attention to solar energy conversion, which break through restrictions in traditional solar cells, such as the high recombination at interfaces of porous TiO2 films/sensitizers/hole conductors/counter electrodes, instability of dyes, and leakage of solution electrolyte, and so the novel solar cells exhibit promising applications in the future. In this Minireview article, the assembling of solar cells including the preparation of TiO2 nanotube array photoanodes, quantum dot preparation and sensitization on photoanodes, filling of hole conductors in TiO2 nanotubes, and selection of counter electrodes are overviewed, and the development course of all-solid-state quantum dot-sensitized TiO2 nanotube array solar cells in recent years are summarized in detail. Moreover, the influences of TiO2 nanotube array photoanodes, quantum dots, solid electrolyte, and counter electrodes on photon-to-current efficiencies of solar cells are summarized. In addition, current problems of solid-state quantum dot-sensitized TiO2 nanotube array solar cells are analyzed, and the corresponding improvements, such as multisensitizers and passivation layers, are proposed to improve the photoelectric conversion efficiency. Finally, this Minireview provides a perspective for the future development of this novel solar cell

  4. Live cell imaging reveals at novel view of DNA

    International Nuclear Information System (INIS)

    Non-homologous end-joining (NHEJ) is the major repair pathway for DNA double-strand breaks (DSBs) that are the most severe form of DNA damages. Recently, live cell imaging techniques coupled with laser micro-irradiation were used to analyze the spatio-temporal behavior of the NHEJ core factors upon DSB induction in living cells. Based on the live cell imaging studies, we proposed a novel two-phase model for DSB sensing and protein assembly in the NHEJ pathway. This new model provides a novel view of the dynamic protein behavior on DSBs and broad implications for the molecular mechanism of NHEJ. (author)

  5. RNAi screen reveals host cell kinases specifically involved in Listeria monocytogenes spread from cell to cell.

    Directory of Open Access Journals (Sweden)

    Ryan Chong

    Full Text Available Intracellular bacterial pathogens, such as Listeria monocytogenes and Rickettsia conorii display actin-based motility in the cytosol of infected cells and spread from cell to cell through the formation of membrane protrusions at the cell cortex. Whereas the mechanisms supporting cytosolic actin-based motility are fairly well understood, it is unclear whether specific host factors may be required for supporting the formation and resolution of membrane protrusions. To address this gap in knowledge, we have developed high-throughput fluorescence microscopy and computer-assisted image analysis procedures to quantify pathogen spread in human epithelial cells. We used the approach to screen a siRNA library covering the human kinome and identified 7 candidate kinases whose depletion led to severe spreading defects in cells infected with L. monocytogenes. We conducted systematic validation procedures with redundant silencing reagents and confirmed the involvement of the serine/threonine kinases, CSNK1A1 and CSNK2B. We conducted secondary assays showing that, in contrast with the situation observed in CSNK2B-depleted cells, L. monocytogenes formed wild-type cytosolic tails and displayed wild-type actin-based motility in the cytosol of CSNK1A1-depleted cells. Furthermore, we developed a protrusion formation assay and showed that the spreading defect observed in CSNK1A1-depleted cells correlated with the formation of protrusion that did not resolve into double-membrane vacuoles. Moreover, we developed sending and receiving cell-specific RNAi procedures and showed that CSNK1A was required in the sending cells, but was dispensable in the receiving cells, for protrusion resolution. Finally, we showed that the observed defects were specific to Listeria monocytogenes, as Rickettsia conorii displayed wild-type cell-to-cell spread in CSNK1A1- and CSNK2B-depleted cells. We conclude that, in addition to the specific host factors supporting cytosolic actin

  6. A Low Velocity Zone along the Chaochou Fault in Southern Taiwan: Seismic Image Revealed by a Linear Seismic Array

    Directory of Open Access Journals (Sweden)

    Hsin-Chieh Pu

    2010-01-01

    Full Text Available The Chaochou fault is one of the major boundary faults in southern Taiwan where strong convergence has taken place between the Eurasian and Philippine Sea plates. The surface fault trace between the Pingtung plain and the Central Range follows a nearly N-S direction and stretches to 80 km in length. In order to examine the subsurface structures along the Chaochou fault, a linear seismic array with 14 short-period stations was deployed across the fault to record seismic data between August and December 2001. Detailed examination of seismic data generated by 10 local earthquakes and recorded by the linear array has shown that the incidence angles of the first P-waves recorded by several seismic stations at the fault zone were significantly larger than those located farther away from the fault zone. This difference might reflect the lateral variation of velocity structures across the Chaochou fault. Further examination of ray-paths of seismic wave propagation indicates that a low-velocity zone along the Chaochou fault is needed to explain the significant change in incidence angles across the fault zone. Although we do not have adequate information to calculate the exact geometry of the fault zone well, the variation in incidence angles across the fault can be explained by the existence of a low-velocity zone that is about 3 km in width on the surface and extends downward to a depth of 5 km. The low-velocity zone along the Chaochou fault might imply that the fault system consists of several splay faults on the hanging wall in the Central Range.

  7. Development of a Microforce Sensor and Its Array Platform for Robotic Cell Microinjection Force Measurement

    Science.gov (United States)

    Xie, Yu; Zhou, Yunlei; Lin, Yuzi; Wang, Lingyun; Xi, Wenming

    2016-01-01

    Robot-assisted cell microinjection, which is precise and can enable a high throughput, is attracting interest from researchers. Conventional probe-type cell microforce sensors have some real-time injection force measurement limitations, which prevent their integration in a cell microinjection robot. In this paper, a novel supported-beam based cell micro-force sensor with a piezoelectric polyvinylidine fluoride film used as the sensing element is described, which was designed to solve the real-time force-sensing problem during a robotic microinjection manipulation, and theoretical mechanical and electrical models of the sensor function are derived. Furthermore, an array based cell-holding device with a trapezoidal microstructure is micro-fabricated, which serves to improve the force sensing speed and cell manipulation rates. Tests confirmed that the sensor showed good repeatability and a linearity of 1.82%. Finally, robot-assisted zebrafish embryo microinjection experiments were conducted. These results demonstrated the effectiveness of the sensor working with the robotic cell manipulation system. Moreover, the sensing structure, theoretical model, and fabrication method established in this study are not scale dependent. Smaller cells, e.g., mouse oocytes, could also be manipulated with this approach. PMID:27058545

  8. Single-Cell Electric Lysis on an Electroosmotic-Driven Microfluidic Chip with Arrays of Microwells

    Directory of Open Access Journals (Sweden)

    Yu-Hung Chen

    2012-05-01

    Full Text Available Accurate analysis at the single-cell level has become a highly attractive tool for investigating cellular content. An electroosmotic-driven microfluidic chip with arrays of 30-µm-diameter microwells was developed for single-cell electric lysis in the present study. The cellular occupancy in the microwells when the applied voltage was 5 V (82.4% was slightly higher than that at an applied voltage of 10 V (81.8%. When the applied voltage was increased to 15 V, the cellular occupancy in the microwells dropped to 64.3%. More than 50% of the occupied microwells contain individual cells. The results of electric lysis experiments at the single-cell level indicate that the cells were gradually lysed as the DC voltage of 30 V was applied; the cell was fully lysed after 25 s. Single-cell electric lysis was demonstrated in the proposed microfluidic chip, which is suitable for high-throughput cell lysis.

  9. Development of a Microforce Sensor and Its Array Platform for Robotic Cell Microinjection Force Measurement.

    Science.gov (United States)

    Xie, Yu; Zhou, Yunlei; Lin, Yuzi; Wang, Lingyun; Xi, Wenming

    2016-01-01

    Robot-assisted cell microinjection, which is precise and can enable a high throughput, is attracting interest from researchers. Conventional probe-type cell microforce sensors have some real-time injection force measurement limitations, which prevent their integration in a cell microinjection robot. In this paper, a novel supported-beam based cell micro-force sensor with a piezoelectric polyvinylidine fluoride film used as the sensing element is described, which was designed to solve the real-time force-sensing problem during a robotic microinjection manipulation, and theoretical mechanical and electrical models of the sensor function are derived. Furthermore, an array based cell-holding device with a trapezoidal microstructure is micro-fabricated, which serves to improve the force sensing speed and cell manipulation rates. Tests confirmed that the sensor showed good repeatability and a linearity of 1.82%. Finally, robot-assisted zebrafish embryo microinjection experiments were conducted. These results demonstrated the effectiveness of the sensor working with the robotic cell manipulation system. Moreover, the sensing structure, theoretical model, and fabrication method established in this study are not scale dependent. Smaller cells, e.g., mouse oocytes, could also be manipulated with this approach. PMID:27058545

  10. Development of a Microforce Sensor and Its Array Platform for Robotic Cell Microinjection Force Measurement.

    Science.gov (United States)

    Xie, Yu; Zhou, Yunlei; Lin, Yuzi; Wang, Lingyun; Xi, Wenming

    2016-04-06

    Robot-assisted cell microinjection, which is precise and can enable a high throughput, is attracting interest from researchers. Conventional probe-type cell microforce sensors have some real-time injection force measurement limitations, which prevent their integration in a cell microinjection robot. In this paper, a novel supported-beam based cell micro-force sensor with a piezoelectric polyvinylidine fluoride film used as the sensing element is described, which was designed to solve the real-time force-sensing problem during a robotic microinjection manipulation, and theoretical mechanical and electrical models of the sensor function are derived. Furthermore, an array based cell-holding device with a trapezoidal microstructure is micro-fabricated, which serves to improve the force sensing speed and cell manipulation rates. Tests confirmed that the sensor showed good repeatability and a linearity of 1.82%. Finally, robot-assisted zebrafish embryo microinjection experiments were conducted. These results demonstrated the effectiveness of the sensor working with the robotic cell manipulation system. Moreover, the sensing structure, theoretical model, and fabrication method established in this study are not scale dependent. Smaller cells, e.g., mouse oocytes, could also be manipulated with this approach.

  11. Development of a Microforce Sensor and Its Array Platform for Robotic Cell Microinjection Force Measurement

    Directory of Open Access Journals (Sweden)

    Yu Xie

    2016-04-01

    Full Text Available Robot-assisted cell microinjection, which is precise and can enable a high throughput, is attracting interest from researchers. Conventional probe-type cell microforce sensors have some real-time injection force measurement limitations, which prevent their integration in a cell microinjection robot. In this paper, a novel supported-beam based cell micro-force sensor with a piezoelectric polyvinylidine fluoride film used as the sensing element is described, which was designed to solve the real-time force-sensing problem during a robotic microinjection manipulation, and theoretical mechanical and electrical models of the sensor function are derived. Furthermore, an array based cell-holding device with a trapezoidal microstructure is micro-fabricated, which serves to improve the force sensing speed and cell manipulation rates. Tests confirmed that the sensor showed good repeatability and a linearity of 1.82%. Finally, robot-assisted zebrafish embryo microinjection experiments were conducted. These results demonstrated the effectiveness of the sensor working with the robotic cell manipulation system. Moreover, the sensing structure, theoretical model, and fabrication method established in this study are not scale dependent. Smaller cells, e.g., mouse oocytes, could also be manipulated with this approach.

  12. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

    OpenAIRE

    Laura-Roxana Stingaciu; Hugh O’Neill; Michelle Liberton; Urban, Volker S.; Himadri B. Pakrasi; Michael Ohl

    2016-01-01

    Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membran...

  13. Geometric determinants of directional cell motility revealed using microcontact printing.

    Science.gov (United States)

    Brock, Amy; Chang, Eric; Ho, Chia-Chi; LeDuc, Philip; Jiang, Xingyu; Whitesides, George M; Ingber, Donald E

    2003-03-01

    Mammalian cells redirect their movement in response to changes in the physical properties of their extracellular matrix (ECM) adhesive scaffolds, including changes in available substrate area, shape, or flexibility. Yet, little is known about the cell's ability to discriminate between different types of spatial signals. Here we utilize a soft-lithography-based, microcontact printing technology in combination with automated computerized image analysis to explore the relationship between ECM geometry and directional motility. When fibroblast cells were cultured on fibronectin-coated adhesive islands with the same area (900 micrometers2) but different geometric forms (square, triangle, pentagon, hexagon, trapezoid, various parallelograms) and aspect ratios, cells preferentially extended new lamellipodia from their corners. In addition, by imposing these simple geometric constraints through ECM, cells were directed to deposit new fibronectin fibrils in these same corner regions. These data indicate that mammalian cells can sense edges within ECM patterns that exhibit a wide range of angularity and that they use these spatial cues to guide where they will deposit ECM and extend new motile processes during the process of directional migration. PMID:14674434

  14. HIV-host interactome revealed directly from infected cells.

    Science.gov (United States)

    Luo, Yang; Jacobs, Erica Y; Greco, Todd M; Mohammed, Kevin D; Tong, Tommy; Keegan, Sarah; Binley, James M; Cristea, Ileana M; Fenyö, David; Rout, Michael P; Chait, Brian T; Muesing, Mark A

    2016-01-01

    Although genetically compact, HIV-1 commandeers vast arrays of cellular machinery to sustain and protect it during cycles of viral outgrowth. Transposon-mediated saturation linker scanning mutagenesis was used to isolate fully replication-competent viruses harbouring a potent foreign epitope tag. Using these viral isolates, we performed differential isotopic labelling and affinity-capture mass spectrometric analyses on samples obtained from cultures of human lymphocytes to classify the vicinal interactomes of the viral Env and Vif proteins as they occur during natural infection. Importantly, interacting proteins were recovered without bias, regardless of their potential for positive, negative or neutral impact on viral replication. We identified specific host associations made with trimerized Env during its biosynthesis, at virological synapses, with innate immune effectors (such as HLA-E) and with certain cellular signalling pathways (for example, Notch1). We also defined Vif associations with host proteins involved in the control of nuclear transcription and nucleoside biosynthesis as well as those interacting stably or transiently with the cytoplasmic protein degradation apparatus. Our approach is broadly applicable to elucidating pathogen-host interactomes, providing high-certainty identification of interactors by their direct access during cycling infection. Understanding the pathophysiological consequences of these associations is likely to provide strategic targets for antiviral intervention. PMID:27572969

  15. A smart fully integrated micromachined separator with soft magnetic micro-pillar arrays for cell isolation

    Science.gov (United States)

    Dong, Tao; Su, Qianhua; Yang, Zhaochu; Zhang, Yulong; Egeland, Eirik B.; Gu, Dan D.; Calabrese, Paolo; Kapiris, Matteo J.; Karlsen, Frank; Minh, Nhut T.; Wang, K.; Jakobsen, Henrik

    2010-11-01

    A smart fully integrated micromachined separator with soft magnetic micro-pillar arrays has been developed and demonstrated, which can merely employ one independent lab-on-chip to realize cell isolation. The simulation, design, microfabrication and test for the new electromagnetic micro separator were executed. The simulation results of the electromagnetic field in the separator show that special soft magnetic micro-pillar arrays can amplify and redistribute the electromagnetic field generated by the micro-coils. The separator can be equipped with a strong magnetic field to isolate the target cells with a considerably low input current. The micro separator was fabricated by micro-processing technology. An electroplating bath was hired to deposit NiCo/NiFe to fabricate the micro-pillar arrays. An experimental system was set up to verify the function of the micro separator by isolating the lymphocytes, in which the human whole blood mixed with Dynabeads® FlowComp Flexi and monoclonal antibody MHCD2704 was used as the sample. The results show that the electromagnetic micro separator with an extremely low input current can recognize and capture the target lymphocytes with a high efficiency, the separation ratio reaching more than 90% at a lower flow rate. For the electromagnetic micro separator, there is no external magnetizing field required, and there is no extra cooling system because there is less Joule heat generated due to the lower current. The magnetic separator is totally reusable, and it can be used to separate cells or proteins with common antigens.

  16. Industrial technology for economic and reliable encapsulation of large surface arrays of solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Anguet, J.; Salles, Y.

    1983-01-01

    Different approaches are described showing, that the technology of sheet glass, which is applied in the fields of civil construction and automobile industry, can be used for the incapsulation of solar cell arrays after some modifications. The behaviour of such pannels during environmental tests is satisfactory and this technology allows to assure a good stability in the electric performance. The results obtained in the course of this contract allow to start up with the final step, that is the investigation and the realisation of the necessary means for the production of sheet glas based solar pannels.

  17. Enhanced Electron Photoemission by Collective Lattice Resonances in Plasmonic Nanoparticle-Array Photodetectors and Solar Cells

    DEFF Research Database (Denmark)

    Zhukovsky, Sergei; Babicheva, Viktoriia; Uskov, Alexander;

    2014-01-01

    We propose to use collective lattice resonances in plasmonic nanoparticle arrays to enhance and tailor photoelectron emission in Schottky barrier photodetectors and solar cells. We show that the interaction between narrow-band lattice resonances (the Rayleigh anomaly) and broader-band individual......-particle excitations (localized surface plasmon resonances) leads to stronger local field enhancement. In turn, this causes a significant increase of the photocurrent compared to the case when only individual-particle excitations are present. The results can be used to design new photodetectors with highly selective...

  18. Phase resetting reveals network dynamics underlying a bacterial cell cycle.

    Directory of Open Access Journals (Sweden)

    Yihan Lin

    Full Text Available Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS.

  19. Modeling of the cell-electrode interface noise for microelectrode arrays.

    Science.gov (United States)

    Guo, Jing; Yuan, Jie; Chan, Mansun

    2012-12-01

    Microelectrodes are widely used in the physiological recording of cell field potentials. As microelectrode signals are generally in the μV range, characteristics of the cell-electrode interface are important to the recording accuracy. Although the impedance of the microelectrode-solution interface has been well studied and modeled in the past, no effective model has been experimentally verified to estimate the noise of the cell-electrode interface. Also in existing interface models, spectral information is largely disregarded. In this work, we developed a model for estimating the noise of the cell-electrode interface from interface impedances. This model improves over existing noise models by including the cell membrane capacitor and frequency dependent impedances. With low-noise experiment setups, this model is verified by microelectrode array (MEA) experiments with mouse muscle myoblast cells. Experiments show that the noise estimated from this model has models. With this model, noise of the cell-electrode interface can be estimated by simply measuring interface impedances. This model also provides insights for micro- electrode design to achieve good recording signal-to-noise ratio.

  20. A Nanoprinted Model of Interstitial Cancer Migration Reveals a Link between Cell Deformability and Proliferation.

    Science.gov (United States)

    Panagiotakopoulou, Magdalini; Bergert, Martin; Taubenberger, Anna; Guck, Jochen; Poulikakos, Dimos; Ferrari, Aldo

    2016-07-26

    Metastatic progression of tumors requires the coordinated dissemination of cancerous cells through interstitial tissues and their replication in distant body locations. Despite their importance in cancer treatment decisions, key factors, such as cell shape adaptation and the role it plays in dense tissue invasion by cancerous cells, are not well understood. Here, we employ a 3D electrohydrodynamic nanoprinting technology to generate vertical arrays of topographical pores that mimic interstitial tissue resistance to the mesenchymal migration of cancerous cells, in order to determine the effect of nuclear size, cell deformability, and cell-to-substrate adhesion on tissue invasion efficiency. The high spatial and temporal resolution of our analysis demonstrates that the ability of cells to deform depends on the cell cycle phase, peaks immediately after mitosis, and is key to the invasion process. Increased pore penetration efficiency by cells in early G1 phase also coincided with their lower nuclear volume and higher cell deformability, compared with the later cell cycle stages. Furthermore, artificial decondensation of chromatin induced an increase in cell and nuclear deformability and improved pore penetration efficiency of cells in G1. Together, these results underline that along the cell cycle cells have different abilities to dynamically remodel their actin cytoskeleton and induce nuclear shape changes, which determines their pore penetration efficiency. Thus, our results support a mechanism in which cell proliferation and pore penetration are functionally linked to favor the interstitial dissemination of metastatic cells. PMID:27268411

  1. Novel Genomic Aberrations in Testicular Germ Cell Tumors by Array-CGH, and Associated Gene Expression Changes

    Directory of Open Access Journals (Sweden)

    Rolf I. Skotheim

    2006-01-01

    Full Text Available Introduction: Testicular germ cell tumors of adolescent and young adult men (TGCTs generally have near triploid and complex karyotypes. The actual genes driving the tumorigenesis remain essentially to be identified. Materials and Methods: To determine the detailed DNA copy number changes, and investigate their impact on gene expression levels, we performed an integrated microarray profiling of TGCT genomes and transcriptomes. We analyzed 17 TGCTs, three precursor lesions, and the embryonal carcinoma cell lines, NTERA2 and 2102Ep, by comparative genomic hybridization microarrays (array-CGH, and integrated the data with transcriptome profiles of the same samples. Results: The gain of chromosome arm 12p was, as expected, the most common aberration, and we found CCND2, CD9, GAPD, GDF3, NANOG, and TEAD4 to be the therein most highly over-expressed genes. Additional frequent genomic aberrations revealed some shorter chromosomal segments, which are novel to TGCT, as well as known aberrations for which we here refined boundaries. These include gains from 7p15.2 and 21q22.2, and losses of 4p16.3 and 22q13.3. Integration of DNA copy number information to gene expression profiles identified that BRCC3, FOS, MLLT11, NES, and RAC1 may act as novel oncogenes in TGCT. Similarly, DDX26, ERCC5, FZD4, NME4, OPTN, and RB1 were both lost and under-expressed genes, and are thus putative TGCT suppressor genes. Conclusion: This first genome-wide integrated array-CGH and gene expression profiling of TGCT provides novel insights into the genome biology underlying testicular tumorigenesis.

  2. Human cell-based micro electrode array platform for studying neurotoxicity

    Directory of Open Access Journals (Sweden)

    Laura eYlä-Outinen

    2010-09-01

    Full Text Available At present, most of the neurotoxicological analyses are based on in vitro and in vivo models utilizing animal cells or animal models. In addition, the used in vitro models are mostly based on molecular biological end-point analyses. Thus, for neurotoxicological screening, human cell-based analysis platforms in which the functional neuronal networks responses for various neurotoxicants can be also detected real-time are highly needed. Microelectrode array (MEA is a method which enables the measurement of functional activity of neuronal cell networks in vitro for long periods of time. Here, we utilize MEA to study the neurotoxicity of methyl mercury chloride (MeHgCl, concentrations 0.5-500 nM to human embryonic stem cell (hESC-derived neuronal cell networks exhibiting spontaneous electrical activity. The neuronal cell cultures were matured on MEAs into networks expressing spontaneous spike train-like activity before exposing the cells to MeHgCl for 72 hours. MEA measurements were performed acutely and 24, 48, and 72 hours after the onset of the exposure. Finally, exposed cells were analyzed with traditional molecular biological methods for cell proliferation, cell survival, and gene and protein expression. Our results show that 500 nM MeHgCl decreases the electrical signaling and alters the pharmacologic response of hESC-derived neuronal networks in delayed manner whereas effects can not be detected with qRT-PCR, immunostainings, or proliferation measurements. Thus, we conclude that human cell-based MEA-platform is a sensitive online method for neurotoxicological screening.

  3. Limb-Brightened Jet of 3C 84 Revealed by the 43-GHz Very-Long-Baseline-Array Observation

    CERN Document Server

    Nagai, H; Giovannini, G; Doi, A; Orienti, M; D'Ammando, F; Kino, M; Nakamura, M; Asada, K; Hada, K; Giroletti, M

    2014-01-01

    We present a study of sub-pc scale radio structure of the radio galaxy 3C 84/NGC 1275 based on the Very Long Baseline Array (VLBA) data at 43 GHz. We discover a limb-brightening in the "restarted" jet associated with the 2005 radio outburst. In the 1990s, the jet structure was ridge-brightening rather than limb-brightening, despite the observations being done with similar angular resolution. This indicates that the transverse jet structure has changed recently. This change in the morphology shows an interesting agreement with the $\\gamma$-ray flux increase, i.e., the $\\gamma$-ray flux in 1990s was at least seven times lower than the current one. One plausible explanation for the limb-brightening is the velocity structure of the jet in the context of the stratified jet, which is a successful scenario to explain the $\\gamma$-ray emission in some active galactic nuclei (AGNs). If this is the case, the change in apparent transverse structure might be caused by the change in the transverse velocity structure. We a...

  4. Design, development, manufacture, testing, and delivery of devices for connection of solar cell panel circuitry to flat conductor cable solar cell array harness

    Science.gov (United States)

    Dillard, P. A.; Waddington, D.

    1971-01-01

    The technology status and problem areas which exist for the application of flat conductor cabling to solar cell arrays are summarized. Details covering the design, connector manufacture, and prototype test results are also summarized.

  5. Effect of Extended Extinction from Gold Nanopillar Arrays on the Absorbance Spectrum of a Bulk Heterojunction Organic Solar Cell

    Directory of Open Access Journals (Sweden)

    Shu-Ju Tsai

    2015-02-01

    Full Text Available We report on the effects of enhanced absorption/scattering from arrays of Au nanopillars of varied size and spacing on the spectral response of a P3HT:PCBM bulk heterojunction solar cell. Nanopillar array-patterned devices do show increased optical extinction within a narrow range of wavelengths compared to control samples without such arrays. The measured external quantum efficiency and calculated absorbance, however, both show a decrease near the corresponding wavelengths. Numerical simulations indicate that for relatively narrow nanopillars, the increased optical extinction is dominated by absorption within the nanopillars, rather than scattering, and is likely dissipated by Joule heating.

  6. Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray) analysis.

    Science.gov (United States)

    Patra, Amlan K; Yu, Zhongtang

    2015-01-01

    In a previous study origanum oil (ORO), garlic oil (GAO), and peppermint oil (PEO) were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L) on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number of operational taxonomic units, OTUs) in the phylum Firmicutes, especially those in the class Clostridia, was decreased by ORO and GAO, but increased by PEO, while that in the phylum Bacteroidetes was increased by ORO and PEO. Species richness in the genus Butyrivibrio was lowered by all the EOs. Increases of Bacteroidetes OTUs mainly resulted from increases of Prevotella OTUs. Overall, 67 individual OTUs showed significant differences (P ≤ 0.05) in relative abundance across the EO treatments. The predominant OTUs affected by EOs were diverse, including those related to Syntrophococcus sucromutans, Succiniclasticum ruminis, and Lachnobacterium bovis, and those classified to Prevotella, Clostridium, Roseburia, Pseudobutyrivibrio, Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Bacteroidales, and Clostridiales. In total, 60 OTUs were found significantly (P ≤ 0.05) correlated with feed degradability, ammonia concentration, and molar percentage of volatile fatty acids. Taken together, this study demonstrated extensive impact of EOs on rumen bacterial communities in an EO type-dependent manner, especially those in the predominant families Prevotellaceae, Lachnospiraceae, and Ruminococcaceae. The information from this study may aid in understanding the effect of EOs on feed digestion and fermentation by rumen bacteria. PMID:25914694

  7. Essential oils affect populations of some rumen bacteria in vitro as revealed by microarray (RumenBactArray analysis

    Directory of Open Access Journals (Sweden)

    Amlan Kumar Patra

    2015-04-01

    Full Text Available In a previous study origanum oil (ORO, garlic oil (GAO, and peppermint oil (PEO were shown to effectively lower methane production, decrease abundance of methanogens, and change abundances of several bacterial populations important to feed digestion in vitro. In this study, the impact of these essential oils (EOs, at 0.50 g/L, on the rumen bacterial community composition and population was further examined using the recently developed RumenBactArray. Species richness (expressed as number of operational taxonomic units, OTUs in the phylum Firmicutes, especially those in the class Clostridia, was decreased by ORO and GAO, but increased by PEO, while that in the phylum Bacteroidetes was increased by ORO and PEO. Species richness in the genus Butyrivibrio was lowered by all the EOs. Increases of Bacteroidetes OTUs mainly resulted from increases of Prevotella OTUs. Overall, 67 individual OTUs showed significant differences (P≤0.05 in relative abundance across the EO treatments. The predominant OTUs affected by EOs were diverse, including those related to Syntrophococcus sucromutans, Succiniclasticum ruminis, and Lachnobacterium bovis, and those classified to Prevotella, Clostridium, Roseburia, Pseudobutyrivibrio, Lachnospiraceae, Ruminococcaceae, Prevotellaceae, Bacteroidales, and Clostridiales. In total, 60 OTUs were found significantly (P≤0.05 correlated with feed degradability, ammonia concentration, and molar percentage of volatile fatty acids. Taken together, this study demonstrated extensive impact of EOs on rumen bacterial communities in an EO type-dependent manner, especially those in the predominant families Prevotellaceae, Lachnospiraceae and Ruminococcaceae. The information from this study may aid in understanding the effect of EOs on feed digestion and fermentation by rumen bacteria.

  8. Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays

    Science.gov (United States)

    Laborde, C.; Pittino, F.; Verhoeven, H. A.; Lemay, S. G.; Selmi, L.; Jongsma, M. A.; Widdershoven, F. P.

    2015-09-01

    Platforms that offer massively parallel, label-free biosensing can, in principle, be created by combining all-electrical detection with low-cost integrated circuits. Examples include field-effect transistor arrays, which are used for mapping neuronal signals and sequencing DNA. Despite these successes, however, bioelectronics has so far failed to deliver a broadly applicable biosensing platform. This is due, in part, to the fact that d.c. or low-frequency signals cannot be used to probe beyond the electrical double layer formed by screening salt ions, which means that under physiological conditions the sensing of a target analyte located even a short distance from the sensor (∼1 nm) is severely hampered. Here, we show that high-frequency impedance spectroscopy can be used to detect and image microparticles and living cells under physiological salt conditions. Our assay employs a large-scale, high-density array of nanoelectrodes integrated with CMOS electronics on a single chip and the sensor response depends on the electrical properties of the analyte, allowing impedance-based fingerprinting. With our platform, we image the dynamic attachment and micromotion of BEAS, THP1 and MCF7 cancer cell lines in real time at submicrometre resolution in growth medium, demonstrating the potential of the platform for label/tracer-free high-throughput screening of anti-tumour drug candidates.

  9. 15% Power Conversion Efficiency from a Gated Nanotube/Silicon Nanowire Array Solar Cell

    Science.gov (United States)

    Petterson, Maureen K.; Lemaitre, Maxime G.; Shen, Yu; Wadhwa, Pooja; Hou, Jie; Vasilyeva, Svetlana V.; Kravchenko, Ivan I.; Rinzler, Andrew G.

    2015-03-01

    Despite their enhanced light trapping ability the performance of silicon nanowire array solar cells have, been stagnant with power conversion efficiencies barely breaking 10%. The problem is understood to be the consequence of a high photo-carrier recombination at the large surface area of the Si nanowire sidewalls. Here, by exploiting 1) electronic gating via an ionic liquid electrolyte to induce inversion in the n-type Si nanowires and 2) using a layer of single wall carbon nanotubes engineered to contact each nanowire tip and extract the minority carriers, we demonstrate silicon nanowire array solar cells with power conversion efficiencies of 15%. Our results allow for discrimination between the two principle means of avoiding front surface recombination: surface passivation and the use of local fields. A deleterious electrochemical reaction of the silicon due to the electrolyte gating is shown to be caused by oxygen/water entrained in the ionic liquid electrolyte. While encapsulation can avoid the issue a non-encapsulation based solution is also described. We gratefully acknowledge support from the National Science Foundation under ECCS-1232018.

  10. Process development for automated solar cell and module production. Task 4: automated array assembly

    Energy Technology Data Exchange (ETDEWEB)

    Hagerty, J.J.

    1980-06-30

    The scope of work under this contract involves specifying a process sequence which can be used in conjunction with automated equipment for the mass production of solar cell modules for terrestrial use. This process sequence is then critically analyzed from a technical and economic standpoint to determine the technological readiness of each process step for implementation. The process steps are ranked according to the degree of development effort required and according to their significance to the overall process. Under this contract the steps receiving analysis were: back contact metallization, automated cell array layup/interconnect, and module edge sealing. For automated layup/interconnect both hard automation and programmable automation (using an industrial robot) were studied. The programmable automation system was then selected for actual hardware development. Economic analysis using the SAMICS system has been performed during these studies to assure that development efforts have been directed towards the ultimate goal of price reduction. Details are given. (WHK)

  11. Engineered red blood cells as carriers for systemic delivery of a wide array of functional probes.

    Science.gov (United States)

    Shi, Jiahai; Kundrat, Lenka; Pishesha, Novalia; Bilate, Angelina; Theile, Chris; Maruyama, Takeshi; Dougan, Stephanie K; Ploegh, Hidde L; Lodish, Harvey F

    2014-07-15

    We developed modified RBCs to serve as carriers for systemic delivery of a wide array of payloads. These RBCs contain modified proteins on their plasma membrane, which can be labeled in a sortase-catalyzed reaction under native conditions without inflicting damage to the target membrane or cell. Sortase accommodates a wide range of natural and synthetic payloads that allow modification of RBCs with substituents that cannot be encoded genetically. As proof of principle, we demonstrate site-specific conjugation of biotin to in vitro-differentiated mouse erythroblasts as well as to mature mouse RBCs. Thus modified, RBCs remain in the bloodstream for up to 28 d. A single domain antibody attached enzymatically to RBCs enables them to bind specifically to target cells that express the antibody target. We extend these experiments to human RBCs and demonstrate efficient sortase-mediated labeling of in vitro-differentiated human reticulocytes.

  12. Towards fast plasma and blood cell separation - pattern and arrangement investigation of post arrays used in deterministic hydrodynamics

    NARCIS (Netherlands)

    Li, J.; Le Gac, S.; Berg, van den A.; Locascio, L.E.; Gaitan, M.; Paegel, B.M.; Ross, D.J.; Vreeland, W.N.

    2008-01-01

    We show that both the post pattern and arrangement have an influence on the cell movement (zigzag vs. bump mode) in deterministic hydrodynamics while the current theory is limited to one parameter, the array row shift ε for cylindrical posts. Besides, a new mechanism of cell movement, the “stair mov

  13. Implementation of exon arrays: alternative splicing during T-cell proliferation as determined by whole genome analysis

    Directory of Open Access Journals (Sweden)

    Whistler Toni

    2010-09-01

    Full Text Available Abstract Background The contribution of alternative splicing and isoform expression to cellular response is emerging as an area of considerable interest, and the newly developed exon arrays allow for systematic study of these processes. We use this pilot study to report on the feasibility of exon array implementation looking to replace the 3' in vitro transcription expression arrays in our laboratory. One of the most widely studied models of cellular response is T-cell activation from exogenous stimulation. Microarray studies have contributed to our understanding of key pathways activated during T-cell stimulation. We use this system to examine whole genome transcription and alternate exon usage events that are regulated during lymphocyte proliferation in an attempt to evaluate the exon arrays. Results Peripheral blood mononuclear cells form healthy donors were activated using phytohemagglutinin, IL2 and ionomycin and harvested at 5 points over a 7 day period. Flow cytometry measured cell cycle events and the Affymetrix exon array platform was used to identify the gene expression and alternate exon usage changes. Gene expression changes were noted in a total of 2105 transcripts, and alternate exon usage identified in 472 transcript clusters. There was an overlap of 263 transcripts which showed both differential expression and alternate exon usage over time. Gene ontology enrichment analysis showed a broader range of biological changes in biological processes for the differentially expressed genes, which include cell cycle, cell division, cell proliferation, chromosome segregation, cell death, component organization and biogenesis and metabolic process ontologies. The alternate exon usage ontological enrichments are in metabolism and component organization and biogenesis. We focus on alternate exon usage changes in the transcripts of the spliceosome complex. The real-time PCR validation rates were 86% for transcript expression and 71% for

  14. Efficient analysis of a small number of cancer cells at the single-cell level using an electroactive double-well array.

    Science.gov (United States)

    Kim, Soo Hyeon; Fujii, Teruo

    2016-07-01

    Analysis of the intracellular materials of a small number of cancer cells at the single-cell level is important to improve our understanding of cellular heterogeneity in rare cells. To analyze an extremely small number of cancer cells (less than hundreds of cells), an efficient system is required in order to analyze target cells with minimal sample loss. Here, we present a novel approach utilizing an advanced electroactive double-well array (EdWA) for on-chip analysis of a small number of cancer cells at the single-cell level with minimal loss of target cells. The EdWA consisted of cell-sized trap-wells for deterministic single-cell trapping using dielectrophoresis and high aspect ratio reaction-wells for confining the cell lysates extracted by lysing trapped single cells via electroporation. We demonstrated a highly efficient single-cell arraying (a cell capture efficiency of 96 ± 3%) by trapping diluted human prostate cancer cells (PC3 cells). On-chip single-cell analysis was performed by measuring the intracellular β-galactosidase (β-gal) activity after lysing the trapped single cells inside a tightly enclosed EdWA in the presence of a fluorogenic enzyme substrate. The PC3 cells showed large cell-to-cell variations in β-gal activity although they were cultured under the same conditions in a culture dish. This simple and effective system has great potential for high throughput single-cell analysis of rare cells.

  15. Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells

    Science.gov (United States)

    Stingaciu, Laura-Roxana; O'Neill, Hugh; Liberton, Michelle; Urban, Volker S.; Pakrasi, Himadri B.; Ohl, Michael

    2016-01-01

    Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.

  16. Single cell activity reveals direct electron transfer in methanotrophic consortia

    Science.gov (United States)

    McGlynn, Shawn E.; Chadwick, Grayson L.; Kempes, Christopher P.; Orphan, Victoria J.

    2015-10-01

    Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.

  17. Cell electroporation with a three-dimensional microelectrode array on a printed circuit board.

    Science.gov (United States)

    Xu, Youchun; Su, Shisheng; Zhou, Changcheng; Lu, Ying; Xing, Wanli

    2015-04-01

    Electroporation is a commonly used approach to rapidly introduce exogenous molecules into cells without permanent damage. Compared to classical electroporation protocols, microchip-based electroporation approaches have the advantages of high transfection efficiency and low consumption, but they also commonly rely on costly and tedious microfabrication technology. Hence, it is desirable to develop a novel, more affordable, and effective approach to facilitate cell electroporation. In this study, we utilized a standard printed circuit board (PCB) technology to fabricate a chip with an interdigitated array of electrodes for electroporation of suspended cells. The electrodes (thickness ~35 μm) fabricated by PCB technology are much thicker than the two-dimensional (2D) planar electrodes (thickness electroporation. HeLa, MCF7, COS7, Jurkat, and 3T3-L1 cells were efficiently transfected with the pEGFP-N1 plasmid using individually optimal electroporation parameters. This work provides a novel method for convenient and rapid cell transfection and thus holds promise for use as a low-cost disposable device in biomedical research.

  18. Nanowire Arrays as Cell Force Sensors To Investigate Adhesin-Enhanced Holdfast of Single Cell Bacteria and Biofilm Stability.

    Science.gov (United States)

    Sahoo, Prasana K; Janissen, Richard; Monteiro, Moniellen P; Cavalli, Alessandro; Murillo, Duber M; Merfa, Marcus V; Cesar, Carlos L; Carvalho, Hernandes F; de Souza, Alessandra A; Bakkers, Erik P A M; Cotta, Monica A

    2016-07-13

    Surface attachment of a planktonic bacteria, mediated by adhesins and extracellular polymeric substances (EPS), is a crucial step for biofilm formation. Some pathogens can modulate cell adhesiveness, impacting host colonization and virulence. A framework able to quantify cell-surface interaction forces and their dependence on chemical surface composition may unveil adhesiveness control mechanisms as new targets for intervention and disease control. Here we employed InP nanowire arrays to dissect factors involved in the early stage biofilm formation of the phytopathogen Xylella fastidiosa. Ex vivo experiments demonstrate single-cell adhesion forces up to 45 nN, depending on the cell orientation with respect to the surface. Larger adhesion forces occur at the cell poles; secreted EPS layers and filaments provide additional mechanical support. Significant adhesion force enhancements were observed for single cells anchoring a biofilm and particularly on XadA1 adhesin-coated surfaces, evidencing molecular mechanisms developed by bacterial pathogens to create a stronger holdfast to specific host tissues. PMID:27336224

  19. Naturally death-resistant precursor cells revealed as the origin of retinoblastoma

    DEFF Research Database (Denmark)

    Trinh, Emmanuelle; Lazzerini Denchi, Eros; Helin, Kristian

    2004-01-01

    The molecular mechanisms and the cell-of-origin leading to retinoblastoma are not well defined. In this issue of Cancer Cell, Bremner and colleagues describe the first inheritable model of retinoblastoma, revealing that loss of the pocket proteins pRb and p107 deregulates cell cycle exit in retinal...

  20. Effects of Titanium Oxide Nanotube Arrays with Different Lengths on the Characteristics of Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Chin-Guo Kuo

    2013-01-01

    Full Text Available The self-aligned highly ordered TiO2 nanotube (TNT arrays were fabricated by potentiostatic anodization of Ti foil, and we found that the TNT-array length and diameter were dependent on the electrolyte (NH4F concentration in ethylene glycol and anodization time. The characteristics of the fabricated TNT arrays were characterized by XRD pattern, FESEM, and absorption spectrum. As the electrolyte NH4F concentration in the presence of H2O (2 vol% with anodization was changed from 0.25 to 0.75 wt% and the anodization period was increased from 1 to 5 h, the TNT-array length was changed from 9.55 to 30.2 μm and the TNT-array diameter also increased. As NH4F concentration was 0.5 wt%, the prepared TNT arrays were also used to fabricate the dye-sensitized solar cells (DSSCs. We would show that the measured photovoltaic performance of the DSSCs was dependent on the TNT-array length.

  1. Design for strong absorption in a nanowire array tandem solar cell

    Science.gov (United States)

    Chen, Yang; Pistol, Mats-Erik; Anttu, Nicklas

    2016-01-01

    Semiconductor nanowires are a promising candidate for next-generation solar cells. However, the optical response of nanowires is, due to diffraction effects, complicated to optimize. Here, we optimize through optical modeling the absorption in a dual-junction nanowire-array solar cell in terms of the Shockley-Quessier detailed balance efficiency limit. We identify efficiency maxima that originate from resonant absorption of photons through the HE11 and the HE12 waveguide modes in the top cell. An efficiency limit above 40% is reached in the band gap optimized Al0.10Ga0.90As/In0.34Ga0.66As system when we allow for different diameter for the top and the bottom nanowire subcell. However, for experiments, equal diameter for the top and the bottom cell might be easier to realize. In this case, we find in our modeling a modest 1–2% drop in the efficiency limit. In the Ga0.51In0.49P/InP system, an efficiency limit of η = 37.3% could be reached. These efficiencies, which include reflection losses and sub-optimal absorption, are well above the 31.0% limit of a perfectly-absorbing, idealized single-junction bulk cell, and close to the 42.0% limit of the idealized dual-junction bulk cell. Our results offer guidance in the choice of materials and dimensions for nanowires with potential for high efficiency tandem solar cells. PMID:27574019

  2. Simulation of the contractile response of cells on an array of micro-posts.

    LENUS (Irish Health Repository)

    McGarry, J P

    2009-09-13

    A bio-chemo-mechanical model has been used to predict the contractile responses of smooth cells on a bed of micro-posts. Predictions obtained for smooth muscle cells reveal that, by converging onto a single set of parameters, the model captures all of the following responses in a self-consistent manner: (i) the scaling of the force exerted by the cells with the number of posts; (ii) actin distributions within the cells, including the rings of actin around the micro-posts; (iii) the curvature of the cell boundaries between the posts; and (iv) the higher post forces towards the cell periphery. Similar correspondences between predictions and measurements have been demonstrated for fibroblasts and mesenchymal stem cells once the maximum stress exerted by the stress fibre bundles has been recalibrated. Consistent with measurements, the model predicts that the forces exerted by the cells will increase with both increasing post stiffness and cell area (or equivalently, post spacing). In conjunction with previous assessments, these findings suggest that this framework represents an important step towards a complete model for the coupled bio-chemo-mechanical responses of cells.

  3. Micro-arrayed human embryonic stem cells-derived cardiomyocytes for in vitro functional assay.

    Directory of Open Access Journals (Sweden)

    Elena Serena

    Full Text Available INTRODUCTION: The heart is one of the least regenerative organs in the body and any major insult can result in a significant loss of heart cells. The development of an in vitro-based cardiac tissue could be of paramount importance for many aspects of the cardiology research. In this context, we developed an in vitro assay based on human cardiomyocytes (hCMs and ad hoc micro-technologies, suitable for several applications: from pharmacological analysis to physio-phatological studies on transplantable hCMs. We focused on the development of an assay able to analyze not only hCMs viability, but also their functionality. METHODS: hCMs were cultured onto a poly-acrylamide hydrogel with tunable tissue-like mechanical properties and organized through micropatterning in a 20×20 array. Arrayed hCMs were characterized by immunofluorescence, GAP-FRAP analyses and live and dead assay. Their functionality was evaluated monitoring the excitation-contraction coupling. RESULTS: Micropatterned hCMs maintained the expression of the major cardiac markers (cTnT, cTnI, Cx43, Nkx2.5, α-actinin and functional properties. The spontaneous contraction frequency was (0.83±0.2 Hz, while exogenous electrical stimulation lead to an increase up to 2 Hz. As proof of concept that our device can be used for screening the effects of pathological conditions, hCMs were exposed to increasing levels of H(2O(2. Remarkably, hCMs viability was not compromised with exposure to 0.1 mM H(2O(2, but hCMs contractility was dramatically suppressed. As proof of concept, we also developed a microfluidic platform to selectively treat areas of the cell array, in the perspective of performing multi-parametric assay. CONCLUSIONS: Such system could be a useful tool for testing the effects of multiple conditions on an in vitro cell model representative of human heart physiology, thus potentially helping the processes of therapy and drug development.

  4. Paper-based microreactor array for rapid screening of cell signaling cascades.

    Science.gov (United States)

    Huang, Chia-Hao; Lei, Kin Fong; Tsang, Ngan-Ming

    2016-08-01

    Investigation of cell signaling pathways is important for the study of pathogenesis of cancer. However, the related operations used in these studies are time consuming and labor intensive. Thus, the development of effective therapeutic strategies may be hampered. In this work, gel-free cell culture and subsequent immunoassay has been successfully integrated and conducted in a paper-based microreactor array. Study of the activation level of different kinases of cells stimulated by different conditions, i.e., IL-6 stimulation, starvation, and hypoxia, was demonstrated. Moreover, rapid screening of cell signaling cascades after the stimulations of HGF, doxorubicin, and UVB irradiation was respectively conducted to simultaneously screen 40 kinases and transcription factors. Activation of multi-signaling pathways could be identified and the correlation between signaling pathways was discussed to provide further information to investigate the entire signaling network. The present technique integrates most of the tedious operations using a single paper substrate, reduces sample and reagent consumption, and shortens the time required by the entire process. Therefore, it provides a first-tier rapid screening tool for the study of complicated signaling cascades. It is expected that the technique can be developed for routine protocol in conventional biological research laboratories. PMID:27377153

  5. Microprocessor control of multiple peak power tracking DC/DC converters for use with solar cell arrays

    Science.gov (United States)

    Frederick, Martin E. (Inventor); Jermakian, Joel (Inventor)

    1991-01-01

    A method and an apparatus is provided for efficiently controlling the power output of a solar cell array string or a plurality of solar cell array strings to achieve a maximum amount of output power from the strings under varying conditions of use. Maximum power output from a solar array string is achieved through control of a pulse width modulated DC/DC buck converter which transfers power from a solar array to a load or battery bus. The input voltage from the solar array to the converter is controlled by a pulse width modulation duty cycle, which in turn is controlled by a differential signal controller. By periodically adjusting the control voltage up or down by a small amount and comparing the power on the load or bus with that generated at different voltage values a maximum power output voltage may be obtained. The system is totally modular and additional solar array strings may be added to the system simply by adding converter boards to the system and changing some constants in the controller's control routines.

  6. Gene expression profiles in squamous cell cervical carcinoma using array-based comparative genomic hybridization analysis.

    Science.gov (United States)

    Choi, Y-W; Bae, S M; Kim, Y-W; Lee, H N; Kim, Y W; Park, T C; Ro, D Y; Shin, J C; Shin, S J; Seo, J-S; Ahn, W S

    2007-01-01

    Our aim was to identify novel genomic regions of interest and provide highly dynamic range information on correlation between squamous cell cervical carcinoma and its related gene expression patterns by a genome-wide array-based comparative genomic hybridization (array-CGH). We analyzed 15 cases of cervical cancer from KangNam St Mary's Hospital of the Catholic University of Korea. Microdissection assay was performed to obtain DNA samples from paraffin-embedded cervical tissues of cancer as well as of the adjacent normal tissues. The bacterial artificial chromosome (BAC) array used in this study consisted of 1440 human BACs and the space among the clones was 2.08 Mb. All the 15 cases of cervical cancer showed the differential changes of the cervical cancer-associated genetic alterations. The analysis limit of average gains and losses was 53%. A significant positive correlation was found in 8q24.3, 1p36.32, 3q27.1, 7p21.1, 11q13.1, and 3p14.2 changes through the cervical carcinogenesis. The regions of high level of gain were 1p36.33-1p36.32, 8q24.3, 16p13.3, 1p36.33, 3q27.1, and 7p21.1. And the regions of homozygous loss were 2q12.1, 22q11.21, 3p14.2, 6q24.3, 7p15.2, and 11q25. In the high level of gain regions, GSDMDC1, RECQL4, TP73, ABCF3, ALG3, HDAC9, ESRRA, and RPS6KA4 were significantly correlated with cervical cancer. The genes encoded by frequently lost clones were PTPRG, GRM7, ZDHHC3, EXOSC7, LRP1B, and NR3C2. Therefore, array-CGH analyses showed that specific genomic alterations were maintained in cervical cancer that were critical to the malignant phenotype and may give a chance to find out possible target genes present in the gained or lost clones.

  7. Solid-state dye-sensitized solar cells based on ZnO nanoparticle and nanorod array hybrid photoanodes

    Directory of Open Access Journals (Sweden)

    Sue Hung-Jue

    2011-01-01

    Full Text Available Abstract The effect of ZnO photoanode morphology on the performance of solid-state dye-sensitized solar cells (DSSCs is reported. Four different structures of dye-loaded ZnO layers have been fabricated in conjunction with poly(3-hexylthiophene. A significant improvement in device efficiency with ZnO nanorod arrays as photoanodes has been achieved by filling the interstitial voids of the nanorod arrays with ZnO nanoparticles. The overall power conversion efficiency increases from 0.13% for a nanorod-only device to 0.34% for a device with combined nanoparticles and nanorod arrays. The higher device efficiency in solid-state DSSCs with hybrid nanorod/nanoparticle photoanodes is originated from both large surface area provided by nanoparticles for dye adsorption and efficient charge transport provided by the nanorod arrays to reduce the recombinations of photogenerated carriers.

  8. Real-time monitoring of cellular dynamics using a microfluidic cell culture system with integrated electrode array and potentiostat

    DEFF Research Database (Denmark)

    Zor, Kinga; Vergani, M.; Heiskanen, Arto;

    2011-01-01

    A versatile microfluidic, multichamber cell culture and analysis system with an integrated electrode array and potentiostat suitable for electrochemical detection and microscopic imaging is presented in this paper. The system, which allows on-line electrode cleaning and modification, was developed...... for real-time monitoring of cellular dynamics, exemplified in this work by monitoring of redox metabolism inside living yeast cells and dopamine release from PC12 cells....

  9. Advanced Solar Cell and Array Technology for NASA Deep Space Missions

    Science.gov (United States)

    Piszczor, Michael; Benson, Scott; Scheiman, David; Finacannon, Homer; Oleson, Steve; Landis, Geoffrey

    2008-01-01

    A recent study by the NASA Glenn Research Center assessed the feasibility of using photovoltaics (PV) to power spacecraft for outer planetary, deep space missions. While the majority of spacecraft have relied on photovoltaics for primary power, the drastic reduction in solar intensity as the spacecraft moves farther from the sun has either limited the power available (severely curtailing scientific operations) or necessitated the use of nuclear systems. A desire by NASA and the scientific community to explore various bodies in the outer solar system and conduct "long-term" operations using using smaller, "lower-cost" spacecraft has renewed interest in exploring the feasibility of using photovoltaics for to Jupiter, Saturn and beyond. With recent advances in solar cell performance and continuing development in lightweight, high power solar array technology, the study determined that photovoltaics is indeed a viable option for many of these missions.

  10. Geometry of the Farallon Slab Revealed by Joint Interpretation of Wavefield Imaging and Tomography Results from the Earthscope Transportable Array

    Science.gov (United States)

    Pavlis, G. L.; Wang, Y.

    2015-12-01

    A significant number of P and S wave tomography models have been produced in the past decade using various subsets of data from the Earthscope USArray and different inversion algorithms. We focus here on published tomography results that span large portions of the final footprint of the USArray. We use 3D visualization techniques to search for common features in different tomography models. We also compare tomography results to features seen in our current generation wavefield images. Recent innovations of our plane wave migration method have yielded what is arguably the highest resolution image ever produced of the mantle in the vicinity of the transition zone. The new results reveal a rich collection of coherent, dipping structures seen throughout the upper mantle and transition zone. These dipping interfaces are judged significant according to a coherence metric. We treat these surfaces as strain markers to assess proposed models for geometry of the 3D geometry of the Farallon Slab under North America. We find the following geologic interpretations are well supported by independent results: 1. The old Farallon under eastern North America and below the base of transition zone is universally seen as a high velocity anomaly. 2. All results support a simple, 3D kinematic model of the updip limit of the Farallon slab window that follows a track from Cape Mendocino, across Nevada, and northern Arizona and New Mexico. 3. All models show a strong low-velocity mantle under the southwestern U.S. 4. A low-velocity features is universally seen related to the Yellowstone-Snake River system. Shorter wavelength features observed in different tomography models are inconsistent showing that the theme of this session is very important to understand what features are in current results are real. Isopach maps of the thickness of the transition show a systematic difference in transition zone thickness in the western and eastern US. The transition zone thickens in the eastern US in

  11. Stoichiometric control of live cell mixing to enable fluidically-encoded co-culture models in perfused microbioreactor arrays.

    Science.gov (United States)

    Occhetta, P; Glass, N; Otte, E; Rasponi, M; Cooper-White, J J

    2016-02-01

    In vivo, tissues are maintained and repaired through interactions between the present (different) cell types, which communicate with each other through both the secretion of paracrine factors and direct cell-cell contacts. In order to investigate and better understand this dynamic, complex interplay among diverse cell populations, we must develop new in vitro co-culture strategies that enable us to recapitulate such native tissue complexity. In this work, a microfluidic mixer based on a staggered herringbone design was computationally designed and experimentally validated that features the ability to mix large, non-diffusive particles (i.e. live cells) in a programmed manner. This is the first time that the herringbone mixer concept has been shown to effectively mix particles of the size range applicable to live cells. The cell mixer allowed for sequentially mixing of two cell types to generate reverse linear concentration co-culture patterns. Once validated, the mixer was integrated into a perfused microbioreactor array as an upstream module to deliver mixed cells to five downstream culture units, each consisting of ten serially-connected circular microculture chambers. This novel cell mixer microbioreactor array (CM-MBA) platform was validated through the establishment of spatio-temporally tunable osteogenic co-culture models, investigating the role of pre-osteoblastic cells (SAOS2) on human mesenchymal stem cells (hMSCs) commitment to an osteogenic endpoint. An increase on expression of alkaline phosphatase in sequential (downstream) chambers, consistent with the initial linear distribution of SAOS2, suggests not only osteoblastic cell-driven hMSCs induction towards the osteogenic phenotype, but also the importance of paracrine signaling. In conclusion, the cell mixer microbioreactor array combines the ability to rapidly establish cell co-culture models in a high-throughput, programmable fashion, with the additional advantage of maintaining cells in culture

  12. Cellular architecture of Treponema pallidum: novel flagellum, periplasmic cone, and cell envelope as revealed by cryo electron tomography.

    Science.gov (United States)

    Liu, Jun; Howell, Jerrilyn K; Bradley, Sherille D; Zheng, Yesha; Zhou, Z Hong; Norris, Steven J

    2010-11-01

    High-resolution cryo electron tomography (cryo-ET) was utilized to visualize Treponema pallidum, the causative agent of syphilis, at the molecular level. Three-dimensional (3D) reconstructions from 304 infectious organisms revealed unprecedented cellular structures of this unusual member of the spirochetal family. High-resolution cryo-ET reconstructions provided detailed structures of the cell envelope, which is significantly different from that of Gram-negative bacteria. The 4-nm lipid bilayer of both outer membrane and cytoplasmic membrane resolved in 3D reconstructions, providing an important marker for interpreting membrane-associated structures. Abundant lipoproteins cover the outer leaflet of the cytoplasmic membrane, in contrast to the rare outer membrane proteins visible by scanning probe microscopy. High-resolution cryo-ET images also provided the first observation of T. pallidum chemoreceptor arrays, as well as structural details of the periplasmically located cone-shaped structure at both ends of the bacterium. Furthermore, 3D subvolume averages of periplasmic flagellar motors and flagellar filaments from living organisms revealed the novel flagellar architectures that may facilitate their rotation within the confining periplasmic space. Our findings provide the most detailed structural understanding of periplasmic flagella and the surrounding cell envelope, which enable this enigmatic bacterium to efficiently penetrate tissue and to escape host immune responses.

  13. Disposable micro-fluidic biosensor array for online parallelized cell adhesion kinetics analysis on quartz crystal resonators

    DEFF Research Database (Denmark)

    Cama, G.; Jacobs, T.; Dimaki, Maria;

    2010-01-01

    In this contribution we present a new disposable micro-fluidic biosensor array for the online analysis of adherent Madin Darby canine kidney (MDCK-II) cells on quartz crystal resonators (QCRs). The device was conceived for the parallel cultivation of cells providing the same experimental conditions...... among all the sensors of the array. As well, dedicated sensor interface electronics were developed and optimized for fast spectra acquisition of all 16 QCRs with a miniaturized impedance analyzer. This allowed performing cell cultivation experiments for the observation of fast cellular reaction kinetics...... with focus on the comparison of the resulting sensor signals influenced by different cell distributions on the sensor surface. To prove the assumption of equal flow circulation within the symmetric micro-channel network and support the hypothesis of identical cultivation conditions for the cells living above...

  14. Microbioreactor array screening of Wnt modulators and microenvironmental factors in osteogenic differentiation of mesenchymal progenitor cells.

    Directory of Open Access Journals (Sweden)

    Jessica E Frith

    Full Text Available Cellular microenvironmental conditions coordinate to regulate stem cell populations and their differentiation. Mesenchymal precursor cells (MPCs, which have significant potential for a wide range of therapeutic applications, can be expanded or differentiated into osteo- chondro- and adipogenic lineages. The ability to establish, screen, and control aspects of the microenvironment is paramount if we are to elucidate the complex interplay of signaling events that direct cell fate. Whilst modulation of Wnt signaling may be useful to direct osteogenesis in MPCs, there is still significant controversy over how the Wnt signaling pathway influences osteogenesis. In this study, we utilised a full-factorial microbioreactor array (MBA to rapidly, combinatorially screen several Wnt modulatory compounds (CHIR99021, IWP-4 and IWR-1 and characterise their effects upon osteogenesis. The MBA screening system showed excellent consistency between donors and experimental runs. CHIR99021 (a Wnt agonist had a profoundly inhibitory effect upon osteogenesis, contrary to expectations, whilst the effects of the IWP-4 and IWR-1 (Wnt antagonists were confirmed to be inhibitory to osteogenesis, but to a lesser extent than observed for CHIR99021. Importantly, we demonstrated that these results were translatable to standard culture conditions. Using RT-qPCR of osteogenic and Wnt pathway markers, we showed that CHIR exerted its effects via inhibition of ALP and SPP1 expression, even though other osteogenic markers (RUNX2, MSX2, DLX, COL1A1 were upregulated. Lastly, this MBA platform, due to the continuous provision of medium from the first to the last of ten serially connected culture chambers, permitted new insight into the impacts of paracrine signaling on osteogenic differentiation in MPCs, with factors secreted by the MPCs in upstream chambers enhancing the differentiation of cells in downstream chambers. Insights provided by this cell-based assay system will be key to

  15. Transcriptomic gene-network analysis of exposure to silver nanoparticle reveals potentially neurodegenerative progression in mouse brain neural cells.

    Science.gov (United States)

    Lin, Ho-Chen; Huang, Chin-Lin; Huang, Yuh-Jeen; Hsiao, I-Lun; Yang, Chung-Wei; Chuang, Chun-Yu

    2016-08-01

    Silver nanoparticles (AgNPs) are commonly used in daily living products. AgNPs can induce inflammatory response in neuronal cells, and potentially develop neurological disorders. The gene networks in response to AgNPs-induced neurodegenerative progression have not been clarified in various brain neural cells. This study found that 3-5nm AgNPs were detectable to enter the nuclei of mouse neuronal cells after 24-h of exposure. The differentially expressed genes in mouse brain neural cells exposure to AgNPs were further identified using Phalanx Mouse OneArray® chip, and permitted to explore the gene network pathway regulating in neurodegenerative progression according to Cytoscape analysis. In focal adhesion pathway of ALT astrocytes, AgNPs induced the gene expression of RasGRF1 and reduced its downstream BCL2 gene for apoptosis. In cytosolic DNA sensing pathway of microglial BV2 cells, AgNPs reduced the gene expression of TREX1 and decreased IRF7 to release pro-inflammatory cytokines for inflammation and cellular activation. In MAPK pathway of neuronal N2a cells, AgNPs elevated GADD45α gene expression, and attenuated its downstream PTPRR gene to interfere with neuron growth and differentiation. Moreover, AgNPs induced beta amyloid deposition in N2a cells, and decreased PSEN1 and PSEN2, which may disrupt calcium homeostasis and presynaptic dysfunction for Alzheimer's disease development. These findings suggested that AgNPs exposure reveals the potency to induce the progression of neurodegenerative disorder. PMID:27131904

  16. Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma.

    Directory of Open Access Journals (Sweden)

    Benjamin A Neely

    Full Text Available Renal cell carcinoma comprises 2 to 3% of malignancies in adults with the most prevalent subtype being clear-cell RCC (ccRCC. This type of cancer is well characterized at the genomic and transcriptomic level and is associated with a loss of VHL that results in stabilization of HIF1. The current study focused on evaluating ccRCC stage dependent changes at the proteome level to provide insight into the molecular pathogenesis of ccRCC progression. To accomplish this, label-free proteomics was used to characterize matched tumor and normal-adjacent tissues from 84 patients with stage I to IV ccRCC. Using pooled samples 1551 proteins were identified, of which 290 were differentially abundant, while 783 proteins were identified using individual samples, with 344 being differentially abundant. These 344 differentially abundant proteins were enriched in metabolic pathways and further examination revealed metabolic dysfunction consistent with the Warburg effect. Additionally, the protein data indicated activation of ESRRA and ESRRG, and HIF1A, as well as inhibition of FOXA1, MAPK1 and WISP2. A subset analysis of complementary gene expression array data on 47 pairs of these same tissues indicated similar upstream changes, such as increased HIF1A activation with stage, though ESRRA and ESRRG activation and FOXA1 inhibition were not predicted from the transcriptomic data. The activation of ESRRA and ESRRG implied that HIF2A may also be activated during later stages of ccRCC, which was confirmed in the transcriptional analysis. This combined analysis highlights the importance of HIF1A and HIF2A in developing the ccRCC molecular phenotype as well as the potential involvement of ESRRA and ESRRG in driving these changes. In addition, cofilin-1, profilin-1, nicotinamide N-methyltransferase, and fructose-bisphosphate aldolase A were identified as candidate markers of late stage ccRCC. Utilization of data collected from heterogeneous biological domains strengthened

  17. Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma.

    Science.gov (United States)

    Neely, Benjamin A; Wilkins, Christopher E; Marlow, Laura A; Malyarenko, Dariya; Kim, Yunee; Ignatchenko, Alexandr; Sasinowska, Heather; Sasinowski, Maciek; Nyalwidhe, Julius O; Kislinger, Thomas; Copland, John A; Drake, Richard R

    2016-01-01

    Renal cell carcinoma comprises 2 to 3% of malignancies in adults with the most prevalent subtype being clear-cell RCC (ccRCC). This type of cancer is well characterized at the genomic and transcriptomic level and is associated with a loss of VHL that results in stabilization of HIF1. The current study focused on evaluating ccRCC stage dependent changes at the proteome level to provide insight into the molecular pathogenesis of ccRCC progression. To accomplish this, label-free proteomics was used to characterize matched tumor and normal-adjacent tissues from 84 patients with stage I to IV ccRCC. Using pooled samples 1551 proteins were identified, of which 290 were differentially abundant, while 783 proteins were identified using individual samples, with 344 being differentially abundant. These 344 differentially abundant proteins were enriched in metabolic pathways and further examination revealed metabolic dysfunction consistent with the Warburg effect. Additionally, the protein data indicated activation of ESRRA and ESRRG, and HIF1A, as well as inhibition of FOXA1, MAPK1 and WISP2. A subset analysis of complementary gene expression array data on 47 pairs of these same tissues indicated similar upstream changes, such as increased HIF1A activation with stage, though ESRRA and ESRRG activation and FOXA1 inhibition were not predicted from the transcriptomic data. The activation of ESRRA and ESRRG implied that HIF2A may also be activated during later stages of ccRCC, which was confirmed in the transcriptional analysis. This combined analysis highlights the importance of HIF1A and HIF2A in developing the ccRCC molecular phenotype as well as the potential involvement of ESRRA and ESRRG in driving these changes. In addition, cofilin-1, profilin-1, nicotinamide N-methyltransferase, and fructose-bisphosphate aldolase A were identified as candidate markers of late stage ccRCC. Utilization of data collected from heterogeneous biological domains strengthened the findings from

  18. Transport and collision dynamics in periodic asymmetric obstacle arrays: Rational design of microfluidic rare-cell immunocapture devices

    Science.gov (United States)

    Gleghorn, Jason P.; Smith, James P.; Kirby, Brian J.

    2013-09-01

    Microfluidic obstacle arrays have been used in numerous applications, and their ability to sort particles or capture rare cells from complex samples has broad and impactful applications in biology and medicine. We have investigated the transport and collision dynamics of particles in periodic obstacle arrays to guide the design of convective, rather than diffusive, transport-based immunocapture microdevices. Ballistic and full computational fluid dynamics simulations are used to understand the collision modes that evolve in cylindrical obstacle arrays with various geometries. We identify previously unrecognized collision mode structures and differential size-based collision frequencies that emerge from these arrays. Previous descriptions of transverse displacements that assume unidirectional flow in these obstacle arrays cannot capture mode transitions properly as these descriptions fail to capture the dependence of the mode transitions on column spacing and the attendant change in the flow field. Using these analytical and computational simulations, we elucidate design parameters that induce high collision rates for all particles larger than a threshold size or selectively increase collision frequencies for a narrow range of particle sizes within a polydisperse population. Furthermore, we investigate how the particle Péclet number affects collision dynamics and mode transitions and demonstrate that experimental observations from various obstacle array geometries are well described by our computational model.

  19. Microchannel-connected SU-8 honeycombs by single-step projection photolithography for positioning cells on silicon oxide nanopillar arrays

    International Nuclear Information System (INIS)

    We report on the fabrication, functionalization and testing of SU-8 microstructures for cell culture and positioning over large areas. The microstructure consists of a honeycomb arrangement of cell containers interconnected by microchannels and centered on nanopillar arrays designed for promoting cell positioning. The containers have been dimensioned to trap single cells and, with a height of 50 µm, prevent cells from escaping. The structures are fabricated using a single ultraviolet photolithography exposure with focus depth in the lower part of the SU-8 resist. With optimized process parameters, microchannels of various aspect ratios are thus produced. The cell containers and microchannels serve for the organization of axonal growth between neurons. The roughly 2 µm-high and 500 nm-wide nanopillars are made of silicon oxide structured by deep reactive ion etching. In future work, beyond their cell positioning purpose, the nanopillars could be functionalized as sensors. The proof of concept of the novel microstructure for organized cell culture is given by the successful growth of interconnected PC12 cells. Promoted by the honeycomb geometry, a dense network of interconnections between the cells has formed and the intended intimate contact of cells with the nanopillar arrays was observed by scanning electron microscopy. This proves the potential of these new devices as tools for the controlled cell growth in an interconnected container system with well-defined 3D geometry. (paper)

  20. Hydrogel Microwell Arrays Allow the Assessment of Protease-Associated Enhancement of Cancer Cell Aggregation and Survival

    Directory of Open Access Journals (Sweden)

    Dietmar W. Hutmacher

    2013-08-01

    Full Text Available Current routine cell culture techniques are only poorly suited to capture the physiological complexity of tumor microenvironments, wherein tumor cell function is affected by intricate three-dimensional (3D, integrin-dependent cell-cell and cell-extracellular matrix (ECM interactions. 3D cell cultures allow the investigation of cancer-associated proteases like kallikreins as they degrade ECM proteins and alter integrin signaling, promoting malignant cell behaviors. Here, we employed a hydrogel microwell array platform to probe using a high-throughput mode how ovarian cancer cell aggregates of defined size form and survive in response to the expression of kallikreins and treatment with paclitaxel, by performing microscopic, quantitative image, gene and protein analyses dependent on the varying microwell and aggregate sizes. Paclitaxel treatment increased aggregate formation and survival of kallikrein-expressing cancer cells and levels of integrins and integrin-related factors. Cancer cell aggregate formation was improved with increasing aggregate size, thereby reducing cell death and enhancing integrin expression upon paclitaxel treatment. Therefore, hydrogel microwell arrays are a powerful tool to screen the viability of cancer cell aggregates upon modulation of protease expression, integrin engagement and anti-cancer treatment providing a micro-scaled yet high-throughput technique to assess malignant progression and drug-resistance.

  1. Evaluation of Platinum-Black Stimulus Electrode Array for Electrical Stimulation of Retinal Cells in Retinal Prosthesis System

    Science.gov (United States)

    Watanabe, Taiichiro; Kobayashi, Risato; Komiya, Ken; Fukushima, Takafumi; Tomita, Hiroshi; Sugano, Eriko; Kurino, Hiroyuki; Tanaka, Tetsu; Tamai, Makoto; Koyanagi, Mitsumasa

    2007-04-01

    A retinal prosthesis system with a three-dimensionally (3D) stacked LSI chip has been proposed. We fabricated a new implantable stimulus electrode array deposited with Platinum-black (Pt-b) on a polyimide-based flexible printed circuit (FPC) for the electrical stimulation of the retinal cells. Impedance measurement of the Pt-b electrode-electrolyte interface in a saline solution was performed and the Pt-b electrode realized a very low impedance. The power consumption at the electrode array when retinal cells were stimulated by a stimulus current was evaluated. The power consumption of the Pt-b stimulus electrode array was 91% lower than that of a previously fabricated Al stimulus electrode array due to a convexo-concave surface. In the cytotoxicity test (CT), we confirmed that Pt implantation induced no cellular degeneration of the rat retina. In the animal experiments, electrically evoked potential (EEP) was successfully recorded using Japanese white rabbits. These results indicate that electrical stimulation using the Pt-b stimulus electrode array can restore visual sensation.

  2. Novel insights of the gastric gland organization revealed by chief cell specific expression of moesin

    Science.gov (United States)

    Zhu, Lixin; Hatakeyama, Jason; Zhang, Bing; Makdisi, Joy; Ender, Cody; Forte, John G.

    2009-01-01

    ERM (ezrin, radixin, and moesin) proteins play critical roles in epithelial and endothelial cell polarity, among other functions. In gastric glands, ezrin is mainly expressed in acid-secreting parietal cells, but not in mucous neck cells or zymogenic chief cells. In looking for other ERM proteins, moesin was found lining the lumen of much of the gastric gland, but it was not expressed in parietal cells. No significant radixin expression was detected in the gastric glands. Moesin showed an increased gradient of expression from the neck to the base of the glands. In addition, the staining pattern of moesin revealed a branched morphology for the gastric lumen. This pattern of short branches extending from the glandular lumen was confirmed by using antibody against zonula occludens-1 (ZO-1) to stain tight junctions. With a mucous neck cell probe (lectin GSII, from Griffonia simplicifolia) and a chief cell marker (pepsinogen C), immunohistochemistry revealed that the mucous neck cells at the top of the glands do not express moesin, but, progressing toward the base, mucous cells showing decreased GSII staining had low or moderate level of moesin expression. The level of moesin expression continued to increase toward the base of the glands and reached a plateau in the base where chief cells and parietal cells abound. The level of pepsinogen expression also increased toward the base. Pepsinogen C was located on cytoplasmic granules and/or more generally distributed in chief cells, whereas moesin was exclusively expressed on the apical membrane. This is a clear demonstration of distinctive cellular expression of two ERM family members in the same tissue. The results provide the first evidence that moesin is involved in the cell biology of chief cells. Novel insights on gastric gland morphology revealed by the moesin and ZO-1 staining provide the basis for a model of cell maturation and migration within the gland. PMID:19074636

  3. Novel insights of the gastric gland organization revealed by chief cell specific expression of moesin.

    Science.gov (United States)

    Zhu, Lixin; Hatakeyama, Jason; Zhang, Bing; Makdisi, Joy; Ender, Cody; Forte, John G

    2009-02-01

    ERM (ezrin, radixin, and moesin) proteins play critical roles in epithelial and endothelial cell polarity, among other functions. In gastric glands, ezrin is mainly expressed in acid-secreting parietal cells, but not in mucous neck cells or zymogenic chief cells. In looking for other ERM proteins, moesin was found lining the lumen of much of the gastric gland, but it was not expressed in parietal cells. No significant radixin expression was detected in the gastric glands. Moesin showed an increased gradient of expression from the neck to the base of the glands. In addition, the staining pattern of moesin revealed a branched morphology for the gastric lumen. This pattern of short branches extending from the glandular lumen was confirmed by using antibody against zonula occludens-1 (ZO-1) to stain tight junctions. With a mucous neck cell probe (lectin GSII, from Griffonia simplicifolia) and a chief cell marker (pepsinogen C), immunohistochemistry revealed that the mucous neck cells at the top of the glands do not express moesin, but, progressing toward the base, mucous cells showing decreased GSII staining had low or moderate level of moesin expression. The level of moesin expression continued to increase toward the base of the glands and reached a plateau in the base where chief cells and parietal cells abound. The level of pepsinogen expression also increased toward the base. Pepsinogen C was located on cytoplasmic granules and/or more generally distributed in chief cells, whereas moesin was exclusively expressed on the apical membrane. This is a clear demonstration of distinctive cellular expression of two ERM family members in the same tissue. The results provide the first evidence that moesin is involved in the cell biology of chief cells. Novel insights on gastric gland morphology revealed by the moesin and ZO-1 staining provide the basis for a model of cell maturation and migration within the gland. PMID:19074636

  4. Detection of Chromosomal Structural Alterations in Single Cells by SNP Arrays: A Systematic Survey of Amplification Bias and Optimized Workflow

    Science.gov (United States)

    Iwamoto, Kazuya; Bundo, Miki; Ueda, Junko; Nakano, Yoko; Ukai, Wataru; Hashimoto, Eri; Saito, Toshikazu; Kato, Tadafumi

    2007-01-01

    Background In single-cell human genome analysis using whole-genome amplified product, a strong amplification bias involving allele dropout and preferential amplification hampers the quality of results. Using an oligonucleotide single nucleotide polymorphism (SNP) array, we systematically examined the nature of this amplification bias, including frequency, degree, and preference for genomic location, and we assessed the effects of this amplification bias on subsequent genotype and chromosomal copy number analyses. Methodology/Principal Findings We found a large variability in amplification bias among the amplified products obtained by multiple displacement amplification (MDA), and this bias had a severe effect on the genotype and chromosomal copy number analyses. We established optimal experimental conditions for pre-screening for high-quality amplified products, processing array data, and analyzing chromosomal structural alterations. Using this optimized protocol, we successfully detected previously unidentified chromosomal structural alterations in single cells from a lymphoblastoid cell line. These alterations were subsequently confirmed by karyotype analysis. In addition, we successfully obtained reproducible chromosomal copy number profiles of single cells from the cell line with a complex karyotype, indicating the applicability and potential of our optimized workflow. Conclusions/Significance Our results suggest that the quality of amplification products should be critically assessed before using them for genomic analyses. The method of MDA-based whole-genome amplification followed by SNP array analysis described here will be useful for exploring chromosomal alterations in single cells. PMID:18074030

  5. A Silicon-Based Nanothin Film Solid Oxide Fuel Cell Array with Edge Reinforced Support for Enhanced Thermal Mechanical Stability.

    Science.gov (United States)

    Baek, Jong Dae; Yu, Chen-Chiang; Su, Pei-Chen

    2016-04-13

    A silicon-based micro-solid oxide fuel cell (μ-SOFC) with electrolyte membrane array embedded in a thin silicon supporting membrane, featuring a unique edge reinforcement structure, was demonstrated by utilizing simple silicon micromachining processes. The square silicon supporting membrane, fabricated by combining deep reactive ion etching and through-wafer wet etching processes, has thicker edges and corners than the center portion of the membrane, which effectively improved the mechanical stability of the entire fuel cell array during cell fabrication and cell operation. The 20 μm thick single crystalline silicon membrane supports a large number of 80 nm thick free-standing yttria-stabilized zirconia (YSZ) electrolytes. The fuel cell array was stably maintained at the open circuit voltage (OCV) of 1.04 V for more than 30 h of operation at 350 °C. A high peak power density of 317 mW/cm(2) was obtained at 400 °C. During a rigorous in situ thermal cycling between 150 and 400 °C at a fast cooling and heating rate of 25 °C/min, the OCV of the μ-SOFC recovered to its high value of 1.07 V without any drop caused by membrane failure, which justifies the superior thermal stability of this novel cell architecture. PMID:26990604

  6. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing.

    Science.gov (United States)

    Venturi, Vanessa; Quigley, Máire F; Greenaway, Hui Yee; Ng, Pauline C; Ende, Zachary S; McIntosh, Tina; Asher, Tedi E; Almeida, Jorge R; Levy, Samuel; Price, David A; Davenport, Miles P; Douek, Daniel C

    2011-04-01

    The human naive T cell repertoire is the repository of a vast array of TCRs. However, the factors that shape their hierarchical distribution and relationship with the memory repertoire remain poorly understood. In this study, we used polychromatic flow cytometry to isolate highly pure memory and naive CD8(+) T cells, stringently defined with multiple phenotypic markers, and used deep sequencing to characterize corresponding portions of their respective TCR repertoires from four individuals. The extent of interindividual TCR sharing and the overlap between the memory and naive compartments within individuals were determined by TCR clonotype frequencies, such that higher-frequency clonotypes were more commonly shared between compartments and individuals. TCR clonotype frequencies were, in turn, predicted by the efficiency of their production during V(D)J recombination. Thus, convergent recombination shapes the TCR repertoire of the memory and naive T cell pools, as well as their interrelationship within and between individuals.

  7. Single-cell lineage tracking analysis reveals that an established cell line comprises putative cancer stem cells and their heterogeneous progeny

    Science.gov (United States)

    Sato, Sachiko; Rancourt, Ann; Sato, Yukiko; Satoh, Masahiko S.

    2016-01-01

    Mammalian cell culture has been used in many biological studies on the assumption that a cell line comprises putatively homogeneous clonal cells, thereby sharing similar phenotypic features. This fundamental assumption has not yet been fully tested; therefore, we developed a method for the chronological analysis of individual HeLa cells. The analysis was performed by live cell imaging, tracking of every single cell recorded on imaging videos, and determining the fates of individual cells. We found that cell fate varied significantly, indicating that, in contrast to the assumption, the HeLa cell line is composed of highly heterogeneous cells. Furthermore, our results reveal that only a limited number of cells are immortal and renew themselves, giving rise to the remaining cells. These cells have reduced reproductive ability, creating a functionally heterogeneous cell population. Hence, the HeLa cell line is maintained by the limited number of immortal cells, which could be putative cancer stem cells. PMID:27003384

  8. Reconfigurable Pico-cell Antenna Array for Indoor Coverage in GSM 900 Band

    Directory of Open Access Journals (Sweden)

    B. Ivsic

    2009-12-01

    Full Text Available This paper proposes a simple antenna array based on three stacked shorted patches aimed to be used as GSM (900 MHz indoor base station antenna. Three same linearly polarized stacked patches are set in three orthogonal planes in space forming pyramid-like structure. The antenna array can be used for nearly omnidirectional coverage as well as for covering three 120º sectors. The proposed array also offers the possibility of polarization diversity.

  9. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq.

    Science.gov (United States)

    Gokce, Ozgun; Stanley, Geoffrey M; Treutlein, Barbara; Neff, Norma F; Camp, J Gray; Malenka, Robert C; Rothwell, Patrick E; Fuccillo, Marc V; Südhof, Thomas C; Quake, Stephen R

    2016-07-26

    The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs) that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states. PMID:27425622

  10. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq

    Directory of Open Access Journals (Sweden)

    Ozgun Gokce

    2016-07-01

    Full Text Available The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.

  11. Genomic profiling of oral squamous cell carcinoma by array-based comparative genomic hybridization.

    Directory of Open Access Journals (Sweden)

    Shunichi Yoshioka

    Full Text Available We designed a study to investigate genetic relationships between primary tumors of oral squamous cell carcinoma (OSCC and their lymph node metastases, and to identify genomic copy number aberrations (CNAs related to lymph node metastasis. For this purpose, we collected a total of 42 tumor samples from 25 patients and analyzed their genomic profiles by array-based comparative genomic hybridization. We then compared the genetic profiles of metastatic primary tumors (MPTs with their paired lymph node metastases (LNMs, and also those of LNMs with non-metastatic primary tumors (NMPTs. Firstly, we found that although there were some distinctive differences in the patterns of genomic profiles between MPTs and their paired LNMs, the paired samples shared similar genomic aberration patterns in each case. Unsupervised hierarchical clustering analysis grouped together 12 of the 15 MPT-LNM pairs. Furthermore, similarity scores between paired samples were significantly higher than those between non-paired samples. These results suggested that MPTs and their paired LNMs are composed predominantly of genetically clonal tumor cells, while minor populations with different CNAs may also exist in metastatic OSCCs. Secondly, to identify CNAs related to lymph node metastasis, we compared CNAs between grouped samples of MPTs and LNMs, but were unable to find any CNAs that were more common in LNMs. Finally, we hypothesized that subpopulations carrying metastasis-related CNAs might be present in both the MPT and LNM. Accordingly, we compared CNAs between NMPTs and LNMs, and found that gains of 7p, 8q and 17q were more common in the latter than in the former, suggesting that these CNAs may be involved in lymph node metastasis of OSCC. In conclusion, our data suggest that in OSCCs showing metastasis, the primary and metastatic tumors share similar genomic profiles, and that cells in the primary tumor may tend to metastasize after acquiring metastasis-associated CNAs.

  12. On-chip clearing of arrays of 3-D cell cultures and micro-tissues.

    Science.gov (United States)

    Grist, S M; Nasseri, S S; Poon, T; Roskelley, C; Cheung, K C

    2016-07-01

    Three-dimensional (3-D) cell cultures are beneficial models for mimicking the complexities of in vivo tissues, especially in tumour studies where transport limitations can complicate response to cancer drugs. 3-D optical microscopy techniques are less involved than traditional embedding and sectioning, but are impeded by optical scattering properties of the tissues. Confocal and even two-photon microscopy limit sample imaging to approximately 100-200 μm depth, which is insufficient to image hypoxic spheroid cores. Optical clearing methods have permitted high-depth imaging of tissues without physical sectioning, but they are difficult to implement for smaller 3-D cultures due to sample loss in solution exchange. In this work, we demonstrate a microfluidic platform for high-throughput on-chip optical clearing of breast cancer spheroids using the SeeDB, Clear(T2), and ScaleSQ clearing methods. Although all three methods are able to effectively clear the spheroids, we find that SeeDB and ScaleSQ more effectively clear the sample than Clear(T2); however, SeeDB induces green autofluorescence while ScaleS causes sample expansion. Our unique on-chip implementation permits clearing arrays of 3-D cultures using perfusion while monitoring the 3-D cultures throughout the process, enabling visualization of the clearing endpoint as well as monitoring of transient changes that could induce image artefacts. Our microfluidic device is compatible with on-chip 3-D cell culture, permitting the use of on-chip clearing at the endpoint after monitoring the same spheroids during their culture. This on-chip method has the potential to improve readout from 3-D cultures, facilitating their use in cell-based assays for high-content drug screening and other applications. PMID:27493703

  13. False positive rate of an arrayCGH platform for single-cell preimplantation genetic screening and subsequent clinical application on day-3

    OpenAIRE

    Mir, Pere; Rodrigo, Lorena; Mercader, Amparo; Buendía Segura, Maria del Pilar; Mateu, Emilia; Milán-Sánchez, Miguel; Peinado, Vanessa; Pellicer Martínez, Antonio; Remohí Giménez, José; Simón, Carlos; Rubio Lluesa, Carmen

    2012-01-01

    In this work, false positive rate of an arrayCGH platform for its use in day-3 single-blastomere analysis was calculated. For this purpose, 38 embryos diagnosed as abnormal on day-3 by FISH were re-biopsied on day-4. Single-cell day-4 arrayCGH diagnosis was then performed. A successful amplification was obtained in 97.4 % (37/38) of the day-4 cells analysed by arrayCGH. Day-3 FISH and day-4 arrayCGH diagnosis were concordant in 35/37 cases. The two discordant embryos were spread and all the c...

  14. Patterned cell arrays and patterned co-cultures on polydopamine-modified poly(vinyl alcohol) hydrogels

    International Nuclear Information System (INIS)

    Live cell arrays are an emerging tool that expand traditional 2D in vitro cell culture, increasing experimental precision and throughput. A patterned cell system was developed by combining the cell-repellent properties of polyvinyl alcohol hydrogels with the cell adhesive properties of self-assembled films of dopamine (polydopamine). It was shown that polydopamine could be patterned onto spin-cast polyvinyl alcohol hydrogels by microcontact printing, which in turn effectively patterned the growth of several cell types (HeLa, human embryonic kidney, human umbilical vein endothelial cells (HUVEC) and prostate cancer). The cells could be patterned in geometries down to single-cell confinement, and it was demonstrated that cell patterns could be maintained for at least 3 weeks. Furthermore, polydopamine could be used to modify poly(vinyl alcohol) in situ using a cell-compatible deposition buffer (1 mg mL−1 dopamine in 25 mM tris with a physiological salt balance). The treatment switched the PVA hydrogel from cell repellent to cell adhesive. Finally, by combining microcontact printing and in situ deposition of polydopamine, patterned co-cultures of the same cell type (HeLa/HeLa) and dissimilar cell types (HeLa/HUVEC) were realized through simple chemistry and could be studied over time. The combination of polyvinyl alcohol and polydopamine was shown to be an attractive route to versatile, patterned cell culture experiments with minimal infrastructure requirements and low complexity. (paper)

  15. Pathway-focused PCR array profiling of enriched populations of laser capture microdissected hippocampal cells after traumatic brain injury.

    Directory of Open Access Journals (Sweden)

    Deborah R Boone

    Full Text Available Cognitive deficits in survivors of traumatic brain injury (TBI are associated with irreversible neurodegeneration in brain regions such as the hippocampus. Comparative gene expression analysis of dying and surviving neurons could provide insight into potential therapeutic targets. We used two pathway-specific PCR arrays (RT2 Profiler Apoptosis and Neurotrophins & Receptors PCR arrays to identify and validate TBI-induced gene expression in dying (Fluoro-Jade-positive or surviving (Fluoro-Jade-negative pyramidal neurons obtained by laser capture microdissection (LCM. In the Apoptosis PCR array, dying neurons showed significant increases in expression of genes associated with cell death, inflammation, and endoplasmic reticulum (ER stress compared with adjacent, surviving neurons. Pro-survival genes with pleiotropic functions were also significantly increased in dying neurons compared to surviving neurons, suggesting that even irreversibly injured neurons are able to mount a protective response. In the Neurotrophins & Receptors PCR array, which consists of genes that are normally expected to be expressed in both groups of hippocampal neurons, only a few genes were expressed at significantly different levels between dying and surviving neurons. Immunohistochemical analysis of selected, differentially expressed proteins supported the gene expression data. This is the first demonstration of pathway-focused PCR array profiling of identified populations of dying and surviving neurons in the brain after TBI. Combining precise laser microdissection of identifiable cells with pathway-focused PCR array analysis is a practical, low-cost alternative to microarrays that provided insight into neuroprotective signals that could be therapeutically targeted to ameliorate TBI-induced neurodegeneration.

  16. Identification of biomarkers to measure HIV-specific mucosal and systemic CD8(+) T-cell immunity using single cell Fluidigm 48.48 Dynamic arrays.

    Science.gov (United States)

    Trivedi, Shubhanshi; Neeman, Teresa; Jackson, Ronald J; Ranasinghe, Roshanka; Jack, Cameron; Ranasinghe, Charani

    2015-12-16

    Thirty genes composed of cytokines, chemokines, granzymes, perforin and integrins were evaluated in gut and splenic K(d)Gag197-205-specific single CD8(+) T cells using Fluidigm 48.48 Dynamic arrays, with the aim of identifying biomarkers to predict effective mucosal and systemic vaccine efficacy. The mRNA expression profiles were analyzed in three ways: (i) the "number" of K(d)Gag197-205-specific CD8(+) T cells expressing the biomarker, (ii) "level" of mRNA expression using principal component analysis (PCA) and (iii) poly-functionality in relation to RANTES expression. In total, 21 genes were found to be differentially expressed between the vaccine groups and the immune compartments tested. Overall, the PCA indicated that IL-13Rα2 or IL-4R antagonist adjuvanted vaccines that previously induced high-avidity mucosal/systemic CD8(+) T cells with better protective efficacy, the "level" of mRNA expression, specifically RANTES, MIP-1β, and integrin α4 in gut K(d)Gag197-205-specific single CD8(+) T cells, were significantly elevated compared to unadjuvanted vaccine. Furthermore, significantly elevated granzymes/perforin levels were detected in IL-13(-/-) mice given the unadjuvanted vaccine, indicating that the degree of IL-13 inhibition (total, transient or no inhibition) can considerably alter the level of T-cell activity/poly-functionality. When splenic- and gut-K(d)Gag197-205-specific CD8(+) T cells were compared, PC1 vs. PC2 scores revealed that not only RANTES, MIP-1β, and integrin α4 mRNA, but also perforin, granzymes A/B, and integrins β1 and β2 mRNA were elevated in spleen. Collectively, data suggest that RANTES, MIP-1β, perforin, and integrins α4, β1 and β7 mRNA in single HIV-specific CD8(+) T cells could be used as a measure of effective mucosal and systemic vaccine efficacy. PMID:26519547

  17. The Influence of Immunization Route, Tissue Microenvironment, and Cytokine Cell Milieu on HIV-Specific CD8+ T Cells Measured Using Fluidigm Dynamic Arrays.

    Science.gov (United States)

    Trivedi, Shubhanshi; Ranasinghe, Charani

    2015-01-01

    Thirty different genes including cytokines, chemokines, granzymes, perforin and specifically integrins were evaluated in Peyer's patch-KdGag197-205-specific CD8+ T cells (pools of 100 cells) using Fluidigm 48.48 Dynamic arrays following three different prime-boost immunization strategies. Data revealed that the route of prime or the booster immunization differentially influenced the integrin expression profile on gut KdGag197-205-specific CD8+ T cells. Specifically, elevated numbers of integrin αE and αD expressing gut KdGag197-205-specific CD8+ T cells were detected following mucosal but not systemic priming. Also, αE/β7 and αD/β2 heterodimerization were more noticeable in an intranasal (i.n.)/i.n. vaccination setting compared to i.n./intramuscular (i.m) or i.m./i.m. vaccinations. Moreover, in all vaccine groups tested α4 appeared to heterodimerize more closely with β7 then β1. Also MIP-1β, RANTES, CCR5, perforin and integrin α4 bio-markers were significantly elevated in i.n./i.m. and i.m./i.m. immunization groups compared to purely mucosal i.n./i.n. delivery. Furthermore, when wild type (WT) BALB/c and IL-13 knockout (KO) mice were immunized using i.n./i.m. strategy, MIP-1α, MIP-1β, RANTES, integrins α4, β1 and β7 mRNA expression levels were found to be significantly different, in mucosal verses systemic KdGag197-205-specific CD8+ T cells. Interestingly, the numbers of gut KdGag197-205-specific CD8+ T cells expressing gut-homing markers α4β7 and CCR9 protein were also significantly elevated in IL-13 KO compared to WT control. Collectively, our findings further corroborate that the route of vaccine delivery, tissue microenvironment and IL-13 depleted cytokine milieu can significantly alter the antigen-specific CD8+ T cell gene expression profiles and in turn modulate their functional avidities as well as homing capabilities. PMID:25946028

  18. The Influence of Immunization Route, Tissue Microenvironment, and Cytokine Cell Milieu on HIV-Specific CD8+ T Cells Measured Using Fluidigm Dynamic Arrays.

    Directory of Open Access Journals (Sweden)

    Shubhanshi Trivedi

    Full Text Available Thirty different genes including cytokines, chemokines, granzymes, perforin and specifically integrins were evaluated in Peyer's patch-KdGag197-205-specific CD8+ T cells (pools of 100 cells using Fluidigm 48.48 Dynamic arrays following three different prime-boost immunization strategies. Data revealed that the route of prime or the booster immunization differentially influenced the integrin expression profile on gut KdGag197-205-specific CD8+ T cells. Specifically, elevated numbers of integrin αE and αD expressing gut KdGag197-205-specific CD8+ T cells were detected following mucosal but not systemic priming. Also, αE/β7 and αD/β2 heterodimerization were more noticeable in an intranasal (i.n./i.n. vaccination setting compared to i.n./intramuscular (i.m or i.m./i.m. vaccinations. Moreover, in all vaccine groups tested α4 appeared to heterodimerize more closely with β7 then β1. Also MIP-1β, RANTES, CCR5, perforin and integrin α4 bio-markers were significantly elevated in i.n./i.m. and i.m./i.m. immunization groups compared to purely mucosal i.n./i.n. delivery. Furthermore, when wild type (WT BALB/c and IL-13 knockout (KO mice were immunized using i.n./i.m. strategy, MIP-1α, MIP-1β, RANTES, integrins α4, β1 and β7 mRNA expression levels were found to be significantly different, in mucosal verses systemic KdGag197-205-specific CD8+ T cells. Interestingly, the numbers of gut KdGag197-205-specific CD8+ T cells expressing gut-homing markers α4β7 and CCR9 protein were also significantly elevated in IL-13 KO compared to WT control. Collectively, our findings further corroborate that the route of vaccine delivery, tissue microenvironment and IL-13 depleted cytokine milieu can significantly alter the antigen-specific CD8+ T cell gene expression profiles and in turn modulate their functional avidities as well as homing capabilities.

  19. TiO2 Nanotube Arrays Composite Film as Photoanode for High-Efficiency Dye-Sensitized Solar Cell

    Directory of Open Access Journals (Sweden)

    Jinghua Hu

    2014-01-01

    Full Text Available A double-layered photoanode made of hierarchical TiO2 nanotube arrays (TNT-arrays as the overlayer and commercial-grade TiO2 nanoparticles (P25 as the underlayer is designed for dye-sensitized solar cells (DSSCs. Crystallized free-standing TNT-arrays films are prepared by two-step anodization process. For photovoltaic applications, DSSCs based on double-layered photoanodes produce a remarkably enhanced power conversion efficiency (PCE of up to 6.32% compared with the DSSCs solely composed of TNT-arrays (5.18% or nanoparticles (3.65% with a similar thickness (24 μm at a constant irradiation of 100 mW cm−2. This is mainly attributed to the fast charge transport paths and superior light-scattering ability of TNT-arrays overlayer and good electronic contact with F-doped tin oxide (FTO glass provided from P25 nanoparticles as a bonding layer.

  20. Use of highly-ordered TiO(2) nanotube arrays in dye-sensitized solar cells.

    Science.gov (United States)

    Mor, Gopal K; Shankar, Karthik; Paulose, Maggie; Varghese, Oomman K; Grimes, Craig A

    2006-02-01

    We describe the use of highly ordered transparent TiO(2) nanotube arrays in dye-sensitized solar cells (DSCs). Highly ordered nanotube arrays of 46-nm pore diameter, 17-nm wall thickness, and 360-nm length were grown perpendicular to a fluorine-doped tin oxide-coated glass substrate by anodic oxidation of a titanium thin film. After crystallization by an oxygen anneal, the nanotube arrays are treated with TiCl(4) to enhance the photogenerated current and then integrated into the DSC structure using a commercially available ruthenium-based dye. Although the negative electrode is only 360-nm-thick, under AM 1.5 illumination the generated photocurrent is 7.87 mA/cm(2), with a photocurrent efficiency of 2.9%. Voltage-decay measurements indicate that the highly ordered TiO(2) nanotube arrays, in comparison to nanoparticulate systems, have superior electron lifetimes and provide excellent pathways for electron percolation. Our results indicate that remarkable photoconversion efficiencies may be obtained, possibly to the ideal limit of approximately 31% for a single photosystem scheme, with an increase of the nanotube-array length to several micrometers. PMID:16464037

  1. Single-Cell Transcriptome Analyses Reveal Signals to Activate Dormant Neural Stem Cells

    OpenAIRE

    Luo, Yuping; Coskun, Volkan; Liang, Aibing; Yu, Juehua; Cheng, Liming; Ge, Weihong; Shi, Zhanping; Zhang, Kunshan; Li, Chun; Cui, Yaru; Lin, Haijun; Luo, Dandan; Wang, Junbang; Lin, Connie; Dai, Zachary

    2015-01-01

    The scarcity of tissue-specific stem cells and the complexity of their surrounding environment have made molecular characterization of these cells particularly challenging. Through single-cell transcriptome and weighted gene co-expression network analysis (WGCNA), we uncovered molecular properties of CD133+/GFAP− ependymal (E) cells in the adult mouse forebrain neurogenic zone. Surprisingly, prominent hub genes of the gene network unique to ependymal CD133+/GFAP− quiescent cells were enriched...

  2. Capturing power at higher voltages from arrays of microbial fuel cells without voltage reversal

    KAUST Repository

    Kim, Younggy

    2011-01-01

    Voltages produced by microbial fuel cells (MFCs) cannot be sustainably increased by linking them in series due to voltage reversal, which substantially reduces stack voltages. It was shown here that MFC voltages can be increased with continuous power production using an electronic circuit containing two sets of multiple capacitors that were alternately charged and discharged (every one second). Capacitors were charged in parallel by the MFCs, but linked in series while discharging to the circuit load (resistor). The parallel charging of the capacitors avoided voltage reversal, while discharging the capacitors in series produced up to 2.5 V with four capacitors. There were negligible energy losses in the circuit compared to 20-40% losses typically obtained with MFCs using DC-DC converters to increase voltage. Coulombic efficiencies were 67% when power was generated via four capacitors, compared to only 38% when individual MFCs were operated with a fixed resistance of 250 Ω. The maximum power produced using the capacitors was not adversely affected by variable performance of the MFCs, showing that power generation can be maintained even if individual MFCs perform differently. Longer capacitor charging and discharging cycles of up to 4 min maintained the average power but increased peak power by up to 2.6 times. These results show that capacitors can be used to easily obtain higher voltages from MFCs, allowing for more useful capture of energy from arrays of MFCs. © 2011 The Royal Society of Chemistry.

  3. Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.

    Science.gov (United States)

    Yu, Tao; Wang, Yongtao; Zhang, Huizhen; Johnson, Caroline H; Jiang, Yiming; Li, Xiangjun; Wu, Zeming; Liu, Tian; Krausz, Kristopher W; Yu, Aiming; Gonzalez, Frank J; Huang, Min; Bi, Huichang

    2016-06-01

    Mycoplasma contamination is a common problem in cell culture and can alter cellular functions. Since cell metabolism is either directly or indirectly involved in every aspect of cell function, it is important to detect changes to the cellular metabolome after mycoplasma infection. In this study, liquid chromatography mass spectrometry (LC/MS)-based metabolomics was used to investigate the effect of mycoplasma contamination on the cellular metabolism of human pancreatic carcinoma cells (PANC-1). Multivariate analysis demonstrated that mycoplasma contamination induced significant metabolic changes in PANC-1 cells. Twenty-three metabolites were identified and found to be involved in arginine and purine metabolism and energy supply. This study demonstrates that mycoplasma contamination significantly alters cellular metabolite levels, confirming the compelling need for routine checking of cell cultures for mycoplasma contamination, particularly when used for metabolomics studies. Graphical abstract Metabolomics reveals mycoplasma contamination changes the metabolome of PANC-1 cells.

  4. A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation

    DEFF Research Database (Denmark)

    Klochendler, Agnes; Weinberg-Corem, Noa; Moran, Maya;

    2012-01-01

    biological material. We describe a transgenic mouse strain, expressing a CyclinB1-GFP fusion reporter, that marks replicating cells in the S/G2/M phases of the cell cycle. Using flow cytometry, we isolate live replicating cells from the liver and compare their transcriptome to that of quiescent cells to......Most adult mammalian tissues are quiescent, with rare cell divisions serving to maintain homeostasis. At present, the isolation and study of replicating cells from their in vivo niche typically involves immunostaining for intracellular markers of proliferation, causing the loss of sensitive...... reveal gene expression programs associated with cell proliferation in vivo. We find that replicating hepatocytes have reduced expression of genes characteristic of liver differentiation. This reporter system provides a powerful platform for gene expression and metabolic and functional studies of...

  5. Metabolomics reveals mycoplasma contamination interferes with the metabolism of PANC-1 cells.

    Science.gov (United States)

    Yu, Tao; Wang, Yongtao; Zhang, Huizhen; Johnson, Caroline H; Jiang, Yiming; Li, Xiangjun; Wu, Zeming; Liu, Tian; Krausz, Kristopher W; Yu, Aiming; Gonzalez, Frank J; Huang, Min; Bi, Huichang

    2016-06-01

    Mycoplasma contamination is a common problem in cell culture and can alter cellular functions. Since cell metabolism is either directly or indirectly involved in every aspect of cell function, it is important to detect changes to the cellular metabolome after mycoplasma infection. In this study, liquid chromatography mass spectrometry (LC/MS)-based metabolomics was used to investigate the effect of mycoplasma contamination on the cellular metabolism of human pancreatic carcinoma cells (PANC-1). Multivariate analysis demonstrated that mycoplasma contamination induced significant metabolic changes in PANC-1 cells. Twenty-three metabolites were identified and found to be involved in arginine and purine metabolism and energy supply. This study demonstrates that mycoplasma contamination significantly alters cellular metabolite levels, confirming the compelling need for routine checking of cell cultures for mycoplasma contamination, particularly when used for metabolomics studies. Graphical abstract Metabolomics reveals mycoplasma contamination changes the metabolome of PANC-1 cells. PMID:27074779

  6. Ultrastructural and molecular distinctions between the porcine inner cell mass and epiblast reveal unique pluripotent cell states

    DEFF Research Database (Denmark)

    Hall, V. J.; Jacobsen, Janus Valentin; Rasmussen, M. A.;

    2010-01-01

    Characterization of the pluripotent cell populations within the porcine embryo is essential for understanding pluripotency and self-renewal regulation in the inner cell mass (ICM) and epiblast. In this study, we perform detailed ultrastructural and molecular characterization of the developing...... pluripotent cell population as it develops from the ICM to the late epiblast. The ultrastructural observations revealed that the outer cells of the ICM have a high nuclear:cytoplasmic ratio but are transcriptionally inactive and contain mitochondria with few cristae. In contrast, the epiblast cells have...... a reduced nuclear:cytoplasmic ratio, are more transcriptionally active, and contain abundant cellular organelles. This study also revealed cavitation and potential unfolding of the epiblast. As the ICM forms the epiblast, SSEA1 is lost and VIMENTIN is lost and re-expressed. The D6 blastocyst expressed high...

  7. Minimizing Platelet Activation-Induced Clogging in Deterministic Lateral Displacement Arrays for High-Throughput Capture of Circulating Tumor Cells

    Science.gov (United States)

    D'Silva, Joseph; Loutherback, Kevin; Austin, Robert; Sturm, James

    2013-03-01

    Deterministic lateral displacement arrays have been used to separate circulating tumor cells (CTCs) from diluted whole blood at flow rates up to 10 mL/min (K. Loutherback et al., AIP Advances, 2012). However, the throughput is limited to 2 mL equivalent volume of undiluted whole blood due to clogging of the array. Since the concentration of CTCs can be as low as 1-10 cells/mL in clinical samples, processing larger volumes of blood is necessary for diagnostic and analytical applications. We have identified platelet activation by the micro-post array as the primary cause of this clogging. In this talk, we (i) show that clogging occurs at the beginning of the micro-post array and not in the injector channels because both acceleration and deceleration in fluid velocity are required for clogging to occur, and (ii) demonstrate how reduction in platelet concentration and decrease in platelet contact time within the device can be used in combination to achieve a 10x increase in the equivalent volume of undiluted whole blood processed. Finally, we discuss experimental efforts to separate the relative contributions of contact activated coagulation and shear-induced platelet activation to clogging and approaches to minimize these, such as surface treatment and post geometry design.

  8. Transcriptome analysis reveals a classical interferon signature induced by IFNλ4 in human primary cells

    DEFF Research Database (Denmark)

    Lauber, Chris; Vieyres, Gabrielle; Terczynska-Dyla, Ewa;

    2015-01-01

    4 could be a tissue-specific regulation of an unknown subset of genes. To address both tissue and subtype specificity in the interferon response, we treated primary human hepatocytes and airway epithelial cells with IFNα, IFNλ3 or IFNλ4 and assessed interferon mediated gene regulation using...... transcriptome sequencing. Our data show a surprisingly similar response to all three subtypes of interferon. We also addressed the tissue specificity of the response, and identified a subset of tissue-specific genes. However, the interferon response is robust in both tissues with the majority of the identified...... genes being regulated in hepatocytes as well as airway epithelial cells. Thus we provide an in-depth analysis of the liver interferon response seen over an array of interferon subtypes and compare it to the response in the lung epithelium....

  9. Effects of Surface Modification of Nanotube Arrays on the Performance of CdS Quantum-Dot-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Danhong Li

    2013-01-01

    Full Text Available CdS-sensitized TiO2 nanotube arrays have been fabricated using the method of successive ionic layer adsorption and reaction and used as a photoanode for quantum-dot-sensitized solar cells. Before being coated with CdS, the surface of TiO2 nanotube arrays was treated with TiCl4, nitric acid (HNO3, potassium hydroxide (KOH, and methyltrimethoxysilane (MTMS, respectively, for the purpose of reducing the interface transfer resistance of quantum-dot-sensitized solar cells. The surfaces of the modified samples represented the characteristics of superhydrophilic and hydrophobic which directly affect the power conversion efficiency of the solar cells. The results showed that surface modification resulted in the reduction of the surface tension, which played a significant role in the connectivity of CdS and TiO2 nanotube arrays. In addition, the solar cells based on CdS/TiO2 electrode treated by HNO3 achieved a maximum power conversion efficiency of 0.17%, which was 42% higher than the reference sample without any modification.

  10. The effect of lance geometry and carbon coating of silicon lances on propidium iodide uptake in lance array nanoinjection of HeLa 229 cells

    International Nuclear Information System (INIS)

    Connecting technology to biologic discovery is a core focus of non-viral gene therapy biotechnologies. One approach that leverages both the physical and electrical function of microelectromechanical systems (MEMS) in cellular engineering is a technology previously described as lance array nanoinjection (LAN). In brief, LAN consists of a silicon chip measuring 2 cm by 2 cm that has been etched to contain an array of 10 μm tall, solid lances that are spaced every 10 μm in a grid pattern. This array of lances is used to physically penetrate hundreds of thousands of cells simultaneously and to then electrically deliver molecular loads into cells. In this present work, two variables related to the microfabrication of the silicon lances, namely lance geometry and coating, are investigated. The purpose of both experimental variables is to assess these parameters’ effect on propidium iodide (PI), a cell membrane impermeable dye, uptake to injected HeLa 229 cells. For the lance geometry experimentation, three different microfabricated lance geometries were used which include a flat/narrow (FN, 1 μm diameter), flat/wide (FW, 2–2.5 μm diameter), and pointed (P, 1 μm diameter) lance geometries. From these tests, it was shown that the FN lances had a slightly better cell viability rate of 91.73% and that the P lances had the best PI uptake rate of 75.08%. For the lance coating experimentation, two different lances were fabricated, both silicon etched lances with some being carbon coated (CC) in a  <100 nm layer of carbon and the other lances being non-coated (Si). Results from this experiment showed no significant difference between lance types at three different nanoinjection protocols (0V, +1.5V DC, and  +5V Pulsed) for both cell viability and PI uptake rates. One exception to this is the comparison of CC/5V Pul and Si/5V Pul samples, where the CC/5V Pul samples had a cell viability rate 5% higher. Both outcomes were unexpected and reveal how to better

  11. Chicken-Specific Kinome Array Reveals that Salmonella enterica Serovar Enteritidis Modulates Host Immune Signaling Pathways in the Cecum to Establish a Persistence Infection

    Science.gov (United States)

    Kogut, Michael H.; Swaggerty, Christina L.; Byrd, James Allen; Selvaraj, Ramesh; Arsenault, Ryan J.

    2016-01-01

    Non-typhoidal Salmonella enterica induces an early, short-lived pro-inflammatory response in chickens that is asymptomatic of clinical disease and results in a persistent colonization of the gastrointestinal (GI) tract that transmits infections to naïve hosts via fecal shedding of bacteria. The underlying mechanisms that control this persistent colonization of the ceca of chickens by Salmonella are only beginning to be elucidated. We hypothesize that alteration of host signaling pathways mediate the induction of a tolerance response. Using chicken-specific kinomic immune peptide arrays and quantitative RT-PCR of infected cecal tissue, we have previously evaluated the development of disease tolerance in chickens infected with Salmonella enterica serovar Enteritidis (S. Enteritidis) in a persistent infection model (4–14 days post infection). Here, we have further outlined the induction of an tolerance defense strategy in the cecum of chickens infected with S. Enteritidis beginning around four days post-primary infection. The response is characterized by alterations in the activation of T cell signaling mediated by the dephosphorylation of phospholipase c-γ1 (PLCG1) that inhibits NF-κB signaling and activates nuclear factor of activated T-cells (NFAT) signaling and blockage of interferon-γ (IFN-γ) production through the disruption of the JAK-STAT signaling pathway (dephosphorylation of JAK2, JAK3, and STAT4). Further, we measured a significant down-regulation reduction in IFN-γ mRNA expression. These studies, combined with our previous findings, describe global phenotypic changes in the avian cecum of Salmonella Enteritidis-infected chickens that decreases the host responsiveness resulting in the establishment of persistent colonization. The identified tissue protein kinases also represent potential targets for future antimicrobial compounds for decreasing Salmonella loads in the intestines of food animals before going to market. PMID:27472318

  12. Optomechanical properties of cancer cells revealed by light-induced deformation and quantitative phase microscopy

    Science.gov (United States)

    Kastl, Lena; Budde, Björn; Isbach, Michael; Rommel, Christina; Kemper, Björn; Schnekenburger, Jürgen

    2015-05-01

    There is a growing interest in cell biology and clinical diagnostics in label-free, optical techniques as the interaction with the sample is minimized and substances like dyes or fixatives do not affect the investigated cells. Such techniques include digital holographic microscopy (DHM) and the optical stretching by fiber optical two beam traps. DHM enables quantitative phase contrast imaging and thereby the determination of the cellular refractive index, dry mass and the volume, whereas optical cell stretching reveals the deformability of cells. Since optical stretching strongly depends on the optical properties and the shape of the investigated material we combined the usage of fiber optical stretching and DHM for the characterization of pancreatic tumor cells. The risk of tumors is their potential to metastasize, spread through the bloodstream and build distal tumors/metastases. The grade of dedifferentiation in which the cells lose their cell type specific properties is a measure for this metastatic potential. The less differentiated the cells are, the higher is their risk to metastasize. Our results demonstrate that pancreatic tumor cells, which are from the same tumor but vary in their grade of differentiation, show significant differences in their deformability. The retrieved data show that differentiated cells have a higher stiffness than less differentiated cells of the same tumor. Even cells that differ only in the expression of a single tumor suppressor gene which is responsible for cell-cell adhesions can be distinguished by their mechanical properties. Additionally, results from DHM measurements yield that the refractive index shows only few variations, indicating that it does not significantly influence optical cell stretching. The obtained results show a promising new approach for the phenotyping of different cell types, especially in tumor cell characterization and cancer diagnostics.

  13. Balanced transcription of cell division genes in Bacillus subtilis as revealed by single cell analysis

    NARCIS (Netherlands)

    Trip, Erik Nico; Veening, Jan-Willem; Stewart, Eric J.; Errington, Jeff; Scheffers, Dirk-Jan

    2013-01-01

    Cell division in bacteria is carried out by a set of conserved proteins that all have to function at the correct place and time. A cell cycle-dependent transcriptional programme drives cell division in bacteria such as Caulobacter crescentus. Whether such a programme exists in the Gram-positive mode

  14. Cell behavior observation and gene expression analysis of melanoma associated with stromal fibroblasts in a three-dimensional magnetic cell culture array.

    Science.gov (United States)

    Okochi, Mina; Matsumura, Taku; Yamamoto, And Shuhei; Nakayama, Eiichi; Jimbow, Kowichi; Honda, Hiroyuki

    2013-01-01

    A three-dimensional (3D) multicellular tumor spheroid culture array has been fabricated using a magnetic force-based cell patterning method, analyzing the effect of stromal fibroblast on the invasive capacity of melanoma. Formation of spheroids was observed when array-like multicellular patterns of melanoma were developed using a pin-holder device made of magnetic soft iron and an external magnet, which enables the assembly of the magnetically labeled cells on the collagen gel-coated surface as array-like cell patterns. The interaction of fibroblast on the invasion of melanoma was investigated using three types of cell interaction models: (i) fibroblasts were magnetically labeled and patterned together in array with melanoma spheroids (direct-interaction model), (ii) fibroblasts coexisting in the upper collagen gel (indirect-interaction model) of melanoma spheroids, and (iii) fibroblast-sheets coexisting under melanoma spheroids (fibroblast-sheet model). The fibroblast-sheet model has largely increased the invasive capacity of melanoma, and the promotion of adhesion, migration, and invasion were also observed. In the fibroblast-sheet model, the expression of IL-8 and MMP-2 increased by 24-fold and 2-fold, respectively, in real time RT-PCR compared to the absence of fibroblasts. The results presented in this study demonstrate the importance of fibroblast interaction to invasive capacity of melanoma in the 3D in vitro bioengineered tumor microenvironment.

  15. Application of highly-ordered TiO2 nanotube-arrays in heterojunction dye-sensitized solar cells

    Science.gov (United States)

    Paulose, Maggie; Shankar, Karthik; Varghese, Oomman K.; Mor, Gopal K.; Grimes, Craig A.

    2006-06-01

    Highly-ordered TiO2 nanotube arrays are made by potentiostatic anodization of a titanium film in a fluoride containing electrolyte. Here we describe the application of this unique material architecture in both front-side and back-side illuminated dye-sensitized solar cells (DSSCs). The back-side illuminated solar cells are based on the use of 6.2 µm long (110 nm pore diameter, 20 nm wall thickness) highly-ordered nanotube-array films made by anodization of a 250 µm thick Ti foil in a KF electrolyte. Front-side illuminated solar cells use a negative electrode composed of optically transparent nanotube arrays, approximately 3600 nm in length (46 nm pore diameter, 17 nm wall thickness), grown on a fluorine doped tin oxide coated glass substrate by anodic oxidation of a previously deposited RF-sputtered titanium thin film in a HF electrolyte. After crystallization by oxygen annealling the nanotube-arrays are treated with TiCl4 to enhance photocurrent amplitudes. The arrays are then sensitized by a self-assembled monolayer of bis(tetrabutylammonium)-cis-(dithiocyanato)-N, N'- bis(4-carboxylato-4'-carboxylic acid-2, 2'-bipyridine)ruthenium(II) (commonly called 'N719'). Superior photoresponse is obtained using acetonitrile as the dye solvent. Voltage decay measurements indicate that the highly-ordered TiO2 nanotube-arrays, in comparison with nanoparticulate systems, provide excellent pathways for electron percolation with superior electron lifetimes. The front-side illuminated DSSCs, show a typical AM 1.5 photocurrent of 10.3 mA cm-2, open circuit voltage of 0.84 V, 0.54 fill factor, and 4.7% efficiency although the transparent nanotube-array negative electrode is only 360 nm thick. The back-side illuminated DSSCs show an AM 1.5 short-circuit current density of 10.6 mA cm-2, 0.82 V open circuit potential and a 0.51 fill factor yielding a solar conversion efficiency of 4.4%.

  16. Microcavity arrays as an in vitro model system of the bone marrow niche for hematopoietic stem cells.

    Science.gov (United States)

    Wuchter, Patrick; Saffrich, Rainer; Giselbrecht, Stefan; Nies, Cordula; Lorig, Hanna; Kolb, Stephanie; Ho, Anthony D; Gottwald, Eric

    2016-06-01

    In previous studies human mesenchymal stromal cells (MSCs) maintained the "stemness" of human hematopoietic progenitor cells (HPCs) through direct cell-cell contact in two-dimensional co-culture systems. We establish a three-dimensional (3D) co-culture system based on a custom-made chip, the 3(D)-KITChip, as an in vitro model system of the human hematopoietic stem cell niche. This array of up to 625 microcavities, with 300 μm size in each orientation, was inserted into a microfluidic bioreactor. The microcavities of the 3(D)-KITChip were inoculated with human bone marrow MSCs together with umbilical cord blood HPCs. MSCs used the microcavities as a scaffold to build a complex 3D mesh. HPCs were distributed three-dimensionally inside this MSC network and formed ß-catenin- and N-cadherin-based intercellular junctions to the surrounding MSCs. Using RT(2)-PCR and western blots, we demonstrate that a proportion of HPCs maintained the expression of CD34 throughout a culture period of 14 days. In colony-forming unit assays, the hematopoietic stem cell plasticity remained similar after 14 days of bioreactor co-culture, whereas monolayer co-cultures showed increasing signs of HPC differentiation and loss of stemness. These data support the notion that the 3D microenvironment created within the microcavity array preserves vital stem cell functions of HPCs more efficiently than conventional co-culture systems. PMID:26829941

  17. Immunoprofiling reveals unique cell-specific patterns of wall epitopes in the expanding Arabidopsis stem.

    Science.gov (United States)

    Hall, Hardy C; Cheung, Jingling; Ellis, Brian E

    2013-04-01

    The Arabidopsis inflorescence stem undergoes rapid directional growth, requiring massive axial cell-wall extension in all its tissues, but, at maturity, these tissues are composed of cell types that exhibit markedly different cell-wall structures. It is not clear whether the cell-wall compositions of these cell types diverge rapidly following axial growth cessation, or whether compositional divergence occurs at earlier stages in differentiation, despite the common requirement for cell-wall extensibility. To examine this question, seven cell types were assayed for the abundance and distribution of 18 major cell-wall glycan classes at three developmental stages along the developing inflorescence stem, using a high-throughput immunolabelling strategy. These stages represent a phase of juvenile growth, a phase displaying the maximum rate of stem extension, and a phase in which extension growth is ceasing. The immunolabelling patterns detected demonstrate that the cell-wall composition of most stem tissues undergoes pronounced changes both during and after rapid extension growth. Hierarchical clustering of the immunolabelling signals identified cell-specific binding patterns for some antibodies, including a sub-group of arabinogalactan side chain-directed antibodies whose epitope targets are specifically associated with the inter-fascicular fibre region during the rapid cell expansion phase. The data reveal dynamic, cell type-specific changes in cell-wall chemistry across diverse cell types during cell-wall expansion and maturation in the Arabidopsis inflorescence stem, and highlight the paradox between this structural diversity and the uniform anisotropic cell expansion taking place across all tissues during stem growth.

  18. Specific lectin biomarkers for isolation of human pluripotent stem cells identified through array-based glycomic analysis

    Institute of Scientific and Technical Information of China (English)

    Yu-Chieh Wang; Trevor R Leonardo; Ying Liu; Suzanne E Peterson; Louise C Laurent; Shinya Yamanaka; Jeanne F Loring; Masato Nakagawa; Ibon Garitaonandia; Ileana Slavin; Gulsah Altun; Robert M Lacharite; Kristopher L Nazor; Ha T Tran; Candace L Lynch

    2011-01-01

    Rapid and dependable methods for isolating human pluripotent stem cell (hPSC) populations are urgently needed for quality control in basic research and in cell-based therapy applications.Using lectin arrays,we analyzed glycoproteins extracted from 26 hPSC samples and 22 differentiated cell samples,and identified a small group of iectins with distinctive binding signatures that were sufficient to distinguish hPSCs from a variety of non-pluripotent cell types.These specific biomarkers were shared by all the 12 human embryonic stem cell and the 14 human induced pluripotent stem cell samples examined,regardless of the laboratory of origin,the culture conditions,the somatic cell type reprogrammed,or the reprogramming method used.We demonstrated a practical application of specific lectin binding by detecting hPSCs within a differentiated cell population with lectin-mediated staining followed by fluorescence microscopy and flow cytometry,and by enriching and purging viable hPSCs from mixed cell populations using lectin-mediated cell separation.Global gene expression analysis showed pluripotency-associated differential expression of specific fucosyltransferases and sialyltransferases,which may underlie these differences in protein glycosylation and lectin binding.Taken together,our results show that protein glycosylation differs considerably between pluripotent and non-pluripotent cells,and demonstrate that lectins may be used as biomarkers to monitor pluripotency in stem cell populations and for removal of viable hPSCs from mixed cell populations.

  19. A robust method to analyze copy number alterations of less than 100 kb in single cells using oligonucleotide array CGH.

    Directory of Open Access Journals (Sweden)

    Birte Möhlendick

    Full Text Available Comprehensive genome wide analyses of single cells became increasingly important in cancer research, but remain to be a technically challenging task. Here, we provide a protocol for array comparative genomic hybridization (aCGH of single cells. The protocol is based on an established adapter-linker PCR (WGAM and allowed us to detect copy number alterations as small as 56 kb in single cells. In addition we report on factors influencing the success of single cell aCGH downstream of the amplification method, including the characteristics of the reference DNA, the labeling technique, the amount of input DNA, reamplification, the aCGH resolution, and data analysis. In comparison with two other commercially available non-linear single cell amplification methods, WGAM showed a very good performance in aCGH experiments. Finally, we demonstrate that cancer cells that were processed and identified by the CellSearch® System and that were subsequently isolated from the CellSearch® cartridge as single cells by fluorescence activated cell sorting (FACS could be successfully analyzed using our WGAM-aCGH protocol. We believe that even in the era of next-generation sequencing, our single cell aCGH protocol will be a useful and (cost- effective approach to study copy number alterations in single cells at resolution comparable to those reported currently for single cell digital karyotyping based on next generation sequencing data.

  20. Kinetic modeling reveals a common death niche for newly formed and mature B cells.

    Directory of Open Access Journals (Sweden)

    Gitit Shahaf

    Full Text Available BACKGROUND: B lymphocytes are subject to elimination following strong BCR ligation in the absence of appropriate second signals, and this mechanism mediates substantial cell losses during late differentiation steps in the bone marrow and periphery. Mature B cells may also be eliminated through this mechanism as well as through normal turnover, but the population containing mature cells destined for elimination has not been identified. Herein, we asked whether the transitional 3 (T3 subset, which contains most newly formed cells undergoing anergic death, could also include mature B cells destined for elimination. METHODOLOGY/PRINCIPAL FINDINGS: To interrogate this hypothesis and its implications, we applied mathematical models to previously generated in vivo labeling data. Our analyses reveal that the death rate of T3 B cells is far higher than the death rates of all other splenic B cell subpopulations. Further, the model, in which the T3 pool includes both newly formed and mature primary B cells destined for apoptotic death, shows that this cell loss may account for nearly all mature B cell turnover. CONCLUSIONS/SIGNIFICANCE: This finding has implications for the mechanism of normal mature B cell turnover.

  1. High-throughput mammalian two-hybrid screening for protein-protein interactions using transfected cell arrays

    Directory of Open Access Journals (Sweden)

    Thamm Sabine

    2008-02-01

    Full Text Available Abstract Background Most of the biological processes rely on the formation of protein complexes. Investigation of protein-protein interactions (PPI is therefore essential for understanding of cellular functions. It is advantageous to perform mammalian PPI analysis in mammalian cells because the expressed proteins can then be subjected to essential post-translational modifications. Until now mammalian two-hybrid assays have been performed on individual gene scale. We here describe a new and cost-effective method for the high-throughput detection of protein-protein interactions in mammalian cells that combines the advantages of mammalian two-hybrid systems with those of DNA microarrays. Results In this cell array protein-protein interaction assay (CAPPIA, mixtures of bait and prey expression plasmids together with an auto-fluorescent reporter are immobilized on glass slides in defined array formats. Adherent cells that grow on top of the micro-array will become fluorescent only if the expressed proteins interact and subsequently trans-activate the reporter. Using known interaction partners and by screening 160 different combinations of prey and bait proteins associated with the human androgen receptor we demonstrate that this assay allows the quantitative detection of specific protein interactions in different types of mammalian cells and under the influence of different compounds. Moreover, different strategies in respect to bait-prey combinations are presented. Conclusion We demonstrate that the CAPPIA assay allows the quantitative detection of specific protein interactions in different types of mammalian cells and under the influence of different compounds. The high number of preys that can be tested per slide together with the flexibility to interrogate any bait of interest and the small amounts of reagents that are required makes this assay currently one of the most economical high-throughput detection assays for protein-protein interactions

  2. Label-free capture of breast cancer cells spiked in buffy coats using carbon nanotube antibody micro-arrays

    Science.gov (United States)

    Khosravi, Farhad; Trainor, Patrick; Rai, Shesh N.; Kloecker, Goetz; Wickstrom, Eric; Panchapakesan, Balaji

    2016-04-01

    We demonstrate the rapid and label-free capture of breast cancer cells spiked in buffy coats using nanotube-antibody micro-arrays. Single wall carbon nanotube arrays were manufactured using photo-lithography, metal deposition, and etching techniques. Anti-epithelial cell adhesion molecule (EpCAM) antibodies were functionalized to the surface of the nanotube devices using 1-pyrene-butanoic acid succinimidyl ester functionalization method. Following functionalization, plain buffy coat and MCF7 cell spiked buffy coats were adsorbed on to the nanotube device and electrical signatures were recorded for differences in interaction between samples. A statistical classifier for the ‘liquid biopsy’ was developed to create a predictive model based on dynamic time warping to classify device electrical signals that corresponded to plain (control) or spiked buffy coats (case). In training test, the device electrical signals originating from buffy versus spiked buffy samples were classified with ˜100% sensitivity, ˜91% specificity and ˜96% accuracy. In the blinded test, the signals were classified with ˜91% sensitivity, ˜82% specificity and ˜86% accuracy. A heatmap was generated to visually capture the relationship between electrical signatures and the sample condition. Confocal microscopic analysis of devices that were classified as spiked buffy coats based on their electrical signatures confirmed the presence of cancer cells, their attachment to the device and overexpression of EpCAM receptors. The cell numbers were counted to be ˜1-17 cells per 5 μl per device suggesting single cell sensitivity in spiked buffy coats that is scalable to higher volumes using the micro-arrays.

  3. Label-free capture of breast cancer cells spiked in buffy coats using carbon nanotube antibody micro-arrays.

    Science.gov (United States)

    Khosravi, Farhad; Trainor, Patrick; Rai, Shesh N; Kloecker, Goetz; Wickstrom, Eric; Panchapakesan, Balaji

    2016-04-01

    We demonstrate the rapid and label-free capture of breast cancer cells spiked in buffy coats using nanotube-antibody micro-arrays. Single wall carbon nanotube arrays were manufactured using photo-lithography, metal deposition, and etching techniques. Anti-epithelial cell adhesion molecule (EpCAM) antibodies were functionalized to the surface of the nanotube devices using 1-pyrene-butanoic acid succinimidyl ester functionalization method. Following functionalization, plain buffy coat and MCF7 cell spiked buffy coats were adsorbed on to the nanotube device and electrical signatures were recorded for differences in interaction between samples. A statistical classifier for the 'liquid biopsy' was developed to create a predictive model based on dynamic time warping to classify device electrical signals that corresponded to plain (control) or spiked buffy coats (case). In training test, the device electrical signals originating from buffy versus spiked buffy samples were classified with ∼100% sensitivity, ∼91% specificity and ∼96% accuracy. In the blinded test, the signals were classified with ∼91% sensitivity, ∼82% specificity and ∼86% accuracy. A heatmap was generated to visually capture the relationship between electrical signatures and the sample condition. Confocal microscopic analysis of devices that were classified as spiked buffy coats based on their electrical signatures confirmed the presence of cancer cells, their attachment to the device and overexpression of EpCAM receptors. The cell numbers were counted to be ∼1-17 cells per 5 μl per device suggesting single cell sensitivity in spiked buffy coats that is scalable to higher volumes using the micro-arrays.

  4. A novel non-overlapping bi-clustering algorithm for network generation using living cell array data

    OpenAIRE

    Yang, E.; Foteinou, P.T.; King, K.R.; Yarmush, M L; Androulakis, I.P.

    2007-01-01

    The living cell array quantifies the contribution of activated transcription factors upon the expression levels of their target genes. The direct manipulation of the regulatory mechanisms offers enormous possibilities for deciphering the machinery that activates and controls gene expression. We propose a novel bi-clustering algorithm for generating non-overlapping clusters of reporter genes and conditions and demonstrate how this information can be interpreted in order to assist in the constr...

  5. Dynamics inside the cancer cell attractor reveal cell heterogeneity, limits of stability, and escape.

    Science.gov (United States)

    Li, Qin; Wennborg, Anders; Aurell, Erik; Dekel, Erez; Zou, Jie-Zhi; Xu, Yuting; Huang, Sui; Ernberg, Ingemar

    2016-03-01

    The observed intercellular heterogeneity within a clonal cell population can be mapped as dynamical states clustered around an attractor point in gene expression space, owing to a balance between homeostatic forces and stochastic fluctuations. These dynamics have led to the cancer cell attractor conceptual model, with implications for both carcinogenesis and new therapeutic concepts. Immortalized and malignant EBV-carrying B-cell lines were used to explore this model and characterize the detailed structure of cell attractors. Any subpopulation selected from a population of cells repopulated the whole original basin of attraction within days to weeks. Cells at the basin edges were unstable and prone to apoptosis. Cells continuously changed states within their own attractor, thus driving the repopulation, as shown by fluorescent dye tracing. Perturbations of key regulatory genes induced a jump to a nearby attractor. Using the Fokker-Planck equation, this cell population behavior could be described as two virtual, opposing influences on the cells: one attracting toward the center and the other promoting diffusion in state space (noise). Transcriptome analysis suggests that these forces result from high-dimensional dynamics of the gene regulatory network. We propose that they can be generalized to all cancer cell populations and represent intrinsic behaviors of tumors, offering a previously unidentified characteristic for studying cancer. PMID:26929366

  6. Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control

    OpenAIRE

    Burke, Jason R.; Hura, Greg L.; Rubin, Seth M.

    2012-01-01

    Rubin and colleagues describe the first structures of full-length and phosphorylated Retinoblastoma (Rb) protein. These structures reveal the mechanism of Rb inactivation and provide valuable insight into this critical tumor suppressor protein's allosteric inhibition via multisite Cdk phosphorylation and its E2F and cell cycle regulation.

  7. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Resch, Michael G.; Donohoe, Byron; Ciesielski, Peter; Nill, Jennifer; McKinney, Kellene; Mittal, Ashutosh; Katahira, Rui; Himmel, Michael; Biddy, Mary; Beckham, Gregg; Decker, Steve

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution.

  8. Semiconductor wire array structures, and solar cells and photodetectors based on such structures

    Science.gov (United States)

    Kelzenberg, Michael D.; Atwater, Harry A.; Briggs, Ryan M.; Boettcher, Shannon W.; Lewis, Nathan S.; Petykiewicz, Jan A.

    2014-08-19

    A structure comprising an array of semiconductor structures, an infill material between the semiconductor materials, and one or more light-trapping elements is described. Photoconverters and photoelectrochemical devices based on such structure also described.

  9. Prognostic Impact of Array-based Genomic Profiles in Esophageal Squamous Cell Cancer

    International Nuclear Information System (INIS)

    Esophageal squamous cell carcinoma (ESCC) is a genetically complex tumor type and a major cause of cancer related mortality. Although distinct genetic alterations have been linked to ESCC development and prognosis, the genetic alterations have not gained clinical applicability. We applied array-based comparative genomic hybridization (aCGH) to obtain a whole genome copy number profile relevant for identifying deranged pathways and clinically applicable markers. A 32 k aCGH platform was used for high resolution mapping of copy number changes in 30 stage I-IV ESCC. Potential interdependent alterations and deranged pathways were identified and copy number changes were correlated to stage, differentiation and survival. Copy number alterations affected median 19% of the genome and included recurrent gains of chromosome regions 5p, 7p, 7q, 8q, 10q, 11q, 12p, 14q, 16p, 17p, 19p, 19q, and 20q and losses of 3p, 5q, 8p, 9p and 11q. High-level amplifications were observed in 30 regions and recurrently involved 7p11 (EGFR), 11q13 (MYEOV, CCND1, FGF4, FGF3, PPFIA, FAD, TMEM16A, CTTS and SHANK2) and 11q22 (PDFG). Gain of 7p22.3 predicted nodal metastases and gains of 1p36.32 and 19p13.3 independently predicted poor survival in multivariate analysis. aCGH profiling verified genetic complexity in ESCC and herein identified imbalances of multiple central tumorigenic pathways. Distinct gains correlate with clinicopathological variables and independently predict survival, suggesting clinical applicability of genomic profiling in ESCC

  10. Principles of bacterial cell-size determination revealed by cell wall synthesis perturbations

    OpenAIRE

    Carolina Tropini; Timothy K. Lee; Jen Hsin; Samantha M. Desmarais; Tristan Ursell; Russell D. Monds; Kerwyn Casey Huang

    2014-01-01

    Although bacterial cell morphology is tightly controlled, the principles of size regulation remain elusive. In Escherichia coli, perturbation of cell-wall synthesis often results in similar morphologies, making it difficult to deconvolve the complex genotype-phenotype relationships underlying morphogenesis. Here we modulated cell width through heterologous expression of sequences encoding the essential enzyme PBP2 and through sublethal treatments with drugs that inhibit PBP2 and the MreB cyto...

  11. Nuclear motility in glioma cells reveals a cell-line dependent role of various cytoskeletal components.

    Directory of Open Access Journals (Sweden)

    Alexa Kiss

    Full Text Available Nuclear migration is a general term for the movement of the nucleus towards a specific site in the cell. These movements are involved in a number of fundamental biological processes, such as fertilization, cell division, and embryonic development. Despite of its importance, the mechanism of nuclear migration is still poorly understood in mammalian cells. In order to shed light on the mechanical processes underlying nuclear movements, we adapted a micro-patterning based assay. C6 rat and U87 human glioma cells seeded on fibronectin patterns--thereby forced into a bipolar morphology--displayed oscillatory movements of the nucleus or the whole cell, respectively. We found that both the actomyosin system and microtubules are involved in the nuclear/cellular movements of both cell lines, but their contributions are cell-/migration-type specific. Dynein activity was necessary for nuclear migration of C6 cells but active myosin-II was dispensable. On the other hand, coupled nuclear and cellular movements of U87 cells were driven by actomyosin contraction. We explain these cell-line dependent effects by the intrinsic differences in the overall mechanical tension due to the various cytoskeletal elements inside the cell. Our observations showed that the movements of the nucleus and the centrosome are strongly correlated and display large variation, indicating a tight but flexible coupling between them. The data also indicate that the forces responsible for nuclear movements are not acting directly via the centrosome. Based on our observations, we propose a new model for nuclear oscillations in C6 cells in which dynein and microtubule dynamics are the main drivers of nuclear movements. This mechanism is similar to the meiotic nuclear oscillations of Schizosaccharomyces pombe and may be evolutionary conserved.

  12. Tumorigenicity of hypoxic respiring cancer cells revealed by a hypoxia–cell cycle dual reporter

    Science.gov (United States)

    Le, Anne; Stine, Zachary E.; Nguyen, Christopher; Afzal, Junaid; Sun, Peng; Hamaker, Max; Siegel, Nicholas M.; Gouw, Arvin M.; Kang, Byung-hak; Yu, Shu-Han; Cochran, Rory L.; Sailor, Kurt A.; Song, Hongjun; Dang, Chi V.

    2014-01-01

    Although aerobic glycolysis provides an advantage in the hypoxic tumor microenvironment, some cancer cells can also respire via oxidative phosphorylation. These respiring (“non-Warburg”) cells were previously thought not to play a key role in tumorigenesis and thus fell from favor in the literature. We sought to determine whether subpopulations of hypoxic cancer cells have different metabolic phenotypes and gene-expression profiles that could influence tumorigenicity and therapeutic response, and we therefore developed a dual fluorescent protein reporter, HypoxCR, that detects hypoxic [hypoxia-inducible factor (HIF) active] and/or cycling cells. Using HEK293T cells as a model, we identified four distinct hypoxic cell populations by flow cytometry. The non-HIF/noncycling cell population expressed a unique set of genes involved in mitochondrial function. Relative to the other subpopulations, these hypoxic “non-Warburg” cells had highest oxygen consumption rates and mitochondrial capacity consistent with increased mitochondrial respiration. We found that these respiring cells were unexpectedly tumorigenic, suggesting that continued respiration under limiting oxygen conditions may be required for tumorigenicity. PMID:25114222

  13. Agrobacterium type IV secretion system and its substrates form helical arrays around the circumference of virulence-induced cells.

    Science.gov (United States)

    Aguilar, Julieta; Zupan, John; Cameron, Todd A; Zambryski, Patricia C

    2010-02-23

    The genetic transformation of plant cells by Agrobacterium tumefaciens results from the transfer of DNA and proteins via a specific virulence (vir) -induced type IV secretion system (T4SS). To better understand T4SS function, we analyzed the localization of its structural components and substrates by deconvolution fluorescence microscopy. GFP fusions to T4SS proteins with cytoplasmic tails, VirB8 and VirD4, or cytoplasmic T4SS substrate proteins, VirD2, VirE2, and VirF, localize in a helical pattern of fluorescent foci around the perimeter of the bacterial cell. All fusion proteins were expressed at native levels of vir induction. Importantly, most fusion proteins are functional and do not exhibit dominant-negative effects on DNA transfer to plant cells. Further, GFP-VirB8 complements a virB8 deletion strain. We also detect native VirB8 localization as a helical array of foci by immunofluorescence microscopy. T4SS foci likely use an existing helical scaffold during their assembly. Indeed, the bacterial cytoskeletal component MinD colocalizes with GFP-VirB8. Helical arrays of foci are found at all times investigated between 12 and 48 h post vir induction at 19 degrees C. These data lead to a model with multiple T4SSs around the bacterial cell that likely facilitate host cell attachment and DNA transfer. In support, we find multiple T pili around vir-induced bacterial cells. PMID:20133577

  14. An enteroendocrine cell-enteric glia connection revealed by 3D electron microscopy.

    Science.gov (United States)

    Bohórquez, Diego V; Samsa, Leigh A; Roholt, Andrew; Medicetty, Satish; Chandra, Rashmi; Liddle, Rodger A

    2014-01-01

    The enteroendocrine cell is the cornerstone of gastrointestinal chemosensation. In the intestine and colon, this cell is stimulated by nutrients, tastants that elicit the perception of flavor, and bacterial by-products; and in response, the cell secretes hormones like cholecystokinin and peptide YY--both potent regulators of appetite. The development of transgenic mice with enteroendocrine cells expressing green fluorescent protein has allowed for the elucidation of the apical nutrient sensing mechanisms of the cell. However, the basal secretory aspects of the enteroendocrine cell remain largely unexplored, particularly because a complete account of the enteroendocrine cell ultrastructure does not exist. Today, the fine ultrastructure of a specific cell can be revealed in the third dimension thanks to the invention of serial block face scanning electron microscopy (SBEM). Here, we bridged confocal microscopy with SBEM to identify the enteroendocrine cell of the mouse and study its ultrastructure in the third dimension. The results demonstrated that 73.5% of the peptide-secreting vesicles in the enteroendocrine cell are contained within an axon-like basal process. We called this process a neuropod. This neuropod contains neurofilaments, which are typical structural proteins of axons. Surprisingly, the SBEM data also demonstrated that the enteroendocrine cell neuropod is escorted by enteric glia--the cells that nurture enteric neurons. We extended these structural findings into an in vitro intestinal organoid system, in which the addition of glial derived neurotrophic factors enhanced the development of neuropods in enteroendocrine cells. These findings open a new avenue of exploration in gastrointestinal chemosensation by unveiling an unforeseen physical relationship between enteric glia and enteroendocrine cells. PMID:24587096

  15. An enteroendocrine cell-enteric glia connection revealed by 3D electron microscopy.

    Directory of Open Access Journals (Sweden)

    Diego V Bohórquez

    Full Text Available The enteroendocrine cell is the cornerstone of gastrointestinal chemosensation. In the intestine and colon, this cell is stimulated by nutrients, tastants that elicit the perception of flavor, and bacterial by-products; and in response, the cell secretes hormones like cholecystokinin and peptide YY--both potent regulators of appetite. The development of transgenic mice with enteroendocrine cells expressing green fluorescent protein has allowed for the elucidation of the apical nutrient sensing mechanisms of the cell. However, the basal secretory aspects of the enteroendocrine cell remain largely unexplored, particularly because a complete account of the enteroendocrine cell ultrastructure does not exist. Today, the fine ultrastructure of a specific cell can be revealed in the third dimension thanks to the invention of serial block face scanning electron microscopy (SBEM. Here, we bridged confocal microscopy with SBEM to identify the enteroendocrine cell of the mouse and study its ultrastructure in the third dimension. The results demonstrated that 73.5% of the peptide-secreting vesicles in the enteroendocrine cell are contained within an axon-like basal process. We called this process a neuropod. This neuropod contains neurofilaments, which are typical structural proteins of axons. Surprisingly, the SBEM data also demonstrated that the enteroendocrine cell neuropod is escorted by enteric glia--the cells that nurture enteric neurons. We extended these structural findings into an in vitro intestinal organoid system, in which the addition of glial derived neurotrophic factors enhanced the development of neuropods in enteroendocrine cells. These findings open a new avenue of exploration in gastrointestinal chemosensation by unveiling an unforeseen physical relationship between enteric glia and enteroendocrine cells.

  16. Atmospheric-pressure plasma-jet from micronozzle array and its biological effects on living cells for cancer therapy

    Science.gov (United States)

    Kim, Kangil; Choi, Jae Duk; Hong, Yong Cheol; Kim, Geunyoung; Noh, Eun Joo; Lee, Jong-Soo; Yang, Sang Sik

    2011-02-01

    We propose a plasma-jet device with a micrometer-sized nozzle array for use in a cancer therapy. Also, we show the biological effects of atmospheric-pressure plasma on living cells. Nitrogen-plasma activated a surrogate DNA damage signal transduction pathway, called the ataxia telangiectasia mutated (ATM)-checkpoint kinase 2 pathway, suggesting that the nitrogen-plasma generates DNA double-strand breaks. Phosphorylation of H2AX and p53 was detected in the plasma-treated cells, leading to apoptotic cell death. Thus, an effect for the nitrogen plasma in the control of apoptotic cell death provides insight into the how biological effects of the nitrogen-plasma can be applied to the control of cell survival, a finding with potential therapeutic implications.

  17. Ordered crystalline TiO2 nanohexagon arrays for improving conversion efficiency of dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Anatase TiO2 nanohexagon arrays were grown by using an anodization process of Ti foil in fluoride containing electrolytes. Photoanode based on the as-grown anatase TiO2 nanohexagon arrays for DSSCs showed a power photoconversion efficiency of 4.01% and incident photon-to-current conversion efficiency of 68%, which are significantly higher than those of the device based on anatase TiO2 nanotube arrays. This improvement in power conversion efficiency should be attributed to the fact that the nanotubes with hexagonal structure have higher surface area to allow the uploading of more dye molecules for light harvesting. Also, the spacing introduced inside the hexagon might allow the dye molecules to cover the interior of the walls. In addition, it is believed that the photoconversion efficiency can be further increased by optimizing the hexagonal structure through the electrochemical conditions. - Graphical abstract: Nanotubes with hexagonal structure have higher surface area to allow the uploading of more dye molecules for light harvesting in dye-sensitized solar cells. - Highlights: • A unique TiO2 nanohexagon arrays were grown by an anodization process. • Higher surface area for dye uploading provided by the hexagon structure. • TiO2 nanohexagon based photoanode has PCE of 4.01% and IPCE of 68%

  18. Ordered crystalline TiO{sub 2} nanohexagon arrays for improving conversion efficiency of dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Javed, Hafiz Muhammad Asif [Electronic Materials Research Laboratory, International Center for Dielectric Research, Key Laboratory of the Ministry of Education, State Key Laboratory for Manufacturing Systems Engineering, Xi' an Jiaotong University, Xi' an, 710049 (China); Que, Wenxiu, E-mail: wxque@mail.xjtu.edu.cn [Electronic Materials Research Laboratory, International Center for Dielectric Research, Key Laboratory of the Ministry of Education, State Key Laboratory for Manufacturing Systems Engineering, Xi' an Jiaotong University, Xi' an, 710049 (China); Yin, Xingtian; Xing, Yonglei; Liu, Xiaobin; Asghar, Ali; Shao, Jinyou [Electronic Materials Research Laboratory, International Center for Dielectric Research, Key Laboratory of the Ministry of Education, State Key Laboratory for Manufacturing Systems Engineering, Xi' an Jiaotong University, Xi' an, 710049 (China); Kong, Ling Bing, E-mail: ELBKong@ntu.edu.sg [School of Materials Science and Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798 (Singapore)

    2015-10-15

    Anatase TiO{sub 2} nanohexagon arrays were grown by using an anodization process of Ti foil in fluoride containing electrolytes. Photoanode based on the as-grown anatase TiO{sub 2} nanohexagon arrays for DSSCs showed a power photoconversion efficiency of 4.01% and incident photon-to-current conversion efficiency of 68%, which are significantly higher than those of the device based on anatase TiO{sub 2} nanotube arrays. This improvement in power conversion efficiency should be attributed to the fact that the nanotubes with hexagonal structure have higher surface area to allow the uploading of more dye molecules for light harvesting. Also, the spacing introduced inside the hexagon might allow the dye molecules to cover the interior of the walls. In addition, it is believed that the photoconversion efficiency can be further increased by optimizing the hexagonal structure through the electrochemical conditions. - Graphical abstract: Nanotubes with hexagonal structure have higher surface area to allow the uploading of more dye molecules for light harvesting in dye-sensitized solar cells. - Highlights: • A unique TiO{sub 2} nanohexagon arrays were grown by an anodization process. • Higher surface area for dye uploading provided by the hexagon structure. • TiO{sub 2} nanohexagon based photoanode has PCE of 4.01% and IPCE of 68%.

  19. Genomic instability of micronucleated cells revealed by single-cell comparative genomic hybridization.

    NARCIS (Netherlands)

    Imle, A.; Polzer, B.; Alexander, S.; Klein, C.A.; Friedl, P.H.A.

    2009-01-01

    Nuclear variation in size and shape and genomic instability are hallmarks of dedifferentiated cancer cells. Although micronuclei are a typical long-term consequence of DNA damage, their contribution to chromosomal instability and clonal diversity in cancer disease is unclear. We isolated cancer cell

  20. Single cell mass cytometry reveals remodeling of human T cell phenotypes by varicella zoster virus.

    Science.gov (United States)

    Sen, Nandini; Mukherjee, Gourab; Arvin, Ann M

    2015-11-15

    The recent application of mass cytometry (CyTOF) to biology provides a 'systems' approach to monitor concurrent changes in multiple host cell factors at the single cell level. We used CyTOF to evaluate T cells infected with varicella zoster virus (VZV) infection, documenting virus-mediated phenotypic and functional changes caused by this T cell tropic human herpesvirus. Here we summarize our findings using two complementary panels of antibodies against surface and intracellular signaling proteins to elucidate the consequences of VZV-mediated perturbations on the surface and in signaling networks of infected T cells. CyTOF data was analyzed by several statistical, analytical and visualization tools including hierarchical clustering, orthogonal scaling, SPADE, viSNE, and SLIDE. Data from the mass cytometry studies demonstrated that VZV infection led to 'remodeling' of the surface architecture of T cells, promoting skin trafficking phenotypes and associated with concomitant activation of T-cell receptor and PI3-kinase pathways. This method offers a novel approach for understanding viral interactions with differentiated host cells important for pathogenesis. PMID:26213183

  1. Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status

    Science.gov (United States)

    Coscia, F.; Watters, K. M.; Curtis, M.; Eckert, M. A.; Chiang, C. Y.; Tyanova, S.; Montag, A.; Lastra, R. R.; Lengyel, E.; Mann, M.

    2016-01-01

    A cell line representative of human high-grade serous ovarian cancer (HGSOC) should not only resemble its tumour of origin at the molecular level, but also demonstrate functional utility in pre-clinical investigations. Here, we report the integrated proteomic analysis of 26 ovarian cancer cell lines, HGSOC tumours, immortalized ovarian surface epithelial cells and fallopian tube epithelial cells via a single-run mass spectrometric workflow. The in-depth quantification of >10,000 proteins results in three distinct cell line categories: epithelial (group I), clear cell (group II) and mesenchymal (group III). We identify a 67-protein cell line signature, which separates our entire proteomic data set, as well as a confirmatory publicly available CPTAC/TCGA tumour proteome data set, into a predominantly epithelial and mesenchymal HGSOC tumour cluster. This proteomics-based epithelial/mesenchymal stratification of cell lines and human tumours indicates a possible origin of HGSOC either from the fallopian tube or from the ovarian surface epithelium. PMID:27561551

  2. Single-cell duplex RT-LATE-PCR reveals Oct4 and Xist RNA gradients in 8-cell embryos

    Directory of Open Access Journals (Sweden)

    Hartung Odelya

    2007-12-01

    combined with PurAmp sample preparation, for quantitative analysis of transcript levels in single cells. With this technique, copy numbers of different RNAs can be accurately measured independently from their relative abundance in a cell, a goal that cannot be achieved using symmetric PCR. The technique illustrated in this work is relevant to a wide array of applications, such as stem cell and cancer cell analysis and preimplantation genetic diagnostics.

  3. On-line observation of cell growth in a three-dimensional matrix on surface modified microelectrode arrays

    OpenAIRE

    Lin, Shu-Ping; Kyriakides, Themis R.; Chen, Jia-Jin J.

    2009-01-01

    Despite many successful applications of microelectrode arrays (MEAs), typical two-dimensional in-vitro cultures do not project the full scale of the cell growth environment in the three-dimensional (3D) in-vivo setting. This study aims to on-line monitor in-vitro cell growth in a 3D matrix on the surface-modified MEAs with a dynamic perfusion culture system. A 3D matrix consisting of poly(ethylene glycol) hydrogel supplemented with poly-D-lysine was subsequently synthesized in-situ on the sel...

  4. Wafer-Scale Integration of Inverted Nanopyramid Arrays for Advanced Light Trapping in Crystalline Silicon Thin Film Solar Cells.

    Science.gov (United States)

    Zhou, Suqiong; Yang, Zhenhai; Gao, Pingqi; Li, Xiaofeng; Yang, Xi; Wang, Dan; He, Jian; Ying, Zhiqin; Ye, Jichun

    2016-12-01

    Crystalline silicon thin film (c-Si TF) solar cells with an active layer thickness of a few micrometers may provide a viable pathway for further sustainable development of photovoltaic technology, because of its potentials in cost reduction and high efficiency. However, the performance of such cells is largely constrained by the deteriorated light absorption of the ultrathin photoactive material. Here, we report an efficient light-trapping strategy in c-Si TFs (~20 μm in thickness) that utilizes two-dimensional (2D) arrays of inverted nanopyramid (INP) as surface texturing. Three types of INP arrays with typical periodicities of 300, 670, and 1400 nm, either on front, rear, or both surfaces of the c-Si TFs, are fabricated by scalable colloidal lithography and anisotropic wet etch technique. With the extra aid of antireflection coating, the sufficient optical absorption of 20-μm-thick c-Si with a double-sided 1400-nm INP arrays yields a photocurrent density of 39.86 mA/cm(2), which is about 76 % higher than the flat counterpart (22.63 mA/cm(2)) and is only 3 % lower than the value of Lambertian limit (41.10 mA/cm(2)). The novel surface texturing scheme with 2D INP arrays has the advantages of excellent antireflection and light-trapping capabilities, an inherent low parasitic surface area, a negligible surface damage, and a good compatibility for subsequent process steps, making it a good alternative for high-performance c-Si TF solar cells. PMID:27071681

  5. Photoelectrochemical cell/dye-sensitized solar cell tandem water splitting systems with transparent and vertically aligned quantum dot sensitized TiO2 nanorod arrays

    Science.gov (United States)

    Shin, Kahee; Yoo, Ji-Beom; Park, Jong Hyeok

    2013-03-01

    The present work reports fabrication of vertically aligned CdS sensitized TiO2 nanorod arrays grown on transparent conducting oxide substrate with high transparency as a photoanode in photoelectrochemical cell for water splitting. To realize an unassisted water splitting system, the photoanode and dye-sensitized solar cell tandem structures are tried and their electrochemical behaviors are also investigated. The hydrothermally grown TiO2 nanorod arrays followed by CdS nanoparticle decoration can improve the light absorption of long wavelength light resulting in increased photocurrent density. Two different techniques (electrodeposition and spray pyrolysis deposition) of CdS nanoparticle sensitization are carried out and their water splitting behaviors in the tandem cell are compared.

  6. Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

    Directory of Open Access Journals (Sweden)

    Dmitri Papatsenko

    2015-08-01

    Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

  7. Power-Law Modeling of Cancer Cell Fates Driven by Signaling Data to Reveal Drug Effects

    Science.gov (United States)

    Zhang, Fan; Wu, Min; Kwoh, Chee Keong; Zheng, Jie

    2016-01-01

    Extracellular signals are captured and transmitted by signaling proteins inside a cell. An important type of cellular responses to the signals is the cell fate decision, e.g., apoptosis. However, the underlying mechanisms of cell fate regulation are still unclear, thus comprehensive and detailed kinetic models are not yet available. Alternatively, data-driven models are promising to bridge signaling data with the phenotypic measurements of cell fates. The traditional linear model for data-driven modeling of signaling pathways has its limitations because it assumes that the a cell fate is proportional to the activities of signaling proteins, which is unlikely in the complex biological systems. Therefore, we propose a power-law model to relate the activities of all the measured signaling proteins to the probabilities of cell fates. In our experiments, we compared our nonlinear power-law model with the linear model on three cancer datasets with phosphoproteomics and cell fate measurements, which demonstrated that the nonlinear model has superior performance on cell fates prediction. By in silico simulation of virtual protein knock-down, the proposed model is able to reveal drug effects which can complement traditional approaches such as binding affinity analysis. Moreover, our model is able to capture cell line specific information to distinguish one cell line from another in cell fate prediction. Our results show that the power-law data-driven model is able to perform better in cell fate prediction and provide more insights into the signaling pathways for cancer cell fates than the linear model. PMID:27764199

  8. A CdSe thin film: a versatile buffer layer for improving the performance of TiO2 nanorod array:PbS quantum dot solar cells

    Science.gov (United States)

    Tan, Furui; Wang, Zhijie; Qu, Shengchun; Cao, Dawei; Liu, Kong; Jiang, Qiwei; Yang, Ying; Pang, Shan; Zhang, Weifeng; Lei, Yong; Wang, Zhanguo

    2016-05-01

    To fully utilize the multiple exciton generation effects in quantum dots and improve the overall efficiency of the corresponding photovoltaic devices, nanostructuralizing the electron conducting layer turns out to be a feasible strategy. Herein, PbS quantum dot solar cells were fabricated on the basis of morphologically optimized TiO2 nanorod arrays. By inserting a thin layer of CdSe quantum dots into the interface of TiO2 and PbS, a dramatic enhancement in the power conversion efficiency from 4.2% to 5.2% was realized and the resulting efficiency is one of the highest values for quantum dot solar cells based on nanostructuralized buffer layers. The constructed double heterojunction with a cascade type-II energy level alignment is beneficial for promoting photogenerated charge separation and reducing charge recombination, thereby responsible for the performance improvement, as revealed by steady-state analyses as well as ultra-fast photoluminescence and photovoltage decays. Thus this paper provides a good buffer layer to the community of quantum dot solar cells.To fully utilize the multiple exciton generation effects in quantum dots and improve the overall efficiency of the corresponding photovoltaic devices, nanostructuralizing the electron conducting layer turns out to be a feasible strategy. Herein, PbS quantum dot solar cells were fabricated on the basis of morphologically optimized TiO2 nanorod arrays. By inserting a thin layer of CdSe quantum dots into the interface of TiO2 and PbS, a dramatic enhancement in the power conversion efficiency from 4.2% to 5.2% was realized and the resulting efficiency is one of the highest values for quantum dot solar cells based on nanostructuralized buffer layers. The constructed double heterojunction with a cascade type-II energy level alignment is beneficial for promoting photogenerated charge separation and reducing charge recombination, thereby responsible for the performance improvement, as revealed by steady

  9. An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.

    Directory of Open Access Journals (Sweden)

    Cecil M Benitez

    2014-10-01

    Full Text Available The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered. Here, we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets, and their endocrine or exocrine progeny. Using probabilistic models to decode the general programs organizing gene expression, we identified co-expressed gene sets in cell subsets that revealed patterns and processes governing progenitor cell development, lineage specification, and endocrine cell maturation. Purification of Neurog3 mutant cells and module network analysis linked established regulators such as Neurog3 to unrecognized gene targets and roles in pancreas development. Iterative module network analysis nominated and prioritized transcriptional regulators, including diabetes risk genes. Functional validation of a subset of candidate regulators with corresponding mutant mice revealed that the transcription factors Etv1, Prdm16, Runx1t1 and Bcl11a are essential for pancreas development. Our integrated approach provides a unique framework for identifying regulatory genes and functional gene sets underlying pancreas development and associated diseases such as diabetes mellitus.

  10. Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells.

    Science.gov (United States)

    Grover, Amit; Sanjuan-Pla, Alejandra; Thongjuea, Supat; Carrelha, Joana; Giustacchini, Alice; Gambardella, Adriana; Macaulay, Iain; Mancini, Elena; Luis, Tiago C; Mead, Adam; Jacobsen, Sten Eirik W; Nerlov, Claus

    2016-01-01

    Aged haematopoietic stem cells (HSCs) generate more myeloid cells and fewer lymphoid cells compared with young HSCs, contributing to decreased adaptive immunity in aged individuals. However, it is not known how intrinsic changes to HSCs and shifts in the balance between biased HSC subsets each contribute to the altered lineage output. Here, by analysing HSC transcriptomes and HSC function at the single-cell level, we identify increased molecular platelet priming and functional platelet bias as the predominant age-dependent change to HSCs, including a significant increase in a previously unrecognized class of HSCs that exclusively produce platelets. Depletion of HSC platelet programming through loss of the FOG-1 transcription factor is accompanied by increased lymphoid output. Therefore, increased platelet bias may contribute to the age-associated decrease in lymphopoiesis. PMID:27009448

  11. Genetically Induced Cell Death in Bulge Stem Cells Reveals Their Redundancy for Hair and Epidermal Regeneration

    OpenAIRE

    Driskell, Iwona; Oeztuerk-Winder, Feride; Humphreys, Peter; Frye, Michaela

    2014-01-01

    Adult mammalian epidermis contains multiple stem cell populations in which quiescent and more proliferative stem and progenitor populations coexist. However, the precise interrelation of these populations in homeostasis remains unclear. Here, we blocked the contribution of quiescent keratin 19 (K19)-expressing bulge stem cells to hair follicle formation through genetic ablation of the essential histone methyltransferase Setd8 that is required for the maintenance of adult skin. Deletion of Set...

  12. Integrated metabolomics and transcriptomics reveal enhanced specialized metabolism in Medicago truncatula root border cells.

    Science.gov (United States)

    Watson, Bonnie S; Bedair, Mohamed F; Urbanczyk-Wochniak, Ewa; Huhman, David V; Yang, Dong Sik; Allen, Stacy N; Li, Wensheng; Tang, Yuhong; Sumner, Lloyd W

    2015-04-01

    Integrated metabolomics and transcriptomics of Medicago truncatula seedling border cells and root tips revealed substantial metabolic differences between these distinct and spatially segregated root regions. Large differential increases in oxylipin-pathway lipoxygenases and auxin-responsive transcript levels in border cells corresponded to differences in phytohormone and volatile levels compared with adjacent root tips. Morphological examinations of border cells revealed the presence of significant starch deposits that serve as critical energy and carbon reserves, as documented through increased β-amylase transcript levels and associated starch hydrolysis metabolites. A substantial proportion of primary metabolism transcripts were decreased in border cells, while many flavonoid- and triterpenoid-related metabolite and transcript levels were increased dramatically. The cumulative data provide compounding evidence that primary and secondary metabolism are differentially programmed in border cells relative to root tips. Metabolic resources normally destined for growth and development are redirected toward elevated accumulation of specialized metabolites in border cells, resulting in constitutively elevated defense and signaling compounds needed to protect the delicate root cap and signal motile rhizobia required for symbiotic nitrogen fixation. Elevated levels of 7,4'-dihydroxyflavone were further increased in border cells of roots exposed to cotton root rot (Phymatotrichopsis omnivora), and the value of 7,4'-dihydroxyflavone as an antimicrobial compound was demonstrated using in vitro growth inhibition assays. The cumulative and pathway-specific data provide key insights into the metabolic programming of border cells that strongly implicate a more prominent mechanistic role for border cells in plant-microbe signaling, defense, and interactions than envisioned previously.

  13. RNAi screen reveals an Abl kinase-dependent host cell pathway involved in Pseudomonas aeruginosa internalization.

    Directory of Open Access Journals (Sweden)

    Julia F Pielage

    2008-03-01

    Full Text Available Internalization of the pathogenic bacterium Pseudomonas aeruginosa by non-phagocytic cells is promoted by rearrangements of the actin cytoskeleton, but the host pathways usurped by this bacterium are not clearly understood. We used RNAi-mediated gene inactivation of approximately 80 genes known to regulate the actin cytoskeleton in Drosophila S2 cells to identify host molecules essential for entry of P. aeruginosa. This work revealed Abl tyrosine kinase, the adaptor protein Crk, the small GTPases Rac1 and Cdc42, and p21-activated kinase as components of a host signaling pathway that leads to internalization of P. aeruginosa. Using a variety of complementary approaches, we validated the role of this pathway in mammalian cells. Remarkably, ExoS and ExoT, type III secreted toxins of P. aeruginosa, target this pathway by interfering with GTPase function and, in the case of ExoT, by abrogating P. aeruginosa-induced Abl-dependent Crk phosphorylation. Altogether, this work reveals that P. aeruginosa utilizes the Abl pathway for entering host cells and reveals unexpected complexity by which the P. aeruginosa type III secretion system modulates this internalization pathway. Our results furthermore demonstrate the applicability of using RNAi screens to identify host signaling cascades usurped by microbial pathogens that may be potential targets for novel therapies directed against treatment of antibiotic-resistant infections.

  14. High copy arrays containing a sequence upstream of mec-3 alter cell migration and axonal morphology in C. elegans

    Directory of Open Access Journals (Sweden)

    Patchen Brandi

    2001-01-01

    Full Text Available Abstract Background The Caenorhabditis elegans gene mec-3 encodes a LIM-homeodomain protein that is a master regulator of touch receptor neuron genes. Two of the touch neurons, the ALM neurons, are generated in the anterior of the animal and then migrate to near the middle of the animal. In animals transformed with a sequence upstream of mec-3, the ALM touch receptor neurons failed to migrate to their normal positions and sometimes migrated in the wrong direction, and the PLM touch receptor neurons showed axonal defects. Here we characterize this effect and identify the sequence causing the cell migration and axonal defects. Results The ALM migration defect did not result from RNA interference (RNAi, nonspecific effects of carrying a transgenic array, expression of GFP, or the marker gene used to make the transformants. Instead, the ALM migration defect resulted from transgenic arrays containing many copies of a specific 104 bp DNA sequence. Transgenic arrays containing this sequence did not affect all cell migrations. Conclusions The mec-3 upstream sequence appeared to be sequestering (titrating out a specific DNA-binding factor that is required for the ALMs to migrate correctly. Because titration of this factor could reverse the direction of ALM migrations, it may be part of a program that specifies both the direction and extent of ALM migrations. mec-3 is a master regulator of touch receptor neuron genes, so the factor or factors that bind this sequence may also be involved in specifying the fate of touch receptor neurons.

  15. 16.1% Efficient Hysteresis-Free Mesostructured Perovskite Solar Cells Based on Synergistically Improved ZnO Nanorod Arrays

    KAUST Repository

    Mahmood, Khalid

    2015-06-01

    Significant efficiency improvements are reported in mesoscopic perovskite solar cells based on the development of a low-temperature solution-processed ZnO nanorod (NR) array exhibiting higher NR aspect ratio, enhanced electron density, and substantially reduced work function than conventional ZnO NRs. These features synergistically result in hysteresis-free, scan-independent, and stabilized devices with an efficiency of 16.1%. Electron-rich, nitrogen-doped ZnO (N:ZnO) NR-based electron transporting materials (ETMs) with enhanced electron mobility produced using ammonium acetate show consistently higher efficiencies by one to three power points than undoped ZnO NRs. Additionally, the preferential electrostatic interaction between the -nonpolar facets of N:ZnO and the conjugated polyelectrolyte polyethylenimine (PEI) has been relied on to promote the hydrothermal growth of high aspect ratio NR arrays and substantially improve the infiltration of the perovskite light absorber into the ETM. Using the same interactions, a conformal PEI coating on the electron-rich high aspect ratio N:ZnO NR arrays is -successfully applied, resulting in a favorable work function shift and altogether leading to the significant boost in efficiency from <10% up to >16%. These results largely surpass the state-of-the-art PCE of ZnO-based perovskite solar cells and highlight the benefits of synergistically combining mesoscale control with doping and surface modification. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. cDNA Expression Array Analysis of Gene Expression in Human Hepatocarcinoma Hep3B Cells Induced By BNIPL-1

    Institute of Scientific and Technical Information of China (English)

    Li XIE; Wen-Xin QIN; Jin-Jun LI; Xiang-Huo HE; Hui-Qun SHU; Gen-Fu YAO; Da-Fang WAN; Jian-Ren GU

    2005-01-01

    Bcl-2/adenovirus E1B 19 kDa interacting protein 2 like-1 (BNIPL-1) is a novel human protein identified in our laboratory, which can interact with Bcl-2 and Cdc42GAP and induce apoptosis via the BNIP-2 and Cdc42GAP homology (BCH) domain. In the present study, we established the Hep3B-Tet-on stable cell line in which expression of BNIPL-1 can be induced by doxycycline. The cell proliferation activity assay showed that the overexpression of BNIPL-1 suppresses Hep3B cell growth in vitro. The differential expression profiles of 588 known genes from BNIPL-1-transfected Hep3B-Tet-on and vector control cells were determined using the Atlas human cDNA expression array. Fifteen genes were differentially expressed between these two cell lines, among which seven genes were up-regulated and eight genes were down-regulated by BINPL-1. Furthermore, the differential expression result was confirmed by semiquantitative RT-PCR. Among these differentially expressed genes, p16INK4, IL-12, TRAIL and the lymphotoxin β gene involved in growth suppression or cell apoptosis were up-regulated, and PTEN involved in cell proliferation was down-regulated by BNIPL-1. These results suggest that BNIPL-1 might inhibit cell growth though cell cycle arrest and/or apoptotic cell death pathway(s).

  17. A high-performance photovoltaic concentrator array - The mini-dome Fresnel lens concentrator with 30 percent efficient GaAs/GaSb tandem cells

    Science.gov (United States)

    Piszczor, M. F.; Brinker, D. J.; Flood, D. J.; Avery, J. E.; Fraas, L. M.; Fairbanks, E. S.; Yerkes, J. W.; O'Neill, M. J.

    1991-01-01

    A high-efficiency, lightweight space photovoltaic concentrator array is described. Previous work on the minidome Fresnel lens concentrator concept is being integrated with Boeing's 30 percent efficient tandem GaAs/GaSb concentrator cells into a high-performance photovoltaic array. Calculations indicate that, in the near term, such an array can achieve 300 W/sq m at a specific power of 100 W/kg. Emphasis of the program has now shifted to integrating the concentrator lens, tandem cell, and supporting panel structure into a space-qualifiable array. A description is presented of the current status of component and prototype panel testing and the development of a flight panel for the Photovoltaic Array Space Power Plus Diagnostics (PASP PLUS) flight experiment.

  18. In vivo fluorescence imaging reveals the promotion of mammary tumorigenesis by mesenchymal stromal cells.

    Directory of Open Access Journals (Sweden)

    Chien-Chih Ke

    Full Text Available Mesenchymal stromal cells (MSCs are multipotent adult stem cells which are recruited to the tumor microenvironment (TME and influence tumor progression through multiple mechanisms. In this study, we examined the effects of MSCs on the tunmorigenic capacity of 4T1 murine mammary cancer cells. It was found that MSC-conditioned medium increased the proliferation, migration, and efficiency of mammosphere formation of 4T1 cells in vitro. When co-injected with MSCs into the mouse mammary fat pad, 4T1 cells showed enhanced tumor growth and generated increased spontaneous lung metastasis. Using in vivo fluorescence color-coded imaging, the interaction between GFP-expressing MSCs and RFP-expressing 4T1 cells was monitored. As few as five 4T1 cells could give rise to tumor formation when co-injected with MSCs into the mouse mammary fat pad, but no tumor was formed when five or ten 4T1 cells were implanted alone. The elevation of tumorigenic potential was further supported by gene expression analysis, which showed that when 4T1 cells were in contact with MSCs, several oncogenes, cancer markers, and tumor promoters were upregulated. Moreover, in vivo longitudinal fluorescence imaging of tumorigenesis revealed that MSCs created a vascularized environment which enhances the ability of 4T1 cells to colonize and proliferate. In conclusion, this study demonstrates that the promotion of mammary cancer progression by MSCs was achieved through the generation of a cancer-enhancing microenvironment to increase tumorigenic potential. These findings also suggest the potential risk of enhancing tumor progression in clinical cell therapy using MSCs. Attention has to be paid to patients with high risk of breast cancer when considering cell therapy with MSCs.

  19. Live Cell Imaging Reveals the Dynamics of Telomerase Recruitment to Telomeres.

    Science.gov (United States)

    Schmidt, Jens C; Zaug, Arthur J; Cech, Thomas R

    2016-08-25

    Telomerase maintains genome integrity by adding repetitive DNA sequences to the chromosome ends in actively dividing cells, including 90% of all cancer cells. Recruitment of human telomerase to telomeres occurs during S-phase of the cell cycle, but the molecular mechanism of the process is only partially understood. Here, we use CRISPR genome editing and single-molecule imaging to track telomerase trafficking in nuclei of living human cells. We demonstrate that telomerase uses three-dimensional diffusion to search for telomeres, probing each telomere thousands of times each S-phase but only rarely forming a stable association. Both the transient and stable association events depend on the direct interaction of the telomerase protein TERT with the telomeric protein TPP1. Our results reveal that telomerase recruitment to telomeres is driven by dynamic interactions between the rapidly diffusing telomerase and the chromosome end. PMID:27523609

  20. Dichotomy of cellular inhibition by small-molecule inhibitors revealed by single-cell analysis

    Science.gov (United States)

    Vogel, Robert M.; Erez, Amir; Altan-Bonnet, Grégoire

    2016-01-01

    Despite progress in drug development, a quantitative and physiological understanding of how small-molecule inhibitors act on cells is lacking. Here, we measure the signalling and proliferative response of individual primary T-lymphocytes to a combination of antigen, cytokine and drug. We uncover two distinct modes of signalling inhibition: digital inhibition (the activated fraction of cells diminishes upon drug treatment, but active cells appear unperturbed), versus analogue inhibition (the activated fraction is unperturbed whereas activation response is diminished). We introduce a computational model of the signalling cascade that accounts for such inhibition dichotomy, and test the model predictions for the phenotypic variability of cellular responses. Finally, we demonstrate that the digital/analogue dichotomy of cellular response as revealed on short (signal transduction) timescales, translates into similar dichotomy on longer (proliferation) timescales. Our single-cell analysis of drug action illustrates the strength of quantitative approaches to translate in vitro pharmacology into functionally relevant cellular settings. PMID:27687249

  1. Effect of TiO2 blocking layer on TiO2 nanorod arrays based dye sensitized solar cells

    Science.gov (United States)

    Sivakumar, R.; Paulraj, M.

    2016-05-01

    Highly ordered rutile titanium dioxide nanorod (TNR) arrays (1.2 to 6.2 μm thickness) were grown on TiO2 blocking layer chemically deposited on fluorine doped tin oxide (FTO) substrate and were used as photo-electrodes to fabricate dye sensitized solar cells (DSSC's). Homogeneous layer of TiO2 on FTO was achieved by using aqueous peroxo- titanium complex (PTC) solutions via chemical bath deposition. Structural and morphological properties of the prepared samples were investigated using X-ray diffraction (XRD), scanning electron microscopy (SEM) measurements. TNR arrays (6.2 μm) with TiO2 blocking layer showed higher energy conversion efficiency (1.46%) than that without TiO2 blocking layer. The reason can be ascertained to the suppression of electron-hole recombination at the semiconductor/electrolyte interface by the effect of TiO2 blocking layer.

  2. Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

    International Nuclear Information System (INIS)

    Prostate cancer cells in primary tumors have been typed CD10-/CD13-/CD24hi/CD26+/CD38lo/CD44-/CD104-. This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. CD26+ cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types

  3. Effect of different agents onto multidrug resistant cells revealed by fluorescence correlation spectroscopy

    Science.gov (United States)

    Boutin, C.; Roche, Y.; Jaffiol, R.; Millot, J.-M.; Millot, C.; Plain, J.; Deturche, R.; Jeannesson, P.; Manfait, M.; Royer, P.

    Fluorescence correlation spectroscopy (FCS), which is a sensitive and non invasive technique, has been used to characterize the plasma membrane fluidity and heterogeneity of multidrug resistant living cells. At the single cell level, the effects of different membrane agents present in the extra-cellular medium have been analyzed. Firstly, we reveal a modification of plasma membrane microviscosity according to the addition of a fluidity modulator, benzyl alcohol. In the other hand, revertant such as verapamil and cyclosporin-A appears to act more specifically on the slow diffusion sites as microdomains.

  4. Functional Features of Trans-differentiated Hair Cells Mediated by Atoh1 Reveals a Primordial Mechanism

    OpenAIRE

    Yang, Juanmei; Bouvron, Sonia; Lv, Ping; Chi, Fanglu; Yamoah, Ebenezer N.

    2012-01-01

    Evolution has transformed a simple ear with few vestibular maculae into a complex 3-dimensional structure consisting of nine distinct endorgans. It is debatable whether the sensory epithelia underwent progressive segregation or emerged from distinct sensory patches. To address these uncertainties we examined the morphological and functional phenotype of trans-differentiated rat hair cells to reveal their primitive or endorgan-specific origins. Additionally, it is uncertain how Atoh1-mediated ...

  5. Gene expression profiling reveals novel regulation by bisphenol-A in estrogen receptor-α-positive human cells

    International Nuclear Information System (INIS)

    Bisphenol-A (BPA) shows proliferative actions in uterus and mammary glands and may influence the development of male and female reproductive tracts in utero or during early postnatal life. Because of its ability to function as an estrogen receptor (ER) agonist, BPA has the potential to disrupt normal endocrine signaling through regulation of ER target genes. Some genes are regulated by both estradiol (E2) and BPA, but those exclusive to either agent have not been described. Using a yeast strain incorporating a vitellogenin A2 ERE-LacZ reporter gene into the genome, we found that BPA induced expression of the reporter in colonies transformed with the ERα expression plasmid, illustrating BPA-mediated regulation within a chromatin context. Additionally, a reporter gene transiently transfected into the endometrial cancer (Ishikawa) cell line also showed BPA activity, although at 100-fold less potency than E2. To compare global gene expression in response to BPA and E2, we used a variant of the MCF-7 breast cancer cell line stably expressing HA-tagged ERα. Cultures were treated for 3 h with an ethanol vehicle, E2 (10-8 M), or BPA (10-6 M), followed by isolation of RNA and microarray analysis with the human U95A probe array (Affymetrix, Santa Clara, CA, USA). More than 300 genes were changed 2-fold or more by either or both agents, with roughly half being up-regulated and half down-regulated. A number of growth- and development-related genes, such as HOXC1 and C6, Wnt5A, Frizzled, TGFβ-2, and STAT inhibitor 2, were found to be affected exclusively by BPA. We used quantitative real-time PCR to verify regulation of the HOXC6 gene, which showed decreased expression of approximately 2.5-fold by BPA. These results reveal novel effects by BPA and E2, raising interesting possibilities regarding the role of endocrine disruptors in sexual development

  6. Stem cell-like differentiation potentials of endometrial side population cells as revealed by a newly developed in vivo endometrial stem cell assay.

    Directory of Open Access Journals (Sweden)

    Kaoru Miyazaki

    Full Text Available BACKGROUND: Endometrial stem/progenitor cells contribute to the cyclical regeneration of human endometrium throughout a woman's reproductive life. Although the candidate cell populations have been extensively studied, no consensus exists regarding which endometrial population represents the stem/progenitor cell fraction in terms of in vivo stem cell activity. We have previously reported that human endometrial side population cells (ESP, but not endometrial main population cells (EMP, exhibit stem cell-like properties, including in vivo reconstitution of endometrium-like tissues when xenotransplanted into immunodeficient mice. The reconstitution efficiency, however, was low presumably because ESP cells alone could not provide a sufficient microenvironment (niche to support their stem cell activity. The objective of this study was to establish a novel in vivo endometrial stem cell assay employing cell tracking and tissue reconstitution systems and to examine the stem cell properties of ESP through use of this assay. METHODOLOGY/PRINCIPAL FINDINGS: ESP and EMP cells isolated from whole endometrial cells were infected with lentivirus to express tandem Tomato (TdTom, a red fluorescent protein. They were mixed with unlabeled whole endometrial cells and then transplanted under the kidney capsule of ovariectomized immunodeficient mice. These mice were treated with estradiol and progesterone for eight weeks and nephrectomized. All of the grafts reconstituted endometrium-like tissues under the kidney capsules. Immunofluorescence revealed that TdTom-positive cells were significantly more abundant in the glandular, stromal, and endothelial cells of the reconstituted endometrium in mice transplanted with TdTom-labeled ESP cells than those with TdTom-labeled EMP cells. CONCLUSIONS/SIGNIFICANCE: We have established a novel in vivo endometrial stem cell assay in which multi-potential differentiation can be identified through cell tracking during in vivo

  7. Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells

    DEFF Research Database (Denmark)

    Hattori, Naoko; Niwa, Tohru; Kimura, Kana;

    2013-01-01

    . Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell......Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which...... population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination...

  8. Peripheral blood mononuclear cell gene array profiles in female patients with involuntary bladder contractions

    Directory of Open Access Journals (Sweden)

    Bluth MH

    2011-06-01

    Full Text Available Wellman Cheung1, Mark J Bluth1, Sohail Khan2, Christopher Johns2, Martin H Bluth31State University of New York Downstate Medical Center, Brooklyn, NY, USA; 2Cold Spring Harbor Laboratory – Microarray Shared Resource, Cold Spring Harbor, NY, USA; 3Wayne State University School of Medicine, Detroit, MI, USABackground: Patients with urgency represent a group of incontinence sufferers whose diagnosis remains difficult to establish. Urodynamic testing demonstrating involuntary bladder contraction provides objective confirmation but represents an invasive approach. We have previously demonstrated that peripheral blood mononuclear cells (PBMC can provide a reporter function in solid organ disease toward biomarker discovery. Here we investigated the utility of using PBMC as marker for patients with confirmed involuntary bladder contraction.Methods: Fifteen female patients were evaluated for involuntary bladder contractions and stress urinary incontinence as demonstrated by urodynamics and also assessed for pelvic prolapse, stress incontinence by history, bladder neck dysfunction, and bladder capacity. PBMC were obtained from patients’ whole blood, and RNA was subjected to microarray gene chip analysis.Results: Microarray analysis revealed that eleven genes were differentially regulated (five upregulated and six downregulated. Of these, PGRMC1 (progesterone receptor membrane component 1, EIF2S3 (eukaryotic initiation factor, C3AR1 (complement receptor, and three unknown genes were downregulated. Upregulated genes included MYOM2 (myomesin M-protein, a cytoskeletal protein; KTN1 (kinectin; and AAK 1 (AP2 associated kinase.Conclusions: Microarray analysis revealed many genes that were differentially regulated in PBMC from patients with involuntary detrusor contractions. These genes may be important in regulating structural integrity of bladder and supporting tissues. These data suggest that PBMC can provide a reporter function for patients with

  9. Single-Molecule Imaging Reveals the Activation Dynamics of Intracellular Protein Smad3 on Cell Membrane

    Science.gov (United States)

    Li, Nan; Yang, Yong; He, Kangmin; Zhang, Fayun; Zhao, Libo; Zhou, Wei; Yuan, Jinghe; Liang, Wei; Fang, Xiaohong

    2016-09-01

    Smad3 is an intracellular protein that plays a key role in propagating transforming growth factor β (TGF-β) signals from cell membrane to nucleus. However whether the transient process of Smad3 activation occurs on cell membrane and how it is regulated remains elusive. Using advanced live-cell single-molecule fluorescence microscopy to image and track fluorescent protein-labeled Smad3, we observed and quantified, for the first time, the dynamics of individual Smad3 molecules docking to and activation on the cell membrane. It was found that Smad3 docked to cell membrane in both unstimulated and stimulated cells, but with different diffusion rates and dissociation kinetics. The change in its membrane docking dynamics can be used to study the activation of Smad3. Our results reveal that Smad3 binds with type I TGF-β receptor (TRI) even in unstimulated cells. Its activation is regulated by TRI phosphorylation but independent of receptor endocytosis. This study offers new information on TGF-β/Smad signaling, as well as a new approach to investigate the activation of intracellular signaling proteins for a better understanding of their functions in signal transduction.

  10. Quantitative proteomics reveals middle infrared radiation-interfered networks in breast cancer cells.

    Science.gov (United States)

    Chang, Hsin-Yi; Li, Ming-Hua; Huang, Tsui-Chin; Hsu, Chia-Lang; Tsai, Shang-Ru; Lee, Si-Chen; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2015-02-01

    Breast cancer is one of the leading cancer-related causes of death worldwide. Treatment of triple-negative breast cancer (TNBC) is complex and challenging, especially when metastasis has developed. In this study, we applied infrared radiation as an alternative approach for the treatment of TNBC. We used middle infrared (MIR) with a wavelength range of 3-5 μm to irradiate breast cancer cells. MIR significantly inhibited cell proliferation in several breast cancer cells but did not affect the growth of normal breast epithelial cells. We performed iTRAQ-coupled LC-MS/MS analysis to investigate the MIR-triggered molecular mechanisms in breast cancer cells. A total of 1749 proteins were identified, quantified, and subjected to functional enrichment analysis. From the constructed functionally enriched network, we confirmed that MIR caused G2/M cell cycle arrest, remodeled the microtubule network to an astral pole arrangement, altered the actin filament formation and focal adhesion molecule localization, and reduced cell migration activity and invasion ability. Our results reveal the coordinative effects of MIR-regulated physiological responses in concentrated networks, demonstrating the potential implementation of infrared radiation in breast cancer therapy. PMID:25556991

  11. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging.

    Science.gov (United States)

    Yan, Jing; Sharo, Andrew G; Stone, Howard A; Wingreen, Ned S; Bassler, Bonnie L

    2016-09-01

    Biofilms are surface-associated bacterial communities that are crucial in nature and during infection. Despite extensive work to identify biofilm components and to discover how they are regulated, little is known about biofilm structure at the level of individual cells. Here, we use state-of-the-art microscopy techniques to enable live single-cell resolution imaging of a Vibrio cholerae biofilm as it develops from one single founder cell to a mature biofilm of 10,000 cells, and to discover the forces underpinning the architectural evolution. Mutagenesis, matrix labeling, and simulations demonstrate that surface adhesion-mediated compression causes V. cholerae biofilms to transition from a 2D branched morphology to a dense, ordered 3D cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture in V. cholerae biofilms, and this growth pattern is controlled by a single gene, rbmA Competition analyses reveal that the dense growth mode has the advantage of providing the biofilm with superior mechanical properties. Our single-cell technology can broadly link genes to biofilm fine structure and provides a route to assessing cell-to-cell heterogeneity in response to external stimuli.

  12. Gene array analysis of neural crest cells identifies transcription factors necessary for direct conversion of embryonic fibroblasts into neural crest cells

    Directory of Open Access Journals (Sweden)

    Tsutomu Motohashi

    2016-03-01

    Full Text Available Neural crest cells (NC cells are multipotent cells that emerge from the edge of the neural folds and migrate throughout the developing embryo. Although the gene regulatory network for generation of NC cells has been elucidated in detail, it has not been revealed which of the factors in the network are pivotal to directing NC identity. In this study we analyzed the gene expression profile of a pure NC subpopulation isolated from Sox10-IRES-Venus mice and investigated whether these genes played a key role in the direct conversion of Sox10-IRES-Venus mouse embryonic fibroblasts (MEFs into NC cells. The comparative molecular profiles of NC cells and neural tube cells in 9.5-day embryos revealed genes including transcription factors selectively expressed in developing trunk NC cells. Among 25 NC cell-specific transcription factor genes tested, SOX10 and SOX9 were capable of converting MEFs into SOX10-positive (SOX10+ cells. The SOX10+ cells were then shown to differentiate into neurons, glial cells, smooth muscle cells, adipocytes and osteoblasts. These SOX10+ cells also showed limited self-renewal ability, suggesting that SOX10 and SOX9 directly converted MEFs into NC cells. Conversely, the remaining transcription factors, including well-known NC cell specifiers, were unable to convert MEFs into SOX10+ NC cells. These results suggest that SOX10 and SOX9 are the key factors necessary for the direct conversion of MEFs into NC cells.

  13. Real-time imaging of microparticles and living cells with CMOS nanocapacitor arrays

    NARCIS (Netherlands)

    Laborde, C.; Pittino, F.; Verhoeven, H.A.; Lemay, S.G.; Selmi, L.; Jongsma, M.A.; Widdershoven, F.P.

    2015-01-01

    Massively parallel, label free biosensing platforms can in principle be realized by combining all-electrical detection with low-cost integrated circuits. Examples include field-effect transistor (FET) arrays used for mapping neuronal signals1,2 and DNA sequencing3,4. Despite these remarkable success

  14. Plasma nitriding induced growth of Pt-nanowire arrays as high performance electrocatalysts for fuel cells

    NARCIS (Netherlands)

    Du, S.; Lin, K.; Malladi, S.R.K.; Lu, Y.; Sun, S.; Xu, Q.; Steinberger-Wilckens, R.; Dong, H.

    2014-01-01

    In this work, we demonstrate an innovative approach, combing a novel active screen plasma (ASP) technique with green chemical synthesis, for a direct fabrication of uniform Pt nanowire arrays on large-area supports. The ASP treatment enables in-situ N-doping and surface modification to the support s

  15. Chick embryo xenograft model reveals a novel perineural niche for human adipose-derived stromal cells

    Directory of Open Access Journals (Sweden)

    Ingrid R. Cordeiro

    2015-09-01

    Full Text Available Human adipose-derived stromal cells (hADSC are a heterogeneous cell population that contains adult multipotent stem cells. Although it is well established that hADSC have skeletal potential in vivo in adult organisms, in vitro assays suggest further differentiation capacity, such as into glia. Thus, we propose that grafting hADSC into the embryo can provide them with a much more instructive microenvironment, allowing the human cells to adopt diverse fates or niches. Here, hADSC spheroids were grafted into either the presumptive presomitic mesoderm or the first branchial arch (BA1 regions of chick embryos. Cells were identified without previous manipulations via human-specific Alu probes, which allows efficient long-term tracing of heterogeneous primary cultures. When grafted into the trunk, in contrast to previous studies, hADSC were not found in chondrogenic or osteogenic territories up to E8. Surprisingly, 82.5% of the hADSC were associated with HNK1+ tissues, such as peripheral nerves. Human skin fibroblasts showed a smaller tropism for nerves. In line with other studies, hADSC also adopted perivascular locations. When grafted into the presumptive BA1, 74.6% of the cells were in the outflow tract, the final goal of cardiac neural crest cells, and were also associated with peripheral nerves. This is the first study showing that hADSC could adopt a perineural niche in vivo and were able to recognize cues for neural crest cell migration of the host. Therefore, we propose that xenografts of human cells into chick embryos can reveal novel behaviors of heterogeneous cell populations, such as response to migration cues.

  16. Screening Metastasis-associated Genes from Anoikis Resistant A549 Lung Cancer Cells by Human Genome Array

    Directory of Open Access Journals (Sweden)

    Xiaoping WANG

    2010-01-01

    Full Text Available Background and objective As a barrier to metastases, cells normally undergo apoptosis after they lose contact with their extra cellular matrix (ECM. This process has been termed “anoikis”. Tumour cells that acquire malignant potential have developed mechanisms to resist anoikis and thereby survive after detachment from their primary site while traveling through the lymphatic and circulatory systems. This “anoikis resistance” is considered the first step to tumor metastases. The aim of this study was to screen metastasis-associated genes from anoikis resistant and adherent growth A549 lung cancer cell by Human Genome Array. Methods Establish anoikis resistant A549 lung cancer cell lines by using poly-hydroxyethyl methacrylate resin processed petri dishes, which causes cell free from adherent. The different expressed gene between anoikis resistant A549 cell and adherent growth A549 cell was tested using human V2.0 whole-genome oligonucleotide microarray, a product of Capitalbio Corporation, Beijing. Screen metastasis-associated genes. Results 745 different expressed genes were screened, including 63 highly metastasis-associated genes. Conclusion The successfully established anoikis resistant A549 cell lines and screened different expressed genes provide us basis for further research on metastasis of lung cancer.

  17. Prodigiosin inhibits motility and activates bacterial cell death revealing molecular biomarkers of programmed cell death.

    Science.gov (United States)

    Darshan, N; Manonmani, H K

    2016-12-01

    The antimicrobial activity of prodigiosin from Serratia nematodiphila darsh1, a bacterial pigment was tested against few food borne bacterial pathogens Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli. The mode of action of prodigiosin was studied. Prodigiosin induced bactericidal activity indicating a stereotypical set of biochemical and morphological feature of Programmed cell death (PCD). PCD involves DNA fragmentation, generation of ROS, and expression of a protein with caspase-like substrate specificity in bacterial cells. Prodigiosin was observed to be internalized into bacterial cells and was localized predominantly in the membrane and the nuclear fraction, thus, facilitating intracellular trafficking and then binding of prodigiosin to the bacterial DNA. Corresponding to an increasing concentration of prodigiosin, the level of certain proteases were observed to increase in bacteria studied, thus initiating the onset of PCD. Prodigiosin at a sub-inhibitory concentration inhibits motility of pathogens. Our observations indicated that prodigiosin could be a promising antibacterial agent and could be used in the prevention of bacterial infections. PMID:27460563

  18. Mammary-Stem-Cell-Based Somatic Mouse Models Reveal Breast Cancer Drivers Causing Cell Fate Dysregulation

    Directory of Open Access Journals (Sweden)

    Zheng Zhang

    2016-09-01

    Full Text Available Cancer genomics has provided an unprecedented opportunity for understanding genetic causes of human cancer. However, distinguishing which mutations are functionally relevant to cancer pathogenesis remains a major challenge. We describe here a mammary stem cell (MaSC organoid-based approach for rapid generation of somatic genetically engineered mouse models (GEMMs. By using RNAi and CRISPR-mediated genome engineering in MaSC-GEMMs, we have discovered that inactivation of Ptpn22 or Mll3, two genes mutated in human breast cancer, greatly accelerated PI3K-driven mammary tumorigenesis. Using these tumor models, we have also identified genetic alterations promoting tumor metastasis and causing resistance to PI3K-targeted therapy. Both Ptpn22 and Mll3 inactivation resulted in disruption of mammary gland differentiation and an increase in stem cell activity. Mechanistically, Mll3 deletion enhanced stem cell activity through activation of the HIF pathway. Thus, our study has established a robust in vivo platform for functional cancer genomics and has discovered functional breast cancer mutations.

  19. Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

    Science.gov (United States)

    Carrot is one of the most economically important vegetables worldwide, however, genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to devel...

  20. Single-Cell-Arrayed Agarose Chip for in Situ Analysis of Cytotoxicity and Genotoxicity of DNA Cross-Linking Agents.

    Science.gov (United States)

    Li, Lili; Wang, Weixing; Ding, Mingyu; Luo, Guoan; Liang, Qionglin

    2016-07-01

    Development of approach or device to allow continuous multiple measurements, such as integrating cytotoxic and genotoxic analysis, is quite appealing for study of the drug's activity and mechanism of action or resistance. In this study, a single-cell-arrayed agarose chip system was developed to combine cell cultivation with subsequent in situ analysis of cytotoxicity and genotoxicity of the chemotherapeutic agent. The modified alkaline comet assay coupled with the Live/Dead assay was used to monitor the interstrand cross-links (ICLs) formation and the cytotoxic effects in different glioma cell lines. In addition, the ICL-induced double strand breaks (DSBs) was measured on the chip to reflect the level of ICLs indirectly. Compared with the traditional methods, the microarray agarose device offers higher throughput, reproducibility, and robustness, exhibiting good potential for high-content drug screening. PMID:27269449

  1. Monolithic in-based III-V compound semiconductor focal plane array cell with single stage CCD output

    Science.gov (United States)

    Fossum, Eric R. (Inventor); Cunningham, Thomas J. (Inventor); Krabach, Timothy N. (Inventor); Staller, Craig O. (Inventor)

    1995-01-01

    A monolithic semiconductor imager includes an indium-based III-V compound semiconductor monolithic active layer of a first conductivity type, an array of plural focal plane cells on the active layer, each of the focal plane cells including a photogate over a top surface of the active layer, a readout circuit dedicated to the focal plane cell including plural transistors formed monolithically with the monolithic active layer and a single-stage charge coupled device formed monolithically with the active layer between the photogate and the readout circuit for transferring photo-generated charge accumulated beneath the photogate during an integration period to the readout circuit. The photogate includes thin epitaxial semiconductor layer of a second conductivity type overlying the active layer and an aperture electrode overlying a peripheral portion of the thin epitaxial semiconductor layer, the aperture electrode being connectable to a photogate bias voltage.

  2. Hydrothermal synthesis of rutile–anatase TiO{sub 2} nanobranched arrays for efficient dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Soon Jin; Im, Hyo Been [Graduate School of Energy Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764 (Korea, Republic of); Nam, Jung Eun; Kang, Jin Kyu [Advanced Convergence Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 50-1, Sang-ri, Hyeonpung-myeon, Dalseong-gun, Daegu 711-873 (Korea, Republic of); Hwang, Taek Sung [Department of Chemical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764 (Korea, Republic of); Yi, Kwang Bok, E-mail: cosy32@cnu.ac.kr [Department of Chemical Engineering Education, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764 (Korea, Republic of)

    2014-11-30

    Highlights: • The unique rutile–anatase TiO{sub 2} nanobranched arrays have been synthesized for DSSC application. • TiO{sub 2} nano-structure consists of anatase nanobranches covering of rutile nanorod surfaces. • The successful attachment of anatase TiO{sub 2} nanobranches to the nanorods is achieved by TiCl{sub 4} treatment. - Abstract: Rutile–anatase TiO{sub 2} nanobranched arrays were prepared in two sequential hydrothermal-synthesis steps. The morphologies and crystalline nanostructures of the samples were investigated by controlling growth time and the concentration of the titanium precursor. All samples were characterized by field-emission scanning electron microscopy and X-ray diffraction analysis. It was found that treating the surfaces of rutile TiO{sub 2} nanorods with aqueous TiCl{sub 4} solutions allows the anatase TiO{sub 2} nanobranches to grow perpendicular to the main rutile TiO{sub 2} nanorods attached to the FTO glass. Irregularly shaped, dense TiO{sub 2} structures formed in the absence of TiCl{sub 4} treatment. A light-to-electricity conversion efficiency of 3.45% was achieved using 2.3 μm tall TiO{sub 2} nanobranched arrays in a dye-sensitized solar cell. This value is significantly higher than that observed for pure rutile TiO{sub 2} nanorods.

  3. Human stem cells from single blastomeres reveal pathways of embryonic or trophoblast fate specification.

    Science.gov (United States)

    Zdravkovic, Tamara; Nazor, Kristopher L; Larocque, Nicholas; Gormley, Matthew; Donne, Matthew; Hunkapillar, Nathan; Giritharan, Gnanaratnam; Bernstein, Harold S; Wei, Grace; Hebrok, Matthias; Zeng, Xianmin; Genbacev, Olga; Mattis, Aras; McMaster, Michael T; Krtolica, Ana; Valbuena, Diana; Simón, Carlos; Laurent, Louise C; Loring, Jeanne F; Fisher, Susan J

    2015-12-01

    Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines (designated UCSFB1-10) from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple. Compared with numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns that were, in part, indicative of trophoblast competence. At a transcriptional level, UCSFB lines from different embryos were often more closely related than those from the same embryo. As predicted by the transcriptomic data, immunolocalization of EOMES, T brachyury, GDF15 and active β-catenin revealed differential expression among blastomeres of 8- to 10-cell human embryos. The UCSFB lines formed derivatives of the three germ layers and CDX2-positive progeny, from which we derived the first human trophoblast stem cell line. Our data suggest heterogeneity among early-stage blastomeres and that the UCSFB lines have unique properties, indicative of a more immature state than conventional lines.

  4. Transcriptomic changes in human renal proximal tubular cells revealed under hypoxic conditions by RNA sequencing.

    Science.gov (United States)

    Yu, Wenmin; Li, Yiping; Wang, Zhi; Liu, Lei; Liu, Jing; Ding, Fengan; Zhang, Xiaoyi; Cheng, Zhengyuan; Chen, Pingsheng; Dou, Jun

    2016-09-01

    Chronic hypoxia often occurs among patients with chronic kidney disease (CKD). Renal proximal tubular cells may be the primary target of a hypoxic insult. However, the underlying transcriptional mechanisms remain undefined. In this study, we revealed the global changes in gene expression in HK‑2 human renal proximal tubular cells under hypoxic and normoxic conditions. We analyzed the transcriptome of HK‑2 cells exposed to hypoxia for 24 h using RNA sequencing. A total of 279 differentially expressed genes was examined, as these genes could potentially explain the differences in HK‑2 cells between hypoxic and normoxic conditions. Moreover, 17 genes were validated by qPCR, and the results were highly concordant with the RNA seqencing results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to better understand the functions of these differentially expressed genes. The upregulated genes appeared to be significantly enriched in the pathyway of extracellular matrix (ECM)-receptor interaction, and in paticular, the pathway of renal cell carcinoma was upregulated under hypoxic conditions. The downregulated genes were enriched in the signaling pathway related to antigen processing and presentation; however, the pathway of glutathione metabolism was downregulated. Our analysis revealed numerous novel transcripts and alternative splicing events. Simultaneously, we also identified a large number of single nucleotide polymorphisms, which will be a rich resource for future marker development. On the whole, our data indicate that transcriptome analysis provides valuable information for a more in depth understanding of the molecular mechanisms in CKD and renal cell carcinoma. PMID:27432315

  5. A new method of linear control for optimum transfer of power from a solar cell array to the distribution network

    Science.gov (United States)

    Ray, G. C.; Jha, R.

    1984-08-01

    The paper describes a new method of linear control for transfer of optimum power from a Solar Cell Array (SCA) to the distribution network. It is shown that the current corresponding to the optimum power varies almost linearly with the level of illumination. By connecting a storage battery in parallel to the SCA, the charging current to the battery is continuously adjusted by sensing the ilumination level and current simultaneously. Variation of the charging current keeps the operating point on the optimum power locus. In the ac distribution network the power is to be fed through a current-source inverter and a step up/down transformer.

  6. Robustness and adaptation reveal plausible cell cycle controlling subnetwork in Saccharomyces cerevisiae.

    Science.gov (United States)

    Huang, Jiun-Yan; Huang, Chi-Wei; Kao, Kuo-Ching; Lai, Pik-Yin

    2013-04-10

    Biological systems are often organized spatially and temporally by multi-scale functional subsystems (modules). A specific subcellular process often corresponds to a subsystem composed of some of these interconnected modules. Accurate identification of system-level modularity organization from the large scale networks can provide valuable information on subsystem models of subcellular processes or physiological phenomena. Computational identification of functional modules from the large scale network is the key approach to solve the complexity of modularity in the past decade, but the overlapping and multi-scale nature of modules often renders unsatisfactory results in these methods. Most current methods for modularity detection are optimization-based and suffered from the drawback of size resolution limit. It is difficult to trace the origin of the unsatisfactory results, which may be due to poor data, inappropriate objective function selection or simply resulted from natural evolution, and hence no system-level accurate modular models for subcellular processes can be offered. Motivated by the idea of evolution with robustness and adaption as guiding principles, we propose a novel approach that can identify significant multi-scale overlapping modules that are sufficiently accurate at the system and subsystem levels, giving biological insights for subcellular processes. The success of our evolution strategy method is demonstrated by applying to the yeast protein-protein interaction network. Functional subsystems of important physiological phenomena can be revealed. In particular, the cell cycle controlling network is selected for detailed discussion. The cell cycle subcellular processes in yeast can be successfully dissected into functional modules of cell cycle control, cell size check point, spindle assembly checkpoint, and DNA damage check point in G2/M and S phases. The interconnections between check points and cell cycle control modules provide clues on the

  7. Robustness and adaptation reveal plausible cell cycle controlling subnetwork in Saccharomyces cerevisiae.

    Science.gov (United States)

    Huang, Jiun-Yan; Huang, Chi-Wei; Kao, Kuo-Ching; Lai, Pik-Yin

    2013-04-10

    Biological systems are often organized spatially and temporally by multi-scale functional subsystems (modules). A specific subcellular process often corresponds to a subsystem composed of some of these interconnected modules. Accurate identification of system-level modularity organization from the large scale networks can provide valuable information on subsystem models of subcellular processes or physiological phenomena. Computational identification of functional modules from the large scale network is the key approach to solve the complexity of modularity in the past decade, but the overlapping and multi-scale nature of modules often renders unsatisfactory results in these methods. Most current methods for modularity detection are optimization-based and suffered from the drawback of size resolution limit. It is difficult to trace the origin of the unsatisfactory results, which may be due to poor data, inappropriate objective function selection or simply resulted from natural evolution, and hence no system-level accurate modular models for subcellular processes can be offered. Motivated by the idea of evolution with robustness and adaption as guiding principles, we propose a novel approach that can identify significant multi-scale overlapping modules that are sufficiently accurate at the system and subsystem levels, giving biological insights for subcellular processes. The success of our evolution strategy method is demonstrated by applying to the yeast protein-protein interaction network. Functional subsystems of important physiological phenomena can be revealed. In particular, the cell cycle controlling network is selected for detailed discussion. The cell cycle subcellular processes in yeast can be successfully dissected into functional modules of cell cycle control, cell size check point, spindle assembly checkpoint, and DNA damage check point in G2/M and S phases. The interconnections between check points and cell cycle control modules provide clues on the

  8. Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency

    Institute of Scientific and Technical Information of China (English)

    R David Hawkins; Zhen Ye; Samantha Kuan; Pengzhi Yu; Hui Liu; Xinmin Zhang; Roland D Green; Victor V Lobanenkov; Ron Stewart; James A Thomson; Bing Ren; Gary C Hon; Chuhu Yang; Jessica E Antosiewicz-Bourget; LeonardKLee; Que-Minh Ngo; Sarit Klugman; Keith A Ching; Lee E Edsall

    2011-01-01

    Pluripotency,the ability of a cell to differentiate and give rise to all embryonic lineages,defines a small number of mammalian cell types such as embryonic stem (ES) cells.While it has been generally held that pluripotency is the product of a transcriptional regulatory network that activates and maintains the expression of key stem cell genes,accumulating evidence is pointing to a critical role for epigenetic processes in establishing and safeguarding the pluripotency of ES cells,as well as maintaining the identity of differentiated cell types.In order to better understand the role of epigenetic mechanisms in pluripotency,we have examined the dynamics of chromatin modifications genomewide in human ES cells (hESCs) undergoing differentiation into a mesendodermal lineage.We found that chromatin modifications at promoters remain largely invariant during differentiation,except at a small number of promoters where a dynamic switch between acetylation and methylation at H3K27 marks the transition between activation and silencing of gene expression,suggesting a hierarchy in cell fate commitment over most differentially expressed genes.We also mapped over 50 000 potential enhancers,and observed much greater dynamics in chromatin modifications,especially H3K4mel and H3K27ac,which correlate with expression of their potential target genes.Further analysis of these enhancers revealed potentially key transcriptional regulators of pluripotency and a chromatin signature indicative of a poised state that may confer developmental competence in hESCs.Our results provide new evidence supporting the role of chromatin modifications in defining enhancers and pluripotency.

  9. Broadband-antireflective hybrid nanopillar array for photovoltaic application

    International Nuclear Information System (INIS)

    Subwavelength structures such as nanopillars, nanoholes, and nanodomes have recently attracted considerable attention as antireflective structures for solar cells. Recent studies on the optical property of nanopillar array revealed that the reflection minimum is related to the diameter, the pitch, and the height of nanopillars. Here, we investigate the “hybrid” nanopillar array, which is composed of different diameters of nanopillars. Finite differential time domain simulations revealed that the photogeneration in a hybrid nanopillar array is spatially heterogeneous: carriers are generated mainly in the narrower pillars for short-wavelength incident light and in the thicker pillars for long-wavelength light, respectively. Hybrid silicon nanopillar arrays fabricated by using electron beam lithography and dry etching show excellent broadband antireflection property. Hybrid nanopillar array is thus highly promising for next-generation antireflection for photovoltaic applications

  10. Heterogeneous flammulina velutipes-like CdTe/TiO{sub 2} nanorod array: A promising composite nanostructure for solar cell application

    Energy Technology Data Exchange (ETDEWEB)

    Luo Bingwei [Beijing Key Laboratory of Special Functional Materials and Film, School of Chemistry and Environment, Beihang University, Beijing 100191 (China); Deng Yuan, E-mail: dengyuan@buaa.edu.cn [Beijing Key Laboratory of Special Functional Materials and Film, School of Chemistry and Environment, Beihang University, Beijing 100191 (China); Wang Yao; Zhang Zhiwei; Tan Ming [Beijing Key Laboratory of Special Functional Materials and Film, School of Chemistry and Environment, Beihang University, Beijing 100191 (China)

    2012-03-15

    Highlights: Black-Right-Pointing-Pointer Core-shell CdTe/TiO{sub 2} nanorod arrays have been prepared via hydrothermal growth and magnetron sputtering method. Black-Right-Pointing-Pointer CdTe nanograins covered on the surface of the TiO{sub 2} nanorod arrays constructing a flammulina velutipe like type-II heterostructure. Black-Right-Pointing-Pointer The spectrum absorption region and the open circuit photocurrent are greatly increased. - Abstract: Core-shell heterogeneous CdTe/TiO{sub 2} nanorod arrays have been prepared by a two-step synthesis route through combined hydrothermal growth and magnetron sputtering. The composition and microstructure of the arrays were investigated by powder X-ray diffraction (XRD), scanning electron microscopy (SEM) and high-resolution transmission electron microscopy (HRTEM), which show that CdTe nanograins coated on the surface of the single-crystalline TiO{sub 2} nanorod arrays to form a type-II heterostructure. Compared with TiO{sub 2} nanorod arrays, the spectrum absorption region of CdTe/TiO{sub 2} core-shell nanostructure is broadened from ultraviolet light to visible light. The photoelectrodes of CdTe/TiO{sub 2} nanorod arrays show better photoelectric properties than those of bare TiO{sub 2} nanorod arrays. The output power of CdTe/TiO{sub 2} nanorod arrays is 25 times higher than that of a bare TiO{sub 2} nanorod array. These results indicate that the photoelectrode of CdTe/TiO{sub 2} nanorod array has a promising application in solar cell.

  11. Human iPSC-Derived Endothelial Cell Sprouting Assay in Synthetic Hydrogel Arrays

    Science.gov (United States)

    Activation of vascular endothelial cells (ECs) by growth factors initiates a cascade of events in vivo consisting of EC tip cell selection, sprout formation, EC stalk cell proliferation, and ultimately vascular stabilization by support cells. Although EC functional assays can rec...

  12. Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers

    OpenAIRE

    Grzebelus, Dariusz; Iorizzo, Massimo; Senalik, Douglas; Ellison, Shelby; Cavagnaro, Pablo; Macko-Podgorni, Alicja; Heller-Uszynska, Kasia; Kilian, Andrzej; Nothnagel, Thomas; Allender, Charlotte; Simon, Philipp W; Baranski, Rafal

    2013-01-01

    Carrot is one of the most economically important vegetables worldwide, but genetic and genomic resources supporting carrot breeding remain limited. We developed a Diversity Arrays Technology (DArT) platform for wild and cultivated carrot and used it to investigate genetic diversity and to develop a saturated genetic linkage map of carrot. We analyzed a set of 900 DArT markers in a collection of plant materials comprising 94 cultivated and 65 wild carrot accessions. The accessions were attribu...

  13. Development of Microelectrode Arrays Using Electroless Plating for CMOS-Based Direct Counting of Bacterial and HeLa Cells.

    Science.gov (United States)

    Niitsu, Kiichi; Ota, Shoko; Gamo, Kohei; Kondo, Hiroki; Hori, Masaru; Nakazato, Kazuo

    2015-10-01

    The development of two new types of high-density, electroless plated microelectrode arrays for CMOS-based high-sensitivity direct bacteria and HeLa cell counting are presented. For emerging high-sensitivity direct pathogen counting, two technical challenges must be addressed. One is the formation of a bacteria-sized microelectrode, and the other is the development of a high-sensitivity and high-speed amperometry circuit. The requirement for microelectrode formation is that the gold microelectrodes are required to be as small as the target cell. By improving a self-aligned electroless plating technique, the dimensions of the microelectrodes on a CMOS sensor chip in this work were successfully reduced to 1.2 μm × 2.05 μm. This is 1/20th of the smallest size reported in the literature. Since a bacteria-sized microelectrode has a severe limitation on the current flow, the amperometry circuit has to have a high sensitivity and high speed with low noise. In this work, a current buffer was inserted to mitigate the potential fluctuation. Three test chips were fabricated using a 0.6- μm CMOS process: two with 1.2 μm × 2.05 μm (1024 × 1024 and 4 × 4) sensor arrays and one with 6- μm square (16 × 16) sensor arrays; and the microelectrodes were formed on them using electroless plating. The uniformity among the 1024 × 1024 electrodes arranged with a pitch of 3.6 μm × 4.45 μm was optically verified. For improving sensitivity, the trenches on each microelectrode were developed and verified optically and electrochemically for the first time. Higher sensitivity can be achieved by introducing a trench structure than by using a conventional microelectrode formed by contact photolithography. Cyclic voltammetry (CV) measurements obtained using the 1.2 μm × 2.05 μm 4 × 4 and 6- μm square 16 × 16 sensor array with electroless-plated microelectrodes successfully demonstrated direct counting of the bacteria-sized microbeads and HeLa cells. PMID:26561481

  14. [Acute intestinal obstruction revealing enteropathy associated t-cell lymphoma, about a case].

    Science.gov (United States)

    Garba, Abdoul Aziz; Adamou, Harissou; Magagi, Ibrahim Amadou; Brah, Souleymane; Habou, Oumarou

    2016-01-01

    Enteropathy associated T-cell lymphoma (EATL) is a rare complication of celiac disease (CD). We report a case of EATL associated with CD revealed by acute intestinal obstruction. A North African woman of 38 years old with a history of infertility and chronic abdominal pain was admitted in emergency with acute intestinal obstruction. During the surgery, we found a tumor on the small intestine with mesenteric lymphadenopathy. Histology and immunohistochemistry of the specimen objectified a digestive T lymphoma CD3+ and immunological assessment of celiac disease was positive. The diagnosis of EATL was thus retained. Chemotherapy (CHOEP protocol) was established as well as gluten-free diet with a complete response to treatment. The EATL is a rare complication of CD that can be revealed by intestinal obstruction. The prognosis can be improved by early treatment involving surgery and chemotherapy. Its prevention requires early diagnosis of celiac and gluten-free diets. PMID:27217874

  15. Electricity from photovoltaic solar cells. Flat-Plate Solar Array Project of the US Department of Energy's National Photovoltaics Program: 10 years of progress

    Science.gov (United States)

    Christensen, Elmer

    1985-01-01

    The objectives were to develop the flat-plate photovoltaic (PV) array technologies required for large-scale terrestrial use late in the 1980s and in the 1990s; advance crystalline silicon PV technologies; develop the technologies required to convert thin-film PV research results into viable module and array technology; and to stimulate transfer of knowledge of advanced PV materials, solar cells, modules, and arrays to the PV community. Progress reached on attaining these goals, along with future recommendations are discussed.

  16. Ultrastructural analysis of aminoglycoside-induced hair cell death in the zebrafish lateral line reveals an early mitochondrial response.

    OpenAIRE

    Owens, Kelly,; Cunningham, Dale,; Macdonald, Glen; Rubel, Edwin,; Raible, David,; Pujol, Remy

    2007-01-01

    Loss of the mechanosensory hair cells in the auditory and vestibular organs leads to hearing and balance deficits. To investigate initial, in vivo events in aminoglycoside-induced hair cell damage, we examined hair cells from the lateral line of the zebrafish, Danio rerio. The mechanosensory lateral line is located externally on the animal and therefore allows direct manipulation and observation of hair cells. Labeling with vital dyes revealed a rapid response of hair cells to the aminoglycos...

  17. Influence of TiO2 Nanorod Arrays on the Bilayered Photoanode for Dye-Sensitized Solar Cells

    Science.gov (United States)

    Cao, Ya; Li, Zhen; Wang, Yang; Zhang, Tao; Li, Yinchang; Liu, Xueqin; Li, Fei

    2016-06-01

    A TiO2 bilayered structure consisting of TiO2 nanoparticles (TiO2NP) as an overlayer and single-crystal rutile TiO2 nanorods (TiO2 NRs) as an underlayer on a transparent conductive fluorine-doped tin oxide substrate was designed as the photoanode of dye-sensitized solar cells (DSSCs) through a facile hydrothermal treatment followed by a doctor-blade method. DSSCs based on the hierarchical TiO2 nano-architecture photoelectrode shows a power conversion efficiency of 7.39% because the relatively large specific surface area of TiO2NP increased the dye absorption, and oriented one-dimensional TiO2 NRs enhanced the light harvesting capability, accelerating interfacial electron transport. In particular, we observed the growth morphology of the TiO2 nanorod arrays in the bilayered photoanode and the influence of the whole solar cell. The result indicated that the TiO2 NRs layer clearly impacted the photoelectron chemical properties, while the vertical and intensive nanorod arrays significantly increased their performance.

  18. Influence of TiO2 Nanorod Arrays on the Bilayered Photoanode for Dye-Sensitized Solar Cells

    Science.gov (United States)

    Cao, Ya; Li, Zhen; Wang, Yang; Zhang, Tao; Li, Yinchang; Liu, Xueqin; Li, Fei

    2016-10-01

    A TiO2 bilayered structure consisting of TiO2 nanoparticles (TiO2NP) as an overlayer and single-crystal rutile TiO2 nanorods (TiO2 NRs) as an underlayer on a transparent conductive fluorine-doped tin oxide substrate was designed as the photoanode of dye-sensitized solar cells (DSSCs) through a facile hydrothermal treatment followed by a doctor-blade method. DSSCs based on the hierarchical TiO2 nano-architecture photoelectrode shows a power conversion efficiency of 7.39% because the relatively large specific surface area of TiO2NP increased the dye absorption, and oriented one-dimensional TiO2 NRs enhanced the light harvesting capability, accelerating interfacial electron transport. In particular, we observed the growth morphology of the TiO2 nanorod arrays in the bilayered photoanode and the influence of the whole solar cell. The result indicated that the TiO2 NRs layer clearly impacted the photoelectron chemical properties, while the vertical and intensive nanorod arrays significantly increased their performance.

  19. Formalin-induced fluorescence reveals cell shape and morphology in biological tissue samples.

    Directory of Open Access Journals (Sweden)

    Ulrich Leischner

    Full Text Available Ultramicroscopy is a powerful tool to reveal detailed three-dimensional structures of large microscopical objects. Using high magnification, we observed that formalin induces fluorescence more in extra-cellular space and stains cellular structures negatively, rendering cells as dark objects in front of a bright background. Here, we show this effect on a three-dimensional image stack of a hippocampus sample, focusing on the CA1 region. This method, called FIF-Ultramicroscopy, allows for the three-dimensional observation of cellular structures in various tissue types without complicated staining techniques.

  20. An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas

    DEFF Research Database (Denmark)

    Cirilo, Priscila Daniele Ramos; Marchi, Fábio Albuquerque; Barros Filho, Mateus de Camargo;

    2013-01-01

    integrated analysis identified the top 30 significant genes (P<0.01), which comprised genes associated with cancer, whereas the protein-protein interaction analysis indicated a strong association between FANCA and BRCA1. Functional in silico analysis revealed target molecules for drugs involved in cell...... transcriptomic approach indicated that FGFR1 and IGFBP5 amplification, as well as the consequent up-regulation of the protein products, plays an important role in the aetiology of ULs and thus provides data for potential drug therapies development to target genes associated with cellular proliferation in ULs....

  1. Integration of niobium oxide-based resistive switching cells with different select properties into nanostructured cross-bar arrays

    International Nuclear Information System (INIS)

    Memristive devices with different underlying physical mechanisms are investigated and compared with respect to their utilization in passive cross-bar arrays for computing and memory applications. Niobium oxide-based metal–insulator–metal structures in various configurations exhibit abrupt filamentary resistive switching, filamentary resistive switching together with a threshold switching effect and analog switching characteristics. It is found that the initial electroforming step, which is mandatory for filamentary cells, causes problems if no individual selector device ensuring internal current compliance is applied. In contrast, cells based on analog switching are forming free and could be operated without difficulty. Thus they might be of value for utilization as passive circuit elements. (paper)

  2. Molecular analysis of T-cell receptor beta genes in cutaneous T-cell lymphoma reveals Jbeta1 bias.

    Science.gov (United States)

    Morgan, Suzanne M; Hodges, Elizabeth; Mitchell, Tracey J; Harris, Susan; Whittaker, Sean J; Smith, John L

    2006-08-01

    Molecular characterization of T-cell receptor junctional region sequences in cutaneous T-cell lymphoma had not been previously reported. We have examined in detail the features of the T-cell receptor beta (TCRB) gene rearrangements in 20 individuals with well-defined stages of cutaneous T-cell lymphoma (CTCL) comprising 10 cases with early-stage mycosis fungoides (MF) and 10 cases with late-stage MF or Sezary syndrome. Using BIOMED-2 PCR primers, we detected a high frequency of clonally rearranged TCR gamma and TCRB genes (17/20 and 15/20 cases, respectively). We carried out sequencing analysis of each complete clonal variable (V)beta-diversity (D)beta-joining(J)beta fingerprint generated by PCR amplification, and determined the primary structure of the Vbeta-Dbeta-Jbeta junctional regions. We observed considerable diversity in the T-cell receptor Vbeta gene usage and complementarity-determining region 3 loops. Although we found that TCRB gene usage in CTCL and normal individuals share common features, our analysis also revealed preferential usage of Jbeta1 genes in all cases with advanced stages of disease.

  3. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2011-11-01

    Full Text Available As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium and prototrophic (minimal medium culture conditions. The differential patterns of genetic interactions detected among > 235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens and an important target.

  4. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells.

    Science.gov (United States)

    Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas; Lyon, David; Mullari, Meeli; Madsen, Maria V; Daniel, Jeremy A; Jensen, Lars J; Nielsen, Michael L

    2016-01-01

    The posttranslational modification of proteins by arginine methylation is functionally important, yet the breadth of this modification is not well characterized. Using high-resolution mass spectrometry, we identified 8030 arginine methylation sites within 3300 human proteins in human embryonic kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified by methylation. Through quantitative proteomics and RNA interference to examine arginine methylation stoichiometry, we unexpectedly found that the protein arginine methyltransferase (PRMT) family of arginine methyltransferases catalyzed methylation independently of arginine sequence context. In contrast to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially regulated the functions of the pre-mRNA splicing factor SRSF2 (serine/arginine-rich splicing factor 2) and the RNA transport ribonucleoprotein HNRNPUL1 (heterogeneous nuclear ribonucleoprotein U-like 1). Knocking down PRMT5 impaired the RNA binding function of SRSF2, whereas knocking down PRMT4 [also known as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human arginine methylome provides a missing piece in the global and integrative view of cellular physiology and protein regulation. PMID:27577262

  5. Retrieval of the vacuolar H-ATPase from phagosomes revealed by live cell imaging.

    Directory of Open Access Journals (Sweden)

    Margaret Clarke

    Full Text Available BACKGROUND: The vacuolar H+-ATPase, or V-ATPase, is a highly-conserved multi-subunit enzyme that transports protons across membranes at the expense of ATP. The resulting proton gradient serves many essential functions, among them energizing transport of small molecules such as neurotransmitters, and acidifying organelles such as endosomes. The enzyme is not present in the plasma membrane from which a phagosome is formed, but is rapidly delivered by fusion with endosomes that already bear the V-ATPase in their membranes. Similarly, the enzyme is thought to be retrieved from phagosome membranes prior to exocytosis of indigestible material, although that process has not been directly visualized. METHODOLOGY: To monitor trafficking of the V-ATPase in the phagocytic pathway of Dictyostelium discoideum, we fed the cells yeast, large particles that maintain their shape during trafficking. To track pH changes, we conjugated the yeast with fluorescein isothiocyanate. Cells were labeled with VatM-GFP, a fluorescently-tagged transmembrane subunit of the V-ATPase, in parallel with stage-specific endosomal markers or in combination with mRFP-tagged cytoskeletal proteins. PRINCIPAL FINDINGS: We find that the V-ATPase is commonly retrieved from the phagosome membrane by vesiculation shortly before exocytosis. However, if the cells are kept in confined spaces, a bulky phagosome may be exocytosed prematurely. In this event, a large V-ATPase-rich vacuole coated with actin typically separates from the acidic phagosome shortly before exocytosis. This vacuole is propelled by an actin tail and soon acquires the properties of an early endosome, revealing an unexpected mechanism for rapid recycling of the V-ATPase. Any V-ATPase that reaches the plasma membrane is also promptly retrieved. CONCLUSIONS/SIGNIFICANCE: Thus, live cell microscopy has revealed both a usual route and alternative means of recycling the V-ATPase in the endocytic pathway.

  6. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill

    Energy Technology Data Exchange (ETDEWEB)

    Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon; Chain, Patrick S. G.; Dubinsky, Eric A.; Fortney, Julian L.; Han, James; Holman, Hoi-Ying N.; Hultman, Jenni; Lamendella, Regina; Mackelprang, Rachel; Malfatti, Stephanie; Tom, Lauren M.; Tringe, Susannah G.; Woyke, Tanja; Zhou, Jizhong; Rubin, Edward M.; Jansson, Janet K.

    2012-06-12

    The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

  7. Broadband photocurrent enhancement and light-trapping in thin film Si solar cells with periodic Al nanoparticle arrays on the front

    DEFF Research Database (Denmark)

    Uhrenfeldt, Christian; Villesen, Thorbjørn Falk; Tetu, Amelie;

    2015-01-01

    on the front of a thin film Si test solar cell. It is demonstrated that the resonances from the Al nanoparticle array cause a broadband photocurrent enhancement ranging from the ultraviolet to the infrared with respect to a reference cell. From the experimental results as well as from numerical simulations...

  8. CAFET algorithm reveals Wnt/PCP signature in lung squamous cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Yue Hu

    Full Text Available We analyzed the gene expression patterns of 138 Non-Small Cell Lung Cancer (NSCLC samples and developed a new algorithm called Coverage Analysis with Fisher's Exact Test (CAFET to identify molecular pathways that are differentially activated in squamous cell carcinoma (SCC and adenocarcinoma (AC subtypes. Analysis of the lung cancer samples demonstrated hierarchical clustering according to the histological subtype and revealed a strong enrichment for the Wnt signaling pathway components in the cluster consisting predominantly of SCC samples. The specific gene expression pattern observed correlated with enhanced activation of the Wnt Planar Cell Polarity (PCP pathway and inhibition of the canonical Wnt signaling branch. Further real time RT-PCR follow-up with additional primary tumor samples and lung cancer cell lines confirmed enrichment of Wnt/PCP pathway associated genes in the SCC subtype. Dysregulation of the canonical Wnt pathway, characterized by increased levels of β-catenin and epigenetic silencing of negative regulators, has been reported in adenocarcinoma of the lung. Our results suggest that SCC and AC utilize different branches of the Wnt pathway during oncogenesis.

  9. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

    Directory of Open Access Journals (Sweden)

    Liang-Hui Chu

    Full Text Available Angiogenesis involves stimulation of endothelial cells (EC by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome" could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A. We used the Short Time-series Expression Miner (STEM to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC and human microvascular EC (MEC. The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

  10. Suicide Gene-Engineered Stromal Cells Reveal a Dynamic Regulation of Cancer Metastasis

    Science.gov (United States)

    Shen, Keyue; Luk, Samantha; Elman, Jessica; Murray, Ryan; Mukundan, Shilpaa; Parekkadan, Biju

    2016-02-01

    Cancer-associated fibroblasts (CAFs) are a major cancer-promoting component in the tumor microenvironment (TME). The dynamic role of human CAFs in cancer progression has been ill-defined because human CAFs lack a unique marker needed for a cell-specific, promoter-driven knockout model. Here, we developed an engineered human CAF cell line with an inducible suicide gene to enable selective in vivo elimination of human CAFs at different stages of xenograft tumor development, effectively circumventing the challenge of targeting a cell-specific marker. Suicide-engineered CAFs were highly sensitive to apoptosis induction in vitro and in vivo by the addition of a simple small molecule inducer. Selection of timepoints for targeted CAF apoptosis in vivo during the progression of a human breast cancer xenograft model was guided by a bi-phasic host cytokine response that peaked at early timepoints after tumor implantation. Remarkably, we observed that the selective apoptosis of CAFs at these early timepoints did not affect primary tumor growth, but instead increased the presence of tumor-associated macrophages and the metastatic spread of breast cancer cells to the lung and bone. The study revealed a dynamic relationship between CAFs and cancer metastasis that has counter-intuitive ramifications for CAF-targeted therapy.

  11. Single-cell analysis reveals a novel uncultivated magnetotactic bacterium within the candidate division OP3.

    Science.gov (United States)

    Kolinko, Sebastian; Jogler, Christian; Katzmann, Emanuel; Wanner, Gerhard; Peplies, Jörg; Schüler, Dirk

    2012-07-01

    Magnetotactic bacteria (MTB) are a diverse group of prokaryotes that orient along magnetic fields using membrane-coated magnetic nanocrystals of magnetite (Fe(3) O(4) ) or greigite (Fe(3) S(4) ), the magnetosomes. Previous phylogenetic analysis of MTB has been limited to few cultivated species and most abundant members of natural populations, which were assigned to Proteobacteria and the Nitrospirae phyla. Here, we describe a single cell-based approach that allowed the targeted phylogenetic and ultrastructural analysis of the magnetotactic bacterium SKK-01, which was low abundant in sediments of Lake Chiemsee. Morphologically conspicuous single cells of SKK-01 were micromanipulated from magnetically collected multi-species MTB populations, which was followed by whole genome amplification and ultrastructural analysis of sorted cells. Besides intracellular sulphur inclusions, the large ovoid cells of SKK-01 harbour ∼175 bullet-shaped magnetosomes arranged in multiple chains that consist of magnetite as revealed by TEM and EDX analysis. Sequence analysis of 16 and 23S rRNA genes from amplified genomic DNA as well as fluorescence in situ hybridization assigned SKK-01 to the candidate division OP3, which so far lacks any cultivated representatives. SKK-01 represents the first morphotype that can be assigned to the OP3 group as well as the first magnetotactic member of the PVC superphylum. PMID:22003954

  12. Combined in silico and in vivo analyses reveal role of Hes1 in taste cell differentiation.

    Directory of Open Access Journals (Sweden)

    Masato S Ota

    2009-04-01

    Full Text Available The sense of taste is of critical importance to animal survival. Although studies of taste signal transduction mechanisms have provided detailed information regarding taste receptor calcium signaling molecules (TRCSMs, required for sweet/bitter/umami taste signal transduction, the ontogeny of taste cells is still largely unknown. We used a novel approach to investigate the molecular regulation of taste system development in mice by combining in silico and in vivo analyses. After discovering that TRCSMs colocalized within developing circumvallate papillae (CVP, we used computational analysis of the upstream regulatory regions of TRCSMs to investigate the possibility of a common regulatory network for TRCSM transcription. Based on this analysis, we identified Hes1 as a likely common regulatory factor, and examined its function in vivo. Expression profile analyses revealed that decreased expression of nuclear HES1 correlated with expression of type II taste cell markers. After stage E18, the CVP of Hes1(-/ (- mutants displayed over 5-fold more TRCSM-immunoreactive cells than did the CVP of their wild-type littermates. Thus, according to our composite analyses, Hes1 is likely to play a role in orchestrating taste cell differentiation in developing taste buds.

  13. Development of a Microforce Sensor and Its Array Platform for Robotic Cell Microinjection Force Measurement

    OpenAIRE

    Yu Xie; Yunlei Zhou; Yuzi Lin; Lingyun Wang,; Wenming Xi

    2016-01-01

    Robot-assisted cell microinjection, which is precise and can enable a high throughput, is attracting interest from researchers. Conventional probe-type cell microforce sensors have some real-time injection force measurement limitations, which prevent their integration in a cell microinjection robot. In this paper, a novel supported-beam based cell micro-force sensor with a piezoelectric polyvinylidine fluoride film used as the sensing element is described, which was designed to solve the real...

  14. Development of advanced catalytic layer based on vertically aligned conductive polymer arrays for thin-film fuel cell electrodes

    Science.gov (United States)

    Jiang, Shangfeng; Yi, Baolian; Cao, Longsheng; Song, Wei; Zhao, Qing; Yu, Hongmei; Shao, Zhigang

    2016-10-01

    The degradation of carbon supports significantly influences the performance of proton exchange membrane fuel cells (PEMFCs), particularly in the cathode, which must be overcome for the wide application of fuel cells. In this study, advanced catalytic layer with electronic conductive polymer-polypyrrole (PPy) nanowire as ordered catalyst supports for PEMFCs is prepared. A platinum-palladium (PtPd) catalyst thin layer with whiskerette shapes forms along the long axis of the PPy nanowires. The resulting arrays are hot-pressed on both sides of a Nafion® membrane to construct a membrane electrode assembly (without additional ionomer). The ordered thin catalyst layer (approximately 1.1 μm) is applied in a single cell as the anode and the cathode without additional Nafion® ionomer. The single cell yields a maximum performance of 762.1 mW cm-2 with a low Pt loading (0.241 mg Pt cm-2, anode + cathode). The advanced catalyst layer indicates better mass transfer in high current density than that of commercial Pt/C-based electrode. The mass activity is 1.08-fold greater than that of DOE 2017 target. Thus, the as-prepared electrodes have the potential for application in fuel cells.

  15. 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.

  16. DNA-based digital tension probes reveal integrin forces during early cell adhesion

    Science.gov (United States)

    Zhang, Yun; Ge, Chenghao; Zhu, Cheng; Salaita, Khalid

    2014-10-01

    Mechanical stimuli profoundly alter cell fate, yet the mechanisms underlying mechanotransduction remain obscure because of a lack of methods for molecular force imaging. Here to address this need, we develop a new class of molecular tension probes that function as a switch to generate a 20- to 30-fold increase in fluorescence upon experiencing a threshold piconewton force. The probes employ immobilized DNA hairpins with tunable force response thresholds, ligands and fluorescence reporters. Quantitative imaging reveals that integrin tension is highly dynamic and increases with an increasing integrin density during adhesion formation. Mixtures of fluorophore-encoded probes show integrin mechanical preference for cyclized RGD over linear RGD peptides. Multiplexed probes with variable guanine-cytosine content within their hairpins reveal integrin preference for the more stable probes at the leading tip of growing adhesions near the cell edge. DNA-based tension probes are among the most sensitive optical force reporters to date, overcoming the force and spatial resolution limitations of traction force microscopy.

  17. Antarctic-wide array of high-resolution ice core records reveals pervasive lead pollution began in 1889 and persists today

    OpenAIRE

    J. R. McConnell; O. J. Maselli; Sigl, M.; P. Vallelonga; Neumann, T; H. Anschütz; R. C. Bales; Curran, M.A.J.; S. B. Das; Edwards, R.; Kipfstuhl, S.; Layman, L; E. R. Thomas

    2014-01-01

    Interior Antarctica is among the most remote places on Earth and was thought to be beyond the reach of human impacts when Amundsen and Scott raced to the South Pole in 1911. Here we show detailed measurements from an extensive array of 16 ice cores quantifying substantial toxic heavy metal lead pollution at South Pole and throughout Antarctica by 1889 - beating polar explorers by more than 22 years. Unlike the Arctic where lead pollution peaked in the 1970s, lead pollution in Antarctica was a...

  18. Cell-Controlled and Spatially Arrayed Gene Delivery from Fibrin Hydrogels

    OpenAIRE

    Lei, Pedro; Padmashali, Roshan; Andreadis, Stelios T.

    2009-01-01

    We investigated fibrin-mediated gene transfer by embedding pDNA within the hydrogel during polymerization and using two modes of gene transfection with cells placed either on the surface (2D transfection) or within the hydrogel (3D transfection). Using this model, we found that cell transfection depended strongly on the local cell-pDNA microenvironment as defined by the 2D vs. 3D context, target cell type and density, as well as fibrinogen and pDNA concentrations. When cells were embedded wit...

  19. Dual transcript and protein quantification in a massive single cell array.

    Science.gov (United States)

    Park, Seung-Min; Lee, Jae Young; Hong, Soongweon; Lee, Sang Hun; Dimov, Ivan K; Lee, Hojae; Suh, Susie; Pan, Qiong; Li, Keyu; Wu, Anna M; Mumenthaler, Shannon M; Mallick, Parag; Lee, Luke P

    2016-10-01

    Recently, single-cell molecular analysis has been leveraged to achieve unprecedented levels of biological investigation. However, a lack of simple, high-throughput single-cell methods has hindered in-depth population-wide studies with single-cell resolution. We report a microwell-based cytometric method for simultaneous measurements of gene and protein expression dynamics in thousands of single cells. We quantified the regulatory effects of transcriptional and translational inhibitors on cMET mRNA and cMET protein in cell populations. We studied the dynamic responses of individual cells to drug treatments, by measuring cMET overexpression levels in individual non-small cell lung cancer (NSCLC) cells with induced drug resistance. Across NSCLC cell lines with a given protein expression, distinct patterns of transcript-protein correlation emerged. We believe this platform is applicable for interrogating the dynamics of gene expression, protein expression, and translational kinetics at the single-cell level - a paradigm shift in life science and medicine toward discovering vital cell regulatory mechanisms. PMID:27546183

  20. Cardiac Metastases of Renal Cell Carcinoma Revealed by Syncope: Diagnosis and Treatment

    Directory of Open Access Journals (Sweden)

    Aziz Bazine

    2014-08-01

    Full Text Available Introduction: Cardiac metastases from renal cell carcinoma are very rare. In this report, we describe a case of ventricular metastases in the absence of vena cava or right atrial involvement. Case Report: We report the case of a 60-year-old man who had a past history of heavy tobacco intake and well-controlled arterial hypertension. He experienced sudden-onset palpitations, lost consciousness and, as a result, was involved in an accident on the public highway. Cardiac arrhythmia was suspected and, therefore, transthoracic echocardiography was suggested, which revealed a large right ventricular mass. Chest and abdominal computed tomography demonstrated a mass in the right ventricle, but without contiguous vena cava involvement, and a right renal mass related to the probable neoplasm. An ultrasound-guided renal biopsy showed a clear-cell renal cell carcinoma. A bone scan revealed a metastatic bone disease. The patient was started on sunitinib treatment, which was well tolerated. However, approximately 8 months later, reevaluation showed pulmonary metastases. The patient was subsequently started on treatment with everolimus, which, however, was poorly tolerated. Two months later, the patient died due to terminal respiratory insufficiency. Discussion: Based on the literature and our observations in this case, targeted antiangiogenic therapy should be considered as a viable therapeutic alternative to metastasectomy for patients with inoperable cardiac metastatic disease as long as there is no baseline systolic or diastolic dysfunction. The case also emphasizes the importance of a thorough history review and physical examination in the workup of patients with syncope.

  1. Functional malignant cell heterogeneity in pancreatic neuroendocrine tumors revealed by targeting of PDGF-DD

    Science.gov (United States)

    Cortez, Eliane; Gladh, Hanna; Braun, Sebastian; Bocci, Matteo; Cordero, Eugenia; Björkström, Niklas K.; Miyazaki, Hideki; Michael, Iacovos P.; Eriksson, Ulf; Folestad, Erika; Pietras, Kristian

    2016-01-01

    Intratumoral heterogeneity is an inherent feature of most human cancers and has profound implications for cancer therapy. As a result, there is an emergent need to explore previously unmapped mechanisms regulating distinct subpopulations of tumor cells and to understand their contribution to tumor progression and treatment response. Aberrant platelet-derived growth factor receptor beta (PDGFRβ) signaling in cancer has motivated the development of several antagonists currently in clinical use, including imatinib, sunitinib, and sorafenib. The discovery of a novel ligand for PDGFRβ, platelet-derived growth factor (PDGF)-DD, opened the possibility of a previously unidentified signaling pathway involved in tumor development. However, the precise function of PDGF-DD in tumor growth and invasion remains elusive. Here, making use of a newly generated Pdgfd knockout mouse, we reveal a functionally important malignant cell heterogeneity modulated by PDGF-DD signaling in pancreatic neuroendocrine tumors (PanNET). Our analyses demonstrate that tumor growth was delayed in the absence of signaling by PDGF-DD. Surprisingly, ablation of PDGF-DD did not affect the vasculature or stroma of PanNET; instead, we found that PDGF-DD stimulated bulk tumor cell proliferation by induction of paracrine mitogenic signaling between heterogeneous malignant cell clones, some of which expressed PDGFRβ. The presence of a subclonal population of tumor cells characterized by PDGFRβ expression was further validated in a cohort of human PanNET. In conclusion, we demonstrate a previously unrecognized heterogeneity in PanNET characterized by signaling through the PDGF-DD/PDGFRβ axis. PMID:26831065

  2. Optical and structural properties of electrochemically deposited ZnO nanorod arrays suitable for improvement of the light harvesting in thin film solar cells

    International Nuclear Information System (INIS)

    The results of study of the optical and structural properties of ZnO nanorods (NR) arrays electrochemically deposited on two type substrates – the ITO surface on the front side of Si heterojunction (SHJ) solar cells and on stainless steel plate used for formation of a-Si:H thin film solar cells, are reported. The surface morphology of the NS arrays is examined by Scanning Electron Microscopy and AFM. The spectra of specular diffused and total reflection, and haze ratio in reflectance are compared before and after deposition of the ZnO NR arrays. In the case of deposition on ITO surface of SHJ solar cells the values of the direct and diffused reflection of the ZnO NR array decrease demonstrating good antireflection properties. Deposition of ZnO NS arrays on stainless steel plates leads to increasing the values of the diffused reflection and the total reflectance. Possible application of ZnO NS structures for the processing of advanced Si based solar cells for increasing light harvesting is discussed

  3. Mosaic Analysis with Double Markers Reveals Cell-Type-Specific Paternal Growth Dominance

    Directory of Open Access Journals (Sweden)

    Simon Hippenmeyer

    2013-03-01

    Full Text Available Genomic imprinting leads to preferred expression of either the maternal or paternal alleles of a subset of genes. Imprinting is essential for mammalian development, and its deregulation causes many diseases. However, the functional relevance of imprinting at the cellular level is poorly understood for most imprinted genes. We used mosaic analysis with double markers (MADM in mice to create uniparental disomies (UPDs and to visualize imprinting effects with single-cell resolution. Although chromosome 12 UPD did not produce detectable phenotypes, chromosome 7 UPD caused highly significant paternal growth dominance in the liver and lung, but not in the brain or heart. A single gene on chromosome 7, encoding the secreted insulin-like growth factor 2 (IGF2, accounts for most of the paternal dominance effect. Mosaic analyses implied additional imprinted loci on chromosome 7 acting cell autonomously to transmit the IGF2 signal. Our study reveals chromosome- and cell-type specificity of genomic imprinting effects.

  4. Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells.

    Science.gov (United States)

    Nguyen, Long V; Pellacani, Davide; Lefort, Sylvain; Kannan, Nagarajan; Osako, Tomo; Makarem, Maisam; Cox, Claire L; Kennedy, William; Beer, Philip; Carles, Annaick; Moksa, Michelle; Bilenky, Misha; Balani, Sneha; Babovic, Sonja; Sun, Ivan; Rosin, Miriam; Aparicio, Samuel; Hirst, Martin; Eaves, Connie J

    2015-12-10

    Most human breast cancers have diversified genomically and biologically by the time they become clinically evident. Early events involved in their genesis and the cellular context in which these events occur have thus been difficult to characterize. Here we present the first formal evidence of the shared and independent ability of basal cells and luminal progenitors, isolated from normal human mammary tissue and transduced with a single oncogene (KRAS(G12D)), to produce serially transplantable, polyclonal, invasive ductal carcinomas within 8 weeks of being introduced either subrenally or subcutaneously into immunodeficient mice. DNA barcoding of the initial cells revealed a dramatic change in the numbers and sizes of clones generated from them within 2 weeks, and the first appearance of many 'new' clones in tumours passaged into secondary recipients. Both primary and secondary tumours were phenotypically heterogeneous and primary tumours were categorized transcriptionally as 'normal-like'. This system challenges previous concepts that carcinogenesis in normal human epithelia is necessarily a slow process requiring the acquisition of multiple driver mutations. It also presents the first description of initial events that accompany the genesis and evolution of malignant human mammary cell populations, thereby contributing new understanding of the rapidity with which heterogeneity in their properties can develop. PMID:26633636

  5. Quantitative phosphoproteomics reveals SLP-76 dependent regulation of PAG and Src family kinases in T cells.

    Directory of Open Access Journals (Sweden)

    Lulu Cao

    Full Text Available The SH2-domain-containing leukocyte protein of 76 kDa (SLP-76 plays a critical scaffolding role in T cell receptor (TCR signaling. As an adaptor protein that contains multiple protein-binding domains, SLP-76 interacts with many signaling molecules and links proximal receptor stimulation to downstream effectors. The function of SLP-76 in TCR signaling has been widely studied using the Jurkat human leukaemic T cell line through protein disruption or site-directed mutagenesis. However, a wide-scale characterization of SLP-76-dependant phosphorylation events is still lacking. Quantitative profiling of over a hundred tyrosine phosphorylation sites revealed new modes of regulation of phosphorylation of PAG, PI3K, and WASP while reconfirming previously established regulation of Itk, PLCγ, and Erk phosphorylation by SLP-76. The absence of SLP-76 also perturbed the phosphorylation of Src family kinases (SFKs Lck and Fyn, and subsequently a large number of SFK-regulated signaling molecules. Altogether our data suggests unique modes of regulation of positive and negative feedback pathways in T cells by SLP-76, reconfirming its central role in the pathway.

  6. Live-cell microscopy reveals small molecule inhibitor effects on MAPK pathway dynamics.

    Directory of Open Access Journals (Sweden)

    Daniel J Anderson

    Full Text Available Oncogenic mutations in the mitogen activated protein kinase (MAPK pathway are prevalent in human tumors, making this pathway a target of drug development efforts. Recently, ATP-competitive Raf inhibitors were shown to cause MAPK pathway activation via Raf kinase priming in wild-type BRaf cells and tumors, highlighting the need for a thorough understanding of signaling in the context of small molecule kinase inhibitors. Here, we present critical improvements in cell-line engineering and image analysis coupled with automated image acquisition that allow for the simultaneous identification of cellular localization of multiple MAPK pathway components (KRas, CRaf, Mek1 and Erk2. We use these assays in a systematic study of the effect of small molecule inhibitors across the MAPK cascade either as single agents or in combination. Both Raf inhibitor priming as well as the release from negative feedback induced by Mek and Erk inhibitors cause translocation of CRaf to the plasma membrane via mechanisms that are additive in pathway activation. Analysis of Erk activation and sub-cellular localization upon inhibitor treatments reveals differential inhibition and activation with the Raf inhibitors AZD628 and GDC0879 respectively. Since both single agent and combination studies of Raf and Mek inhibitors are currently in the clinic, our assays provide valuable insight into their effects on MAPK signaling in live cells.

  7. Modelling TFE renal cell carcinoma in mice reveals a critical role of WNT signaling

    Science.gov (United States)

    Calcagnì, Alessia; kors, Lotte; Verschuren, Eric; De Cegli, Rossella; Zampelli, Nicolina; Nusco, Edoardo; Confalonieri, Stefano; Bertalot, Giovanni; Pece, Salvatore; Settembre, Carmine; Malouf, Gabriel G; Leemans, Jaklien C; de Heer, Emile; Salvatore, Marco; Peters, Dorien JM; Di Fiore, Pier Paolo; Ballabio, Andrea

    2016-01-01

    TFE-fusion renal cell carcinomas (TFE-fusion RCCs) are caused by chromosomal translocations that lead to overexpression of the TFEB and TFE3 genes (Kauffman et al., 2014). The mechanisms leading to kidney tumor development remain uncharacterized and effective therapies are yet to be identified. Hence, the need to model these diseases in an experimental animal system (Kauffman et al., 2014). Here, we show that kidney-specific TFEB overexpression in transgenic mice, resulted in renal clear cells, multi-layered basement membranes, severe cystic pathology, and ultimately papillary carcinomas with hepatic metastases. These features closely recapitulate those observed in both TFEB- and TFE3-mediated human kidney tumors. Analysis of kidney samples revealed transcriptional induction and enhanced signaling of the WNT β-catenin pathway. WNT signaling inhibitors normalized the proliferation rate of primary kidney cells and significantly rescued the disease phenotype in vivo. These data shed new light on the mechanisms underlying TFE-fusion RCCs and suggest a possible therapeutic strategy based on the inhibition of the WNT pathway. DOI: http://dx.doi.org/10.7554/eLife.17047.001

  8. Comparison of Pyranometers vs. PV Reference Cells for Evaluation of PV Array Performance

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, L.; Gostein, M.; Emery, K.

    2012-09-01

    As the photovoltaics (PV) industry has grown, the need for accurately monitoring the solar resource of PV power plants has increased. Historically, the PV industry has relied on thermopile pyranometers for irradiance measurements, and a large body of historical irradiance data taken with pyranometers exists. However, interest in PV reference devices is increasing. In this paper, we discuss why PV reference devices are better suited for PV applications, and estimate the typical uncertainties in irradiance measurements made with both pyranometers and PV reference devices. We assert that the quantity of interest in monitoring a PV power plant is the equivalent irradiance under the IEC 60904-3 reference solar spectrum that would produce the same electrical response in the PV array as the incident solar radiation. For PV-plant monitoring applications, we find the uncertainties in irradiance measurements of this type to be on the order of +/-5% for thermopile pyranometers and +/-2.4% for PV reference devices.

  9. Enhanced photoelectrochemical performance of CdSe/Mn-CdS/TiO{sub 2} nanorod arrays solar cell

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Libo; Li, Zhen; Liu, Yingbo; Cheng, Fa; Sun, Shuqing, E-mail: sunshuqing@tju.edu.cn

    2014-08-01

    Vertically oriented single-crystalline one-dimensional TiO{sub 2} nanorod arrays was synthesized directly on transparent fluorine-doped tin oxide (FTO) conducting glass substrate by a facile hydrothermal method and was applied as photoanode in CdSe/Mn-doped CdS quantum dots sensitized solar cells (QDSSCs). The effect of coating cycles of QDs on the photovoltaic performance was investigated to find the optimal combination is 10 cycles of Mn-doped CdS and 9 cycles of CdSe, the CdSe(9)/Mn-CdS(10)/TiO{sub 2} solar cell exhibited the best performance due to the complementary effect in the light absorption of Mn-doped CdS and CdSe QDs. The power conversion efficiency of CdSe(9)/Mn-CdS(10)/TiO{sub 2} solar cell reached to 2.40% under one sun illumination (AM 1.5 G, 100 mW/cm{sup 2}), which was 46.34% higher than that of CdSe(9)/CdS(10)/TiO{sub 2} solar cell without doping of Mn (1.64%).

  10. Fabrication of TiO2 nanoparticles/nanorod composite arrays via a two-step method for efficient dye-sensitized solar cells

    Directory of Open Access Journals (Sweden)

    Jingyang Wang

    2014-12-01

    Full Text Available TiO2 nanoparticles/nanorod composite arrays were prepared on the F-doped tin oxide (FTO substrate through a two-step method of hydrothermal and d.c. magnetron sputtering. The microstructure and optical properties of the samples were characterized respectively by means of X-ray diffraction (XRD, field-emission scanning electron microscopy (FESEM and UV–vis spectrometer. The results showed that the TiO2 composite nanorod arrays possess the nature of high surface area for more dye molecule absorption and the strong light scattering effects. The dye sensitized solar cells (DSSCs based on TiO2 composite nanorod arrays exhibited a 80% improvement in the overall energy conversion efficiency compared with the pure TiO2 nanorod arrays photoanode.

  11. 3D-printed concentrator arrays for external light trapping on thin film solar cells

    NARCIS (Netherlands)

    van Dijk, Lourens; Marcus, E. A. Pepijn; Oostra, A. Jolt; Schropp, Ruud E. I.; Di Vece, Marcel

    2015-01-01

    After our recent demonstration of a 3D-printed external light trap on a small solar cell, we now consider its potential for large solar panels. An external light trap consists of a parabolic concentrator and a spacer that redirects the photons that are reflected by the solar cell back towards the so

  12. Individually programmable cell stretching microwell arrays actuated by a Braille display.

    Science.gov (United States)

    Kamotani, Yoko; Bersano-Begey, Tommaso; Kato, Nobuhiro; Tung, Yi-Chung; Huh, Dongeun; Song, Jonathan W; Takayama, Shuichi

    2008-06-01

    Cell culture systems are often static and are therefore nonphysiological. In vivo, many cells are exposed to dynamic surroundings that stimulate cellular responses in a process known as mechanotransduction. To recreate this environment, stretchable cell culture substrate systems have been developed, however, these systems are limited by being macroscopic and low throughput. We have developed a device consisting of 24 miniature cell stretching chambers with flexible bottom membranes that are deformed using the computer-controlled, piezoelectrically actuated pins of a Braille display. We have also developed efficient image capture and analysis protocols to quantify morphological responses of the cells to applied strain. Human dermal microvascular endothelial cells (HDMECs) were found to show increasing degrees of alignment and elongation perpendicular to the radial strain in response to cyclic stretch at increasing frequencies of 0.2, 1, and 5 Hz, after 2, 4, and 12h. Mouse myogenic C2C12 cells were also found to align in response to the stretch, while A549 human lung adenocarcinoma epithelial cells did not respond to stretch.

  13. Assessment of genome integrity in cattle transgenic cell lines using array CGH

    Science.gov (United States)

    Transgenic cattle carrying multiple genomic modifications have been produced by serial rounds of somatic cell chromatin transfer (cloning) of sequentially genetically targeted somatic cells. However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that mult...

  14. Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells

    Directory of Open Access Journals (Sweden)

    Yener Bülent

    2007-10-01

    Full Text Available Abstract Background Recently, we demonstrated that human mesenchymal stem cells (hMSC stimulated with dexamethazone undergo gene focusing during osteogenic differentiation (Stem Cells Dev 14(6: 1608–20, 2005. Here, we examine the protein expression profiles of three additional populations of hMSC stimulated to undergo osteogenic differentiation via either contact with pro-osteogenic extracellular matrix (ECM proteins (collagen I, vitronectin, or laminin-5 or osteogenic media supplements (OS media. Specifically, we annotate these four protein expression profiles, as well as profiles from naïve hMSC and differentiated human osteoblasts (hOST, with known gene ontologies and analyze them as a tensor with modes for the expressed proteins, gene ontologies, and stimulants. Results Direct component analysis in the gene ontology space identifies three components that account for 90% of the variance between hMSC, osteoblasts, and the four stimulated hMSC populations. The directed component maps the differentiation stages of the stimulated stem cell populations along the differentiation axis created by the difference in the expression profiles of hMSC and hOST. Surprisingly, hMSC treated with ECM proteins lie closer to osteoblasts than do hMSC treated with OS media. Additionally, the second component demonstrates that proteomic profiles of collagen I- and vitronectin-stimulated hMSC are distinct from those of OS-stimulated cells. A three-mode tensor analysis reveals additional focus proteins critical for characterizing the phenotypic variations between naïve hMSC, partially differentiated hMSC, and hOST. Conclusion The differences between the proteomic profiles of OS-stimulated hMSC and ECM-hMSC characterize different transitional phenotypes en route to becoming osteoblasts. This conclusion is arrived at via a three-mode tensor analysis validated using hMSC plated on laminin-5.

  15. Quantitative trait loci mapping reveals candidate pathways regulating cell cycle duration in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Siwo Geoffrey

    2010-10-01

    Full Text Available Abstract Background Elevated parasite biomass in the human red blood cells can lead to increased malaria morbidity. The genes and mechanisms regulating growth and development of Plasmodium falciparum through its erythrocytic cycle are not well understood. We previously showed that strains HB3 and Dd2 diverge in their proliferation rates, and here use quantitative trait loci mapping in 34 progeny from a cross between these parent clones along with integrative bioinformatics to identify genetic loci and candidate genes that control divergences in cell cycle duration. Results Genetic mapping of cell cycle duration revealed a four-locus genetic model, including a major genetic effect on chromosome 12, which accounts for 75% of the inherited phenotype variation. These QTL span 165 genes, the majority of which have no predicted function based on homology. We present a method to systematically prioritize candidate genes using the extensive sequence and transcriptional information available for the parent lines. Putative functions were assigned to the prioritized genes based on protein interaction networks and expression eQTL from our earlier study. DNA metabolism or antigenic variation functional categories were enriched among our prioritized candidate genes. Genes were then analyzed to determine if they interact with cyclins or other proteins known to be involved in the regulation of cell cycle. Conclusions We show that the divergent proliferation rate between a drug resistant and drug sensitive parent clone is under genetic regulation and is segregating as a complex trait in 34 progeny. We map a major locus along with additional secondary effects, and use the wealth of genome data to identify key candidate genes. Of particular interest are a nucleosome assembly protein (PFL0185c, a Zinc finger transcription factor (PFL0465c both on chromosome 12 and a ribosomal protein L7Ae-related on chromosome 4 (PFD0960c.

  16. In vivo evaluation of an episcleral multielectrode array for stimulation of the retina with reduced retinal ganglion cell mass.

    Science.gov (United States)

    Siu, Timothy L; Morley, John W

    2008-05-01

    A visual prosthesis is an experimental device designed to activate residual functional neurons in the visual pathway to generate artificial vision for blind patients. Specifically, for photoreceptor disease, a microelectrode array applied to the surface of the sclera could potentially serve to stimulate the remaining interneurons in the retina to produce topographically mapped visual percepts. However, of those neurons spared in the disease process, the retinal ganglion cells (RGC), which represent the final output neurons of the retina, can be markedly reduced in number. Using an albino rabbit model with RGC deficits, acute recording of cortical electrical evoked potential was performed to ascertain whether such a stimulation strategy is feasible. By analyzing the strength-duration curve (current threshold vs. pulse duration) and cortical activation profiles, our results prove that bioelectrically safe and spatially differentiated stimulation of the retina is feasible notwithstanding the condition of markedly reduced RGC counts.

  17. Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages.

    Science.gov (United States)

    Casero, David; Sandoval, Salemiz; Seet, Christopher S; Scholes, Jessica; Zhu, Yuhua; Ha, Vi Luan; Luong, Annie; Parekh, Chintan; Crooks, Gay M

    2015-12-01

    To elucidate the transcriptional 'landscape' that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitor cells spanning the earliest stages of B lymphoid and T lymphoid specification. Over 3,000 genes encoding previously unknown long non-coding RNAs (lncRNAs) were revealed through the analysis of these rare populations. Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage specific and were more lineage specific than those of protein-coding genes. Protein-coding genes co-expressed with neighboring lncRNA genes showed enrichment for ontologies related to lymphoid differentiation. The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships among the earliest progenitor cells in the human bone marrow and thymus.

  18. Facile preparation of titanium dioxide nano-capsule arrays used as photo-anode for dye sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Su, Penglei; Li, Hongyi, E-mail: lhy06@bjut.edu.cn; Wang, Jinshu, E-mail: wangjsh@bjut.edu.cn; Wu, Junshu; Zhao, Bingxin; Wang, Fei

    2015-08-30

    Graphical abstract: - Highlights: • TiO{sub 2} nanoparticles have been introduced into TiO{sub 2} nanotube using a facile liquid phase deposition method at low temperature in atmosphere. • Dye solar cells have been assembled on flexible titanium substrate. • The incident photo-electron conversion efficiency has been improved 76% compared with pure TiO{sub 2} nanotube arrays. - Abstract: To improve titanium dioxide (TiO{sub 2}) nanotube arrays’ performance on dye sensitized solar cells (DSSCs), TiO{sub 2} nano-capsule arrays (TNCP) have been designed and prepared by planting TiO{sub 2} nanoparticles into TiO{sub 2} nanotube (TNT) using a facile liquid phase deposition (LPD) route which does not require any special equipment and both improve the specific surface area and surface energy of TNT at low temperature. It has been found that TiO{sub 2} nanoparticles are homogeneously distributed along the wall of TNT and their crystal size is calculated to be 5–10 nm. The obtained TNCP's specific surface area and surface energy have been increased from 27.1 (for pure TNT) to 33.4 m{sup 2}/g and from 67.7 (for pure TNT) to 76.4 mJ/m{sup 2}, respectively. When used as photo-anodes of DSSCs, TNCP shows higher energy conversion efficiency, which is 1.7 times that of pure TNT. Therefore, the present work provides one effective strategy to better TNT's performance on DSSCs, which can be assembled on metal substrate in large scale.

  19. Facile preparation of titanium dioxide nano-capsule arrays used as photo-anode for dye sensitized solar cells

    International Nuclear Information System (INIS)

    Graphical abstract: - Highlights: • TiO2 nanoparticles have been introduced into TiO2 nanotube using a facile liquid phase deposition method at low temperature in atmosphere. • Dye solar cells have been assembled on flexible titanium substrate. • The incident photo-electron conversion efficiency has been improved 76% compared with pure TiO2 nanotube arrays. - Abstract: To improve titanium dioxide (TiO2) nanotube arrays’ performance on dye sensitized solar cells (DSSCs), TiO2 nano-capsule arrays (TNCP) have been designed and prepared by planting TiO2 nanoparticles into TiO2 nanotube (TNT) using a facile liquid phase deposition (LPD) route which does not require any special equipment and both improve the specific surface area and surface energy of TNT at low temperature. It has been found that TiO2 nanoparticles are homogeneously distributed along the wall of TNT and their crystal size is calculated to be 5–10 nm. The obtained TNCP's specific surface area and surface energy have been increased from 27.1 (for pure TNT) to 33.4 m2/g and from 67.7 (for pure TNT) to 76.4 mJ/m2, respectively. When used as photo-anodes of DSSCs, TNCP shows higher energy conversion efficiency, which is 1.7 times that of pure TNT. Therefore, the present work provides one effective strategy to better TNT's performance on DSSCs, which can be assembled on metal substrate in large scale

  20. Controllable preparation of TiO{sub 2} nanowire arrays on titanium mesh for flexible dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Wenwu; Lu, Hui; Zhang, Mei; Guo, Min, E-mail: guomin@ustb.edu.cn

    2015-08-30

    Graphical abstract: TiO{sub 2} nanowire arrays with controlled morphology and density have been synthesized on Ti mesh substrates by hydrothermal approach for flexible dye-sensitized solar cells which showed well photovoltaic efficiency of 3.42%. - Highlights: • Flexible titanium mesh was first used for hydrothermal preparation of TiO{sub 2} NWAs. • The formation mechanism of the TiO{sub 2} nanostructures was discussed. • The density, average diameter, and morphology of TiO{sub 2} NWAs can be controlled. • The effects of the sensitization temperature and time on the properties were studied. - Abstract: TiO{sub 2} nanowire arrays (NWAs) with an average diameter of 80 nm have been successfully synthesized on titanium (Ti) mesh substrates via hydrothermal method. The effects of preparing conditions such as concentration of NaOH solution, reaction time, and hydrothermal temperature on the growth of TiO{sub 2} nanoarrays and its related photovoltaic properties were systematically investigated by scanning electron microscopy, X-ray diffraction, and photovoltaic properties test. The growth mechanism of the Ti mesh-supported TiO{sub 2} nanostructures was discussed in detail. Moreover, a parametric study was performed to determine the optimized temperature and time of the dye sensitized process for the flexible dye-sensitized solar cell (DSSC). It is demonstrated that hydrothermal parameters had obvious influence on the morphology and growth density of the as-prepared TiO{sub 2} nanoarrays. In addition, the performance of the flexible DSSC depended strongly on the sensitization temperature and time. By utilizing Ti mesh-supported TiO{sub 2} NWAs (with a length of about 14 μm) as a photoanode, the flexible DSSC with a short circuit current density of 10.49 mA cm{sup −2}, an open-circuit voltage of 0.69 V, and an overall power conversion efficiency of 3.42% was achieved.

  1. Revealing nonergodic dynamics in living cells from a single particle trajectory.

    Science.gov (United States)

    Lanoiselée, Yann; Grebenkov, Denis S

    2016-05-01

    We propose the improved ergodicity and mixing estimators to identify nonergodic dynamics from a single particle trajectory. The estimators are based on the time-averaged characteristic function of the increments and can thus capture additional information on the process as compared to the conventional time-averaged mean-square displacement. The estimators are first investigated and validated for several models of anomalous diffusion, such as ergodic fractional Brownian motion and diffusion on percolating clusters, and nonergodic continuous-time random walks and scaled Brownian motion. The estimators are then applied to two sets of earlier published trajectories of mRNA molecules inside live Escherichia coli cells and of Kv2.1 potassium channels in the plasma membrane. These statistical tests did not reveal nonergodic features in the former set, while some trajectories of the latter set could be classified as nonergodic. Time averages along such trajectories are thus not representative and may be strongly misleading. Since the estimators do not rely on ensemble averages, the nonergodic features can be revealed separately for each trajectory, providing a more flexible and reliable analysis of single-particle tracking experiments in microbiology.

  2. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells.

    Science.gov (United States)

    Carlile, Thomas M; Rojas-Duran, Maria F; Zinshteyn, Boris; Shin, Hakyung; Bartoli, Kristen M; Gilbert, Wendy V

    2014-11-01

    Post-transcriptional modification of RNA nucleosides occurs in all living organisms. Pseudouridine, the most abundant modified nucleoside in non-coding RNAs, enhances the function of transfer RNA and ribosomal RNA by stabilizing the RNA structure. Messenger RNAs were not known to contain pseudouridine, but artificial pseudouridylation dramatically affects mRNA function--it changes the genetic code by facilitating non-canonical base pairing in the ribosome decoding centre. However, without evidence of naturally occurring mRNA pseudouridylation, its physiological relevance was unclear. Here we present a comprehensive analysis of pseudouridylation in Saccharomyces cerevisiae and human RNAs using Pseudo-seq, a genome-wide, single-nucleotide-resolution method for pseudouridine identification. Pseudo-seq accurately identifies known modification sites as well as many novel sites in non-coding RNAs, and reveals hundreds of pseudouridylated sites in mRNAs. Genetic analysis allowed us to assign most of the new modification sites to one of seven conserved pseudouridine synthases, Pus1-4, 6, 7 and 9. Notably, the majority of pseudouridines in mRNA are regulated in response to environmental signals, such as nutrient deprivation in yeast and serum starvation in human cells. These results suggest a mechanism for the rapid and regulated rewiring of the genetic code through inducible mRNA modifications. Our findings reveal unanticipated roles for pseudouridylation and provide a resource for identifying the targets of pseudouridine synthases implicated in human disease.

  3. 3D reconstruction of VZV infected cell nuclei and PML nuclear cages by serial section array scanning electron microscopy and electron tomography.

    Directory of Open Access Journals (Sweden)

    Mike Reichelt

    Full Text Available Varicella-zoster virus (VZV is a human alphaherpesvirus that causes varicella (chickenpox and herpes zoster (shingles. Like all herpesviruses, the VZV DNA genome is replicated in the nucleus and packaged into nucleocapsids that must egress across the nuclear membrane for incorporation into virus particles in the cytoplasm. Our recent work showed that VZV nucleocapsids are sequestered in nuclear cages formed from promyelocytic leukemia protein (PML in vitro and in human dorsal root ganglia and skin xenografts in vivo. We sought a method to determine the three-dimensional (3D distribution of nucleocapsids in the nuclei of herpesvirus-infected cells as well as the 3D shape, volume and ultrastructure of these unique PML subnuclear domains. Here we report the development of a novel 3D imaging and reconstruction strategy that we term Serial Section Array-Scanning Electron Microscopy (SSA-SEM and its application to the analysis of VZV-infected cells and these nuclear PML cages. We show that SSA-SEM permits large volume imaging and 3D reconstruction at a resolution sufficient to localize, count and distinguish different types of VZV nucleocapsids and to visualize complete PML cages. This method allowed a quantitative determination of how many nucleocapsids can be sequestered within individual PML cages (sequestration capacity, what proportion of nucleocapsids are entrapped in single nuclei (sequestration efficiency and revealed the ultrastructural detail of the PML cages. More than 98% of all nucleocapsids in reconstructed nuclear volumes were contained in PML cages and single PML cages sequestered up to 2,780 nucleocapsids, which were shown by electron tomography to be embedded and cross-linked by an filamentous electron-dense meshwork within these unique subnuclear domains. This SSA-SEM analysis extends our recent characterization of PML cages and provides a proof of concept for this new strategy to investigate events during virion assembly at the

  4. Current Approach in Surface Plasmons for Thin Film and Wire Array Solar Cell Applications

    OpenAIRE

    Keya Zhou; Zhongyi Guo; Shutian Liu; Jung-Ho Lee

    2015-01-01

    Surface plasmons, which exist along the interface of a metal and a dielectric, have been proposed as an efficient alternative method for light trapping in solar cells during the past ten years. With unique properties such as superior light scattering, optical trapping, guide mode coupling, near field concentration, and hot-electron generation, metallic nanoparticles or nanostructures can be tailored to a certain geometric design to enhance solar cell conversion efficiency and to reduce the ma...

  5. Dislocation dynamics. II. Applications to the formation of persistent slip bands, planar arrays, and dislocation cells

    International Nuclear Information System (INIS)

    The dynamic organization of dislocations into spatially heterogeneous substructures is demonstrated by applying the principles of dislocation dynamics that were outlined in the preceding paper. Here it is shown that the formation of persistent slip bands is a consequence of the competition between dipole formation and annihilation of dislocations of opposite Burgers vectors in the absence of temperature-enhanced climb recovery under cyclic stress conditions. Planar arrays, which are also uniaxial structures, are shown to arise from enhanced dislocation multiplication and the formation of stable dipole configurations along a slip plane at lower temperatures where climb is unimportant. Biaxial dislocation systems experience additional degrees of freedom compared with uniaxial systems because of available motion along additional slip systems. It is demonstrated that for a system of orthogonal slip directions at high temperatures in which climb and glide motion are competitive, dislocation cellular structures form as a result of immobile dipole and junction formation and by the internal elastic strain energy minimization caused by long-range self-shielding. It is shown that the internal elastic strain energy is reduced by the self-organization process. However, the short-range nonlinear processes (i.e., dipole and junction formation) are shown not to allow absolute elastic energy minimization

  6. Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor

    Energy Technology Data Exchange (ETDEWEB)

    Copp& #233; , Jean-Philippe; Patil, Christopher; Rodier, Francis; Sun, Yu; Munoz, Denise; Goldstein, Joshua; Nelson, Peter; Desprez, Pierre-Yves; Campisi, Judith

    2008-10-24

    Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP) developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA-damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial-mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL)-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced senescence. Moreover, they suggest a cell-nonautonomous mechanism by which p53 can restrain, and oncogenic RAS can promote, the development of age-related cancer by altering the tissue microenvironment.

  7. Senescence-associated secretory phenotypes reveal cell-nonautonomous functions of oncogenic RAS and the p53 tumor suppressor.

    Directory of Open Access Journals (Sweden)

    Jean-Philippe Coppé

    2008-12-01

    Full Text Available Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA-damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial-mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced senescence. Moreover, they suggest a cell-nonautonomous mechanism by which p53 can restrain, and oncogenic RAS can promote, the development of age-related cancer by altering the tissue microenvironment.

  8. In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cells

    Science.gov (United States)

    Robijns, J.; Molenberghs, F.; Sieprath, T.; Corne, T. D. J.; Verschuuren, M.; de Vos, W. H.

    2016-07-01

    The nuclear lamina is a critical regulator of nuclear structure and function. Nuclei from laminopathy patient cells experience repetitive disruptions of the nuclear envelope, causing transient intermingling of nuclear and cytoplasmic components. The exact causes and consequences of these events are not fully understood, but their stochastic occurrence complicates in-depth analyses. To resolve this, we have established a method that enables quantitative investigation of spontaneous nuclear ruptures, based on co-expression of a firmly bound nuclear reference marker and a fluorescent protein that shuttles between the nucleus and cytoplasm during ruptures. Minimally invasive imaging of both reporters, combined with automated tracking and in silico synchronization of individual rupture events, allowed extracting information on rupture frequency and recovery kinetics. Using this approach, we found that rupture frequency correlates inversely with lamin A/C levels, and can be reduced in genome-edited LMNA knockout cells by blocking actomyosin contractility or inhibiting the acetyl-transferase protein NAT10. Nuclear signal recovery followed a kinetic that is co-determined by the severity of the rupture event, and could be prolonged by knockdown of the ESCRT-III complex component CHMP4B. In conclusion, our approach reveals regulators of nuclear rupture induction and repair, which may have critical roles in disease development.

  9. Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control

    Energy Technology Data Exchange (ETDEWEB)

    Burke, Jason R.; Hura, Greg L.; Rubin, Seth M. (UCSC); (LBNL)

    2012-07-18

    Cyclin-dependent kinase (Cdk) phosphorylation of the Retinoblastoma protein (Rb) drives cell proliferation through inhibition of Rb complexes with E2F transcription factors and other regulatory proteins. We present the first structures of phosphorylated Rb that reveal the mechanism of its inactivation. S608 phosphorylation orders a flexible 'pocket' domain loop such that it mimics and directly blocks E2F transactivation domain (E2F{sup TD}) binding. T373 phosphorylation induces a global conformational change that associates the pocket and N-terminal domains (RbN). This first multidomain Rb structure demonstrates a novel role for RbN in allosterically inhibiting the E2F{sup TD}-pocket association and protein binding to the pocket 'LxCxE' site. Together, these structures detail the regulatory mechanism for a canonical growth-repressive complex and provide a novel example of how multisite Cdk phosphorylation induces diverse structural changes to influence cell cycle signaling.

  10. Whole-brain circuit dissection in free-moving animals reveals cell-specific mesocorticolimbic networks

    Science.gov (United States)

    Michaelides, Michael; Anderson, Sarah Ann R.; Ananth, Mala; Smirnov, Denis; Thanos, Panayotis K.; Neumaier, John F.; Wang, Gene-Jack; Volkow, Nora D.; Hurd, Yasmin L.

    2013-01-01

    The ability to map the functional connectivity of discrete cell types in the intact mammalian brain during behavior is crucial for advancing our understanding of brain function in normal and disease states. We combined designer receptor exclusively activated by designer drug (DREADD) technology and behavioral imaging with μPET and [18F]fluorodeoxyglucose (FDG) to generate whole-brain metabolic maps of cell-specific functional circuits during the awake, freely moving state. We have termed this approach DREADD-assisted metabolic mapping (DREAMM) and documented its ability in rats to map whole-brain functional anatomy. We applied this strategy to evaluating changes in the brain associated with inhibition of prodynorphin-expressing (Pdyn-expressing) and of proenkephalin-expressing (Penk-expressing) medium spiny neurons (MSNs) of the nucleus accumbens shell (NAcSh), which have been implicated in neuropsychiatric disorders. DREAMM revealed discrete behavioral manifestations and concurrent engagement of distinct corticolimbic networks associated with dysregulation of Pdyn and Penk in MSNs of the NAcSh. Furthermore, distinct neuronal networks were recruited in awake versus anesthetized conditions. These data demonstrate that DREAMM is a highly sensitive, molecular, high-resolution quantitative imaging approach. PMID:24231358

  11. Coupled electrophysiological recording and single cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation.

    Science.gov (United States)

    Chen, Xiaoying; Zhang, Kunshan; Zhou, Liqiang; Gao, Xinpei; Wang, Junbang; Yao, Yinan; He, Fei; Luo, Yuping; Yu, Yongchun; Li, Siguang; Cheng, Liming; Sun, Yi E

    2016-03-01

    The mammalian brain is heterogeneous, containing billions of neurons and trillions of synapses forming various neural circuitries, through which sense, movement, thought, and emotion arise. The cellular heterogeneity of the brain has made it difficult to study the molecular logic of neural circuitry wiring, pruning, activation, and plasticity, until recently, transcriptome analyses with single cell resolution makes decoding of gene regulatory networks underlying aforementioned circuitry properties possible. Here we report success in performing both electrophysiological and whole-genome transcriptome analyses on single human neurons in culture. Using Weighted Gene Coexpression Network Analyses (WGCNA), we identified gene clusters highly correlated with neuronal maturation judged by electrophysiological characteristics. A tight link between neuronal maturation and genes involved in ubiquitination and mitochondrial function was revealed. Moreover, we identified a list of candidate genes, which could potentially serve as biomarkers for neuronal maturation. Coupled electrophysiological recording and single cell transcriptome analysis will serve as powerful tools in the future to unveil molecular logics for neural circuitry functions. PMID:26883038

  12. Characterization of genetic rearrangements in esophageal squamous carcinoma cell lines by a combination of M-FISH and array-CGH: further confirmation of some split genomic regions in primary tumors

    International Nuclear Information System (INIS)

    Chromosomal and genomic aberrations are common features of human cancers. However, chromosomal numerical and structural aberrations, breakpoints and disrupted genes have yet to be identified in esophageal squamous cell carcinoma (ESCC). Using multiplex-fluorescence in situ hybridization (M-FISH) and oligo array-based comparative hybridization (array-CGH), we identified aberrations and breakpoints in six ESCC cell lines. Furthermore, we detected recurrent breakpoints in primary tumors by dual-color FISH. M-FISH and array-CGH results revealed complex numerical and structural aberrations. Frequent gains occurred at 3q26.33-qter, 5p14.1-p11, 7pter-p12.3, 8q24.13-q24.21, 9q31.1-qter, 11p13-p11, 11q11-q13.4, 17q23.3-qter, 18pter-p11, 19 and 20q13.32-qter. Losses were frequent at 18q21.1-qter. Breakpoints that clustered within 1 or 2 Mb were identified, including 9p21.3, 11q13.3-q13.4, 15q25.3 and 3q28. By dual-color FISH, we observed that several recurrent breakpoint regions in cell lines were also present in ESCC tumors. In particular, breakpoints clustered at 11q13.3-q13.4 were identified in 43.3% (58/134) of ESCC tumors. Both 11q13.3-q13.4 splitting and amplification were significantly correlated with lymph node metastasis (LNM) (P = 0.004 and 0.022) and advanced stages (P = 0.004 and 0.039). Multivariate logistic regression analysis revealed that only 11q13.3-q13.4 splitting was an independent predictor for LNM (P = 0.026). The combination of M-FISH and array-CGH helps produce more accurate karyotypes. Our data provide significant, detailed information for appropriate uses of these ESCC cell lines for cytogenetic and molecular biological studies. The aberrations and breakpoints detected in both the cell lines and primary tumors will contribute to identify affected genes involved in the development and progression of ESCC

  13. Microelectrode arrays of diamond-insulated graphitic channels for real time detection of exocytotic events from cultured chromaffin cells and slices of adrenal glands

    CERN Document Server

    Picollo, F; Bernardi, E; Marcantoni, A; Pasquarelli, A; Carbone, E; Olivero, P; Carabelli, V

    2016-01-01

    A microstructured graphitic 4x4 multielectrode array was embedded in a single crystal diamond substrate (4x4 {uG-SCD MEA) for real-time monitoring of exocytotic events from cultured chromaffin cells and adrenal slices. The current approach relies on the development of a parallel ion beam lithographic technique, which assures the time effective fabrication of extended arrays with reproducible electrode dimensions. The reported device is suitable for performing amperometric and voltammetric recordings with high sensitivity and temporal resolution, by simultaneously acquiring data from 16 rectangularly shaped microelectrodes (20x3.5 um^2) separated by 200 um gaps. Taking advantage of the array geometry we addressed the following specific issues: i) detect both the spontaneous and KCl-evoked secretion simultaneously from several chromaffin cells directly cultured on the device surface, ii) resolve the waveform of different subsets of exocytotic events, iii) monitoring quantal secretory events from thin slices of ...

  14. Low temperature grown ZnO@TiO{sub 2} core shell nanorod arrays for dye sensitized solar cell application

    Energy Technology Data Exchange (ETDEWEB)

    Goh, Gregory Kia Liang [Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology, and Research), 3 Research Link, 117602 Singapore (Singapore); Le, Hong Quang, E-mail: lehq@imre.a-star.edu.sg [Institute of Materials Research and Engineering, A*STAR (Agency for Science, Technology, and Research), 3 Research Link, 117602 Singapore (Singapore); Huang, Tang Jiao; Hui, Benjamin Tan Tiong [Department of Materials Science and Engineering (DMSE), Faculty of Engineering National University of Singapore (NUS) BLK E3A, #04-10, 7 Engineering Drive 1, Singapore 117574 (Singapore)

    2014-06-01

    High aspect ratio ZnO nanorod arrays were synthesized on fluorine-doped tin oxide glasses via a low temperature solution method. By adjusting the growth condition and adding polyethylenimine, ZnO nanorod arrays with tunable length were successfully achieved. The ZnO@TiO{sub 2} core shells structures were realized by a fast growth method of immersion into a (NH{sub 4}){sub 2}·TiF{sub 6} solution. Transmission electron microscopy, X-ray Diffraction and energy dispersive X-ray measurements all confirmed the existence of a titania shell uniformly covering the ZnO nanorod's surface. Results of solar cell testing showed that addition of a TiO{sub 2} shell to the ZnO nanorod significantly increased short circuit current (from 4.2 to 5.2 mA/cm{sup 2}), open circuit voltage (from 0.6 V to 0.8 V) and fill factor (from 42.8% to 73.02%). The overall cell efficiency jumped from 1.1% for bare ZnO nanorod to 3.03% for a ZnO@TiO{sub 2} core shell structured solar cell with a 18–22 nm shell thickness, a nearly threefold increase. - Graphical abstract: The synthesis process of coating TiO{sub 2} shell onto ZnO nanorod core is shown schematically. A thin, uniform, and conformal shell had been grown on the surface of the ZnO core after immersing in the (NH{sub 4}){sub 2}·TiF{sub 6} solution for 5–15 min. - Highlights: • ZnO@TiO{sub 2} core shell nanorod has been grown on FTO substrate using low temperature solution method. • TEM, XRD, EDX results confirmed the existing of titana shell, uniformly covered rod's surface. • TiO{sub 2} shell suppressed recombination, demonstrated significant enhancement in cell's efficiency. • Core shell DSSC's efficiency achieved as high as 3.03%, 3 times higher than that of ZnO nanorods.

  15. Cell model of catecholaminergic polymorphic ventricular tachycardia reveals early and delayed afterdepolarizations.

    Directory of Open Access Journals (Sweden)

    Kirsi Kujala

    Full Text Available BACKGROUND: Induced pluripotent stem cells (iPSC provide means to study the pathophysiology of genetic disorders. Catecholaminergic polymorphic ventricular tachycardia (CPVT is a malignant inherited ion channel disorder predominantly caused by mutations in the cardiac ryanodine receptor (RyR2. In this study the cellular characteristics of CPVT are investigated and whether the electrophysiological features of this mutation can be mimicked using iPSC -derived cardiomyocytes (CM. METHODOLOGY/PRINCIPAL FINDINGS: Spontaneously beating CMs were differentiated from iPSCs derived from a CPVT patient carrying a P2328S mutation in RyR2 and from two healthy controls. Calcium (Ca(2+ cycling and electrophysiological properties were studied by Ca(2+ imaging and patch-clamp techniques. Monophasic action potential (MAP recordings and 24h-ECGs of CPVT-P2328S patients were analyzed for the presence of afterdepolarizations. We found defects in Ca(2+ cycling and electrophysiology in CPVT CMs, reflecting the cardiac phenotype observed in the patients. Catecholaminergic stress led to abnormal Ca(2+ signaling and induced arrhythmias in CPVT CMs. CPVT CMs also displayed reduced sarcoplasmic reticulum (SR Ca(2+ content, indicating leakage of Ca(2+ from the SR. Patch-clamp recordings of CPVT CMs revealed both delayed afterdepolarizations (DADs during spontaneous beating and in response to adrenaline and also early afterdepolarizations (EADs during spontaneous beating, recapitulating the changes seen in MAP and 24h-ECG recordings of patients carrying the same mutation. CONCLUSIONS/SIGNIFICANCE: This cell model shows aberrant Ca(2+ cycling characteristic of CPVT and in addition to DADs it displays EADs. This cell model for CPVT provides a platform to study basic pathology, to screen drugs, and to optimize drug therapy.

  16. Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane.

    Science.gov (United States)

    Ferreira, Savio Siqueira; Hotta, Carlos Takeshi; Poelking, Viviane Guzzo de Carli; Leite, Debora Chaves Coelho; Buckeridge, Marcos Silveira; Loureiro, Marcelo Ehlers; Barbosa, Marcio Henrique Pereira; Carneiro, Monalisa Sampaio; Souza, Glaucia Mendes

    2016-05-01

    Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. Expression of sugar transporters might explain sucrose differences among genotypes, but an unexpected differential expression of histones were also identified between high and low Brix° genotypes. Lignin biosynthetic genes and bioenergetics-related genes were up-regulated in the high lignin genotype, suggesting that these genes are important for S. spontaneum to allocate carbon to lignin, while S. officinarum allocates it to sucrose storage. Co-expression network analysis identified 18 transcription factors possibly related to cell wall biosynthesis while in silico analysis detected cis-elements involved in cell wall biosynthesis in their promoters. Our results provide information to elucidate regulatory networks underlying traits of interest that will allow the improvement of sugarcane for biofuel and chemicals production. PMID:26820137

  17. Evaluation of reverse phase protein array (RPPA)-based pathway-activation profiling in 84 non-small cell lung cancer (NSCLC) cell lines as platform for cancer proteomics and biomarker discovery.

    Science.gov (United States)

    Ummanni, Ramesh; Mannsperger, Heiko A; Sonntag, Johanna; Oswald, Marcus; Sharma, Ashwini K; König, Rainer; Korf, Ulrike

    2014-05-01

    The reverse phase protein array (RPPA) approach was employed for a quantitative analysis of 71 cancer-relevant proteins and phosphoproteins in 84 non-small cell lung cancer (NSCLC) cell lines and by monitoring the activation state of selected receptor tyrosine kinases, PI3K/AKT and MEK/ERK1/2 signaling, cell cycle control, apoptosis, and DNA damage. Additional information on NSCLC cell lines such as that of transcriptomic data, genomic aberrations, and drug sensitivity was analyzed in the context of proteomic data using supervised and non-supervised approaches for data analysis. First, the unsupervised analysis of proteomic data indicated that proteins clustering closely together reflect well-known signaling modules, e.g. PI3K/AKT- and RAS/RAF/ERK-signaling, cell cycle regulation, and apoptosis. However, mutations of EGFR, ERBB2, RAF, RAS, TP53, and PI3K were found dispersed across different signaling pathway clusters. Merely cell lines with an amplification of EGFR and/or ERBB2 clustered closely together on the proteomic, but not on the transcriptomic level. Secondly, supervised data analysis revealed that sensitivity towards anti-EGFR drugs generally correlated better with high level EGFR phosphorylation than with EGFR abundance itself. High level phosphorylation of RB and high abundance of AURKA were identified as candidates that can potentially predict sensitivity towards the aurora kinase inhibitor VX680. Examples shown demonstrate that the RPPA approach presents a useful platform for targeted proteomics with high potential for biomarker discovery. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. PMID:24361481

  18. Antarctic-Wide Array of High-Resolution Ice Core Records Reveals Pervasive Lead Pollution Began in 1889 and Persists Today

    Science.gov (United States)

    McConnell, J. R.; Maselli, O. J.; Sigl, M.; Vallelonga, P.; Neumann, Thomas Allen; Anschutz, H.; Bales, R. C.; Curran, M. A. J.; Das, S. B.; Edwards, R.; Kipfstuhl, S.; Layman, L.; Thomas, E. R.

    2014-01-01

    Interior Antarctica is among the most remote places on Earth and was thought to be beyond the reach of human impacts when Amundsen and Scott raced to the South Pole in 1911. Here we show detailed measurements from an extensive array of 16 ice cores quantifying substantial toxic heavy metal lead pollution at South Pole and throughout Antarctica by 1889 - beating polar explorers by more than 22 years. Unlike the Arctic where lead pollution peaked in the 1970s, lead pollution in Antarctica was as high in the early 20th century as at any time since industrialization. The similar timing and magnitude of changes in lead deposition across Antarctica, as well as the characteristic isotopic signature of Broken Hill lead found throughout the continent, suggest that this single emission source in southern Australia was responsible for the introduction of lead pollution into Antarctica at the end of the 19th century and remains a significant source today. An estimated 660 t of industrial lead have been deposited over Antarctica during the past 130 years as a result of mid-latitude industrial emissions, with regional-to-global scale circulation likely modulating aerosol concentrations. Despite abatement efforts, significant lead pollution in Antarctica persists into the 21st century.

  19. Ultra-high efficient solar cell based on decagonal arrays of silicon nanowires

    Science.gov (United States)

    Hussein, Mohamed; Hameed, Mohamed Farhat O.; Areed, Nihal F. F.; Obayya, Salah Sabry A.

    2014-11-01

    Silicon nanowires (SiNWs) are the subject of intense research in solar energy harvesting due to their unique electrical and optical characteristics. The transmission, reflection, and absorption spectra of decagonal Si NWs (D-SiNWs) solar cells have been calculated using a three-dimensional finite-difference time-domain method to present a design guideline for ultra-high efficiency SiNW in solar cell applications. In this study, the structure geometrical parameters of the suggested design are tuned to maximize light absorption. The ultimate efficiency is used to quantify the absorption enhancement of the SiNWs solar cells. A maximum ultimate efficiency of 39.3% is achieved for the reported D-SiNWs, which is greater than that of the previous work of slanting Si NWs by 17.49%.

  20. Process development for automated solar cell and module production. Task 4: Automated array assembly

    Science.gov (United States)

    Hagerty, J. J.

    1981-01-01

    Progress in the development of automated solar cell and module production is reported. The unimate robot is programmed for the final 35 cell pattern to be used in the fabrication of the deliverable modules. The mechanical construction of the automated lamination station and final assembly station phases are completed and the first operational testing is underway. The final controlling program is written and optimized. The glass reinforced concrete (GRC) panels to be used for testing and deliverables are in production. Test routines are grouped together and defined to produce the final control program.

  1. Optimization of interdigitated electrode (IDE) arrays for impedance based evaluation of Hs 578T cancer cells

    Science.gov (United States)

    Alexander, Frank, Jr.; Price, Dorielle T.; Bhansali, Shekhar

    2010-04-01

    This paper examines the effect of electrode width and spacing of interdigitated electrodes (IDEs) for impedance-based cancer detection and characterization. IDEs are desired for bioimpedance measurements because their fabrication process is simple and inexpensive, and the geometry presents a potential for improved sensitivity over other microelectrode designs. Optimizing the geometry will eliminate this problem and increase the sensitivity of these devices for bioimpedance measurement applications. This paper evaluates the effect of IDE geometry on the sensitivity of breast cancer cell impedance measurements. Equivalent circuit data analysis was conducted to quantify and characterize the cells.

  2. Fabrication and doping methods for silicon nano- and micropillar arrays for solar cell applications: a review

    NARCIS (Netherlands)

    Elbersen, R.; Vijselaar, W.J.C.; Tiggelaar, R.M.; Gardeniers, J.G.E.; Huskens, J.

    2015-01-01

    Silicon is one of the main components of commercial solar cells and is used in many other solar-light-harvesting devices. The overall efficiency of these devices can be increased by the use of structured surfaces that contain nanometer- to micrometer-sized pillars with radial p/n junctions. High den

  3. Proteome array identification of bioactive soluble proteins/peptides in matrigel; relevance to stem cell responses

    Science.gov (United States)

    Matrigel and similar commercial products are extracts of the Engelbreth-Holm-Swarm sarcoma that provide a basement-membrane-like attachment factor or gel that is used to grow cells on or in. To ascertain further what proteins may be present in Matrigel, besides its major basement-membrane constitue...

  4. Modeling and Characteristic Parameters Analysis of a Trough Concentrating Photovoltaic/Thermal System with GaAs and Super Cell Arrays

    Directory of Open Access Journals (Sweden)

    Xu Ji

    2012-01-01

    Full Text Available The paper established the one-dimension steady models of a trough concentrating photovoltaic/thermal system with a super cell array and a GaAs cell array, respectively, and verified the models by experiments. The gaps between calculation results and experimental results were less than 5%. Utilizing the models, the paper analyzed the influences of the characteristic parameters on the performances of the TCPV/T system with a super cell array and a GaAs cell array, respectively. The reflectivity of the parabolic mirror in the TCPV/T system was an important factor to determine the utilizing efficiency of solar energy. The performances of the TCPV/T system can be optimized by improving the mirror reflectivity and the thermal solar radiation absorptivity of the lighting plate and pursuing a suitable focal line with uniform light intensity distribution. All these works will benefit to the utilization of the trough concentrating system and the combined heat/power supply.

  5. Reuse of E-plate cell sensor arrays in the xCELLigence Real-Time Cell Analyzer.

    Science.gov (United States)

    Stefanowicz-Hajduk, Justyna; Adamska, Anna; Bartoszewski, Rafal; Ochocka, J Renata

    2016-01-01

    The xCELLigence Real-Time Cell Analyzer (RTCA) is a non-invasive, impedence-based biosensor system that can measure cell viability, migration, growth, spreading, and proliferation. Changes in cell morphology and behavior are continuously monitored in real time using microelectronics located in the wells of RTCA E-plates. According to the manufacturer's recommendation, E-plates are single-use and disposable. Here, we show that E-plates can be regenerated and reused several times without significantly effecting experimental results. PMID:27625205

  6. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Resch, M.

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution imaging techniques. Also, translating findings between model substrates to intact biomass is critical for evaluating enzyme performance. Here we employ a fungal free enzyme cocktail, a complexed cellulosomal system, and a combination of the two to investigate saccharification mechanisms on cellulose I, II and III along with corn stover from Clean Fractionation (CF), which is an Organosolv pretreatment. The insoluble Cellulose Enriched Fraction (CEF) from CF contains mainly cellulose with minor amounts of residual hemicellulose and lignin, the amount of which depends on the CF pretreatment severity. Enzymatic digestions at both low and high-solids loadings demonstrate that CF reduces the amount of enzyme required to depolymerize polysaccharides relative to deacetylated, dilute acid pretreated corn stover. Transmission and scanning electron microscopy of the biomass provides evidence for the different mechanisms of enzymatic deconstruction between free and complexed enzyme systems, and reveals the basis for the synergistic relationship between the two enzyme paradigms on a process-relevant substrate for the first time. These results also demonstrate that the presence of lignin, rather than cellulose morphology, is more detrimental to cellulosome action than to free cellulases. As enzyme costs are a major economic driver for biorefineries, this study provides key inputs for the evaluation of CF as a pretreatment method for biomass conversion.

  7. Optimizing laser beam profiles using micro-lens arrays for efficient material processing: applications to solar cells

    Science.gov (United States)

    Hauschild, Dirk; Homburg, Oliver; Mitra, Thomas; Ivanenko, Mikhail; Jarczynski, Manfred; Meinschien, Jens; Bayer, Andreas; Lissotschenko, Vitalij

    2009-02-01

    High power laser sources are used in various production tools for microelectronic products and solar cells, including the applications annealing, lithography, edge isolation as well as dicing and patterning. Besides the right choice of the laser source suitable high performance optics for generating the appropriate beam profile and intensity distribution are of high importance for the right processing speed, quality and yield. For industrial applications equally important is an adequate understanding of the physics of the light-matter interaction behind the process. In advance simulations of the tool performance can minimize technical and financial risk as well as lead times for prototyping and introduction into series production. LIMO has developed its own software founded on the Maxwell equations taking into account all important physical aspects of the laser based process: the light source, the beam shaping optical system and the light-matter interaction. Based on this knowledge together with a unique free-form micro-lens array production technology and patented micro-optics beam shaping designs a number of novel solar cell production tool sub-systems have been built. The basic functionalities, design principles and performance results are presented with a special emphasis on resilience, cost reduction and process reliability.

  8. Commercialisation of CMOS Integrated Circuit Technology in Multi-Electrode Arrays for Neuroscience and Cell-Based Biosensors

    Directory of Open Access Journals (Sweden)

    Chris R. Bowen

    2011-05-01

    Full Text Available The adaptation of standard integrated circuit (IC technology as a transducer in cell-based biosensors in drug discovery pharmacology, neural interface systems and electrophysiology requires electrodes that are electrochemically stable, biocompatible and affordable. Unfortunately, the ubiquitous Complementary Metal Oxide Semiconductor (CMOS IC technology does not meet the first of these requirements. For devices intended only for research, modification of CMOS by post-processing using cleanroom facilities has been achieved. However, to enable adoption of CMOS as a basis for commercial biosensors, the economies of scale of CMOS fabrication must be maintained by using only low-cost post-processing techniques. This review highlights the methodologies employed in cell-based biosensor design where CMOS-based integrated circuits (ICs form an integral part of the transducer system. Particular emphasis will be placed on the application of multi-electrode arrays for in vitro neuroscience applications. Identifying suitable IC packaging methods presents further significant challenges when considering specific applications. The various challenges and difficulties are reviewed and some potential solutions are presented.

  9. Commercialisation of CMOS integrated circuit technology in multi-electrode arrays for neuroscience and cell-based biosensors.

    Science.gov (United States)

    Graham, Anthony H D; Robbins, Jon; Bowen, Chris R; Taylor, John

    2011-01-01

    The adaptation of standard integrated circuit (IC) technology as a transducer in cell-based biosensors in drug discovery pharmacology, neural interface systems and electrophysiology requires electrodes that are electrochemically stable, biocompatible and affordable. Unfortunately, the ubiquitous Complementary Metal Oxide Semiconductor (CMOS) IC technology does not meet the first of these requirements. For devices intended only for research, modification of CMOS by post-processing using cleanroom facilities has been achieved. However, to enable adoption of CMOS as a basis for commercial biosensors, the economies of scale of CMOS fabrication must be maintained by using only low-cost post-processing techniques. This review highlights the methodologies employed in cell-based biosensor design where CMOS-based integrated circuits (ICs) form an integral part of the transducer system. Particular emphasis will be placed on the application of multi-electrode arrays for in vitro neuroscience applications. Identifying suitable IC packaging methods presents further significant challenges when considering specific applications. The various challenges and difficulties are reviewed and some potential solutions are presented.

  10. Commercialisation of CMOS Integrated Circuit Technology in Multi-Electrode Arrays for Neuroscience and Cell-Based Biosensors

    Science.gov (United States)

    Graham, Anthony H. D.; Robbins, Jon; Bowen, Chris R.; Taylor, John

    2011-01-01

    The adaptation of standard integrated circuit (IC) technology as a transducer in cell-based biosensors in drug discovery pharmacology, neural interface systems and electrophysiology requires electrodes that are electrochemically stable, biocompatible and affordable. Unfortunately, the ubiquitous Complementary Metal Oxide Semiconductor (CMOS) IC technology does not meet the first of these requirements. For devices intended only for research, modification of CMOS by post-processing using cleanroom facilities has been achieved. However, to enable adoption of CMOS as a basis for commercial biosensors, the economies of scale of CMOS fabrication must be maintained by using only low-cost post-processing techniques. This review highlights the methodologies employed in cell-based biosensor design where CMOS-based integrated circuits (ICs) form an integral part of the transducer system. Particular emphasis will be placed on the application of multi-electrode arrays for in vitro neuroscience applications. Identifying suitable IC packaging methods presents further significant challenges when considering specific applications. The various challenges and difficulties are reviewed and some potential solutions are presented. PMID:22163884

  11. Microalterations of inherently unstable genomic regions in rat mammary carcinomas as revealed by long oligonucleotide array-based comparative genomic hybridization

    NARCIS (Netherlands)

    Adamovic, T.; McAllister, D.; Guryev, V.; Wang, X.; Andrae, J.W.; Cuppen, E.; Jacob, H.; Sugg, S.L.

    2009-01-01

    The presence of copy number variants in normal genomes poses a challenge to identify small genuine somatic copy number changes in high-resolution cancer genome profiling studies due to the use of unpaired reference DNA. Another problem is the well-known rearrangements of immunoglobulin and T-cell re

  12. Microalterations of Inherently Unstable Genomic Regions in Rat Mammary Carcinomas as Revealed by Long Oligonucleotide Array-Based Comparative Genomic Hybridization

    NARCIS (Netherlands)

    Adamovic, Tatjana; McAllister, Donna; Guryev, Victor; Wang, Xujing; Andrae, Jaime Wendt; Cuppen, Edwin; Jacob, Howard J.; Sugg, Sonia L.

    2009-01-01

    The presence of copy number variants in normal genomes poses a challenge to identify small genuine somatic copy number changes in high-resolution cancer genome profiling studies due to the use of unpaired reference DNA. Another problem is the well-known rearrangements of immunoglobulin and T-cell re

  13. Array Analysis of Simian Varicella Virus Gene Transcription in Productively Infected Cells in Tissue Culture

    OpenAIRE

    Deitch, Steven B.; Gilden, Donald H.; Wellish, Mary; Smith, John; Cohrs, Randall J.; Mahalingam, Ravi

    2005-01-01

    Simian varicella virus (SVV) is a neurotropic alphaherpesvirus of monkeys that is a model for varicella pathogenesis and latency. Like human varicella-zoster virus (VZV), SVV causes chicken pox (varicella), becomes latent in ganglia along the entire neuraxis, and reactivates to produce shingles (zoster). We developed macroarrays to determine the extent of viral transcription from all 70 predicted SVV open reading frames (ORFs) in infected cells in tissue culture. Cloned fragments (200 to 400 ...

  14. Microfabricated ion trap array

    Science.gov (United States)

    Blain, Matthew G.; Fleming, James G.

    2006-12-26

    A microfabricated ion trap array, comprising a plurality of ion traps having an inner radius of order one micron, can be fabricated using surface micromachining techniques and materials known to the integrated circuits manufacturing and microelectromechanical systems industries. Micromachining methods enable batch fabrication, reduced manufacturing costs, dimensional and positional precision, and monolithic integration of massive arrays of ion traps with microscale ion generation and detection devices. Massive arraying enables the microscale ion traps to retain the resolution, sensitivity, and mass range advantages necessary for high chemical selectivity. The reduced electrode voltage enables integration of the microfabricated ion trap array with on-chip circuit-based rf operation and detection electronics (i.e., cell phone electronics). Therefore, the full performance advantages of the microfabricated ion trap array can be realized in truly field portable, handheld microanalysis systems.

  15. Improved flow cytometric assessment reveals distinct microvesicle (cell-derived microparticle signatures in joint diseases.

    Directory of Open Access Journals (Sweden)

    Bence György

    Full Text Available INTRODUCTION: Microvesicles (MVs, earlier referred to as microparticles, represent a major type of extracellular vesicles currently considered as novel biomarkers in various clinical settings such as autoimmune disorders. However, the analysis of MVs in body fluids has not been fully standardized yet, and there are numerous pitfalls that hinder the correct assessment of these structures. METHODS: In this study, we analyzed synovial fluid (SF samples of patients with osteoarthritis (OA, rheumatoid arthritis (RA and juvenile idiopathic arthritis (JIA. To assess factors that may confound MV detection in joint diseases, we used electron microscopy (EM, Nanoparticle Tracking Analysis (NTA and mass spectrometry (MS. For flow cytometry, a method commonly used for phenotyping and enumeration of MVs, we combined recent advances in the field, and used a novel approach of differential detergent lysis for the exclusion of MV-mimicking non-vesicular signals. RESULTS: EM and NTA showed that substantial amounts of particles other than MVs were present in SF samples. Beyond known MV-associated proteins, MS analysis also revealed abundant plasma- and immune complex-related proteins in MV preparations. Applying improved flow cytometric analysis, we demonstrate for the first time that CD3(+ and CD8(+ T-cell derived SF MVs are highly elevated in patients with RA compared to OA patients (p=0.027 and p=0.009, respectively, after Bonferroni corrections. In JIA, we identified reduced numbers of B cell-derived MVs (p=0.009, after Bonferroni correction. CONCLUSIONS: Our results suggest that improved flow cytometric assessment of MVs facilitates the detection of previously unrecognized disease-associated vesicular signatures.

  16. Array analysis for potential biomarker of gemcitabine identification in non-small cell lung cancer cell lines.

    Science.gov (United States)

    Zhang, Hai-Hong; Zhang, Zhi-Yi; Che, Chun-Li; Mei, Yi-Fang; Shi, Yu-Zhi

    2013-01-01

    Gemcitabine is one of the most widely used drugs for the treatment of advanced Non-small cell lung cancer (NSCLC), but modest objective response rate of patients to gemcitabine makes it necessary to identify novel biomarkers for patients who can benefit from gemcitabine-based therapy and to improve the effect of clinical therapy. In this work, 3 NSCLC cell lines displaying different sensitivities to gemcitabine were applied for mRNA and microRNA (miR) expression chips to figure out the biomarkers for gemcitabine sensitivity. Genes whose expression increased dramatically in sensitive cell lines were mainly enriched in cell adhesion (NRP2, CXCR3, CDK5R1, IL32 and CDH2) and secretory granule (SLC11A1, GP5, CD36 and IGF1), while genes with significantly upregulated expression in resistant cell line were mainly clustered in methylation modification (HIST1H2BF, RAB23 and TP53) and oxidoreductase (TP53I3, CYP27B1 and SOD3). The most intriguing is the activation of Wnt/β-catenin signaling in gemcitabine resistant NSCLC cell lines. The miR-155, miR-10a, miR-30a, miR-24-2* and miR-30c-2* were upregulated in sensitive cell lines, while expression of miR-200c, miR-203, miR-885-5p, miR-195 and miR-25* was increased in resistant cell line. Genes with significantly altered expression and putatively mediated by the expression-changed miRs were mainly enriched in chromatin assembly (MAF, HLF, BCL2, and IGSF3), anti-apoptosis (BCL2, IGF1 and IKBKB), protein kinase (NRP2, PAK7 and CDK5R1) (all the above genes were upregulated in sensitive cells) and small GTPase mediated signal transduction (GNA13, RAP2A, ARHGAP5 and RAB23, down-regulated in sensitive cells). Our results might provide potential biomarkers for gemcitabine sensitivity prediction and putative targets to overcome gemcitabine resistance in NSCLC patients. PMID:24040438

  17. The metabolic enzyme ManA reveals a link between cell wall integrity and chromosome morphology.

    OpenAIRE

    Maya Elbaz; Sigal Ben-Yehuda

    2010-01-01

    Author Summary The bacterial cell is resistant to extremes of osmotic pressure and protected against mechanical damages by the existence of a rigid outer shell defined as the cell wall. The strength of the cell wall is achieved by the presence of long glycan strands cross-linked by peptide side bridges. The cell wall is a dynamic structure continuously being synthesized and modified to allow for cell growth and division. Damaging the cell wall leads to abnormal cellular morphologies and cell ...

  18. Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis

    Directory of Open Access Journals (Sweden)

    Chavez Adela

    2008-07-01

    Full Text Available Abstract Background Anaplasma phagocytophilum (Ap is an obligate intracellular bacterium and the agent of human granulocytic anaplasmosis, an emerging tick-borne disease. Ap alternately infects ticks and mammals and a variety of cell types within each. Understanding the biology behind such versatile cellular parasitism may be derived through the use of tiling microarrays to establish high resolution, genome-wide transcription profiles of the organism as it infects cell lines representative of its life cycle (tick; ISE6 and pathogenesis (human; HL-60 and HMEC-1. Results Detailed, host cell specific transcriptional behavior was revealed. There was extensive differential Ap gene transcription between the tick (ISE6 and the human (HL-60 and HMEC-1 cell lines, with far fewer differentially transcribed genes between the human cell lines, and all disproportionately represented by membrane or surface proteins. There were Ap genes exclusively transcribed in each cell line, apparent human- and tick-specific operons and paralogs, and anti-sense transcripts that suggest novel expression regulation processes. Seven virB2 paralogs (of the bacterial type IV secretion system showed human or tick cell dependent transcription. Previously unrecognized genes and coding sequences were identified, as were the expressed p44/msp2 (major surface proteins paralogs (of 114 total, through elevated signal produced to the unique hypervariable region of each – 2/114 in HL-60, 3/114 in HMEC-1, and none in ISE6. Conclusion Using these methods, whole genome transcription profiles can likely be generated for Ap, as well as other obligate intracellular organisms, in any host cells and for all stages of the cell infection process. Visual representation of comprehensive transcription data alongside an annotated map of the genome renders complex transcription into discernable patterns.

  19. Transcriptome analysis of exosome-compromised human cells using high-density tiling arrays

    DEFF Research Database (Denmark)

    Jensen, Torben Heick

    The extent of RNA degradation in the nucleus has traditionally been underestimated. However, all major RNA species are synthesized, processed and can be degraded in this compartment and consequently an enormous amount of nucleosides are turned over and recycled. The RNA exosome, a multisubunit...... complex of 3’-5’ exoribonucleases, is a key player in these processive/degradative pathways. The exosome is highly conserved between yeast and man, and exists in a cytoplasmic and a nuclear form; the 3’-5’ exoribonuclease Rrp6 (human homologue PM/Scl100) is a specific component of the nuclear exosome.......Studies in yeast using exosome-mutant strains has revealed specific functions of the nuclear exosome: (i) processing or degradation of small nuclear/nucleolar RNAs (snRNAs, snoRNAs), (ii) surveillance and degradation of malformed mRNAs and (iii) processing or degradation of ribosomal precursor RNA to mature r...

  20. Study on sickle cell disease haplotypes reveals the African origin of Amapá's population

    Directory of Open Access Journals (Sweden)

    Natália de Morais Castelo

    2014-04-01

    Full Text Available Introduction:Sickle cell disease (SCD is a hereditary, hematologic, multifactorial disease, with high prevalence worldwide; its cause is a mutation in the sixth codon of the beta globin gene (βs.Objective:To identify the haplotypes present in people with SCD in Amapá, and relate them to African descent.Methods:We analyzed, by molecular techniques, 46 blood samples from people with SCD in Macapá, the capital of Amapá, with the purpose of obtaining information about haplotype frequency distribution, which helps understand the ethnic background of Amapá's population.Results:Our study revealed that the most frequent haplotype is Bantu (61.2%, followed by Benin (26.6% and Senegal (12.2%. Results showed statistical differences from studies conducted in other regions. A high frequency of the Senegal haplotype stands out, in comparison with some Brazilian studies.Conclusion:Amapá's results exhibit unique characteristics when compared to haplotypes in other regions, with high frequency of Senegal and Benin haplotypes, absence of atypical, Cameroon and Saudi, confirming that Brazil shows ethnic background diversity, as well as different haplotype frequencies.

  1. Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity.

    Science.gov (United States)

    Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

    2014-01-01

    The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4(+)SNS-Cre/TdTomato(+), 2) IB4(-)SNS-Cre/TdTomato(+), and 3) Parv-Cre/TdTomato(+) cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. PMID:25525749

  2. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells.

    Science.gov (United States)

    Kim, Daesik; Kim, Jungeun; Hur, Junho K; Been, Kyung Wook; Yoon, Sun-Heui; Kim, Jin-Soo

    2016-08-01

    Programmable clustered regularly interspaced short palindromic repeats (CRISPR) Cpf1 endonucleases are single-RNA-guided (crRNA) enzymes that recognize thymidine-rich protospacer-adjacent motif (PAM) sequences and produce cohesive double-stranded breaks (DSBs). Genome editing with CRISPR-Cpf1 endonucleases could provide an alternative to CRISPR-Cas9 endonucleases, but the determinants of targeting specificity are not well understood. Using mismatched crRNAs we found that Cpf1 could tolerate single or double mismatches in the 3' PAM-distal region, but not in the 5' PAM-proximal region. Genome-wide analysis of cleavage sites in vitro for eight Cpf1 nucleases using Digenome-seq revealed that there were 6 (LbCpf1) and 12 (AsCpf1) cleavage sites per crRNA in the human genome, fewer than are present for Cas9 nucleases (>90). Most Cpf1 off-target cleavage sites did not produce mutations in cells. We found mismatches in either the 3' PAM-distal region or in the PAM sequence of 12 off-target sites that were validated in vivo. Off-target effects were completely abrogated by using preassembled, recombinant Cpf1 ribonucleoproteins.

  3. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-09

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  4. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells

    OpenAIRE

    Jichuan Zhang; Jingyi Fei; Leslie, Benjamin J.; Kyu Young Han; Kuhlman, Thomas E; Taekjip Ha

    2015-01-01

    Live cell RNA imaging using genetically encoded fluorescent labels is an important tool for monitoring RNA activities. A recently reported RNA aptamer-fluorogen system, the Spinach, in which an RNA aptamer binds and induces the fluorescence of a GFP-like 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) ligand, can be readily tagged to the RNA of interest. Although the aptamer–fluorogen system is sufficient for imaging highly abundant non-coding RNAs (tRNAs, rRNAs, etc.), it performs po...

  5. Low dose irradiation of thyroid cells reveals a unique transcriptomic and epigenetic signature in RET/PTC-positive cells

    Energy Technology Data Exchange (ETDEWEB)

    Abou-El-Ardat, Khalil, E-mail: kabouela@sckcen.be [Radiobiology Unit, Molecular and Cellular Biology, GKD Building, Studiecentrum voor Kernenergie - Centre d' Etude de l' Energie Nucleaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); Monsieurs, Pieter [Radiobiology Unit, Molecular and Cellular Biology, GKD Building, Studiecentrum voor Kernenergie - Centre d' Etude de l' Energie Nucleaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); Anastasov, Natasa; Atkinson, Mike [Department of Radiation Sciences, Helmholtz Zentrum Muenchen, Munich (Germany); Derradji, Hanane [Radiobiology Unit, Molecular and Cellular Biology, GKD Building, Studiecentrum voor Kernenergie - Centre d' Etude de l' Energie Nucleaire (SCK-CEN), Boeretang 200, 2400 Mol (Belgium); De Meyer, Tim [Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); Department of Applied Mathematics, Biometrics and Process Control, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); Bekaert, Sofie [Clinical Research Center, Faculty for Medicine and Health Sciences, Universiteit Gent, 185 De Pintelaan, 9000 Ghent (Belgium); Van Criekinge, Wim [Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Universiteit Gent, 9000 Ghent (Belgium); and others

    2012-03-01

    The high doses of radiation received in the wake of the Chernobyl incident and the atomic bombing of Hiroshima and Nagasaki have been linked to the increased appearance of thyroid cancer in the children living in the vicinity of the site. However, the data gathered on the effect of low doses of radiation on the thyroid remain limited. We have examined the genome wide transcriptional response of a culture of TPC-1 human cell line of papillary thyroid carcinoma origin with a RET/PTC1 translocation to various doses (0.0625, 0.5, and 4 Gy) of X-rays and compared it to response of thyroids with a RET/PTC3 translocation and against wild-type mouse thyroids irradiated with the same doses using Affymetrix microarrays. We have found considerable overlap at a high dose of 4 Gy in both RET/PTC-positive systems but no common genes at 62.5 mGy. In addition, the response of RET/PTC-positive system at all doses was distinct from the response of wild-type thyroids with both systems signaling down different pathways. Analysis of the response of microRNAs in TPC-1 cells revealed a radiation-responsive signature of microRNAs in addition to dose-responsive microRNAs. Our results point to the fact that a low dose of X-rays seems to have a significant proliferative effect on normal thyroids. This observation should be studied further as opposed to its effect on RET/PTC-positive thyroids which was subtle, anti-proliferative and system-dependent.

  6. Low dose irradiation of thyroid cells reveals a unique transcriptomic and epigenetic signature in RET/PTC-positive cells.

    Science.gov (United States)

    Abou-El-Ardat, Khalil; Monsieurs, Pieter; Anastasov, Nataša; Atkinson, Mike; Derradji, Hanane; De Meyer, Tim; Bekaert, Sofie; Van Criekinge, Wim; Baatout, Sarah

    2012-03-01

    The high doses of radiation received in the wake of the Chernobyl incident and the atomic bombing of Hiroshima and Nagasaki have been linked to the increased appearance of thyroid cancer in the children living in the vicinity of the site. However, the data gathered on the effect of low doses of radiation on the thyroid remain limited. We have examined the genome wide transcriptional response of a culture of TPC-1 human cell line of papillary thyroid carcinoma origin with a RET/PTC1 translocation to various doses (0.0625, 0.5, and 4Gy) of X-rays and compared it to response of thyroids with a RET/PTC3 translocation and against wild-type mouse thyroids irradiated with the same doses using Affymetrix microarrays. We have found considerable overlap at a high dose of 4Gy in both RET/PTC-positive systems but no common genes at 62.5mGy. In addition, the response of RET/PTC-positive system at all doses was distinct from the response of wild-type thyroids with both systems signaling down different pathways. Analysis of the response of microRNAs in TPC-1 cells revealed a radiation-responsive signature of microRNAs in addition to dose-responsive microRNAs. Our results point to the fact that a low dose of X-rays seems to have a significant proliferative effect on normal thyroids. This observation should be studied further as opposed to its effect on RET/PTC-positive thyroids which was subtle, anti-proliferative and system-dependent. PMID:22027090

  7. Highly ordered mesoporous carbon arrays from natural wood materials as counter electrode for dye-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Q.W.; Li, G.R.; Wang, F.; Gao, X.P. [Institute of New Energy Material Chemistry, Tianjin Key Laboratory of Metal and Molecule Based Material Chemistry, Nankai University, Tianjin 300071 (China)

    2010-07-15

    Highly ordered mesoporous carbon arrays are prepared by a facile carbonization of the natural bamboo and oak wood in argon atmosphere. The as-prepared oak mesoporous carbon arrays have good electrocatalytic activity and high conductivity, based on their well connected framework, highly ordered microtexture, wider mesopores and larger surface area. Consequentially, the photovoltaic performance of the DSSC with the oak mesoporous carbon array film as counter electrode is excellent and comparable to that of the DSSC with FTO/Pt counter electrode. In addition, it is a simple method for a mass production of mesoporous carbon arrays with natural wood materials. (author)

  8. Smooth bumps in H/V curves over a broad area from single-station ambient noise recordings are meaningful and reveal the importance of Q in array processing: The Boumerdes (Algeria) case

    Science.gov (United States)

    Guillier, B.; Chatelain, J.-L.; Hellel, M.; Machane, D.; Mezouer, N.; Ben Salem, R.; Oubaiche, E. H.

    2005-12-01

    Single-station H/V curves from ambient noise recordings in Boumerdes (Algeria) show smooth bumps around 1 and 3 Hz. A complementary microtremor study, based on two 34 and 134-meter aperture arrays, evidences that these bumps are indeed real peaks produced by two strong VS contrasts at 37 and 118 meters depth, strongly smoothed by very high S-wave attenuation in the two sedimentary layers. These two H/V bumps, observed over a broad area, are meaningful and reveal the importance of Q in S-wave velocity modeling from microtremor array data processing. It also appears that Tertiary rocks should be, at least in some cases, taken into account, together with the Quaternary sediments, to explain single-station H/V frequency peaks, and therefore that considering only the first 30 m of soil for VS amplification evaluation, as usually recommended, sometimes leads to flaky results by artificially eliminating non-explained low-frequency peaks from the analysis.

  9. Side Population Cells from Human Melanoma Tumors Reveal Diverse Mechanisms for Chemoresistance

    OpenAIRE

    Luo, Yuchun; Ellis, Lixia Z; Dallaglio, Katiuscia; Takeda, Moe; Robinson, William A.; Robinson, Steven; Liu, Weimin; Lewis, Karl D.; McCarter, Martin D; Gonzalez, Rene; David A Norris; Roop, Dennis R.; Spritz, Richard A.; Ahn, Natalie G.; Fujita, Mayumi

    2012-01-01

    Side population (SP) is identified as cells capable of excluding the fluorescent Hoechst dye and anticancer drugs, and represents hematopoietic stem cells and chemoresistant cells from several solid tumors. In this study, we confirmed the presence of SP cells in tumors from melanoma patients. Melanoma SP cells overexpressed ATP-binding-cassette (ABC) transporters, ABCB1 and ABCB5. We generated a direct in vivo xenograft model, and demonstrated that SP cells were resistant to paclitaxel, a sub...

  10. Biomarker screening of oral cancer cell lines revealed sub-populations of CD133-, CD44-, CD24- and ALDH1- positive cancer stem cells

    Directory of Open Access Journals (Sweden)

    Kendall K

    2013-05-01

    Full Text Available Head and neck squamous cell carcinoma (HNSCC ranks sixth worldwide for cancer-related mortality. For the past several decades the mainstay of treatment for HNSCC has been surgery and external beam radiation, although more recent trials combining chemotherapy and radiation have demonstrated improvements. However, cancer recurrence and treatment failures continue to occur in a significant percentage of patients. Recent advances in tumor biology have led to the discovery that many cancers, including HNSCC, may contain subpopulations of cells with stem cell-like properties that may explain relapse and recurrence. The objective of this study was to screen existing oral cancer cell lines for biomarkers specific for cells with stem cell-like properties. RNA was isolated for RT-PCR screening using primers for specific mRNA of the biomarkers: CD44, CD24, CD133, NANOG, Nestin, ALDH1, and ABCG2 in CAL27, SCC25 and SCC15 cells. This analysis revealed that some oral cancer cell lines (CAL27 and SCC25 may contain small subpopulations of adhesion- and contact-independent cells (AiDC that also express tumor stem cell markers, including CD44, CD133, and CD24. In addition, CAL27 cells also expressed the intracellular tumor stem cell markers, ALDH1 and ABCG2. Isolation and culture of the adhesion- and contact-independent cells from CAL27 and SCC25 populations revealed differential proliferation rates and more robust inhibition by the MEK inhibitor PD98059, as well as the chemotherapeutic agents Cisplatin and Paclitaxel, within the AiDC CAL27 cells. At least one oral cancer cell line (CAL27 contained subpopulations of cells that express specific biomarkers associated with tumor stem cells which were morphologically and phenotypically distinct from other cells within this cell line.

  11. Lamination And Microstructuring Technology for a Bio-Cell Multiwell array

    CERN Document Server

    Jung, E; Neumann, A; Bottcher, L; Braun, T; Bauer, J; Reichl, H; Iafelice, B; Destro, F; Gambari, R

    2008-01-01

    Microtechnology becomes a versatile tool for biological and biomedical applications. Microwells have been established long but remained non-intelligent up to now. Merging new fabrication techniques and handling concepts with microelectronics enables to realize intelligent microwells suitable for future improved cancer treatment. The described technology depicts the basis for the fabrication of a elecronically enhanced microwell. Thin aluminium sheets are structured by laser micro machining and laminated successively to obtain registration tolerances of the respective layers of 5..10\\^A$\\mu$m. The microwells lasermachined into the laminate are with 50..80\\^A$\\mu$m diameter, allowing to hold individual cells within the well. The individual process steps are described and results on the microstructuring are given.

  12. Preparation of Vertical Array of ZnO Nano rods via a Seed-Mediated Growth Method for Photoelectrochemical Solar Cell

    International Nuclear Information System (INIS)

    The preparation of vertical array ZnO nano rods on the FTO coated glass was demonstrated via a one-dimensional crystal growth of attached-nano seeds in an aqueous mixture of zinc acetate and ammonia at room temperature. In typical process, ZnO nano rods were characterized with vertical array oriented with diameter and length of 25 nm and ca. 190-218 nm, respectively that was grown throughout the surface by using four cycle growth process. The photoelectrochemical cell property was studied by fabricating solar cell with structure FTO/ ZnO nano rod/ electrolyte/ platinum. The JSC and VOC of the cell were found to be 0.22 mA/ cm2 and 0.44 V, respectively. (author)

  13. Genome-wide copy number profiling using a 100K SNP array reveals novel disease-related genes BORIS and TSHZ1 in juvenile angiofibroma.

    Science.gov (United States)

    Schick, Bernhard; Wemmert, Silke; Willnecker, Vivienne; Dlugaiczyk, Julia; Nicolai, Piero; Siwiec, Henryk; Thiel, Christian T; Rauch, Anita; Wendler, Olaf

    2011-11-01

    Juvenile angiofibroma (JA) is a unique fibrovascular tumor, which is almost exclusively found in the posterior nasal cavity of adolescent males. Although histologically classified as benign, the tumor often shows an aggressive growth pattern and has been associated with chromosomal imbalances, amplification of oncogenes and epigenetic dysregulation. We present the first genome-wide profiling of JAs (n=14) with a 100K single nucleotide polymorphism (SNP) microarray. Among the 30 novel JA-specific amplifications detected on autosomal chromosomes with this technique, the genes encoding the cancer-testis antigen BORIS (brother of the regulator of imprinted sites) and the developmental regulator protein TSHZ1 (teashirt zinc finger homeobox 1) were selected for further analysis. Gains for both BORIS (20q13.3) and TSHZ1 (18q22.3) were confirmed by quantitative genomic PCR. Furthermore, quantitative RT-PCR revealed a significant up-regulation of BORIS (ptool for identifying novel disease-related genes in JAs and newly implicates BORIS and TSHZ1 overexpression in the pathogenesis of JAs. Detection of BORIS in JAs is described with special regard to tumor proliferation and epigenetic dysregulation, and the finding of TSHZ1 amplifications is discussed with special respect to the hypothesis of JAs as malformations of the first branchial arch artery.

  14. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality

    Directory of Open Access Journals (Sweden)

    Shahin S Ali

    2015-08-01

    Full Text Available Moniliophthora roreri is the fungal pathogen that causes frosty pod rot (FPR disease of Theobroma cacao L., the source of chocolate. FPR occurs in most of the cacao producing countries in the Western Hemisphere, causing yield losses up to 80%. Genetic diversity within the FPR pathogen population may allow the population to adapt to changing environmental conditions and adapt to enhanced resistance in the host plant. The present study developed SNP markers from RNASeq results for 13 M. roreri isolates and validated the markers for their ability to reveal genetic diversity in an international M. roreri collection. The SNP resources reported herein represent the first study of RNASeq-derived SNP validation in M. roreri and demonstrates the utility of RNASeq as an approach for de novo SNP identification in M. roreri. A total of 88 polymorphic SNPs were used to evaluate the genetic diversity of 172 M. roreri cacao isolates resulting in 37 distinct genotypes (including 14 synonymous groups. Absence of heterozygosity for the 88 SNP markers indicates reproduction in M. roreri is clonal and likely due to a homothallic life style. The upper Magdalena Valley of Colombia showed the highest levels of genetic diversity with 20 distinct genotypes of which 13 were limited to this region, and indicates this region as the possible center of origin for M. roreri.

  15. Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions

    Science.gov (United States)

    Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja; Richter, Michael; Schulz-Vogt, Heide N.; Flood, Beverly E.; Bailey, Jake V.; Mußmann, Marc

    2016-01-01

    Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a chain-forming “Candidatus Thiomargarita nelsonii Thio36”, and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. “Ca. T. nelsonii Thio36” is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that “Ca. T. nelsonii Thio36” can function as a chemolithoautotroph. Carbon can be fixed via the Calvin–Benson–Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation pathway. Surprisingly, “Ca. T. nelsonii Thio36” also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na+-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae “Ca. T. nelsonii Thio36” encodes many genes similar to those of (filamentous) cyanobacteria. In summary, the genome of “Ca. T. nelsonii Thio36” provides additional insight into the ecology of

  16. Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

    Directory of Open Access Journals (Sweden)

    Beverly E. Flood

    2016-05-01

    Full Text Available The genus Thiomargarita includes the world’s largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria.Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence transposable elements and miniature inverted-repeat transposable elements (MITEs. In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsr

  17. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

    Science.gov (United States)

    Flood, Beverly E.; Fliss, Palmer; Jones, Daniel S.; Dick, Gregory J.; Jain, Sunit; Kaster, Anne-Kristin; Winkel, Matthias; Mußmann, Marc; Bailey, Jake

    2016-01-01

    The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group

  18. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity.

    Science.gov (United States)

    Flood, Beverly E; Fliss, Palmer; Jones, Daniel S; Dick, Gregory J; Jain, Sunit; Kaster, Anne-Kristin; Winkel, Matthias; Mußmann, Marc; Bailey, Jake

    2016-01-01

    The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group

  19. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity.

    Science.gov (United States)

    Flood, Beverly E; Fliss, Palmer; Jones, Daniel S; Dick, Gregory J; Jain, Sunit; Kaster, Anne-Kristin; Winkel, Matthias; Mußmann, Marc; Bailey, Jake

    2016-01-01

    The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group

  20. Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions.

    Science.gov (United States)

    Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja; Richter, Michael; Schulz-Vogt, Heide N; Flood, Beverly E; Bailey, Jake V; Mußmann, Marc

    2016-01-01

    Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a chain-forming "Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. "Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that "Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation pathway. Surprisingly, "Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na(+)-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae "Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In summary, the genome of "Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur

  1. A Systematic Analysis of Cell Cycle Regulators in Yeast Reveals That Most Factors Act Independently of Cell Size to Control Initiation of Division

    OpenAIRE

    Scott A Hoose; Jeremy A Rawlings; Kelly, Michelle M.; M Camille Leitch; Ababneh, Qotaiba O; Robles, Juan P.; David Taylor; Hoover, Evelyn M.; Bethel Hailu; McEnery, Kayla A.; S Sabina Downing; Deepika Kaushal; Yi Chen; Alex Rife; Kirtan A Brahmbhatt

    2012-01-01

    Upstream events that trigger initiation of cell division, at a point called START in yeast, determine the overall rates of cell proliferation. The identity and complete sequence of those events remain unknown. Previous studies relied mainly on cell size changes to identify systematically genes required for the timely completion of START. Here, we evaluated panels of non-essential single gene deletion strains for altered DNA content by flow cytometry. This analysis revealed that most gene dele...

  2. General Route to ZnO Nanorod Arrays on Conducting Substrates via Galvanic-cell-based approach

    Science.gov (United States)

    Zheng, Zhaoke; Lim, Zhi Shiuh; Peng, Yuan; You, Lu; Chen, Lang; Wang, Junling

    2013-08-01

    Wurtzite ZnO nanorod exhibits many unique properties, which make it promising for various optoelectronic applications. To grow well-aligned ZnO nanorod arrays on various substrates, a seed layer is usually required to improve the density and vertical alignment. The reported works about seedless hydrothermal synthesis either require special substrates, or require external electrical field to enhance the ZnO nucleation. Here, we report a general method for the one-pot synthesis of homogenous and well-aligned ZnO nanorods on common conducting substrates without a seed layer. This method, based on the galvanic-cell structure, makes use of the contact potential between different materials as the driving force for ZnO growth. It is applicable to different conducting substrates at low temperature. More importantly, the as-grown ZnO nanorods show enhanced photoelectric response. This unique large scale low-temperature processing method could be of great importance for the application of ZnO nanostructures.

  3. Novel insights of the gastric gland organization revealed by chief cell specific expression of moesin

    OpenAIRE

    Zhu, Lixin; Hatakeyama, Jason; Zhang, Bing; Makdisi, Joy; Ender, Cody; Forte, John G.

    2008-01-01

    ERM (ezrin, radixin, and moesin) proteins play critical roles in epithelial and endothelial cell polarity, among other functions. In gastric glands, ezrin is mainly expressed in acid-secreting parietal cells, but not in mucous neck cells or zymogenic chief cells. In looking for other ERM proteins, moesin was found lining the lumen of much of the gastric gland, but it was not expressed in parietal cells. No significant radixin expression was detected in the gastric glands. Moesin showed an inc...

  4. Combination of hydrogel nanoparticles and proteomics to reveal secreted proteins associated with decidualization of human uterine stromal cells

    Directory of Open Access Journals (Sweden)

    Stephens Andrew N

    2011-09-01

    Full Text Available Abstract Background Identification of secreted proteins of low abundance is often limited by abundant and high molecular weight (MW proteins. We have optimised a procedure to overcome this limitation. Results Low MW proteins in the conditioned media of cultured cells were first captured using dual-size exclusion/affinity hydrogel nanoparticles and their identities were then revealed by proteomics. Conclusions This technique enables the analysis of secreted proteins of cultured cells low MW and low abundance.

  5. Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction

    Directory of Open Access Journals (Sweden)

    Redondo-Nieto Miguel

    2013-01-01

    Full Text Available Abstract Background Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported. Results Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins. Conclusions The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.

  6. Mitogenic activation of B cells in vitro: the properties of adherent accessory cells as revealed by partition analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kettman, J.R.; Soederberg, A.; Lefkovits, I.

    1986-08-15

    The requirement of B cells activated by mitogen (dextran sulfate plus lipopolysaccharide) for accessory cells was studied by partition analysis. Small numbers of splenic B cells were activated to clonal growth, as determined by visual inspection, and to immunoglobulin (Ig) synthesis, as determined by release of Ig into the culture fluid. By placing irradiated adherent cells in the periphery of the microculture wells and forcing responding cells to different areas of the well (slant experiments), it was observed that no cell contact was necessary for B cell activation, and that promoted contact (Rock and Roll experiments) does not increase the efficiency of activation. Sequential microcultures suggest that only some irradiated adherent cells act as accessory cells, but they can perform this function to more than one B cell. Attempts to perform limiting dilution analysis by varying irradiated adherent cell input showed non-single-hit behavior. When the data were rearranged, taking into account the distribution of irradiated adherent cells, then single-hit behavior with about 1 to 5% of irradiated adherent cells acting as an accessory cells for B cell clonal activation was observed. The evidence suggests that an uncommon irradiated adherent cell releases a soluble factor necessary for B cell activation and/or clonal proliferation.

  7. High-Throughput siRNA Screening to Reveal GATA-2 Upstream Transcriptional Mechanisms in Hematopoietic Cells.

    Directory of Open Access Journals (Sweden)

    Yo Saito

    Full Text Available Hematopoietic stem cells can self-renew and differentiate into all blood cell types. The transcription factor GATA-2 is expressed in both hematopoietic stem and progenitor cells and is essential for cell proliferation, survival, and differentiation. Recently, evidence from studies of aplastic anemia, MonoMAC syndrome, and lung cancer has demonstrated a mechanistic link between GATA-2 and human pathophysiology. GATA-2-dependent disease processes have been extensively analyzed; however, the transcriptional mechanisms upstream of GATA-2 remain less understood. Here, we conducted high-throughput small-interfering-RNA (siRNA library screening and showed that YN-1, a human erythroleukemia cell line, expressed high levels of GATA-2 following the activation of the hematopoietic-specific 1S promoter. As transient luciferase reporter assay in YN-1 cells revealed the highest promoter activity in the 1S promoter fused with GATA-2 intronic enhancer (+9.9 kb/1S; therefore, we established a cell line capable of stably expressing +9.9 kb/1S-Luciferase. Subsequently, we screened 995 transcription factor genes and revealed that CITED2 acts as a GATA-2 activator in human hematopoietic cells. These results provide novel insights into and further identify the regulatory mechanism of GATA-2.

  8. Conveniently fabricated heterojunction ZnO/TiO2 electrodes using TiO2 nanotube arrays for dye-sensitized solar cells

    Science.gov (United States)

    Liu, Rui; Yang, Wein-Duo; Qiang, Liang-Sheng; Liu, Hsin-Yi

    2012-12-01

    TiO2 nanotube arrays with an inner average pore diameter of 83 nm and a length of 14 μm are grown on Ti foils by electrochemical anodization in ammonium fluoride-water-glycerol solution. ZnO is introduced into the TiO2 nanotube arrays by a convenient electrodeposition technique. ZnO/TiO2 nanocomposites supported on Ti substrate are used as the photo-anode electrode for dye-sensitized solar cells (DSSCs). The morphology, structure and electrochemical properties are investigated using field-emission scanning electron microscopy, transmission electron microscopy, X-ray diffraction, UV-vis diffusion reflection spectroscopy, X-ray photoelectron spectroscopy and cyclic voltammetry measurements. It is found that ZnO have been embedded in the TiO2 nanotube arrays, and changed some photoelectric properties. The conversion efficiency of the dye-sensitized solar cells is more than doubled, compared with that of bare TiO2 nanotube arrays with deposited 60 min. This improvement comes from the synergetic effect between ZnO and TiO2, which increases dye absorption, electron transport and electron lifetime.

  9. Differential expression of cellular microRNAs in HPV-11 transfected cells. An analysis by three different array platforms and qRT-PCR

    DEFF Research Database (Denmark)

    Dreher, Anita; Rossing, Maria; Kaczkowski, Bogumil;

    2010-01-01

    Human papillomavirus type 11 (HPV-11) infects the genital and the respiratory tract leading to condylomas and respiratory papillomatosis. HPV infections are restricted to epithelial tissue and the progression through the virus lifecycle is tightly coordinated to the differentiation of the host cell....... The changes of cellular microRNAs by HPV-11 gene expression were investigated in a cell culture model of HaCaT cells transfected with HPV-11, with the goal of understanding which cellular processes were affected by the virus. Human microRNA profiling was conducted on three different array platform systems...

  10. A VIN1 GUS::GFP fusion reveals activated sucrose metabolism programming occurring in interspersed cells during tomato fruit ripening.

    Science.gov (United States)

    Estornell, Leandro Hueso; Pons, Clara; Martínez, Alicia; O'Connor, José Enrique; Orzaez, Diego; Granell, Antonio

    2013-08-15

    The tomato is a model for fleshy fruit development and ripening. Here we report on the identification of a novel unique cell autonomous/cellular pattern of expression that was detected in fruits of transgenic tomato lines carrying a GFP GUS driven by the fruit specific vacuolar invertase promoter VIN1. The VIN1 promoter sequence faithfully reproduced the global endogenous VIN expression by conferring a biphasic pattern of expression with a second phase clearly associated to fruit ripening. A closer view revealed a salt and pepper pattern of expression characterized by individual cells exhibiting a range of expression levels (from high to low) surrounded by cells with no expression. This type of pattern was detected across different fruit tissues and cell types with some preferences for vascular, sub-epidermal layer and the inner part of the fruit. Cell ability to show promoter activity was neither directly associated with overall ripening - as we find VIN+ and - VIN- cells at all stages of ripening, nor with cell size. Nevertheless the number of cells with active VIN-driven expression increased with ripening and the activity of the VIN promoter seems to be inversely correlated with cell size in VIN+ cells. Gene expression analysis of FACS-sorted VIN+ cells revealed a transcriptionally distinct subpopulation of cells defined by increased expression of genes related to sucrose metabolism, and decreased activity in protein synthesis and chromatin remodeling. This finding suggests that local micro heterogeneity may underlie some aspects (i.e. the futile cycles involving sucrose metabolism) of an otherwise more uniform looking ripening program.

  11. Ascl3 knockout and cell ablation models reveal complexity of salivary gland maintenance and regeneration.

    Science.gov (United States)

    Arany, Szilvia; Catalán, Marcelo A; Roztocil, Elisa; Ovitt, Catherine E

    2011-05-15

    Expression of the transcription factor, Ascl3, marks a population of adult progenitor cells, which can give rise to both acinar and duct cell types in the murine salivary glands. Using a previously reported Ascl3(EGFP-Cre/+) knock-in strain, we demonstrate that Ascl3-expressing cells represent a molecularly distinct, and proliferating population of progenitor cells located in salivary gland ducts. To investigate both the role of the Ascl3 transcription factor, and the role of the cells in which it is expressed, we generated knockout and cell-specific ablation models. Ascl3 knockout mice develop smaller salivary glands than wild type littermates, but secrete saliva normally. They display a lower level of cell proliferation, consistent with their smaller size. In the absence of Ascl3, the cells maintain their progenitor function and continue to generate both acinar and duct cells. To directly test the role of the progenitor cells, themselves, in salivary gland development and regeneration, we used Cre-activated expression of diphtheria toxin (DTA) in the Ascl3-expressing (Ascl3+) cell population, resulting in specific cell ablation of Ascl3+ cells. In the absence of the Ascl3+ progenitor cells, the mice developed morphologically normal, albeit smaller, salivary glands able to secrete saliva. Furthermore, in a ductal ligation model of salivary gland injury, the glands of these mice were able to regenerate acinar cells. Our results indicate that Ascl3+ cells are active proliferating progenitors, but they are not the only precursors for salivary gland development or regeneration. We conclude that maintenance of tissue homeostasis in the salivary gland must involve more than one progenitor cell population.

  12. Modelling the spatio-temporal cell dynamics reveals novel insights on cell differentiation and proliferation in the small intestinal crypt.

    Directory of Open Access Journals (Sweden)

    Carmen Pin

    Full Text Available We developed a slow structural relaxation model to describe cellular dynamics in the crypt of the mouse small intestine. Cells are arranged in a three dimensional spiral the size of which dynamically changes according to cell production demands of adjacent villi. Cell differentiation and proliferation is regulated through Wnt and Notch signals, the strength of which depends on the local cell composition. The highest level of Wnt activity is associated with maintaining equipotent stem cells (SC, Paneth cells and common goblet-Paneth cell progenitors (CGPCPs intermingling at the crypt bottom. Low levels of Wnt signalling area are associated with stem cells giving rise to secretory cells (CGPCPs, enteroendocrine or Tuft cells and proliferative absorptive progenitors. Deciding between these two fates, secretory and stem/absorptive cells, depends on Notch signalling. Our model predicts that Notch signalling inhibits secretory fate if more than 50% of cells they are in contact with belong to the secretory lineage. CGPCPs under high Wnt signalling will differentiate into Paneth cells while those migrating out from the crypt bottom differentiate into goblet cells. We have assumed that mature Paneth cells migrating upwards undergo anoikis. Structural relaxation explains the localisation of Paneth cells to the crypt bottom in the absence of active forces. The predicted crypt generation time from one SC is 4-5 days with 10-12 days needed to reach a structural steady state. Our predictions are consistent with experimental observations made under altered Wnt and Notch signalling. Mutations affecting stem cells located at the crypt floor have a 50% chance of being propagated throughout the crypt while mutations in cells above are rarely propagated. The predicted recovery time of an injured crypt losing half of its cells is approximately 2 days.

  13. agged tumor cells reveal regulatory steps during earliest stages of tumor progression and micrometastasis

    OpenAIRE

    Culp, L A; Lin, W.C.

    1999-01-01

    Histochemical marker genes were used to "tag" mouse fibrosarcoma or human neuroblastoma cells, providing a better understanding of their subsequent progression and metastasis mechanisms in nude mice. Micrometastases in the lung were initiated from clusters of 2-6 cells rather than single cells in most cases; tumor cells were also visualized binding to the endothelium of small blood vessels to initiate these micrometastases. Shortterm, these mechanisms relied ...

  14. Computational models reveal a passive mechanism for cell migration in the crypt.

    Directory of Open Access Journals (Sweden)

    Sara-Jane Dunn

    Full Text Available Cell migration in the intestinal crypt is essential for the regular renewal of the epithelium, and the continued upward movement of cells is a key characteristic of healthy crypt dynamics. However, the driving force behind this migration is unknown. Possibilities include mitotic pressure, active movement driven by motility cues, or negative pressure arising from cell loss at the crypt collar. It is possible that a combination of factors together coordinate migration. Here, three different computational models are used to provide insight into the mechanisms that underpin cell movement in the crypt, by examining the consequence of eliminating cell division on cell movement. Computational simulations agree with existing experimental results, confirming that migration can continue in the absence of mitosis. Importantly, however, simulations allow us to infer mechanisms that are sufficient to generate cell movement, which is not possible through experimental observation alone. The results produced by the three models agree and suggest that cell loss due to apoptosis and extrusion at the crypt collar relieves cell compression below, allowing cells to expand and move upwards. This finding suggests that future experiments should focus on the role of apoptosis and cell extrusion in controlling cell migration in the crypt.

  15. Dental pulp stem cells differentiation reveals new insights in Oct4A dynamics.

    Directory of Open Access Journals (Sweden)

    Federico Ferro

    Full Text Available Although the role played by the core transcription factor network, which includes c-Myc, Klf4, Nanog, and Oct4, in the maintenance of embryonic stem cell (ES pluripotency and in the reprogramming of adult cells is well established, its persistence and function in adult stem cells are still debated. To verify its persistence and clarify the role played by these molecules in adult stem cell function, we investigated the expression pattern of embryonic and adult stem cell markers in undifferentiated and fully differentiated dental pulp stem cells (DPSC. A particular attention was devoted to the expression pattern and intracellular localization of the stemness-associated isoform A of Oct4 (Oct4A. Our data demonstrate that: Oct4, Nanog, Klf4 and c-Myc are expressed in adult stem cells and, with the exception of c-Myc, they are significantly down-regulated following differentiation. Cell differentiation was also associated with a significant reduction in the fraction of DPSC expressing the stem cell markers CD10, CD29 and CD117. Moreover, a nuclear to cytoplasm shuttling of Oct4A was identified in differentiated cells, which was associated with Oct4A phosphorylation. The present study would highlight the importance of the post-translational modifications in DPSC stemness maintenance, by which stem cells balance self-renewal versus differentiation. Understanding and controlling these mechanisms may be of great importance for stemness maintenance and stem cells clinical use, as well as for cancer research.

  16. The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

    NARCIS (Netherlands)

    H. Kempe; A. Schwabe; F. Crémazy; P.J. Verschure; F.J. Bruggeman

    2015-01-01

    Transcriptional stochasticity can be measured by counting the number of mRNA molecules per cell. Cell-to-cell variability is best captured in terms of concentration rather than molecule counts, because reaction rates depend on concentrations. We combined single-molecule mRNA counting with single-cel

  17. Analysis of chlorophyll fluorescence reveals stage specific patterns of chloroplast-containing cells during Arabidopsis embryogenesis.

    Science.gov (United States)

    Tejos, Ricardo I; Mercado, Ana V; Meisel, Lee A

    2010-01-01

    The basic body plan of a plant is established early in embryogenesis when cells differentiate, giving rise to the apical and basal regions of the embryo. Using chlorophyll fluorescence as a marker for chloroplasts, we have detected specific patterns of chloroplast-containing cells at specific stages of embryogenesis. Non-randomly distributed chloroplast-containing cells are seen as early as the globular stage of embryogenesis in Arabidopsis. In the heart stage of embryogenesis, chloroplast containing cells are detected in epidermal cells as well as a central region of the heart stage embryo, forming a triangular septum of chloroplast-containing cells that divides the embryo into three equal sectors. Torpedo stage embryos have chloroplast-containing epidermal cells and a central band of chloroplast-containing cells in the cortex layer, just below the shoot apical meristem. In the walking-stick stage of embryogenesis, chloroplasts are present in the epidermal, cortex and endodermal cells. The chloroplasts appear reduced or absent from the provascular and columella cells of walking-stick stage embryos. These results suggest that there is a tight regulation of plastid differentiation during embryogenesis that generates specific patterns of chloroplast-containing cells in specific cell layers at specific stages of embryogenesis.

  18. Fluorescent labelling of intestinal epithelial cells reveals independent long-lived intestinal stem cells in a crypt

    Energy Technology Data Exchange (ETDEWEB)

    Horita, Nobukatsu [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan); Tsuchiya, Kiichiro, E-mail: kii.gast@tmd.ac.jp [Department of Advanced Therapeutics for Gastrointestinal Diseases, Graduate School, Tokyo Medical and Dental University (Japan); Hayashi, Ryohei [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan); Department of Gastroenterology and Metabolism, Hiroshima University (Japan); Fukushima, Keita; Hibiya, Shuji; Fukuda, Masayoshi; Kano, Yoshihito; Mizutani, Tomohiro; Nemoto, Yasuhiro; Yui, Shiro [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan); Okamoto, Ryuichi; Nakamura, Tetsuya [Department of Advanced Therapeutics for Gastrointestinal Diseases, Graduate School, Tokyo Medical and Dental University (Japan); Watanabe, Mamoru [Department of Gastroenterology and Hepatology, Graduate School, Tokyo Medical and Dental University (Japan)

    2014-11-28

    Highlights: • Lentivirus mixed with Matrigel enables direct infection of intestinal organoids. • Our original approach allows the marking of a single stem cell in a crypt. • Time-lapse imaging shows the dynamics of a single stem cell. • Our lentivirus transgene system demonstrates plural long-lived stem cells in a crypt. - Abstract: Background and aims: The dynamics of intestinal stem cells are crucial for regulation of intestinal function and maintenance. Although crypt stem cells have been identified in the intestine by genetic marking methods, identification of plural crypt stem cells has not yet been achieved as they are visualised in the same colour. Methods: Intestinal organoids were transferred into Matrigel® mixed with lentivirus encoding mCherry. The dynamics of mCherry-positive cells was analysed using time-lapse imaging, and the localisation of mCherry-positive cells was analysed using 3D immunofluorescence. Results: We established an original method for the introduction of a transgene into an organoid generated from mouse small intestine that resulted in continuous fluorescence of the mCherry protein in a portion of organoid cells. Three-dimensional analysis using confocal microscopy showed a single mCherry-positive cell in an organoid crypt that had been cultured for >1 year, which suggested the presence of long-lived mCherry-positive and -negative stem cells in the same crypt. Moreover, a single mCherry-positive stem cell in a crypt gave rise to both crypt base columnar cells and transit amplifying cells. Each mCherry-positive and -negative cell contributed to the generation of organoids. Conclusions: The use of our original lentiviral transgene system to mark individual organoid crypt stem cells showed that long-lived plural crypt stem cells might independently serve as intestinal epithelial cells, resulting in the formation of a completely functional villus.

  19. Fluorescent labelling of intestinal epithelial cells reveals independent long-lived intestinal stem cells in a crypt

    International Nuclear Information System (INIS)

    Highlights: • Lentivirus mixed with Matrigel enables direct infection of intestinal organoids. • Our original approach allows the marking of a single stem cell in a crypt. • Time-lapse imaging shows the dynamics of a single stem cell. • Our lentivirus transgene system demonstrates plural long-lived stem cells in a crypt. - Abstract: Background and aims: The dynamics of intestinal stem cells are crucial for regulation of intestinal function and maintenance. Although crypt stem cells have been identified in the intestine by genetic marking methods, identification of plural crypt stem cells has not yet been achieved as they are visualised in the same colour. Methods: Intestinal organoids were transferred into Matrigel® mixed with lentivirus encoding mCherry. The dynamics of mCherry-positive cells was analysed using time-lapse imaging, and the localisation of mCherry-positive cells was analysed using 3D immunofluorescence. Results: We established an original method for the introduction of a transgene into an organoid generated from mouse small intestine that resulted in continuous fluorescence of the mCherry protein in a portion of organoid cells. Three-dimensional analysis using confocal microscopy showed a single mCherry-positive cell in an organoid crypt that had been cultured for >1 year, which suggested the presence of long-lived mCherry-positive and -negative stem cells in the same crypt. Moreover, a single mCherry-positive stem cell in a crypt gave rise to both crypt base columnar cells and transit amplifying cells. Each mCherry-positive and -negative cell contributed to the generation of organoids. Conclusions: The use of our original lentiviral transgene system to mark individual organoid crypt stem cells showed that long-lived plural crypt stem cells might independently serve as intestinal epithelial cells, resulting in the formation of a completely functional villus

  20. Real-time motion analysis reveals cell directionality as an indicator of breast cancer progression.

    Directory of Open Access Journals (Sweden)

    Michael C Weiger

    Full Text Available Cancer cells alter their migratory properties during tumor progression to invade surrounding tissues and metastasize to distant sites. However, it remains unclear how migratory behaviors differ between tumor cells of different malignancy and whether these migratory behaviors can be utilized to assess the malignant potential of tumor cells. Here, we analyzed the migratory behaviors of cell lines representing different stages of breast cancer progression using conventional migration assays or time-lapse imaging and particle image velocimetry (PIV to capture migration dynamics. We find that the number of migrating cells in transwell assays, and the distance and speed of migration in unconstrained 2D assays, show no correlation with malignant potential. However, the directionality of cell motion during 2D migration nicely distinguishes benign and tumorigenic cell lines, with tumorigenic cell lines harboring less directed, more random motion. Furthermore, the migratory behaviors of epithelial sheets observed under basal conditions and in response to stimulation with epidermal growth factor (EGF or lysophosphatitic acid (LPA are distinct for each cell line with regard to cell speed, directionality, and spatiotemporal motion patterns. Surprisingly, treatment with LPA promotes a more cohesive, directional sheet movement in lung colony forming MCF10CA1a cells compared to basal conditions or EGF stimulation, implying that the LPA signaling pathway may alter the invasive potential of MCF10CA1a cells. Together, our findings identify cell directionality as a promising indicator for assessing the tumorigenic potential of breast cancer cell lines and show that LPA induces more cohesive motility in a subset of metastatic breast cancer cells.

  1. Cationic Antimicrobial Peptides Derived from Crocodylus siamensis Leukocyte Extract, Revealing Anticancer Activity and Apoptotic Induction on Human Cervical Cancer Cells.

    Science.gov (United States)

    Theansungnoen, Tinnakorn; Maijaroen, Surachai; Jangpromma, Nisachon; Yaraksa, Nualyai; Daduang, Sakda; Temsiripong, Theeranan; Daduang, Jureerut; Klaynongsruang, Sompong

    2016-06-01

    Known antimicrobial peptides KT2 and RT2 as well as the novel RP9 derived from the leukocyte extract of the freshwater crocodile (Crocodylus siamensis) were used to evaluate the ability in killing human cervical cancer cells. RP9 in the extract was purified by a combination of anion exchange column and reversed-phase HPLC, and its sequence was analyzed by mass spectrometry. The novel peptide could inhibit Gram-negative Vibrio cholerae (clinical isolation) and Gram-positive Bacillus pumilus TISTR 905, and its MIC values were 61.2 µM. From scanning electron microscopy, the peptide was seen to affect bacterial surfaces directly. KT2 and RT2, which are designed antimicrobial peptides using the C. siamensis Leucrocin I template, as well as RP9 were chemically synthesized for investigation of anticancer activity. By Sulforhodamine B colorimetric assay, these antimicrobial peptides could inhibit both HeLa and CaSki cancer cell lines. The IC50 values of KT2 and RT2 for HeLa and CaSki cells showed 28.7-53.4 and 17.3-30.8 µM, while those of RP9 were 126.2 and 168.3 µM, respectively. Additionally, the best candidate peptides KT2 and RT2 were used to determine the apoptotic induction on cancer cells by human apoptosis array assay. As a result, KT2 and RT2 were observed to induce apoptotic cell death in HeLa cells. Therefore, these results indicate that KT2 and RT2 with antimicrobial activity have a highly potent ability to kill human cervical cancer cells. PMID:27129462

  2. A novel molecule integrating therapeutic and diagnostic activities reveals multiple aspects of stem cell-based therapy.

    Science.gov (United States)

    Hingtgen, Shawn D; Kasmieh, Randa; van de Water, Jeroen; Weissleder, Ralph; Shah, Khalid

    2010-04-01

    Stem cells are promising therapeutic delivery vehicles; however pre-clinical and clinical applications of stem cell-based therapy would benefit significantly from the ability to simultaneously determine therapeutic efficacy and pharmacokinetics of therapies delivered by engineered stem cells. In this study, we engineered and screened numerous fusion variants that contained therapeutic (TRAIL) and diagnostic (luciferase) domains designed to allow simultaneous investigation of multiple events in stem cell-based therapy in vivo. When various stem cell lines were engineered with the optimized molecule, SRL(O)L(2)TR, diagnostic imaging showed marked differences in the levels and duration of secretion between stem cell lines, while the therapeutic activity of the molecule showed the different secretion levels translated to significant variability in tumor cell killing. In vivo, simultaneous diagnostic and therapeutic monitoring revealed that stem cell-based delivery significantly improved pharmacokinetics and anti-tumor effectiveness of the therapy compared to intravenous or intratumoral delivery. As treatment for highly malignant brain tumor xenografts, tracking SRL(O)L(2)TR showed stable stem cell-mediated delivery significantly regressed peripheral and intracranial tumors. Together, the integrated diagnostic and therapeutic properties of SRL(O)L(2)TR answer critical questions necessary for successful utilization of stem cells as novel therapeutic vehicles. PMID:20127797

  3. Lineage relationship of CD8+ T cell subsets is revealed by progressive changes in the epigenetic landscape

    Science.gov (United States)

    Crompton, Joseph G.; Narayanan, Manikandan; Cuddapah, Suresh; Roychoudhuri, Rahul; Ji, Yun; Yang, Wenjing; Patel, Shashank J.; Sukumar, Madhusudhanan; Palmer, Douglas C.; Peng, Weiqun; Wang, Ena; Marincola, Francesco M.; Klebanoff, Christopher A.; Zhao, Keji; Tsang, John S.; Gattinoni, Luca; Restifo, Nicholas P.

    2016-01-01

    To better elucidate epigenetic mechanisms that correlate with the dynamic gene expression program observed upon T-cell differentiation, we investigated the genomic landscape of histone modifications in naive and memory CD8+ T cells. Using a ChIP-Seq approach coupled with global gene expression profiling, we generated genome-wide histone H3 lysine 4 (H3K4me3) and H3 lysine 27 (H3K27me3) trimethylation maps in naive, T memory stem cells, central memory cells, and effector memory cells in order to gain insight into how histone architecture is remodeled during T cell differentiation. We show that H3K4me3 histone modifications are associated with activation of genes, while H3K27me3 is negatively correlated with gene expression at canonical loci and enhancers associated with T-cell metabolism, effector function, and memory. Our results also reveal histone modifications and gene expression signatures that distinguish the recently identified T memory stem cells from other CD8+ T-cell subsets. Taken together, our results suggest that CD8+ lymphocytes undergo chromatin remodeling in a progressive fashion. These findings have major implications for our understanding of peripheral T-cell ontogeny and the formation of immunological memory. PMID:25914936

  4. Evaluation of in-plane local stress distribution in stacked IC chip using dynamic random access memory cell array for highly reliable three-dimensional IC

    Science.gov (United States)

    Tanikawa, Seiya; Kino, Hisashi; Fukushima, Takafumi; Koyanagi, Mitsumasa; Tanaka, Tetsu

    2016-04-01

    As three-dimensional (3D) ICs have many advantages, IC performances can be enhanced without scaling down of transistor size. However, 3D IC has mechanical stresses inside Si substrates owing to its 3D stacking structure, which induces negative effects on transistor performances such as carrier mobility changes. One of the mechanical stresses is local bending stress due to organic adhesive shrinkage among stacked IC chips. In this paper, we have proposed an evaluation method for in-plane local stress distribution in the stacked IC chips using retention time modulation of a dynamic random access memory (DRAM) cell array. We fabricated a test structure composed of a DRAM chip bonded on a Si interposer with dummy Cu/Sn microbumps. As a result, we clarified that the DRAM cell array can precisely evaluate the in-plane local stress distribution in the stacked IC chips.

  5. Expression weighted cell type enrichments reveal genetic and cellular nature of major brain disorders

    Directory of Open Access Journals (Sweden)

    Nathan Gerald Skene

    2016-01-01

    Full Text Available The cell types that trigger the primary pathology in many brain diseases remain largely unknown. One route to understanding the primary pathological