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Sample records for cell arrays reveal

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

    International Nuclear Information System (INIS)

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

    2012-01-01

    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. (paper)

  2. SNP array profiling of mouse cell lines identifies their strains of origin and reveals cross-contamination and widespread aneuploidy.

    Science.gov (United States)

    Didion, John P; Buus, Ryan J; Naghashfar, Zohreh; Threadgill, David W; Morse, Herbert C; de Villena, Fernando Pardo-Manuel

    2014-10-03

    The crisis of Misidentified and contaminated cell lines have plagued the biological research community for decades. Some repositories and journals have heeded calls for mandatory authentication of human cell lines, yet misidentification of mouse cell lines has received little publicity despite their importance in sponsored research. Short tandem repeat (STR) profiling is the standard authentication method, but it may fail to distinguish cell lines derived from the same inbred strain of mice. Additionally, STR profiling does not reveal karyotypic changes that occur in some high-passage lines and may have functional consequences. Single nucleotide polymorphism (SNP) profiling has been suggested as a more accurate and versatile alternative to STR profiling; however, a high-throughput method for SNP-based authentication of mouse cell lines has not been described. We have developed computational methods (Cell Line Authentication by SNP Profiling, CLASP) for cell line authentication and copy number analysis based on a cost-efficient SNP array, and we provide a reference database of commonly used mouse strains and cell lines. We show that CLASP readily discriminates among cell lines of diverse taxonomic origins, including multiple cell lines derived from a single inbred strain, intercross or wild caught mouse. CLASP is also capable of detecting contaminants present at concentrations as low as 5%. Of the 99 cell lines we tested, 15 exhibited substantial divergence from the reported genetic background. In all cases, we were able to distinguish whether the authentication failure was due to misidentification (one cell line, Ba/F3), the presence of multiple strain backgrounds (five cell lines), contamination by other cells and/or the presence of aneuploid chromosomes (nine cell lines). Misidentification and contamination of mouse cell lines is potentially as widespread as it is in human cell culture. This may have substantial implications for studies that are dependent on the

  3. Si Microwire Array Solar Cells

    Energy Technology Data Exchange (ETDEWEB)

    Putnam, Morgan C.; Boettcher, Shannon W.; Kelzenberg, Michael D.; Turner-Evans, Daniel B.; Spurgeon, Joshua M.; Warren, Emily L.; Briggs, Ryan M.; Lewis, Nathan S.; Atwater, Harry A.

    2010-01-01

    Si microwire-array solar cells with Air Mass 1.5 Global conversion efficiencies of up to 7.9% have been fabricated using an active volume of Si equivalent to a 4 μm thick Si wafer. These solar cells exhibited open-circuit voltages of 500 mV, short-circuit current densities (J{sub sc}) of up to 24 mA cm{sup -2}, and fill factors >65% and employed Al{sub 2}O{sub 3} dielectric particles that scattered light incident in the space between the wires, a Ag back reflector that prevented the escape of incident illumination from the back surface of the solar cell, and an a-SiN{sub x}:H passivation/anti-reflection layer. Wire-array solar cells without some or all of these design features were also fabricated to demonstrate the importance of the light-trapping elements in achieving a high J{sub sc}. Scanning photocurrent microscopy images of the microwire-array solar cells revealed that the higher J{sub sc} of the most advanced cell design resulted from an increased absorption of light incident in the space between the wires. Spectral response measurements further revealed that solar cells with light-trapping elements exhibited improved red and infrared response, as compared to solar cells without light-trapping elements.

  4. Solar cell array interconnects

    Science.gov (United States)

    Carey, Paul G.; Thompson, Jesse B.; Colella, Nicolas J.; Williams, Kenneth A.

    1995-01-01

    Electrical interconnects for solar cells or other electronic components using a silver-silicone paste or a lead-tin (Pb-Sn) no-clean fluxless solder cream, whereby the high breakage of thin (copper strips which are secured to the solar cells by a silver-silicone conductive paste which can be used at room temperature, or by a Pb-Sn solder cream which eliminates undesired residue on the active surfaces of the solar cells. Electrical testing using the interconnects of this invention has shown that no degradation of the interconnects developed under high current testing, while providing a very low contact resistance value.

  5. Sorting white blood cells in microfabricated arrays

    Science.gov (United States)

    Castelino, Judith Andrea Rose

    Fractionating white cells in microfabricated arrays presents the potential for detecting cells with abnormal adhesive or deformation properties. A possible application is separating nucleated fetal red blood cells from maternal blood. Since fetal cells are nucleated, it is possible to extract genetic information about the fetus from them. Separating fetal cells from maternal blood would provide a low cost noninvasive prenatal diagnosis for genetic defects, which is not currently available. We present results showing that fetal cells penetrate further into our microfabricated arrays than adult cells, and that it is possible to enrich the fetal cell fraction using the arrays. We discuss modifications to the array which would result in further enrichment. Fetal cells are less adhesive and more deformable than adult white cells. To determine which properties limit penetration, we compared the penetration of granulocytes and lymphocytes in arrays with different etch depths, constriction size, constriction frequency, and with different amounts of metabolic activity. The penetration of lymphocytes and granulocytes into constrained and unconstrained arrays differed qualitatively. In constrained arrays, the cells were activated by repeated shearing, and the number of cells stuck as a function of distance fell superexponentially. In unconstrained arrays the number of cells stuck fell slower than an exponential. We attribute this result to different subpopulations of cells with different sticking parameters. We determined that penetration in unconstrained arrays was limited by metabolic processes, and that when metabolic activity was reduced penetration was limited by deformability. Fetal cells also contain a different form of hemoglobin with a higher oxygen affinity than adult hemoglobin. Deoxygenated cells are paramagnetic and are attracted to high magnetic field gradients. We describe a device which can separate cells using 10 μm magnetic wires to deflect the paramagnetic

  6. 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....

  7. Radiation hard solar cell and array

    International Nuclear Information System (INIS)

    Russell, R.L.

    1975-01-01

    A power generating solar cell for a spacecraft solar array is hardened against transient response to nuclear radiation while permitting normal operation of the cell in a solar radiation environment by shunting the cell with a second solar cell whose contacts are reversed relative to the power cell to form a cell module, exposing the power cell only to the solar radiation in a solar radiation environment to produce an electrical output at the module terminals, and exposing both cells to the nuclear radiation in a nuclear radiation environment so that the radiation induced currents generated by the cells suppress one another

  8. Si Wire-Array Solar Cells

    Science.gov (United States)

    Boettcher, Shannon

    2010-03-01

    Micron-scale Si wire arrays are three-dimensional photovoltaic absorbers that enable orthogonalization of light absorption and carrier collection and hence allow for the utilization of relatively impure Si in efficient solar cell designs. The wire arrays are grown by a vapor-liquid-solid-catalyzed process on a crystalline (111) Si wafer lithographically patterned with an array of metal catalyst particles. Following growth, such arrays can be embedded in polymethyldisiloxane (PDMS) and then peeled from the template growth substrate. The result is an unusual photovoltaic material: a flexible, bendable, wafer-thickness crystalline Si absorber. In this paper I will describe: 1. the growth of high-quality Si wires with controllable doping and the evaluation of their photovoltaic energy-conversion performance using a test electrolyte that forms a rectifying conformal semiconductor-liquid contact 2. the observation of enhanced absorption in wire arrays exceeding the conventional light trapping limits for planar Si cells of equivalent material thickness and 3. single-wire and large-area solid-state Si wire-array solar cell results obtained to date with directions for future cell designs based on optical and device physics. In collaboration with Michael Kelzenberg, Morgan Putnam, Joshua Spurgeon, Daniel Turner-Evans, Emily Warren, Nathan Lewis, and Harry Atwater, California Institute of Technology.

  9. Sub-megabase resolution tiling (SMRT array-based comparative genomic hybridization profiling reveals novel gains and losses of chromosomal regions in Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma cell lines

    Directory of Open Access Journals (Sweden)

    Lam Wan L

    2008-01-01

    Full Text Available Abstract Background Hodgkin lymphoma (HL and Anaplastic Large Cell Lymphoma (ALCL, are forms of malignant lymphoma defined by unique morphologic, immunophenotypic, genotypic, and clinical characteristics, but both overexpress CD30. We used sub-megabase resolution tiling (SMRT array-based comparative genomic hybridization to screen HL-derived cell lines (KMH2 and L428 and ALCL cell lines (DEL and SR-786 in order to identify disease-associated gene copy number gains and losses. Results Significant copy number gains and losses were observed on several chromosomes in all four cell lines. Assessment of copy number alterations with 26,819 DNA segments identified an average of 20 genetic alterations. Of the recurrent minimally altered regions identified, 11 (55% were within previously published regions of chromosomal alterations in HL and ALCL cell lines while 9 (45% were novel alterations not previously reported. HL cell lines L428 and KMH2 shared gains in chromosome cytobands 2q23.1-q24.2, 7q32.2-q36.3, 9p21.3-p13.3, 12q13.13-q14.1, and losses in 13q12.13-q12.3, and 18q21.32-q23. ALCL cell lines SR-786 and DEL, showed gains in cytobands 5p15.32-p14.3, 20p12.3-q13.11, and 20q13.2-q13.32. Both pairs of HL and ALCL cell lines showed losses in 18q21.32-18q23. Conclusion This study is considered to be the first one describing HL and ALCL cell line genomes at sub-megabase resolution. This high-resolution analysis allowed us to propose novel candidate target genes that could potentially contribute to the pathogenesis of HL and ALCL. FISH was used to confirm the amplification of all three isoforms of the trypsin gene (PRSS1/PRSS2/PRSS3 in KMH2 and L428 (HL and DEL (ALCL cell lines. These are novel findings that have not been previously reported in the lymphoma literature, and opens up an entirely new area of research that has not been previously associated with lymphoma biology. The findings raise interesting possibilities about the role of signaling

  10. Cell Proliferation Tracking Using Graphene Sensor Arrays

    Directory of Open Access Journals (Sweden)

    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. New Array Approaches to Explore Single Cells Genomes

    Science.gov (United States)

    Vanneste, Evelyne; Bittman, Lilach; Van der Aa, Niels; Voet, Thierry; Vermeesch, Joris Robert

    2011-01-01

    Microarray analysis enables the genome-wide detection of copy number variations and the investigation of chromosomal instability. Whereas array techniques have been well established for the analysis of unamplified DNA derived from many cells, it has been more challenging to enable the accurate analysis of single cell genomes. In this review, we provide an overview of single cell DNA amplification techniques, the different array approaches, and discuss their potential applications to study human embryos. PMID:22509179

  12. STED super-resolution microscopy reveals an array of MINOS clusters along human mitochondria.

    Science.gov (United States)

    Jans, Daniel C; Wurm, Christian A; Riedel, Dietmar; Wenzel, Dirk; Stagge, Franziska; Deckers, Markus; Rehling, Peter; Jakobs, Stefan

    2013-05-28

    The mitochondrial inner membrane organizing system (MINOS) is a conserved large hetero-oligomeric protein complex in the mitochondrial inner membrane, crucial for the maintenance of cristae morphology. MINOS has been suggested to represent the core of an extended protein network that controls mitochondrial function and structure, and has been linked to several human diseases. The spatial arrangement of MINOS within mitochondria is ill-defined, however. Using super-resolution stimulated emission depletion (STED) microscopy and immunogold electron microscopy, we determined the distribution of three known human MINOS subunits (mitofilin, MINOS1, and CHCHD3) in mammalian cells. Super-resolution microscopy revealed that all three subunits form similar clusters within mitochondria, and that MINOS is more abundant in mitochondria around the nucleus than in peripheral mitochondria. At the submitochondrial level, mitofilin, a core MINOS subunit, is preferentially localized at cristae junctions. In primary human fibroblasts, mitofilin labeling uncovered a regularly spaced pattern of clusters arranged in parallel to the cell growth surfaces. We suggest that this array of MINOS complexes might explain the observed phenomenon of largely horizontally arranged cristae junctions that connect the inner boundary membrane to lamellar cristae. The super-resolution images demonstrate an unexpectedly high level of regularity in the nanoscale distribution of the MINOS complex in human mitochondria, supporting an integrating role of MINOS in the structural organization of the organelle.

  13. Multijunction Ultralight Solar Cells and Arrays, Phase II

    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...

  14. Multijunction Ultralight Solar Cells and Arrays, Phase I

    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...

  15. Monitoring of cell cultures with LTCC microelectrode array.

    Science.gov (United States)

    Ciosek, P; Zawadzki, K; Łopacińska, J; Skolimowski, M; Bembnowicz, P; Golonka, L J; Brzózka, Z; Wróblewski, W

    2009-04-01

    Monitoring of cell cultures in microbioreactors is a crucial task in cell bioassays and toxicological tests. In this work a novel tool based on a miniaturized sensor array fabricated using low-temperature cofired ceramics (LTCC) technology is presented. The developed device is applied to the monitoring of cell-culture media change, detection of the growth of various species, and in toxicological studies performed with the use of cells. Noninvasive monitoring performed with the LTCC microelectrode array can be applied for future cell-engineering purposes.

  16. Gene array analysis of PD-1H overexpressing monocytes reveals a pro-inflammatory profile

    Directory of Open Access Journals (Sweden)

    Preeti Bharaj

    2018-02-01

    Full Text Available We have previously reported that overexpression of Programmed Death -1 Homolog (PD-1H in human monocytes leads to activation and spontaneous secretion of multiple pro inflammatory cytokines. Here we evaluate changes in monocytes gene expression after enforced PD-1H expression by gene array. The results show that there are significant alterations in 51 potential candidate genes that relate to immune response, cell adhesion and metabolism. Genes corresponding to pro-inflammatory cytokines showed the highest upregulation, 7, 3.2, 3.0, 5.8, 4.4 and 3.1 fold upregulation of TNF-α, IL-1 β, IFN-α, γ, λ and IL-27 relative to vector control. The data are in agreement with cytometric bead array analysis showing induction of proinflammatory cytokines, IL-6, IL-1β and TNF-α by PD-1H. Other genes related to inflammation, include transglutaminase 2 (TG2, NF-κB (p65 and p50 and toll like receptors (TLR 3 and 4 were upregulated 5, 4.5 and 2.5 fold, respectively. Gene set enrichment analysis (GSEA also revealed that signaling pathways related to inflammatory response, such as NFκB, AT1R, PYK2, MAPK, RELA, TNFR1, MTOR and proteasomal degradation, were significantly upregulated in response to PD-1H overexpression. We validated the results utilizing a standard inflammatory sepsis model in humanized BLT mice, finding that PD-1H expression was highly correlated with proinflammatory cytokine production. We therefore conclude that PD-1H functions to enhance monocyte activation and the induction of a pro-inflammatory gene expression profile.

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

    International Nuclear Information System (INIS)

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

    2009-01-01

    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. (semiconductor devices)

  18. 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

  19. Radiation hard memory cell and array thereof

    International Nuclear Information System (INIS)

    Gunckel, T.L. II; Rovell, A.; Nielsen, R.L.

    1978-01-01

    A memory cell configuration that is implemented to be relatively hard to the adverse effects of a nuclear event is discussed. The presently disclosed memory cell can be interconnected with other like memory cells to form a high speed radiation hard register file. Information is selectively written into and read out of a memory cell comprising the register file, which memory cell preserves previously stored data without alteration in the event of exposure to high levels of nuclear radiation

  20. A Novel Robot of Manufacturing Space Solar Cell Arrays

    Directory of Open Access Journals (Sweden)

    Wu Yuexin

    2008-11-01

    Full Text Available This paper presents a novel robot employed to manufacture space solar cell arrays. First of all including the mechanical configuration and control system, the architecture of the robot is described. Then the flow velocity field of adhesive in the dispensing needles is acquired based on hydrodynamics. The accurate section form model of adhesive dispensed on the solar cells is obtained, which is essential for the robot to control the uniformity of dispensing adhesive. Finally the experiment validates the feasibility and reliability of the robot system. The application of robots instead of manual work in manufacturing space solar cell arrays will enhance the development of space industry.

  1. A Novel Robot of Manufacturing Space Solar Cell Arrays

    Directory of Open Access Journals (Sweden)

    Wu Yuexin

    2007-03-01

    Full Text Available This paper presents a novel robot employed to manufacture space solar cell arrays. First of all including the mechanical configuration and control system, the architecture of the robot is described. Then the flow velocity field of adhesive in the dispensing needles is acquired based on hydrodynamics. The accurate section form model of adhesive dispensed on the solar cells is obtained, which is essential for the robot to control the uniformity of dispensing adhesive. Finally the experiment validates the feasibility and reliability of the robot system. The application of robots instead of manual work in manufacturing space solar cell arrays will enhance the development of space industry.

  2. Single cell array impedance analysis in a microfluidic device

    Science.gov (United States)

    Altinagac, Emre; Taskin, Selen; Kizil, Huseyin

    2016-10-01

    Impedance analysis of single cells is presented in this paper. Following the separation of a target cell type by dielectrophoresis in our previous work, this paper focuses on capturing the cells as a single array and performing impedance analysis to point out the signature difference between each cell type. Lab-on-a-chip devices having a titanium interdigitated electrode layer on a glass substrate and a PDMS microchannel are fabricated to capture each cell in a single form and perform impedance analysis. HCT116 (homosapiens colon colorectal carcin) and HEK293 (human embryonic kidney) cells are used in our experiments.

  3. Interspace modification of titania-nanorod arrays for efficient mesoscopic perovskite solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Peng; Jin, Zhixin; Wang, Yinglin, E-mail: wangyl100@nenu.edu.cn; Wang, Meiqi; Chen, Shixin; Zhang, Yang; Wang, Lingling; Zhang, Xintong, E-mail: xtzhang@nenu.edu.cn; Liu, Yichun, E-mail: ycliu@nenu.edu.cn

    2017-04-30

    Highlights: • The fabrication of perovskite solar cells utilizing TiO{sub 2} NR arrays. • Investigation of the interspace effect of TiO{sub 2} NR on perovskite layer. • Understanding of the balance between perovskite capping layer and pore filling. - Abstract: Morphology of electron transport layers (ETLs) has an important influence on the device architecture and electronic processes of mesostructured solar cells. In this work, we thoroughly investigated the effect of the interspace of TiO{sub 2} nanorod (NR) arrays on the photovoltaic performance of the perovskite solar cells (PSCs). Along with the interspace in TiO{sub 2}-NR arrays increasing, the thickness as well as the crystal size of perovskite capping layer are reduced accordingly, and the filling of perovskite in the channel becomes incomplete. Electrochemical impedance spectroscopy measurements reveal that this variation of perovskite absorber layer, induced by interspace of TiO{sub 2} NR arrays, causes the change of charge recombination process at the TiO{sub 2}/perovskite interface, suggesting that a balance between capping layer and the perovskite filling is critical to obtain high charge collection efficiency of PSCs. A power conversion efficiency of 10.3% could be achieved through careful optimization of interspace in TiO{sub 2}-NR arrays. Our research will shed light on the morphology control of ETLs with 1D structure for heterojunction solar cells fabricated by solution-deposited method.

  4. Interspace modification of titania-nanorod arrays for efficient mesoscopic perovskite solar cells

    International Nuclear Information System (INIS)

    Chen, Peng; Jin, Zhixin; Wang, Yinglin; Wang, Meiqi; Chen, Shixin; Zhang, Yang; Wang, Lingling; Zhang, Xintong; Liu, Yichun

    2017-01-01

    Highlights: • The fabrication of perovskite solar cells utilizing TiO 2 NR arrays. • Investigation of the interspace effect of TiO 2 NR on perovskite layer. • Understanding of the balance between perovskite capping layer and pore filling. - Abstract: Morphology of electron transport layers (ETLs) has an important influence on the device architecture and electronic processes of mesostructured solar cells. In this work, we thoroughly investigated the effect of the interspace of TiO 2 nanorod (NR) arrays on the photovoltaic performance of the perovskite solar cells (PSCs). Along with the interspace in TiO 2 -NR arrays increasing, the thickness as well as the crystal size of perovskite capping layer are reduced accordingly, and the filling of perovskite in the channel becomes incomplete. Electrochemical impedance spectroscopy measurements reveal that this variation of perovskite absorber layer, induced by interspace of TiO 2 NR arrays, causes the change of charge recombination process at the TiO 2 /perovskite interface, suggesting that a balance between capping layer and the perovskite filling is critical to obtain high charge collection efficiency of PSCs. A power conversion efficiency of 10.3% could be achieved through careful optimization of interspace in TiO 2 -NR arrays. Our research will shed light on the morphology control of ETLs with 1D structure for heterojunction solar cells fabricated by solution-deposited method.

  5. An advanced space photovoltaic concentrator array using Fresnel lenses, gallium arsenide cells, and prismatic cell covers

    Science.gov (United States)

    O'Neill, Mark J.; Piszczor, Michael F.

    1988-01-01

    The current status of a space concentrator array which uses refractive optics, gallium arsenide cells, and prismatic cell covers to achieve excellent performance at a very low array mass is documented. The prismatically covered cells have established records for space cell performance (24.2 percent efficient at 100 AM0 suns and 25 C) and terrestrial single-junction cell performance (29.3 percent efficient at 200 AM1.5 suns and 25 C).

  6. 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.

  7. Y-doping TiO2 nanorod arrays for efficient perovskite solar cells

    Science.gov (United States)

    Deng, Xinlian; Wang, Yanqing; Cui, Zhendong; Li, Long; Shi, Chengwu

    2018-05-01

    To improve the electron transportation in TiO2 nanorod arrays and charge separation in the interface of TiO2/perovskite, Y-doping TiO2 nanorod arrays with the length of 200 nm, diameter of 11 nm and areal density of 1050 μm-2 were successfully prepared by the hydrothermal method and the influence of Y/Ti molar ratios of 0%, 3%, 5% in the hydrothermal grown solutions on the growth of TiO2 nanorod arrays was investigated. The results revealed that the appropriate Y/Ti molar ratios can increase the areal density of the corresponding TiO2 nanorod arrays and improve the charge separation in the interface of the TiO2/perovskite. The Y-doping TiO2 nanorod array perovskite solar cells with the Y/Ti molar ratio of 3% exhibited a photoelectric conversion efficiency (PCE) of 18.11% along with an open-circuit voltage (Voc) of 1.06 V, short-circuit photocurrent density (Jsc) of 22.50 mA cm-2 and fill factor (FF) of 76.16%, while the un-doping TiO2 nanorod array perovskite solar cells gave a PCE of 16.42% along with Voc of 1.04 V, Jsc of 21.66 mA cm-2 and FF of 72.97%.

  8. 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.

  9. Micro-magnet arrays for specific single bacterial cell positioning

    Energy Technology Data Exchange (ETDEWEB)

    Pivetal, Jérémy, E-mail: jeremy.piv@netcmail.com [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Royet, David [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Ciuta, Georgeta [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Frenea-Robin, Marie [Université de Lyon, Université Lyon 1, CNRS UMR 5005, Laboratoire Ampère, F-69622 Villeurbanne (France); Haddour, Naoufel [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Dempsey, Nora M. [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Dumas-Bouchiat, Frédéric [Univ Limoges, CNRS, SPCTS UMR 7513, 12 Rue Atlantis, F-87068 Limoges (France); Simonet, Pascal [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France)

    2015-04-15

    In various contexts such as pathogen detection or analysis of microbial diversity where cellular heterogeneity must be taken into account, there is a growing need for tools and methods that enable microbiologists to analyze bacterial cells individually. One of the main challenges in the development of new platforms for single cell studies is to perform precise cell positioning, but the ability to specifically target cells is also important in many applications. In this work, we report the development of new strategies to selectively trap single bacterial cells upon large arrays, based on the use of micro-magnets. Escherichia coli bacteria were used to demonstrate magnetically driven bacterial cell organization. In order to provide a flexible approach adaptable to several applications in the field of microbiology, cells were magnetically and specifically labeled using two different strategies, namely immunomagnetic labeling and magnetic in situ hybridization. Results show that centimeter-sized arrays of targeted, isolated bacteria can be successfully created upon the surface of a flat magnetically patterned hard magnetic film. Efforts are now being directed towards the integration of a detection tool to provide a complete micro-system device for a variety of microbiological applications. - Highlights: 1.We report a new approach to selectively micropattern bacterial cells individually upon micro-magnet arrays. 2.Permanent micro-magnets of a size approaching that of bacteria could be fabricated using a Thermo-Magnetic Patterning process. 3.Bacterial cells were labeled using two different magnetic labeling strategies providing flexible approach adaptable to several applications in the field of microbiology.

  10. Size Specific Transfection to Mammalian Cells by Micropillar Array Electroporation

    Science.gov (United States)

    Zu, Yingbo; Huang, Shuyan; Lu, Yang; Liu, Xuan; Wang, Shengnian

    2016-12-01

    Electroporation serves as a promising non-viral gene delivery approach, while its current configuration carries several drawbacks associated with high-voltage electrical pulses and heterogeneous treatment on individual cells. Here we developed a new micropillar array electroporation (MAE) platform to advance the electroporation-based delivery of DNA and RNA probes into mammalian cells. By introducing well-patterned micropillar array texture on the electrode surface, the number of pillars each cell faces varies with its plasma membrane surface area, despite their large population and random locations. In this way, cell size specific electroporation is conveniently carried out, contributing to a 2.5~3 fold increase on plasmid DNA transfection and an additional 10-55% transgene knockdown with siRNA probes, respectively. The delivery efficiency varies with the number and size of micropillars as well as their pattern density. As MAE works like many single cell electroporation are carried out in parallel, the electrophysiology response of individual cells is representative, which has potentials to facilitate the tedious, cell-specific protocol screening process in current bulk electroporation (i.e., electroporation to a large population of cells). Its success might promote the wide adoption of electroporation as a safe and effective non-viral gene delivery approach needed in many biological research and clinical treatments.

  11. Iron-copper metallization for flexible solar/cell arrays

    Science.gov (United States)

    Lavendel, H. W.

    1983-01-01

    The feasibility of a copper-base metallization for shallow-junction cells applied in flexible solar arrays in space is discussed. This type of metallization will reduce usage of precious metals (such as silver), increase case of bonding (by welding or by soldering) and eliminate heavy high Z interconnects (such as molybdenum). The main points of concern are stability against thermally induced diffusion of copper into silicon which causes degradation of shallow cell junctions, and low series resistance of the contact with semiconductor which promotes cell efficiency.

  12. Micropillar arrays enabling single microbial cell encapsulation in hydrogels.

    Science.gov (United States)

    Park, Kyun Joo; Lee, Kyoung G; Seok, Seunghwan; Choi, Bong Gill; Lee, Moon-Keun; Park, Tae Jung; Park, Jung Youn; Kim, Do Hyun; Lee, Seok Jae

    2014-06-07

    Single microbial cell encapsulation in hydrogels is an important task to find valuable biological resources for human welfare. The conventional microfluidic designs are mainly targeted only for highly dispersed spherical bioparticles. Advanced structures should be taken into consideration for handling such aggregated and non-spherical microorganisms. Here, to address the challenge, we propose a new type of cylindrical-shaped micropillar array in a microfluidic device for enhancing the dispersion of cell clusters and the isolation of individual cells into individual micro-hydrogels for potential practical applications. The incorporated micropillars act as a sieve for the breaking of Escherichia coli (E. coli) clusters into single cells in a polymer mixture. Furthermore, the combination of hydrodynamic forces and a flow-focusing technique will improve the probability of encapsulation of a single cell into each hydrogel with a broad range of cell concentrations. This proposed strategy and device would be a useful platform for genetically modified microorganisms for practical applications.

  13. Advanced Data Mining of Leukemia Cells Micro-Arrays

    OpenAIRE

    Richard S. Segall; Ryan M. Pierce

    2009-01-01

    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 pro...

  14. 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.

  15. 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

    2016-01-01

    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. PMID:26856884

  16. Recent Advances in Genetic Technique of Microbial Report Cells and Their Applications in Cell Arrays

    Directory of Open Access Journals (Sweden)

    Do Hyun Kim

    2015-01-01

    Full Text Available Microbial cell arrays have attracted consistent attention for their ability to provide unique global data on target analytes at low cost, their capacity for readily detectable and robust cell growth in diverse environments, their high degree of convenience, and their capacity for multiplexing via incorporation of molecularly tailored reporter cells. To highlight recent progress in the field of microbial cell arrays, this review discusses research on genetic engineering of reporter cells, technologies for patterning live cells on solid surfaces, cellular immobilization in different polymers, and studies on their application in environmental monitoring, disease diagnostics, and other related fields. On the basis of these results, we discuss current challenges and future prospects for novel microbial cell arrays, which show promise for use as potent tools for unraveling complex biological processes.

  17. 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.

  18. Digital cell counting device integrated with a single-cell array.

    Directory of Open Access Journals (Sweden)

    Tatsuya Saeki

    Full Text Available In this paper, we present a novel cell counting method accomplished using a single-cell array fabricated on an image sensor, complementary metal oxide semiconductor sensor. The single-cell array was constructed using a microcavity array, which can trap up to 7,500 single cells on microcavities periodically arranged on a plane metallic substrate via the application of a negative pressure. The proposed method for cell counting is based on shadow imaging, which uses a light diffraction pattern generated by the microcavity array and trapped cells. Under illumination, the cell-occupied microcavities are visualized as shadow patterns in an image recorded by the complementary metal oxide semiconductor sensor due to light attenuation. The cell count is determined by enumerating the uniform shadow patterns created from one-on-one relationships with single cells trapped on the microcavities in digital format. In the experiment, all cell counting processes including entrapment of non-labeled HeLa cells from suspensions on the array and image acquisition of a wide-field-of-view of 30 mm(2 in 1/60 seconds were implemented in a single integrated device. As a result, the results from the digital cell counting had a linear relationship with those obtained from microscopic observation (r(2  = 0.99. This platform could be used at extremely low cell concentrations, i.e., 25-15,000 cells/mL. Our proposed system provides a simple and rapid miniaturized cell counting device for routine laboratory use.

  19. Distributed hydrophone array based on liquid crystal cell

    Science.gov (United States)

    Brodzeli, Zourab; Ladouceur, Francois; Silvestri, Leonardo; Michie, Andrew; Chigrinov, Vladimir; Guo, Grace Qi; Pozhidaev, Eugene P.; Kiselev, Alexei D.

    2012-02-01

    We describe a fibre optic hydrophone array system that could be used for underwater acoustic surveillance applications e.g. military, counter terrorist and customs authorities in protecting ports and harbors, offshore production facilities or coastal approaches as well as various marine applications. In this paper we propose a new approach to underwater sonar systems using voltage-controlled Liquid Crystals (LC) and simple multiplexing method. The proposed method permits measurements of sound under water at multiple points along an optical fibre using low cost components (LC cells), standard single mode fibre, without complex interferometric measurement techniques, electronics or demodulation software.

  20. Relationship between thunderstorm electrification and storm kinetics revealed by phased array weather radar

    Science.gov (United States)

    Yoshida, S.; Adachi, T.; Kusunoki, K.; Hayashi, S.; Wu, T.; Ushio, T.; Yoshikawa, E.

    2017-04-01

    We examine 3-D lightning location data and radar data obtained through multiple radar observation stations, including two X-band phased array weather radars (PAWRs), in order to understand the relationship between thunderstorm electrification and storm kinetics. In an investigated convective cell, both intracloud (IC) and cloud-to-ground (CG) flash rates drastically change within 25 min. First, the IC flash rate shows a steep increase with a peak at 10 min-1, and then, the CG flash rate peaks 7 min afterward. During the increase phase of the IC flash rate, the radar observation indicates that the echo top height and updraft echo volume in the upper level increase. The upper positive charge regions removed by IC flashes are located in or near the updraft region at high altitudes. On the contrary, the IC flash rate decreases when the updraft at high altitudes weakens. The IC flash rate is well correlated with a proxy for updraft volume in 1 min interval comparison. These results indicate that the IC flash rate has a strong connection with updraft at high altitudes. The CG flash rate peaks when precipitation particles, probably involving graupel, from high altitudes arrive at approximately the -10°C isotherm level. We speculate that graupel from high altitudes might contribute to the initiations of CG flashes. We show an abrupt ascent of the upper positive charge region involved in IC flashes. PAWR observation results indicate that the updraft might have contributed to the ascent of the upper positive lightning charge region.

  1. Light absorption and emission in nanowire array solar cells.

    Science.gov (United States)

    Kupec, Jan; Stoop, Ralph L; Witzigmann, Bernd

    2010-12-20

    Inorganic nanowires are under intense research for large scale solar power generation intended to ultimately contribute a substantial fraction to the overall power mix. Their unique feature is to allow different pathways for the light absorption and carrier transport. In this publication we investigate the properties of a nanowire array acting as a photonic device governed by wave-optical phenomena. We solve the Maxwell equations and calculate the light absorption efficiency for the AM1.5d spectrum and give recommendations on the design. Due to concentration of the incident sunlight at a microscopic level the absorptivity of nanowire solar cells can exceed the absorptivity of an equal amount of material used in thin-film devices. We compute the local density of photon states to assess the effect of emission enhancement, which influences the radiative lifetime of excess carriers. This allows us to compute the efficiency limit within the framework of detailed balance. The efficiency is highly sensitive with respect to the diameter and distance of the nanowires. Designs featuring nanowires below a certain diameter will intrinsically feature low short-circuit current that cannot be compensated even by increasing the nanowire density. Optimum efficiency is not achieved in densely packed arrays, in fact spacing the nanowires further apart (simultaneously decreasing the material use) can even improve efficiency in certain scenarios. We observe absorption enhancement reducing the material use. In terms of carrier generation per material use, nanowire devices can outperform thin-film devices by far.

  2. 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

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

    International Nuclear Information System (INIS)

    Wang, Xiaolin; Gou, Xue; Chen, Shuxun; Yan, Xiao; Sun, Dong

    2013-01-01

    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)

  4. Anatomical Reconstruction and Functional Imaging Reveal an Ordered Array of Skylight Polarization Detectors in Drosophila.

    Science.gov (United States)

    Weir, Peter T; Henze, Miriam J; Bleul, Christiane; Baumann-Klausener, Franziska; Labhart, Thomas; Dickinson, Michael H

    2016-05-11

    Many insects exploit skylight polarization as a compass cue for orientation and navigation. In the fruit fly, Drosophila melanogaster, photoreceptors R7 and R8 in the dorsal rim area (DRA) of the compound eye are specialized to detect the electric vector (e-vector) of linearly polarized light. These photoreceptors are arranged in stacked pairs with identical fields of view and spectral sensitivities, but mutually orthogonal microvillar orientations. As in larger flies, we found that the microvillar orientation of the distal photoreceptor R7 changes in a fan-like fashion along the DRA. This anatomical arrangement suggests that the DRA constitutes a detector for skylight polarization, in which different e-vectors maximally excite different positions in the array. To test our hypothesis, we measured responses to polarized light of varying e-vector angles in the terminals of R7/8 cells using genetically encoded calcium indicators. Our data confirm a progression of preferred e-vector angles from anterior to posterior in the DRA, and a strict orthogonality between the e-vector preferences of paired R7/8 cells. We observed decreased activity in photoreceptors in response to flashes of light polarized orthogonally to their preferred e-vector angle, suggesting reciprocal inhibition between photoreceptors in the same medullar column, which may serve to increase polarization contrast. Together, our results indicate that the polarization-vision system relies on a spatial map of preferred e-vector angles at the earliest stage of sensory processing. The fly's visual system is an influential model system for studying neural computation, and much is known about its anatomy, physiology, and development. The circuits underlying motion processing have received the most attention, but researchers are increasingly investigating other functions, such as color perception and object recognition. In this work, we investigate the early neural processing of a somewhat exotic sense, called

  5. Cost competitiveness of a solar cell array power source for ATS-6 educational TV terminal

    Science.gov (United States)

    Masters, R. M.

    1975-01-01

    A cost comparison is made between a terrestrial solar cell array power system and a variety of other power sources for the ATS-6 Satellite Instructional Television Experiment (SITE) TV terminals in India. The solar array system was sized for a typical Indian location, Lahore. Based on present capital and fuel costs, the solar cell array power system is a close competitor to the least expensive alternate power system. A feasibility demonstration of a terrestrial solar cell array system powering an ATS-6 receiver terminal at Cleveland, Ohio is described.

  6. Design to improve photoelectric efficiency for photovoltaic cell array for laser power beaming

    Science.gov (United States)

    Li, Xiaojiang; Li, Beibei

    2017-02-01

    Photovoltaic cell (PV) array is a photovoltaic conversion device for laser power beaming, and uneven distribution of laser beam energy will have negative influence on the photovoltaic efficiency of PV array. In order to improve the photovoltaic efficiency under uneven laser irradiation, an optimized and efficient parallel-series PV array is designed. Based on the mathematical model and MATLB/Simulink simulation model of PV array , the influencing factors of photovoltaic efficiency are analyzed, and the concept and scheme to improve the photovoltaic efficiency of parallel-series PV array are proposed. Finally, compared with typical PV array, the effects improving efficiency of optimized array is simulated and analyzed. The simulation results show that under uneven laser irradiation, the optimized parallel-series PV array can obtain higher photovoltaic efficiency.

  7. Read margin analysis of crossbar arrays using the cell-variability-aware simulation method

    Science.gov (United States)

    Sun, Wookyung; Choi, Sujin; Shin, Hyungsoon

    2018-02-01

    This paper proposes a new concept of read margin analysis of crossbar arrays using cell-variability-aware simulation. The size of the crossbar array should be considered to predict the read margin characteristic of the crossbar array because the read margin depends on the number of word lines and bit lines. However, an excessively high-CPU time is required to simulate large arrays using a commercial circuit simulator. A variability-aware MATLAB simulator that considers independent variability sources is developed to analyze the characteristics of the read margin according to the array size. The developed MATLAB simulator provides an effective method for reducing the simulation time while maintaining the accuracy of the read margin estimation in the crossbar array. The simulation is also highly efficient in analyzing the characteristic of the crossbar memory array considering the statistical variations in the cell characteristics.

  8. Morphology of living cells cultured on nanowire arrays with varying nanowire densities and diameters.

    Science.gov (United States)

    Li, Zhen; Persson, Henrik; Adolfsson, Karl; Oredsson, Stina; Prinz, Christelle N

    2018-04-02

    Vertical nanowire arrays are increasingly investigated for their applications in steering cell behavior. The geometry of the array is an important parameter, which influences the morphology and adhesion of cells. Here, we investigate the effects of array geometry on the morphology of MCF7 cancer cells and MCF10A normal-like epithelial cells. Different gallium phosphide nanowire array-geometries were produced by varying the nanowire density and diameter. Our results show that the cell size is smaller on nanowires compared to flat gallium phosphide. The cell area decreases with increasing the nanowire density on the substrate. We observed an effect of the nanowire diameter on MCF10A cells, with a decreased cell area on 40 nm diameter nanowires, compared to 60 and 80 nm diameter nanowires in high-density arrays. The focal adhesion morphology depends on the extent to which cells are contacting the substrate. For low nanowire densities and diameters, cells are lying on the substrate and we observed large focal adhesions at the cell edges. In contrast, for high nanowire densities and diameters, cells are lying on top of the nanowires and we observed point-like focal adhesions distributed over the whole cell. Our results constitute a step towards the ability to fine-tune cell behavior on nanowire arrays.

  9. 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.

  10. 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......). To date, no reported criteria are sensitive enough to discriminate reliably between KA and SCC, and consequently there is a clinical need for discriminating markers. Our previous study analyzed 132 KAs and 29 SCCs and revealed significantly different regions of genomic aberrations using chromosomal...

  11. Array-based sensing of normal, cancerous, and metastatic cells using conjugated fluorescent polymers.

    Science.gov (United States)

    Bajaj, Avinash; Miranda, Oscar R; Phillips, Ronnie; Kim, Ik-Bum; Jerry, D Joseph; Bunz, Uwe H F; Rotello, Vincent M

    2010-01-27

    A family of conjugated fluorescent polymers was used to create an array for cell sensing. Fluorescent conjugated polymers with pendant charged residues provided multivalent interactions with cell membranes, allowing the detection of subtle differences between different cell types on the basis of cell surface features. Highly reproducible characteristic patterns were obtained from different cell types as well as from isogenic cell lines, enabling the identification of the cell type as well differentiating between normal, cancerous, and metastatic isogenic cell types with high accuracy.

  12. 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.

  13. 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.

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

    International Nuclear Information System (INIS)

    Man, Tsz-Kwong; Rao, Pulivarthi H; Lu, Xin-Yan; Jaeweon, Kim; Perlaky, Laszlo; Harris, Charles P; Shah, Shishir; Ladanyi, Marc; Gorlick, Richard; Lau, Ching C

    2004-01-01

    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. Basic principles of STT-MRAM cell operation in memory arrays

    International Nuclear Information System (INIS)

    Khvalkovskiy, A V; Apalkov, D; Watts, S; Chepulskii, R; Beach, R S; Ong, A; Tang, X; Driskill-Smith, A; Lottis, D; Chen, E; Nikitin, V; Krounbi, M; Butler, W H; Visscher, P B

    2013-01-01

    For reliable operation, individual cells of an STT-MRAM memory array must meet specific requirements on their performance. In this work we review some of these requirements and discuss the fundamental physical principles of STT-MRAM operation, covering the range from device level to chip array performance, and methodology for its development. (paper)

  16. Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.

    Science.gov (United States)

    Wacker, Irene; Chockley, Peter; Bartels, Carolin; Spomer, Waldemar; Hofmann, Andreas; Gengenbach, Ulrich; Singh, Sachin; Thaler, Marlene; Grabher, Clemens; Schröder, Rasmus R

    2015-08-01

    For 3D reconstructions of whole immune cells from zebrafish, isolated from adult animals by FAC-sorting we employed array tomography on hundreds of serial sections deposited on silicon wafers. Image stacks were either recorded manually or automatically with the newly released ZEISS Atlas 5 Array Tomography platform on a Zeiss FEGSEM. To characterize different populations of immune cells, organelle inventories were created by segmenting individual cells. In addition, arrays were used for quantification of cell populations with respect to the various cell types they contained. The detection of immunological synapses in cocultures of cell populations from thymus or WKM with cancer cells helped to identify the cytotoxic nature of these cells. Our results demonstrate the practicality and benefit of AT for high-throughput ultrastructural imaging of substantial volumes. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  17. 3D shear wave velocity structure revealed with ambient noise tomography on a DAS array

    Science.gov (United States)

    Zeng, X.; Thurber, C. H.; Wang, H. F.; Fratta, D.

    2017-12-01

    An 8700-m Distributed Acoustic Sensing (DAS) cable was deployed at Brady's Hot Springs, Nevada in March 2016 in a 1.5 by 0.5 km study area. The layout of the DAS array was designed with a zig-zag geometry to obtain relatively uniform areal and varied angular coverage, providing very dense coverage with a one-meter channel spacing. This array continuously recorded signals of a vibroseis truck, earthquakes, and traffic noise during the 15-day deployment. As shown in a previous study (Zeng et al., 2017), ambient noise tomography can be applied to DAS continuous records to image shear wave velocity structure in the near surface. To avoid effects of the vibroseis truck operation, only continuous data recorded during the nighttime was used to compute noise cross-correlation functions for channel pairs within a given linear segment. The frequency band of whitening was set at 5 to 15 Hz and the length of the cross-correlation time window was set to 60 second. The phase velocities were determined using the multichannel analysis of surface waves (MASW) methodology. The phase velocity dispersion curve was then used to invert for shear wave velocity profiles. A preliminarily velocity model at Brady's Hot Springs (Lawrence Livermore National Laboratory, 2015) was used as the starting model and the sensitivity kernels of Rayleigh wave group and phase velocities were computed with this model. As the sensitivity kernel shows, shear wave velocity in the top 200 m can be constrained with Rayleigh wave group and phase velocities in our frequency band. With the picked phase velocity data, the shear wave velocity structure can be obtained via Occam's inversion (Constable et al., 1987; Lai 1998). Shear wave velocity gradually increases with depth and it is generally faster than the Lawrence Livermore National Laboratory (2015) model. Furthermore, that model has limiting constraints at shallow depth. The strong spatial variation is interpreted to reflect the different sediments and

  18. Precisely Assembled Nanofiber Arrays as a Platform to Engineer Aligned Cell Sheets for Biofabrication

    Directory of Open Access Journals (Sweden)

    Vince Beachley

    2014-08-01

    Full Text Available A hybrid cell sheet engineering approach was developed using ultra-thin nanofiber arrays to host the formation of composite nanofiber/cell sheets. It was found that confluent aligned cell sheets could grow on uniaxially-aligned and crisscrossed nanofiber arrays with extremely low fiber densities. The porosity of the nanofiber sheets was sufficient to allow aligned linear myotube formation from differentiated myoblasts on both sides of the nanofiber sheets, in spite of single-side cell seeding. The nanofiber content of the composite cell sheets is minimized to reduce the hindrance to cell migration, cell-cell contacts, mass transport, as well as the foreign body response or inflammatory response associated with the biomaterial. Even at extremely low densities, the nanofiber component significantly enhanced the stability and mechanical properties of the composite cell sheets. In addition, the aligned nanofiber arrays imparted excellent handling properties to the composite cell sheets, which allowed easy processing into more complex, thick 3D structures of higher hierarchy. Aligned nanofiber array-based composite cell sheet engineering combines several advantages of material-free cell sheet engineering and polymer scaffold-based cell sheet engineering; and it represents a new direction in aligned cell sheet engineering for a multitude of tissue engineering applications.

  19. Cultivating liver cells on printed arrays of hepatocyte growth factor.

    Science.gov (United States)

    Jones, Caroline N; Tuleuova, Nazgul; Lee, Ji Youn; Ramanculov, Erlan; Reddi, A Hari; Zern, Mark A; Revzin, Alexander

    2009-08-01

    Growth factors are commonly present in soluble form during in vitro cell cultivation experiments in order to provide signals for cellular proliferation or differentiation. In contrast to these traditional experiments, we investigated solid-phase presentation of a hepatocyte growth factor (HGF), a protein important in liver development and regeneration, on microarrays of extracellular matrix (ECM) proteins. In our experiments, HGF was mixed in solution with ECM proteins (collagen (I), (IV) or laminin) and robotically printed onto silane-modified glass slides. Primary rat hepatocytes were seeded onto HGF/ECM protein microarrays and formed cellular clusters that corresponded in size to the dimensions of individual protein spots (500 microm diameter). Analysis of liver-specific products, albumin and alpha1-antitrypsin, revealed several fold higher levels of expression of these proteins in hepatocytes cultured on HGF/ECM microarrays compared to cells cultivated on ECM proteins alone. In addition, cultivation of hepatocytes on HGF/ECM protein spots led to spontaneous reorganization of cellular clusters from a monolayer into three-dimensional spheroids. We also investigated the effects of surface-tethered HGF on hepatocytes co-cultivated with stromal cells and observed a significantly higher level of albumin in co-cultures where hepatocytes were stimulated by HGF/ECM spots compared to co-cultures created on ECM protein islands without the growth factor. In summary, our study suggests that incorporation of HGF into ECM protein microarrays has a profound and long-lasting effect on the morphology and phenotype of primary hepatocytes. In the future, the number of growth factors printed on ECM microarrays will be expanded to enable multiplexed and combinatorial screening of inducers of cellular differentiation or proliferation.

  20. Molecular Motor Propelled Filaments Reveal Light-Guiding in Nanowire Arrays for Enhanced Biosensing

    Science.gov (United States)

    2013-01-01

    Semiconductor nanowire arrays offer significant potential for biosensing applications with optical read-out due to their high surface area and due to the unique optical properties of one-dimensional materials. A challenge for optical read-out of analyte-binding to the nanowires is the need to efficiently collect and detect light from a three-dimensional volume. Here we show that light from fluorophores attached along several μm long vertical Al2O3 coated gallium phosphide nanowires couples into the wires, is guided along them and emitted at the tip. This enables effective collection of light emitted by fluorescent analytes located at different focal planes along the nanowire. We unequivocally demonstrate the light-guiding effect using a novel method whereby the changes in emitted fluorescence intensity are observed when fluorescent cytoskeletal filaments are propelled by molecular motors along the wires. The findings are discussed in relation to nanobiosensor developments, other nanotechnological applications, and fundamental studies of motor function. PMID:24367994

  1. Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences

    Directory of Open Access Journals (Sweden)

    Alessandra Traini

    2013-01-01

    Full Text Available Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

  2. Efficient Template-Based Nanomanufacturing of Carbon Nanotube Arrays for Cell Applications

    Science.gov (United States)

    Ahmed, Adeel

    Carbon nanotube arrays have been found to be highly effective at carrying out intracellular delivery of cargo at high efficiencies while ensuring cell viability. Template based chemical vapor deposition is a commonly used process to fabricate these arrays. However, current etching methods used to expose carbon nanotubes from templates are expensive and time consuming. The high cost and time-consuming processes currently required to fabricate such arrays are factors which limit the commercialization of this technology and inhibit scope for larger research programs. In this thesis, alternative nanofabrication methods were explored with the aim of making the fabrication of CNT arrays cost effective and efficient. Mechanical polishing coupled with wet chemical etching is shown as a feasible alternative option to dry etching. The effects of process variables on physical properties of CNT arrays have been studied and quantified in order to demonstrate control over the process. Scanning Electron Microscopy has been used to qualitatively understand the differences between CNT arrays fabricated using dry etching and the alternative process. Cell culture has been demonstrated on the CNT arrays and the potential to use 3D printing to fabricate a nanofluidic device is also demonstrated. The alternative process can save etching time by 97% while maintaining a similar level of control over the process. This study, therefore, opens the path to quicker production of CNT arrays at low cost for biomedical use.

  3. Photovoltaic Performance of a Nanowire/Quantum Dot Hybrid Nanostructure Array Solar Cell.

    Science.gov (United States)

    Wu, Yao; Yan, Xin; Zhang, Xia; Ren, Xiaomin

    2018-02-23

    An innovative solar cell based on a nanowire/quantum dot hybrid nanostructure array is designed and analyzed. By growing multilayer InAs quantum dots on the sidewalls of GaAs nanowires, not only the absorption spectrum of GaAs nanowires is extended by quantum dots but also the light absorption of quantum dots is dramatically enhanced due to the light-trapping effect of the nanowire array. By incorporating five layers of InAs quantum dots into a 500-nm high-GaAs nanowire array, the power conversion efficiency enhancement induced by the quantum dots is six times higher than the power conversion efficiency enhancement in thin-film solar cells which contain the same amount of quantum dots, indicating that the nanowire array structure can benefit the photovoltaic performance of quantum dot solar cells.

  4. 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...

  5. New Aspects Regarding Evolution and Virulence of Listeria monocytogenes Revealed by Comparative Genomics and DNA Arrays

    Science.gov (United States)

    Doumith, Michel; Cazalet, Christel; Simoes, Natalie; Frangeul, Lionel; Jacquet, Christine; Kunst, Frank; Martin, Paul; Cossart, Pascale; Glaser, Philippe; Buchrieser, Carmen

    2004-01-01

    Listeria monocytogenes is a food-borne bacterial pathogen that causes a wide spectrum of diseases, such as meningitis, septicemia, abortion, and gastroenteritis, in humans and animals. Among the 13 L. monocytogenes serovars described, invasive disease is mostly associated with serovar 4b strains. To investigate the genetic diversity of L. monocytogenes strains with different virulence potentials, we partially sequenced an epidemic serovar 4b strain and compared it with the complete sequence of the nonepidemic L. monocytogenes EGDe serovar 1/2a strain. We identified an unexpected genetic divergence between the two strains, as about 8% of the sequences were serovar 4b specific. These sequences included seven genes coding for surface proteins, two of which belong to the internalin family, and three genes coding for transcriptional regulators, all of which might be important in different steps of the infectious process. Based on the sequence information, we then characterized the gene content of 113 Listeria strains by using a newly designed Listeria array containing the “flexible” part of the sequenced Listeria genomes. Hybridization results showed that all of the previously identified virulence factors of L. monocytogenes were present in the 93 L. monocytogenes strains tested. However, distinct patterns of the presence or absence of other genes were identified among the different L. monocytogenes serovars and Listeria species. These results allow new insights into the evolution of L. monocytogenes, suggesting that early divergence of the ancestral L. monocytogenes serovar 1/2c strains from the serovar 1/2b strains led to two major phylogenetic lineages, one of them including the serogroup 4 strains, which branched off the serovar 1/2b ancestral lineage, leading (mostly by gene loss) to the species Listeria innocua. The identification of 30 L. monocytogenes-specific and several serovar-specific marker genes, such as three L. monocytogenes serovar 4b

  6. Whole-body single-cell sequencing reveals transcriptional domains in the annelid larval body.

    Science.gov (United States)

    Achim, Kaia; Eling, Nils; Vergara, Hernando Martinez; Bertucci, Paola Yanina; Musser, Jacob; Vopalensky, Pavel; Brunet, Thibaut; Collier, Paul; Benes, Vladimir; Marioni, John C; Arendt, Detlev

    2018-01-24

    Animal bodies comprise diverse arrays of cells. To characterise cellular identities across an entire body, we have compared the transcriptomes of single cells randomly picked from dissociated whole larvae of the marine annelid Platynereis dumerilii. We identify five transcriptionally distinct groups of differentiated cells, each expressing a unique set of transcription factors and effector genes that implement cellular phenotypes. Spatial mapping of cells into a cellular expression atlas, and wholemount in situ hybridisation of group-specific genes reveals spatially coherent transcriptional domains in the larval body, comprising e.g. apical sensory-neurosecretory cells vs. neural/epidermal surface cells. These domains represent new, basic subdivisions of the annelid body based entirely on differential gene expression, and are composed of multiple, transcriptionally similar cell types. They do not represent clonal domains, as revealed by developmental lineage analysis. We propose that the transcriptional domains that subdivide the annelid larval body represent families of related cell types that have arisen by evolutionary diversification. Their possible evolutionary conservation makes them a promising tool for evo-devo research. (167/250). © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  7. A microneedle array able to inject tens of thousands of cells simultaneously

    Science.gov (United States)

    Teichert, Gregory H.; Burnett, Sandra; Jensen, Brian D.

    2013-09-01

    This paper presents a biological microelectromechanical system for injecting foreign particles into thousands of cells simultaneously. The system inserts an array of microneedles into a monolayer of cells, and the foreign particles enter the cells by diffusion. The needle array is fabricated using a series of deep reactive ion etches and produces about 4 million needles that average 1 μm in diameter and 8 μm in length with 10 μm spacing. The insertion of the needles is controlled through a compliant suspension. The compliant suspension was designed to provide for needle motion into the cells while restraining rotations or transverse motions that could result in tearing of the cell membranes. Testing was performed using propidium iodide, a membrane impermeable dye, injected into HeLa cells. Average cell survivability was found to be 97.7%, and up to 97.9% of the surviving cells received the propidium iodide.

  8. A microneedle array able to inject tens of thousands of cells simultaneously

    International Nuclear Information System (INIS)

    Teichert, Gregory H; Jensen, Brian D; Burnett, Sandra

    2013-01-01

    This paper presents a biological microelectromechanical system for injecting foreign particles into thousands of cells simultaneously. The system inserts an array of microneedles into a monolayer of cells, and the foreign particles enter the cells by diffusion. The needle array is fabricated using a series of deep reactive ion etches and produces about 4 million needles that average 1 μm in diameter and 8 μm in length with 10 μm spacing. The insertion of the needles is controlled through a compliant suspension. The compliant suspension was designed to provide for needle motion into the cells while restraining rotations or transverse motions that could result in tearing of the cell membranes. Testing was performed using propidium iodide, a membrane impermeable dye, injected into HeLa cells. Average cell survivability was found to be 97.7%, and up to 97.9% of the surviving cells received the propidium iodide. (paper)

  9. Light trapping characteristics of glass substrate with hemisphere pit arrays in thin film Si solar cells

    International Nuclear Information System (INIS)

    Chen Le; Wang Qing-Kang; Wangyang Pei-Hua; Huang Kun; Shen Xiang-Qian

    2015-01-01

    In this paper, the light trapping characteristics of glass substrate with hemisphere pit (HP) arrays in thin film Si solar cells are theoretically studied via a numerical approach. It is found that the HP glass substrate has good antireflection properties. Its surface reflectance can be reduced by ∼ 50% compared with planar glass. The HP arrays can make the unabsorbed light return to the absorbing layer of solar cells, and the ratio of second absorption approximately equals 30%. Thus, the glass substrate with the hemisphere pit arrays (HP glass) can effectively reduce the total reflectivity of a solar cell from 20% to 13%. The HP glass can also prolong the optical path length. The numerical results show that the total optical path length of the thin film Si solar cell covered with the HP glass increases from 2ω to 4ω. These results are basically consistent with the experimental results. (paper)

  10. 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.

  11. High-frequency microrheology reveals cytoskeleton dynamics in living cells

    Science.gov (United States)

    Rigato, Annafrancesca; Miyagi, Atsushi; Scheuring, Simon; Rico, Felix

    2017-08-01

    Living cells are viscoelastic materials, dominated by an elastic response on timescales longer than a millisecond. On shorter timescales, the dynamics of individual cytoskeleton filaments are expected to emerge, but active microrheology measurements on cells accessing this regime are scarce. Here, we develop high-frequency microrheology experiments to probe the viscoelastic response of living cells from 1 Hz to 100 kHz. We report the viscoelasticity of different cell types under cytoskeletal drug treatments. On previously inaccessible short timescales, cells exhibit rich viscoelastic responses that depend on the state of the cytoskeleton. Benign and malignant cancer cells revealed remarkably different scaling laws at high frequencies, providing a unique mechanical fingerprint. Microrheology over a wide dynamic range--up to the frequency characterizing the molecular components--provides a mechanistic understanding of cell mechanics.

  12. 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.

  13. Carbon-Ring Microelectrode Arrays for Electrochemical Imaging of Single Cell Exocytosis: Fabrication and Characterization

    Science.gov (United States)

    Lin, Yuqing; Trouillon, Raphaël; Svensson, Maria I.; Keighron, Jacqueline D.; Cans, Ann-Sofie; Ewing, Andrew G.

    2012-01-01

    Fabrication of carbon microelectrode arrays, with up to 15 electrodes in total tips as small as 10 to 50 μm, is presented. The support structures of microelectrodes were obtained by pulling multiple quartz capillaries together to form hollow capillary arrays before carbon deposition. Carbon ring microelectrodes were deposited by pyrolysis of acetylene in the lumen of these quartz capillary arrays. Each carbon deposited array tip was filled with epoxy, followed by beveling of the tip of the array to form a deposited carbon-ring microelectrode array (CRMA). Both the number of the microelectrodes in the array and the tip size are independently tunable. These CRMAs have been characterized using scanning electron microscopy, energy dispersive X-ray spectroscopy, and electrogenerated chemiluminescence. Additionally, the electrochemical properties were investigated with steady-state voltammetry. In order to demonstrate the utility of these fabricated microelectrodes in neurochemistry, CRMAs containing eight microring electrodes were used for electrochemical monitoring of exocytotic events from single PC12 cells. Subcellular temporal heterogeneities in exocytosis (ie. cold spots vs. hot spots) were successfully detected with the CRMAs. PMID:22339586

  14. 'Big bang' of B-cell development revealed.

    Science.gov (United States)

    Murre, Cornelis

    2018-01-15

    Earlier studies have identified transcription factors that specify B-cell fate, but the underlying mechanisms remain to be revealed. Two new studies by Miyai and colleagues (pp. 112-126) and Li and colleagues (pp. 96-111) in this issue of Genes & Development provide new and unprecedented insights into the genetic and epigenetic mechanisms that establish B-cell identity. © 2018 Murre; Published by Cold Spring Harbor Laboratory Press.

  15. 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.

  16. Life on magnets: stem cell networking on micro-magnet arrays.

    Science.gov (United States)

    Zablotskii, Vitalii; Dejneka, Alexandr; Kubinová, Šárka; Le-Roy, Damien; Dumas-Bouchiat, Frédéric; Givord, Dominique; Dempsey, Nora M; Syková, Eva

    2013-01-01

    Interactions between a micro-magnet array and living cells may guide the establishment of cell networks due to the cellular response to a magnetic field. To manipulate mesenchymal stem cells free of magnetic nanoparticles by a high magnetic field gradient, we used high quality micro-patterned NdFeB films around which the stray field's value and direction drastically change across the cell body. Such micro-magnet arrays coated with parylene produce high magnetic field gradients that affect the cells in two main ways: i) causing cell migration and adherence to a covered magnetic surface and ii) elongating the cells in the directions parallel to the edges of the micro-magnet. To explain these effects, three putative mechanisms that incorporate both physical and biological factors influencing the cells are suggested. It is shown that the static high magnetic field gradient generated by the micro-magnet arrays are capable of assisting cell migration to those areas with the strongest magnetic field gradient, thereby allowing the build up of tunable interconnected stem cell networks, which is an elegant route for tissue engineering and regenerative medicine.

  17. Life on magnets: stem cell networking on micro-magnet arrays.

    Directory of Open Access Journals (Sweden)

    Vitalii Zablotskii

    Full Text Available Interactions between a micro-magnet array and living cells may guide the establishment of cell networks due to the cellular response to a magnetic field. To manipulate mesenchymal stem cells free of magnetic nanoparticles by a high magnetic field gradient, we used high quality micro-patterned NdFeB films around which the stray field's value and direction drastically change across the cell body. Such micro-magnet arrays coated with parylene produce high magnetic field gradients that affect the cells in two main ways: i causing cell migration and adherence to a covered magnetic surface and ii elongating the cells in the directions parallel to the edges of the micro-magnet. To explain these effects, three putative mechanisms that incorporate both physical and biological factors influencing the cells are suggested. It is shown that the static high magnetic field gradient generated by the micro-magnet arrays are capable of assisting cell migration to those areas with the strongest magnetic field gradient, thereby allowing the build up of tunable interconnected stem cell networks, which is an elegant route for tissue engineering and regenerative medicine.

  18. 3D Nanochannel Array Platform for High-throughput Cell Manipulation and Nano-electroporation

    Science.gov (United States)

    Chang, Lingqian

    Electroporation is one of the most common non-viral methods for gene delivery. Recent progress in gene therapy has offered special opportunities to electroporation for in vitro and in vivo applications. However, conventional bulk electroporation (BEP) inevitably causes serious cell damage and stochastic transfection between cells. Microfluidic electroporation (MEP) has been claimed to provide benign single cell transfection for the last decade. Nevertheless, the intracellular transport in both MEP and BEP systems is highly diffusion-dominant, which prevents precise dose control and high uniformity. In this Ph.D. research, we developed a 3D nanochannel-electroporation (3D NEP) platform for mass cell transfection. A silicon-based nanochannel array (3D NEP) chip was designed and fabricated for cell manipulation and electroporation. The chip, designed as Z-directional microchannel - nanochannel array, was fabricated by clean room techniques including projection photolithography and deep reactive-ion etching (DRIE). The fabricated 3D NEP chip is capable of handling 40,000 cells per 1 cm2, up to 1 million per wafer (100 mm diameter). High-throughput cell manipulation technologies were investigated for precise alignment of individual cells to the nanochannel array, a key step for NEP to achieve dose control. We developed three techniques for cell trapping in this work. (1) Magnetic tweezers (MTs) were integrated on the chip to remotely control cells under a programmed magnetic field. (2) A positive dielectrophoresis (pDEP) power system was built as an alternative to trap cells onto the nanochannel array using DEP force. (3) A novel yet simple 'dipping-trap' method was used to rapidly trap cells onto a nanochannel array, aligned by a micro-cap array pattern on the 3D NEP chip, which eventually offered 70 - 90 % trapping efficiency and 90 % specificity. 3D NEP platforms were assembled for cell transfection based on the Si-based nanochannel array chip and cell manipulation

  19. Deterministic Capture of Individual Circulating Tumor Cells Using a Flow-Restricted Microfluidic Trap Array

    Directory of Open Access Journals (Sweden)

    Yousang Yoon

    2018-03-01

    Full Text Available Circulating tumor cells (CTCs are regarded as a strong biomarker which includes clinically valuable information. However, CTCs are very rare and require precise separation and detection for effective clinical applications. Furthermore, downstream analysis has become necessary to identify the distinct sub-population of CTCs that causes metastasis. Here, we report a flow-restricted microfluidic trap array capable of deterministic single-cell capture of CTCs. The extent of flow restriction, correlating with the device geometry, was then optimized using a highly invasive breast cancer cell line (LM2 MDA-MB-231 to achieve 97% capture efficiency with a single-cell capture rate of 99%. Single-cell capture of CTCs from mice with full-blown metastasis was also demonstrated. The single-CTC capturing ability of the flow-restricted trap array not only showed cell enumerating ability but also high prospects for application in future automated downstream analysis.

  20. 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

  1. 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.

  2. Magnetic Microfluidic Linear Halbach Array Configuration for Cell Separation

    Directory of Open Access Journals (Sweden)

    Saeed Omer

    2018-01-01

    Full Text Available The different type of blood entities like red blood cells (RBCs, white blood cell (WBCs and platelets counts is a critical point in routine medical tests. Circulating tumor cells (CTCs counting and analysing in the blood is indicative of the stage and origin of cancer in particular time. Here we are describing a proposed microfluidic device, used a magnetic means for CTCs separation from a blood or buffer sample. The device characterizations were simulated using COMSOL MULTIPHYSICS software as well as practically validated. Using a known spiked number of CTCs in the sample, the purity and recovery rate were calculated to be 93% and respectively.

  3. Combinatorial electrochemical cell array for high throughput screening of micro-fuel-cells and metal/air batteries

    Science.gov (United States)

    Jiang, Rongzhong

    2007-07-01

    An electrochemical cell array was designed that contains a common air electrode and 16 microanodes for high throughput screening of both fuel cells (based on polymer electrolyte membrane) and metal/air batteries (based on liquid electrolyte). Electrode materials can easily be coated on the anodes of the electrochemical cell array and screened by switching a graphite probe from one cell to the others. The electrochemical cell array was used to study direct methanol fuel cells (DMFCs), including high throughput screening of electrode catalysts and determination of optimum operating conditions. For screening of DMFCs, there is about 6% relative standard deviation (percentage of standard deviation versus mean value) for discharge current from 10to20mA/cm2. The electrochemical cell array was also used to study tin/air batteries. The effect of Cu content in the anode electrode on the discharge performance of the tin/air battery was investigated. The relative standard deviations for screening of metal/air battery (based on zinc/air) are 2.4%, 3.6%, and 5.1% for discharge current at 50, 100, and 150mA/cm2, respectively.

  4. PVSIM{copyright}: A simulation program for photovoltaic cells, modules, and arrays

    Energy Technology Data Exchange (ETDEWEB)

    King, D.L.; Dudley, J.K.; Boyson, W.E.

    1996-06-01

    An electrical simulation model for photovoltaic cells, modules, and arrays has been developed that will be useful to a wide range of analysts in the photovoltaic industry. The Microsoft{reg_sign} Windows{trademark} based program can be used to analyze individual cells, to analyze the effects of cell mismatch or reverse bias(`hot spot`) heating in modules and to analyze the performance of large arrays of modules including bypass and blocking diodes. User defined statistical variance can be applied to the fundamental parameters used to simulate the cells and diodes. The model is most appropriate for cells that can be accurately modeled using a two-diode equivalent circuit. This paper describes the simulation program and illustrates its versatility with examples.

  5. Opto-acoustic microscopy reveals adhesion mechanics of single cells

    Science.gov (United States)

    Abi Ghanem, Maroun; Dehoux, Thomas; Liu, Liwang; Le Saux, Guillaume; Plawinski, Laurent; Durrieu, Marie-Christine; Audoin, Bertrand

    2018-01-01

    Laser-generated GHz-ultrasonic-based technologies have shown the ability to image single cell adhesion and stiffness simultaneously. Using this new modality, we here demonstrate quantitative indicators to investigate contact mechanics and adhesion processes of the cell. We cultured human cells on a rigid substrate, and we used an inverted pulsed opto-acoustic microscope to generate acoustic pulses containing frequencies up to 100 GHz in the substrate. We map the reflection of the acoustic pulses at the cell-substrate interface to obtain images of the acoustic impedance of the cell, Zc, as well as of the stiffness of the interface, K, with 1 μm lateral resolution. Our results show that the standard deviation ΔZc reveals differences between different cell types arising from the multiplicity of local conformations within the nucleus. From the distribution of K-values within the nuclear region, we extract a mean interfacial stiffness, Km, that quantifies the average contact force in areas of the cell displaying weak bonding. By analogy with classical contact mechanics, we also define the ratio of the real to nominal contact areas, Sr/St. We show that Km can be interpreted as a quantitative indicator of passive contact at metal-cell interfaces, while Sr/St is sensitive to active adhesive processes in the nuclear region. The ability to separate the contributions of passive and active adhesion processes should allow gaining insight into cell-substrate interactions, with important applications in tissue engineering.

  6. Growth behavior in plant cell cultures based on emissions detected by a multisensor array.

    Science.gov (United States)

    Komaraiah, Palle; Navratil, Marian; Carlsson, Maria; Jeffers, Paul; Brodelius, Maria; Brodelius, Peter E; Kieran, Patricia M; Mandenius, Carl-Fredrik

    2004-01-01

    The use of a multisensor array based on chemical gas sensors to monitor plant cell cultures is described. The multisensor array, also referred to as an electronic nose, consisted of 19 different metal oxide semiconductor sensors and one carbon dioxide sensor. The device was used to continuously monitor the off-gas from two plant cell suspension cultures, Morinda citrifolia and Nicotiana tabacum, cultivated under batch conditions. By analyzing the multiarray responses using two pattern recognition methods, principal component analysis and artificial neural networks, it was possible to monitor the course of the cultivations and, in turn, to predict (1) the biomass concentration in both systems and (2) the formation of the secondary metabolite, antraquinone, by M. citrifolia. The results identify the multisensor array method as a potentially useful analytical tool for monitoring plant process variables that are otherwise difficult to analyze on-line.

  7. 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.

  8. Stochastic model explains formation of cell arrays on H/O-diamond patterns

    Czech Academy of Sciences Publication Activity Database

    Ukraintsev, Egor; Brož, A.; Hubálek Kalbáčová, M.; Kromka, Alexander; Rezek, Bohuslav

    2015-01-01

    Roč. 10, č. 4 (2015), "041006-1"-"041006-9" ISSN 1934-8630 R&D Projects: GA ČR GA15-01687S Institutional support: RVO:68378271 Keywords : cell migration * biofilm array * diamond surface * stochastic simulations Subject RIV: BO - Biophysics Impact factor: 2.105, year: 2015

  9. 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-...

  10. Directing Stem Cell Differentiation via Electrochemical Reversible Switching between Nanotubes and Nanotips of Polypyrrole Array.

    Science.gov (United States)

    Wei, Yan; Mo, Xiaoju; Zhang, Pengchao; Li, Yingying; Liao, Jingwen; Li, Yongjun; Zhang, Jinxing; Ning, Chengyun; Wang, Shutao; Deng, Xuliang; Jiang, Lei

    2017-06-27

    Control of stem cell behaviors at solid biointerfaces is critical for stem-cell-based regeneration and generally achieved by engineering chemical composition, topography, and stiffness. However, the influence of dynamic stimuli at the nanoscale from solid biointerfaces on stem cell fate remains unclear. Herein, we show that electrochemical switching of a polypyrrole (Ppy) array between nanotubes and nanotips can alter surface adhesion, which can strongly influence mechanotransduction activation and guide differentiation of mesenchymal stem cells (MSCs). The Ppy array, prepared via template-free electrochemical polymerization, can be reversibly switched between highly adhesive hydrophobic nanotubes and poorly adhesive hydrophilic nanotips through an electrochemical oxidation/reduction process, resulting in dynamic attachment and detachment to MSCs at the nanoscale. Multicyclic attachment/detachment of the Ppy array to MSCs can activate intracellular mechanotransduction and osteogenic differentiation independent of surface stiffness and chemical induction. This smart surface, permitting transduction of nanoscaled dynamic physical inputs into biological outputs, provides an alternative to classical cell culture substrates for regulating stem cell fate commitment. This study represents a general strategy to explore nanoscaled interactions between stem cells and stimuli-responsive surfaces.

  11. 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.

  12. Patterned arrays for the efficient detection of whole cells

    Science.gov (United States)

    Alexander, Troy A.

    2006-10-01

    Surface-Enhanced-Raman-Spectroscopy (SERS) is potentially a very sensitive technique for the detection of biological agents (i.e., proteins, viruses or whole cell bacteria). However, since initial reports, its utility has not been realized. Its limited acceptance as a routine analysis technique for both chemical and biological agents is largely due to the lack of reproducible SERS-active substrates. Most established SERS substrate fabrication schemes are based on selfassembly of the metallic (typically, Au, Ag, Pt, Pd or Cu) surfaces responsible for enhancement. Further, these protocols do not lend themselves to the stringent control over the enhancing feature shape, size, and placement on a nanometer scale. SERS can be made a more robust and attractive spectroscopic technique for biological agents by developing quantifiable, highly sensitive, and highly selective SERS-active substrates. Recently, novel SERS-active substrates, fabricated from nano-patterned Si and Au have been commercialized and are easily obtained in the marketplace. Commercialized Au SERS-active substrates fabricated using semiconductor manipulation and routine metal vapor deposition techniques used for the spectral analysis of intact bacterial cells. This talk will focus on the substrate characterization (microscopic and spectral) and application towards whole cells.

  13. Genome-wide array-CGH analysis reveals YRF1 gene copy number variation that modulates genetic stability in distillery yeasts.

    Science.gov (United States)

    Deregowska, Anna; Skoneczny, Marek; Adamczyk, Jagoda; Kwiatkowska, Aleksandra; Rawska, Ewa; Skoneczna, Adrianna; Lewinska, Anna; Wnuk, Maciej

    2015-10-13

    Industrial yeasts, economically important microorganisms, are widely used in diverse biotechnological processes including brewing, winemaking and distilling. In contrast to a well-established genome of brewer's and wine yeast strains, the comprehensive evaluation of genomic features of distillery strains is lacking. In the present study, twenty two distillery yeast strains were subjected to electrophoretic karyotyping and array-based comparative genomic hybridization (array-CGH). The strains analyzed were assigned to the Saccharomyces sensu stricto complex and grouped into four species categories: S. bayanus, S. paradoxus, S. cerevisiae and S. kudriavzevii. The genomic diversity was mainly revealed within subtelomeric regions and the losses and/or gains of fragments of chromosomes I, III, VI and IX were the most frequently observed. Statistically significant differences in the gene copy number were documented in six functional gene categories: 1) telomere maintenance via recombination, DNA helicase activity or DNA binding, 2) maltose metabolism process, glucose transmembrane transporter activity; 3) asparagine catabolism, cellular response to nitrogen starvation, localized in cell wall-bounded periplasmic space, 4) siderophore transport, 5) response to copper ion, cadmium ion binding and 6) L-iditol 2- dehydrogenase activity. The losses of YRF1 genes (Y' element ATP-dependent helicase) were accompanied by decreased level of Y' sequences and an increase in DNA double and single strand breaks, and oxidative DNA damage in the S. paradoxus group compared to the S. bayanus group. We postulate that naturally occurring diversity in the YRF1 gene copy number may promote genetic stability in the S. bayanus group of distillery yeast strains.

  14. Computer modeling of inversion layer MOS solar cells and arrays

    Science.gov (United States)

    Ho, Fat Duen

    1991-02-01

    A two dimensional numerical model of the inversion layer metal insulator semiconductor (IL/MIS) solar cell is proposed by using the finite element method. The two-dimensional current flow in the device is taken into account in this model. The electrostatic potential distribution, the electron concentration distribution, and the hole concentration distribution for different terminal voltages are simulated. The results of simple calculation are presented. The existing problems for this model are addressed. Future work is proposed. The MIS structures are studied and some of the results are reported.

  15. Interfacing Inorganic Nanowire Arrays and Living Cells for Cellular Function Analysis.

    Science.gov (United States)

    Kwak, Minsuk; Han, Lin; Chen, Jonathan J; Fan, Rong

    2015-11-11

    Inorganic nanowires are among the most attractive functional materials, which have emerged in the past two decades. They have demonstrated applications in information technology and energy conversion, but their utility in biological or biomedical research remains relatively under-explored. Although nanowire-based sensors have been frequently reported for biomolecular detection, interfacing nanowire arrays and living mammalian cells for the direct analysis of cellular functions is a very recent endeavor. Cell-penetrating nanowires enabled effective delivery of biomolecules, electrical and optical stimulation and recording of intracellular signals over a long period of time. Non-penetrating, high-density nanowire arrays display rich interactions between the nanostructured substrate and the micro/nanoscale features of cell surfaces. Such interactions enable efficient capture of rare cells including circulating tumor cells and trafficking leukocytes from complex biospecimens. It also serves as a platform for probing cell traction force and neuronal guidance. The most recent advances in the field that exploits nanowire arrays (both penetrating and non-penetrating) to perform rapid analysis of cellular functions potentially for disease diagnosis and monitoring are reviewed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. High-content analysis screening for cell cycle regulators using arrayed synthetic crRNA libraries.

    Science.gov (United States)

    Strezoska, Žaklina; Perkett, Matthew R; Chou, Eldon T; Maksimova, Elena; Anderson, Emily M; McClelland, Shawn; Kelley, Melissa L; Vermeulen, Annaleen; Smith, Anja van Brabant

    2017-06-10

    The CRISPR-Cas9 system has been utilized for large-scale, loss-of-function screens mainly using lentiviral pooled formats and cell-survival phenotypic assays. Screening in an arrayed format expands the types of phenotypic readouts that can be used to now include high-content, morphology-based assays, and with the recent availability of synthetic crRNA libraries, new studies are emerging. Here, we use a cell cycle reporter cell line to perform an arrayed, synthetic crRNA:tracrRNA screen targeting 169 genes (>600 crRNAs) and used high content analysis (HCA) to identify genes that regulate the cell cycle. Seven parameters were used to classify cells into cell cycle categories and multiple parameters were combined using a new analysis technique to identify hits. Comprehensive hit follow-up experiments included target gene expression analysis, confirmation of DNA insertions/deletions, and validation with orthogonal reagents. Our results show that most hits had three or more independent crRNAs per gene that demonstrated a phenotype with consistent individual parameters, indicating that our screen produced high-confidence hits with low off-target effects and allowed us to identify hits with more subtle phenotypes. The results of our screen demonstrate the power of using arrayed, synthetic crRNAs for functional phenotypic screening using multiparameter HCA assays. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  17. 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.

  18. High-resolution Antibody Array Analysis of Childhood Acute Leukemia Cells*

    Science.gov (United States)

    Kanderova, Veronika; Kuzilkova, Daniela; Stuchly, Jan; Vaskova, Martina; Brdicka, Tomas; Fiser, Karel; Hrusak, Ondrej; Lund-Johansen, Fridtjof

    2016-01-01

    Acute leukemia is a disease pathologically manifested at both genomic and proteomic levels. Molecular genetic technologies are currently widely used in clinical research. In contrast, sensitive and high-throughput proteomic techniques for performing protein analyses in patient samples are still lacking. Here, we used a technology based on size exclusion chromatography followed by immunoprecipitation of target proteins with an antibody bead array (Size Exclusion Chromatography-Microsphere-based Affinity Proteomics, SEC-MAP) to detect hundreds of proteins from a single sample. In addition, we developed semi-automatic bioinformatics tools to adapt this technology for high-content proteomic screening of pediatric acute leukemia patients. To confirm the utility of SEC-MAP in leukemia immunophenotyping, we tested 31 leukemia diagnostic markers in parallel by SEC-MAP and flow cytometry. We identified 28 antibodies suitable for both techniques. Eighteen of them provided excellent quantitative correlation between SEC-MAP and flow cytometry (p leukemia. In this assay, we used 632 different antibodies and detected 501 targets. Of those, 47 targets were differentially expressed between at least two of the three acute leukemia subgroups. The CD markers correlated with immunophenotypic categories as expected. From non-CD markers, we found DBN1, PAX5, or PTK2 overexpressed in B-cell precursor acute lymphoblastic leukemias, LAT, SH2D1A, or STAT5A overexpressed in T-cell acute lymphoblastic leukemias, and HCK, GLUD1, or SYK overexpressed in acute myeloid leukemias. In addition, OPAL1 overexpression corresponded to ETV6-RUNX1 chromosomal translocation. In summary, we demonstrated that SEC-MAP technology is a powerful tool for detecting hundreds of proteins in clinical samples obtained from pediatric acute leukemia patients. It provides information about protein size and reveals differences in protein expression between particular leukemia subgroups. Forty-seven of SEC-MAP identified

  19. Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

    Science.gov (United States)

    Mueller, Nikola S.; Krumsiek, Jan; Theis, Fabian J.; Böhm, Christian; Meyer-Bäse, Anke

    2011-06-01

    Advances in high-throughput measurements of biological specimens necessitate the development of biologically driven computational techniques. To understand the molecular level of many human diseases, such as cancer, lipid quantifications have been shown to offer an excellent opportunity to reveal disease-specific regulations. The data analysis of the cell lipidome, however, remains a challenging task and cannot be accomplished solely based on intuitive reasoning. We have developed a method to identify a lipid correlation network which is entirely disease-specific. A powerful method to correlate experimentally measured lipid levels across the various samples is a Gaussian Graphical Model (GGM), which is based on partial correlation coefficients. In contrast to regular Pearson correlations, partial correlations aim to identify only direct correlations while eliminating indirect associations. Conventional GGM calculations on the entire dataset can, however, not provide information on whether a correlation is truly disease-specific with respect to the disease samples and not a correlation of control samples. Thus, we implemented a novel differential GGM approach unraveling only the disease-specific correlations, and applied it to the lipidome of immortal Glioblastoma tumor cells. A large set of lipid species were measured by mass spectrometry in order to evaluate lipid remodeling as a result to a combination of perturbation of cells inducing programmed cell death, while the other perturbations served solely as biological controls. With the differential GGM, we were able to reveal Glioblastoma-specific lipid correlations to advance biomedical research on novel gene therapies.

  20. 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.

  1. Poisson statistics-mediated particle/cell counting in microwell arrays.

    Science.gov (United States)

    Ahrberg, Christian D; Lee, Jong Min; Chung, Bong Geun

    2018-02-05

    Precise determination of particle or cell numbers is of importance for a wide array of applications in environmental studies, medical and biological applications, or manufacturing and monitoring applications in industrial production processes. A number of techniques ranging from manual counting to sophisticated equipment (e.g., flow cytometry) are available for this task. However, these methods are either labour intensive, prone to error, or require expensive equipment. Here, we present a fast, simple method for determining the number density of cells or microparticles using a microwell array. We analyze the light transmission of the microwells and categorize the microwells into two groups. As particles/cells contained in a microwell locally reduce the light transmission, these wells displayed a lower average transmission compared to unoccupied microwells. The number density of particles/cells can be calculated by Poisson statistics from the ratio of occupied to unoccupied microwells. Following this approach, the number densities of two different types of microparticles, as well as HeLa and E. Coli cells, ranging over four orders of magnitude were determined. Through the microwell array defined by microfabrication, a simple image recognition algorithm can be used with the formation of aggregates or irregular shaped samples providing no additional difficulty to the microwell recognition. Additionally, this method can be carried out using only simple equipment and data analysis automated by a computer program.

  2. Discrimination of micromass-induced chondrocytes from human mesenchymal stem cells by focal plane array-Fourier transform infrared microspectroscopy.

    Science.gov (United States)

    Chonanant, Chirapond; Bambery, Keith R; Jearanaikoon, Nichada; Chio-Srichan, Sirinart; Limpaiboon, Temduang; Tobin, Mark J; Heraud, Philip; Jearanaikoon, Patcharee

    2014-12-01

    Rapid and sensitive methods for identifying stem cell differentiation state are required for facilitating future stem cell therapies. We aimed to evaluate the capability of focal plane array-Fourier transform infrared (FPA-FTIR) microspectroscopy for characterising the differentiation of chondrocytes from human mesenchymal stem cells (hMSCs). Successful induction was validated by reverse transcription polymerase chain reaction (RT-PCR) and Western blot analysis for collagen and aggrecan expression as chondrocyte markers in parallel with the spectroscopy. Spectra derived from chondrocyte-induced cells revealed strong IR absorbance bands attributed to collagen near 1338 and 1234 cm(-1) and proteoglycan at 1245 and 1175-960 cm(-1) compared to the non-induced cells. In addition, spectra from control and induced cells are segregated into separate clusters in partial least squares discriminant analysis score plots at the very early stages of induction and discrimination of an independent set of validation spectra with 100% accuracy. The predominant bands responsible for this discrimination were associated with collagen and aggrecan protein concordant with those obtained from RT-PCR and Western blot techniques. Our findings support the capability of FPA-FTIR microspectroscopy as a label-free tool for stem cell characterization allowing rapid and sensitive detection of macromolecular changes during chondrogenic differentiation. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Microbioreactor arrays for full factorial screening of exogenous and paracrine factors in human embryonic stem cell differentiation.

    Directory of Open Access Journals (Sweden)

    Drew M Titmarsh

    Full Text Available Timed exposure of pluripotent stem cell cultures to exogenous molecules is widely used to drive differentiation towards desired cell lineages. However, screening differentiation conditions in conventional static cultures can become impractical in large parameter spaces, and is intrinsically limited by poor spatiotemporal control of the microenvironment that also makes it impossible to determine whether exogenous factors act directly or through paracrine-dependent mechanisms. We detail here the development of a continuous flow microbioreactor array platform that combines full-factorial multiplexing of input factors with progressive accumulation of paracrine factors through serially-connected culture chambers, and further, the use of this system to explore the combinatorial parameter space of both exogenous and paracrine factors involved in human embryonic stem cell (hESC differentiation to a MIXL1-GFP(+ primitive streak-like population. We show that well known inducers of primitive streak (BMP, Activin and Wnt signals do not simply act directly on hESC to induce MIXL1 expression, but that this requires accumulation of surplus, endogenous factors; and, that conditioned medium or FGF-2 supplementation is able to offset this. Our approach further reveals the presence of a paracrine, negative feedback loop to the MIXL1-GFP(+ population, which can be overcome with GSK-3β inhibitors (BIO or CHIR99021, implicating secreted Wnt inhibitory signals such as DKKs and sFRPs as candidate effectors. Importantly, modulating paracrine effects identified in microbioreactor arrays by supplementing FGF-2 and CHIR in conventional static culture vessels resulted in improved differentiation outcomes. We therefore demonstrate that this microbioreactor array platform uniquely enables the identification and decoding of complex soluble factor signalling hierarchies, and that this not only challenges prevailing strategies for extrinsic control of hESC differentiation, but

  4. Capture, isolation and release of cancer cells with aptamer-functionalized glass bead array.

    Science.gov (United States)

    Wan, Yuan; Liu, Yaling; Allen, Peter B; Asghar, Waseem; Mahmood, M Arif Iftakher; Tan, Jifu; Duhon, Holli; Kim, Young-tae; Ellington, Andrew D; Iqbal, Samir M

    2012-11-21

    Early detection and isolation of circulating tumor cells (CTC) can enable better prognosis for cancer patients. A Hele-Shaw device with aptamer functionalized glass beads is designed, modeled, and fabricated to efficiently isolate cancer cells from a cellular mixture. The glass beads are functionalized with anti-epidermal growth factor receptor (EGFR) aptamer and sit in ordered array of pits in polydimethylsiloxane (PDMS) channel. A PDMS encapsulation is then used to cover the channel and to flow through cell solution. The beads capture cancer cells from flowing solution depicting high selectivity. The cell-bound glass beads are then re-suspended from the device surface followed by the release of 92% cells from glass beads using combination of soft shaking and anti-sense RNA. This approach ensures that the cells remain in native state and undisturbed during capture, isolation and elution for post-analysis. The use of highly selective anti-EGFR aptamer with the glass beads in an array and subsequent release of cells with antisense molecules provide multiple levels of binding and release opportunities that can help in defining new classes of CTC enumeration devices.

  5. Identification of T-cell epitopes using ELISpot and peptide pool arrays.

    Science.gov (United States)

    Tobery, Timothy W; Caulfield, Michael J

    2004-01-01

    Here we describe a method for T-cell epitope identification using a modified ELISpot assay that is both simple and efficient. By using a carefully constructed array of pools of overlapping peptides spanning the entire antigen sequence to stimulate T-cell responses, we are able to detect antigen-specific cytokine responses by both CD8+ and CD4+ T cells and identify the specific peptides to which the cells are responding. Additionally, by performing magnetic bead depletion of either CD8+ or CD4+ cells prior to the assay, we are able to determine the phenotype of the responding cells to each of the peptide epitopes identified. Use of this method will allow the identification of both CD4+ and CD8+ T-cell epitopes without the need for MHC allele-matched reagents and without the need for highly specialized instrumentation. By using an array of peptide pools, this method also dramatically reduces the number of immune cells required to test the entire antigen sequence, often a limiting factor in vaccine testing and other studies.

  6. Parallel alignment of bacteria using near-field optical force array for cell sorting

    Science.gov (United States)

    Zhao, H. T.; Zhang, Y.; Chin, L. K.; Yap, P. H.; Wang, K.; Ser, W.; Liu, A. Q.

    2017-08-01

    This paper presents a near-field approach to align multiple rod-shaped bacteria based on the interference pattern in silicon nano-waveguide arrays. The bacteria in the optical field will be first trapped by the gradient force and then rotated by the scattering force to the equilibrium position. In the experiment, the Shigella bacteria is rotated 90 deg and aligned to horizontal direction in 9.4 s. Meanwhile, 150 Shigella is trapped on the surface in 5 min and 86% is aligned with angle < 5 deg. This method is a promising toolbox for the research of parallel single-cell biophysical characterization, cell-cell interaction, etc.

  7. Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples.

    Science.gov (United States)

    Zhou, Qinghua; Wu, Shen-Yin; Amato, Katherine; DiAdamo, Autumn; Li, Peining

    2016-03-20

    Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene-dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genomic hybridization (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate (ADR) of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis (IPA) was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomal trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization (FISH) testing with probes of chromosomes X/Y/18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples. Copyright © 2016 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

  8. Aluminum oxide passivated radial junction sub-micrometre pillar array textured silicon solar cells

    Science.gov (United States)

    Pudasaini, Pushpa Raj; Elam, David; Ayon, Arturo A.

    2013-06-01

    We report radial, p-n junction, sub-micrometre, pillar array textured solar cells, fabricated on an n-type Czochralski silicon wafer. Relatively simple processing schemes such as metal-assisted chemical etching and spin on dopant techniques were employed for the fabrication of the proposed solar cells. Atomic layer deposition (ALD) grown aluminum oxide (Al2O3) was employed as a surface passivation layer on the B-doped emitter surface. In spite of the fact that the sub-micrometre pillar array textured surface has a relatively high surface-to-volume ratio, we observed an open circuit voltage (VOC) and a short circuit current density (JSC) as high as 572 mV and 29.9 mA cm-2, respectively, which leads to a power conversion efficiency in excess of 11.30%, for the optimized structure of the solar cell described herein. Broadband omnidirectional antireflection effects along with the light trapping property of the sub-micrometre, pillar array textured surface and the excellent passivation quality of the ALD-grown Al2O3 on the B-doped emitter surface were responsible for the enhanced electrical performance of the proposed solar cells.

  9. Development of the nanotiter plate for use in antibody and cell array technologies

    Science.gov (United States)

    Ramdutt, Devin; Lui, Rodney; Davies, Kerrie; Boswell, Rod W.; dos Remedios, Cristobal G.; Charles, Christine; Bilek, Marcela M.; McKenzie, David R.

    2005-02-01

    The design and fabrication of biomedical tools using techniques common in microelectronics is becoming established procedure. In our research, we use gaseous plasma dry etching to form microstructures on silicon wafers. These are intended for use in capturing and binding antibodies and live cells in an array to be used in High Throughput Screening (HTS) and High Content Screening (HCS) of new pharmaceuticals. We call this new arraying plate the "Nanotiter" plate. The benefit of our design (100 x 100 wells in a 25 x 25 mm array) over current 96-, 384- and 1056-well microtiter plates are that the number of samples (wells) that can be tested in one plate scan can be substantially increased, the wells can be rapidly and effectively washed, and the well surfaces can be modified to modulate ligand binding. Simple crowding of wells on a plate can result in cross contamination of samples in adjacent wells during the washing. Furthermore, motile cells may migrate between the wells. 1056 microtiter plates currently cannot be washed, and washing 384 plates is problematic. Our design incorporates plasma-deposited polymers that functionally bind antibodies (or other proteins) in but not between wells. Furthermore, the wells can be shaped to minimize cell migration. Inverting the plate on a wash solution allows unbound cells to simply fall away under gravity thus minimising the contamination of adjacent wells. Thus, our Nanotiter plate represents a substantial improvement over existing technology.

  10. Plasmonic Photovoltaic Cells with Dual-Functional Gold, Silver, and Copper Half-Shell Arrays.

    Science.gov (United States)

    Wu, Ling; Kim, Gyu Min; Nishi, Hiroyasu; Tatsuma, Tetsu

    2017-09-12

    Solid-state photovoltaic cells based on plasmon-induced charge separation (PICS) have attracted growing attention during the past decade. However, the power conversion efficiency (PCE) of the previously reported devices, which are generally loaded with dispersed metal nanoparticles as light absorbers, has not been sufficiently high. Here we report simpler plasmonic photovoltaic cells with interconnected Au, Ag, and Cu half-shell arrays deposited on SiO 2 @TiO 2 colloidal crystals, which serve both as a plasmonic light absorber and as a current collector. The well-controlled and easily prepared plasmonic structure allows precise comparison of the PICS efficiency between different plasmonic metal species. The cell with the Ag half-shell array has higher photovoltaic performance than the cells with Au and Cu half-shell arrays because of the high population of photogenerated energetic electrons, which gives a high electron injection efficiency and suppressed charge recombination probability, achieving the highest PCE among the solid-state PICS devices even without a hole transport layer.

  11. Study of the magnetization behavior of ferromagnetic nanowire array: Existence of growth defects revealed by micromagnetic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen Vien, G., E-mail: gilles.nguyen@univ-brest.fr [Laboratoire de Magnétisme de Bretagne, EA 4522, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France); Rioual, S. [Laboratoire de Magnétisme de Bretagne, EA 4522, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France); Gloaguen, F. [Chimie, Electrochimie Moléculaires et Chimie Analytique, UMR CNRS 6521, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France); Rouvellou, B.; Lescop, B. [Laboratoire de Magnétisme de Bretagne, EA 4522, Université de Bretagne Occidentale, CS 93837, 29238 Brest-Cedex 3 (France)

    2016-03-01

    High aspect ratio nanowires were electrodeposited in nanoporous anodic alumina template by a potentiostatic method. The angular dependence of the coercive field and remanence magnetization extracted from magnetometry measurements are compared with micromagnetic simulations. Inclusion of magnetostatic interactions between Ni nanowires in simulations is required to explain some of the properties of the magnetization reversal. However, it is not sufficient to reproduce fully the angular dependence of the coercive field. Due to the polycrystalline nature of nanowires and thus to the presence of grain boundaries, defects are included in simulations. A good agreement between theory and experiment is then clearly highlighted, in particular in the nanowire easy axis direction. The achieved results allow a description of several experimental data published in the literature and consequently to get a better understanding of reversal mechanisms that operate in such nanowire arrays. A complementary study of composite nanowire array is successfully performed to prove the adequacy of the simulations method to describe the magnetic properties of nanowire array. - Highlights: • High axial squareness nanowire array are synthetized by a potentiostatic method. • Nanowires are modeled as non-ideal magnetic particles. • Segmentation of nanowire is required to describe the angular dependence of coercivity. • Respective role of magnetostatic coupling and nanowire segmentation in nanowire array are studied. • Micromagnetic simulations lead to quantitative agreement for well-defined composite nanowire array.

  12. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.

    Science.gov (United States)

    Pei, Weike; Feyerabend, Thorsten B; Rössler, Jens; Wang, Xi; Postrach, Daniel; Busch, Katrin; Rode, Immanuel; Klapproth, Kay; Dietlein, Nikolaus; Quedenau, Claudia; Chen, Wei; Sauer, Sascha; Wolf, Stephan; Höfer, Thomas; Rodewald, Hans-Reimer

    2017-08-24

    Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure.

  13. Handheld mechanical cell lysis chip with ultra-sharp silicon nano-blade arrays for rapid intracellular protein extraction.

    Science.gov (United States)

    Yun, Sung-Sik; Yoon, Sang Youl; Song, Min-Kyung; Im, Sin-Hyeog; Kim, Sohee; Lee, Jong-Hyun; Yang, Sung

    2010-06-07

    This paper presents a handheld mechanical cell lysis chip with ultra-sharp nano-blade arrays fabricated by simple and cost effective crystalline wet etching of (110) silicon. The ultra-sharp nano-blade array is simply formed by the undercutting of (110) silicon during the crystalline wet etching process. Cells can be easily disrupted by the silicon nano-blade array without the help of additional reagents or electrical sources. Based on the bench-top test of the proposed device, a handheld mechanical cell lysis chip with the nano-blade arrays is designed and fabricated for direct connection to a commercial syringe. The direct connection to a syringe provides rapid cell lysis, easy handling, and minimization of the lysate dead volume. The protein concentration in the cell lysate obtained by the proposed lysis chip is quantitatively comparable to the one prepared by a conventional chemical lysis method.

  14. 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

    Nanowires (NWs) are attracting more and more interest due to their potential cellular applications, such as delivery of compounds or sensing platforms. Arrays of vertical indium-arsenide (InAs) NWs are interfaced with human embryonic kidney cells and rat embryonic dorsal root ganglion neurons....... 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...

  15. 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...... platform will be used for high-throughput identification of combinatorial and native-like scaffolds for tissue engineering of functional organs....

  16. Characterization of a Ga-assisted GaAs nanowire array solar cell on si substrate

    DEFF Research Database (Denmark)

    Boulanger, J. P.; Chia, A. C. E.; Wood, B.

    2016-01-01

    A single-junction core-shell GaAs nanowire (NW) solar cell on Si (1 1 1) substrates is presented. A Ga-assisted vapor–liquid–solid growth mechanism was used for the formation of a patterned array of radial p-i-n GaAs NWs encapsulated in AlInP passivation. Novel device fabrication utilizing facet......-dependent properties to minimize passivation layer removal for electrical contacting is demonstrated. Thorough electrical characterization and analysis of the cell is reported. The electrostatic potential distribution across the radial p-i-n junction GaAs NW is investigated by off-axis electron holography....

  17. Parallel recognition of cancer cells using an addressable array of solid-state micropores.

    Science.gov (United States)

    Ilyas, Azhar; Asghar, Waseem; Kim, Young-tae; Iqbal, Samir M

    2014-12-15

    Early stage detection and precise quantification of circulating tumor cells (CTCs) in the peripheral blood of cancer patients are important for early diagnosis. Early diagnosis improves the effectiveness of the therapy and results in better prognosis. Several techniques have been used for CTC detection but are limited by their need for dye tagging, low throughput and lack of statistical reliability at single cell level. Solid-state micropores can characterize each cell in a sample providing interesting information about cellular populations. We report a multi-channel device which utilized solid-state micropores array assembly for simultaneous measurement of cell translocation. This increased the throughput of measurement and as the cells passed the micropores, tumor cells showed distinctive current blockade pulses, when compared to leukocytes. The ionic current across each micropore channel was continuously monitored and recorded. The measurement system not only increased throughput but also provided on-chip cross-relation. The whole blood was lysed to get rid of red blood cells, so the blood dilution was not needed. The approach facilitated faster processing of blood samples with tumor cell detection efficiency of about 70%. The design provided a simple and inexpensive method for rapid and reliable detection of tumor cells without any cell staining or surface functionalization. The device can also be used for high throughput electrophysiological analysis of other cell types. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. 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...

  19. Dynamic transcriptional signature and cell fate analysis reveals plasticity of individual neural plate border cells.

    Science.gov (United States)

    Roellig, Daniela; Tan-Cabugao, Johanna; Esaian, Sevan; Bronner, Marianne E

    2017-03-29

    The 'neural plate border' of vertebrate embryos contains precursors of neural crest and placode cells, both defining vertebrate characteristics. How these lineages segregate from neural and epidermal fates has been a matter of debate. We address this by performing a fine-scale quantitative temporal analysis of transcription factor expression in the neural plate border of chick embryos. The results reveal significant overlap of transcription factors characteristic of multiple lineages in individual border cells from gastrula through neurula stages. Cell fate analysis using a Sox2 (neural) enhancer reveals that cells that are initially Sox2+ cells can contribute not only to neural tube but also to neural crest and epidermis. Moreover, modulating levels of Sox2 or Pax7 alters the apportionment of neural tube versus neural crest fates. Our results resolve a long-standing question and suggest that many individual border cells maintain ability to contribute to multiple ectodermal lineages until or beyond neural tube closure.

  20. Electro-Deformation of Fused Cells in a Microfluidic Array Device

    Directory of Open Access Journals (Sweden)

    Yan Liu

    2016-11-01

    Full Text Available We present a new method of analyzing the deformability of fused cells in a microfluidic array device. Electrical stresses—generated by applying voltages (4–20 V across discrete co-planar microelectrodes along the side walls of a microfluidic channel—have been used to electro-deform fused and unfused stem cells. Under an electro-deformation force induced by applying an alternating current (AC signal, we observed significant electro-deformation phenomena. The experimental results show that the fused stem cells were stiffer than the unfused stem cells at a relatively low voltage (<16 V. However, at a relatively high voltage, the fused stem cells were more easily deformed than were the unfused stem cells. In addition, the electro-deformation process is modeled based on the Maxwell stress tensor and structural mechanics of cells. The theoretical results show that a positive correlation is found between the deformation of the cell and the applied voltage, which is consistent with the experimental results. Combined with a numerical analysis and experimental study, the results showed that the significant difference of the deformation ratio of the fused and unfused cells is not due to their size difference. This demonstrates that some other properties of cell membranes (such as the membrane structure were also changed in the electrofusion process, in addition to the size modification of that process.

  1. Hollow nanoneedle array and its utilization for repeated administration of biomolecules to the same cells.

    Science.gov (United States)

    Peer, Elad; Artzy-Schnirman, Arbel; Gepstein, Lior; Sivan, Uri

    2012-06-26

    We present a novel hollow nanoneedle array (NNA) device capable of simultaneously delivering diverse cargo into a group of cells in a culture over prolonged periods. The silica needles are fed by a common reservoir whose content can be replenished and modified in real time while maintaining contact with the same cells. The NNA, albeit its submicrometer features, is fabricated in a silicon-on-insulator wafer using conventional, large scale, silicon technology. 3T3-NIH fibroblast cells and HEK293 human embryonic kidney cells are shown to grow and proliferate successfully on the NNAs. Cargo delivery from the reservoir through the needles to a group of HEK293 cells in the culture is demonstrated by repeated administration of fluorescently labeled dextran to the same cells and transfection with DNA coding for red fluorescent protein. The capabilities demonstrated by the NNA device open the door to large scale studies of the effect of selected cells on their environment as encountered, for instance, in the study of cell-fate decisions, the role of cell-autonomous versus nonautonomous mechanisms in developmental biology, and in the study of excitable cell-networks.

  2. Conical nano-structure arrays of Platinum cathode catalyst for enhanced cell performance in PEMFC (proton exchange membrane fuel cell)

    International Nuclear Information System (INIS)

    Khan, Aziz; Nath, Bhabesh Kumar; Chutia, Joyanti

    2015-01-01

    Conical nanostructure arrays of Pt (Platinum) as cathode catalyst are developed using a novel integrated plasma sputtering technique. The integration method involves successive deposition of Pt catalyst arrays one upon another maintaining a uniform time gap. Deposition by integrated approach results in the formation of dense arrays of Pt nanostructure as compared to continuous deposition. These high number density integrated arrays with low Pt loading of 0.10 mg cm −2 at the cathode provide enhanced performance compared to non-integrated cathode catalyst prepared by continuous deposition and standard commercial electrodes with Pt loadings of 1 mg cm −2 . The performance is compared on the basis of polarization curve measurements and the calculated power density values. PEM fuel cell with dual integrated cathode showed an improved power density of 0.90 W cm −2 , which is higher than continuously deposited cathode catalyst with maximum power density of 0.67 W cm −2 for the same Pt loading of 0.10 mg cm −2 . - Highlights: • Conical nanostructures with high number density are prepared by a novel integrated deposition technique. • Electrode with such catalyst shows maximum performance of 0.9 W cm −2 . • Integrated catalyst performs better than continuously prepared nanostructure catalyst.

  3. Real-time Detection of Breast Cancer Cells Using Peptide-functionalized Microcantilever Arrays

    Science.gov (United States)

    Etayash, Hashem; Jiang, Keren; Azmi, Sarfuddin; Thundat, Thomas; Kaur, Kamaljit

    2015-01-01

    Ligand-directed targeting and capturing of cancer cells is a new approach for detecting circulating tumor cells (CTCs). Ligands such as antibodies have been successfully used for capturing cancer cells and an antibody based system (CellSearch®) is currently used clinically to enumerate CTCs. Here we report the use of a peptide moiety in conjunction with a microcantilever array system to selectively detect CTCs resulting from cancer, specifically breast cancer. A sensing microcantilever, functionalized with a breast cancer specific peptide 18-4 (WxEAAYQrFL), showed significant deflection on cancer cell (MCF7 and MDA-MB-231) binding compared to when exposed to noncancerous (MCF10A and HUVEC) cells. The peptide-functionalized microcantilever allowed efficient capture and detection of cancer cells in MCF7 spiked human blood samples emulating CTCs in human blood. A detection limit of 50–100 cancer cells mL−1 from blood samples was achieved with a capture yield of 80% from spiked whole blood samples. The results emphasize the potential of peptide 18-4 as a novel peptide for capturing and detecting cancer cells in conjunction with nanomechanical cantilever platform. The reported peptide-based cantilever platform represents a new analytical approach that can lead to an alternative to the various detection platforms and can be leveraged to further study CTCs. PMID:26434765

  4. Single-Cell Chemical Lysis on Microfluidic Chips with Arrays of Microwells

    Directory of Open Access Journals (Sweden)

    Nikolay A. Maslov

    2011-12-01

    Full Text Available Many conventional biochemical assays are performed using populations of cells to determine their quantitative biomolecular profiles. However, population averages do not reflect actual physiological processes in individual cells, which occur either on short time scales or nonsynchronously. Therefore, accurate analysis at the single-cell level has become a highly attractive tool for investigating cellular content. Microfluidic chips with arrays of microwells were developed for single-cell chemical lysis in the present study. The cellular occupancy in 30-mm-diameter microwells (91.45% was higher than that in 20-mm-diameter microwells (83.19% at an injection flow rate of 2.8 mL/min. However, most of the occupied 20-mm-diameter microwells contained individual cells. The results of chemical lysis experiments at the single-cell level indicate that cell membranes were gradually lysed as the lysis buffer was injected; they were fully lysed after 12 s. Single-cell chemical lysis was demonstrated in the proposed microfluidic chip, which is suitable for high-throughput cell lysis.

  5. Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions.

    Directory of Open Access Journals (Sweden)

    Weitao Chen

    2016-07-01

    Full Text Available Mating of budding yeast cells is a model system for studying cell-cell interactions. Haploid yeast cells secrete mating pheromones that are sensed by the partner which responds by growing a mating projection toward the source. The two projections meet and fuse to form the diploid. Successful mating relies on precise coordination of dynamic extracellular signals, signaling pathways, and cell shape changes in a noisy background. It remains elusive how cells mate accurately and efficiently in a natural multi-cell environment. Here we present the first stochastic model of multiple mating cells whose morphologies are driven by pheromone gradients and intracellular signals. Our novel computational framework encompassed a moving boundary method for modeling both a-cells and α-cells and their cell shape changes, the extracellular diffusion of mating pheromones dynamically coupled with cell polarization, and both external and internal noise. Quantification of mating efficiency was developed and tested for different model parameters. Computer simulations revealed important robustness strategies for mating in the presence of noise. These strategies included the polarized secretion of pheromone, the presence of the α-factor protease Bar1, and the regulation of sensing sensitivity; all were consistent with data in the literature. In addition, we investigated mating discrimination, the ability of an a-cell to distinguish between α-cells either making or not making α-factor, and mating competition, in which multiple a-cells compete to mate with one α-cell. Our simulations were consistent with previous experimental results. Moreover, we performed a combination of simulations and experiments to estimate the diffusion rate of the pheromone a-factor. In summary, we constructed a framework for simulating yeast mating with multiple cells in a noisy environment, and used this framework to reproduce mating behaviors and to identify strategies for robust cell-cell

  6. 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.

  7. Cellular Homeostasis and Antioxidant Response in Epithelial HT29 Cells on Titania Nanotube Arrays Surface

    Directory of Open Access Journals (Sweden)

    Rabiatul Basria SMN Mydin

    2017-01-01

    Full Text Available Cell growth and proliferative activities on titania nanotube arrays (TNA have raised alerts on genotoxicity risk. Present toxicogenomic approach focused on epithelial HT29 cells with TNA surface. Fledgling cell-TNA interaction has triggered G0/G1 cell cycle arrests and initiates DNA damage surveillance checkpoint, which possibly indicated the cellular stress stimuli. A profound gene regulation was observed to be involved in cellular growth and survival signals such as p53 and AKT expressions. Interestingly, the activation of redox regulator pathways (antioxidant defense was observed through the cascade interactions of GADD45, MYC, CHECK1, and ATR genes. These mechanisms furnish to protect DNA during cellular division from an oxidative challenge, set in motion with XRRC5 and RAD50 genes for DNA damage and repair activities. The cell fate decision on TNA-nanoenvironment has been reported to possibly regulate proliferative activities via expression of p27 and BCL2 tumor suppressor proteins, cogent with SKP2 and BCL2 oncogenic proteins suppression. Findings suggested that epithelial HT29 cells on the surface of TNA may have a positive regulation via cell-homeostasis mechanisms: a careful circadian orchestration between cell proliferation, survival, and death. This nanomolecular knowledge could be beneficial for advanced medical applications such as in nanomedicine and nanotherapeutics.

  8. Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infection.

    Science.gov (United States)

    Matula, Petr; Kumar, Anil; Wörz, Ilka; Erfle, Holger; Bartenschlager, Ralf; Eils, Roland; Rohr, Karl

    2009-04-01

    The identification of eukaryotic genes involved in virus entry and replication is important for understanding viral infection. Our goal is to develop a siRNA-based screening system using cell arrays and high-throughput (HT) fluorescence microscopy. A central issue is efficient, robust, and automated single-cell-based analysis of massive image datasets. We have developed an image analysis approach that comprises (i) a novel, gradient-based thresholding scheme for cell nuclei segmentation which does not require subsequent postprocessing steps for separation of clustered nuclei, (ii) quantification of the virus signal in the neighborhood of cell nuclei, (iii) localization of regions with transfected cells by combining model-based circle fitting and grid fitting, (iv) cell classification as infected or noninfected, and (v) image quality control (e.g., identification of out-of-focus images). We compared the results of our nucleus segmentation approach with a previously developed scheme of adaptive thresholding with subsequent separation of nuclear clusters. Our approach, which does not require a postprocessing step for the separation of nuclear clusters, correctly segmented 97.1% of the nuclei, whereas the previous scheme achieved 95.8%. Using our algorithm for the detection of out-of-focus images, we obtained a high discrimination power of 99.4%. Our overall approach has been applied to more than 55,000 images of cells infected by either hepatitis C or dengue virus. Reduced infection rates were correctly detected in positive siRNA controls, as well as for siRNAs targeting, for example, cellular genes involved in viral infection. Our image analysis approach allows for the automatic and accurate determination of changes in viral infection based on high-throughput single-cell-based siRNA cell array imaging experiments. (c) 2008 International Society for Advancement of Cytometry.

  9. Optical simulations of P3HT/Si nanowire array hybrid solar cells.

    Science.gov (United States)

    Wang, Wenbo; Li, Xinhua; Wen, Long; Zhao, Yufeng; Duan, Huahua; Zhou, Bukang; Shi, Tongfei; Zeng, Xuesong; Li, Ning; Wang, Yuqi

    2014-01-01

    An optical simulation of poly(3-hexylthiophene) (P3HT)/Si nanowire array (NWA) hybrid solar cells was investigated to evaluate the optical design requirements of the system by using finite-difference time-domain (FDTD) method. Steady improvement of light absorption was obtained with increased P3HT coating shell thickness from 0 to 80 nm on Si NWA. Further increasing the thickness caused dramatic decrease of the light absorption. Combined with the analysis of ultimate photocurrents, an optimum geometric structure with a coating P3HT thickness of 80 nm was proposed. At this structure, the hybrid solar cells show the most efficient light absorption. The optimization of the geometric structure and further understanding of the optical characteristics may contribute to the development for the practical experiment of the promising hybrid solar cells.

  10. 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.

  11. Bilateral CMUT Cells and Arrays: Equivalent Circuits, Diffraction Constants, and Substrate Impedance.

    Science.gov (United States)

    Koymen, Hayrettin; Atalar, Abdullah; Tasdelen, A Sinan

    2017-02-01

    We introduce the large-signal and small-signal equivalent circuit models for a capacitive micromachined ultrasonic transducer (CMUT) cell, which has radiating plates on both sides. We present the diffraction coefficient of baffled and unbaffled CMUT cells. We show that the substrate can be modeled as a very thick radiating plate on one side, which can be readily incorporated in the introduced model. In the limiting case, the reactance of this backing impedance is entirely compliant for substrate materials with a Poisson's ratio less than 1/3. We assess the dependence of the radiation performance of the front plate on the thickness of the back plate by simulating an array of bilateral CMUT cells. We find that the small-signal linear model is sufficiently accurate for large-signal excitation, for the purpose of the determining the fundamental component. To determine harmonic distortion, the large-signal model must be used with harmonic balance analysis. Rayleigh-Bloch waves are excited at the front and back surfaces similar to conventional CMUT arrays.

  12. Colony Lysate Arrays for Proteomic Profiling of Drug-Tolerant Persisters of Cancer Cell.

    Science.gov (United States)

    Kume, Kohei; Nishizuka, Satoshi S

    2017-09-05

    Functional heterogeneity of cancer cells is one of the key properties to understanding relapse after drug treatment. Hence, clarification is needed with regard to which types of subgroups of cancer cells dominantly contribute to the initiation of relapse. Recently, we established the colony lysate array (CoLA), which is a method that allows comparison of individual colonies at the protein level to assess the initiation of anticancer drug-tolerant persisters (DTPs) based on the reverse-phase protein array (RPPA) system. DTPs grow in various drug concentrations and types showing 2-dimensional growth (∼1 mm) on a flat surface. The size of DTPs are larger than spheroids (∼0.3 mm) in agarose gel, which makes them easy to handle for a number of assays. DTPs provide functional information during the process of their formation, initiating from the origin of a drug-tolerant single cell. Using >2000 DTPs generated from various drugs and doses profiled on the basis of 44 proteins, we demonstrate that the DTPs are clustered on the basis of their proteomic profiles changing in response to drugs and doses. Of interest, nine transcription factors in the DTPs, such as STAT3 and OCT4A, were identified as having decreased or increased levels of proteins in response to gefitinib. Importantly, these results can be obtained only by individual proteomic colony profiling, which may identify alternative therapeutic targets and biomarkers for DTPs that may harbor critical mechanisms for cancer relapse.

  13. The applicability of DOE solar cell and array technology to space power

    Science.gov (United States)

    Scott-Monck, J. A.; Stella, P. M.; Berman, P. A.

    1980-01-01

    Current trends in terrestrial photovoltaics that might benefit future space power needs are reviewed. Emphasis is placed on the Low-Cost Solar Array Project with attention given to the materials task, the silicon sheet task, the production processes and equipment task, and encapsulation. The Photovoltaic Concentrator Technology Development Project is also discussed. It is concluded that terrestrial photovoltaic technology that has either been developed to date or is currently under development will not have any significant effect on the performance or cost of solar cells and panels for space over the near term (1980-1990).

  14. Anti-reflective microstructure array and its performance evaluation in thin film flexible solar cells

    Science.gov (United States)

    Chen, Fei; Zhan, Xinghua; Gao, Mengyu; Tie, Shengnian; Gao, Wei

    2017-07-01

    The anti-reflective (AR) structure greatly reduces the light reflection. When it is applied on solar cells, it enables more light to be absorbed by the cells, increasing the energy of the incident light and improving the light-to-electricity conversion efficiency. In this study, the optical properties of AR microstructures are investigated followed by the performance evaluation of solar cells. The AR microstructure is arrayed in a uniform and periodic fashion. When it is applied on PMMA, only 1.0% of the light is reflected away while 2.6% of the light is reflected on glass. The angular dependence performance is also improved with AR structure with 9.4% more light absorption, which can increase the effective energy generation duration for the solar cell. The AR structure is applied to amorphous silicon thin film solar cells by nano-imprinting technology. The solar cell with AR structure gained 8.63% more power compared to the conventional solar cells.

  15. Arrayed mutant haploid embryonic stem cell libraries facilitate phenotype-driven genetic screens.

    Science.gov (United States)

    Liu, Guang; Wang, Xue; Liu, Yufang; Zhang, Meili; Cai, Tao; Shen, Zhirong; Jia, Yuyan; Huang, Yue

    2017-12-15

    Forward genetic screens using mammalian embryonic stem (ES) cells have identified genes required for numerous cellular processes. However, loss-of-function screens are more difficult to conduct in diploid cells because, in most cases, both alleles of a gene must be mutated to exhibit a phenotype. Recently, mammalian haploid ES cell lines were successfully established and applied to several recessive genetic screens. However, all these screens were performed in mixed pools of mutant cells and were mainly based on positive selection. In general, negative screening is not easy to apply to these mixed pools, although quantitative deep sequencing of mutagen insertions can help to identify some 'missing' mutants. Moreover, the interplay between different mutant cells in the mixed pools would interfere with the readout of the screens. Here, we developed a method for rapidly generating arrayed haploid mutant libraries in which the proportion of homozygous mutant clones can reach 85%. After screening thousands of individual mutant clones, we identified a number of novel factors required for the onset of differentiation in ES cells. A negative screen was also conducted to discover mutations conferring cells with increased sensitivity to DNA double-strand breaks induced by the drug doxorubicin. Both of these screens illustrate the value of this system. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. 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

  17. 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.

  18. Pseudotemporal Ordering of Single Cells Reveals Metabolic Control of Postnatal β Cell Proliferation.

    Science.gov (United States)

    Zeng, Chun; Mulas, Francesca; Sui, Yinghui; Guan, Tiffany; Miller, Nathanael; Tan, Yuliang; Liu, Fenfen; Jin, Wen; Carrano, Andrea C; Huising, Mark O; Shirihai, Orian S; Yeo, Gene W; Sander, Maike

    2017-05-02

    Pancreatic β cell mass for appropriate blood glucose control is established during early postnatal life. β cell proliferative capacity declines postnatally, but the extrinsic cues and intracellular signals that cause this decline remain unknown. To obtain a high-resolution map of β cell transcriptome dynamics after birth, we generated single-cell RNA-seq data of β cells from multiple postnatal time points and ordered cells based on transcriptional similarity using a new analytical tool. This analysis captured signatures of immature, proliferative β cells and established high expression of amino acid metabolic, mitochondrial, and Srf/Jun/Fos transcription factor genes as their hallmark feature. Experimental validation revealed high metabolic activity in immature β cells and a role for reactive oxygen species and Srf/Jun/Fos transcription factors in driving postnatal β cell proliferation and mass expansion. Our work provides the first high-resolution molecular characterization of state changes in postnatal β cells and paves the way for the identification of novel therapeutic targets to stimulate β cell regeneration. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. A multilevel fast spectral domain algorithm for electromagnetic analysis of infinite periodic arrays with large unit cells

    Directory of Open Access Journals (Sweden)

    T. F. Eibert

    2006-01-01

    Full Text Available A multilevel fast spectral domain algorithm (MLFSDA is introduced for the efficient evaluation of the matrix vector products due to the boundary integral (BI operator within a hybrid finite element - BI (FEBI method for the analysis of infinite periodic arrays. The MLFSDA utilizes the diagonalization property of the spectral domain (SD BI representation and handles the large numbers of Floquet modes required for large (with respect to wavelength periodic unit cells by similar hierarchical techniques as applied in the multilevel fast multipole method/algorithm (MLFMM/MLFMA. With the capability of the MLFSDA to handle very large periodic unit cells, it becomes possible to model finite antennas and scatterers with the infinite periodic array model. For a cavity-backed antenna element and for a semi-finite array of 4 cavity-backed antenna elements in the finite direction, the dependence of the input impedances on the unit cell sizes is investigated and it is found that array resonances disappear for reasonably large unit cell dimensions. Finally, a semi-finite array of antipodal Vivaldi antenna elements is considered and simulation results for infinite periodic, finite, and semi-finite array configurations are compared to measured data.

  20. Analytical Formulation of the Electric Field Induced by Electrode Arrays: Towards Automated Dielectrophoretic Cell Sorting

    Directory of Open Access Journals (Sweden)

    Vladimir Gauthier

    2017-08-01

    Full Text Available Dielectrophoresis is defined as the motion of an electrically polarisable particle in a non-uniform electric field. Current dielectrophoretic devices enabling sorting of cells are mostly controlled in open-loop applying a predefined voltage on micro-electrodes. Closed-loop control of these devices would enable to get advanced functionalities and also more robust behavior. Currently, the numerical models of dielectrophoretic force are too complex to be used in real-time closed-loop control. The aim of this paper is to propose a new type of models usable in this framework. We propose an analytical model of the electric field based on Fourier series to compute the dielectrophoretic force produced by parallel electrode arrays. Indeed, this method provides an analytical expression of the electric potential which decouples the geometrical factors (parameter of our system, the voltages applied on electrodes (input of our system, and the position of the cells (output of our system. Considering the Newton laws on each cell, it enables to generate easily a dynamic model of the cell positions (output function of the voltages on electrodes (input. This dynamic model of our system is required to design the future closed-loop control law. The predicted dielectrophoretic forces are compared to a numerical simulation based on finite element model using COMSOL software. The model presented in this paper enables to compute the dielectrophoretic force applied to a cell by an electrode array in a few tenths of milliseconds. This model could be consequently used in future works for closed-loop control of dielectrophoretic devices.

  1. 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.

  2. Rapid prototyping of arrayed microfluidic systems in polystyrene for cell-based assays

    Science.gov (United States)

    Young, Edmond W.K.; Berthier, Erwin; Guckenberger, David J.; Sackmann, Eric; Lamers, Casey; Meyvantsson, Ivar; Huttenlocher, Anna; Beebe, David J.

    2011-01-01

    Microfluidic cell-based systems have enabled the study of cellular phenomena with improved spatiotemporal control of the microenvironment and at increased throughput. While PDMS has emerged as the most popular material in microfluidics research, it has specific limitations that prevent microfluidic platforms from achieving their full potential. We present here a complete process, ranging from mold design to embossing and bonding, that describes the fabrication of polystyrene (PS) microfluidic devices with similar cost and time expenditures as PDMS-based devices. Emphasis was placed on creating methods that can compete with PDMS fabrication methods in terms of robustness, complexity and time requirements. To achieve this goal several improvements were made to remove critical bottlenecks in existing PS embossing methods. First, traditional lithography techniques were adapted to fabricate bulk epoxy molds capable of resisting high temperatures and pressures. Second, a method was developed to emboss through-holes in a PS layer, enabling creation of large arrays of independent microfluidic systems on a single device without need to manually create access ports. Third, thermal bonding of PS layers was optimized in order to achieve quality bonding over large arrays of microsystems. The choice of materials and methods were validated for biological function using two different cell-based applications to demonstrate the versatility of our streamlined fabrication process. PMID:21261280

  3. 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.

  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. 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)

  7. 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

  8. Inertial picobalance reveals fast mass fluctuations in mammalian cells

    Science.gov (United States)

    Martínez-Martín, David; Fläschner, Gotthold; Gaub, Benjamin; Martin, Sascha; Newton, Richard; Beerli, Corina; Mercer, Jason; Gerber, Christoph; Müller, Daniel J.

    2017-10-01

    The regulation of size, volume and mass in living cells is physiologically important, and dysregulation of these parameters gives rise to many diseases. Cell mass is largely determined by the amount of water, proteins, lipids, carbohydrates and nucleic acids present in a cell, and is tightly linked to metabolism, proliferation and gene expression. Technologies have emerged in recent years that make it possible to track the masses of single suspended cells and adherent cells. However, it has not been possible to track individual adherent cells in physiological conditions at the mass and time resolutions required to observe fast cellular dynamics. Here we introduce a cell balance (a ‘picobalance’), based on an optically excited microresonator, that measures the total mass of single or multiple adherent cells in culture conditions over days with millisecond time resolution and picogram mass sensitivity. Using our technique, we observe that the mass of living mammalian cells fluctuates intrinsically by around one to four per cent over timescales of seconds throughout the cell cycle. Perturbation experiments link these mass fluctuations to the basic cellular processes of ATP synthesis and water transport. Furthermore, we show that growth and cell cycle progression are arrested in cells infected with vaccinia virus, but mass fluctuations continue until cell death. Our measurements suggest that all living cells show fast and subtle mass fluctuations throughout the cell cycle. As our cell balance is easy to handle and compatible with fluorescence microscopy, we anticipate that our approach will contribute to the understanding of cell mass regulation in various cell states and across timescales, which is important in areas including physiology, cancer research, stem-cell differentiation and drug discovery.

  9. 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.

  10. Flexible and twistable non-volatile memory cell array with all-organic one diode-one resistor architecture.

    Science.gov (United States)

    Ji, Yongsung; Zeigler, David F; Lee, Dong Su; Choi, Hyejung; Jen, Alex K-Y; Ko, Heung Cho; Kim, Tae-Wook

    2013-01-01

    Flexible organic memory devices are one of the integral components for future flexible organic electronics. However, high-density all-organic memory cell arrays on malleable substrates without cross-talk have not been demonstrated because of difficulties in their fabrication and relatively poor performances to date. Here we demonstrate the first flexible all-organic 64-bit memory cell array possessing one diode-one resistor architectures. Our all-organic one diode-one resistor cell exhibits excellent rewritable switching characteristics, even during and after harsh physical stresses. The write-read-erase-read output sequence of the cells perfectly correspond to the external pulse signal regardless of substrate deformation. The one diode-one resistor cell array is clearly addressed at the specified cells and encoded letters based on the standard ASCII character code. Our study on integrated organic memory cell arrays suggests that the all-organic one diode-one resistor cell architecture is suitable for high-density flexible organic memory applications in the future.

  11. Optimization of processing parameters on the controlled growth of ZnO nanorod arrays for the performance improvement of solid-state dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Lee, Yi-Mu; Yang, Hsi-Wen

    2011-01-01

    High-transparency and high quality ZnO nanorod arrays were grown on the ITO substrates by a two-step chemical bath deposition (CBD) method. The effects of processing parameters including reaction temperature (25-95 o C) and solution concentration (0.01-0.1 M) on the crystal growth, alignment, optical and electrical properties were systematically investigated. It has been found that these process parameters are critical for the growth, orientation and aspect ratio of the nanorod arrays, showing different structural and optical properties. Experimental results reveal that the hexagonal ZnO nanorod arrays prepared under reaction temperature of 95 o C and solution concentration of 0.03 M possess highest aspect ratio of ∼21, and show the well-aligned orientation and optimum optical properties. Moreover the ZnO nanorod arrays based heterojunction electrodes and the solid-state dye-sensitized solar cells (SS-DSSCs) were fabricated with an improved optoelectrical performance. -- Graphical abstract: The ZnO nanorod arrays demonstrate well-alignment, high aspect ratio (L/D∼21) and excellent optical transmittance by low-temperature chemical bath deposition (CBD). Display Omitted Research highlights: → Investigate the processing parameters of CBD on the growth of ZnO nanorod arrays. → Optimization of CBD process parameters: 0.03 M solution concentration and reaction temperature of 95 o C. → The prepared ZnO samples possess well-alignment and high aspect ratio (L/D∼21). → An n-ZnO/p-NiO heterojunction: great rectifying behavior and low leakage current. → SS-DSSC has J SC of 0.31 mA/cm 2 and V OC of 590 mV, and an improved η of 0.059%.

  12. Enhancement of hydrogenated amorphous silicon solar cells with front-surface hexagonal plasmonic arrays from nanoscale lithography

    Science.gov (United States)

    Zhang, Chenlong; Gwamuri, Jephias; Cvetanovic, Sandra; Sadatgol, Mehdi; Guney, Durdu O.; Pearce, Joshua M.

    2017-07-01

    The study first uses numerical simulations of hexagonal triangle and sphere arrays to optimize the performance of hydrogenated amorphous silicon (a-Si:H) photovoltaic devices. The simulations indicated the potential for a sphere array to provide optical enhancement (OE) up to 7.4% compared to a standard cell using a nanosphere radius of 250 nm and silver film thickness of 50 nm. Next a detailed series of a-Si:H cells were fabricated and tested for quantum efficiency and characteristic and current-voltage (I-V) profiles using a solar simulator. Triangle and sphere array based cells, as well as the uncoated reference cells are analyzed and the results find that the simulation does not precisely predict the observed enhancement, but it forecasts a trend and can be used to guide fabrication. In general, the measured OE follows the simulated trend: (1) for triangular arrays no enhancement is observed and as the silver thickness increases the more degradation of the cell; (2) for annealed arrays both measured and simulated OE occur with the thinner silver thickness. Measured efficiency enhancement reached 20.2% and 10.9% for nanosphere diameter D = 500 nm, silver thicknesses h = 50 nm and 25 nm, respectively. These values, which surpass simulation results, indicate that this method is worth additional investigation.

  13. Alterations in gene array patterns in dendritic cells from aged humans.

    Directory of Open Access Journals (Sweden)

    Jia-ning Cao

    Full Text Available Dendritic cells (DCs are major antigen-presenting cells that play a key role in initiating and regulating innate and adaptive immune responses. DCs are critical mediators of tolerance and immunity. The functional properties of DCs decline with age. The purpose of this study was to define the age-associated molecular changes in DCs by gene array analysis using Affymatrix GeneChips. The expression levels of a total of 260 genes (1.8% were significantly different (144 down-regulated and 116 upregulated in monocyte-derived DCs (MoDCs from aged compared to young human donors. Of the 260 differentially expressed genes, 24% were down-regulated by more than 3-fold, suggesting that a large reduction in expression occurred for a notable number of genes in the aged. Our results suggest that the genes involved in immune response to pathogens, cell migration and T cell priming display significant age-related changes. Furthermore, downregulated genes involved in cell cycle arrest and DNA replication may play a critical role in aging-associated genetic instability. These changes in gene expression provide molecular based evidence for age-associated functional abnormalities in human DCs that may be responsible for the defects in adaptive immunity observed in the elderly.

  14. Thin-film-transistor array: an exploratory attempt for high throughput cell manipulation using electrowetting principle

    Science.gov (United States)

    Shaik, F. Azam; Cathcart, G.; Ihida, S.; Lereau-Bernier, M.; Leclerc, E.; Sakai, Y.; Toshiyoshi, H.; Tixier-Mita, A.

    2017-05-01

    In lab-on-a-chip (LoC) devices, microfluidic displacement of liquids is a key component. electrowetting on dielectric (EWOD) is a technique to move fluids, with the advantage of not requiring channels, pumps or valves. Fluids are discretized into droplets on microelectrodes and moved by applying an electric field via the electrodes to manipulate the contact angle. Micro-objects, such as biological cells, can be transported inside of these droplets. However, the design of conventional microelectrodes, made by standard micro-fabrication techniques, fixes the path of the droplets, and limits the reconfigurability of paths and thus limits the parallel processing of droplets. In that respect, thin film transistor (TFT) technology presents a great opportunity as it allows infinitely reconfigurable paths, with high parallelizability. We propose here to investigate the possibility of using TFT array devices for high throughput cell manipulation using EWOD. A COMSOL based 2D simulation coupled with a MATLAB algorithm was used to simulate the contact angle modulation, displacement and mixing of droplets. These simulations were confirmed by experimental results. The EWOD technique was applied to a droplet of culture medium containing HepG2 carcinoma cells and demonstrated no negative effects on the viability of the cells. This confirms the possibility of applying EWOD techniques to cellular applications, such as parallel cell analysis.

  15. The fine specificity of mannose-binding and galactose-binding lectins revealed using outlier motif analysis of glycan array data.

    Science.gov (United States)

    Maupin, Kevin A; Liden, Daniel; Haab, Brian B

    2012-01-01

    Glycan-binding proteins are commonly used as analytical reagents to detect the levels of specific glycan structures in biological samples. A detailed knowledge of the specificities of glycan-binding proteins is required for properly interpreting their binding data. A powerful technology for characterizing glycan-binding specificity is the glycan array. However, the interpretation of glycan-array data can be difficult due to the complex fine specificities of certain glycan-binding proteins. We developed a systematic approach, called outlier-motif analysis, for extracting fine-specificity information from glycan-array data, and we applied the method to the study of four commonly used lectins: two mannose binders (concanavalin A and Lens culinaris) and two galactose binders (Bauhinia purpurea and peanut agglutinin). The study confirmed the known, primary specificity of each lectin and also revealed new insights into their binding preferences. Lens culinaris's main specificity may be non-terminal, α-linked mannose with a single linkage at its 2' carbon, which is more restricted than previous definitions. We found broader specificity for bauhinea purpurea (BPL) than previously reported, showing that BPL can bind terminal N-acetylgalactosamine (GalNAc) and penultimate β-linked galactose under certain limitations. Peanut agglutinin may bind terminal Galβ1,3Gal, a glycolipid motif, in addition to terminal Galβ1,3GalNAc, a common O-linked glycoprotein motif. These results could be used to more accurately interpret data obtained using these well-studied lectins. Furthermore, this study demonstrates a systematic and general approach for extracting fine-specificity information from glycan-array data.

  16. High-Throughput Selective Capture of Single Circulating Tumor Cells by Dielectrophoresis at a Wireless Electrode Array.

    Science.gov (United States)

    Li, Min; Anand, Robbyn K

    2017-07-05

    We demonstrate continuous high-throughput selective capture of circulating tumor cells by dielectrophoresis at arrays of wireless electrodes (bipolar electrodes, BPEs). The use of BPEs removes the requirement of ohmic contact to individual array elements, thus enabling otherwise unattainable device formats. Capacitive charging of the electrical double layer at opposing ends of each BPE allows an AC electric field to be transmitted across the entire device. Here, two such designs are described and evaluated. In the first design, BPEs interconnect parallel microchannels. Pockets extruding from either side of the microchannels volumetrically control the number of cells captured at each BPE tip and enhance trapping. High-fidelity single-cell capture was achieved when the pocket dimensions were matched to those of the cells. A second, open design allows many non-targeted cells to pass through. These devices enable high-throughput capture of rare cells and single-cell analysis.

  17. 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.

  18. Understanding InP Nanowire Array Solar Cell Performance by Nanoprobe-Enabled Single Nanowire Measurements.

    Science.gov (United States)

    Otnes, Gaute; Barrigón, Enrique; Sundvall, Christian; Svensson, K Erik; Heurlin, Magnus; Siefer, Gerald; Samuelson, Lars; Åberg, Ingvar; Borgström, Magnus T

    2018-04-27

    III-V solar cells in the nanowire geometry might hold significant synthesis-cost and device-design advantages as compared to thin films and have shown impressive performance improvements in recent years. To continue this development there is a need for characterization techniques giving quick and reliable feedback for growth development. Further, characterization techniques which can improve understanding of the link between nanowire growth conditions, subsequent processing, and solar cell performance are desired. Here, we present the use of a nanoprobe system inside a scanning electron microscope to efficiently contact single nanowires and characterize them in terms of key parameters for solar cell performance. Specifically, we study single as-grown InP nanowires and use electron beam induced current characterization to understand the charge carrier collection properties, and dark current-voltage characteristics to understand the diode recombination characteristics. By correlating the single nanowire measurements to performance of fully processed nanowire array solar cells, we identify how the performance limiting parameters are related to growth and/or processing conditions. We use this understanding to achieve a more than 7-fold improvement in efficiency of our InP nanowire solar cells, grown from a different seed particle pattern than previously reported from our group. The best cell shows a certified efficiency of 15.0%; the highest reported value for a bottom-up synthesized InP nanowire solar cell. We believe the presented approach have significant potential to speed-up the development of nanowire solar cells, as well as other nanowire-based electronic/optoelectronic devices.

  19. Nanotube antibody biosensor arrays for the detection of circulating breast cancer cells

    Science.gov (United States)

    Shao, Ning; Wickstrom, Eric; Panchapakesan, Balaji

    2008-11-01

    Recent reports have shown that nanoscale electronic devices can be used to detect a change in electrical properties when receptor proteins bind to their corresponding antibodies functionalized on the surface of the device, in extracts from as few as ten lysed tumor cells. We hypothesized that nanotube-antibody devices could sensitively and specifically detect entire live cancer cells. We report for the first time a single nanotube field effect transistor array, functionalized with IGF1R-specific and Her2-specific antibodies, which exhibits highly sensitive and selective sensing of live, intact MCF7 and BT474 human breast cancer cells in human blood. Those two cell lines both overexpress IGF1R and Her2, at different levels. Single or small bundle of nanotube devices that were functionalized with IGF1R-specific or Her2-specific antibodies showed 60% decreases in conductivity upon interaction with BT474 or MCF7 breast cancer cells in two µl drops of blood. Control experiments with non-specific antibodies or with MCF10A control breast cells produced a less than 5% decrease in electrical conductivity, illustrating the high sensitivity for whole cell binding by these single nanotube-antibody devices. We postulate that the free energy change due to multiple simultaneous cell-antibody binding events exerted stress along the nanotube surface, decreasing its electrical conductivity due to an increase in band gap. Because the free energy change upon cell-antibody binding, the stress exerted on the nanotube, and the change in conductivity are specific to a specific antigen-antibody interaction; these properties might be used as a fingerprint for the molecular sensing of circulating cancer cells. From optical microscopy observations during sensing, it appears that the binding of a single cell to a single nanotube field effect transistor produced the change in electrical conductivity. Thus we report a nanoscale oncometer with single cell sensitivity with a diameter 1000 times

  20. In vivo single cell analysis reveals Gata2 dynamics in cells transitioning to hematopoietic fate.

    Science.gov (United States)

    Eich, Christina; Arlt, Jochen; Vink, Chris S; Solaimani Kartalaei, Parham; Kaimakis, Polynikis; Mariani, Samanta A; van der Linden, Reinier; van Cappellen, Wiggert A; Dzierzak, Elaine

    2018-01-02

    Cell fate is established through coordinated gene expression programs in individual cells. Regulatory networks that include the Gata2 transcription factor play central roles in hematopoietic fate establishment. Although Gata2 is essential to the embryonic development and function of hematopoietic stem cells that form the adult hierarchy, little is known about the in vivo expression dynamics of Gata2 in single cells. Here, we examine Gata2 expression in single aortic cells as they establish hematopoietic fate in Gata2Venus mouse embryos. Time-lapse imaging reveals rapid pulsatile level changes in Gata2 reporter expression in cells undergoing endothelial-to-hematopoietic transition. Moreover, Gata2 reporter pulsatile expression is dramatically altered in Gata2 +/- aortic cells, which undergo fewer transitions and are reduced in hematopoietic potential. Our novel finding of dynamic pulsatile expression of Gata2 suggests a highly unstable genetic state in single cells concomitant with their transition to hematopoietic fate. This reinforces the notion that threshold levels of Gata2 influence fate establishment and has implications for transcription factor-related hematologic dysfunctions. © 2018 Eich et al.

  1. 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.

  2. Construction of synthetic nucleoli in human cells reveals how a major functional nuclear domain is formed and propagated through cell division.

    Science.gov (United States)

    Grob, Alice; Colleran, Christine; McStay, Brian

    2014-02-01

    Human cell nuclei are functionally organized into structurally stable yet dynamic bodies whose cell cycle inheritance is poorly understood. Here, we investigate the biogenesis and propagation of nucleoli, sites of ribosome biogenesis and key regulators of cellular growth. Nucleolar and cell cycles are intimately connected. Nucleoli disappear during mitosis, reforming around prominent uncharacterized chromosomal features, nucleolar organizer regions (NORs). By examining the effects of UBF depletion on both endogenous NORs and synthetic pseudo-NORs, we reveal its essential role in maintaining competency and establishing a bookmark on mitotic NORs. Furthermore, we demonstrate that neo-NORs, UBF-binding site arrays coupled with rDNA transcription units, direct the de novo biogenesis of functional compartmentalized neonucleoli irrespective of their site of chromosomal integration. For the first time, we establish the sequence requirements for nucleolar biogenesis and provide proof that this is a staged process where UBF-dependent mitotic bookmarking precedes function-dependent nucleolar assembly.

  3. 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.

  4. 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....

  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. Prognostic impact of array-based genomic profiles in esophageal squamous cell cancer

    DEFF Research Database (Denmark)

    Carneiro, Ana; Isinger, Anna; Karlsson, Anna

    2008-01-01

    p13.3 independently predicted poor survival in multivariate analysis. CONCLUSION: 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......BACKGROUND: 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. METHODS: A 32 k aCGH platform was used for high resolution mapping of copy number changes in 30 stage I-IV ESCC. Potential...

  7. Energy distribution design on the photovoltaic cell array of the SSPS-OMEGA concept

    Science.gov (United States)

    Yang, Yang; Zhang, Yiqun; Fan, Guanheng; Wang, Dongxu; Li, Xun

    2017-05-01

    Solar energy collection and conversion is of great significance to the power transmission of the Space Solar Power Station (SSPS), and has influences on the overall system, technologically and economically. For the proposed SSPS-OMEGA concept, the original conceptual design had non-uniform energy distribution and excessive energy density in local areas, which would cause decreases in its optical and electric performance. Aiming at this point, firstly, this paper evaluates the optical performance of the OMEGA concept via ray trace technique. Secondly, the generatrix geometry design of the photovoltaic (PV) cell array based on Bézier curve is carried out to obtain optimal optical performance available for efficient response to sunrays. After that numerical examples achieve good collection efficiency and suitable energy distribution. Finally, modular construction for the main concentrator and its influence on optical performance are investigated. Moreover, the effect of the orbital motion and tracking error are analyzed to provide reference for the realization of the OMEGA.

  8. Three Dimensional Lithospheric Electrical Structure of the Tibetan Plateau as Revealed by SinoProbe Long Period Magnetotelluric Array Data

    Science.gov (United States)

    Wei, Wenbo; Zhang, Letian; Jin, Sheng; Ye, Gaofeng; Jing, Jianen; Dong, Hao; Xie, Chengliang; Yin, Yaotian

    2017-04-01

    The on-going continent-continent collision between the Indian and Eurasian plates since 55 Ma has created the spectacular topography of the Tibetan plateau. However, many first order questions remain to be answered as to the mechanisms behind this young orogenic process. Under the auspices of the SinoProbe Project, a three dimensional (3-D) Magnetotelluric (MT) array have been deployed on the Tibetan Plateau from 2010 to 2013 to better understand this orogeny. By the end of 2013, 1099 MT stations have been completed, including 102 combined broadband MT (BBMT) and long period MT (LMT) stations. In this study, MT data of these 102 combined stations have been used to investigate the deep lithospheric electrical structure of the Tibetan Plateau. MT impedances within the period range of 10 - 50000 s were extracted to be used for 3-D inversions with the ModEM code using the standard NLCG algorithm. The resulting lithospheric electrical structure of the Tibetan Plateau shows a distinct pattern of strong variation not only vertically, but also horizontally. Conductors are found to be widespread in the middle to lower crust. But their geometries are quite complex, and not obviously consistent with the hypothesis of continuous eastward channel flow. Instead, most crustal conductors in central and southern Tibet display a pattern of N-S extension. In the depth range of the upper mantle, two more conductive regions can be identified in the southern Qiangtang Terrane and in the central Lhasa Terrane. Resistor associated with the underthrust Inidan plate can be traced beneath the Bangong-Nujiang suture in western Tibet, but only beneath the central Lhasa terrane in central Tibet. * This work was jointly supported by the grants from Project SinoProbe-01 and National Natural Science Foundation of China (41404060).

  9. 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.

  10. Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status

    Directory of Open Access Journals (Sweden)

    Wei Jun S

    2011-04-01

    Full Text Available Abstract Background Neuroblastoma (NB tumors are well known for their pronounced clinical and molecular heterogeneity. The global gene expression and DNA copy number alterations have been shown to have profound differences in tumors of low or high stage and those with or without MYCN amplification. RNA splicing is an important regulatory mechanism of gene expression, and differential RNA splicing may be associated with the clinical behavior of a tumor. Methods In this study, we used exon array profiling to investigate global alternative splicing pattern of 47 neuroblastoma samples in stage 1 and stage 4 with normal or amplified MYCN copy number (stage 1-, 4- and 4+. The ratio of exon-level expression to gene-level expression was used to detect alternative splicing events, while the gene-level expression was applied to characterize whole gene expression change. Results Principal component analysis (PCA demonstrated distinct splicing pattern in three groups of samples. Pairwise comparison identified genes with splicing changes and/or whole gene expression changes in high stage tumors. In stage 4- compared with stage 1- tumors, alternatively spliced candidate genes had little overlap with genes showing whole gene expression changes, and most of them were involved in different biological processes. In contrast, a larger number of genes exhibited either exon-level splicing, gene-level expression or both changes in stage 4+ versus stage 1- tumors. Those biological processes involved in stage 4- tumors were disrupted to a greater extent by both splicing and transcription regulations in stage 4+ tumors. Conclusions Our results demonstrated a significant role of alternative splicing in high stage neuroblastoma, and suggested a MYCN-associated splicing regulation pathway in stage 4+ tumors. The identification of differentially spliced genes and pathways in neuroblastoma tumors of different stages and molecular subtypes may be important to the

  11. Cytotoxicity and gene array analysis of alveolar epithelial A549 cells exposed to paraquat.

    Science.gov (United States)

    Mitsopoulos, Panagiotis; Suntres, Zacharias E

    2010-12-05

    Paraquat (PQ), a commonly used herbicide, is highly toxic to humans and animals. The primary injury occurs in the lung, where PQ is actively taken up by alveolar epithelial cells and consequently produces damaging reactive oxygen species (ROS) via redox cycling. ROS have also been shown to induce expression of several early response genes and to activate transcription factors, which may contribute to the inflammatory response associated with PQ injury. In order to further elucidate the mechanism(s) of PQ injury, we investigated its effects on the cellular status and gene expression profile of immortalized human alveolar epithelial A549 cells in vitro. Incubation of cells with PQ resulted in concentration- and time-dependent PQ uptake, which correlated with increases in intracellular ROS levels and decreases in intracellular glutathione content, mitochondrial membrane potential, and cell viability. Gene array analysis showed differential expression in response to PQ exposure over time, particularly increases in: (i) the expression of growth arrest and cell cycle-related genes (e.g. CDKN1A, DDIT3 GADD45A, GDF15, MDM2, EGR1, CASP10, CASP8) and (ii) the expression of pro-inflammatory genes (e.g. IL1A, IL6, IL18, NFKB1, SERPINE1), which correlated with increases in the secretion of pro-inflammatory cytokines (e.g. IL-8, IL-6). These data suggest that uptake of PQ by A549 cells altered the cellular redox status and the expression of several early response genes, including the inflammatory response, all of which might contribute to the overall cytotoxicity of PQ. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  12. 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.

  13. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer.

    NARCIS (Netherlands)

    Wilhelm, M.; Veltman, J.A.; Olshen, A.B.; Jain, A.N.; Moore, D.H.; Presti Jr, J.C.; Kovacs, G.; Waldman, F.M.

    2002-01-01

    Array-based comparative genomic hybridization (CGH) uses multiple genomic clones arrayed on a slide to detect relative copy number of tumor DNA sequences. Application of array CGH to tumor specimens makes genetic diagnosis of cancers possible and may help to differentiate relevant subsets of tumors,

  14. Hybrid heterojunction solar cell based on organic-inorganic silicon nanowire array architecture.

    Science.gov (United States)

    Shen, Xiaojuan; Sun, Baoquan; Liu, Dong; Lee, Shuit-Tong

    2011-12-07

    Silicon nanowire arrays (SiNWs) on a planar silicon wafer can be fabricated by a simple metal-assisted wet chemical etching method. They can offer an excellent light harvesting capability through light scattering and trapping. In this work, we demonstrated that the organic-inorganic solar cell based on hybrid composites of conjugated molecules and SiNWs on a planar substrate yielded an excellent power conversion efficiency (PCE) of 9.70%. The high efficiency was ascribed to two aspects: one was the improvement of the light absorption by SiNWs structure on the planar components; the other was the enhancement of charge extraction efficiency, resulting from the novel top contact by forming a thin organic layer shell around the individual silicon nanowire. On the contrary, the sole planar junction solar cell only exhibited a PCE of 6.01%, due to the lower light trapping capability and the less hole extraction efficiency. It indicated that both the SiNWs structure and the thin organic layer top contact were critical to achieve a high performance organic/silicon solar cell. © 2011 American Chemical Society

  15. Generation of electrical power under human skin by subdermal solar cell arrays for implantable bioelectronic devices.

    Science.gov (United States)

    Song, Kwangsun; Han, Jung Hyun; Yang, Hyung Chae; Nam, Kwang Il; Lee, Jongho

    2017-06-15

    Medical electronic implants can significantly improve people's health and quality of life. These implants are typically powered by batteries, which usually have a finite lifetime and therefore must be replaced periodically using surgical procedures. Recently, subdermal solar cells that can generate electricity by absorbing light transmitted through skin have been proposed as a sustainable electricity source to power medical electronic implants in bodies. However, the results to date have been obtained with animal models. To apply the technology to human beings, electrical performance should be characterized using human skin covering the subdermal solar cells. In this paper, we present electrical performance results (up to 9.05mW/cm 2 ) of the implantable solar cell array under 59 human skin samples isolated from 10 cadavers. The results indicate that the power densities depend on the thickness and tone of the human skin, e.g., higher power was generated under thinner and brighter skin. The generated power density is high enough to operate currently available medical electronic implants such as pacemakers that require tens of microwatt. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Live cell imaging reveals at novel view of DNA

    International Nuclear Information System (INIS)

    Moritomi-Yano, Keiko; Yano, Ken-ichi

    2010-01-01

    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)

  17. Single cell Hi-C reveals cell-to-cell variability in chromosome structure

    Science.gov (United States)

    Schoenfelder, Stefan; Yaffe, Eitan; Dean, Wendy; Laue, Ernest D.; Tanay, Amos; Fraser, Peter

    2013-01-01

    Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. PMID:24067610

  18. Catch and Release: A dense, longitudinal array of water quality sondes reveals spatial and temporal complexities in suspended sediment flux

    Science.gov (United States)

    Guilinger, J. J.; Crosby, B. T.

    2017-12-01

    Excessive suspended sediment in streams is one of the most common causes for industrial, ecological and recreational stream impairment in the US. Identifying the primary geomorphic or anthropogenic sources of sediment is a key step in the effective mitigation of impairment. This study seeks to identify sources of suspended sediment in an agriculturally impaired watershed, Marsh Creek, in southeast Idaho. We employ thirteen multi-parameter water quality sensors to simultaneously measure stage, turbidity, temperature and conductivity every 15 minutes over a full calendar year. Examined at both the event and annual scale, these data enable mass balance calculations for mainstem and tributary contributions. Revealed in this monitoring is an approximately eight-fold longitudinal increase in sediment flux over 74 km that is largely augmented by eroding mainstem banks in reaches with higher stream power in the lower 30 km, with less than 20% contributed from tributaries. Independent data confirming the bank source were acquired through cost-effective sediment fingerprinting using 15N and C:N signatures from potential soil endmembers. Additionally, Google Street View-type longitudinal imagery of banks was collected via a kayak survey to confirm the spatial extent and magnitude of bank erosion along Marsh Creek. These data converge on bank erosion as the primary source of fine sediment. Sediment load at various hierarchical temporal and spatial scales is impacted by in-stream storage and remobilization, especially over shorter timescales ranging from daily to seasonal periods. Once averaged over the annual scale, local, temporary in-channel storage is overcome and these data reveal source reaches that can be prioritized for restoration and mitigation projects.

  19. Creation of defined single cell resolution neuronal circuits on microelectrode arrays

    Science.gov (United States)

    Pirlo, Russell Kirk

    2009-12-01

    The way cell-cell organization of neuronal networks influences activity and facilitates function is not well understood. Microelectrode arrays (MEAs) and advancing cell patterning technologies have enabled access to and control of in vitro neuronal networks spawning much new research in neuroscience and neuroengineering. We propose that small, simple networks of neurons with defined circuitry may serve as valuable research models where every connection can be analyzed, controlled and manipulated. Towards the goal of creating such neuronal networks we have applied microfabricated elastomeric membranes, surface modification and our unique laser cell patterning system to create defined neuronal circuits with single-cell precision on MEAs. Definition of synaptic connectivity was imposed by the 3D physical constraints of polydimethylsiloxane elastomeric membranes. The membranes had 20mum clear-through holes and 2-3mum deep channels which when applied to the surface of the MEA formed microwells to confine neurons to electrodes connected via shallow tunnels to direct neurite outgrowth. Tapering and turning of channels was used to influence neurite polarity. Biocompatibility of the membranes was increased by vacuum baking, oligomer extraction, and autoclaving. Membranes were bound to the MEA by oxygen plasma treatment and heated pressure. The MEA/membrane surface was treated with oxygen plasma, poly-D-lysine and laminin to improve neuron attachment, survival and neurite outgrowth. Prior to cell patterning the outer edge of culture area was seeded with 5x10 5 cells per cm and incubated for 2 days. Single embryonic day 7 chick forebrain neurons were then patterned into the microwells and onto the electrodes using our laser cell patterning system. Patterned neurons successfully attached to and were confined to the electrodes. Neurites extended through the interconnecting channels and connected with adjacent neurons. These results demonstrate that neuronal circuits can be

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

    International Nuclear Information System (INIS)

    Larramendy, Florian; Paul, Oliver; Blatche, Marie Charline; Mazenq, Laurent; Laborde, Adrian; Temple-Boyer, Pierre

    2015-01-01

    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)

  1. 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

    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...

  2. Ultrastructure of a hexagonal array in exosporium of a highly sporogenic mutant of Clostridium botulinum type A revealed by electron microscopy using optical diffraction and filtration.

    Science.gov (United States)

    Masuda, K; Kawata, T; Takumi, K; Kinouchi, T

    1980-01-01

    The ultrastructure of a hexagonal array in the exosporium from spores of a highly sporogenic mutant of Clostridium botulinum type A strain 190L was studied by electron microscopy of negatively stained exosporium fragments using optical diffraction and filtration. The exosporium was composed of three or more lamellae showing and equilateral, hexagonal periodicity. Images of the single exosporium layer from which the noise had been filtered optically revealed that the hexagonally arranged, morphological unit of the exosporium was composed of three globular subunits about 2.1 nm in diameter which were arranged at the vertices of an equilateral triangle with sides of about 2.4 nm. The morphological units were arranged with a spacing of about 4.5 nm. the adjacent globular subunits appeared to be interconnected by delicate linkers.

  3. Pt-Ni/WC Alloy Nanorods Arrays as ORR Catalyst for PEM Fuel Cells

    Energy Technology Data Exchange (ETDEWEB)

    Begum, Mahbuba; Yurukcu, Mesut; Yurtsever, Fatma; Ergul, Busra; Kariuki, Nancy; Myers, Deborah J.; Karabacak, Tansel

    2017-08-24

    Polymer electrolyte membrane fuel cells (PEMFCs) among the other types of fuel cell technology are attractive power sources, especially for electric vehicle applications. While significant progress and plausible prospects of PEMFCs have been achieved, there are still some challenges related to the performance, durability, and cost that need to be overcome to make them economically viable for widespread commercialization. Our strategy is to develop thin films of high-active and stable catalyst coated on vertically aligned nanorod arrays of conductive and stable support. In this work, we fabricated tungsten carbide (WC) nanorods as support and coated them with a platinum-nickel (Pt-Ni) alloy shell denoted as Pt-Ni/WC catalysts. The Pt- Ni/WC nanorods were deposited on glassy carbon disks as well as on silicon substrates for evaluation of their electrocatalytic oxygen reduction reaction (ORR) activity and physical properties. Cyclic voltammetry experiments using rotating disk electrode were performed in perchloric acid (0.1 M HClO4) electrolyte at room temperature to characterize the ORR activity and stability of Pt-Ni/WC nanorods catalysts. Scanning electron microscopy and X-ray diffraction techniques were utilized to study the morphology and crystallographic properties, respectively.

  4. Cell lineage tracing reveals a biliary origin of intrahepatic cholangiocarcinoma

    Science.gov (United States)

    Guest, Rachel V; Boulter, Luke; Kendall, Timothy J; Minnis-Lyons, Sarah E; Walker, Robert; Wigmore, Stephen J; Sansom, Owen J; Forbes, Stuart J

    2014-01-01

    Intrahepatic cholangiocarcinoma (ICC) is a treatment refractory malignancy with a high mortality and an increasing incidence worldwide. Recent studies have observed that activation of Notch and AKT signalling within mature hepatocytes is able to induce the formation of tumours displaying biliary lineage markers, thereby raising the suggestion that it is hepatocytes, rather than cholangiocytes or hepatic progenitor cells that represent the cell of origin of this tumour. Here we utilise a cholangiocyte-lineage tracing system to target p53 loss to biliary epithelia and observe the appearance of labelled biliary lineage tumours in response to chronic injury. Consequent to this, up-regulation of native functional Notch signalling is observed to occur spontaneously within cholangiocytes and hepatocytes in this model as well as in human ICC. These data prove that in the context of chronic inflammation and p53 loss, frequent occurrences in human disease, biliary epithelia are a target of transformation and an origin of ICC. PMID:24310400

  5. Toward Wearable Energy Storage Devices: Paper-Based Biofuel Cells based on a Screen-Printing Array Structure.

    Science.gov (United States)

    Shitanda, Isao; Momiyama, Misaki; Watanabe, Naoto; Tanaka, Tomohiro; Tsujimura, Seiya; Hoshi, Yoshinao; Itagaki, Masayuki

    2017-10-01

    A novel paper-based biofuel cell with a series/parallel array structure has been fabricated, in which the cell voltage and output power can easily be adjusted as required by printing. The output of the fabricated 4-series/4-parallel biofuel cell reached 0.97±0.02 mW at 1.4 V, which is the highest output power reported to date for a paper-based biofuel cell. This work contributes to the development of flexible, wearable energy storage device.

  6. 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

  7. 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.

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

    Science.gov (United States)

    Yoshioka, Shunichi; Tsukamoto, Yoshiyuki; Hijiya, Naoki; Nakada, Chisato; Uchida, Tomohisa; Matsuura, Keiko; Takeuchi, Ichiro; Seto, Masao; Kawano, Kenji; Moriyama, Masatsugu

    2013-01-01

    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.

  9. Process Development of Gallium Nitride Phosphide Core-Shell Nanowire Array Solar Cell

    Science.gov (United States)

    Chuang, Chen

    Dilute Nitride GaNP is a promising materials for opto-electronic applications due to its band gap tunability. The efficiency of GaNxP1-x /GaNyP1-y core-shell nanowire solar cell (NWSC) is expected to reach as high as 44% by 1% N and 9% N in the core and shell, respectively. By developing such high efficiency NWSCs on silicon substrate, a further reduction of the cost of solar photovoltaic can be further reduced to 61$/MWh, which is competitive to levelized cost of electricity (LCOE) of fossil fuels. Therefore, a suitable NWSC structure and fabrication process need to be developed to achieve this promising NWSC. This thesis is devoted to the study on the development of fabrication process of GaNxP 1-x/GaNyP1-y core-shell Nanowire solar cell. The thesis is divided into two major parts. In the first parts, previously grown GaP/GaNyP1-y core-shell nanowire samples are used to develop the fabrication process of Gallium Nitride Phosphide nanowire solar cell. The design for nanowire arrays, passivation layer, polymeric filler spacer, transparent col- lecting layer and metal contact are discussed and fabricated. The property of these NWSCs are also characterized to point out the future development of Gal- lium Nitride Phosphide NWSC. In the second part, a nano-hole template made by nanosphere lithography is studied for selective area growth of nanowires to improve the structure of core-shell NWSC. The fabrication process of nano-hole templates and the results are presented. To have a consistent features of nano-hole tem- plate, the Taguchi Method is used to optimize the fabrication process of nano-hole templates.

  10. 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.

  11. Screen for Slit/Robo signaling in trunk neural cells reveals new players.

    Science.gov (United States)

    Martinez, Darwin; Zuhdi, Nora; Reyes, Michelle; Ortega, Blanca; Giovannone, Dion; Lee, Vivian M; de Bellard, Maria Elena

    2018-02-07

    Slits ligands and their Robo receptors are involved in quite disparate cell signaling pathways that include axon guidance, cell proliferation, cell motility and angiogenesis. Neural crest cells emerge by delamination from neural cells in the dorsal neural tube, and give rise to various components of the peripheral nervous system in vertebrates. It is well established that these cells change from a non-migratory to a highly migratory state allowing them to reach distant regions before they differentiate. However, but the mechanism controlling this delamination and subsequent migration are still not fully understood. The repulsive Slit ligand family members, have been classified also as true tumor suppressor molecules. The present study explored in further detail what possible Slit/Robo signals are at play in the trunk neural cells and neural crest cells by carrying out a microarray after Slit2 gain of function in trunk neural tubes. We found that in addition to molecules known to be downstream of Slit/Robo signaling, there were a large set of molecules known to be important in maintaining cells in non-motile, epithelia phenotype. Furthermore, we found new molecules previously not associated with Slit/Robo signaling: cell proliferation markers, Ankyrins and RAB intracellular transporters. Our findings suggest that neural crest cells use and array of different Slit/Robo pathways during their transformation from non-motile to highly motile cells. Copyright © 2018. Published by Elsevier B.V.

  12. 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.

  13. Hybrid Solar Cells Based on Silicon Nanowire Arrays for Remote Chemical Sensing

    Directory of Open Access Journals (Sweden)

    Joël DAVENAS

    2014-05-01

    Full Text Available Disordered arrays of silicon nanowires have been produced by the OAG technique. The UV-visible absorption spectrum of the SiNWs shows a main increase of the absorption extending in the near infrared and similar absorption than bulk crystalline silicon below 400 nm. T EMT simulation of the UV absorption of silicon nanowires predicts a main optical absorption for a nanowire orientation parallel to the electric field vector of the incident light, as expected for SiNW lying with a dominant orientation parallel to the substrate. The enhanced optical absorption tail extending above 400 nm has been attributed to the combination of band gap opening shown by the PL emission and high densities of silicon surface states at high surface/volume ratio. Hybrid solar cells have been fabricated through the dispersion of silicon nanowires in a poly(3-hexylthiophene thin film leading to a 1.14 % conversion yield, which was increased to 3.04 % upon SiNW surface functionalization, opening new perspectives for self sufficient power supplies applicable to remote sensing.

  14. 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.

  15. High-Density Dielectrophoretic Microwell Array for Detection, Capture, and Single-Cell Analysis of Rare Tumor Cells in Peripheral Blood.

    Directory of Open Access Journals (Sweden)

    Atsushi Morimoto

    Full Text Available Development of a reliable platform and workflow to detect and capture a small number of mutation-bearing circulating tumor cells (CTCs from a blood sample is necessary for the development of noninvasive cancer diagnosis. In this preclinical study, we aimed to develop a capture system for molecular characterization of single CTCs based on high-density dielectrophoretic microwell array technology. Spike-in experiments using lung cancer cell lines were conducted. The microwell array was used to capture spiked cancer cells, and captured single cells were subjected to whole genome amplification followed by sequencing. A high detection rate (70.2%-90.0% and excellent linear performance (R2 = 0.8189-0.9999 were noted between the observed and expected numbers of tumor cells. The detection rate was markedly higher than that obtained using the CellSearch system in a blinded manner, suggesting the superior sensitivity of our system in detecting EpCAM- tumor cells. Isolation of single captured tumor cells, followed by detection of EGFR mutations, was achieved using Sanger sequencing. Using a microwell array, we established an efficient and convenient platform for the capture and characterization of single CTCs. The results of a proof-of-principle preclinical study indicated that this platform has potential for the molecular characterization of captured CTCs from patients.

  16. Gene expression profile of coronary artery cells treated with nonsteroidal anti-inflammatory drugs reveals off-target effects.

    Science.gov (United States)

    Palayoor, Sanjeewani T; J-Aryankalayil, Molykutty; Makinde, Adeola Y; Cerna, David; Falduto, Michael T; Magnuson, Scott R; Coleman, C Norman

    2012-06-01

    Nonsteroidal anti-inflammatory drugs (NSAIDs) have come under scrutiny because of the gastrointestinal, renal, and cardiovascular toxicity associated with prolonged use of these drugs. The purpose of this study was to identify molecular targets for NSAIDs related to cellular toxicity with a view to optimize drug efficacy in the clinic. Coronary artery smooth muscle cells and endothelial cells were treated with low (clinically achievable) and high (typically used in preclinical studies) concentrations of celecoxib, NS398, and ibuprofen for 24 hours. NSAIDs-induced gene expression changes were evaluated by microarray analysis and validated by real-time reverse-transcription polymerase chain reaction and western blotting. The functional significance of differentially expressed genes was evaluated by Ingenuity Pathway Analysis. At high concentrations, NSAIDs altered the expression of genes regulating cell proliferation and cell death. NSAIDs also altered genes associated with cardiovascular functions including inflammation, thrombosis, fibrinolysis, coronary artery disease, and hypertension. The gene expression was most impacted by ibuprofen, celecoxib, and NS398, in that order. This study revealed that NSAIDs altered expression of an array of genes associated with cardiovascular events and emphasizes the potential for fingerprinting drugs in preclinical studies to assess the potential drug toxicity and to optimize the drug efficacy in clinical settings.

  17. Optimizing the size of a solar cell array; Optimiser la taille d'un panneau solaire

    Energy Technology Data Exchange (ETDEWEB)

    Shannon, J. [Linear Technology, 94 - Rungis (France)

    2006-06-15

    The electronic power conversion system is a strategic part of solar power supply systems. An ideal diode controller combined to a compensated switching regulator allows to optimize the operation of the battery and to optimize the dimensioning of the solar cells array. The ideal diode controller limits the discharge of the battery inside the non-exposed solar cells and limits the related direct voltage drop and loss of power. The switching regulator charger lowers the solar cells voltage to charge the battery and ensures the optimum operation of the solar elements. (J.S.)

  18. Experimental study on direct-contact liquid film cooling simulated dense-array solar cells in high concentrating photovoltaic system

    International Nuclear Information System (INIS)

    Wang, Yiping; Shi, Xusheng; Huang, Qunwu; Cui, Yong; Kang, Xue

    2017-01-01

    Highlights: • Direct-contact liquid film cooling dense-array solar cells was first proposed. • Average temperature was controlled well below 80 °C. • The maximum temperature difference was less than 10 °C. • The heat transfer coefficient reached up to 11.91 kW/(m 2 ·K) under 589X. - Abstract: This paper presented a new method of cooling dense-array solar cells in high concentrating photovoltaic system by direct-contact liquid film, and water was used as working fluid. An electric heating plate was designed to simulate the dense-array solar cells in high concentrating photovoltaic system. The input power of electric heating plate simulated the concentration ratios. By heat transfer experiments, the effect of water temperatures and flow rates on heat transfer performance was investigated. The results indicated that: the average temperature of simulated solar cells was controlled well below 80 °C under water temperature of 30 °C and flow rate of 300 L/h when concentration ratio ranged between 300X and 600X. The maximum temperature difference among temperature measurement points was less than 10 °C, which showed the temperature distribution was well uniform. The heat transfer coefficient reached up to 11.91 kW/(m 2 ·K) under concentration ratio of 589X. To improve heat transfer performance and obtain low average temperature of dense-array solar cells, lower water temperature and suitable water flow rate are preferred.

  19. 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.

  20. 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

  1. 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)

    Sessions, John W; Hanks, Brad W; Jensen, Brian D; Lindstrom, Dallin L; Hope, Sandra

    2016-01-01

    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

  2. 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.

  3. Raman spectrum reveals Mesenchymal stem cells inhibiting HL60 cells growth

    Science.gov (United States)

    Su, Xin; Fang, Shaoyin; Zhang, Daosen; Zhang, Qinnan; Lu, Xiaoxu; Tian, Jindong; Fan, Jinping; Zhong, Liyun

    2017-04-01

    Though some research results reveals that Mesenchymal stem cells (MSCs) have the ability of inhibiting tumor cells proliferation, it remains controversial about the precise interaction mechanism during MSCs and tumor cells co-culture. In this study, combing Raman spectroscopic data and principle component analysis (PCA), the biochemical changes of MSCs or Human promyelocytic leukemia (HL60) cells during their co-culture were presented. The obtained results showed that some main Raman peaks of HL60 assigned to nucleic acids or proteins were greatly higher in intensity in the late stage of co-culture than those in the early stage of co-culture while they were still lower relative to the control group, implicating that the effect of MSCs inhibiting HL60 proliferation appeared in the early stage but gradually lost the inhibiting ability in the late stage of co-culture. Moreover, some other peaks of HL60 assigned to proteins were decreased in intensity in the early stage of co-culture relative to the control group but rebounded to the level similar to the control group in the late stage, showing that the content and structure changes of these proteins might be generated in the early stage but returned to the original state in the late stage of co-culture. As a result, in the early stage of MSCs-HL60 co-culture, along with the level of Akt phosphorylation of HL60 was lowered relative to its control group, the proliferation rate of HL60 cells was decreased. And in the late stage of co-culture, along with the level of Akt phosphorylation was rebounded, the reverse transfer of Raman peaks within 875-880 cm- 1 appeared, thus MSCs lost the ability to inhibit HL60 growth and HL60 proliferation was increased. In addition, it was observed that the peak at 811 cm- 1, which is a marker of RNA, was higher in intensity in the late stage than that in the control group, indicating that MSCs might be differentiated into myofibroblast-like MSCs. In addition, PCA results also exhibited

  4. MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells.

    Science.gov (United States)

    Liu, Zongzhi; Li, Ao; Schulz, Vincent; Chen, Min; Tuck, David

    2010-06-01

    Genotyping platforms such as single nucleotide polymorphism (SNP) arrays are powerful tools to study genomic aberrations in cancer samples. Allele specific information from SNP arrays provides valuable information for interpreting copy number variation (CNV) and allelic imbalance including loss-of-heterozygosity (LOH) beyond that obtained from the total DNA signal available from array comparative genomic hybridization (aCGH) platforms. Several algorithms based on hidden Markov models (HMMs) have been designed to detect copy number changes and copy-neutral LOH making use of the allele information on SNP arrays. However heterogeneity in clinical samples, due to stromal contamination and somatic alterations, complicates analysis and interpretation of these data. We have developed MixHMM, a novel hidden Markov model using hidden states based on chromosomal structural aberrations. MixHMM allows CNV detection for copy numbers up to 7 and allows more complete and accurate description of other forms of allelic imbalance, such as increased copy number LOH or imbalanced amplifications. MixHMM also incorporates a novel sample mixing model that allows detection of tumor CNV events in heterogeneous tumor samples, where cancer cells are mixed with a proportion of stromal cells. We validate MixHMM and demonstrate its advantages with simulated samples, clinical tumor samples and a dilution series of mixed samples. We have shown that the CNVs of cancer cells in a tumor sample contaminated with up to 80% of stromal cells can be detected accurately using Illumina BeadChip and MixHMM. The MixHMM is available as a Python package provided with some other useful tools at http://genecube.med.yale.edu:8080/MixHMM.

  5. MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells.

    Directory of Open Access Journals (Sweden)

    Zongzhi Liu

    Full Text Available BACKGROUND: Genotyping platforms such as single nucleotide polymorphism (SNP arrays are powerful tools to study genomic aberrations in cancer samples. Allele specific information from SNP arrays provides valuable information for interpreting copy number variation (CNV and allelic imbalance including loss-of-heterozygosity (LOH beyond that obtained from the total DNA signal available from array comparative genomic hybridization (aCGH platforms. Several algorithms based on hidden Markov models (HMMs have been designed to detect copy number changes and copy-neutral LOH making use of the allele information on SNP arrays. However heterogeneity in clinical samples, due to stromal contamination and somatic alterations, complicates analysis and interpretation of these data. METHODS: We have developed MixHMM, a novel hidden Markov model using hidden states based on chromosomal structural aberrations. MixHMM allows CNV detection for copy numbers up to 7 and allows more complete and accurate description of other forms of allelic imbalance, such as increased copy number LOH or imbalanced amplifications. MixHMM also incorporates a novel sample mixing model that allows detection of tumor CNV events in heterogeneous tumor samples, where cancer cells are mixed with a proportion of stromal cells. CONCLUSIONS: We validate MixHMM and demonstrate its advantages with simulated samples, clinical tumor samples and a dilution series of mixed samples. We have shown that the CNVs of cancer cells in a tumor sample contaminated with up to 80% of stromal cells can be detected accurately using Illumina BeadChip and MixHMM. AVAILABILITY: The MixHMM is available as a Python package provided with some other useful tools at http://genecube.med.yale.edu:8080/MixHMM.

  6. 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.

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

    International Nuclear Information System (INIS)

    Carneiro, Ana; Isinger, Anna; Karlsson, Anna; Johansson, Jan; Jönsson, Göran; Bendahl, Pär-Ola; Falkenback, Dan; Halvarsson, Britta; Nilbert, Mef

    2008-01-01

    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

  8. Calcium Imaging of GPCR Activation Using Arrays of Reverse Transfected HEK293 Cells in a Microfluidic System.

    Science.gov (United States)

    Roelse, Margriet; Henquet, Maurice G L; Verhoeven, Harrie A; de Ruijter, Norbert C A; Wehrens, Ron; van Lenthe, Marco S; Witkamp, Renger F; Hall, Robert D; Jongsma, Maarten A

    2018-02-16

    Reverse-transfected cell arrays in microfluidic systems have great potential to perform large-scale parallel screening of G protein-coupled receptor (GPCR) activation. Here, we report the preparation of a novel platform using reverse transfection of HEK293 cells, imaging by stereo-fluorescence microscopy in a flowcell format, real-time monitoring of cytosolic calcium ion fluctuations using the fluorescent protein Cameleon and analysis of GPCR responses to sequential sample exposures. To determine the relationship between DNA concentration and gene expression, we analyzed cell arrays made with variable concentrations of plasmid DNA encoding fluorescent proteins and the Neurokinin 1 (NK1) receptor. We observed pronounced effects on gene expression of both the specific and total DNA concentration. Reverse transfected spots with NK1 plasmid DNA at 1% of total DNA still resulted in detectable NK1 activation when exposed to its ligand. By varying the GPCR DNA concentration in reverse transfection, the sensitivity and robustness of the receptor response for sequential sample exposures was optimized. An injection series is shown for an array containing the NK1 receptor, bitter receptor TAS2R8 and controls. Both receptors were exposed 14 times to alternating samples of two ligands. Specific responses remained reproducible. This platform introduces new opportunities for high throughput screening of GPCR libraries.

  9. Live cell linear dichroism imaging reveals extensive membrane ruffling within the docking structure of natural killer cell immune synapses

    DEFF Research Database (Denmark)

    Benninger, Richard K P; Vanherberghen, Bruno; Young, Stephen

    2009-01-01

    We have applied fluorescence imaging of two-photon linear dichroism to measure the subresolution organization of the cell membrane during formation of the activating (cytolytic) natural killer (NK) cell immune synapse (IS). This approach revealed that the NK cell plasma membrane is convoluted...... into ruffles at the periphery, but not in the center of a mature cytolytic NK cell IS. Time-lapse imaging showed that the membrane ruffles formed at the initial point of contact between NK cells and target cells and then spread radialy across the intercellular contact as the size of the IS increased, becoming...

  10. Real-time quantification of protein expression and translocation at individual cell resolution using imaging-dish-based live cell array.

    Science.gov (United States)

    Ravid-Hermesh, Orit; Zurgil, Naomi; Shafran, Yana; Sobolev, Maria; Galmidi, Moti; Badihi, Yoav; Israel, Liron Limor; Lellouche, Jean Paul; Lellouche, Emmanuel; Michaeli, Shulamit; Deutsch, Mordechai

    2014-11-01

    Cell populations represent intrinsically heterogeneous systems with a high level of spatiotemporal complexity. Monitoring and understanding cell-to-cell diversity is essential for the research and application of intra- and interpopulation variations. Optical analysis of live cells is challenging since both adherent and nonadherent cells change their spatial location. However, most currently available single-cell techniques do not facilitate treatment and monitoring of the same live cells over time throughout multistep experiments. An imaging-dish-based live cell array (ID-LCA) has been developed and produced for cell handling, culturing, and imaging of numerous live cells. The dish is composed of an array of pico scale cavities-pico wells (PWs) embossed on its glass bottom. Cells are seeded, cultured, treated, and spatiotemporally measured on the ID-LCA, while each cell or small group of cells are locally constrained in the PWs. Finally, predefined cells can be retrieved for further evaluation. Various types of ID-LCAs were used in this proof-of-principle work, to demonstrate on-ID-LCA transfection of fluorescently tagged chimeric proteins, as well as the detection and kinetic analysis of their induced translocation. High variability was evident within cell populations with regard to protein expression levels as well as the extent and dynamics of protein redistribution. The association of these parameters with cell morphology and functional parameters was examined. Both the new methodology and the device facilitate research of the translocation process at individual cell resolution within large populations and thus, can potentially be used in high-throughput fashion.

  11. 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%.

  12. Array-CGH analysis of cell-free fetal DNA in 10 mL of amniotic fluid supernatant.

    Science.gov (United States)

    Lapaire, Olav; Lu, Xin-Yan; Johnson, Kirby L; Jarrah, Zina; Stroh, Helene; Cowan, Janet M; Tantravahi, Umadevi; Bianchi, Diana W

    2007-07-01

    Previously, we showed that analysis of amniotic fluid (AF) supernatant cell-free fetal (cff) DNA using DNA microarrays (array-CGH) allows for detection of whole chromosome differences between test and reference DNA. Subsequent technical advances have increased both the yield and quality of extracted cffDNA. Here we determined whether array-CGH using smaller volumes of both fresh and frozen AF cffDNA could identify fetal aneuploidy. CffDNA was extracted from 10 mL of residual AF supernatant. The test AF samples (n = 10) included one with a normal karyotype, and nine with the following fetal aneuploidies: trisomies 13 (n = 1), 18 (n = 3), 21 (n = 2), trisomy 9 mosaicism (47,XX,+ 9[18]/46,XX[2]), triploidy (69,XXY) and Turner syndrome (45,X). Array-CGH using AF cffDNA from aneuploid fetuses, compared to euploid reference AF cffDNA, detected whole chromosome aneuploidy in 8 of 9 cases tested, including the case of trisomy 9 mosaicism. The case of triploidy was not detected. CffDNA extracted from 10 mL AF supernatant can be analyzed using array-CGH to correctly identify human chromosome abnormalities. This technology allows for rapid screening of AF samples for whole chromosomal changes by using routinely discarded supernatant, and may augment standard prenatal karyotyping techniques by providing additional molecular information.

  13. Gene expression profiling revealed novel mechanism of action of Taxotere and Furtulon in prostate cancer cells

    Directory of Open Access Journals (Sweden)

    Li Ran

    2005-01-01

    Full Text Available Abstract Background Both Taxotere and Capecitabine have shown anti-cancer activity against various cancers including prostate cancer. In combination, Taxotere plus Capecitabine has demonstrated higher anti-cancer activity in advanced breast cancers. However, the molecular mechanisms of action of Taxotere and Capecitabine have not been fully elucidated in prostate cancer. Methods The total RNA from PC3 and LNCaP prostate cells untreated and treated with 2 nM Taxotere, 110 μM Furtulon (active metabolite of Capecitabine, or 1 nM Taxotere plus 50 μM Furtulon for 6, 36, and 72 hours, was subjected to Affymetrix Human Genome U133A Array analysis. Real-time PCR and Western Blot analysis were conducted to confirm microarray data. Results Taxotere and Furtulon down-regulated some genes critical for cell proliferation, cell cycle progression, transcription factor, cell signaling, and oncogenesis, and up-regulated some genes related to the induction of apoptosis, cell cycle arrest, and differentiation in both cell lines. Taxotere and Furtulon also up-regulated some genes responsible for chemotherapeutic resistance, suggesting the induction of cancer cell resistance to these agents. Conclusions Taxotere and Furtulon caused the alternation of a large number of genes, many of which may contribute to the molecular mechanisms by which Taxotere and Furtulon inhibit the growth of prostate cancer cells. This information could be utilized for further mechanistic research and for devising optimized therapeutic strategies against prostate cancer.

  14. 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.

  15. Transcriptome analysis reveals determinant stages controlling human embryonic stem cell commitment to neuronal cells.

    Science.gov (United States)

    Li, Yuanyuan; Wang, Ran; Qiao, Nan; Peng, Guangdun; Zhang, Ke; Tang, Ke; Han, Jing-Dong J; Jing, Naihe

    2017-12-01

    Proper neural commitment is essential for ensuring the appropriate development of the human brain and for preventing neurodevelopmental diseases such as autism spectrum disorders, schizophrenia, and intellectual disorders. However, the molecular mechanisms underlying the neural commitment in humans remain elusive. Here, we report the establishment of a neural differentiation system based on human embryonic stem cells (hESCs) and on comprehensive RNA sequencing analysis of transcriptome dynamics during early hESC differentiation. Using weighted gene co-expression network analysis, we reveal that the hESC neurodevelopmental trajectory has five stages: pluripotency (day 0); differentiation initiation (days 2, 4, and 6); neural commitment (days 8-10); neural progenitor cell proliferation (days 12, 14, and 16); and neuronal differentiation (days 18, 20, and 22). These stages were characterized by unique module genes, which may recapitulate the early human cortical development. Moreover, a comparison of our RNA-sequencing data with several other transcriptome profiling datasets from mice and humans indicated that Module 3 associated with the day 8-10 stage is a critical window of fate switch from the pluripotency to the neural lineage. Interestingly, at this stage, no key extrinsic signals were activated. In contrast, using CRISPR/Cas9-mediated gene knockouts, we also found that intrinsic hub transcription factors, including the schizophrenia-associated SIX3 gene and septo-optic dysplasia-related HESX1 gene, are required to program hESC neural determination. Our results improve the understanding of the mechanism of neural commitment in the human brain and may help elucidate the etiology of human mental disorders and advance therapies for managing these conditions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Live cell imaging reveals marked variability in myoblast proliferation and fate

    Science.gov (United States)

    2013-01-01

    Background During the process of muscle regeneration, activated stem cells termed satellite cells proliferate, and then differentiate to form new myofibers that restore the injured area. Yet not all satellite cells contribute to muscle repair. Some continue to proliferate, others die, and others become quiescent and are available for regeneration following subsequent injury. The mechanisms that regulate the adoption of different cell fates in a muscle cell precursor population remain unclear. Methods We have used live cell imaging and lineage tracing to study cell fate in the C2 myoblast line. Results Analyzing the behavior of individual myoblasts revealed marked variability in both cell cycle duration and viability, but similarities between cells derived from the same parental lineage. As a consequence, lineage sizes and outcomes differed dramatically, and individual lineages made uneven contributions toward the terminally differentiated population. Thus, the cohort of myoblasts undergoing differentiation at the end of an experiment differed dramatically from the lineages present at the beginning. Treatment with IGF-I increased myoblast number by maintaining viability and by stimulating a fraction of cells to complete one additional cell cycle in differentiation medium, and as a consequence reduced the variability of the terminal population compared with controls. Conclusion Our results reveal that heterogeneity of responses to external cues is an intrinsic property of cultured myoblasts that may be explained in part by parental lineage, and demonstrate the power of live cell imaging for understanding how muscle differentiation is regulated. PMID:23638706

  17. 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.

  18. Protein activation dynamics in cells and tumor micro arrays assessed by time resolved Förster resonance energy transfer.

    Science.gov (United States)

    Calleja, Véronique; Leboucher, Pierre; Larijani, Banafshé

    2012-01-01

    Analytical time resolved Förster resonance energy transfer (FRET) can be exploited for assessing, in cells and tumor micro arrays, the activation status and dynamics of oncoproteins such as epidermal growth factor receptor (EGFR1) and their downstream effectors such as protein kinase B (PKB) and 3-phosphoinositide-dependent protein kinase 1 (PDK1). The outcome of our research involving the application of quantitative imaging for investigating molecular mechanisms of phosphoinositide-dependant enzymes, such as PKB and PDK1, has resulted in a refined model describing the dynamics and regulation of these two oncoproteins in live cells. Our translational research exploits a quantitative FRET method for establishing the activation status of predictive biomarkers in tumor micro arrays. We developed a two-site FRET assay monitored by automated frequency domain Fluorescence lifetime imaging microscopy (FLIM). As a proof of principle, we tested our methodology by assessing EGFR1 activation status in tumor micro arrays from head and neck patients. Our two-site FRET assay, by high-throughput frequency domain FLIM, has great potential to provide prognostic and perhaps predictive biomarkers. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. The influence of passivation and photovoltaic properties of α-Si:H coverage on silicon nanowire array solar cells

    Science.gov (United States)

    2013-01-01

    Silicon nanowire (SiNW) arrays for radial p-n junction solar cells offer potential advantages of light trapping effects and quick charge collection. Nevertheless, lower open circuit voltages (Voc) lead to lower energy conversion efficiencies. In such cases, the performance of the solar cells depends critically on the quality of the SiNW interfaces. In this study, SiNW core-shell solar cells have been fabricated by growing crystalline silicon (c-Si) nanowires via the metal-assisted chemical etching method and by depositing hydrogenated amorphous silicon (α-Si:H) via the plasma-enhanced chemical vapor deposition (PECVD) method. The influence of deposition parameters on the coverage and, consequently, the passivation and photovoltaic properties of α-Si:H layers on SiNW solar cells have been analyzed. PMID:24059343

  20. Identification of cellular responses to low-dose radiation by antibody array in human B-lymphoblasts IM-9 cells

    Energy Technology Data Exchange (ETDEWEB)

    Eom, Hyeon Soo; Kim, Ji Young; Nam, Seon Young [Low-dose Radiation Research Team, Radiation Health Institute, Korea Hydro and Nuclear Power Co. LTD., Seoul (Korea, Republic of)

    2017-04-15

    The low-dose radiation (LDR)-induced various responses can reduce genetic mutation, enhance cell survival, and increase infection resistance (1). The antibody array for global analysis of phosphorylated proteins might be very useful to study signaling networks of LDR-induced cellular responses (2). Therefore, global analysis of phospho- proteins in cells exposed to radiation is important to understand the signaling mechanisms induced by changes of protein phosphorylation which lead to various biological effects by radiation. The aim is to explore the possibility of LDR-specific signaling for various beneficial effects and elucidate the potential signaling pathways representing LDR responses. Our results suggest that LDR did not affect cell death and that the increased proteins phosphorylation by LDR might be involved in various cellular responses for cell homeostasis. These results might be useful to further studies aimed at investigating potential regulatory markers that represent responses to LDR.

  1. The influence of passivation and photovoltaic properties of α-Si:H coverage on silicon nanowire array solar cells.

    Science.gov (United States)

    Li, Kuntang; Wang, Xiuqin; Lu, Pengfei; Ding, Jianning; Yuan, Ningyi

    2013-09-23

    Silicon nanowire (SiNW) arrays for radial p-n junction solar cells offer potential advantages of light trapping effects and quick charge collection. Nevertheless, lower open circuit voltages (Voc) lead to lower energy conversion efficiencies. In such cases, the performance of the solar cells depends critically on the quality of the SiNW interfaces. In this study, SiNW core-shell solar cells have been fabricated by growing crystalline silicon (c-Si) nanowires via the metal-assisted chemical etching method and by depositing hydrogenated amorphous silicon (α-Si:H) via the plasma-enhanced chemical vapor deposition (PECVD) method. The influence of deposition parameters on the coverage and, consequently, the passivation and photovoltaic properties of α-Si:H layers on SiNW solar cells have been analyzed.

  2. Multiplex flow cytometry barcoding and antibody arrays identify surface antigen profiles of primary and metastatic colon cancer cell lines.

    Directory of Open Access Journals (Sweden)

    Kumar Sukhdeo

    Full Text Available Colon cancer is a deadly disease affecting millions of people worldwide. Current treatment challenges include management of disease burden as well as improvements in detection and targeting of tumor cells. To identify disease state-specific surface antigen signatures, we combined fluorescent cell barcoding with high-throughput flow cytometric profiling of primary and metastatic colon cancer lines (SW480, SW620, and HCT116. Our multiplexed technique offers improvements over conventional methods by permitting the simultaneous and rapid screening of cancer cells with reduced effort and cost. The method uses a protein-level analysis with commercially available antibodies on live cells with intact epitopes to detect potential tumor-specific targets that can be further investigated for their clinical utility. Multiplexed antibody arrays can easily be applied to other tumor types or pathologies for discovery-based approaches to target identification.

  3. High-efficiency thin and compact concentrator photovoltaics with micro-solar cells directly attached to a lens array.

    Science.gov (United States)

    Hayashi, Nobuhiko; Inoue, Daijiro; Matsumoto, Mitsuhiro; Matsushita, Akio; Higuchi, Hiroshi; Aya, Youichirou; Nakagawa, Tohru

    2015-06-01

    We propose a thin and compact concentrator photovoltaic (CPV) module, about 20 mm thick, one tenth thinner than those of conventional CPVs that are widely deployed for mega-solar systems, to broaden CPV application scenarios. We achieved an energy conversion efficiency of 37.1% at a module temperature of 25 °C under sunlight irradiation optimized for our module. Our CPV module has a lens array consisting of 10 mm-square unit lenses and micro solar cells that are directly attached to the lens array, to reduce the focal length of the concentrator and to reduce optical losses due to reflection. The optical loss of the lens in our module is about 9.0%, which is lower than that of conventional CPV modules with secondary optics. This low optical loss enables our CPV module to achieve a high energy conversion efficiency.

  4. 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.

  5. Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.

    Science.gov (United States)

    Hochgerner, Hannah; Zeisel, Amit; Lönnerberg, Peter; Linnarsson, Sten

    2018-02-01

    The dentate gyrus of the hippocampus is a brain region in which neurogenesis persists into adulthood; however, the relationship between developmental and adult dentate gyrus neurogenesis has not been examined in detail. Here we used single-cell RNA sequencing to reveal the molecular dynamics and diversity of dentate gyrus cell types in perinatal, juvenile, and adult mice. We found distinct quiescent and proliferating progenitor cell types, linked by transient intermediate states to neuroblast stages and fully mature granule cells. We observed shifts in the molecular identity of quiescent and proliferating radial glia and granule cells during the postnatal period that were then maintained through adult stages. In contrast, intermediate progenitor cells, neuroblasts, and immature granule cells were nearly indistinguishable at all ages. These findings demonstrate the fundamental similarity of postnatal and adult neurogenesis in the hippocampus and pinpoint the early postnatal transformation of radial glia from embryonic progenitors to adult quiescent stem cells.

  6. A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, human and rat

    Directory of Open Access Journals (Sweden)

    Nap Jan-Peter

    2007-04-01

    Full Text Available Abstract Background The Affymetrix GeneChip technology uses multiple probes per gene to measure its expression level. Individual probe signals can vary widely, which hampers proper interpretation. This variation can be caused by probes that do not properly match their target gene or that match multiple genes. To determine the accuracy of Affymetrix arrays, we developed an extensive verification protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome databases. Results Applying this protocol to Affymetrix Mouse Genome arrays (the earlier U74Av2 and the newer 430 2.0 array, the number of sequence-verified probes with perfect matches was no less than 85% and 95%, respectively; and for 74% and 85% of the probe sets all probes were sequence verified. The latter percentages increased to 80% and 94% after discarding one or two unverifiable probes per probe set, and even further to 84% and 97% when, in addition, allowing for one or two mismatches between probe and target gene. Similar results were obtained for other mouse arrays, as well as for human and rat arrays. Based on these data, refined chip definition files for all arrays are provided online. Researchers can choose the version appropriate for their study to (reanalyze expression data. Conclusion The accuracy of Affymetrix probe sequences is higher than previously reported, particularly on newer arrays. Yet, refined probe set definitions have clear effects on the detection of differentially expressed genes. We demonstrate that the interpretation of the results of Affymetrix arrays is improved when the new chip definition files are used.

  7. Single-cell multiplexed cytokine profiling of CD19 CAR-T cells reveals a diverse landscape of polyfunctional antigen-specific response.

    Science.gov (United States)

    Xue, Qiong; Bettini, Emily; Paczkowski, Patrick; Ng, Colin; Kaiser, Alaina; McConnell, Timothy; Kodrasi, Olja; Quigley, Máire F; Heath, James; Fan, Rong; Mackay, Sean; Dudley, Mark E; Kassim, Sadik H; Zhou, Jing

    2017-11-21

    It remains challenging to characterize the functional attributes of chimeric antigen receptor (CAR)-engineered T cell product targeting CD19 related to potency and immunotoxicity ex vivo, despite promising in vivo efficacy in patients with B cell malignancies. We employed a single-cell, 16-plex cytokine microfluidics device and new analysis techniques to evaluate the functional profile of CD19 CAR-T cells upon antigen-specific stimulation. CAR-T cells were manufactured from human PBMCs transfected with the lentivirus encoding the CD19-BB-z transgene and expanded with anti-CD3/anti-CD28 coated beads. The enriched CAR-T cells were stimulated with anti-CAR or control IgG beads, stained with anti-CD4 RPE and anti-CD8 Alexa Fluor 647 antibodies, and incubated for 16 h in a single-cell barcode chip (SCBC). Each SCBC contains ~12,000 microchambers, covered with a glass slide that was pre-patterned with a complete copy of a 16-plex antibody array. Protein secretions from single CAR-T cells were captured and subsequently analyzed using proprietary software and new visualization methods. We demonstrate a new method for single-cell profiling of CD19 CAR-T pre-infusion products prepared from 4 healthy donors. CAR-T single cells exhibited a marked heterogeneity of cytokine secretions and polyfunctional (2+ cytokine) subsets specific to anti-CAR bead stimulation. The breadth of responses includes anti-tumor effector (Granzyme B, IFN-γ, MIP-1α, TNF-α), stimulatory (GM-CSF, IL-2, IL-8), regulatory (IL-4, IL-13, IL-22), and inflammatory (IL-6, IL-17A) functions. Furthermore, we developed two new bioinformatics tools for more effective polyfunctional subset visualization and comparison between donors. Single-cell, multiplexed, proteomic profiling of CD19 CAR-T product reveals a diverse landscape of immune effector response of CD19 CAR-T cells to antigen-specific challenge, providing a new platform for capturing CAR-T product data for correlative analysis. Additionally, such high

  8. Effects of ZnS layer on the performance improvement of the photosensitive ZnO nanowire arrays 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, 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, Xi' an Jiaotong University, Xi' an, 710049 (China); Gao, Yanping; Xing, Yonglei [Electronic Materials Research Laboratory, International Center for Dielectric Research, Key Laboratory of the Ministry of Education, 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, 639798 (Singapore)

    2016-08-01

    The impact of ZnS layer as an interface modification on the photosensitive ZnO nanowire arrays solar cells was studied. CdS, CdSe and ZnS were deposited on ZnO nanowire arrays by SILAR method. When a ZnS layer was deposited, the quantum dot barrier was indirectly become in contact with the electrolyte, which thus restrained the flow of electrons. The CdS sensitized solar cells has an efficiency of 0.55% with the deposition of the ZnS(3) layer, that is, with a deposition of three times, whereas the CdS/CdSe co-sensitized solar cells has an efficiency of 2.03% with the deposition of the ZnS(1) layer. It was also noted that as the thickness of the of ZnS layer was increased, V{sub oc}, I{sub sc} and efficiencies of both the solar cells were first increased and then decreased. In addition, the CdS/N719 solar cells has an efficiency of 0.75% with the deposition of the ZnS(2) layer. - Highlights: • The impact of ZnS layer on the photosensitive ZnO nanowire solar cells was studied. • ZnS layer restrained the flow of electrons to the electrolyte. • CdS/CdSe co-sensitized solar cells have higher efficiency than CdS solar cells. • When ZnS layer was increased, V{sub oc} and I{sub sc} firstly increased and then decreased.

  9. Radioresistance of intermediate TCR cells and their localization in the body of mice revealed by irradiation

    International Nuclear Information System (INIS)

    Kimura, Motohiko; Watanabe, Hisami; Ohtsuka, Kazuo; Iiai, Tsuneo; Tsuchida, Masanori; Sato, Shotaro; Abo, Toru

    1993-01-01

    Extrathymic generation of T cells in the liver and in the intestine was recently demonstrated. We investigated herein whether such T cells, especially those in the liver, are present in other organs of mice. This investigation is possible employing our recently introduced method with which even a minor proportion of extrathymic, intermediate T-cell receptor (TCR) cells in organs other than the liver can be identified. Intermediate TCR cells expressed higher levels of IL-2Rβ and lymphocyte function-associated antigen-1 (LFA-1) than bright TCR cells (i.e., T cells of thymic origin) as revealed by two-color staining. Although intermediate TCR cells were present at a small proportion in the spleen and thymus, they predominated in these organs after irradiation (9 Gy) and bone marrow reconstitution, or after low dose irradiation (6 Gy). This was due to that intermediate TCR cells were relatively radioresistant, whereas bright TCR cells were radiosensitive. Microscopic observation and immunochemical staining showed that intermediate TCR cells in the spleen localized in the red pulp and those in the thymus localized in the medulla. These intermediate TCR cells displayed a large light scatter, similar to such cells in the liver. The present results suggest that intermediate TCR cells may proliferate at multiple sites in the body. (author)

  10. Combination of short-length TiO{sub 2} nanorod arrays and compact PbS quantum-dot thin films for efficient solid-state quantum-dot-sensitized solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Zhengguo [School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009 (China); School of Chemistry and Chemical Engineering, Beifang University of Nationalities, Yinchuan 750021 (China); Shi, Chengwu, E-mail: shicw506@foxmail.com [School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009 (China); Chen, Junjun; Xiao, Guannan; Li, Long [School of Chemistry and Chemical Engineering, Hefei University of Technology, Hefei 230009 (China)

    2017-07-15

    Graphical abstract: The TiO{sub 2} nanorod array with the length of 600 nm, the diameter of 20 nm, the areal density of 500 μm{sup −2} was successfully prepared. The compact PbS quantum-dot thin film was firstly obtained on the TiO{sub 2} nanorod array by spin-coating-assisted successive ionic layer absorption and reaction with using 1,2-ethanedithiol. The photoelectric conversion efficiency (PCE) of the compact PbS quantum-dot thin film sensitized solar cells achieved 4.10% using spiro-OMeTAD as a hole transporting layer, while the PCE of the PbS quantum-dot sensitized solar cells was only 0.54%. - Highlights: • Preparation of TiO{sub 2} nanorod arrays with the length of 600 nm, diameter of 20 nm. • The compact PbS QD thin film and short-length TiO{sub 2} nanorod array were combined. • EDT addition improved PbS nanoparticle coverage and photovoltaic performance. • The compact PbS QD thin film sensitized solar cell achieved the PCE of 4.10%. - Abstract: Considering the balance of the hole diffusion length and the loading quantity of quantum-dots, the rutile TiO{sub 2} nanorod array with the length of 600 nm, the diameter of 20 nm, and the areal density of 500 μm{sup −2} is successfully prepared by the hydrothermal method using the aqueous grown solution of 38 mM titanium isopropoxide and 6 M hydrochloric acid at 170 °C for 105 min. The compact PbS quantum-dot thin film on the TiO{sub 2} nanorod array is firstly obtained by the spin-coating-assisted successive ionic layer absorption and reaction with using 1,2-ethanedithiol (EDT). The result reveals that the strong interaction between lead and EDT is very important to control the crystallite size of PbS quantum-dots and obtain the compact PbS quantum-dot thin film on the TiO{sub 2} nanorod array. The all solid-state sensitized solar cell with the combination of the short-length, high-density TiO{sub 2} nanorod array and the compact PbS quantum-dot thin film achieves the photoelectric conversion

  11. Alternative Routes to Induced Pluripotent Stem Cells Revealed by Reprogramming of the Neural Lineage.

    Science.gov (United States)

    Jackson, Steven A; Olufs, Zachariah P G; Tran, Khoa A; Zaidan, Nur Zafirah; Sridharan, Rupa

    2016-03-08

    During the reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells, the activation of pluripotency genes such as NANOG occurs after the mesenchymal to epithelial transition. Here we report that both adult stem cells (neural stem cells) and differentiated cells (astrocytes) of the neural lineage can activate NANOG in the absence of cadherin expression during reprogramming. Gene expression analysis revealed that only the NANOG+E-cadherin+ populations expressed stabilization markers, had upregulated several cell cycle genes; and were transgene independent. Inhibition of DOT1L activity enhanced both the numbers of NANOG+ and NANOG+E-cadherin+ colonies in neural stem cells. Expressing SOX2 in MEFs prior to reprogramming did not alter the ratio of NANOG colonies that express E-cadherin. Taken together these results provide a unique pathway for reprogramming taken by cells of the neural lineage. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  12. 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...... precursors. The authors show that a subset of these precursors contain an inherent resistance to apoptosis, and that while most terminally differentiate, some are likely to acquire additional mutations, leading to tumor formation. Thus, this work defines the cell-of-origin of retinoblastoma and suggests...... that mutations giving increased proliferative capacity are required for retinoblastoma development....

  13. Detection of Her2-overexpressing cancer cells using keyhole shaped chamber array employing a magnetic droplet-handling system.

    Science.gov (United States)

    Okochi, Mina; Koike, Shinji; Tanaka, Masayoshi; Honda, Hiroyuki

    2017-07-15

    An on-chip gene expression analysis compartmentalized in droplets was developed for detection of cancer cells at a single-cell level. The chip consists of a keyhole-shaped reaction chamber with hydrophobic modification employing a magnetic bead-droplet-handling system with a gate for bead separation. Using three kinds of water-based droplets in oil, a droplet with sample cells, a lysis buffer with magnetic beads, and RT-PCR buffer, parallel magnetic manipulation and fusion of droplets were performed using a magnet-handling device containing small external magnet patterns in an array. The actuation with the magnet offers a simple system for droplet manipulation that allows separation and fusion of droplets containing magnetic beads. After reverse transcription and amplification by thermal cycling, fluorescence was obtained for detection of overexpressing genes. For clinical detection of gastric cancer cells in peritoneal washing, the Her2-overexpressing gastric cancer cells spiked within normal cells was detected by gene expression analysis of droplets containing an average of 2.5 cells. Our developed droplet-based cancer detection system manipulated by external magnetic force without pumps or valves offers a simple and flexible set-up for transcriptional detection of cancer cells, and will be greatly advantageous for less-invasive clinical diagnosis and prognostic prediction. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Endometrial natural killer (NK) cells reveal a tissue-specific receptor repertoire.

    Science.gov (United States)

    Feyaerts, D; Kuret, T; van Cranenbroek, B; van der Zeeuw-Hingrez, S; van der Heijden, O W H; van der Meer, A; Joosten, I; van der Molen, R G

    2018-02-13

    Is the natural killer (NK) cell receptor repertoire of endometrial NK (eNK) cells tissue-specific? The NK cell receptor (NKR) expression profile in pre-pregnancy endometrium appears to have a unique tissue-specific phenotype, different from that found in NK cells in peripheral blood, suggesting that these cells are finely tuned towards the reception of an allogeneic fetus. NK cells are important for successful pregnancy. After implantation, NK cells encounter extravillous trophoblast cells and regulate trophoblast invasion. NK cell activity is amongst others regulated by C-type lectin heterodimer (CD94/NKG2) and killer cell immunoglobulin-like (KIR) receptors. KIR expression on decidual NK cells is affected by the presence of maternal HLA-C and biased towards KIR2D expression. However, little is known about NKR expression on eNK cells prior to pregnancy. In this study, matched peripheral and menstrual blood (a source of endometrial cells) was obtained from 25 healthy females with regular menstrual cycles. Menstrual blood was collected during the first 36 h of menstruation using a menstrual cup, a non-invasive technique to obtain endometrial cells. KIR and NKG2 receptor expression on eNK cells was characterized by 10-color flow cytometry, and compared to matched pbNK cells of the same female. KIR and HLA-C genotypes were determined by PCR-SSOP techniques. Anti-CMV IgG antibodies in plasma were measured by chemiluminescence immunoassay. KIR expression patterns of eNK cells collected from the same female do not differ over consecutive menstrual cycles. The percentage of NK cells expressing KIR2DL2/L3/S2, KIR2DL3, KIR2DL1, LILRB1 and/or NKG2A was significantly higher in eNK cells compared to pbNK cells, while no significant difference was observed for NKG2C, KIR2DL1/S1, and KIR3DL1. The NKR repertoire of eNK cells was clearly different from pbNK cells, with eNK cells co-expressing more than three NKR simultaneously. In addition, outlier analysis revealed 8 and 15 NKR

  15. Extraordinary electromagnetic transmission by antenna arrays and frequency selective surfaces having compound unit cells with dissimilar elements

    Energy Technology Data Exchange (ETDEWEB)

    Loui, Hung; Strassner, II, Bernd H.

    2018-03-20

    The various embodiments presented herein relate to extraordinary electromagnetic transmission (EEMT) to enable multiple inefficient (un-matched) but coupled radiators and/or apertures to radiate and/or pass electromagnetic waves efficiently. EEMT can be utilized such that signal transmission from a plurality of antennas and/or apertures occurs at a transmission frequency different to transmission frequencies of the individual antennas and/or aperture elements. The plurality of antennas/apertures can comprise first antenna/aperture having a first radiating area and material(s) and second antenna/aperture having a second radiating area and material(s), whereby the first radiating/aperture area and second radiating/aperture area can be co-located in a periodic compound unit cell. Owing to mutual coupling between the respective antennas/apertures in their arrayed configuration, the transmission frequency of the array can be shifted from the transmission frequencies of the individual elements. EEMT can be utilized for an array of evanescent of inefficient radiators connected to a transmission line(s).

  16. A paper-based microbial fuel cell array for rapid and high-throughput screening of electricity-producing bacteria.

    Science.gov (United States)

    Choi, Gihoon; Hassett, Daniel J; Choi, Seokheun

    2015-06-21

    There is a large global effort to improve microbial fuel cell (MFC) techniques and advance their translational potential toward practical, real-world applications. Significant boosts in MFC performance can be achieved with the development of new techniques in synthetic biology that can regulate microbial metabolic pathways or control their gene expression. For these new directions, a high-throughput and rapid screening tool for microbial biopower production is needed. In this work, a 48-well, paper-based sensing platform was developed for the high-throughput and rapid characterization of the electricity-producing capability of microbes. 48 spatially distinct wells of a sensor array were prepared by patterning 48 hydrophilic reservoirs on paper with hydrophobic wax boundaries. This paper-based platform exploited the ability of paper to quickly wick fluid and promoted bacterial attachment to the anode pads, resulting in instant current generation upon loading of the bacterial inoculum. We validated the utility of our MFC array by studying how strategic genetic modifications impacted the electrochemical activity of various Pseudomonas aeruginosa mutant strains. Within just 20 minutes, we successfully determined the electricity generation capacity of eight isogenic mutants of P. aeruginosa. These efforts demonstrate that our MFC array displays highly comparable performance characteristics and identifies genes in P. aeruginosa that can trigger a higher power density.

  17. 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

  18. Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types.

    Science.gov (United States)

    Giotti, Bruno; Joshi, Anagha; Freeman, Tom C

    2017-01-05

    Cell division is central to the physiology and pathology of all eukaryotic organisms. The molecular machinery underpinning the cell cycle has been studied extensively in a number of species and core aspects of it have been found to be highly conserved. Similarly, the transcriptional changes associated with this pathway have been studied in different organisms and different cell types. In each case hundreds of genes have been reported to be regulated, however there seems to be little consensus in the genes identified across different studies. In a recent comparison of transcriptomic studies of the cell cycle in different human cell types, only 96 cell cycle genes were reported to be the same across all studies examined. Here we perform a systematic re-examination of published human cell cycle expression data by using a network-based approach to identify groups of genes with a similar expression profile and therefore function. Two clusters in particular, containing 298 transcripts, showed patterns of expression consistent with cell cycle occurrence across the four human cell types assessed. Our analysis shows that there is a far greater conservation of cell cycle-associated gene expression across human cell types than reported previously, which can be separated into two distinct transcriptional networks associated with the G 1 /S-S and G 2 -M phases of the cell cycle. This work also highlights the benefits of performing a re-analysis on combined datasets.

  19. 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.

  20. A quorum-sensing factor in vegetative Dictyostelium discoideum cells revealed by quantitative migration analysis.

    Directory of Open Access Journals (Sweden)

    Laurent Golé

    Full Text Available BACKGROUND: Many cells communicate through the production of diffusible signaling molecules that accumulate and once a critical concentration has been reached, can activate or repress a number of target genes in a process termed quorum sensing (QS. In the social amoeba Dictyostelium discoideum, QS plays an important role during development. However little is known about its effect on cell migration especially in the growth phase. METHODS AND FINDINGS: To investigate the role of cell density on cell migration in the growth phase, we use multisite timelapse microscopy and automated cell tracking. This analysis reveals a high heterogeneity within a given cell population, and the necessity to use large data sets to draw reliable conclusions on cell motion. In average, motion is persistent for short periods of time (t ≤ 5 min, but normal diffusive behavior is recovered over longer time periods. The persistence times are positively correlated with the migrated distances. Interestingly, the migrated distance decreases as well with cell density. The adaptation of cell migration to cell density highlights the role of a secreted quorum sensing factor (QSF on cell migration. Using a simple model describing the balance between the rate of QSF generation and the rate of QSF dilution, we were able to gather all experimental results into a single master curve, showing a sharp cell transition between high and low motile behaviors with increasing QSF. CONCLUSION: This study unambiguously demonstrates the central role played by QSF on amoeboid motion in the growth phase.

  1. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells

    OpenAIRE

    Cai, Xuezhong; Lu, Shihua; Zhang, Zhihong; Gonzalez, Carlos M.; Damania, Blossom; Cullen, Bryan R.

    2005-01-01

    MicroRNAs (miRNAs) are an endogenously encoded class of small RNAs that have been proposed to function as key posttranscriptional regulators of gene expression in a range of eukaryotic species, including humans. The small size of miRNA precursors makes them potentially ideal for use by viruses as inhibitors of host cell defense pathways. Here, we demonstrate that the pathogenic human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) encodes an array of 11 distinct miRNAs, all of whic...

  2. 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 co......) tiling array that covers discrete regions from different chromosomes to represent a range of gene content and exonic/nonexonic conservation grades of the human genome....

  3. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies.

    Science.gov (United States)

    Bakker, Bjorn; Taudt, Aaron; Belderbos, Mirjam E; Porubsky, David; Spierings, Diana C J; de Jong, Tristan V; Halsema, Nancy; Kazemier, Hinke G; Hoekstra-Wakker, Karina; Bradley, Allan; de Bont, Eveline S J M; van den Berg, Anke; Guryev, Victor; Lansdorp, Peter M; Colomé-Tatché, Maria; Foijer, Floris

    2016-05-31

    Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all lymphoma cells. This suggests that chromosome instability is somehow suppressed in the aneuploid lymphomas or that selection for frequently lost/gained chromosomes out-competes the CIN-imposed mis-segregation. To distinguish between these explanations and to examine karyotype dynamics in chromosome instable lymphoma, we use a newly developed single-cell whole genome sequencing (scWGS) platform that provides a complete and unbiased overview of copy number variations (CNV) in individual cells. To analyse these scWGS data, we develop AneuFinder, which allows annotation of copy number changes in a fully automated fashion and quantification of CNV heterogeneity between cells. Single-cell sequencing and AneuFinder analysis reveals high levels of copy number heterogeneity in chromosome instability-driven murine T-cell lymphoma samples, indicating ongoing chromosome instability. Application of this technology to human B cell leukaemias reveals different levels of karyotype heterogeneity in these cancers. Our data show that even though aneuploid tumours select for particular and recurring chromosome combinations, single-cell analysis using AneuFinder reveals copy number heterogeneity. This suggests ongoing chromosome instability that other platforms fail to detect. As chromosome instability might drive tumour evolution, karyotype analysis using single-cell sequencing technology could become an essential tool for cancer treatment stratification.

  4. Calcium Imaging Reveals Coordinated Simple Spike Pauses in Populations of Cerebellar Purkinje Cells

    Directory of Open Access Journals (Sweden)

    Jorge E. Ramirez

    2016-12-01

    Full Text Available The brain’s control of movement is thought to involve coordinated activity between cerebellar Purkinje cells. The results reported here demonstrate that somatic Ca2+ imaging is a faithful reporter of Na+-dependent “simple spike” pauses and enables us to optically record changes in firing rates in populations of Purkinje cells in brain slices and in vivo. This simultaneous calcium imaging of populations of Purkinje cells reveals a striking spatial organization of pauses in Purkinje cell activity between neighboring cells. The source of this organization is shown to be the presynaptic gamma-Aminobutyric acid producing (GABAergic network, and blocking ionotropic gamma-Aminobutyric acid receptor (GABAARs abolishes the synchrony. These data suggest that presynaptic interneurons synchronize (inactivity between neighboring Purkinje cells, and thereby maximize their effect on downstream targets in the deep cerebellar nuclei.

  5. Localised electrochemical impedance measurements of a polymer electrolyte fuel cell using a reference electrode array to give cathode-specific measurements and examine membrane hydration dynamics

    Science.gov (United States)

    Engebretsen, Erik; Hinds, Gareth; Meyer, Quentin; Mason, Tom; Brightman, Edward; Castanheira, Luis; Shearing, Paul R.; Brett, Daniel J. L.

    2018-04-01

    Advances in bespoke diagnostic techniques for polymer electrolyte fuel cells continue to provide unique insight into the internal operation of these devices and lead to improved performance and durability. Localised measurements of current density have proven to be extremely useful in designing better fuel cells and identifying optimal operating strategies, with electrochemical impedance spectroscopy (EIS) now routinely used to deconvolute the various losses in fuel cells. Combining the two techniques provides another dimension of understanding, but until now each localised EIS has been based on 2-electrode measurements, composed of both the anode and cathode responses. This work shows that a reference electrode array can be used to give individual electrode-specific EIS responses, in this case the cathode is focused on to demonstrate the approach. In addition, membrane hydration dynamics are studied under current load steps from open circuit voltage. A three-stage process is identified associated with an initial rapid reduction in membrane resistance after 10 s of applying a current step, followed by a slower ramp to approximately steady state, which was achieved after ∼250 s. These results support previously published work that has looked at membrane swelling dynamics and reveal that membrane hydration/membrane resistance is highly heterogeneous.

  6. Lead field theory provides a powerful tool for designing microelectrode array impedance measurements for biological cell detection and observation.

    Science.gov (United States)

    Böttrich, Marcel; Tanskanen, Jarno M A; Hyttinen, Jari A K

    2017-06-26

    Our aim is to introduce a method to enhance the design process of microelectrode array (MEA) based electric bioimpedance measurement systems for improved detection and viability assessment of living cells and tissues. We propose the application of electromagnetic lead field theory and reciprocity for MEA design and measurement result interpretation. Further, we simulated impedance spectroscopy (IS) with two- and four-electrode setups and a biological cell to illustrate the tool in the assessment of the capabilities of given MEA electrode constellations for detecting cells on or in the vicinity of the microelectrodes. The results show the power of the lead field theory in electromagnetic simulations of cell-microelectrode systems depicting the fundamental differences of two- and four-electrode IS measurement configurations to detect cells. Accordingly, the use in MEA system design is demonstrated by assessing the differences between the two- and four-electrode IS configurations. Further, our results show how cells affect the lead fields in these MEA system, and how we can utilize the differences of the two- and four-electrode setups in cell detection. The COMSOL simulator model is provided freely in public domain as open source. Lead field theory can be successfully applied in MEA design for the IS based assessment of biological cells providing the necessary visualization and insight for MEA design. The proposed method is expected to enhance the design and usability of automated cell and tissue manipulation systems required for bioreactors, which are intended for the automated production of cell and tissue grafts for medical purposes. MEA systems are also intended for toxicology to assess the effects of chemicals on living cells. Our results demonstrate that lead field concept is expected to enhance also the development of such methods and devices.

  7. Transmission electron microscopy reveals distinct macrophage- and tick cell-specific morphological stages of Ehrlichia chaffeensis.

    Directory of Open Access Journals (Sweden)

    Sarah E Dedonder

    Full Text Available BACKGROUND: Ehrlichia chaffeensis is an emerging tick-borne rickettsial pathogen responsible for human monocytic ehrlichiosis. Despite the induction of an active host immune response, the pathogen has evolved to persist in its vertebrate and tick hosts. Understanding how the organism progresses in tick and vertebrate host cells is critical in identifying effective strategies to block the pathogen transmission. Our recent molecular and proteomic studies revealed differences in numerous expressed proteins of the organism during its growth in different host environments. METHODOLOGY/PRINCIPAL FINDINGS: Transmission electron microscopy analysis was performed to assess morphological changes in the bacterium within macrophages and tick cells. The stages of pathogen progression observed included the attachment of the organism to the host cells, its engulfment and replication within a morulae by binary fission and release of the organisms from infected host cells by complete host cell lysis or by exocytosis. E. chaffeensis grown in tick cells was highly pleomorphic and appears to replicate by both binary fission and filamentous type cell divisions. The presence of Ehrlichia-like inclusions was also observed within the nucleus of both macrophages and tick cells. This observation was confirmed by confocal microscopy and immunoblot analysis. CONCLUSIONS/SIGNIFICANCE: Morphological differences in the pathogen's progression, replication, and processing within macrophages and tick cells provide further evidence that E. chaffeensis employs unique host-cell specific strategies in support of adaptation to vertebrate and tick cell environments.

  8. Modular expression analysis reveals functional conservation between human Langerhans cells and mouse cross-priming dendritic cells

    OpenAIRE

    Artyomov, Maxim N.; Munk, Adiel; Gorvel, Laurent; Korenfeld, Daniel; Cella, Marina; Tung, Thomas; Klechevsky, Eynav

    2015-01-01

    Characterization of functionally distinct dendritic cell (DC) subsets in mice has fueled interest in whether analogous counterparts exist in humans. Transcriptional modules of coordinately expressed genes were used for defining shared functions between the species. Comparing modules derived from four human skin DC subsets and modules derived from the Immunological Genome Project database for all mouse DC subsets revealed that human Langerhans cells (LCs) and the mouse XCR1+CD8?+CD103+ DCs sha...

  9. Process development for automated solar cell and module production. Task 4. Automated array assembly. Quarterly report No. 1

    Energy Technology Data Exchange (ETDEWEB)

    Hagerty, J. J.

    1980-10-15

    Work has been divided into five phases. The first phase is to modify existing hardware and controlling computer software to: (1) improve cell-to-cell placement accuracy, (2) improve the solder joint while reducing the amount of solder and flux smear on the cell's surface, and (3) reduce the system cycle time to 10 seconds. The second phase involves expanding the existing system's capabilities to be able to reject broken cells and make post-solder electrical tests. Phase 3 involves developing new hardware to allow for the automated encapsulation of solar modules. This involves three discrete pieces of hardware: (1) a vacuum platen end effector for the robot which allows it to pick up the 1' x 4' array of 35 inter-connected cells. With this, it can also pick up the cover glass and completed module, (2) a lamination preparation station which cuts the various encapsulation components from roll storage and positions them for encapsulation, and (3) an automated encapsulation chamber which interfaces with the above two and applies the heat and vacuum to cure the encapsulants. Phase 4 involves the final assembly of the encapsulated array into a framed, edge-sealed module completed for installation. For this we are using MBA's Glass Reinforced Concrete (GRC) in panels such as those developed by MBA for JPL under contract No. 955281. The GRC panel plays the multiple role of edge frame, substrate and mounting structure. An automated method of applying the edge seal will also be developed. The final phase (5) is the fabrication of six 1' x 4' electrically active solar modules using the above developed equipment. Progress is reported. (WHK)

  10. 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.

  11. 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.

  12. Phylogenetic analysis of the Neks reveals early diversification of ciliary-cell cycle kinases.

    Directory of Open Access Journals (Sweden)

    Jeremy D K Parker

    2007-10-01

    Full Text Available NIMA-related kinases (Neks have been studied in diverse eukaryotes, including the fungus Aspergillus and the ciliate Tetrahymena. In the former, a single Nek plays an essential role in cell cycle regulation; in the latter, which has more than 30 Neks in its genome, multiple Neks regulate ciliary length. Mammalian genomes encode an intermediate number of Neks, several of which are reported to play roles in cell cycle regulation and/or localize to centrosomes. Previously, we reported that organisms with cilia typically have more Neks than organisms without cilia, but were unable to establish the evolutionary history of the gene family.We have performed a large-scale analysis of the Nek family using Bayesian techniques, including tests of alternate topologies. We find that the Nek family had already expanded in the last common ancestor of eukaryotes, a ciliated cell which likely expressed at least five Neks. We suggest that Neks played an important role in the common ancestor in regulating cilia, centrioles, and centrosomes with respect to mitotic entry, and that this role continues today in organisms with cilia. Organisms that lack cilia generally show a reduction in the number of Nek clades represented, sometimes associated with lineage specific expansion of a single clade, as has occurred in the plants.This is the first rigorous phylogenetic analysis of a kinase family across a broad array of phyla. Our findings provide a coherent framework for the study of Neks and their roles in coordinating cilia and cell cycle progression.

  13. B-Cell-Specific Diversion of Glucose Carbon Utilization Reveals a Unique Vulnerability in B Cell Malignancies.

    Science.gov (United States)

    Xiao, Gang; Chan, Lai N; Klemm, Lars; Braas, Daniel; Chen, Zhengshan; Geng, Huimin; Zhang, Qiuyi Chen; Aghajanirefah, Ali; Cosgun, Kadriye Nehir; Sadras, Teresa; Lee, Jaewoong; Mirzapoiazova, Tamara; Salgia, Ravi; Ernst, Thomas; Hochhaus, Andreas; Jumaa, Hassan; Jiang, Xiaoyan; Weinstock, David M; Graeber, Thomas G; Müschen, Markus

    2018-04-05

    B cell activation during normal immune responses and oncogenic transformation impose increased metabolic demands on B cells and their ability to retain redox homeostasis. While the serine/threonine-protein phosphatase 2A (PP2A) was identified as a tumor suppressor in multiple types of cancer, our genetic studies revealed an essential role of PP2A in B cell tumors. Thereby, PP2A redirects glucose carbon utilization from glycolysis to the pentose phosphate pathway (PPP) to salvage oxidative stress. This unique vulnerability reflects constitutively low PPP activity in B cells and transcriptional repression of G6PD and other key PPP enzymes by the B cell transcription factors PAX5 and IKZF1. Reflecting B-cell-specific transcriptional PPP-repression, glucose carbon utilization in B cells is heavily skewed in favor of glycolysis resulting in lack of PPP-dependent antioxidant protection. These findings reveal a gatekeeper function of the PPP in a broad range of B cell malignancies that can be efficiently targeted by small molecule inhibition of PP2A and G6PD. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. MCF10A and MDA-MB-231 human breast basal epithelial cell co-culture in silicon micro-arrays.

    Science.gov (United States)

    Nikkhah, Mehdi; Strobl, Jeannine S; Schmelz, Eva M; Roberts, Paul C; Zhou, Hui; Agah, Masoud

    2011-10-01

    We developed istotropically etched silicon chip micro-arrays for co-culture of metastatic human breast cancer (MDA-MB-231) and non-tumorigenic human breast (MCF10A) cells. The micro-arrays were fabricated using a single-mask, single-etch step process. Each chip contained a 16×16 array of cavities 140 μm wide by 60 μm deep separated by planar silicon surfaces. Cells occupied 97-100% of the etched cavities. The cavities were enriched three-fold in MDA-MB-231 cells relative to the seeding ratio of, MDA-MB-231(1): MCF10A(10) cells. Micro co-cultures comprised of both MCF10A and MDA-MB-231 cells formed in 26% of cavities and contained 2-10 cells per cavity. Heterotropic cell interactions were seen in co-culture, and sites of these interactions were enriched with vinculin spikes. A selective morphological response to the histone deacetylase inhibitor (HDI), SAHA (suberoylanilide hydroxamic acid), occurred in MDA-MB-231 cells which was quantified by significant increases in cell length and cell area on flat surfaces and in the number of stretched cells inside the etched cavities. The morphology of MCF10A cells was unaltered in response to SAHA. Real time imaging showed the formation of highly dynamic and randomly orienting cytoplasmic extensions in MDA-MB-231 cells 1h after adding SAHA; this is the first report of a rapid, morphological response in breast tumor cells to a histone deacetylase inhibitor. The findings demonstrate the utility of etched silicon micro-arrays for the propagation of human breast cell co-cultures and the application of HDI as a potential marker to distinguish metastatic breast cancer cells in a background of normal breast cell types. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Controlled synthesis of ZnO branched nanorod arrays by hierarchical solution growth and application in dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Fang Xiaoming; Peng Lihua; Shang Xiaoying; Zhang Zhengguo

    2011-01-01

    We demonstrate the controlled synthesis of ZnO branched nanorod arrays on fluorine-doped SnO 2 -coated glass substrates by the hierarchical solution growth method. In the secondary growth, the concentration of Zn(NO 3 ) 2 /hexamethylenetetramine plays an important role in controlling the morphology of the branched nanorod arrays, besides that of diaminopropane used as a structure-directing agent to induce the growth of branches. The population density and morphology of the branched nanorod arrays depend on those of the nanorod arrays obtained from the primary growth, which can be modulated though the concentration of Zn(NO 3 ) 2 /hexamethylenetetramine in the primary growth solution. The dye-sensitized ZnO branched nanorod arrays exhibit much stronger optical absorption as compared with its corresponding primary nanorod arrays, suggesting that the addition of the branches improves light harvesting. The dye-sensitized solar cell based on the optimized ZnO branched nanorod array reaches a conversion efficiency of 1.66% under the light radiation of 1000 W/m 2 . The branched nanorod arrays can also be applied in other application fields of ZnO.

  16. GaSb solar cells grown on GaAs via interfacial misfit arrays for use in the III-Sb multi-junction cell

    Science.gov (United States)

    Nelson, George T.; Juang, Bor-Chau; Slocum, Michael A.; Bittner, Zachary S.; Laghumavarapu, Ramesh B.; Huffaker, Diana L.; Hubbard, Seth M.

    2017-12-01

    Growth of GaSb with low threading dislocation density directly on GaAs may be possible with the strategic strain relaxation of interfacial misfit arrays. This creates an opportunity for a multi-junction solar cell with access to a wide range of well-developed direct bandgap materials. Multi-junction cells with a single layer of GaSb/GaAs interfacial misfit arrays could achieve higher efficiency than state-of-the-art inverted metamorphic multi-junction cells while forgoing the need for costly compositionally graded buffer layers. To develop this technology, GaSb single junction cells were grown via molecular beam epitaxy on both GaSb and GaAs substrates to compare homoepitaxial and heteroepitaxial GaSb device results. The GaSb-on-GaSb cell had an AM1.5g efficiency of 5.5% and a 44-sun AM1.5d efficiency of 8.9%. The GaSb-on-GaAs cell was 1.0% efficient under AM1.5g and 4.5% at 44 suns. The lower performance of the heteroepitaxial cell was due to low minority carrier Shockley-Read-Hall lifetimes and bulk shunting caused by defects related to the mismatched growth. A physics-based device simulator was used to create an inverted triple-junction GaInP/GaAs/GaSb model. The model predicted that, with current GaSb-on-GaAs material quality, the not-current-matched, proof-of-concept cell would provide 0.5% absolute efficiency gain over a tandem GaInP/GaAs cell at 1 sun and 2.5% gain at 44 suns, indicating that the effectiveness of the GaSb junction was a function of concentration.

  17. 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.

  18. Survey reveals public open to ban on hand-held cell phone use and texting.

    Science.gov (United States)

    2013-01-01

    A study performed by the Bureau of Transportation Statistics : (BTS) reveals that the public is open to a ban on : hand-held cell phone use while driving. The study is based : on data from 2009s Omnibus Household Survey (OHS), : which is administe...

  19. Magnetic arrays

    Science.gov (United States)

    Trumper, D.L.; Kim, W.; Williams, M.E.

    1997-05-20

    Electromagnet arrays are disclosed which can provide selected field patterns in either two or three dimensions, and in particular, which can provide single-sided field patterns in two or three dimensions. These features are achieved by providing arrays which have current densities that vary in the windings both parallel to the array and in the direction of array thickness. 12 figs.

  20. Magnetic arrays

    Energy Technology Data Exchange (ETDEWEB)

    Trumper, David L. (Plaistow, NH); Kim, Won-jong (Cambridge, MA); Williams, Mark E. (Pelham, NH)

    1997-05-20

    Electromagnet arrays which can provide selected field patterns in either two or three dimensions, and in particular, which can provide single-sided field patterns in two or three dimensions. These features are achieved by providing arrays which have current densities that vary in the windings both parallel to the array and in the direction of array thickness.

  1. Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

    NARCIS (Netherlands)

    Semrau, Stefan; Goldmann, Johanna E; Soumillon, Magali; Mikkelsen, Tarjei S; Jaenisch, Rudolf; van Oudenaarden, Alexander

    2017-01-01

    Gene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measure the gene expression

  2. Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.

    Science.gov (United States)

    Zheng, Chunhong; Zheng, Liangtao; Yoo, Jae-Kwang; Guo, Huahu; Zhang, Yuanyuan; Guo, Xinyi; Kang, Boxi; Hu, Ruozhen; Huang, Julie Y; Zhang, Qiming; Liu, Zhouzerui; Dong, Minghui; Hu, Xueda; Ouyang, Wenjun; Peng, Jirun; Zhang, Zemin

    2017-06-15

    Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8 + T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8 + T cells and Tregs and represses the CD8 + T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Genetically induced cell death in bulge stem cells reveals their redundancy for hair and epidermal regeneration.

    Science.gov (United States)

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

    2015-03-01

    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 Setd8 eliminated the contribution of bulge cells to hair follicle regeneration through inhibition of cell division and induction of cell death, but the growth and morphology of hair follicles were unaffected. Furthermore, ablation of Setd8 in the hair follicle bulge blocked the contribution of K19-postive stem cells to wounded epidermis, but the wound healing process was unaltered. Our data indicate that quiescent bulge stem cells are dispensable for hair follicle regeneration and epidermal injury in the short term and support the hypothesis that quiescent and cycling stem cell populations are equipotent. © 2014 AlphaMed Press.

  4. Single-cell paired-end genome sequencing reveals structural variation per cell cycle

    Science.gov (United States)

    Voet, Thierry; Kumar, Parveen; Van Loo, Peter; Cooke, Susanna L.; Marshall, John; Lin, Meng-Lay; Zamani Esteki, Masoud; Van der Aa, Niels; Mateiu, Ligia; McBride, David J.; Bignell, Graham R.; McLaren, Stuart; Teague, Jon; Butler, Adam; Raine, Keiran; Stebbings, Lucy A.; Quail, Michael A.; D’Hooghe, Thomas; Moreau, Yves; Futreal, P. Andrew; Stratton, Michael R.; Vermeesch, Joris R.; Campbell, Peter J.

    2013-01-01

    The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although single-cell genome analyses could resolve these problems, such analyses are error-prone because of whole-genome amplification (WGA) artefacts and are limited in the types of DNA mutation that can be discerned. We developed methods for paired-end sequence analysis of single-cell WGA products that enable (i) detecting multiple classes of DNA mutation, (ii) distinguishing DNA copy number changes from allelic WGA-amplification artefacts by the discovery of matching aberrantly mapping read pairs among the surfeit of paired-end WGA and mapping artefacts and (iii) delineating the break points and architecture of structural variants. By applying the methods, we capture DNA copy number changes acquired over one cell cycle in breast cancer cells and in blastomeres derived from a human zygote after in vitro fertilization. Furthermore, we were able to discover and fine-map a heritable inter-chromosomal rearrangement t(1;16)(p36;p12) by sequencing a single blastomere. The methods will expedite applications in basic genome research and provide a stepping stone to novel approaches for clinical genetic diagnosis. PMID:23630320

  5. Traumatic brain injury reveals novel cell lineage relationships within the subventricular zone

    Directory of Open Access Journals (Sweden)

    Gretchen M. Thomsen

    2014-07-01

    Full Text Available The acute response of the rodent subventricular zone (SVZ to traumatic brain injury (TBI involves a physical expansion through increased cell proliferation. However, the cellular underpinnings of these changes are not well understood. Our analyses have revealed that there are two distinct transit-amplifying cell populations that respond in opposite ways to injury. Mash1+ transit-amplifying cells are the primary SVZ cell type that is stimulated to divide following TBI. In contrast, the EGFR+ population, which has been considered to be a functionally equivalent progenitor population to Mash1+ cells in the uninjured brain, becomes significantly less proliferative after injury. Although normally quiescent GFAP+ stem cells are stimulated to divide in SVZ ablation models, we found that the GFAP+ stem cells do not divide more after TBI. We found, instead, that TBI results in increased numbers of GFAP+/EGFR+ stem cells via non-proliferative means—potentially through the dedifferentiation of progenitor cells. EGFR+ progenitors from injured brains only were competent to revert to a stem cell state following brief exposure to growth factors. Thus, our results demonstrate previously unknown changes in lineage relationships that differ from conventional models and likely reflect an adaptive response of the SVZ to maintain endogenous brain repair after TBI.

  6. MRI reveals slow clearance of dead cell transplants in mouse forelimb muscles

    Science.gov (United States)

    Zhang, Yanhui; Zhang, Hongyan; Ding, Lijun; Zhang, Hailu; Zhang, Pengli; Jiang, Haizhen; Tan, Bo; Deng, Zongwu

    2017-01-01

    A small molecule tetraazacyclododecane-1,4,7,10-tetraacetic acid (Gd-DOTA)4-TPP agent is used to label human mesenchymal stem cells (hMSCs) via electroporation (EP). The present study assessed the cytotoxicity of cell labeling, in addition to its effect on cell differentiation potential. There were no significant adverse effects on cell viability or differentiation induced by either EP or cellular uptake of (Gd-DOTA)4-TPP. Labeled live and dead hMSCs were transplanted into mouse forelimb muscles. T2-weighted magnetic resonance imaging (MRI) was used to track the in vivo fate of the cell transplants. The labeling and imaging strategy allowed long term tracking of the cell transplants and unambiguous distinguishing of the cell transplants from their surrounding tissues. Cell migration was observed for live hMSCs injected into subcutaneous tissues, however not for either live or dead hMSCS injected into limb muscles. A slow clearance process occurred of the dead cell transplants in the limb muscular tissue. The MRI results therefore reveal that the fate and physiological activities of cell transplants depend on the nature of their host tissue. PMID:28765924

  7. 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.

  8. 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.

  9. Self-cooling mono-container fuel cell generators and power plants using an array of such generators

    Science.gov (United States)

    Gillett, James E.; Dederer, Jeffrey T.; Zafred, Paolo R.

    1998-01-01

    A mono-container fuel cell generator (10) contains a layer of interior insulation (14), a layer of exterior insulation (16) and a single housing (20) between the insulation layers, where fuel cells, containing electrodes and electrolyte, are surrounded by the interior insulation (14) in the interior (12) of the generator, and the generator is capable of operating at temperatures over about 650.degree. C., where the combination of interior and exterior insulation layers have the ability to control the temperature in the housing (20) below the degradation temperature of the housing material. The housing can also contain integral cooling ducts, and a plurality of these generators can be positioned next to each other to provide a power block array with interior cooling.

  10. Prognostic impact of array-based genomic profiles in esophageal squamous cell cancer

    DEFF Research Database (Denmark)

    Carneiro, Ana; Isinger, Anna; Karlsson, Anna

    2008-01-01

    applied array-based comparative genomic hybridization (aCGH) to obtain a whole genome copy number profile relevant for identifying deranged pathways and clinically applicable markers. METHODS: A 32 k aCGH platform was used for high resolution mapping of copy number changes in 30 stage I-IV ESCC. Potential......p13.3 independently predicted poor survival in multivariate analysis. CONCLUSION: 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...

  11. Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

    DEFF Research Database (Denmark)

    Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas

    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...... 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...

  12. Array CGH analysis of chronic lymphocytic leukemia reveals frequent cryptic monoallelic and biallelic deletions of chromosome 22q11 that include the PRAME gene

    NARCIS (Netherlands)

    Gunn, Shelly R.; Bolla, Aswani R.; Barron, Lynn L.; Gorre, Mercedes E.; Mohammed, Mansoor S.; Bahler, David W.; Mellink, Clemens H. M.; van Oers, Marinus H. J.; Keating, Michael J.; Ferrajoli, Alessandra; Coombes, Kevin R.; Abruzzo, Lynne V.; Robetorye, Ryan S.

    2009-01-01

    We used BAC array-based CGH to detect genomic imbalances in 187 CLL cases. Submicroscopic deletions of chromosome 22q11 were observed in 28 cases (15%), and the frequency of these deletions was second only to loss of the 13q14 region, the most common genomic aberration in CLL. Oligonucleotide-based

  13. 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

    (CGH) for copy number changes and single-copy number polymorphism (SNP) microarrays for allelic loss (LOH). Many array-based CGH changes were not found by LOH because they did not cause true reduction-to-homozygosity. Conversely, many regions of SNP-LOH occurred in the absence of copy number change...

  14. Antarctic-wide array of high-resolution ice core records reveals pervasive lead pollution began in 1889 and persists today

    DEFF Research Database (Denmark)

    McConnell, J.R.; Maselli, OJ; Sigl, Michael

    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...

  15. Zebrafish B Cell Development without a Pre-B Cell Stage, Revealed by CD79 Fluorescence Reporter Transgenes.

    Science.gov (United States)

    Liu, Xingjun; Li, Yue-Sheng; Shinton, Susan A; Rhodes, Jennifer; Tang, Lingjuan; Feng, Hui; Jette, Cicely A; Look, A Thomas; Hayakawa, Kyoko; Hardy, Richard R

    2017-09-01

    CD79a and CD79b proteins associate with Ig receptors as integral signaling components of the B cell Ag receptor complex. To study B cell development in zebrafish, we isolated orthologs of these genes and performed in situ hybridization, finding that their expression colocalized with IgH-μ in the kidney, which is the site of B cell development. CD79 transgenic lines were made by linking the promoter and upstream regulatory segments of CD79a and CD79b to enhanced GFP to identify B cells, as demonstrated by PCR analysis of IgH-μ expression in sorted cells. We crossed these CD79-GFP lines to a recombination activating gene (Rag)2:mCherry transgenic line to identify B cell development stages in kidney marrow. Initiation of CD79:GFP expression in Rag2:mCherry + cells and the timing of Ig H and L chain expression revealed simultaneous expression of both IgH-μ- and IgL-κ-chains, without progressing through the stage of IgH-μ-chain alone. Rag2:mCherry + cells without CD79:GFP showed the highest Rag1 and Rag2 mRNAs compared with CD79a and CD79b:GFP + B cells, which showed strongly reduced Rag mRNAs. Thus, B cell development in zebrafish does not go through a Rag hi CD79 + IgH-μ + pre-B cell stage, different from mammals. After the generation of CD79:GFP + B cells, decreased CD79 expression occurred upon differentiation to Ig secretion, as detected by alteration from membrane to secreted IgH-μ exon usage, similar to in mammals. This confirmed a conserved role for CD79 in B cell development and differentiation, without the requirement of a pre-B cell stage in zebrafish. Copyright © 2017 by The American Association of Immunologists, Inc.

  16. 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

    . 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...

  17. Solar fuel production in a novel polymeric electrolyte membrane photoelectrochemical (PEM-PEC) cell with a web of titania nanotube arrays as photoanode and gaseous reactants

    NARCIS (Netherlands)

    Stoll, T.; Zafeiropoulos, G.; Tsampas, M. N.

    2016-01-01

    A novel photoelectrochemical (PEC) cell design is proposed and investigated for H-2 production with gaseous reactants. The core of the cell is a membrane electrode assembly (MEA) that consists of a TiO2 nanotube arrays photoanode, a Pt/C cathode, a Pt/C reference electrode and a proton conducting

  18. The Molecular Architecture of Cell Adhesion: Dynamic Remodeling Revealed by Videonanoscopy

    Directory of Open Access Journals (Sweden)

    Arnauld eSergé

    2016-05-01

    Full Text Available The plasma membrane delimits the cell, which is the basic unit of living organisms, and is also a privileged site for cell communication with the environment. Cell adhesion can occur through cell-cell and cell-matrix contacts. Adhesion proteins such as integrins and cadherins also constitute receptors for inside-out and outside-in signaling within proteolipidic platforms. Adhesion molecule targeting and stabilization relies on specific features such as preferential segregation by the sub-membrane cytoskeleton meshwork and within membrane proteolipidic microdomains. This review presents an overview of the recent insights brought by the latest developments in microscopy, to unravel the molecular remodeling occurring at cell contacts. The dynamic aspect of cell adhesion was recently highlighted by super-resolution videomicroscopy, also named videonanoscopy. By circumventing the diffraction limit of light, nanoscopy has allowed the monitoring of molecular localization and behavior at the single-molecule level, on fixed and living cells. Accessing molecular-resolution details such as quantitatively monitoring components entering and leaving cell contacts by lateral diffusion and reversible association has revealed an unexpected plasticity. Adhesion structures can be highly specialized, such as focal adhesion in motile cells, as well as immune and neuronal synapses. Spatiotemporal reorganization of adhesion molecules, receptors and adaptors directly relates to structure/function modulation. Assembly of these supramolecular complexes is continuously balanced by dynamic events, remodeling adhesions on various timescales, notably by molecular conformation switches, lateral diffusion within the membrane and endo/exocytosis. Pathological alterations in cell adhesion are involved in cancer evolution, through cancer stem cell interaction with stromal niches, growth, extravasation and metastasis.

  19. Single exosome study reveals subpopulations distributed among cell lines with variability related to membrane content

    Directory of Open Access Journals (Sweden)

    Zachary J. Smith

    2015-12-01

    Full Text Available Current analysis of exosomes focuses primarily on bulk analysis, where exosome-to-exosome variability cannot be assessed. In this study, we used Raman spectroscopy to study the chemical composition of single exosomes. We measured spectra of individual exosomes from 8 cell lines. Cell-line-averaged spectra varied considerably, reflecting the variation in total exosomal protein, lipid, genetic, and cytosolic content. Unexpectedly, single exosomes isolated from the same cell type also exhibited high spectral variability. Subsequent spectral analysis revealed clustering of single exosomes into 4 distinct groups that were not cell-line specific. Each group contained exosomes from multiple cell lines, and most cell lines had exosomes in multiple groups. The differences between these groups are related to chemical differences primarily due to differing membrane composition. Through a principal components analysis, we identified that the major sources of spectral variation among the exosomes were in cholesterol content, relative expression of phospholipids to cholesterol, and surface protein expression. For example, exosomes derived from cancerous versus non-cancerous cell lines can be largely separated based on their relative expression of cholesterol and phospholipids. We are the first to indicate that exosome subpopulations are shared among cell types, suggesting distributed exosome functionality. The origins of these differences are likely related to the specific role of extracellular vesicle subpopulations in both normal cell function and carcinogenesis, and they may provide diagnostic potential at the single exosome level.

  20. 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)

    Pascal, Laura E; Liu, Alvin Y; Vêncio, Ricardo ZN; Page, Laura S; Liebeskind, Emily S; Shadle, Christina P; Troisch, Pamela; Marzolf, Bruz; True, Lawrence D; Hood, Leroy E

    2009-01-01

    Prostate cancer cells in primary tumors have been typed CD10 - /CD13 - /CD24 hi /CD26 + /CD38 lo /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

  1. 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.

  2. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells

    Science.gov (United States)

    Cai, Xuezhong; Lu, Shihua; Zhang, Zhihong; Gonzalez, Carlos M.; Damania, Blossom; Cullen, Bryan R.

    2005-01-01

    MicroRNAs (miRNAs) are an endogenously encoded class of small RNAs that have been proposed to function as key posttranscriptional regulators of gene expression in a range of eukaryotic species, including humans. The small size of miRNA precursors makes them potentially ideal for use by viruses as inhibitors of host cell defense pathways. Here, we demonstrate that the pathogenic human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) encodes an array of 11 distinct miRNAs, all of which are expressed at readily detectable levels in latently KSHV infected cells. Individual KSHV miRNAs were expressed at up to 2,200 copies per cell. The KSHV miRNAs are expressed from what appears to be a single genetic locus that largely coincides with an ≈4-kb noncoding sequence located between the KSHV v-cyclin and K12/Kaposin genes, both of which are also expressed in latently infected cells. Computer analysis of potential mRNA targets for these viral miRNAs identified a number of interesting candidate genes, including several mRNAs previously shown to be down-regulated in KSHV-infected cells. We hypothesize that these viral miRNAs play a critical role in the establishment and/or maintenance of KSHV latent infection in vivo and, hence, in KSHV-induced oncogenesis. PMID:15800047

  3. Performance enhancement of quantum dot sensitized solar cells under TiO2 nanotube arrays membranes optimization

    Science.gov (United States)

    Peng, Zhuoyin; Liu, Yueli; Zhao, Yinghan; Liao, Lida; Chen, Jian

    2017-07-01

    One-dimensional single crystalline TiO2 nanotube arrays with different length are prepared, and transferred onto the FTO glass substrate with different concentration of Ti-precursor. The relationships between the concentration of Ti-precursor and the optical properties, as well as the photovoltaic performance of the as-prepared solar cells have been investigated. The optical absorption intensity is obviously enhanced and optical absorption edge is expanded to 800 nm for the CdSe/CdS/TiO2 NTs solar cells. In addition, 20 μm - CdSe/CdS/TiO2 NTs solar cells with 0.1 M Ti-precursor have the great photovoltaic conversion efficiency of 4.18%. The excellent photovoltaic performance is attributed to the suitable TiO2 connection layer from 0.1 M Ti-precursor and length of TiO2 NTs, which greatly enhances the electron-hole generation and charge transfer performance in the solar cells. Finally, the photovoltaic efficiency of the as-fabricated solar cells can be further enhanced to 4.51% through the ZnS passivation layer deposition.[Figure not available: see fulltext.

  4. Rapid and specific electrochemical detection of prostate cancer cells using an aperture sensor array.

    Science.gov (United States)

    Moscovici, Mario; Bhimji, Alyajahan; Kelley, Shana O

    2013-03-07

    A rapid, simple and specific cancer cell counting sensor would allow for early detection and better disease management. We have developed a novel cell counting device that can specifically count 125 prostate cancer cells in both complex media with serum and a mixed cell population containing non-target cells within 15 min. The microfabricated glass chip with exposed gold apertures utilizes the anti-EpCAM antibody to selectively count prostate cancer cells via differential pulse voltammetry. The newly developed sensor exhibits excellent sensitivity and selectivity. The cells remain viable throughout the counting process and can be used for further analysis. This device could have utility for future applications in early stage cancer diagnosis.

  5. 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.

  6. Genome-wide profiling of pluripotent cells reveals a unique molecular signature of human embryonic germ cells.

    Directory of Open Access Journals (Sweden)

    Nikta Pashai

    Full Text Available Human embryonic germ cells (EGCs provide a powerful model for identifying molecules involved in the pluripotent state when compared to their progenitors, primordial germ cells (PGCs, and other pluripotent stem cells. Microarray and Principal Component Analysis (PCA reveals for the first time that human EGCs possess a transcription profile distinct from PGCs and other pluripotent stem cells. Validation with qRT-PCR confirms that human EGCs and PGCs express many pluripotency-associated genes but with quantifiable differences compared to pluripotent embryonic stem cells (ESCs, induced pluripotent stem cells (IPSCs, and embryonal carcinoma cells (ECCs. Analyses also identified a number of target genes that may be potentially associated with their unique pluripotent states. These include IPO7, MED7, RBM26, HSPD1, and KRAS which were upregulated in EGCs along with other pluripotent stem cells when compared to PGCs. Other potential target genes were also found which may contribute toward a primed ESC-like state. These genes were exclusively up-regulated in ESCs, IPSCs and ECCs including PARP1, CCNE1, CDK6, AURKA, MAD2L1, CCNG1, and CCNB1 which are involved in cell cycle regulation, cellular metabolism and DNA repair and replication. Gene classification analysis also confirmed that the distinguishing feature of EGCs compared to ESCs, ECCs, and IPSCs lies primarily in their genetic contribution to cellular metabolism, cell cycle, and cell adhesion. In contrast, several genes were found upregulated in PGCs which may help distinguish their unipotent state including HBA1, DMRT1, SPANXA1, and EHD2. Together, these findings provide the first glimpse into a unique genomic signature of human germ cells and pluripotent stem cells and provide genes potentially involved in defining different states of germ-line pluripotency.

  7. Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells

    Science.gov (United States)

    Pashai, Nikta; Hao, Haiping; All, Angelo; Gupta, Siddharth; Chaerkady, Raghothama; De Los Angeles, Alejandro; Gearhart, John D.; Kerr, Candace L.

    2012-01-01

    Human embryonic germ cells (EGCs) provide a powerful model for identifying molecules involved in the pluripotent state when compared to their progenitors, primordial germ cells (PGCs), and other pluripotent stem cells. Microarray and Principal Component Analysis (PCA) reveals for the first time that human EGCs possess a transcription profile distinct from PGCs and other pluripotent stem cells. Validation with qRT-PCR confirms that human EGCs and PGCs express many pluripotency-associated genes but with quantifiable differences compared to pluripotent embryonic stem cells (ESCs), induced pluripotent stem cells (IPSCs), and embryonal carcinoma cells (ECCs). Analyses also identified a number of target genes that may be potentially associated with their unique pluripotent states. These include IPO7, MED7, RBM26, HSPD1, and KRAS which were upregulated in EGCs along with other pluripotent stem cells when compared to PGCs. Other potential target genes were also found which may contribute toward a primed ESC-like state. These genes were exclusively up-regulated in ESCs, IPSCs and ECCs including PARP1, CCNE1, CDK6, AURKA, MAD2L1, CCNG1, and CCNB1 which are involved in cell cycle regulation, cellular metabolism and DNA repair and replication. Gene classification analysis also confirmed that the distinguishing feature of EGCs compared to ESCs, ECCs, and IPSCs lies primarily in their genetic contribution to cellular metabolism, cell cycle, and cell adhesion. In contrast, several genes were found upregulated in PGCs which may help distinguish their unipotent state including HBA1, DMRT1, SPANXA1, and EHD2. Together, these findings provide the first glimpse into a unique genomic signature of human germ cells and pluripotent stem cells and provide genes potentially involved in defining different states of germ-line pluripotency. PMID:22737227

  8. Combination of short-length TiO2 nanorod arrays and compact PbS quantum-dot thin films for efficient solid-state quantum-dot-sensitized solar cells

    Science.gov (United States)

    Zhang, Zhengguo; Shi, Chengwu; Chen, Junjun; Xiao, Guannan; Li, Long

    2017-07-01

    Considering the balance of the hole diffusion length and the loading quantity of quantum-dots, the rutile TiO2 nanorod array with the length of 600 nm, the diameter of 20 nm, and the areal density of 500 μm-2 is successfully prepared by the hydrothermal method using the aqueous grown solution of 38 mM titanium isopropoxide and 6 M hydrochloric acid at 170 °C for 105 min. The compact PbS quantum-dot thin film on the TiO2 nanorod array is firstly obtained by the spin-coating-assisted successive ionic layer absorption and reaction with using 1,2-ethanedithiol (EDT). The result reveals that the strong interaction between lead and EDT is very important to control the crystallite size of PbS quantum-dots and obtain the compact PbS quantum-dot thin film on the TiO2 nanorod array. The all solid-state sensitized solar cell with the combination of the short-length, high-density TiO2 nanorod array and the compact PbS quantum-dot thin film achieves the photoelectric conversion efficiency of 4.10%, along with an open-circuit voltage of 0.52 V, a short-circuit photocurrent density of 13.56 mA cm-2 and a fill factor of 0.58.

  9. 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.

  10. The new anti-actin agent dihydrohalichondramide reveals fenestrae-forming centers in hepatic endothelial cells

    Directory of Open Access Journals (Sweden)

    Menu Eline

    2002-03-01

    Full Text Available Abstract Background Liver sinusoidal endothelial cells (LSECs react to different anti-actin agents by increasing their number of fenestrae. A new structure related to fenestrae formation could be observed when LSECs were treated with misakinolide. In this study, we investigated the effects of two new actin-binding agents on fenestrae dynamics. High-resolution microscopy, including immunocytochemistry and a combination of fluorescence- and scanning electron microscopy was applied. Results Halichondramide and dihydrohalichondramide disrupt microfilaments within 10 minutes and double the number of fenestrae in 30 minutes. Dihydrohalichondramide induces fenestrae-forming centers, whereas halichondramide only revealed fenestrae-forming centers without attached rows of fenestrae with increasing diameter. Correlative microscopy showed the absence of actin filaments (F-actin in sieve plates and fenestrae-forming centers. Comparable experiments on umbilical vein endothelial cells and bone marrow sinusoidal endothelial cells revealed cell contraction without the appearance of fenestrae or fenestrae-forming centers. Conclusion (I A comparison of all anti-actin agents tested so far, revealed that the only activity that misakinolide and dihydrohalichondramide have in common is their barbed end capping activity; (II this activity seems to slow down the process of fenestrae formation to such extent that it becomes possible to resolve fenestrae-forming centers; (III fenestrae formation resulting from microfilament disruption is probably unique to LSECs.

  11. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Brückner, Michael [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Becker, Katja [Justus Liebig University Giessen, Biochemistry and Molecular Biology, 35392 Giessen (Germany); Popp, Jürgen [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany); Frosch, Torsten, E-mail: torsten.frosch@uni-jena.de [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany)

    2015-09-24

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

  12. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

    International Nuclear Information System (INIS)

    Brückner, Michael; Becker, Katja; Popp, Jürgen; Frosch, Torsten

    2015-01-01

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

  13. 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 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.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.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 endometrial tissue reconstitution. Using this assay, we demonstrated that ESP

  14. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo salar).

    Science.gov (United States)

    Bourret, Vincent; Kent, Matthew P; Primmer, Craig R; Vasemägi, Anti; Karlsson, Sten; Hindar, Kjetil; McGinnity, Philip; Verspoor, Eric; Bernatchez, Louis; Lien, Sigbjørn

    2013-02-01

    Atlantic salmon (Salmo salar) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this study, we describe the development of a medium-density Atlantic salmon single nucleotide polymorphism (SNP) array based on expressed sequence tags (ESTs) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNPs were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated European and North American populations, and within Europe, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In Europe, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing Baltic populations to all others. We also discuss the potential future applications of the SNP array for conservation, management and aquaculture. © 2012 Blackwell Publishing Ltd.

  16. Analyses of absorption distribution of a rubidium cell side-pumped by a Laser-Diode-Array (LDA)

    Science.gov (United States)

    Yu, Hang; Han, Juhong; Rong, Kepeng; Wang, Shunyan; Cai, He; An, Guofei; Zhang, Wei; Yu, Qiang; Wu, Peng; Wang, Hongyuan; Wang, You

    2018-01-01

    A diode-pumped alkali laser (DPAL) has been regarded as one of the most potential candidates to achieve high power performances of next generation. In this paper, we investigate the physical properties of a rubidium cell side-pumped by a Laser-Diode-Array (LDA) in this study. As the saturated concentration of a gain medium inside a vapor cell is extremely sensitive to the temperature, the populations of every energy-level of the atomic alkali are strongly relying on the vapor temperature. Thus, the absorption characteristics of a DPAL are mainly dominated by the temperature distribution. In this paper, the temperature, absorption, and lasing distributions in the cross-section of a rubidium cell side-pumped by a LDA are obtained by means of a complicated mathematic procedure. Based on the original end-pumped mode we constructed before, a novel one-direction side-pumped theoretical mode has been established to explore the distribution properties in the transverse section of a rubidium vapor cell by combining the procedures of heat transfer and laser kinetics together. It has been thought the results might be helpful for design of a side-pumped configuration in a high-powered DPAL.

  17. Carbon fiber/Co9S8 nanotube arrays hybrid structures for flexible quantum dot-sensitized solar cells.

    Science.gov (United States)

    Guo, Wenxi; Chen, Chang; Ye, Meidan; Lv, Miaoqiang; Lin, Changjian

    2014-04-07

    Recently, hybrid carbon materials and inorganic nanocrystals have received an intensive amount of attention and have opened up an exciting new field in the design and fabrication of high-performance catalysts. Here we present a novel kind of hybrid counter electrode (CE) consisting of a carbon fiber (CF) and Co9S8 nanotube arrays (NTs) for fiber-shaped flexible quantum dot-sensitized solar cells (QDSSCs). The growth mechanisms of Co(CO3)0.35Cl0.20(OH)1.10 nanowire arrays (NWs) on the CFs were discussed, and the catalytic activity of the CF, Pt and Co9S8/CF hybrid structure (Co9S8@CF) were elucidated systematically as well. An absolute energy conversion efficiency of 3.79% has been demonstrated under 100 mW cm(-2) AM 1.5 illumination by using Co9S8@CF as a CE. This work not only demonstrates an innovative approach for growing cobalt sulfide NTs on flexible substrates that can be applied in flexible devices for energy harvesting and storage, but also provides a kind of hybrid structure and high-efficiency CE for QDSSCs.

  18. 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...

  19. Early transcriptional and epigenetic regulation of CD8+ T cell differentiation revealed by single-cell RNA-seq

    Science.gov (United States)

    Kakaradov, Boyko; Arsenio, Janilyn; Widjaja, Christella E.; He, Zhaoren; Aigner, Stefan; Metz, Patrick J.; Yu, Bingfei; Wehrens, Ellen J.; Lopez, Justine; Kim, Stephanie H.; Zuniga, Elina I.; Goldrath, Ananda W.; Chang, John T.; Yeo, Gene W.

    2017-01-01

    SUMMARY During microbial infection, responding CD8+ T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA sequencing approach and analyzed individual CD8+ T lymphocytes sequentially throughout the course of a viral infection in vivo. Our analyses revealed a striking transcriptional divergence among cells that had undergone their first division and identified previously unknown molecular determinants controlling CD8+ T lymphocyte fate specification. These findings suggest a model of terminal effector cell differentiation initiated by an early burst of transcriptional activity and subsequently refined by epigenetic silencing of transcripts associated with memory lymphocytes, highlighting the power and necessity of single-cell approaches. PMID:28218746

  20. 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

    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

  1. Fabrication of micropatterned arrays of gold nanoparticles for photothermal manipulation of living cells.

    Science.gov (United States)

    Polleux, Julien; Baffou, Guillaume

    2014-01-01

    The fabrication of micro/nanostructured surfaces functionalized with stimulus-responsive chemical groups proved to be an interesting approach to simultaneously confine cell adhesion and manipulate cell-substrate interactions down to the single cell level. However, reversibility of stimulus-triggered systems is often not possible or exhibits slow switching kinetics. In contrast to such setups, gold nanoparticles have the properties to efficiently and reversibly generate heat under illumination at their plasmon resonance band. Thus, photo-induced heating could be used to directly and locally interface living cells and dynamically tailor the interactions to their adhesive environment. In the present chapter, we will first detail the preparation of micropatterned and functionalized gold nanoparticles immobilized on glass coverslips, and then report how to reliably characterize the photothermal properties of such substrates that enable the dynamic manipulation of cells. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. 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.

  3. 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

    2016-09-06

    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.

  4. Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation.

    Science.gov (United States)

    Yu, Bingfei; Zhang, Kai; Milner, J Justin; Toma, Clara; Chen, Runqiang; Scott-Browne, James P; Pereira, Renata M; Crotty, Shane; Chang, John T; Pipkin, Matthew E; Wang, Wei; Goldrath, Ananda W

    2017-05-01

    Dynamic changes in the expression of transcription factors (TFs) can influence the specification of distinct CD8 + T cell fates, but the observation of equivalent expression of TFs among differentially fated precursor cells suggests additional underlying mechanisms. Here we profiled the genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8 + T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that the expression and binding of TFs contributed to the establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal key TFs that influence the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8 + T cell differentiation, regulated the formation of terminal-effector cell fates and memory-precursor cell fates, respectively. Our data define the epigenetic landscape of differentiation intermediates and facilitate the identification of TFs with previously unappreciated roles in CD8 + T cell differentiation.

  5. 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.

  6. Single cell amperometry reveals curcuminoids modulate the release of neurotransmitters during exocytosis from PC12 cells

    Science.gov (United States)

    Li, Xianchan; Mohammadi, Amir Saeid; Ewing, Andrew G.

    2016-01-01

    We used single cell amperometry to examine whether curcumin and bisdemethoxycurcumin (BDMC), substances that are suggested to affect learning and memory, can modulate monoamine release from PC12 cells. Our results indicate both curcumin and BDMC need long-term treatment (72 h in this study) to influence exocytosis effectively. By analyzing the parameters calculated from single exocytosis events, it can be concluded that curcumin and BDMC affect exocytosis through different mechanisms. Curcumin accelerates the event dynamics with no significant change of the monoamine amount released from single exocytotic events, whereas BDMC attenuates the amount from single exocytotic event with no significant change of the event dynamics. This comparison of the effect of curcumin and BDMC on exocytosis at the single cell level brings insight into their different mechanisms, which might lead to different biological actions. The effect of curcumin and BDMC on the opening and closing of the exocytotic fusion pore were also investigated. These results might be helpful for understanding the improvement of learning and memory and the anti-depression properties of curcuminoids. PMID:28579928

  7. 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.

  8. Intracellular CHO Cell Metabolite Profiling Reveals Steady-State Dependent Metabolic Fingerprints in Perfusion Culture.

    Science.gov (United States)

    Karst, Daniel J; Steinhoff, Robert F; Kopp, Marie R G; Serra, Elisa; Soos, Miroslav; Zenobi, Renato; Morbidelli, Massimo

    2017-07-01

    Perfusion cell culture processes allow the steady-state culture of mammalian cells at high viable cell density, which is beneficial for overall product yields and homogeneity of product quality in the manufacturing of therapeutic proteins. In this study, the extent of metabolic steady state and the change of the metabolite profile between different steady states of an industrial Chinese hamster ovary (CHO) cell line producing a monoclonal antibody (mAb) was investigated in stirred tank perfusion bioreactors. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) of daily cell extracts revealed more than a hundred peaks, among which 76 metabolites were identified by tandem MS (MS/MS) and high resolution Fourier transform ion cyclotron resonance (FT-ICR) MS. Nucleotide ratios (Uridine (U)-ratio, nucleotide triphosphate (NTP)-ratio and energy charge (EC)) and multivariate analysis of all features indicated a consistent metabolite profile for a stable culture performed at 40 × 10 6 cells/mL over 26 days of culture. Conversely, the reactor was operated continuously so as to reach three distinct steady states one after the other at 20, 60, and 40 × 10 6 cells/mL. In each case, a stable metabolite profile was achieved after an initial transient phase of approximately three days at constant cell density when varying between these set points. Clear clustering according to cell density was observed by principal component analysis, indicating steady-state dependent metabolite profiles. In particular, varying levels of nucleotides, nucleotide sugar, and lipid precursors explained most of the variance between the different cell density set points. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:879-890, 2017. © 2016 American Institute of Chemical Engineers.

  9. Single-cell tracking reveals antibiotic-induced changes in mycobacterial energy metabolism.

    Science.gov (United States)

    Maglica, Željka; Özdemir, Emre; McKinney, John D

    2015-02-17

    ATP is a key molecule of cell physiology, but despite its importance, there are currently no methods for monitoring single-cell ATP fluctuations in live bacteria. This is a major obstacle in studies of bacterial energy metabolism, because there is a growing awareness that bacteria respond to stressors such as antibiotics in a highly individualistic manner. Here, we present a method for long-term single-cell tracking of ATP levels in Mycobacterium smegmatis based on a combination of microfluidics, time-lapse microscopy, and Förster resonance energy transfer (FRET)-based ATP biosensors. Upon treating cells with antibiotics, we observed that individual cells undergo an abrupt and irreversible switch from high to low intracellular ATP levels. The kinetics and extent of ATP switching clearly discriminate between an inhibitor of ATP synthesis and other classes of antibiotics. Cells that resume growth after 24 h of antibiotic treatment maintain high ATP levels throughout the exposure period. In contrast, antibiotic-treated cells that switch from ATP-high to ATP-low states never resume growth after antibiotic washout. Surprisingly, only a subset of these nongrowing ATP-low cells stains with propidium iodide (PI), a widely used live/dead cell marker. These experiments also reveal a cryptic subset of cells that do not resume growth after antibiotic washout despite remaining ATP high and PI negative. We conclude that ATP tracking is a more dynamic, sensitive, reliable, and discriminating marker of cell viability than staining with PI. This method could be used in studies to evaluate antimicrobial effectiveness and mechanism of action, as well as for high-throughput screening. New antimicrobials are urgently needed to stem the rising tide of antibiotic-resistant bacteria. All antibiotics are expected to affect bacterial energy metabolism, directly or indirectly, yet tools to assess the impact of antibiotics on the ATP content of individual bacterial cells are lacking. The

  10. A microfluidic device for separation of amniotic fluid mesenchymal stem cells utilizing louver-array structures.

    Science.gov (United States)

    Wu, Huei-Wen; Lin, Xi-Zhang; Hwang, Shiaw-Min; Lee, Gwo-Bin

    2009-12-01

    Human mesenchymal stem cells can differentiate into multiple lineages for cell therapy and, therefore, have attracted considerable research interest recently. This study presents a new microfluidic device for bead and cell separation utilizing a combination of T-junction focusing and tilted louver-like structures. For the first time, a microfluidic device is used for continuous separation of amniotic stem cells from amniotic fluids. An experimental separation efficiency as high as 82.8% for amniotic fluid mesenchymal stem cells is achieved. Furthermore, a two-step separation process is performed to improve the separation efficiency to 97.1%. These results are based on characterization experiments that show that this microfluidic chip is capable of separating beads with diameters of 5, 10, 20, and 40 microm by adjusting the volume-flow-rate ratio between the flows in the main and side channels of the T-junction focusing structure. An optimal volume-flow-rate ratio of 0.5 can lead to high separation efficiencies of 87.8% and 85.7% for 5-microm and 10-microm beads, respectively, in a one-step separation process. The development of this microfluidic chip may be promising for future research into stem cells and for cell therapy.

  11. In Vivo Expansion of Melanoma-Specific T Cells Using Microneedle Arrays Coated with Immune-Polyelectrolyte Multilayers.

    Science.gov (United States)

    Zeng, Qin; Gammon, Joshua M; Tostanoski, Lisa H; Chiu, Yu-Chieh; Jewell, Christopher M

    2017-02-13

    Microneedles (MNs) are micron-scale polymeric or metallic structures that offer distinct advantages for vaccines by efficiently targeting skin-resident immune cells, eliminating injection-associated pain, and improving patient compliance. These advantages, along with recent studies showing therapeutic benefits achieved using traditional intradermal injections in human cancer patients, suggest MN delivery might enhance cancer vaccines and immunotherapies. We recently developed a new class of polyelectrolyte multilayers based on the self-assembly of model peptide antigens and molecular toll-like receptor agonists (TLRa) into ultrathin, conformal coatings. Here, we reasoned that these immune polyelectrolyte multilayers (iPEMs) might be a useful platform for assembling cancer vaccine components on MN arrays for intradermal delivery from these substrates. Using conserved human melanoma antigens and a potent TLRa vaccine adjuvant, CpG, we show that iPEMs can be assembled on MNs in an automated fashion. These films, prepared with up to 128 layers, are approximately 200 nm thick but provide cancer vaccine cargo loading >225 μg/cm 2 . In cell culture, iPEM cargo released from MNs is internalized by primary dendritic cells, promotes activation of these cells, and expands T cells during coculture. In mice, application of iPEM-coated MNs results in the codelivery of tumor antigen and CpG through the skin, expanding tumor-specific T cells during initial MN applications and resulting in larger memory recall responses during a subsequent booster MN application. This study support MNs coated with PEMs built from tumor vaccine components as a well-defined, modular system for generating tumor-specific immune responses, enabling new approaches that can be explored in combination with checkpoint blockade or other combination cancer therapies.

  12. Revealing the sequence of interactions of PuroA peptide with Candida albicans cells by live-cell imaging

    Science.gov (United States)

    Shagaghi, Nadin; Bhave, Mrinal; Palombo, Enzo A.; Clayton, Andrew H. A.

    2017-03-01

    To determine the mechanism(s) of action of antimicrobial peptides (AMPs) it is desirable to provide details of their interaction kinetics with cellular, sub-cellular and molecular targets. The synthetic peptide, PuroA, displays potent antimicrobial activities which have been attributed to peptide-induced membrane destabilization, or intracellular mechanisms of action (DNA-binding) or both. We used time-lapse fluorescence microscopy and fluorescence lifetime imaging microscopy (FLIM) to directly monitor the localization and interaction kinetics of a FITC- PuroA peptide on single Candida albicans cells in real time. Our results reveal the sequence of events leading to cell death. Within 1 minute, FITC-PuroA was observed to interact with SYTO-labelled nucleic acids, resulting in a noticeable quenching in the fluorescence lifetime of the peptide label at the nucleus of yeast cells, and cell-cycle arrest. A propidium iodide (PI) influx assay confirmed that peptide translocation itself did not disrupt the cell membrane integrity; however, PI entry occurred 25-45 minutes later, which correlated with an increase in fractional fluorescence of pores and an overall loss of cell size. Our results clarify that membrane disruption appears to be the mechanism by which the C. albicans cells are killed and this occurs after FITC-PuroA translocation and binding to intracellular targets.

  13. Modeling chronic myeloid leukemia in immunodeficient mice reveals expansion of aberrant mast cells and accumulation of pre-B cells

    International Nuclear Information System (INIS)

    Askmyr, M; Ågerstam, H; Lilljebjörn, H; Hansen, N; Karlsson, C; Palffy, S von; Landberg, N; Högberg, C; Lassen, C; Rissler, M; Richter, J; Ehinger, M; Järås, M; Fioretos, T

    2014-01-01

    Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm that, if not treated, will progress into blast crisis (BC) of either myeloid or B lymphoid phenotype. The BCR-ABL1 fusion gene, encoding a constitutively active tyrosine kinase, is thought to be sufficient to cause chronic phase (CP) CML, whereas additional genetic lesions are needed for progression into CML BC. To generate a humanized CML model, we retrovirally expressed BCR-ABL1 in the cord blood CD34 + cells and transplanted these into NOD-SCID (non-obese diabetic/severe-combined immunodeficient) interleukin-2-receptor γ-deficient mice. In primary mice, BCR-ABL1 expression induced an inflammatory-like state in the bone marrow and spleen, and mast cells were the only myeloid lineage specifically expanded by BCR-ABL1. Upon secondary transplantation, the pronounced inflammatory phenotype was lost and mainly human mast cells and macrophages were found in the bone marrow. Moreover, a striking block at the pre-B-cell stage was observed in primary mice, resulting in an accumulation of pre-B cells. A similar block in B-cell differentiation could be confirmed in primary cells from CML patients. Hence, this humanized mouse model of CML reveals previously unexplored features of CP CML and should be useful for further studies to understand the disease pathogenesis of CML

  14. miRNA array screening reveals cooperative MGMT-regulation between miR-181d-5p and miR-409-3p in glioblastoma

    Science.gov (United States)

    Khalil, Susanna; Fabbri, Enrica; Santangelo, Alessandra; Bezzerri, Valentino; Cantù, Cinzia; Gennaro, Gianfranco Di; Finotti, Alessia; Ghimenton, Claudio; Eccher, Albino; Dechecchi, Maria; Scarpa, Aldo; Hirshman, Brian; Chen, Clark; Ferracin, Manuela; Negrini, Massimo; Gambari, Roberto; Cabrini, Giulio

    2016-01-01

    The levels of expression of O6-methylguanine-DNA methyltransferase (MGMT) are relevant in predicting the response to the alkylating chemotherapy in patients affected by glioblastoma. MGMT promoter methylation and the published MGMT regulating microRNAs (miRNAs) do not completely explain the expression pattern of MGMT in clinical glioblastoma specimens. Here we used a genome-wide microarray-based approach to identify MGMT regulating miRNAs. Our screen unveiled three novel MGMT regulating miRNAs, miR-127-3p, miR-409-3p, and miR-124-3p, in addition to the previously identified miR-181d-5p. Transfection of these three novel miRNAs into the T98G glioblastoma cell line suppressed MGMT mRNA and protein expression. However, their MGMT- suppressive effects are 30–50% relative that seen with miR-181d-5p transfection. In silico analyses of The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) revealed that miR-181d-5p is the only miRNA that consistently exhibited inverse correlation with MGMT mRNA expression. However, statistical models incorporating both miR-181d-5p and miR-409-3p expression better predict MGMT expression relative to models involving either miRNA alone. Our results confirmed miR-181d-5p as the key MGMT-regulating miRNA. Other MGMT regulating miRNAs, including the miR-409-3p identified in this report, modify the effect of miR-181d-5p on MGMT expression. MGMT expression is, thus, regulated by cooperative interaction between key MGMT-regulating miRNAs. PMID:27057640

  15. Controllable preparation of TiO2 nanowire arrays on titanium mesh for flexible dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Liu, Wenwu; Lu, Hui; Zhang, Mei; Guo, Min

    2015-01-01

    Graphical abstract: TiO 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 2 NWAs. • The formation mechanism of the TiO 2 nanostructures was discussed. • The density, average diameter, and morphology of TiO 2 NWAs can be controlled. • The effects of the sensitization temperature and time on the properties were studied. - Abstract: TiO 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 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 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 2 nanoarrays. In addition, the performance of the flexible DSSC depended strongly on the sensitization temperature and time. By utilizing Ti mesh-supported TiO 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 −2 , an open-circuit voltage of 0.69 V, and an overall power conversion efficiency of 3.42% was achieved

  16. 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.

  17. Proteomic analysis reveals the differential histone programs between male germline cells and vegetative cells in Lilium davidii.

    Science.gov (United States)

    Yang, Hao; Yang, Ning; Wang, Tai

    2016-03-01

    In flowering plants, male germline fate is determined after asymmetric division of the haploid microspore. Daughter cells have distinct fates: the generative cell (GC) undergoes further mitosis to generate sperm cells (SCs), and the vegetative cell (VC) terminally differentiates. However, our understanding of the mechanisms underlying germline development remains limited. Histone variants and modifications define chromatin states, and contribute to establishing and maintaining cell identities by affecting gene expression. Here, we constructed a lily protein database, then extracted and detailed histone entries into a comprehensive lily histone database. We isolated large amounts of nuclei from VCs, GCs and SCs from lily, and profiled histone variants of all five histone families in all three cell types using proteomics approaches. We revealed 92 identities representing 32 histone variants: six for H1, 11 for H2A, eight for H2B, five for H3 and two for H4. Nine variants, including five H1, two H2B, one H3 and one H4 variant, specifically accumulated in GCs and SCs. We also detected H3 modification patterns in the three cell types. GCs and SCs had almost identical histone profiles and similar H3 modification patterns, which were significantly different from those of VCs. Our study also revealed the presence of multiple isoforms, and differential expression patterns between isoforms of a variant. The results suggest that differential histone programs between the germline and companion VCs may be established following the asymmetric division, and are important for identity establishment and differentiation of the male germline as well as the VC. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  18. Preparation and photovoltaic properties of perovskite solar cell based on ZnO nanorod arrays

    Science.gov (United States)

    Xu, Yang; Liu, Tian; Li, Zhaosong; Feng, Bingjie; Li, Siqian; Duan, Jinxia; Ye, Cong; Zhang, Jun; Wang, Hao

    2016-12-01

    A careful control of ZnO nanorod arrays with various densities and thickness were achieved by hydrothermal method. An obvious increase in the ZnO nanorod density is observed as the concentrations of zinc acetate dropped as expected through the surface SEM images. On the other hand, samples with and without TiO2 compact layer were also studied and results had been analyzed to seek for an optimized substrate structure for light absorbing layer and increase the efficiency. What's more, a deep research for the drying temperature for perovskite layer was also conducted. As a result, SEM images discribe a promising surface appearance of perovskite layer which is finely attached onto the nanorod structure. Final power conversion efficiency (PCE) of FTO/ZnO seed layer/ZnO nanorods/perovskite/spiro-OMe-TAD/Au electrode photovoltaic device reached ∼9.15% together with open-circuit voltage of 957 mV, short-circuit current density of 17.8 mA/cm2 and fill factor of 0.537.

  19. BAC array CGH in patients with Velocardiofacial syndrome-like features reveals genomic aberrations on chromosome region 1q21.1

    Directory of Open Access Journals (Sweden)

    Estivill Xavier

    2009-12-01

    Full Text Available Abstract Background Microdeletion of the chromosome 22q11.2 region is the most common genetic aberration among patients with velocardiofacial syndrome (VCFS but a subset of subjects do not show alterations of this chromosome region. Methods We analyzed 18 patients with VCFS-like features by comparative genomic hybridisation (aCGH array and performed a face-to-face slide hybridization with two different arrays: a whole genome and a chromosome 22-specific BAC array. Putative rearrangements were confirmed by FISH and MLPA assays. Results One patient carried a combination of rearrangements on 1q21.1, consisting in a microduplication of 212 kb and a close microdeletion of 1.15 Mb, previously reported in patients with variable phenotypes, including mental retardation, congenital heart defects (CHD and schizophrenia. While 326 control samples were negative for both 1q21.1 rearrangements, one of 73 patients carried the same 212-kb microduplication, reciprocal to TAR microdeletion syndrome. Also, we detected four copy number variants (CNVs inherited from one parent (a 744-kb duplication on 10q11.22; a 160 kb duplication and deletion on 22q11.21 in two cases; and a gain of 140 kb on 22q13.2, not present in control subjects, raising the potential role of these CNVs in the VCFS-like phenotype. Conclusions Our results confirmed aCGH as a successful strategy in order to characterize additional submicroscopic aberrations in patients with VCF-like features that fail to show alterations in 22q11.2 region. We report a 212-kb microduplication on 1q21.1, detected in two patients, which may contribute to CHD.

  20. Local seismicity in the area of Tornio River (northern Fennoscandia) revealed by analysis of local events registered by the POLENET/LAPNET array

    Science.gov (United States)

    Kozlovskaya, E.; Usoltseva, O.; Konstantinovskaya, N.

    2012-04-01

    The region of Tornio river (22-26 deg E and 66.5-69 deg N) is very interesting for seismological studies because it is crossed by systems of tectonic faults spreading in two different directions. 56 local earthquakes originated from this region were recorded by the POLENET/LAPNET temporary array from May, 2007 to May, 2009. Hypocenter depths of earthquakes are in the range of 1-35 km and their magnitudes vary from 0.8 to 2.2. For events detection we used the bulletin of the Institute of Seismology (Helsinki university) and Norway Global Beam Forming bulletin, compiled on the base of automatic detection of events, using the data of Noress, Arcess, Finess, SPA, HFS, APA arrays. In addition to local earthquakes, the array recorded 364 blasts from this region during the POLENET/LAPNET observation period. The events were relocated using manually measured travel times of refracted P waves from events at local distances (less than 200 km) and the 1-D velocity model along the wide-angle reflection and refraction HUKKA profile. The epicenters of relocated events show good correlation with known faults in the region. For each earthquake we constructed travel-time curves with reduction velocity of 8 km/s and compared them with the theoretical travel-time curves, in order to avoid phase misinterpretation. We found out that the largest reduction of travel time residuals during relocation was reached for deep earthquakes, due to more precise depth determination. The other aim of our study was to estimate what part of travel time residuals is not connected with the reference 1D velocity model and accuracy of location, but is rather due to 3-D heterogeneities in the crust. We also analyzed the amplitude characteristics of P-wave arrivals from different layers in the crust and upper mantle and also compared spectrograms of deep earthquakes, shallow earthquakes and blasts.

  1. CoS acicular nanorod arrays for the counter electrode of an efficient dye-sensitized solar cell.

    Science.gov (United States)

    Kung, Chung-Wei; Chen, Hsin-Wei; Lin, Chia-Yu; Huang, Kuan-Chieh; Vittal, R; Ho, Kuo-Chuan

    2012-08-28

    One-dimensional cobalt sulfide (CoS) acicular nanorod arrays (ANRAs) were obtained on a fluorine-doped tin oxide (FTO) substrate by a two-step approach. First, Co(3)O(4) ANRAs were synthesized, and then they were converted to CoS ANRAs for various periods. The compositions of the films obtained after various conversion periods were verified by X-ray diffraction, UV-visible spectrophotometry, and X-ray photoelectron spectroscopy; their morphologies were examined at different periods by scanning electron microscopic and transmission electron microscopic images. Electrocatalytic abilities of the films toward I(-)/I(3)(-) were verified through cyclic voltammetry (CV) and Tafel polarization curves. Long-term stability of the films in I(-)/I(3)(-) electrolyte was studied by CV. The FTO substrates with CoS ANRAs were used as the counter electrodes for dye-sensitized solar cells; a maximum power conversion efficiency of 7.67% was achieved for a cell with CoS ANRAs, under 100 mW/cm(2), which is nearly the same as that of a cell with a sputtered Pt counter electrode (7.70%). Electrochemical impedance spectroscopy was used to substantiate the photovoltaic parameters.

  2. Time-dependent Increase in the Network Response to the Stimulation of Neuronal Cell Cultures on Micro-electrode Arrays.

    Science.gov (United States)

    Gertz, Monica L; Baker, Zachary; Jose, Sharon; Peixoto, Nathalia

    2017-05-29

    Micro-electrode arrays (MEAs) can be used to investigate drug toxicity, design paradigms for next-generation personalized medicine, and study network dynamics in neuronal cultures. In contrast with more traditional methods, such as patch-clamping, which can only record activity from a single cell, MEAs can record simultaneously from multiple sites in a network, without requiring the arduous task of placing each electrode individually. Moreover, numerous control and stimulation configurations can be easily applied within the same experimental setup, allowing for a broad range of dynamics to be explored. One of the key dynamics of interest in these in vitro studies has been the extent to which cultured networks display properties indicative of learning. Mouse neuronal cells cultured on MEAs display an increase in response following training induced by electrical stimulation. This protocol demonstrates how to culture neuronal cells on MEAs; successfully record from over 95% of the plated dishes; establish a protocol to train the networks to respond to patterns of stimulation; and sort, plot, and interpret the results from such experiments. The use of a proprietary system for stimulating and recording neuronal cultures is demonstrated. Software packages are also used to sort neuronal units. A custom-designed graphical user interface is used to visualize post-stimulus time histograms, inter-burst intervals, and burst duration, as well as to compare the cellular response to stimulation before and after a training protocol. Finally, representative results and future directions of this research effort are discussed.

  3. A cell-based, high content screening assay reveals activators and inhibitors of cancer cell invasion

    Science.gov (United States)

    Quintavalle, Manuela; Elia, Leonardo; Price, Jeffrey H.; Heynen-Genel, Susanne; Courtneidge, Sara A.

    2012-01-01

    Acquisition of invasive cell behavior underlies tumor progression and metastasis. To define in more molecular detail the mechanisms underlying invasive behavior, we developed a high throughput screening strategy to quantitate invadopodia; actin-rich membrane protrusions of cancer cells which contribute to tissue invasion and matrix remodeling. We developed a high content, imaged-based assay, and tested the LOPAC 1280 collection of pharmacologically active agents. We found compounds that potently inhibited invadopodia formation without overt toxicity, as well as compounds that increased invadopodia number. One of the two compounds that increased both invadopodia number and invasive behavior was the chemotherapeutic agent paclitaxel, which has potential clinical implications for its use in the neoadjuvant and resistance settings. Several of the invasion inhibitors were annotated as cyclin-dependent kinase (cdk) inhibitors. Loss-of-function experiments determined that Cdk5 was the relevant target. We further determined that the mechanism by which Cdk5 promotes both invadopodia formation and cancer invasion is by phosphorylation and down regulation of the actin regulatory protein caldesmon. PMID:21791703

  4. Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

    Science.gov (United States)

    Liu, Mingshan; Liu, Yang; Di, Jiabo; Su, Zhe; Yang, Hong; Jiang, Beihai; Wang, Zaozao; Zhuang, Meng; Bai, Fan; Su, Xiangqian

    2017-11-23

    Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-region whole-exome sequencing and single-cell whole-genome sequencing to examine the genomic intratumor heterogeneity (ITH) of rectal tumors. We sequenced nine tumor regions and 88 single cells from two rectal cancer patients with tumors of the same molecular classification and characterized their mutation profiles and somatic copy number alterations (SCNAs) at the multi-region and the single-cell levels. A variable extent of genomic heterogeneity was observed between the two patients, and the degree of ITH increased when analyzed on the single-cell level. We found that major SCNAs were early events in cancer development and inherited steadily. Single-cell sequencing revealed mutations and SCNAs which were hidden in bulk sequencing. In summary, we studied the ITH of rectal cancer at regional and single-cell resolution and demonstrated that variable heterogeneity existed in two patients. The mutational scenarios and SCNA profiles of two patients with treatment naïve from the same molecular subtype are quite different. Our results suggest each tumor possesses its own architecture, which may result in different diagnosis, prognosis, and drug responses. Remarkable ITH exists in the two patients we have studied, providing a preliminary impression of ITH in rectal cancer.

  5. Intracellular stress tomography reveals stress focusing and structural anisotropy in cytoskeleton of living cells

    Science.gov (United States)

    Hu, Shaohua; Chen, Jianxin; Fabry, Ben; Numaguchi, Yasushi; Gouldstone, Andrew; Ingber, Donald E.; Fredberg, Jeffrey J.; Butler, James P.; Wang, Ning

    2003-01-01

    We describe a novel synchronous detection approach to map the transmission of mechanical stresses within the cytoplasm of an adherent cell. Using fluorescent protein-labeled mitochondria or cytoskeletal components as fiducial markers, we measured displacements and computed stresses in the cytoskeleton of a living cell plated on extracellular matrix molecules that arise in response to a small, external localized oscillatory load applied to transmembrane receptors on the apical cell surface. Induced synchronous displacements, stresses, and phase lags were found to be concentrated at sites quite remote from the localized load and were modulated by the preexisting tensile stress (prestress) in the cytoskeleton. Stresses applied at the apical surface also resulted in displacements of focal adhesion sites at the cell base. Cytoskeletal anisotropy was revealed by differential phase lags in X vs. Y directions. Displacements and stresses in the cytoskeleton of a cell plated on poly-L-lysine decayed quickly and were not concentrated at remote sites. These data indicate that mechanical forces are transferred across discrete cytoskeletal elements over long distances through the cytoplasm in the living adherent cell.

  6. Epigenetic landscapes reveal transcription factors regulating CD8+ T cell differentiation

    Science.gov (United States)

    Yu, Bingfei; Zhang, Kai; Milner, J. Justin; Toma, Clara; Chen, Runqiang; Scott-Browne, James P.; Pereira, Renata M.; Crotty, Shane; Chang, John T.; Pipkin, Matthew E.; Wang, Wei; Goldrath, Ananda W.

    2017-01-01

    Dynamic changes in the expression of transcription factors (TFs) can influence specification of distinct CD8+ T cell fates, but the observation of equivalent expression of TF among differentially-fated precursor cells suggests additional underlying mechanisms. Here, we profiled genome-wide histone modifications, open chromatin and gene expression of naive, terminal-effector, memory-precursor and memory CD8+ T cell populations induced during the in vivo response to bacterial infection. Integration of these data suggested that TF expression and binding contributed to establishment of subset-specific enhancers during differentiation. We developed a new bioinformatics method using the PageRank algorithm to reveal novel TFs influencing the generation of effector and memory populations. The TFs YY1 and Nr3c1, both constitutively expressed during CD8+ T cell differentiation, regulated the formation of terminal-effector and memory-precursor cell-fates, respectively. Our data define the epigenetic landscape of differentiation intermediates, facilitating identification of TFs with previously unappreciated roles in CD8+ T cell differentiation. PMID:28288100

  7. Study on direct-contact phase-change liquid immersion cooling dense-array solar cells under high concentration ratios

    International Nuclear Information System (INIS)

    Kang, Xue; Wang, Yiping; Huang, Qunwu; Cui, Yong; Shi, Xusheng; Sun, Yong

    2016-01-01

    Highlights: • Direct-contact phase-change liquid immersion cooling for solar cells was proposed. • A self-regulating system investigated the feasibility in temperature control. • Temperature was well controlled between 87.3 °C and 88.5 °C. • Surface heat transfer coefficient was up to 23.49 kW/(m 2 ·K) under 398.4×. • A model illustrated the interface function was the main reason to affect light. - Abstract: A new cooling method by directly immersing the solar cells into phase-change liquid was put forward to cool dense-array solar cells in high concentrating photovoltaic system. A self-running system was built to study the feasibility of temperature control and the effect of bubbles generated by ethanol phase change under concentration ratio ranged between 219.8× and 398.4×. The results show that the cooling system is self-regulating without consuming extra energy and ethanol flow rate reaches up to 180.6 kg/(s·m 2 ) under 398.4×. The temperature of solar cells distributes in the range between 87.3 °C and 88.5 °C, the surface heat transfer coefficient of electric heating plate is up to 23.49 kW/(m 2 ·K) under 398.4×. The bubble effect on electrical performance of triple-junction solar cells is reported and the results show that I sc and P max decline 10.2% and 7.3%, respectively. A model based on bubble images illustrates that light loss at the interface between ethanol and bubble is the main reason to cut down the electrical performance.

  8. Fast time-domain modeling of fluid-coupled cMUT cells: from the single cell to the 1-D linear array element.

    Science.gov (United States)

    Sénégond, Nicolas; Boulmé, Audren; Plag, Camille; Teston, Franck; Certon, Dominique

    2013-07-01

    We report a fast time-domain model of fluid-coupled cMUTs developed to predict the transient response-i.e., the impulse pressure response--of an element of a linear 1-D array. Mechanical equations of the cMUT diaphragm are solved with 2-D finite-difference schemes. The time-domain solving method is a fourth--order Runge-Kutta algorithm. The model takes into account the electrostatic nonlinearity and the contact with the bottom electrode when the membrane is collapsed. Mutual acoustic coupling between cells is introduced through the numerical implementation of analytical solutions of the impulse diffraction theory established in the case of acoustic sources with rectangular geometry. Processing times are very short: they vary from a few minutes for a single cell to a maximum of 30 min for one element of an array. After a description of the model, the impact of the nonlinearity and the pull-in/pull-out phenomena on the dynamic behavior of the cMUT diaphragm is discussed. Experimental results of mechanical displacements obtained by interferometric measurements and the acoustic pressure field are compared with simulations. Different excitation signals-high-frequency bandwidth pulses and toneburst excitations of varying central frequency-were chosen to compare theory with experimental results.

  9. Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains

    Science.gov (United States)

    Van der Aa, Niels; Cheng, Jiqiu; Mateiu, Ligia; Esteki, Masoud Zamani; Kumar, Parveen; Dimitriadou, Eftychia; Vanneste, Evelyne; Moreau, Yves; Vermeesch, Joris Robert; Voet, Thierry

    2013-01-01

    Single-cell genomics is revolutionizing basic genome research and clinical genetic diagnosis. However, none of the current research or clinical methods for single-cell analysis distinguishes between the analysis of a cell in G1-, S- or G2/M-phase of the cell cycle. Here, we demonstrate by means of array comparative genomic hybridization that charting the DNA copy number landscape of a cell in S-phase requires conceptually different approaches to that of a cell in G1- or G2/M-phase. Remarkably, despite single-cell whole-genome amplification artifacts, the log2 intensity ratios of single S-phase cells oscillate according to early and late replication domains, which in turn leads to the detection of significantly more DNA imbalances when compared with a cell in G1- or G2/M-phase. Although these DNA imbalances may, on the one hand, be falsely interpreted as genuine structural aberrations in the S-phase cell’s copy number profile and hence lead to misdiagnosis, on the other hand, the ability to detect replication domains genome wide in one cell has important applications in DNA-replication research. Genome-wide cell-type-specific early and late replicating domains have been identified by analyses of DNA from populations of cells, but cell-to-cell differences in DNA replication may be important in genome stability, disease aetiology and various other cellular processes. PMID:23295674

  10. Ovalbumin-coated pH-sensitive microneedle arrays effectively induce ovalbumin-specific antibody and T-cell responses in mice.

    Science.gov (United States)

    van der Maaden, Koen; Varypataki, Eleni Maria; Romeijn, Stefan; Ossendorp, Ferry; Jiskoot, Wim; Bouwstra, Joke

    2014-10-01

    The aim of this work was to study the applicability of antigen-coated pH-sensitive microneedle arrays for effective vaccination strategies. Therefore, a model antigen (ovalbumin) was coated onto pH-sensitive (pyridine-modified) microneedle arrays to test pH-triggered antigen release by applying the coated arrays onto ex vivo human skin, and by conducting a dermal immunization study in mice. The release of antigen into ex vivo human skin from the coated microneedles was determined by using radioactively labeled ovalbumin. To investigate the induction of antigen-specific IgG, and CD4(+) and CD8(+) T-cell responses, BALB/c mice were immunized with antigen-coated pH-sensitive microneedles by the 'coat and poke' approach. These responses were compared to responses induced by the 'poke and patch' approach, and subcutaneous and intradermal vaccination with classic hypodermic needles. The pH-sensitive microneedle arrays were efficiently coated with ovalbumin (95% coating efficiency) and upon application of six microneedle arrays 4.27 of 7 μg ovalbumin was delivered into the skin, showing a release efficiency of 70%. In contrast, the 'poke and patch' approach led to a delivery of only 6.91 of 100 μg ovalbumin (7% delivery efficiency). Immunization by means of ovalbumin-coated microneedles resulted in robust CD4(+) and CD8(+) T-cell responses comparable to those obtained after subcutaneous or intradermal immunization with conventional needles. Moreover, it effectively induced IgG responses; however, it required prime-boost immunizations before antibodies were produced. In conclusion, antigen delivery into ex vivo human skin by antigen-coated pH-sensitive microneedle arrays is more efficient than the 'poke-and-patch' approach and in vivo vaccination studies show the applicability of pH-sensitive microneedles for the induction of both T cell and B cell responses. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. 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...

  12. Exploring Nanostructure Arrays for Single-Cell and Subcellular Manipulation and Detection

    DEFF Research Database (Denmark)

    Buch-Månson, Nina

    Structures on the nanoscale, such as quantum dots, carbon nanotubes, or nanowires, are highlyinteresting to apply in biological research, since their nanoscale dimension is compatible withcrucial biomolecules, such as proteins, and several orders of magnitude smaller than amammalian cell. Among t...

  13. Comprehensive SNP array study of frequently used neuroblastoma cell lines; copy neutral loss of heterozygosity is common in the cell lines but uncommon in primary tumors

    Directory of Open Access Journals (Sweden)

    Kogner Per

    2011-09-01

    Full Text Available Abstract Background Copy neutral loss of heterozygosity (CN-LOH refers to a special case of LOH occurring without any resulting loss in copy number. These alterations is sometimes seen in tumors as a way to inactivate a tumor suppressor gene and have been found to be important in several types of cancer. Results We have used high density single nucleotide polymorphism arrays in order to investigate the frequency and distribution of CN-LOH and other allelic imbalances in neuroblastoma (NB tumors and cell lines. Our results show that the frequency of these near-CN-LOH events is significantly higher in the cell lines compared to the primary tumors and that the types of CN-LOH differ between the groups. We also show that the low-risk neuroblastomas that are generally considered to have a "triploid karyotype" often present with a complex numerical karyotype (no segmental changes with 2-5 copies of each chromosome. Furthermore a comparison has been made between the three related cell lines SK-N-SH, SH-EP and SH-SY5Y with respect to overall genetic aberrations, and several aberrations unique to each of the cell lines has been found. Conclusions We have shown that the NB tumors analyzed contain several interesting allelic imbalances that would either go unnoticed or be misinterpreted using other genome-wide techniques. These findings indicate that the genetics underlying NB might be even more complex than previously known and that SNP arrays are important analysis tools. We have also showed that these near-CN-LOH events are more frequently seen in NB cell lines compared to NB tumors and that a set of highly related cell lines have continued to evolve secondary to the subcloning event. Taken together our analysis highlights that cell lines in many cases differ substantially from the primary tumors they are thought to represent, and that caution should be taken when drawing conclusions from cell line-based studies.

  14. RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival.

    Science.gov (United States)

    González-Ballester, David; Casero, David; Cokus, Shawn; Pellegrini, Matteo; Merchant, Sabeeha S; Grossman, Arthur R

    2010-06-01

    The Chlamydomonas reinhardtii transcriptome was characterized from nutrient-replete and sulfur-depleted wild-type and snrk2.1 mutant cells. This mutant is null for the regulatory Ser-Thr kinase SNRK2.1, which is required for acclimation of the alga to sulfur deprivation. The transcriptome analyses used microarray hybridization and RNA-seq technology. Quantitative RT-PCR evaluation of the results obtained by these techniques showed that RNA-seq reports a larger dynamic range of expression levels than do microarray hybridizations. Transcripts responsive to sulfur deprivation included those encoding proteins involved in sulfur acquisition and assimilation, synthesis of sulfur-containing metabolites, Cys degradation, and sulfur recycling. Furthermore, we noted potential modifications of cellular structures during sulfur deprivation, including the cell wall and complexes associated with the photosynthetic apparatus. Moreover, the data suggest that sulfur-deprived cells accumulate proteins with fewer sulfur-containing amino acids. Most of the sulfur deprivation responses are controlled by the SNRK2.1 protein kinase. The snrk2.1 mutant exhibits a set of unique responses during both sulfur-replete and sulfur-depleted conditions that are not observed in wild-type cells; the inability of this mutant to acclimate to S deprivation probably leads to elevated levels of singlet oxygen and severe oxidative stress, which ultimately causes cell death. The transcriptome results for wild-type and mutant cells strongly suggest the occurrence of massive changes in cellular physiology and metabolism as cells become depleted for sulfur and reveal aspects of acclimation that are likely critical for cell survival.

  15. A novel immunotoxin reveals a new role for CD321 in endothelial cells.

    Science.gov (United States)

    Fukuhara, Takeshi; Kim, Jia; Hokaiwado, Shintaro; Nawa, Makiko; Okamoto, Hayato; Kogiso, Tomohiko; Watabe, Tetsuro; Hattori, Nobutaka

    2017-01-01

    There are currently several antibody therapies that directly target tumors, and antibody-drug conjugates represent a novel moiety as next generation therapeutics. Here, we used a unique screening probe, DT3C, to identify functional antibodies that recognized surface molecules and functional epitopes, and which provided toxin delivery capability. Accordingly, we generated the 90G4 antibody, which induced DT3C-dependent cytotoxicity in endothelial cells. Molecular analysis revealed that 90G4 recognized CD321, a protein localized at tight junctions. Although CD321 plays a pivotal role in inflammation and lymphocyte trans-endothelial migration, little is known about its mechanism of action in endothelial cells. Targeting of CD321 by the 90G4 immunotoxin induced cell death. Moreover, 90G4 immunotoxin caused cytotoxicity primarily in migratory endothelial cells, but not in those forming sheets, suggesting a critical role for CD321 in tumor angiogenesis. We also found that hypoxia triggered redistribution of CD321 to a punctate localization on the basal side of cells, resulting in functional impairment of tight junctions and increased motility. Thus, our findings raise the intriguing possibility that endothelial CD321 presented cellular localization in tight junction as well as multifunctional dynamics in several conditions, leading to illuminate the importance of widely-expressed CD321 as a potential target for antitumor therapy.

  16. A novel immunotoxin reveals a new role for CD321 in endothelial cells.

    Directory of Open Access Journals (Sweden)

    Takeshi Fukuhara

    Full Text Available There are currently several antibody therapies that directly target tumors, and antibody-drug conjugates represent a novel moiety as next generation therapeutics. Here, we used a unique screening probe, DT3C, to identify functional antibodies that recognized surface molecules and functional epitopes, and which provided toxin delivery capability. Accordingly, we generated the 90G4 antibody, which induced DT3C-dependent cytotoxicity in endothelial cells. Molecular analysis revealed that 90G4 recognized CD321, a protein localized at tight junctions. Although CD321 plays a pivotal role in inflammation and lymphocyte trans-endothelial migration, little is known about its mechanism of action in endothelial cells. Targeting of CD321 by the 90G4 immunotoxin induced cell death. Moreover, 90G4 immunotoxin caused cytotoxicity primarily in migratory endothelial cells, but not in those forming sheets, suggesting a critical role for CD321 in tumor angiogenesis. We also found that hypoxia triggered redistribution of CD321 to a punctate localization on the basal side of cells, resulting in functional impairment of tight junctions and increased motility. Thus, our findings raise the intriguing possibility that endothelial CD321 presented cellular localization in tight junction as well as multifunctional dynamics in several conditions, leading to illuminate the importance of widely-expressed CD321 as a potential target for antitumor therapy.

  17. Metabolomics Analysis Reveals that AICAR Affects Glycerolipid, Ceramide and Nucleotide Synthesis Pathways in INS-1 Cells.

    Science.gov (United States)

    ElAzzouny, Mahmoud A; Evans, Charles R; Burant, Charles F; Kennedy, Robert T

    2015-01-01

    AMPK regulates many metabolic pathways including fatty acid and glucose metabolism, both of which are closely associated with insulin secretion in pancreatic β-cells. Insulin secretion is regulated by metabolic coupling factors such as ATP/ADP ratio and other metabolites generated by the metabolism of nutrients such as glucose, fatty acid and amino acids. However, the connection between AMPK activation and insulin secretion in β-cells has not yet been fully elucidated at a metabolic level. To study the effect of AMPK activation on glucose stimulated insulin secretion, we applied the pharmacological activator 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) to an INS-1 (832/13) β-cell line. We measured the change in 66 metabolites in the presence or absence of AICAR using different stable isotopic labeled nutrients to probe selected pathways. AMPK activation by AICAR increased basal insulin secretion and reduced the glucose stimulation index. Although ATP/ADP ratios were not strongly affected by AICAR, several other metabolites and pathways important for insulin secretion were affected by AICAR treatment including long-chain CoAs, malonyl-CoA, 3-hydroxy-3 methylglutaryl CoA, diacylglycerol, and farnesyl pyrophosphate. Tracer studies using 13C-glucose revealed lower glucose flux in the purine and pyrimidine pathway and in the glycerolipid synthesis pathway. Untargeted metabolomics revealed reduction in ceramides caused by AICAR that may explain the beneficial role of AMPK in protecting β-cells from lipotoxicity. Taken together, the results provide an overall picture of the metabolic changes associated with AICAR treatment and how it modulates insulin secretion and β-cell survival.

  18. Porous ZnO nanosheet arrays constructed on weaved metal wire for flexible dye-sensitized solar cells

    Science.gov (United States)

    Dai, Hui; Zhou, Yong; Chen, Liang; Guo, Binglei; Li, Aidong; Liu, Jianguo; Yu, Tao; Zou, Zhigang

    2013-05-01

    Porous zinc oxide (ZnO) nanosheet (NS) arrays constructed by connected nanocrystallites were built on weaved metal wire (WMW) via hydrothermal treatment followed by calcination, and used as photoanodes for flexible dye-sensitized solar cells (DSSCs). An overall light-to-electricity conversion efficiency (η) of 2.70% was achieved for the DSSC under 100 mW cm-2 illumination, and this η was found to be much higher than that of the DSSC with ZnO nanowire (NW) as the photoanode (0.71%). The far superior performance of the DSSC with ZnO-NS is essentially attributed to: (i) the film consisting of nanosheets with interconnected nanocrystallites can allow relatively direct pathways for the transportation of electrons as the nanosheets have a regular structure with the sheets being oriented to the electrode; (ii) the nanocrystallites assembly and porous character of the nanosheets can provide a large surface area for dye adsorption, which is in favor of enhancing the light absorption and the light propagation; (iii) the nanopores embedded in the nanosheet can act as ``branch lines'' for more efficient electrolyte diffusion into the interstice of the densely packed nanosheets in the array. A further improvement in the efficiency of the DSSC with ZnO-NS was achieved through the atomic layer deposition (ALD) of an ultrathin titanium oxide (TiO2) layer onto the ZnO-NS layer. The larger charge transfer resistance along with the introduction of a TiO2 shell is thought to reduce the surface recombination and thus contribute to the increase in the open circuit voltage (Voc) of the DSCs and higher conversion efficiency (3.09%).Porous zinc oxide (ZnO) nanosheet (NS) arrays constructed by connected nanocrystallites were built on weaved metal wire (WMW) via hydrothermal treatment followed by calcination, and used as photoanodes for flexible dye-sensitized solar cells (DSSCs). An overall light-to-electricity conversion efficiency (η) of 2.70% was achieved for the DSSC under 100 mW cm

  19. Live-cell CRISPR imaging in plants reveals dynamic telomere movements.

    Science.gov (United States)

    Dreissig, Steven; Schiml, Simon; Schindele, Patrick; Weiss, Oda; Rutten, Twan; Schubert, Veit; Gladilin, Evgeny; Mette, Michael F; Puchta, Holger; Houben, Andreas

    2017-08-01

    Elucidating the spatiotemporal organization of the genome inside the nucleus is imperative to our understanding of the regulation of genes and non-coding sequences during development and environmental changes. Emerging techniques of chromatin imaging promise to bridge the long-standing gap between sequencing studies, which reveal genomic information, and imaging studies that provide spatial and temporal information of defined genomic regions. Here, we demonstrate such an imaging technique based on two orthologues of the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 (Cas9). By fusing eGFP/mRuby2 to catalytically inactive versions of Streptococcus pyogenes and Staphylococcus aureus Cas9, we show robust visualization of telomere repeats in live leaf cells of Nicotiana benthamiana. By tracking the dynamics of telomeres visualized by CRISPR-dCas9, we reveal dynamic telomere movements of up to 2 μm over 30 min during interphase. Furthermore, we show that CRISPR-dCas9 can be combined with fluorescence-labelled proteins to visualize DNA-protein interactions in vivo. By simultaneously using two dCas9 orthologues, we pave the way for the imaging of multiple genomic loci in live plants cells. CRISPR imaging bears the potential to significantly improve our understanding of the dynamics of chromosomes in live plant cells. © 2017 The Authors The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

  20. Revealing Glycoproteins in the Secretome of MCF-7 Human Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Aik-Aun Tan

    2015-01-01

    Full Text Available Breast cancer is one of the major issues in the field of oncology, reported with a higher prevalence rate in women worldwide. In attempt to reveal the potential biomarkers for breast cancer, the findings of differentially glycosylated haptoglobin and osteonectin in previous study have drawn our attention towards glycoproteins of secretome from the MCF-7 cancer cell line. In the present study, further analyses were performed on the medium of MCF-7 cells by subjecting it to two-dimensional analyses followed by image analysis in contrast to the medium of human mammary epithelial cells (HMEpC as a negative control. Carboxypeptidase A4 (CPA4, alpha-1-antitrypsin (AAT, haptoglobin (HP, and HSC70 were detected in the medium of MCF-7, while only CPA4 and osteonectin (ON were detected in HMEpC medium. In addition, CPA4 was detected as upregulated in the MCF-7 medium. Further analysis by lectin showed that CPA4, AAT, HP, and HSC70 were secreted as N-glycan in the medium of MCF-7, with HP also showing differentially N-glycosylated isoforms. For the HMEpC, only CPA4 was detected as N-glycan. No O-glycan was detected in the medium of HMEpC but MCF-7 expressed O-glycosylated CPA4 and HSC70. All these revealed that glycoproteins could be used as glycan-based biomarkers for the prognosis of breast cancer.

  1. Live cell CRISPR-imaging in plants reveals dynamic telomere movements

    KAUST Repository

    Dreissig, Steven

    2017-05-16

    Elucidating the spatio-temporal organization of the genome inside the nucleus is imperative to understand the regulation of genes and non-coding sequences during development and environmental changes. Emerging techniques of chromatin imaging promise to bridge the long-standing gap between sequencing studies which reveal genomic information and imaging studies that provide spatial and temporal information of defined genomic regions. Here, we demonstrate such an imaging technique based on two orthologues of the bacterial CRISPR-Cas9 system. By fusing eGFP/mRuby2 to the catalytically inactive version of Streptococcus pyogenes and Staphylococcus aureus Cas9, we show robust visualization of telomere repeats in live leaf cells of Nicotiana benthamiana. By tracking the dynamics of telomeres visualized by CRISPR-dCas9, we reveal dynamic telomere movements of up to 2 μm within 30 minutes during interphase. Furthermore, we show that CRISPR-dCas9 can be combined with fluorescence-labelled proteins to visualize DNA-protein interactions in vivo. By simultaneously using two dCas9 orthologues, we pave the way for imaging of multiple genomic loci in live plants cells. CRISPR-imaging bears the potential to significantly improve our understanding of the dynamics of chromosomes in live plant cells.

  2. Remanence and switching sensitivity in nanodot magnetic arrays.

    Science.gov (United States)

    Gawroński, Przemysław; Kułakowski, Krzysztof

    2008-06-01

    New results are reported of the computer simulations on the magnetic behaviour of magnetic arrays of nanoscopic dots, placed in cells of the square lattice. We show that the remanence magnetization M(r) decreases with the array size. For arrays 50 x 50, we investigate also the stability of the magnetic structure of an array in an oscillating magnetic field. The damage spreading technique reveals that this stability increases with the standard deviation sigma of the switching field of individual elements of the array. On the other hand, M(r) decreases with sigma. An optimalization of the system (large M(r) and large stability) can then be reached at some intermediate value of sigma.

  3. Life on magnets: stem cell networking on micro-magnet arrays

    Czech Academy of Sciences Publication Activity Database

    Zablotskyy, Vitaliy A.; Dejneka, Alexandr; Kubinová, Šárka; Le-Roy, D.; Dumas-Bouchiat, F.; Givord, D.; Dempsey, N.; Syková, Eva

    2013-01-01

    Roč. 8, č. 8 (2013), e70416 E-ISSN 1932-6203 R&D Projects: GA ČR GAP304/11/0653; GA ČR(CZ) GAP304/12/1370 Grant - others:AV ČR(CZ) M100101219 Institutional support: RVO:68378271 ; RVO:68378041 Keywords : micro- magnet * stem cells Subject RIV: BM - Solid Matter Physics ; Magnet ism; FH - Neurology (UEM-P) Impact factor: 3.534, year: 2013

  4. High-resolution Antibody Array Analysis of Childhood Acute Leukemia Cells

    Czech Academy of Sciences Publication Activity Database

    Kanderová, V.; Kuzilkova, D.; Stuchlý, J.; Vašková, M.; Brdička, Tomáš; Fišer, K.; Hrušák, O.; Lund-Johansen, F.; Kalina, T.

    2016-01-01

    Roč. 15, č. 4 (2016), s. 1246-1261 ISSN 1535-9476 R&D Projects: GA MŠk 2B06064 Institutional support: RVO:68378050 Keywords : acute lymphoblastic-leukemia * acute promyelocytic leukemia * cytometric immunobead assay * caspase-dependent cleavage * acute myeloid-leukemia * gene-expression * fusion proteins * flow-cytometry * pcr data * b-cells Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.540, year: 2016

  5. Halide perovskite solar cells using monocrystalline TiO2 nanorod arrays as electron transport layers: impact of nanorod morphology

    Science.gov (United States)

    Thakur, Ujwal Kumar; Askar, Abdelrahman M.; Kisslinger, Ryan; Wiltshire, Benjamin D.; Kar, Piyush; Shankar, Karthik

    2017-07-01

    This is the first report of a 17.6% champion efficiency solar cell architecture comprising monocrystalline TiO2 nanorods (TNRs) coupled with perovskite, and formed using facile solution processing without non-routine surface conditioning. Vertically oriented TNR ensembles are desirable as electron transporting layers (ETLs) in halide perovskite solar cells (HPSCs) because of potential advantages such as vectorial electron percolation pathways to balance the longer hole diffusion lengths in certain halide perovskite semiconductors, ease of incorporating nanophotonic enhancements, and optimization between a high contact surface area for charge transfer (good) versus high interfacial recombination (bad). These advantages arise from the tunable morphology of hydrothermally grown rutile TNRs, which is a strong function of the growth conditions. Fluorescence lifetime imaging microscopy of the HPSCs demonstrated a stronger quenching of the perovskite PL when using TNRs as compared to mesoporous/compact TiO2 thin films. Due to increased interfacial contact area between the ETL and perovskite with easier pore filling, charge separation efficiency is dramatically enhanced. Additionally, solid-state impedance spectroscopy results strongly suggested the suppression of interfacial charge recombination between TNRs and perovskite layer, compared to other ETLs. The optimal ETL morphology in this study was found to consist of an array of TNRs ∼300 nm in length and ∼40 nm in width. This work highlights the potential of TNR ETLs to achieve high performance solution-processed HPSCs.

  6. Large scale single-crystal Cu(In,Ga)Se2 nanotip arrays for high efficiency solar cell.

    Science.gov (United States)

    Liu, Chin-Hung; Chen, Chia-Hsiang; Chen, Szu-Ying; Yen, Yu-Ting; Kuo, Wei-Chen; Liao, Yu-Kuang; Juang, Jenh-Yih; Kuo, Hao-Chung; Lai, Chih-Huang; Chen, Lih-Juann; Chueh, Yu-Lun

    2011-10-12

    In this paper, we demonstrated direct formation of large area Cu(In,Ga)Se(2) nanotip arrays (CIGS NTRs) by using one step Ar(+) milling process without template. By controlling milling time and incident angles, the length of CIGS NTRs with adjustable tilting orientations can be precisely controlled. Formation criteria of these CIGS NTRs have been discussed in terms of surface curvature, multiple components, and crystal quality, resulting in a highly anisotropic milling effect. The CIGS NTRs have very low reflectance solar cell were measured to be ∼390 mV and ∼22.56 mA/cm(2), yielding the filling factor and the efficiency of 59 and 5.2%, respectively. In contrast to CIGS thin film solar cell with efficiency of 3.2%, the nanostructured CIGS NTRs can have efficiency enhancement of ∼160% due to the higher light absorption ability because of the nanostructure. The merits of current approach include the latest way via template-free direct creating process of nanostructured CIGS NTRs with controllable dimensionality and large scale production without postselenization process.

  7. Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates.

    Science.gov (United States)

    Shi, Handuo; Colavin, Alexandre; Lee, Timothy K; Huang, Kerwyn Casey

    2017-02-01

    Single-cell microscopy is a powerful tool for studying gene functions using strain libraries, but it suffers from throughput limitations. Here we describe the Strain Library Imaging Protocol (SLIP), which is a high-throughput, automated microscopy workflow for large strain collections that requires minimal user involvement. SLIP involves transferring arrayed bacterial cultures from multiwell plates onto large agar pads using inexpensive replicator pins and automatically imaging the resulting single cells. The acquired images are subsequently reviewed and analyzed by custom MATLAB scripts that segment single-cell contours and extract quantitative metrics. SLIP yields rich data sets on cell morphology and gene expression that illustrate the function of certain genes and the connections among strains in a library. For a library arrayed on 96-well plates, image acquisition can be completed within 4 min per plate.

  8. Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

    Science.gov (United States)

    Kowalczyk, Monika S.; Tirosh, Itay; Heckl, Dirk; Rao, Tata Nageswara; Dixit, Atray; Haas, Brian J.; Schneider, Rebekka K.; Wagers, Amy J.; Ebert, Benjamin L.; Regev, Aviv

    2015-01-01

    Both intrinsic cell state changes and variations in the composition of stem cell populations have been implicated as contributors to aging. We used single-cell RNA-seq to dissect variability in hematopoietic stem cell (HSC) and hematopoietic progenitor cell populations from young and old mice from two strains. We found that cell cycle dominates the variability within each population and that there is a lower frequency of cells in the G1 phase among old compared with young long-term HSCs, suggesting that they traverse through G1 faster. Moreover, transcriptional changes in HSCs during aging are inversely related to those upon HSC differentiation, such that old short-term (ST) HSCs resemble young long-term (LT-HSCs), suggesting that they exist in a less differentiated state. Our results indicate both compositional changes and intrinsic, population-wide changes with age and are consistent with a model where a relationship between cell cycle progression and self-renewal versus differentiation of HSCs is affected by aging and may contribute to the functional decline of old HSCs. PMID:26430063

  9. Functional Definition of Progenitors Versus Mature Endothelial Cells Reveals Key SoxF-Dependent Differentiation Process.

    Science.gov (United States)

    Patel, Jatin; Seppanen, Elke J; Rodero, Mathieu P; Wong, Ho Yi; Donovan, Prudence; Neufeld, Zoltan; Fisk, Nicholas M; Francois, Mathias; Khosrotehrani, Kiarash

    2017-02-21

    During adult life, blood vessel formation is thought to occur via angiogenic processes involving branching from existing vessels. An alternate proposal suggests that neovessels form from endothelial progenitors able to assemble the intimal layers. We here aimed to define vessel-resident endothelial progenitors in vivo in a variety of tissues in physiological and pathological situations such as normal aorta, lungs, and wound healing, tumors, and placenta, as well. Based on protein expression levels of common endothelial markers using flow cytometry, 3 subpopulations of endothelial cells could be identified among VE-Cadherin+ and CD45- cells. Lineage tracing by using Cdh5cre ERt2 /Rosa-YFP reporter strategy demonstrated that the CD31-/loVEGFR2lo/intracellular endothelial population was indeed an endovascular progenitor (EVP) of an intermediate CD31intVEGFR2lo/intracellular transit amplifying (TA) and a definitive differentiated (D) CD31hiVEGFR2hi/extracellular population. EVP cells arose from vascular-resident beds that could not be transferred by bone marrow transplantation. Furthermore, EVP displayed progenitor-like status with a high proportion of cells in a quiescent cell cycle phase as assessed in wounds, tumors, and aorta. Only EVP cells and not TA and D cells had self-renewal capacity as demonstrated by colony-forming capacity in limiting dilution and by transplantation in Matrigel plugs in recipient mice. RNA sequencing revealed prominent gene expression differences between EVP and D cells. In particular, EVP cells highly expressed genes related to progenitor function including Sox9 , Il33 , Egfr , and Pdfgrα. Conversely, D cells highly expressed genes related to differentiated endothelium including Ets1&2 , Gata2 , Cd31 , Vwf , and Notch . The RNA sequencing also pointed to an essential role of the Sox18 transcription factor. The role of SOX18 in the differentiation process was validated by using lineage-tracing experiments based on S ox18Cre ERt2 /Rosa

  10. Tunable, Highly Ordered TiO2 Nanotube Arrays on Indium Tin Oxide Coated PET for Flexible Bio-sensitized Solar Cells

    Science.gov (United States)

    2011-08-01

    closed together using an electrolyte and indium tin dioxide-coated PET . 201 3. Results and Discussion Figure 5 shows the effects of methanol...Oxide Coated PET for Flexible Bio-sensitized Solar Cells JOSHUA J. MARTIN, UNIVERSITY OF DELAWARE MENTORS: DR. SHASHI KARNA AND DR. MARK GRIEP U.S...4. TITLE AND SUBTITLE Tunable, Highly Ordered TiO2 Nanotube Arrays On Indium Tin Oxide Coated PET For Flexible Bio-sensitized Solar Cells 5a

  11. Application of the pMHC Array to Characterise Tumour Antigen Specific T Cell Populations in Leukaemia Patients at Disease Diagnosis.

    Directory of Open Access Journals (Sweden)

    Suzanne E Brooks

    Full Text Available Immunotherapy treatments for cancer are becoming increasingly successful, however to further improve our understanding of the T-cell recognition involved in effective responses and to encourage moves towards the development of personalised treatments for leukaemia immunotherapy, precise antigenic targets in individual patients have been identified. Cellular arrays using peptide-MHC (pMHC tetramers allow the simultaneous detection of different antigen specific T-cell populations naturally circulating in patients and normal donors. We have developed the pMHC array to detect CD8+ T-cell populations in leukaemia patients that recognise epitopes within viral antigens (cytomegalovirus (CMV and influenza (Flu and leukaemia antigens (including Per Arnt Sim domain 1 (PASD1, MelanA, Wilms' Tumour (WT1 and tyrosinase. We show that the pMHC array is at least as sensitive as flow cytometry and has the potential to rapidly identify more than 40 specific T-cell populations in a small sample of T-cells (0.8-1.4 x 10(6. Fourteen of the twenty-six acute myeloid leukaemia (AML patients analysed had T cells that recognised tumour antigen epitopes, and eight of these recognised PASD1 epitopes. Other tumour epitopes recognised were MelanA (n = 3, tyrosinase (n = 3 and WT1(126-134 (n = 1. One of the seven acute lymphocytic leukaemia (ALL patients analysed had T cells that recognised the MUC1(950-958 epitope. In the future the pMHC array may be used provide point of care T-cell analyses, predict patient response to conventional therapy and direct personalised immunotherapy for patients.

  12. Stimulated emission depletion-based raster image correlation spectroscopy reveals biomolecular dynamics in live cells.

    Science.gov (United States)

    Hedde, Per Niklas; Dörlich, René M; Blomley, Rosmarie; Gradl, Dietmar; Oppong, Emmanuel; Cato, Andrew C B; Nienhaus, G Ulrich

    2013-01-01

    Raster image correlation spectroscopy is a powerful tool to study fast molecular dynamics such as protein diffusion or receptor-ligand interactions inside living cells and tissues. By analysing spatio-temporal correlations of fluorescence intensity fluctuations from raster-scanned microscopy images, molecular motions can be revealed in a spatially resolved manner. Because of the diffraction-limited optical resolution, however, conventional raster image correlation spectroscopy can only distinguish larger regions of interest and requires low fluorophore concentrations in the nanomolar range. Here, to overcome these limitations, we combine raster image correlation spectroscopy with stimulated emission depletion microscopy. With imaging experiments on model membranes and live cells, we show that stimulated emission depletion-raster image correlation spectroscopy offers an enhanced multiplexing capability because of the enhanced spatial resolution as well as access to 10-100 times higher fluorophore concentrations.

  13. 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.

  14. 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.

  15. Retrieval of the vacuolar H-ATPase from phagosomes revealed by live cell imaging.

    Directory of Open Access Journals (Sweden)

    Margaret Clarke

    2010-01-01

    Full Text Available 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.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.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.Thus, live cell microscopy has revealed both a usual route and alternative means of recycling the V-ATPase in the endocytic pathway.

  16. 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.

  17. Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line.

    Science.gov (United States)

    Yusufi, Faraaz Noor Khan; Lakshmanan, Meiyappan; Ho, Ying Swan; Loo, Bernard Liat Wen; Ariyaratne, Pramila; Yang, Yuansheng; Ng, Say Kong; Tan, Tessa Rui Min; Yeo, Hock Chuan; Lim, Hsueh Lee; Ng, Sze Wai; Hiu, Ai Ping; Chow, Chung Ping; Wan, Corrine; Chen, Shuwen; Teo, Gavin; Song, Gao; Chin, Ju Xin; Ruan, Xiaoan; Sung, Ken Wing Kin; Hu, Wei-Shou; Yap, Miranda Gek Sim; Bardor, Muriel; Nagarajan, Niranjan; Lee, Dong-Yup

    2017-05-24

    Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected. Subsequent integration of transcriptomic data with a genome-scale metabolic model showed a substantial increase in energy metabolism in the antibody producer. Metabolomics, lipidomics, and glycomics analyses revealed an elevation in long-chain lipid species, potentially associated with protein transport and secretion requirements, and a surprising stability of N-glycosylation profiles between both cell lines. Overall, the proposed knowledge-based systems biotechnology framework can further accelerate mammalian cell-line engineering in a targeted manner. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. 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.

  19. The laminA/NF-Y protein complex reveals an unknown transcriptional mechanism on cell proliferation.

    Science.gov (United States)

    Cicchillitti, Lucia; Manni, Isabella; Mancone, Carmine; Regazzo, Giulia; Spagnuolo, Manuela; Alonzi, Tonino; Carlomosti, Fabrizio; Dell'Anna, Maria Lucia; Dell'Omo, Giulia; Picardo, Mauro; Ciana, Paolo; Capogrossi, Maurizio C; Tripodi, Marco; Magenta, Alessandra; Rizzo, Maria Giulia; Gurtner, Aymone; Piaggio, Giulia

    2017-01-10

    Lamin A is a component of the nuclear matrix that also controls proliferation by largely unknown mechanisms. NF-Y is a ubiquitous protein involved in cell proliferation composed of three subunits (-YA -YB -YC) all required for the DNA binding and transactivation activity. To get clues on new NF-Y partner(s) we performed a mass spectrometry screening of proteins that co-precipitate with the regulatory subunit of the complex, NF-YA. By this screening we identified lamin A as a novel putative NF-Y interactor. Co-immunoprecipitation experiments and confocal analysis confirmed the interaction between the two endogenous proteins. Interestingly, this association occurs on euchromatin regions, too. ChIP experiments demonstrate lamin A enrichment in several promoter regions of cell cycle related genes in a NF-Y dependent manner. Gain and loss of function experiments reveal that lamin A counteracts NF-Y transcriptional activity. Taking advantage of a recently generated transgenic reporter mouse, called MITO-Luc, in which an NF-Y-dependent promoter controls luciferase expression, we demonstrate that lamin A counteracts NF-Y transcriptional activity not only in culture cells but also in living animals. Altogether, our data demonstrate the occurrence of lamin A/NF-Y interaction and suggest a possible role of this protein complex in regulation of NF-Y function in cell proliferation.

  20. 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.

  1. A graphene-based physiometer array for the analysis of single biological cells

    Science.gov (United States)

    Paulus, Geraldine L. C.; Nelson, Justin T.; Lee, Katherine Y.; Wang, Qing Hua; Reuel, Nigel F.; Grassbaugh, Brittany R.; Kruss, Sebastian; Landry, Markita P.; Kang, Jeon Woong; Vander Ende, Emma; Zhang, Jingqing; Mu, Bin; Dasari, Ramachandra R.; Opel, Cary F.; Wittrup, K. Dane; Strano, Michael S.

    2014-01-01

    A significant advantage of a graphene biosensor is that it inherently represents a continuum of independent and aligned sensor-units. We demonstrate a nanoscale version of a micro-physiometer – a device that measures cellular metabolic activity from the local acidification rate. Graphene functions as a matrix of independent pH sensors enabling subcellular detection of proton excretion. Raman spectroscopy shows that aqueous protons p-dope graphene – in agreement with established doping trajectories, and that graphene displays two distinct pKa values (2.9 and 14.2), corresponding to dopants physi- and chemisorbing to graphene respectively. The graphene physiometer allows micron spatial resolution and can differentiate immunoglobulin (IgG)-producing human embryonic kidney (HEK) cells from non-IgG-producing control cells. Population-based analyses allow mapping of phenotypic diversity, variances in metabolic activity, and cellular adhesion. Finally we show this platform can be extended to the detection of other analytes, e.g. dopamine. This work motivates the application of graphene as a unique biosensor for (sub)cellular interrogation. PMID:25359450

  2. Peculiarities of living cell response to the external stimuli revealed via quasistatic mode of atomic force microscopy

    Science.gov (United States)

    Khalisov, M. M.; Ankudinov, A. V.; Penniyaynen, V. A.; Timoshenko, T. E.; Timoshchuk, K. I.; Samsonov, M. V.; Shirinsky, V. P.

    2017-10-01

    The technique of atomic force microscopy allows revealing living cell morphology and mechanical properties characterization under physiologically relevant conditions. Here, we review our recent results on living cell reaction to different external influences obtained by this technique. The Bruker PeakForce QNM quasistatic mode was used to study living fibroblasts, erythrocytes, sensory neurons, and endothelial cells.

  3. Photovoltaic array reliability optimization

    Science.gov (United States)

    Ross, R. G., Jr.

    1982-01-01

    An overview of the photovoltaic array reliability problem is presented, and a high reliability/minimum cost approach to this problem is presented. Design areas covered are cell failure, interconnect fatigue, and electrical insulation breakdown, and three solution strategies are discussed. The first involves controlling component failures in the solar cell (cell cracking, cell interconnects) and at the module level (must be statistically treated). Second, a fault tolerant circuit is designed which reduces array degradation, improves module yield losses, and controls hot-spot heating. Third, cost optimum module replacement strategies are also effective in reducing array degradation. This can be achieved by minimizing the life-cycle energy cost of the photovoltaic system. The integration of these solutions is aimed at reducing the 0.01% failure rate.

  4. Phosphoproteomics Reveals Regulatory T Cell-Mediated DEF6 Dephosphorylation That Affects Cytokine Expression in Human Conventional T Cells

    KAUST Repository

    Joshi, Rubin N.

    2017-09-25

    Regulatory T cells (Tregs) control key events of immune tolerance, primarily by suppression of effector T cells. We previously revealed that Tregs rapidly suppress T cell receptor (TCR)-induced calcium store depletion in conventional CD4CD25 T cells (Tcons) independently of IP levels, consequently inhibiting NFAT signaling and effector cytokine expression. Here, we study Treg suppression mechanisms through unbiased phosphoproteomics of primary human Tcons upon TCR stimulation and Treg-mediated suppression, respectively. Tregs induced a state of overall decreased phosphorylation as opposed to TCR stimulation. We discovered novel phosphosites (T595_S597) in the DEF6 (SLAT) protein that were phosphorylated upon TCR stimulation and conversely dephosphorylated upon coculture with Tregs. Mutation of these DEF6 phosphosites abrogated interaction of DEF6 with the IP receptor and affected NFAT activation and cytokine transcription in primary Tcons. This novel mechanism and phosphoproteomics data resource may aid in modifying sensitivity of Tcons to Treg-mediated suppression in autoimmune disease or cancer.

  5. Gene Expression Profile of Coronary Artery cells Treated with Non-steroidal Anti-inflammatory Drugs Reveals Off-target Effects

    Science.gov (United States)

    Palayoor, Sanjeewani T.; J-Aryankalayil, Molykutty; Makinde, Adeola. Y.; Cerna, David; Falduto, Michael T.; Magnuson, Scott. R.; Coleman, C. Norman

    2012-01-01

    Non-steroidal anti-inflammatory drugs (NSAIDs) have come under scrutiny because of the gastrointestinal, renal and cardiovascular toxicity associated with prolonged use of these drugs. The purpose of this study was to identify molecular targets for NSAIDs related to cellular toxicity with a view to optimize drug efficacy in clinic. Coronary artery smooth muscle cells (CASMC) and endothelial cells (HCAEC) were treated with low (clinically achievable) and high (typically used in preclinical studies) concentrations of celecoxib (CXB), NS398 (NS) and ibuprofen (IBU) for 24h. NSAIDs-induced gene expression changes were evaluated by microarray analysis and validated by real-time RT-PCR and western blotting. The functional significance of differentially expressed genes was evaluated by Ingenuity Pathway Analysis (IPA). At high concentrations, NSAIDs altered the expression of genes regulating cell proliferation and cell death. NSAIDs also altered genes associated with cardiovascular functions including inflammation, thrombosis, fibrinolysis, coronary artery disease and hypertension. The gene expression was most impacted by IBU, CXB and NS, in that order. This study revealed that NSAIDs altered expression of an array of genes associated with cardiovascular events and emphasizes the potential for fingerprinting drugs in preclinical studies to assess the potential drug toxicity and to optimize the drug efficacy in clinical settings. PMID:22668799

  6. 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.

  7. Near-continuous tremor and low-frequency earthquake activities in the Alaska-Aleutian subduction zone revealed by a mini seismic array

    Science.gov (United States)

    Li, Bo; Ghosh, Abhijit

    2017-06-01

    Tectonic tremor and low-frequency earthquakes (LFEs) are relatively poorly studied in the Alaska-Aleutian subduction zone due to the limited data availability, difficult logistics, and rugged terrain. Using 2 months of continuous data recorded by a mini seismic array in the Akutan Island, we detect near-continuous tremor activity with an average of 1.3 h of tectonic tremor per day using a beam backprojection method. Tremor sources are clustered in two patches with an 25 km gap in between them. In addition, we visually identify three low-frequency earthquakes, and using them as templates, we detect 1300 additional LFEs applying a matched-filter method. Tremor and LFE activities agree well in space and time, and LFEs show a much smaller recurrence interval during tremor than during non-tremor time periods. Tremor sources propagate both along the strike and dip directions of the subduction fault with velocities ranging between 13 and 110 km/h. Prolific patchy tremor and LFE activities suggest lateral heterogeneity in the locked to freely slipping transition zone, indicating that slow earthquakes may play an important role in the earthquake cycles in this subduction zone.

  8. Analysis of pigmented villonodular synovitis with genome-wide complementary DNA microarray and tissue array technology reveals insight into potential novel therapeutic approaches.

    Science.gov (United States)

    Finis, Katharina; Sültmann, Holger; Ruschhaupt, Markus; Buness, Andreas; Helmchen, Birgit; Kuner, Ruprecht; Gross, Marie-Luise; Fink, Bernd; Schirmacher, Peter; Poustka, Annemarie; Berger, Irina

    2006-03-01

    To characterize the gene expression profile and determine potential diagnostic markers and therapeutic targets in pigmented villonodular synovitis (PVNS). Gene expression patterns in 11 patients with PVNS, 18 patients with rheumatoid arthritis (RA), and 19 patients with osteoarthritis (OA) were investigated using genome-wide complementary DNA microarrays. Validation of differentially expressed genes was performed by real-time quantitative polymerase chain reaction and immunohistochemical analysis on tissue arrays (80 patients with PVNS, 51 patients with RA, and 20 patients with OA). The gene expression profile in PVNS was clearly distinct from those in RA and OA. One hundred forty-one up-regulated genes and 47 down-regulated genes were found in PVNS compared with RA, and 153 up-regulated genes and 89 down-regulated genes were found in PVNS compared with OA (fold change > or = 1.5; Q MOAP1, and SPP1). The gene expression signature in PVNS is similar to that of activated macrophages and is consistent with the local destructive course of the disease. The gene and protein expression patterns suggest that the ongoing proliferation in PVNS is sustained by apoptosis resistance. This result suggests the possibility of a potential novel therapeutic intervention against PVNS.

  9. Identification of colonic fibroblast secretomes reveals secretory factors regulating colon cancer cell proliferation.

    Science.gov (United States)

    Chen, Sun-Xia; Xu, Xiao-En; Wang, Xiao-Qing; Cui, Shu-Jian; Xu, Lei-Lei; Jiang, Ying-Hua; Zhang, Yang; Yan, Hai-Bo; Zhang, Qian; Qiao, Jie; Yang, Peng-Yuan; Liu, Feng

    2014-10-14

    Stromal microenvironment influences tumor cell proliferation and migration. Fibroblasts represent the most abundant stromal constituents. Here, we established two pairs of normal fibroblast (NF) and cancer-associated fibroblast (CAF) cultures from colorectal adenocarcinoma tissues and the normal counterparts. The NFs and CAFs were stained positive for typical fibroblast markers and inhibited colon cancer (CC) cell proliferation in in vitro cocultures and in xenograft mouse models. The fibroblast conditioned media were analyzed using LC-MS and 227 proteins were identified at a false discovery rate of 1.3%, including 131 putative secretory and 20 plasma membrane proteins. These proteins were enriched for functional categories of extracellular matrix, adhesion, cell motion, inflammatory response, redox homeostasis and peptidase inhibitor. Secreted protein acidic and rich in cysteine, transgelin, follistatin-related protein 1 (FSTL1) and decorin was abundant in the fibroblast secretome as confirmed by Western blot. Silencing of FSTL1 and transgelin in colonic fibroblast cell line CCD-18Co induced an accelerated proliferation of CC cells in cocultures. Exogenous FSTL1 attenuates CC cell proliferation in a negative fashion. FSTL1 was upregulated in CC patient plasma and cancerous tissues but had no implication in prognosis. Our results provided novel insights into the molecular signatures and modulatory role of CC associated fibroblasts. In this study, a label-free LC-MS was performed to analyze the secretomes of two paired primary fibroblasts, which were isolated from fresh surgical specimen of colorectal adenocarcinoma and adjacent normal colonic tissues and exhibited negative modulatory activity for colon cancer cell growth in in vitro cocultures and in vivo xenograph mouse models. Follistatin-related protein 1 was further revealed to be one of the stroma-derived factors of potential suppression role for colon cancer cell proliferation. Our results provide novel

  10. The use of reverse phase protein arrays (RPPA) to explore protein expression variation within individual renal cell cancers.

    Science.gov (United States)

    O'Mahony, Fiach C; Nanda, Jyoti; Laird, Alexander; Mullen, Peter; Caldwell, Helen; Overton, Ian M; Eory, Lel; O'Donnell, Marie; Faratian, Dana; Powles, Thomas; Harrison, David J; Stewart, Grant D

    2013-01-22

    Currently there is no curative treatment for metastatic clear cell renal cell cancer, the commonest variant of the disease. A key factor in this treatment resistance is thought to be the molecular complexity of the disease. Targeted therapy such as the tyrosine kinase inhibitor (TKI)-sunitinib have been utilized, but only 40% of patients will respond, with the overwhelming majority of these patients relapsing within 1 year. As such the question of intrinsic and acquired resistance in renal cell cancer patients is highly relevant. In order to study resistance to TKIs, with the ultimate goal of developing effective, personalized treatments, sequential tissue after a specific period of targeted therapy is required, an approach which had proved successful in chronic myeloid leukaemia. However the application of such a strategy in renal cell carcinoma is complicated by the high level of both inter- and intratumoral heterogeneity, which is a feature of renal cell carcinoma as well as other solid tumors. Intertumoral heterogeneity due to transcriptomic and genetic differences is well established even in patients with similar presentation, stage and grade of tumor. In addition it is clear that there is great morphological (intratumoral) heterogeneity in RCC, which is likely to represent even greater molecular heterogeneity. Detailed mapping and categorization of RCC tumors by combined morphological analysis and Fuhrman grading allows the selection of representative areas for proteomic analysis. Protein based analysis of RCC is attractive due to its widespread availability in pathology laboratories; however, its application can be problematic due to the limited availability of specific antibodies. Due to the dot blot nature of the Reverse Phase Protein Arrays (RPPA), antibody specificity must be pre-validated; as such strict quality control of antibodies used is of paramount importance. Despite this limitation the dot blot format does allow assay miniaturization, allowing

  11. Ribosome profiling reveals translational regulation of mammalian cells in response to hypoxic stress.

    Science.gov (United States)

    Jiang, Zhiwen; Yang, Jiaqi; Dai, Aimei; Wang, Yuming; Li, Wei; Xie, Zhi

    2017-08-21

    Retinal pigment epithelium (RPE) cells transfer oxygen and nutrients from choroid to the neural retina. Reduced oxygen to RPE perturbs development and functions of blood vessels in retina. Previous efforts of genome-wide studies have been largely focused on transcriptional changes of cells in response to hypoxia. Recently developed ribosome profiling provides an opportunity to study genome-wide translational changes. To gain systemic insights into the transcriptional and translational regulation of cellular in response to hypoxic stress, we used simultaneous RNA sequencing and ribosome profiling on an RPE cells line, ARPE-19, under hypoxia condition. Both HIF-1α and EPAS1 (HIF-2α) proteins were stabilized in ARPE-19 under hypoxic stress treatment at 1 h, 2 h and 4 h. Analysis of simultaneous RNA sequencing and ribosome profiling data showed genome-wide gene expression changes at both transcriptional and translational levels. Comparative analysis of ribosome profiling and RNA-seq data revealed that hypoxia induced changes of more genes at the translational than the transcriptional levels. Ribosomes densities at 5' untranslated region (UTR) significantly increased under hypoxic stress. Interestingly, the increase in ribosome densities at 5' UTR is positively correlated with the presence of upstream open reading frames (uORFs) in the 5' UTR of mRNAs. Our results characterized translational profiles of mRNAs for a RPE cell line in response to hypoxia. In particular, uORFs play important roles in the regulation of translation efficiency by affecting ribosomes loading onto mRNAs. This study provides the first attempt to understand translational response of mammalian cells under hypoxic condition.

  12. Multiplex and genome-wide analyses reveal distinctive properties of KIR+ and CD56+ T cells in human blood

    Science.gov (United States)

    Chan, Wing Keung; Rujkijyanont, Piya; Neale, Geoffrey; Yang, Jie; Bari, Rafijul; Gupta, Neha Das; Holladay, Martha; Rooney, Barbara; Leung, Wing

    2014-01-01

    Killer-cell immunoglobulin-like receptors (KIRs) on natural killer (NK) cells have been linked to a wide spectrum of health conditions such as chronic infections, autoimmune diseases, pregnancy complications, cancers, and transplant failures. A small subset of effector memory T cells also expresses KIRs. Here, we use modern analytic tools including genome-wide and multiplex molecular, phenotypic, and functional assays to characterize the KIR+ T cells in human blood. We find that KIR+ T cells primarily reside in the CD56+ T population that is distinctively DNAM-1high with a genome-wide quiescent transcriptome, short telomere, and limited TCR excision circles. During cytomegalovirus (CMV) reactivation in bone marrow transplant recipients, KIR+CD56+ T cells rapidly expanded in real-time, but not KIR+CD56− T cells or KIR+ NK cells. In CMV+ asymptomatic donors, as much as 50% of CD56+ T cells are KIR+, and most are distinguishably KIR2DL2/3+NKG2C+CD57+. Functionally, the KIR+CD56+ T-cell subset lyses cancer cells and CMVpp65-pulsed target cells in a dual KIR-dependent and TCR-dependent manner. Analysis of metabolic transcriptome confirms the immunological memory status of KIR+CD56+ T cells, in contrast to KIR−CD56+ T cells that are more active in energy metabolism and effector differentiation. KIR−CD56+ T cells have >25-fold higher level of expression of RORC than the KIR+ counterpart and are a previously unknown producer of IL-13 rather than IL-17 in multiplex cytokine arrays. Our data provide fundamental insights intoKIR + T cells biologically and clinically. PMID:23858032

  13. Array capabilities and future arrays

    International Nuclear Information System (INIS)

    Radford, D.

    1993-01-01

    Early results from the new third-generation instruments GAMMASPHERE and EUROGAM are confirming the expectation that such arrays will have a revolutionary effect on the field of high-spin nuclear structure. When completed, GAMMASHPERE will have a resolving power am order of magnitude greater that of the best second-generation arrays. When combined with other instruments such as particle-detector arrays and fragment mass analysers, the capabilites of the arrays for the study of more exotic nuclei will be further enhanced. In order to better understand the limitations of these instruments, and to design improved future detector systems, it is important to have some intelligible and reliable calculation for the relative resolving power of different instrument designs. The derivation of such a figure of merit will be briefly presented, and the relative sensitivities of arrays currently proposed or under construction presented. The design of TRIGAM, a new third-generation array proposed for Chalk River, will also be discussed. It is instructive to consider how far arrays of Compton-suppressed Ge detectors could be taken. For example, it will be shown that an idealised open-quote perfectclose quotes third-generation array of 1000 detectors has a sensitivity an order of magnitude higher again than that of GAMMASPHERE. Less conventional options for new arrays will also be explored

  14. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi.

    Science.gov (United States)

    Zhao, Zhongtao; Liu, Huiquan; Wang, Chenfang; Xu, Jin-Rong

    2013-04-23

    Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex

  15. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2013-01-01

    Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 103 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed. Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also

  16. Three-dimensional architecture hybrid perovskite solar cells using CdS nanorod arrays as an electron transport layer

    Science.gov (United States)

    Song, Zihang; Tong, Guoqing; Li, Huan; Li, Guopeng; Ma, Shuai; Yu, Shimeng; Liu, Qian; Jiang, Yang

    2018-01-01

    Three-dimensional (3D) architecture perovskite solar cells (PSCs) using CdS nanorod (NR) arrays as an electron transport layer were designed and prepared layer-by-layer via a physical-chemical vapor deposition (P-CVD) process. The CdS NRs not only provided a scaffold to the perovskite film, but also increased the interfacial contact between the perovskite film and electron transport layer. As an optimized result, a high power conversion efficiency of 12.46% with a short-circuit current density of 19.88 mA cm‑2, an open-circuit voltage of 1.01 V and a fill factor of 62.06% was obtained after 12 h growth of CdS NRs. It was four times the efficiency of contrast planar structure with a similar thickness. The P-CVD method assisted in achieving flat and voidless CH3NH3PbI3‑x Cl x perovskite film and binding the CdS NRs and perovskite film together. The different density of CdS NRs had obvious effects on light transmittance of 350–550 nm, the interfacial area and the difficulty of combining layers. Moreover, the efficient 1D transport paths for electrons and multiple absorption of light, which are generated in 3D architecture, were beneficial to realize a decent power conversion efficiency.

  17. One-Dimensional Self-Standing TiO2Nanotube Array Layers Designed for Perovskite Solar Cell Applications.

    Science.gov (United States)

    Zhang, Jie; Pauporté, Thierry

    2015-08-03

    Nanotube (NT) layers of TiO 2 are important one-dimensional nanostructures for advanced applications. ZnO nanowire arrays prepared through electrochemical deposition with tuned morphological properties are converted into anatase TiO 2 NTs by using a titanate solution adjusted to an ad hoc pH. The tubes are polycrystalline and their diameter and length can be tuned to obtain nanostructures of tailored dimensions. The layers are integrated in CH 3 NH 3 PbI 3 perovskite solar cells (PSCs). Their morphology is optimized for maximum performance and is compared to mesoscopic TiO 2 PSCs. As compared to the latter, the use of NTs improved the perovskite absorbance in the green-to-near-infrared solar spectral region. Moreover, it is shown that the surface treatment of the TiO 2 NTs with TiCl 4 optimizes the interface between the oxide and CH 3 NH 3 PbI 3 , which leads to better charge injection between the perovskite layer and the TiO 2 NTs. The current density-voltage curve hysteresis index is low for the best NT morphology and significantly increases with tube length and diameter. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Integrative Single-Cell Transcriptomics Reveals Molecular Networks Defining Neuronal Maturation During Postnatal Neurogenesis.

    Science.gov (United States)

    Gao, Yu; Wang, Feifei; Eisinger, Brian E; Kelnhofer, Laurel E; Jobe, Emily M; Zhao, Xinyu

    2017-03-01

    In mammalian hippocampus, new neurons are continuously produced from neural stem cells throughout life. This postnatal neurogenesis may contribute to information processing critical for cognition, adaptation, learning, and memory, and is implicated in numerous neurological disorders. During neurogenesis, the immature neuron stage defined by doublecortin (DCX) expression is the most sensitive to regulation by extrinsic factors. However, little is known about the dynamic biology within this critical interval that drives maturation and confers susceptibility to regulatory signals. This study aims to test the hypothesis that DCX-expressing immature neurons progress through developmental stages via activity of specific transcriptional networks. Using single-cell RNA-seq combined with a novel integrative bioinformatics approach, we discovered that individual immature neurons can be classified into distinct developmental subgroups based on characteristic gene expression profiles and subgroup-specific markers. Comparisons between immature and more mature subgroups revealed novel pathways involved in neuronal maturation. Genes enriched in less mature cells shared significant overlap with genes implicated in neurodegenerative diseases, while genes positively associated with neuronal maturation were enriched for autism-related gene sets. Our study thus discovers molecular signatures of individual immature neurons and unveils potential novel targets for therapeutic approaches to treat neurodevelopmental and neurological diseases. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  19. Alteration in Fluidity of Cell Plasma Membrane in Huntington Disease Revealed by Spectral Phasor Analysis.

    Science.gov (United States)

    Sameni, Sara; Malacrida, Leonel; Tan, Zhiqun; Digman, Michelle A

    2018-01-15

    Huntington disease (HD) is a late-onset genetic neurodegenerative disorder caused by expansion of cytosine-adenine-guanine (CAG) trinucleotide in the exon 1 of the gene encoding the polyglutamine (polyQ). It has been shown that protein degradation and lipid metabolism is altered in HD. In many neurodegenerative disorders, impaired lipid homeostasis is one of the early events in the disease onset. Yet, little is known about how mutant huntingtin may affect phospholipids membrane fluidity. Here, we investigated how membrane fluidity in the living cells (differentiated PC12 and HEK293 cell lines) are affected using a hyperspectral imaging of widely used probes, LAURDAN. Using phasor approach, we characterized the fluorescence of LAURDAN that is sensitive to the polarity of the immediate environment. LAURDAN is affected by the physical order of phospholipids (lipid order) and reports the membrane fluidity. We also validated our results using a different fluorescent membrane probe, Nile Red (NR). The plasma membrane in the cells expressing expanded polyQ shows a shift toward increased membrane fluidity revealed by both LAURDAN and NR spectral phasors. This finding brings a new perspective in the understanding of the early stages of HD that can be used as a target for drug screening.

  20. Morphology-based mammalian stem cell tests reveal potential developmental toxicity of donepezil.

    Science.gov (United States)

    Lau, Caroline G Y; Marikawa, Yusuke

    2014-11-01

    Various compounds, including therapeutic drugs, can adversely impact the survival and development of embryos in the uterus. Identification of such development-interfering agents is a challenging task, although multi-angle approaches--including the use of in vitro toxicology studies involving embryonic stem cells--should alleviate some of the current difficulties. In the present study, we utilized the in vitro elongation of embryoid bodies (EBs) derived from mouse embryonal carcinoma stem cell line P19C5 as a model of early embryological events, specifically that of gastrulation and axial patterning. From our study, we identified donepezil, a medication indicated for the management of Alzheimer's disease, as a potential developmental toxicant. The extent of P19C5 EB axial elongation was diminished by donepezil in a dose-dependent manner. Although donepezil is a known inhibitor of acetylcholinesterase, interference of elongation was not mediated through this enzyme. Quantitative reverse-transcriptase PCR revealed that donepezil altered the expression pattern of a specific set of developmental regulator genes involved in patterning along the anterior-posterior body axis. When tested in mouse whole embryo culture, donepezil caused morphological abnormalities including impaired somitogenesis. Donepezil also diminished elongation morphogenesis of EBs generated from human embryonic stem cells. These results suggest that donepezil interferes with axial elongation morphogenesis of early embryos by altering the expression pattern of regulators of axial development. © 2014 Wiley Periodicals, Inc.

  1. Deep sequencing reveals new aspects of progesterone receptor signaling in breast cancer cells.

    Directory of Open Access Journals (Sweden)

    Anastasia Kougioumtzi

    Full Text Available Despite the pleiotropic effects of the progesterone receptor in breast cancer, the molecular mechanisms in play remain largely unknown. To gain a global view of the PR-orchestrated networks, we used next-generation sequencing to determine the progestin-regulated transcriptome in T47D breast cancer cells. We identify a large number of PR target genes involved in critical cellular programs, such as regulation of transcription, apoptosis, cell motion and angiogenesis. Integration of the transcriptomic data with the PR-binding profiling of hormonally treated cells identifies numerous components of the small-GTPases signaling pathways as direct PR targets. Progestin-induced deregulation of the small GTPases may contribute to the PR's role in mammary tumorigenesis. Transcript expression analysis reveals significant expression changes of specific transcript variants in response to the extracellular hormonal stimulus. Using the NET1 gene as an example, we show that the PR can dictate alternative promoter usage leading to the upregulation of an isoform that may play a role in metastatic breast cancer. Future studies should aim to characterize these selectively regulated variants and evaluate their clinical utility in prognosis and targeted therapy of hormonally responsive breast tumors.

  2. 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.

  3. The Influence of Geography and Geology on Seismic Background Noise Levels Across the United States as Revealed by the Transportable Array

    Science.gov (United States)

    Anthony, R. E.; Ringler, A. T.; Holland, A. A.; Wilson, D. C.

    2017-12-01

    The EarthScope USArray Transportable Array (TA) has now covered the US with 3-component broadband seismometers at approximately 70 km station spacing and deployment durations of approximately 2 years. This unprecedented coverage, combined with high-quality and near homogenous installation techniques, offers a novel dataset in which to characterize spatially varying levels of background seismic noise across the United States. We present background noise maps in period bands of interest to earthquake and imaging seismology across the US (lower 48 states and Alaska). Early results from the contiguous 48 states demonstrate that ambient noise levels within the body wave period band (1-5 s) vary by > 20 dB (rel. 1 (m/s2)2/Hz) with the highest noise levels occurring at stations located within sedimentary basins and lowest within the mountain ranges of the Western US. Additionally, stations around the Great Lakes observe heightened noise levels in this band beyond the aforementioned basin amplification. We attribute this observation to local swell activity in the Great Lakes generating short-period microseism signals. This suggests that lake-generated microseisms may be a significant source of noise for Alaskan deployments situated in close proximity to lakes to facilitate float plane access. We further investigate how basin amplification and short-period lake microseism signals may noticeably impact detection and signal-to-noise of teleseismic body wave signals during certain time periods. At longer-periods (> 20 s), we generally observe larger noise levels on the horizontal components of stations situated in basins or on soft sediment, likely caused by locally induced tilt of the sensor. We will present similar analysis from the initial Alaska TA dataset to quantitatively assess how utilization of posthole sensors affects signal-to-noise for the long-period horizontal wavefield.

  4. Design of a large-scale femtoliter droplet array for single-cell analysis of drug-tolerant and drug-resistant bacteria

    Directory of Open Access Journals (Sweden)

    Ryota eIino

    2013-10-01

    Full Text Available Single-cell analysis is a powerful method to assess the heterogeneity among individual cells, enabling the identification of very rare cells with properties that differ from those of the majority. In this Methods Article, we describe the use of a large-scale femtoliter droplet array to enclose, isolate, and analyze individual bacterial cells. As a first example, we describe the single-cell detection of drug-tolerant persisters of Pseudomonas aeruginosa treated with the antibiotic carbenicillin. As a second example, this method was applied to the single-cell evaluation of drug efflux activity, which causes acquired antibiotic resistance of bacteria. The activity of the MexAB-OprM multidrug efflux pump system from Pseudomonas aeruginosa was expressed in Escherichia coli and the effect of an inhibitor D13-9001 were assessed at the single cell level.

  5. Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

    Directory of Open Access Journals (Sweden)

    Liu Liwen

    2009-09-01

    Full Text Available Abstract Background Fission yeast Schizosaccharomyces pombe and budding yeast Saccharomyces cerevisiae are among the original model organisms in the study of the cell-division cycle. Unlike budding yeast, no large-scale regulatory network has been constructed for fission yeast. It has only been partially characterized. As a result, important regulatory cascades in budding yeast have no known or complete counterpart in fission yeast. Results By integrating genome-wide data from multiple time course cell cycle microarray experiments we reconstructed a gene regulatory network. Based on the network, we discovered in addition to previously known regulatory hubs in M phase, a new putative regulatory hub in the form of the HMG box transcription factor SPBC19G7.04. Further, we inferred periodic activities of several less known transcription factors over the course of the cell cycle, identified over 500 putative regulatory targets and detected many new phase-specific and conserved cis-regulatory motifs. In particular, we show that SPBC19G7.04 has highly significant periodic activity that peaks in early M phase, which is coordinated with the late G2 activity of the forkhead transcription factor fkh2. Finally, using an enhanced Bayesian algorithm to co-cluster the expression data, we obtained 31 clusters of co-regulated genes 1 which constitute regulatory modules from different phases of the cell cycle, 2 whose phase order is coherent across the 10 time course experiments, and 3 which lead to identification of phase-specific control elements at both the transcriptional and post-transcriptional levels in S. pombe. In particular, the ribosome biogenesis clusters expressed in G2 phase reveal new, highly conserved RNA motifs. Conclusion Using a systems-level analysis of the phase-specific nature of the S. pombe cell cycle gene regulation, we have provided new testable evidence for post-transcriptional regulation in the G2 phase of the fission yeast cell cycle

  6. Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

    Science.gov (United States)

    Tsang, Jason C H; Yu, Yong; Burke, Shannon; Buettner, Florian; Wang, Cui; Kolodziejczyk, Aleksandra A; Teichmann, Sarah A; Lu, Liming; Liu, Pentao

    2015-09-21

    Hematopoietic stem cells (HSCs) are a rare cell type with the ability of long-term self-renewal and multipotency to reconstitute all blood lineages. HSCs are typically purified from the bone marrow using cell surface markers. Recent studies have identified significant cellular heterogeneities in the HSC compartment with subsets of HSCs displaying lineage bias. We previously discovered that the transcription factor Bcl11a has critical functions in the lymphoid development of the HSC compartment. In this report, we employ single-cell transcriptomic analysis to dissect the molecular heterogeneities in HSCs. We profile the transcriptomes of 180 highly purified HSCs (Bcl11a (+/+) and Bcl11a (-/-)). Detailed analysis of the RNA-seq data identifies cell cycle activity as the major source of transcriptomic variation in the HSC compartment, which allows reconstruction of HSC cell cycle progression in silico. Single-cell RNA-seq profiling of Bcl11a (-/-) HSCs reveals abnormal proliferative phenotypes. Analysis of lineage gene expression suggests that the Bcl11a (-/-) HSCs are constituted of two distinct myeloerythroid-restricted subpopulations. Remarkably, similar myeloid-restricted cells could also be detected in the wild-type HSC compartment, suggesting selective elimination of lymphoid-competent HSCs after Bcl11a deletion. These defects are experimentally validated in serial transplantation experiments where Bcl11a (-/-) HSCs are myeloerythroid-restricted and defective in self-renewal. Our study demonstrates the power of single-cell transcriptomics in dissecting cellular process and lineage heterogeneities in stem cell compartments, and further reveals the molecular and cellular defects in the Bcl11a-deficient HSC compartment.

  7. Short-length and high-density TiO2 nanorod arrays for the efficient charge separation interface in perovskite solar cells

    International Nuclear Information System (INIS)

    Xiao, Guannan; Shi, Chengwu; Zhang, Zhengguo; Li, Nannan; Li, Long

    2017-01-01

    The TiO 2 nanorod arrays with the length of 70 nm, the diameter of 20 nm, and the areal density of 1000 µm −2 were firstly prepared by the hydrothermal method using the aqueous grown solution of 38 mM titanium isopropoxide and 6 M hydrochloric acid at 170 °C for 60 min. Over-500 nm-thickness CH 3 NH 3 PbI 3−x Br x absorber layers were successfully obtained by sequential deposition routes using 1.7 M PbI 2 ·DMSO complex precursor solution and 0.465 M isopropanol solution of the methylammonium halide mixture with the molar ratio of CH 3 NH 3 I/CH 3 NH 3 Br=85/15. The perovskite solar cells based on the TiO 2 nanorod array and 560 nm-thickness CH 3 NH 3 PbI 3−x Br x absorber layer exhibited the best photoelectric conversion efficiency (PCE) of 15.93%, while the corresponding planar perovskite solar cells without the TiO 2 nanorod array and with 530 nm-thickness CH 3 NH 3 PbI 3−x Br x absorber layer gave the best PCE of 12.82% at the relative humidity of 50–54%. - Graphical abstract: The TiO 2 nanorod arrays with the length of 70 nm, the diameter of 20 nm, and the areal density of 1000 µm −2 were prepared by the hydrothermal method using the aqueous grown solution of 38 mM titanium isopropoxide and 6 M hydrochloric acid at 170 °C for 60 min. The optimal annealing temperature of TiO 2 nanorod arrays was 450 °C. The perovskite solar cells based on the TiO 2 nanorod array and 560 nm-thickness CH 3 NH 3 PbI 3−x Br x absorber layer exhibited the best photoelectric conversion efficiency (PCE) of 15.93% and the average PCE of 13.41±2.52%, while the corresponding planar perovskite solar cells without the TiO 2 nanorod array and with 530 nm-thickness CH 3 NH 3 PbI 3−x Br x absorber layer gave the best PCE of 12.82% and the average PCE of 10.54±2.28% at the relative humidity of 50–54%. - Highlights: • Preparation of TiO 2 nanorod array with length of 70 nm and density of 1000 µm −2 . • Influence of annealing temperatures on the -OH content of Ti

  8. Short-length and high-density TiO{sub 2} nanorod arrays for the efficient charge separation interface in perovskite solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Guannan; Shi, Chengwu, E-mail: shicw506@foxmail.com; Zhang, Zhengguo; Li, Nannan; Li, Long

    2017-05-15

    The TiO{sub 2} nanorod arrays with the length of 70 nm, the diameter of 20 nm, and the areal density of 1000 µm{sup −2} were firstly prepared by the hydrothermal method using the aqueous grown solution of 38 mM titanium isopropoxide and 6 M hydrochloric acid at 170 °C for 60 min. Over-500 nm-thickness CH{sub 3}NH{sub 3}PbI{sub 3−x}Br{sub x} absorber layers were successfully obtained by sequential deposition routes using 1.7 M PbI{sub 2}·DMSO complex precursor solution and 0.465 M isopropanol solution of the methylammonium halide mixture with the molar ratio of CH{sub 3}NH{sub 3}I/CH{sub 3}NH{sub 3}Br=85/15. The perovskite solar cells based on the TiO{sub 2} nanorod array and 560 nm-thickness CH{sub 3}NH{sub 3}PbI{sub 3−x}Br{sub x} absorber layer exhibited the best photoelectric conversion efficiency (PCE) of 15.93%, while the corresponding planar perovskite solar cells without the TiO{sub 2} nanorod array and with 530 nm-thickness CH{sub 3}NH{sub 3}PbI{sub 3−x}Br{sub x} absorber layer gave the best PCE of 12.82% at the relative humidity of 50–54%. - Graphical abstract: The TiO{sub 2} nanorod arrays with the length of 70 nm, the diameter of 20 nm, and the areal density of 1000 µm{sup −2} were prepared by the hydrothermal method using the aqueous grown solution of 38 mM titanium isopropoxide and 6 M hydrochloric acid at 170 °C for 60 min. The optimal annealing temperature of TiO{sub 2} nanorod arrays was 450 °C. The perovskite solar cells based on the TiO{sub 2} nanorod array and 560 nm-thickness CH{sub 3}NH{sub 3}PbI{sub 3−x}Br{sub x} absorber layer exhibited the best photoelectric conversion efficiency (PCE) of 15.93% and the average PCE of 13.41±2.52%, while the corresponding planar perovskite solar cells without the TiO{sub 2} nanorod array and with 530 nm-thickness CH{sub 3}NH{sub 3}PbI{sub 3−x}Br{sub x} absorber layer gave the best PCE of 12.82% and the average PCE of 10.54±2.28% at the relative humidity of 50–54%. - Highlights:

  9. 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.

  10. Mouse model of chromosome mosaicism reveals lineage-specific depletion of aneuploid cells and normal developmental potential.

    Science.gov (United States)

    Bolton, Helen; Graham, Sarah J L; Van der Aa, Niels; Kumar, Parveen; Theunis, Koen; Fernandez Gallardo, Elia; Voet, Thierry; Zernicka-Goetz, Magdalena

    2016-03-29

    Most human pre-implantation embryos are mosaics of euploid and aneuploid cells. To determine the fate of aneuploid cells and the developmental potential of mosaic embryos, here we generate a mouse model of chromosome mosaicism. By treating embryos with a spindle assembly checkpoint inhibitor during the four- to eight-cell division, we efficiently generate aneuploid cells, resulting in embryo death during peri-implantation development. Live-embryo imaging and single-cell tracking in chimeric embryos, containing aneuploid and euploid cells, reveal that the fate of aneuploid cells depends on lineage: aneuploid cells in the fetal lineage are eliminated by apoptosis, whereas those in the placental lineage show severe proliferative defects. Overall, the proportion of aneuploid cells is progressively depleted from the blastocyst stage onwards. Finally, we show that mosaic embryos have full developmental potential, provided they contain sufficient euploid cells, a finding of significance for the assessment of embryo vitality in the clinic.

  11. Mouse model of chromosome mosaicism reveals lineage-specific depletion of aneuploid cells and normal developmental potential

    Science.gov (United States)

    Bolton, Helen; Graham, Sarah J. L.; Van der Aa, Niels; Kumar, Parveen; Theunis, Koen; Fernandez Gallardo, Elia; Voet, Thierry; Zernicka-Goetz, Magdalena

    2016-01-01

    Most human pre-implantation embryos are mosaics of euploid and aneuploid cells. To determine the fate of aneuploid cells and the developmental potential of mosaic embryos, here we generate a mouse model of chromosome mosaicism. By treating embryos with a spindle assembly checkpoint inhibitor during the four- to eight-cell division, we efficiently generate aneuploid cells, resulting in embryo death during peri-implantation development. Live-embryo imaging and single-cell tracking in chimeric embryos, containing aneuploid and euploid cells, reveal that the fate of aneuploid cells depends on lineage: aneuploid cells in the fetal lineage are eliminated by apoptosis, whereas those in the placental lineage show severe proliferative defects. Overall, the proportion of aneuploid cells is progressively depleted from the blastocyst stage onwards. Finally, we show that mosaic embryos have full developmental potential, provided they contain sufficient euploid cells, a finding of significance for the assessment of embryo vitality in the clinic. PMID:27021558

  12. 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.

  13. Co-cultures with stem cell-derived human sensory neurons reveal regulators of peripheral myelination.

    Science.gov (United States)

    Clark, Alex J; Kaller, Malte S; Galino, Jorge; Willison, Hugh J; Rinaldi, Simon; Bennett, David L H

    2017-04-01

    See Saporta and Shy (doi:10.1093/awx048) for a scientific commentary on this article.Effective bidirectional signalling between axons and Schwann cells is essential for both the development and maintenance of peripheral nerve function. We have established conditions by which human induced pluripotent stem cell-derived sensory neurons can be cultured with rat Schwann cells, and have produced for the first time long-term and stable myelinating co-cultures with human neurons. These cultures contain the specialized domains formed by axonal interaction with myelinating Schwann cells, such as clustered voltage-gated sodium channels at the node of Ranvier and Shaker-type potassium channel (Kv1.2) at the juxtaparanode. Expression of type III neuregulin-1 (TIIINRG1) in induced pluripotent stem cell-derived sensory neurons strongly enhances myelination, while conversely pharmacological blockade of the NRG1-ErbB pathway prevents myelination, providing direct evidence for the ability of this pathway to promote the myelination of human sensory axons. The β-secretase, BACE1 is a protease needed to generate active NRG1 from the full-length form. Due to the fact that it also cleaves amyloid precursor protein, BACE1 is a therapeutic target in Alzheimer's disease, however, consistent with its role in NRG1 processing we find that BACE1 inhibition significantly impairs myelination in our co-culture system. In order to exploit co-cultures to address other clinically relevant problems, they were exposed to anti-disialosyl ganglioside antibodies, including those derived from a patient with a sensory predominant, inflammatory neuropathy with mixed axonal and demyelinating electrophysiology. The co-cultures reveal that both mouse and human disialosyl antibodies target the nodal axolemma, induce acute axonal degeneration in the presence of complement, and impair myelination. The human, neuropathy-associated IgM antibody is also shown to induce complement-independent demyelination

  14. SNP Arrays

    Directory of Open Access Journals (Sweden)

    Jari Louhelainen

    2016-10-01

    Full Text Available The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.

  15. High throughput transcriptome profiling of lithium stimulated human mesenchymal stem cells reveals priming towards osteoblastic lineage.

    Directory of Open Access Journals (Sweden)

    Neeraj Kumar Satija

    Full Text Available Human mesenchymal stem cells (hMSCs present in the bone marrow are the precursors of osteoblasts, chondrocytes and adipocytes, and hold tremendous potential for osteoregenerative therapy. However, achieving directed differentiation into osteoblasts has been a major concern. The use of lithium for enhancing osteogenic differentiation has been documented in animal models but its effect in humans is not clear. We, therefore, performed high throughput transcriptome analysis of lithium-treated hMSCs to identify altered gene expression and its relevance to osteogenic differentiation. Our results show suppression of proliferation and enhancement of alkaline phosphatase (ALP activity upon lithium treatment of hMSCs under non-osteogenic conditions. Microarray profiling of lithium-stimulated hMSC revealed decreased expression of adipogenic genes (CEBPA, CMKLR1, HSD11B1 and genes involved in lipid biosynthesis. Interestingly, osteoclastogenic factors and immune responsive genes (IL7, IL8, CXCL1, CXCL12, CCL20 were also downregulated. Negative transcriptional regulators of the osteogenic program (TWIST1 and PBX1 were suppressed while genes involved in mineralization like CLEC3B and ATF4 were induced. Gene ontology analysis revealed enrichment of upregulated genes related to mesenchymal cell differentiation and signal transduction. Lithium priming led to enhanced collagen 1 synthesis and osteogenic induction of lithium pretreated MSCs resulted in enhanced expression of Runx2, ALP and bone sialoprotein. However, siRNA-mediated knockdown of RRAD, CLEC3B and ATF4 attenuated lithium-induced osteogenic priming, identifying a role for RRAD, a member of small GTP binding protein family, in osteoblast differentiation. In conclusion, our data highlight the transcriptome reprogramming potential of lithium resulting in higher propensity of lithium "primed" MSCs for osteoblastic differentiation.

  16. High throughput transcriptome profiling of lithium stimulated human mesenchymal stem cells reveals priming towards osteoblastic lineage.

    Science.gov (United States)

    Satija, Neeraj Kumar; Sharma, Deepa; Afrin, Farhat; Tripathi, Rajendra P; Gangenahalli, Gurudutta

    2013-01-01

    Human mesenchymal stem cells (hMSCs) present in the bone marrow are the precursors of osteoblasts, chondrocytes and adipocytes, and hold tremendous potential for osteoregenerative therapy. However, achieving directed differentiation into osteoblasts has been a major concern. The use of lithium for enhancing osteogenic differentiation has been documented in animal models but its effect in humans is not clear. We, therefore, performed high throughput transcriptome analysis of lithium-treated hMSCs to identify altered gene expression and its relevance to osteogenic differentiation. Our results show suppression of proliferation and enhancement of alkaline phosphatase (ALP) activity upon lithium treatment of hMSCs under non-osteogenic conditions. Microarray profiling of lithium-stimulated hMSC revealed decreased expression of adipogenic genes (CEBPA, CMKLR1, HSD11B1) and genes involved in lipid biosynthesis. Interestingly, osteoclastogenic factors and immune responsive genes (IL7, IL8, CXCL1, CXCL12, CCL20) were also downregulated. Negative transcriptional regulators of the osteogenic program (TWIST1 and PBX1) were suppressed while genes involved in mineralization like CLEC3B and ATF4 were induced. Gene ontology analysis revealed enrichment of upregulated genes related to mesenchymal cell differentiation and signal transduction. Lithium priming led to enhanced collagen 1 synthesis and osteogenic induction of lithium pretreated MSCs resulted in enhanced expression of Runx2, ALP and bone sialoprotein. However, siRNA-mediated knockdown of RRAD, CLEC3B and ATF4 attenuated lithium-induced osteogenic priming, identifying a role for RRAD, a member of small GTP binding protein family, in osteoblast differentiation. In conclusion, our data highlight the transcriptome reprogramming potential of lithium resulting in higher propensity of lithium "primed" MSCs for osteoblastic differentiation.

  17. Proteomics investigation reveals cell death-associated proteins of basidiomycete fungus Trametes versicolor treated with Ferruginol.

    Science.gov (United States)

    Chen, Yu-Han; Yeh, Ting-Feng; Chu, Fang-Hua; Hsu, Fu-Lan; Chang, Shang-Tzen

    2015-01-14

    Ferruginol has antifungal activity against wood-rot fungi (basidiomycetes). However, specific research on the antifungal mechanisms of ferruginol is scarce. Two-dimensional gel electrophoresis and fluorescent image analysis were employed to evaluate the differential protein expression of wood-rot fungus Trametes versicolor treated with or without ferruginol. Results from protein identification of tryptic peptides via liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI-MS/MS) analyses revealed 17 protein assignments with differential expression. Downregulation of cytoskeleton β-tubulin 3 indicates that ferruginol has potential to be used as a microtubule-disrupting agent. Downregulation of major facilitator superfamily (MFS)–multiple drug resistance (MDR) transporter and peroxiredoxin TSA1 were observed, suggesting reduction in self-defensive capabilities of T. versicolor. In addition, the proteins involved in polypeptide sorting and DNA repair were also downregulated, while heat shock proteins and autophagy-related protein 7 were upregulated. These observations reveal that such cellular dysfunction and damage caused by ferruginol lead to growth inhibition and autophagic cell death of fungi.

  18. Tilted hexagonal post arrays: DNA electrophoresis in anisotropic media

    Science.gov (United States)

    Chen, Zhen; Dorfman, Kevin D.

    2013-01-01

    Using Brownian dynamics simulations, we show that DNA electrophoresis in a hexagonal array of micron-sized posts changes qualitatively when the applied electric field vector is not coincident with the lattice vectors of the array. DNA electrophoresis in such “tilted” post arrays is superior to the standard “un-tilted” approach; while the time required to achieve a resolution of unity in a tilted post array is similar to an un-tilted array at a low electric field strengths, this time (i) decreases exponentially with electric field strength in a tilted array and (ii) increases exponentially with electric field strength in an un-tilted array. Although the DNA dynamics in a post array are complicated, the electrophoretic mobility results indicate that the “free path”, i.e., the average distance of ballistic trajectories of point sized particles launched from random positions in the unit cell until they intersect the next post, is a useful proxy for the detailed DNA trajectories. The analysis of the free path reveals a fundamental connection between anisotropy of the medium and DNA transport therein that goes beyond simply improving the separation device. PMID:23868490

  19. Solution-processed all-oxide bulk heterojunction solar cells based on CuO nanaorod array and TiO2nanocrystals.

    Science.gov (United States)

    Wu, Fan; Qiao, Qiquan; Bahrami, Behzad; Chen, Ke; Pathak, Rajesh; Tong, Yanhua; Li, Xiaoyi; Zhang, Tiansheng; Jian, Ronghua

    2018-05-25

    We present a method to synthesize CuO nanorod array/TiO 2 nanocrystals bulk heterojunction (BHJ) on fluorine-tin-oxide (FTO) glass, in which single-crystalline p-type semiconductor of the CuO nanorod array is grown on the FTO glass by hydrothermal reaction and the n-type semiconductor of the TiO 2 precursor is filled into the CuO nanorods to form well-organized nano-interpenetrating BHJ after air annealing. The interface charge transfer in CuO nanorod array/TiO 2 heterojunction is studied by Kelvin probe force microscopy (KPFM). KPFM results demonstrate that the CuO nanorod array/TiO 2 heterojunction can realize the transfer of photo-generated electrons from the CuO nanorod array to TiO 2 . In this work, a solar cell with the structure FTO/CuO nanoarray/TiO 2 /Al is successfully fabricated, which exhibits an open-circuit voltage (V oc ) of 0.20 V and short-circuit current density (J sc ) of 0.026 mA cm -2 under AM 1.5 illumination. KPFM studies indicate that the very low performance is caused by an undesirable interface charge transfer. The interfacial surface potential (SP) shows that the electron concentration in the CuO nanorod array changes considerably after illumination due to increased photo-generated electrons, but the change in the electron concentration in TiO 2 is much less than in CuO, which indicates that the injection efficiency of the photo-generated electrons from CuO to TiO 2 is not satisfactory, resulting in an undesirable J sc in the solar cell. The interface photovoltage from the KPFM measurement shows that the low V oc results from the small interfacial SP difference between CuO and TiO 2 because the low injected electron concentration cannot raise the Fermi level significantly in TiO 2 . This conclusion agrees with the measured work function results under illumination. Hence, improvement of the interfacial electron injection is primary for the CuO nanorod array/TiO 2 heterojunction solar cells.

  20. Solution-processed all-oxide bulk heterojunction solar cells based on CuO nanaorod array and TiO2 nanocrystals

    Science.gov (United States)

    Wu, Fan; Qiao, Qiquan; Bahrami, Behzad; Chen, Ke; Pathak, Rajesh; Tong, Yanhua; Li, Xiaoyi; Zhang, Tiansheng; Jian, Ronghua

    2018-05-01

    We present a method to synthesize CuO nanorod array/TiO2 nanocrystals bulk heterojunction (BHJ) on fluorine-tin-oxide (FTO) glass, in which single-crystalline p-type semiconductor of the CuO nanorod array is grown on the FTO glass by hydrothermal reaction and the n-type semiconductor of the TiO2 precursor is filled into the CuO nanorods to form well-organized nano-interpenetrating BHJ after air annealing. The interface charge transfer in CuO nanorod array/TiO2 heterojunction is studied by Kelvin probe force microscopy (KPFM). KPFM results demonstrate that the CuO nanorod array/TiO2 heterojunction can realize the transfer of photo-generated electrons from the CuO nanorod array to TiO2. In this work, a solar cell with the structure FTO/CuO nanoarray/TiO2/Al is successfully fabricated, which exhibits an open-circuit voltage (V oc) of 0.20 V and short-circuit current density (J sc) of 0.026 mA cm‑2 under AM 1.5 illumination. KPFM studies indicate that the very low performance is caused by an undesirable interface charge transfer. The interfacial surface potential (SP) shows that the electron concentration in the CuO nanorod array changes considerably after illumination due to increased photo-generated electrons, but the change in the electron concentration in TiO2 is much less than in CuO, which indicates that the injection efficiency of the photo-generated electrons from CuO to TiO2 is not satisfactory, resulting in an undesirable J sc in the solar cell. The interface photovoltage from the KPFM measurement shows that the low V oc results from the small interfacial SP difference between CuO and TiO2 because the low injected electron concentration cannot raise the Fermi level significantly in TiO2. This conclusion agrees with the measured work function results under illumination. Hence, improvement of the interfacial electron injection is primary for the CuO nanorod array/TiO2 heterojunction solar cells.

  1. 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.

  2. Ag Nanoparticle-Functionalized Open-Ended Freestanding TiO₂ Nanotube Arrays with a Scattering Layer for Improved Energy Conversion Efficiency in Dye-Sensitized Solar Cells.

    Science.gov (United States)

    Rho, Won-Yeop; Chun, Myeung-Hwan; Kim, Ho-Sub; Kim, Hyung-Mo; Suh, Jung Sang; Jun, Bong-Hyun

    2016-06-15

    Dye-sensitized solar cells (DSSCs) were fabricated using open-ended freestanding TiO₂ nanotube arrays functionalized with Ag nanoparticles (NPs) in the channel to create a plasmonic effect, and then coated with large TiO₂ NPs to create a scattering effect in order to improve energy conversion efficiency. Compared to closed-ended freestanding TiO₂ nanotube array-based DSSCs without Ag or large TiO₂ NPs, the energy conversion efficiency of closed-ended DSSCs improved by 9.21% (actual efficiency, from 5.86% to 6.40%) with Ag NPs, 6.48% (actual efficiency, from 5.86% to 6.24%) with TiO₂ NPs, and 14.50% (actual efficiency, from 5.86% to 6.71%) with both Ag NPs and TiO₂ NPs. By introducing Ag NPs and/or large TiO₂ NPs to open-ended freestanding TiO₂ nanotube array-based DSSCs, the energy conversion efficiency was improved by 9.15% (actual efficiency, from 6.12% to 6.68%) with Ag NPs and 8.17% (actual efficiency, from 6.12% to 6.62%) with TiO₂ NPs, and by 15.20% (actual efficiency, from 6.12% to 7.05%) with both Ag NPs and TiO₂ NPs. Moreover, compared to closed-ended freestanding TiO₂ nanotube arrays, the energy conversion efficiency of open-ended freestanding TiO₂ nanotube arrays increased from 6.71% to 7.05%. We demonstrate that each component-Ag NPs, TiO₂ NPs, and open-ended freestanding TiO₂ nanotube arrays-enhanced the energy conversion efficiency, and the use of a combination of all components in DSSCs resulted in the highest energy conversion efficiency.

  3. Development of Electrolysis System Powered by Solar-Cell Array to Supply Hydrogen Gas for Fuel-Cell Energy Resource Systems

    Science.gov (United States)

    Priambodo, Purnomo Sidi; Yusivar, Feri; Subiantoro, Aries; Gunawan, Ridwan

    2009-09-01

    The huge demand of energy worldwide and the depletion of fossil based energy, is a strong reason to rapidly develop any kind of renewable energy resources, which has economical advantages and zero pollution effect. One of the renewable energy technologies aimed in this paper is the generation of electric-energy based on fuel-cell technology, where the input hydrogen (H2) gas is supplied by electrolysis system powered by renewable energy system based on solar cell. In this paper, the authors explain the development of electrolysis system which is powered by solar cell array to supply hydrogen for fuel-cell system. The authors explain in detail how to design an efficient electrolysis system to obtain high ratio conversion of electric energy to hydrogen gas volume. It includes the explanation of the usage of multiple anodes with a single cathode for many solar cell inputs in a single electrolysis system. Hereinafter this is referred as multiple anode electrolysis system. This multiple anode electrolysis system makes the management of hydrogen gas becomes more efficient and effective by using only a single hydrogen gas storage system. This paper also explain the careful design of the resistance value of the electrolysis system to protect or avoid the solar cell panel to deliver excessive current to the electrolysis system which can cause damage on the solar cell panel. Moreover, the electrolyte volume detector is applied on the system as a tool to measure the electrolyte concentration to assure the system resistance is still in the allowed range. Further, the hydrogen gas produced by electrolysis system is stored into the gas storage which consists of silica-gel purifier, first stage low pressure gas bottle, vacuum pump, and second stage high pressure gas bottle. In the first step, the pump will vacuum the first bottle. The first bottle will collect the hydrogen from the electrolysis system through the silica gel to get rid of water vapor. When the first bottle

  4. Efficient Capture of Cancer Cells by Their Replicated Surfaces Reveals Multiscale Topographic Interactions Coupled with Molecular Recognition.

    Science.gov (United States)

    Wang, Wenshuo; Cui, Haijun; Zhang, Pengchao; Meng, Jingxin; Zhang, Feilong; Wang, Shutao

    2017-03-29

    Cell-surface topographic interactions can direct the design of biointerfaces, which have been widely used in isolation of circulating tumor cells or fundamental cell biological research. By using three kinds of cancer cell-replicated surfaces with differentiated structures, we uncover that multiscale-cooperative topographic interactions (at both nanoscale and microscale) coupled with molecular recognition enable efficient and specific isolation of cancer cells. The cell replicas precisely inherit the structural features from the original cancer cells, providing not only preferable structures for matching with cancer cells but also a unique platform to interrogate whether certain cancer cells can optimally match with their own replicated surfaces. The results reveal that cancer cells do not show preferential recognitions to their respective replicas, while the capture agent-modified surfaces with hierarchical structures exhibit improved cancer cell capture efficiencies. Two levels of topographic interactions between cancer cells and cell replica surfaces exist. Nanoscale filopodia on cancer cells can topographically interact with different nanostructures on replica surfaces. In addition, microscale concave/convex on surfaces provide suitable sites for trapping cancer cells. This study may promote smart design of multiscale biofunctional materials that can specifically recognize cancer cells.

  5. Lowering data retention voltage in static random access memory array by post fabrication self-improvement of cell stability by multiple stress application

    Science.gov (United States)

    Mizutani, Tomoko; Takeuchi, Kiyoshi; Saraya, Takuya; Kobayashi, Masaharu; Hiramoto, Toshiro

    2018-04-01

    We propose a new version of the post fabrication static random access memory (SRAM) self-improvement technique, which utilizes multiple stress application. It is demonstrated that, using a device matrix array (DMA) test element group (TEG) with intrinsic channel fully depleted (FD) silicon-on-thin-buried-oxide (SOTB) six-transistor (6T) SRAM cells fabricated by the 65 nm technology, the lowering of data retention voltage (DRV) is more effectively achieved than using the previously proposed single stress technique.

  6. A High Modulation Bandwidth, 110 GHz Power DAC Cell forIQ Transmitter Arrays With Direct Amplitude and PhaseModulation

    Science.gov (United States)

    2014-06-23

    transmission line. Some parasitic capacitance and parasitic inductance asymmetry is inherent to the layout of the Gilbert cell due to the metal crossing at the...design imperfections and differential circuit layout inductive and capacitive parasitic asymmetries. An array element output power ON/OFF ratio better...has traditionallybeen used for automotive and military radar applica- tions. In recent years, the ever-increasing bandwidth needs of users streaming

  7. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

    Science.gov (United States)

    2014-01-01

    . Importantly, cellulases of some GH families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Conclusions Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity. PMID:24422981

  8. Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi.

    Science.gov (United States)

    Zhao, Zhongtao; Liu, Huiquan; Wang, Chenfang; Xu, Jin-Rong

    2014-01-03

    families are present in fungi that are not known to have cellulose-degrading ability. In addition, our results also showed that in general, plant pathogenic fungi have the highest number of CAZymes. Biotrophic fungi tend to have fewer CAZymes than necrotrophic and hemibiotrophic fungi. Pathogens of dicots often contain more pectinases than fungi infecting monocots. Interestingly, besides yeasts, many saprophytic fungi that are highly active in degrading plant biomass contain fewer CAZymes than plant pathogenic fungi. Furthermore, analysis of the gene expression profile of the wheat scab fungus Fusarium graminearum revealed that most of the CAZyme genes related to cell wall degradation were up-regulated during plant infection. Phylogenetic analysis also revealed a complex history of lineage-specific expansions and attritions for the PL1 family. Our study provides insights into the variety and expansion of fungal CAZyme classes and revealed the relationship of CAZyme size and diversity with their nutritional strategy and host specificity.

  9. Modular expression analysis reveals functional conservation between human Langerhans cells and mouse cross-priming dendritic cells.

    Science.gov (United States)

    Artyomov, Maxim N; Munk, Adiel; Gorvel, Laurent; Korenfeld, Daniel; Cella, Marina; Tung, Thomas; Klechevsky, Eynav

    2015-05-04

    Characterization of functionally distinct dendritic cell (DC) subsets in mice has fueled interest in whether analogous counterparts exist in humans. Transcriptional modules of coordinately expressed genes were used for defining shared functions between the species. Comparing modules derived from four human skin DC subsets and modules derived from the Immunological Genome Project database for all mouse DC subsets revealed that human Langerhans cells (LCs) and the mouse XCR1(+)CD8α(+)CD103(+) DCs shared the class I-mediated antigen processing and cross-presentation transcriptional modules that were not seen in mouse LCs. Furthermore, human LCs were enriched in a transcriptional signature specific to the blood cross-presenting CD141/BDCA-3(+) DCs, the proposed equivalent to mouse CD8α(+) DCs. Consistent with our analysis, LCs were highly adept at inducing primary CTL responses. Thus, our study suggests that the function of LCs may not be conserved between mouse and human and supports human LCs as an especially relevant therapeutic target. © 2015 Artyomov et al.

  10. Design review of a compact and low cost elementary radiating cell for satellite broadcasting automotive receiving arrays

    OpenAIRE

    Torres-Sanchez, R.; Mosig, J. R.; Vaccaro, S.; Llorens Del Rio, D.

    2011-01-01

    This communication presents a review of the developments carried out towards the electromagnetic modeling, design and practical implementation of the basic building block of a planar antenna for the reception of Ku-band satellite broadcasting services from user terminals on board automotive platforms. The antenna is conceived as a low profile phased array with fully electronic beam steering and polarization tracking capabilities. This phased array is intended to address the market of low cost...

  11. 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

    Science.gov (United States)

    Ali, Shahin S.; Shao, Jonathan; Strem, Mary D.; Phillips-Mora, Wilberth; Zhang, Dapeng; Meinhardt, Lyndel W.; Bailey, Bryan A.

    2015-01-01

    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 single nucleotide polymorphism (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 RNA sequencing (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. PMID:26379633

  12. Array-Comparative Genomic Hybridization Analysis in Fetuses with Major Congenital Malformations Reveals that 24% of Cases Have Pathogenic Deletions/Duplications.

    Science.gov (United States)

    Di Gregorio, Eleonora; Gai, Giorgia; Botta, Giovanni; Calcia, Alessandro; Pappi, Patrizia; Talarico, Flavia; Savin, Elisa; Ribotta, Marisa; Zonta, Andrea; Mancini, Cecilia; Giorgio, Elisa; Cavalieri, Simona; Restagno, Gabriella; Ferrero, Giovanni B; Viora, Elsa; Pasini, Barbara; Grosso, Enrico; Brusco, Alfredo; Brussino, Alessandro

    2015-01-01

    Karyotyping and aCGH are routinely used to identify genetic determinants of major congenital malformations (MCMs) in fetal deaths or terminations of pregnancy after prenatal diagnosis. Pathogenic rearrangements are found with a variable rate of 9-39% for aCGH. We collected 33 fetuses, 9 with a single MCM and 24 with MCMs involving 2-4 organ systems. aCGH revealed copy number variants in 14 out of 33 cases (42%). Eight were classified as pathogenic which account for a detection rate of 24% (8/33) considering fetuses with 1 or more MCMs and 33% (8/24) taking into account fetuses with multiple malformations only. Three of the pathogenic variants were known microdeletion syndromes (22q11.21 deletion, central chromosome 22q11.21 deletion, and TAR syndrome) and 5 were large rearrangements, adding up to >11 Mb per subject and comprising strong phenotype-related genes. One of those was a de novo complex rearrangement, and the remaining 4 duplications and 2 deletions were 130-900 kb in size, containing 1-7 genes, and were classified as variants of unknown clinical significance. Our study confirms aCGH as a powerful technique to ascertain the genetic etiology of fetal major congenital malformations. © 2015 S. Karger AG, Basel.

  13. 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.

  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.

    Science.gov (United States)

    Ali, Shahin S; Shao, Jonathan; Strem, Mary D; Phillips-Mora, Wilberth; Zhang, Dapeng; Meinhardt, Lyndel W; Bailey, Bryan A

    2015-01-01

    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 single nucleotide polymorphism (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 RNA sequencing (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. Enhanced omnidirectional and weatherability of Cu2ZnSnSe4solar cells with ZnO functional nanorod arrays.

    Science.gov (United States)

    Lai, Fang-I; Yang, Jui-Fu; Liao, Wei-Xiang; Kuo, Shou-Yi

    2017-11-02

    This paper presents the use of nanorods of different sizes, deposited from a chemical solution, as an antireflection layer in copper-zinc-tin selenide (CZTSe) solar cells. With the aid of the nanorods, the surface reflection of the CZTSe solar cells was reduced from 7.76% to 2.97%, and a cell efficiency of 14% was obtained as a result. Omni-directional anti-reflection was verified by the angle-dependent reflection measurements. The nanorod arrays also provided the CZTSe solar cells with a hydrophobic surface, allowing it to exhibit high resistance against humidity during weatherability tests. This shows that the surface passivation brought by the nanorod layer at the surface could effectively extend the lifetime of the CZTSe solar cells. The rate of efficiency decay of the CZTSe solar cells was reduced by 46.85% from that of the device without a nanorod array at the surface, indicating that this surface layer not only provided effective resistance against reflection at the device surface, but also served as a passivation layer and humidity-resistant surface-protection layer.

  16. Cellular dynamics of regeneration reveals role of two distinct Pax7 stem cell populations in larval zebrafish muscle repair.

    Science.gov (United States)

    Pipalia, Tapan G; Koth, Jana; Roy, Shukolpa D; Hammond, Christina L; Kawakami, Koichi; Hughes, Simon M

    2016-06-01

    Heterogeneity of stem cells or their niches is likely to influence tissue regeneration. Here we reveal stem/precursor cell diversity during wound repair in larval zebrafish somitic body muscle using time-lapse 3D confocal microscopy on reporter lines. Skeletal muscle with incision wounds rapidly regenerates both slow and fast muscle fibre types. A swift immune response is followed by an increase in cells at the wound site, many of which express the muscle stem cell marker Pax7. Pax7(+) cells proliferate and then undergo terminal differentiation involving Myogenin accumulation and subsequent loss of Pax7 followed by elongation and fusion to repair fast muscle fibres. Analysis of pax7a and pax7b transgenic reporter fish reveals that cells expressing each of the duplicated pax7 genes are distinctly localised in uninjured larvae. Cells marked by pax7a only or by both pax7a and pax7b enter the wound rapidly and contribute to muscle wound repair, but each behaves differently. Low numbers of pax7a-only cells form nascent fibres. Time-lapse microscopy revealed that the more numerous pax7b-marked cells frequently fuse to pre-existing fibres, contributing more strongly than pax7a-only cells to repair of damaged fibres. pax7b-marked cells are more often present in rows of aligned cells that are observed to fuse into a single fibre, but more rarely contribute to nascent regenerated fibres. Ablation of a substantial portion of nitroreductase-expressing pax7b cells with metronidazole prior to wounding triggered rapid pax7a-only cell accumulation, but this neither inhibited nor augmented pax7a-only cell-derived myogenesis and thus altered the cellular repair dynamics during wound healing. Moreover, pax7a-only cells did not regenerate pax7b cells, suggesting a lineage distinction. We propose a modified founder cell and fusion-competent cell model in which pax7a-only cells initiate fibre formation and pax7b cells contribute to fibre growth. This newly discovered cellular complexity

  17. Cellular dynamics of regeneration reveals role of two distinct Pax7 stem cell populations in larval zebrafish muscle repair

    Directory of Open Access Journals (Sweden)

    Tapan G. Pipalia

    2016-06-01

    Full Text Available Heterogeneity of stem cells or their niches is likely to influence tissue regeneration. Here we reveal stem/precursor cell diversity during wound repair in larval zebrafish somitic body muscle using time-lapse 3D confocal microscopy on reporter lines. Skeletal muscle with incision wounds rapidly regenerates both slow and fast muscle fibre types. A swift immune response is followed by an increase in cells at the wound site, many of which express the muscle stem cell marker Pax7. Pax7+ cells proliferate and then undergo terminal differentiation involving Myogenin accumulation and subsequent loss of Pax7 followed by elongation and fusion to repair fast muscle fibres. Analysis of pax7a and pax7b transgenic reporter fish reveals that cells expressing each of the duplicated pax7 genes are distinctly localised in uninjured larvae. Cells marked by pax7a only or by both pax7a and pax7b enter the wound rapidly and contribute to muscle wound repair, but each behaves differently. Low numbers of pax7a-only cells form nascent fibres. Time-lapse microscopy revealed that the more numerous pax7b-marked cells frequently fuse to pre-existing fibres, contributing more strongly than pax7a-only cells to repair of damaged fibres. pax7b-marked cells are more often present in rows of aligned cells that are observed to fuse into a single fibre, but more rarely contribute to nascent regenerated fibres. Ablation of a substantial portion of nitroreductase-expressing pax7b cells with metronidazole prior to wounding triggered rapid pax7a-only cell accumulation, but this neither inhibited nor augmented pax7a-only cell-derived myogenesis and thus altered the cellular repair dynamics during wound healing. Moreover, pax7a-only cells did not regenerate pax7b cells, suggesting a lineage distinction. We propose a modified founder cell and fusion-competent cell model in which pax7a-only cells initiate fibre formation and pax7b cells contribute to fibre growth. This newly discovered

  18. Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states

    Science.gov (United States)

    Toan, Ngo Minh; Thirumalai, D.

    2018-03-01

    Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling experiments using atomic force spectroscopy on leukocyte function-associated antigen-1 (LFA-1), expressed in T-cells, bound to intercellular adhesion molecules (ICAM), we performed constant loading rate (rf) and constant force (F) simulations using the self-organized polymer model to describe the mechanism of ligand rupture from CACs. The simulations reproduce the major experimental finding on the kinetics of the rupture process, namely, the dependence of the most probable rupture forces (f*s) on ln rf (rf is the loading rate) exhibits two distinct linear regimes. The first, at low rf, has a shallow slope, whereas the slope at high rf is much larger, especially for a LFA-1/ICAM-1 complex with the transition between the two occurring over a narrow rf range. Locations of the two transition states (TSs) extracted from the simulations show an abrupt change from a high value at low rf or constant force, F, to a low value at high rf or F. This unusual behavior in which the CACs switch from one brittle (TS position is a constant over a range of forces) state to another brittle state is not found in forced-rupture in other protein complexes. We explain this novel behavior by constructing the free energy profiles, F(Λ)s, as a function of a collective reaction coordinate (Λ), involving many key charged residues and a critical metal ion (Mg2+). The TS positions in F(Λ), which quantitatively agree with the parameters extracted using the Bell-Evans model, change abruptly at a critical force, demonstrating that it, rather than the molecular extension, is a good reaction coordinate. Our combined analyses using simulations performed in both the pulling modes (constant rf and F) reveal a new mechanism for the two loading regimes observed in the

  19. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

    Directory of Open Access Journals (Sweden)

    Raymond Kiu

    2017-12-01

    Full Text Available Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an “open” pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc, enterotoxin (cpe, and Perfringolysin O (pfo or pfoA, although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56 of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet and anti-defensins genes (mprF were consistently detected in silico (tet: 75%; mprF: 100%. However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

  20. Wire Array Photovoltaics

    Science.gov (United States)

    Turner-Evans, Dan

    Over the past five years, the cost of solar panels has dropped drastically and, in concert, the number of installed modules has risen exponentially. However, solar electricity is still more than twice as expensive as electricity from a natural gas plant. Fortunately, wire array solar cells have emerged as a promising technology for further lowering the cost of solar. Si wire array solar cells are formed with a unique, low cost growth method and use 100 times less material than conventional Si cells. The wires can be embedded in a transparent, flexible polymer to create a free-standing array that can be rolled up for easy installation in a variety of form factors. Furthermore, by incorporating multijunctions into the wire morphology, higher efficiencies can be achieved while taking advantage of the unique defect relaxation pathways afforded by the 3D wire geometry. The work in this thesis shepherded Si wires from undoped arrays to flexible, functional large area devices and laid the groundwork for multijunction wire array cells. Fabrication techniques were developed to turn intrinsic Si wires into full p-n junctions and the wires were passivated with a-Si:H and a-SiNx:H. Single wire devices yielded open circuit voltages of 600 mV and efficiencies of 9%. The arrays were then embedded in a polymer and contacted with a transparent, flexible, Ni nanoparticle and Ag nanowire top contact. The contact connected >99% of the wires in parallel and yielded flexible, substrate free solar cells featuring hundreds of thousands of wires. Building on the success of the Si wire arrays, GaP was epitaxially grown on the material to create heterostructures for photoelectrochemistry. These cells were limited by low absorption in the GaP due to its indirect bandgap, and poor current collection due to a diffusion length of only 80 nm. However, GaAsP on SiGe offers a superior combination of materials, and wire architectures based on these semiconductors were investigated for multijunction

  1. 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.

  2. Note: Multi-confocal fluorescence correlation spectroscopy in living cells using a complementary metal oxide semiconductor-single photon avalanche diode array

    Science.gov (United States)

    Kloster-Landsberg, M.; Tyndall, D.; Wang, I.; Walker, R.; Richardson, J.; Henderson, R.; Delon, A.

    2013-07-01

    Living cells are heterogeneous and rapidly changing biological samples. It is thus desirable to measure molecular concentration and dynamics in many locations at the same time. In this note, we present a multi-confocal setup capable of performing simultaneous fluorescence correlation spectroscopy measurements, by focusing the spots with a spatial light modulator and acquiring data with a monolithic 32 × 32 single-photon avalanche photodiode array. A post-processing method is proposed to correct cross-talk effects between neighboring spots. We demonstrate the applicability of our system by simultaneously measuring the diffusion of free enhanced Green Fluorescent Protein (eGFP) molecules at nine different points in living cells.

  3. 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

    it is shown that this broadband enhancement is due to single particle resonances that give rise to light-trapping in the infrared spectral range and to collective resonances that ensure an efficient in-coupling of light in the ultraviolet-blue spectral range. © 2015 Optical Society of America....... 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...

  4. Static micro-array isolation, dynamic time series classification, capture and enumeration of spiked breast cancer cells in blood: the nanotube-CTC chip

    Science.gov (United States)

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

    2016-11-01

    We demonstrate the rapid and label-free capture of breast cancer cells spiked in blood using nanotube-antibody micro-arrays. 76-element single wall carbon nanotube arrays were manufactured using photo-lithography, metal deposition, and etching techniques. Anti-epithelial cell adhesion molecule (anti-EpCAM), Anti-human epithelial growth factor receptor 2 (anti-Her2) and non-specific IgG antibodies were functionalized to the surface of the nanotube devices using 1-pyrene-butanoic acid succinimidyl ester. Following device functionalization, blood spiked with SKBR3, MCF7 and MCF10A cells (100/1000 cells per 5 μl per device, 170 elements totaling 0.85 ml of whole blood) were adsorbed on to the nanotube device arrays. Electrical signatures were recorded from each device to screen the samples for differences in interaction (specific or non-specific) between samples and devices. A zone classification scheme enabled the classification of all 170 elements in a single map. A kernel-based statistical classifier for the ‘liquid biopsy’ was developed to create a predictive model based on dynamic time warping series to classify device electrical signals that corresponded to plain blood (control) or SKBR3 spiked blood (case) on anti-Her2 functionalized devices with ˜90% sensitivity, and 90% specificity in capture of 1000 SKBR3 breast cancer cells in blood using anti-Her2 functionalized devices. Screened devices that gave positive electrical signatures were confirmed using optical/confocal microscopy to hold spiked cancer cells. Confocal microscopic analysis of devices that were classified to hold spiked blood based on their electrical signatures confirmed the presence of cancer cells through staining for DAPI (nuclei), cytokeratin (cancer cells) and CD45 (hematologic cells) with single cell sensitivity. We report 55%-100% cancer cell capture yield depending on the active device area for blood adsorption with mean of 62% (˜12 500 captured off 20 000 spiked cells in 0.1 ml

  5. 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.

  6. Embedded vertically aligned cadmium telluride nanorod arrays grown by one-step electrodeposition for enhanced energy conversion efficiency in three-dimensional nanostructured solar cells.

    Science.gov (United States)

    Wang, Jun; Liu, Shurong; Mu, Yannan; Liu, Li; A, Runa; Yang, Jiandong; Zhu, Guijie; Meng, Xianwei; Fu, Wuyou; Yang, Haibin

    2017-11-01

    Vertically aligned CdTe nanorods (NRs) arrays are successfully grown by a simple one-step and template-free electrodeposition method, and then embedded in the CdS window layer to form a novel three-dimensional (3D) heterostructure on flexible substrates. The parameters of electrodeposition such as deposition potential and pH of the solution are varied to analyze their important role in the formation of high quality CdTe NRs arrays. The photovoltaic conversion efficiency of the solar cell based on the 3D heterojunction structure is studied in detail. In comparison with the standard planar heterojunction solar cell, the 3D heterojunction solar cell exhibits better photovoltaic performance, which can be attributed to its enhanced optical absorption ability, increased heterojunction area and improved charge carrier transport. The better photoelectric property of the 3D heterojunction solar cell suggests great application potential in thin film solar cells, and the simple electrodeposition process represents a promising technique for large-scale fabrication of other nanostructured solar energy conversion devices. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. 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.

  8. ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology

    Science.gov (United States)

    De Col, Valentina; Fuchs, Philippe; Nietzel, Thomas; Elsässer, Marlene; Voon, Chia Pao; Candeo, Alessia; Seeliger, Ingo; Fricker, Mark D; Grefen, Christopher; Møller, Ian Max; Bassi, Andrea; Lim, Boon Leong; Zancani, Marco; Meyer, Andreas J; Costa, Alex; Wagner, Stephan; Schwarzländer, Markus

    2017-01-01

    Growth and development of plants is ultimately driven by light energy captured through photosynthesis. ATP acts as universal cellular energy cofactor fuelling all life processes, including gene expression, metabolism, and transport. Despite a mechanistic understanding of ATP biochemistry, ATP dynamics in the living plant have been largely elusive. Here, we establish MgATP2- measurement in living plants using the fluorescent protein biosensor ATeam1.03-nD/nA. We generate Arabidopsis sensor lines and investigate the sensor in vitro under conditions appropriate for the plant cytosol. We establish an assay for ATP fluxes in isolated mitochondria, and demonstrate that the sensor responds rapidly and reliably to MgATP2- changes in planta. A MgATP2- map of the Arabidopsis seedling highlights different MgATP2- concentrations between tissues and within individual cell types, such as root hairs. Progression of hypoxia reveals substantial plasticity of ATP homeostasis in seedlings, demonstrating that ATP dynamics can be monitored in the living plant. DOI: http://dx.doi.org/10.7554/eLife.26770.001 PMID:28716182

  9. ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology.

    Science.gov (United States)

    De Col, Valentina; Fuchs, Philippe; Nietzel, Thomas; Elsässer, Marlene; Voon, Chia Pao; Candeo, Alessia; Seeliger, Ingo; Fricker, Mark D; Grefen, Christopher; Møller, Ian Max; Bassi, Andrea; Lim, Boon Leong; Zancani, Marco; Meyer, Andreas J; Costa, Alex; Wagner, Stephan; Schwarzländer, Markus

    2017-07-18

    Growth and development of plants is ultimately driven by light energy captured through photosynthesis. ATP acts as universal cellular energy cofactor fuelling all life processes, including gene expression, metabolism, and transport. Despite a mechanistic understanding of ATP biochemistry, ATP dynamics in the living plant have been largely elusive. Here, we establish MgATP 2- measurement in living plants using the fluorescent protein biosensor ATeam1.03-nD/nA. We generate Arabidopsis sensor lines and investigate the sensor in vitro under conditions appropriate for the plant cytosol. We establish an assay for ATP fluxes in isolated mitochondria, and demonstrate that the sensor responds rapidly and reliably to MgATP 2- changes in planta. A MgATP 2- map of the Arabidopsis seedling highlights different MgATP 2- concentrations between tissues and within individual cell types, such as root hairs. Progression of hypoxia reveals substantial plasticity of ATP homeostasis in seedlings, demonstrating that ATP dynamics can be monitored in the living plant.

  10. 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. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

  11. Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures.

    Directory of Open Access Journals (Sweden)

    Moon Young Lee

    Full Text Available Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC, which serve as slow-wave electrical pacemakers for gastrointestinal (GI smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies.

  12. Mutations at the Subunit Interface of Yeast Proliferating Cell Nuclear Antigen Reveal a Versatile Regulatory Domain.

    Directory of Open Access Journals (Sweden)

    Miklos Halmai

    Full Text Available Proliferating cell nuclear antigen (PCNA plays a key role in many cellular processes and due to that it interacts with a plethora of proteins. The main interacting surfaces of Saccharomyces cerevisiae PCNA have been mapped to the interdomain connecting loop and to the carboxy-terminal domain. Here we report that the subunit interface of yeast PCNA also has regulatory roles in the function of several DNA damage response pathways. Using site-directed mutagenesis we engineered mutations at both sides of the interface and investigated the effect of these alleles on DNA damage response. Genetic experiments with strains bearing the mutant alleles revealed that mutagenic translesion synthesis, nucleotide excision repair, and homologous recombination are all regulated through residues at the subunit interface. Moreover, genetic characterization of one of our mutants identifies a new sub-branch of nucleotide excision repair. Based on these results we conclude that residues at the subunit boundary of PCNA are not only important for the formation of the trimer structure of PCNA, but they constitute a regulatory protein domain that mediates different DNA damage response pathways, as well.

  13. 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.

  14. 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.

  15. Filter arrays

    Energy Technology Data Exchange (ETDEWEB)

    Page, Ralph H.; Doty, Patrick F.

    2017-08-01

    The various technologies presented herein relate to a tiled filter array that can be used in connection with performance of spatial sampling of optical signals. The filter array comprises filter tiles, wherein a first plurality of filter tiles are formed from a first material, the first material being configured such that only photons having wavelengths in a first wavelength band pass therethrough. A second plurality of filter tiles is formed from a second material, the second material being configured such that only photons having wavelengths in a second wavelength band pass therethrough. The first plurality of filter tiles and the second plurality of filter tiles can be interspersed to form the filter array comprising an alternating arrangement of first filter tiles and second filter tiles.

  16. Short-length and high-density TiO2 nanorod arrays for the efficient charge separation interface in perovskite solar cells

    Science.gov (United States)

    Xiao, Guannan; Shi, Chengwu; Zhang, Zhengguo; Li, Nannan; Li, Long

    2017-05-01

    The TiO2 nanorod arrays with the length of 70 nm, the diameter of 20 nm, and the areal density of 1000 μm-2 were firstly prepared by the hydrothermal method using the aqueous grown solution of 38 mM titanium isopropoxide and 6 M hydrochloric acid at 170 °C for 60 min. Over-500 nm-thickness CH3NH3PbI3-xBrx absorber layers were successfully obtained by sequential deposition routes using 1.7 M PbI2·DMSO complex precursor solution and 0.465 M isopropanol solution of the methylammonium halide mixture with the molar ratio of CH3NH3I/CH3NH3Br=85/15. The perovskite solar cells based on the TiO2 nanorod array and 560 nm-thickness CH3NH3PbI3-xBrx absorber layer exhibited the best photoelectric conversion efficiency (PCE) of 15.93%, while the corresponding planar perovskite solar cells without the TiO2 nanorod array and with 530 nm-thickness CH3NH3PbI3-xBrx absorber layer gave the best PCE of 12.82% at the relative humidity of 50-54%.

  17. Molecular Characterization of Down Syndrome Embryonic Stem Cells Reveals a Role for RUNX1 in Neural Differentiation

    Directory of Open Access Journals (Sweden)

    Tomer Halevy

    2016-10-01

    Full Text Available Down syndrome (DS is the leading genetic cause of mental retardation and is caused by a third copy of human chromosome 21. The different pathologies of DS involve many tissues with a distinct array of neural phenotypes. Here we characterize embryonic stem cell lines with DS (DS-ESCs, and focus on the neural aspects of the disease. Our results show that neural progenitor cells (NPCs differentiated from five independent DS-ESC lines display increased apoptosis and downregulation of forehead developmental genes. Analysis of differentially expressed genes suggested RUNX1 as a key transcription regulator in DS-NPCs. Using genome editing we were able to disrupt all three copies of RUNX1 in DS-ESCs, leading to downregulation of several RUNX1 target developmental genes accompanied by reduced apoptosis and neuron migration. Our work sheds light on the role of RUNX1 and the importance of dosage balance in the development of neural phenotypes in DS.

  18. Single cell time-lapse analysis reveals that podoplanin enhances cell survival and colony formation capacity of squamous cell carcinoma cells.

    Science.gov (United States)

    Miyashita, Tomoyuki; Higuchi, Youichi; Kojima, Motohiro; Ochiai, Atsushi; Ishii, Genichiro

    2017-01-06

    Tumor initiating cells (TICs) are characterized by high clonal expansion capacity. We previously reported that podoplanin is a TIC-specific marker for the human squamous cell carcinoma cell line A431. The aim of this study is to explore the molecular mechanism underlying the high clonal expansion potential of podoplanin-positive A431cells using Fucci imaging. Single podoplanin-positive cells created large colonies at a significantly higher frequency than single podoplanin-negative cells, whereas no difference was observed between the two types of cells with respect to cell cycle status. Conversely, the cell death ratio of progenies derived from podoplanin-positive single cell was significantly lower than that of cells derived from podoplanin-negative cells. Single A431 cells, whose podoplanin expression was suppressed by RNA interference, exhibited increased cell death ratios and decreased frequency of large colony forming. Moreover, the frequency of large colony forming decreased significantly when podoplanin-positive single cells was treated with a ROCK (Rho-associated coiled-coil kinase) inhibitor, whereas no difference was observed in single podoplanin-negative cells. Our current study cleared that high clonal expansion capacity of podoplanin-positive TICs populations was the result of reduced cell death by podoplanin-mediated signaling. Therefore, podoplanin activity may be a therapeutic target in the treatment of squamous cell carcinomas.

  19. A 'fragile cell' sub-population revealed during cytometric assessment of Saccharomyces cerevisiae viability in lipid-limited alcoholic fermentation.

    Science.gov (United States)

    Delobel, P; Pradal, M; Blondin, B; Tesniere, C

    2012-11-01

    To show that in anaerobic fermentation with limiting lipid nutrients, cell preparation impacts the viability assessment of yeast cells, and to identify the factors involved. Saccharomyces cerevisiae viability was determined using propidium iodide staining and the flow cytometry. Analyses identified intact cells, dead cells and, under certain conditions, the presence of a third subpopulation of apparently damaged cells. This intermediate population could account for up to 40% of the entire cell population. We describe, analyse and discuss the effects of different solutions for cell resuspension on the respective proportion of these three populations, in particular that of the intermediate population. We show that this intermediate cell population forms in the absence of Ca(2+)/Mg(2+). Cell preparation significantly impacts population viability assessment by FCM. The intermediate population, revealed under certain conditions, could be renamed as 'fragile cells'. For these cells, Ca(2+) and Mg(2+) reduce cell membrane permeability to PI. This is the first study that analyses and discusses the factors influencing the formation of an intermediate population when studying viability in yeast alcoholic fermentation. With a wider application in biological research, this study provides important support to the relatively new questioning of propidium iodide staining as a universal cell death indicator. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

  20. Effect of hexamethylenetetramine (HMT) concentration on the properties of boron doped ZnO nanotubes array films and the performance of dye-sensitized solar cell (DSSC)

    Science.gov (United States)

    Roza, Liszulfah; Iwantono, I.; Andika, Gusyeri; Umar, Akrajas Ali; Rahman, Mohd. Yusri. Abd

    2018-02-01

    This paper reports the effect of hexamethylenetetramine (HMT) concentration on the structural, morphological and optical properties of B-doped ZnO nanotubes arrays. B-doped ZnO nanotubes were employed as anode in dye-sensitized solar cells (DSSCs). The effect of these properties on the photovoltaic performance was also studied. B-doped ZnO nanotube arrays were prepared via hydrothermal technique on FTO substrate at constant concentration of zinc nitrate. The field emission scanning electron microscopy (FESEM) images indicate that the density and length of B-doped ZnO nanotubes increase with the concentration of HMT. However, the diameter decreases with the increase of HMT concentration. The JSC, VOC, FF and η of 1.48 mA cm-2, 0.38 V, 0.39 and 0.224% respectively have been obtained by the DSSC utilizing B-doped ZnO nanotube prepared at 0.06 M HMT.

  1. Metabolic profiling reveals potential metabolic markers associated with Hypoxia Inducible Factor-mediated signalling in hypoxic cancer cells.

    Science.gov (United States)

    Armitage, Emily G; Kotze, Helen L; Allwood, J William; Dunn, Warwick B; Goodacre, Royston; Williams, Kaye J

    2015-10-28

    Hypoxia inducible factors (HIFs) plays an important role in oxygen compromised environments and therefore in tumour survival. In this research, metabolomics has been applied to study HIFs metabolic function in two cell models: mouse hepatocellular carcinoma and human colon carcinoma, whereby the metabolism has been profiled for a range of oxygen potentials. Wild type cells have been compared to cells deficient in HIF signalling to reveal its effect on cellular metabolism under normal oxygen conditions as well as low oxygen, hypoxic and anoxic environments. Characteristic responses to hypoxia that were conserved across both cell models involved the anti-correlation between 2-hydroxyglutarate, 2-oxoglutarate, fructose, hexadecanoic acid, hypotaurine, pyruvate and octadecenoic acid with 4-hydroxyproline, aspartate, cysteine, glutamine, lysine, malate and pyroglutamate. Further to this, network-based correlation analysis revealed HIF specific pathway responses to each oxygen condition that were also conserved between cell models. From this, 4-hydroxyproline was revealed as a regulating hub in low oxygen survival of WT cells while fructose appeared to be in HIF deficient cells. Pathways surrounding these hubs were built from the direct connections of correlated metabolites that look beyond traditional pathways in order to understand the mechanism of HIF response to low oxygen environments.

  2. The role of cell wall revealed by the visualization of Saccharomyces cerevisiae transformation.

    Science.gov (United States)

    Pham, Tuan Anh; Kawai, Shigeyuki; Kono, Emi; Murata, Kousaku

    2011-03-01

    Transformation is an indispensable method for the manipulation of Saccharomyces cerevisiae cell. The spf1 cell, in which the gene encoding an endoplasmic reticulum-located P-type ATPase is deleted, has been known to show the high-transformation phenotype. In this study, fluorescent microscopic observation of transformation process of S. cerevisiae using plasmid DNA labelled with fluorescent DNA probe, YOYO-1, suggested that the spf1 cell absorbed more plasmid DNA on cellular surface than did the wild-type cell and the unwashed cell did more plasmid DNA than the washed cell. The amounts of the absorbed DNA correlated with the transformation efficiency (number of transformants per μg plasmid DNA) and frequency (transformation efficiency per viable cell number). The high-transformation phenotype of spf1 cell and the effect of heat shock, which effectively induces the transformation of intact cell, disappeared upon cell wall digestion. Electron microscopic observation of the transformation process using negatively charged Nanogold as a mimic of plasmid DNA supported the result obtained using YOYO-1 and implied that plasmid DNA enters into cell together with membrane structure. These data strongly suggest that during the transformation of intact cell, plasmid DNA is initially absorbed on the cell wall, passes through the cell wall with the aid of heat shock, reaches to the membrane, and enters into the cell together with the membrane structure and that the capacity of the cell wall to absorb DNA is at least one of the determinants of transformation efficiency and frequency.

  3. 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.

  4. Mitogenic activation of B cells in vitro: the properties of adherent accessory cells as revealed by partition analysis

    International Nuclear Information System (INIS)

    Kettman, J.R.; Soederberg, A.; Lefkovits, I.

    1986-01-01

    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

  5. Genomic Analyses Reveal Global Functional Alterations That Promote Tumor Growth and Novel Tumor Suppressor Genes in Natural Killer-Cell Malignancies

    DEFF Research Database (Denmark)

    Kucuk, Can; Iqbal, Javeed; J. deLeeuw, Ronald

    in the gene expression profile, we performed GEP and array-CGH studies on seven clinically well defined cases and eight well characterized cell lines derived from NKL patients. Methods: Array-CGH was performed on a tiling BAC array and GEP on an Affymetrix 133 plus2 array.The two data sets were correlated...... to identify functional alterations associated with the genetic abnormalities.Candidate genes on del 6q21 were identified and further studied for mutations and promoter methylation. Results: Our aCGH study identified frequent recurrent gains (> 25 %) in 1q, 2p, 7q, 13q, 17q and 20pter-qter. Regions of loss...

  6. Comparative transcriptional profiling analysis of the two daughter cells from tobacco zygote reveals the transcriptome differences in the apical and basal cells

    Directory of Open Access Journals (Sweden)

    Hu Tian-Xiang

    2010-08-01

    Full Text Available Abstract Background In angiosperm, after the first asymmetric zygotic cell division, the apical and basal daughter cells follow distinct development pathways. Global transcriptome analysis of these two cells is essential in understanding their developmental differences. However, because of the difficulty to isolate the in vivo apical and basal cells of two-celled proembryo from ovule and ovary in higher plants, the transcriptome analysis of them hasn't been reported. Results In this study, we developed a procedure for isolating the in vivo apical and basal cells of the two-celled proembryo from tobacco (Nicotiana tabacum, and then performed a comparative transcriptome analysis of the two cells by suppression subtractive hybridization (SSH combined with macroarray screening. After sequencing, we identified 797 differentially expressed ESTs corresponding to 299 unigenes. Library sequence analysis successfully identified tobacco homologies of genes involved in embryogenesis and seed development. By quantitative real-time PCR, we validated the differential expression of 40 genes, with 6 transcripts of them specifically expressed in the apical or basal cell. Expression analysis also revealed some transcripts displayed cell specific activation in one of the daughter cells after zygote division. These differential expressions were further validated by in situ hybridization (ISH. Tissue expression pattern analysis also revealed some potential roles of these candidate genes in development. Conclusions The results show that some differential or specific transcripts in the apical and basal cells of two-celled proembryo were successfully isolated, and the identification of these transcripts reveals that these two daughter cells possess distinct transcriptional profiles after zygote division. Further functional work on these differentially or specifically expressed genes will promote the elucidation of molecular mechanism controlling early embryogenesis.

  7. 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

  8. Encapsulation task of the low-cost silicon solar array project. Investigation of test methods, material properties, and processes for solar cell encapsulants

    Science.gov (United States)

    Willis, P. B.; Baum, B.; White, R. A.

    1978-01-01

    The results of an investigation of solar module encapsulation systems applicable to the Low-Cost Solar Array Project 1986 cost and performance goals are presented. Six basic construction elements were identified and their specific uses in module construction defined. A uniform coating basis was established for each element. The survey results were also useful in revealing price ranges for classes of materials and estimating the cost allocation for each element within the encapsulating cost goal. The six construction elements were considered to be substrates, superstrates, pottants, adhesives, outer covers and back covers.

  9. Expression profiling of CD34+ hematopoietic stem/ progenitor cells reveals distinct subtypes of therapy-related acute myeloid leukemia

    OpenAIRE

    Qian, Zhijian; Fernald, Anthony A.; Godley, Lucy A.; Larson, Richard A.; Le Beau, Michelle M.

    2002-01-01

    One of the most serious consequences of cytotoxic cancer therapy is the development of therapy-related acute myeloid leukemia (t-AML), a neoplastic disorder arising from a multipotential hematopoietic stem cell. To gain insights into the molecular basis of this disease, we performed gene expression profiling of CD34+ hematopoietic progenitor cells from t-AML patients. Our analysis revealed that there are distinct subtypes of t-AML that have a characteristic gene expression pattern. Common to ...

  10. Single-Cell Gene Expression Analysis of a Human ESC Model of Pancreatic Endocrine Development Reveals Different Paths to β-Cell Differentiation.

    Science.gov (United States)

    Petersen, Maja Borup Kjær; Azad, Ajuna; Ingvorsen, Camilla; Hess, Katja; Hansson, Mattias; Grapin-Botton, Anne; Honoré, Christian

    2017-10-10

    The production of insulin-producing β cells from human embryonic stem cells (hESCs) in vitro represents a promising strategy for a cell-based therapy for type 1 diabetes mellitus. To explore the cellular heterogeneity and temporal progression of endocrine progenitors and their progeny, we performed single-cell qPCR on more than 500 cells across several stages of in vitro differentiation of hESCs and compared them with human islets. We reveal distinct subpopulations along the endocrine differentiation path and an early lineage bifurcation toward either polyhormonal cells or β-like cells. We uncover several similarities and differences with mouse development and reveal that cells can take multiple paths to the same differentiation state, a principle that could be relevant to other systems. Notably, activation of the key β-cell transcription factor NKX6.1 can be initiated before or after endocrine commitment. The single-cell temporal resolution we provide can be used to improve the production of functional β cells. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  11. A comparative mechanical analysis of plant and animal cells reveals convergence across kingdoms.

    Science.gov (United States)

    Durand-Smet, Pauline; Chastrette, Nicolas; Guiroy, Axel; Richert, Alain; Berne-Dedieu, Annick; Szecsi, Judit; Boudaoud, Arezki; Frachisse, Jean-Marie; Bendahmane, Mohammed; Bendhamane, Mohammed; Hamant, Oliver; Asnacios, Atef

    2014-11-18

    Plant and animals have evolved different strategies for their development. Whether this is linked to major differences in their cell mechanics remains unclear, mainly because measurements on plant and animal cells relied on independent experiments and setups, thus hindering any direct comparison. In this study we used the same micro-rheometer to compare animal and plant single cell rheology. We found that wall-less plant cells exhibit the same weak power law rheology as animal cells, with comparable values of elastic and loss moduli. Remarkably, microtubules primarily contributed to the rheological behavior of wall-less plant cells whereas rheology of animal cells was mainly dependent on the actin network. Thus, plant and animal cells evolved different molecular strategies to reach a comparable cytoplasmic mechanical core, suggesting that evolutionary convergence could include the internal biophysical properties of cells.

  12. Synthetic Genetic Arrays: Automation of Yeast Genetics.

    Science.gov (United States)

    Kuzmin, Elena; Costanzo, Michael; Andrews, Brenda; Boone, Charles

    2016-04-01

    Genome-sequencing efforts have led to great strides in the annotation of protein-coding genes and other genomic elements. The current challenge is to understand the functional role of each gene and how genes work together to modulate cellular processes. Genetic interactions define phenotypic relationships between genes and reveal the functional organization of a cell. Synthetic genetic array (SGA) methodology automates yeast genetics and enables large-scale and systematic mapping of genetic interaction networks in the budding yeast,Saccharomyces cerevisiae SGA facilitates construction of an output array of double mutants from an input array of single mutants through a series of replica pinning steps. Subsequent analysis of genetic interactions from SGA-derived mutants relies on accurate quantification of colony size, which serves as a proxy for fitness. Since its development, SGA has given rise to a variety of other experimental approaches for functional profiling of the yeast genome and has been applied in a multitude of other contexts, such as genome-wide screens for synthetic dosage lethality and integration with high-content screening for systematic assessment of morphology defects. SGA-like strategies can also be implemented similarly in a number of other cell types and organisms, includingSchizosaccharomyces pombe,Escherichia coli, Caenorhabditis elegans, and human cancer cell lines. The genetic networks emerging from these studies not only generate functional wiring diagrams but may also play a key role in our understanding of the complex relationship between genotype and phenotype. © 2016 Cold Spring Harbor Laboratory Press.

  13. Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness.

    Science.gov (United States)

    Bogeas, Alexandra; Morvan-Dubois, Ghislaine; El-Habr, Elias A; Lejeune, François-Xavier; Defrance, Matthieu; Narayanan, Ashwin; Kuranda, Klaudia; Burel-Vandenbos, Fanny; Sayd, Salwa; Delaunay, Virgile; Dubois, Luiz G; Parrinello, Hugues; Rialle, Stéphanie; Fabrega, Sylvie; Idbaih, Ahmed; Haiech, Jacques; Bièche, Ivan; Virolle, Thierry; Goodhardt, Michele; Chneiweiss, Hervé; Junier, Marie-Pierre

    2018-02-01

    Although a growing body of evidence indicates that phenotypic plasticity exhibited by glioblastoma cells plays a central role in tumor development and post-therapy recurrence, the master drivers of their aggressiveness remain elusive. Here we mapped the changes in active (H3K4me3) and repressive (H3K27me3) histone modifications accompanying the repression of glioblastoma stem-like cells tumorigenicity. Genes with changing histone marks delineated a network of transcription factors related to cancerous behavior, stem state, and neural development, highlighting a previously unsuspected association between repression of ARNT2 and loss of cell tumorigenicity. Immunohistochemistry confirmed ARNT2 expression in cell sub-populations within proliferative zones of patients' glioblastoma. Decreased ARNT2 expression was consistently observed in non-tumorigenic glioblastoma cells, compared to tumorigenic cells. Moreover, ARNT2 expression correlated with a tumorigenic molecular signature at both the tissue level within the tumor core and at the single cell level in the patients' tumors. We found that ARNT2 knockdown decreased the expression of SOX9, POU3F2 and OLIG2, transcription factors implicated in glioblastoma cell tumorigenicity, and repressed glioblastoma stem-like cell tumorigenic properties in vivo. Our results reveal ARNT2 as a pivotal component of the glioblastoma cell tumorigenic signature, located at a node of a transcription factor network controlling glioblastoma cell aggressiveness.

  14. Long-Term Live Cell Imaging