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Sample records for cell throughput maximization

  1. Cell Culture Microfluidic Biochips: Experimental Throughput Maximization

    DEFF Research Database (Denmark)

    Minhass, Wajid Hassan; Pop, Paul; Madsen, Jan

    2011-01-01

    Microfluidic biochips offer a promising alternative to a conventional biochemical laboratory, integrating all necessary functionalities on-chip in order to perform biochemical applications. Researchers have started to propose computer-aided design tools for the synthesis of such biochips. Our foc...... metaheuristic for experimental design generation for the cell culture microfluidic biochips, and we have evaluated our approach using multiple experimental setups....

  2. Aspects of multiuser MIMO for cell throughput maximization

    DEFF Research Database (Denmark)

    Bauch, Gerhard; Tejera, Pedro; Guthy, Christian

    2007-01-01

    . The potential for cell throughput improvement is demonstrated by capacity results based on measured channels in a large office environment. Finally, video streaming is used as a potential application with high data rate and low latency demands. It is shown that the proposed method has the potential to exploit...... multiuser diversity while still providing stable video streams even though QoS constraints are not explicitly taken into account by the scheduler....

  3. Improved Algorithm for Throughput Maximization in MC-CDMA

    OpenAIRE

    Hema Kale; C.G. Dethe; M.M. Mushrif

    2012-01-01

    The Multi-Carrier Code Division Multiple Access (MC-CDMA) is becoming a very significant downlink multiple access technique for high-rate data transmission in the fourth generation wireless communication systems. By means of efficient resource allocation higher data rate i.e. throughput can be achieved. This paper evaluates the performance of criteria used for group (subchannel) allocation employed in downlink transmission, which results in throughput maximization. Proposed algorithm gives th...

  4. MANAGING CONTENTION AVOIDANCE AND MAXIMIZING THROUGHPUT IN OBS NETWORK

    Directory of Open Access Journals (Sweden)

    AMIT KUMAR GARG

    2013-04-01

    Full Text Available Optical Burst Switching (OBS is a promising technology for future optical networks. Due to its less complicated implementation using current optical and electrical components, OBS is seen as the first step towards the future Optical Packet Switching (OPS. In OBS, a key problem is to schedule bursts on wavelength channels whose bandwidth may become fragmented with the so-called void (or idle intervals with both fast and bandwidth efficient algorithms so as to reduce burst loss. In this paper, a new scheme has been proposed to improve the throughput and to avoid the contention in the OBS network. The proposed scheme offers the same node complexity as that in general OBS networks with optical buffers. Also, it avoids burst blockings in transit nodes, turning it into an efficient and simple burst contention avoidance mechanism. Simulation results show that the proposed scheme has improvement of 15% in terms of burst loss probability as compared to OBS existing schemes and also maximizes the throughput of the network without deteriorating excessively other parameters such as end to end delay or ingress queues.

  5. Throughput maximization for buffer-aided hybrid half-/full-duplex relaying with self-interference

    KAUST Repository

    Khafagy, Mohammad Galal

    2015-06-01

    In this work, we consider a two-hop cooperative setting where a source communicates with a destination through an intermediate relay node with a buffer. Unlike the existing body of work on buffer-aided half-duplex relaying, we consider a hybrid half-/full-duplex relaying scenario with loopback interference in the full-duplex mode. Depending on the channel outage and buffer states that are assumed available at the transmitters, the source and relay may either transmit simultaneously or revert to orthogonal transmission. Specifically, a joint source/relay scheduling and relaying mode selection mechanism is proposed to maximize the end-to-end throughput. The throughput maximization problem is converted to a linear program where the exact global optimal solution is efficiently obtained via standard convex/linear numerical optimization tools. Finally, the theoretical findings are corroborated with event-based simulations to provide the necessary performance validation.

  6. Optimal power allocation based on sum-throughput maximization for energy harvesting cognitive radio networks

    Science.gov (United States)

    Xie, Zhenwei; Zhu, Qi

    2017-01-01

    In this study, an optimal power allocation algorithm by maximizing the sum-throughput in energy harvesting cognitive radio networks is proposed. Under the causality constraints of the harvested energy by solar radiation, electromagnetic waves and so on in the two secondary users (SUs), and the interference constraint in the primary user (PU), the sum-throughput maximization problem is formulated. The algorithm decomposes the interference threshold constraint to the power upper bounds of the two SUs. Then, the power allocation problems of the two SUs can be solved by a directional water-filling algorithm (DWA) with the power upper bounds, respectively. The paper gives the algorithm steps and simulation results, and the simulation results verify that the proposed algorithm has obvious advantages over the other two algorithms.

  7. Throughput Maximization for Cognitive Radio Networks Using Active Cooperation and Superposition Coding

    KAUST Repository

    Hamza, Doha R.

    2015-02-13

    We propose a three-message superposition coding scheme in a cognitive radio relay network exploiting active cooperation between primary and secondary users. The primary user is motivated to cooperate by substantial benefits it can reap from this access scenario. Specifically, the time resource is split into three transmission phases: The first two phases are dedicated to primary communication, while the third phase is for the secondary’s transmission. We formulate two throughput maximization problems for the secondary network subject to primary user rate constraints and per-node power constraints with respect to the time durations of primary transmission and the transmit power of the primary and the secondary users. The first throughput maximization problem assumes a partial power constraint such that the secondary power dedicated to primary cooperation, i.e. for the first two communication phases, is fixed apriori. In the second throughput maximization problem, a total power constraint is assumed over the three phases of communication. The two problems are difficult to solve analytically when the relaying channel gains are strictly greater than each other and strictly greater than the direct link channel gain. However, mathematically tractable lowerbound and upperbound solutions can be attained for the two problems. For both problems, by only using the lowerbound solution, we demonstrate significant throughput gains for both the primary and the secondary users through this active cooperation scheme. We find that most of the throughput gains come from minimizing the second phase transmission time since the secondary nodes assist the primary communication during this phase. Finally, we demonstrate the superiority of our proposed scheme compared to a number of reference schemes that include best relay selection, dual-hop routing, and an interference channel model.

  8. Throughput Maximization for Sensor-Aided Cognitive Radio Networks with Continuous Energy Arrivals.

    Science.gov (United States)

    Nguyen, Thanh-Tung; Koo, Insoo

    2015-11-27

    We consider a Sensor-Aided Cognitive Radio Network (SACRN) in which sensors capable of harvesting energy are distributed throughout the network to support secondary transmitters for sensing licensed channels in order to improve both energy and spectral efficiency. Harvesting ambient energy is one of the most promising solutions to mitigate energy deficiency, prolong device lifetime, and partly reduce the battery size of devices. So far, many works related to SACRN have considered single secondary users capable of harvesting energy in whole slot as well as short-term throughput. In the paper, we consider two types of energy harvesting sensor nodes (EHSN): Type-I sensor nodes will harvest ambient energy in whole slot duration, whereas type-II sensor nodes will only harvest energy after carrying out spectrum sensing. In the paper, we also investigate long-term throughput in the scheduling window, and formulate the throughput maximization problem by considering energy-neutral operation conditions of type-I and -II sensors and the target detection probability. Through simulations, it is shown that the sensing energy consumption of all sensor nodes can be efficiently managed with the proposed scheme to achieve optimal long-term throughput in the window.

  9. Generalized Encoding CRDSA: Maximizing Throughput in Enhanced Random Access Schemes for Satellite

    Directory of Open Access Journals (Sweden)

    Manlio Bacco

    2014-12-01

    Full Text Available This work starts from the analysis of the literature about the Random Access protocols with contention resolution, such as Contention Resolution Diversity Slotted Aloha (CRDSA, and introduces a possible enhancement, named Generalized Encoding Contention Resolution Diversity Slotted Aloha (GE-CRDSA. The GE-CRDSA aims at improving the aggregated throughput when the system load is less than 50%, playing on the opportunity of transmitting an optimal combination of information and parity packets frame by frame. This paper shows the improvement in terms of throughput, by performing traffic estimation and adaptive choice of information and parity rates, when a satellite network undergoes a variable traffic load profile.

  10. Method and apparatus for maximizing throughput of indirectly heated rotary kilns

    Science.gov (United States)

    Coates, Ralph L; Smoot, Douglas L.; Hatfield, Kent E

    2016-06-21

    An apparatus and method for achieving improved throughput capacity of indirectly heated rotary kilns used to produce pyrolysis products such as shale oils or coal oils that are susceptible to decomposition by high kiln wall temperatures is disclosed. High throughput is achieved by firing the kiln such that optimum wall temperatures are maintained beginning at the point where the materials enter the heating section of the kiln and extending to the point where the materials leave the heated section. Multiple high velocity burners are arranged such that combustion products directly impact on the area of the kiln wall covered internally by the solid material being heated. Firing rates for the burners are controlled to maintain optimum wall temperatures.

  11. Method and apparatus for maximizing throughput of indirectly heated rotary kilns

    Science.gov (United States)

    Coates, Ralph L; Smoot, L. Douglas; Hatfield, Kent E

    2012-10-30

    An apparatus and method for achieving improved throughput capacity of indirectly heated rotary kilns used to produce pyrolysis products such as shale oils or coal oils that are susceptible to decomposition by high kiln wall temperatures is disclosed. High throughput is achieved by firing the kiln such that optimum wall temperatures are maintained beginning at the point where the materials enter the heating section of the kiln and extending to the point where the materials leave the heated section. Multiple high velocity burners are arranged such that combustion products directly impact on the area of the kiln wall covered internally by the solid material being heated. Firing rates for the burners are controlled to maintain optimum wall temperatures.

  12. Scanning droplet cell for high throughput electrochemical and photoelectrochemical measurements

    Science.gov (United States)

    Gregoire, John M.; Xiang, Chengxiang; Liu, Xiaonao; Marcin, Martin; Jin, Jian

    2013-02-01

    High throughput electrochemical techniques are widely applied in material discovery and optimization. For many applications, the most desirable electrochemical characterization requires a three-electrode cell under potentiostat control. In high throughput screening, a material library is explored by either employing an array of such cells, or rastering a single cell over the library. To attain this latter capability with unprecedented throughput, we have developed a highly integrated, compact scanning droplet cell that is optimized for rapid electrochemical and photoeletrochemical measurements. Using this cell, we screened a quaternary oxide library as (photo)electrocatalysts for the oxygen evolution (water splitting) reaction. High quality electrochemical measurements were carried out and key electrocatalytic properties were identified for each of 5456 samples with a throughput of 4 s per sample.

  13. High-throughput cell mechanical phenotyping for label-free titration assays of cytoskeletal modifications.

    Science.gov (United States)

    Golfier, Stefan; Rosendahl, Philipp; Mietke, Alexander; Herbig, Maik; Guck, Jochen; Otto, Oliver

    2017-08-01

    The mechanical fingerprint of cells is inherently linked to the structure of the cytoskeleton and can serve as a label-free marker for cell homeostasis or pathologic states. How cytoskeletal composition affects the physical response of cells to external loads has been intensively studied with a spectrum of techniques, yet quantitative and statistically powerful investigations in the form of titration assays are hampered by the low throughput of most available methods. In this study, we employ real-time deformability cytometry (RT-DC), a novel microfluidic tool to examine the effects of biochemically modified F-actin and microtubule stability and nuclear chromatin structure on cell deformation in a human leukemia cell line (HL60). The high throughput of our method facilitates extensive titration assays that allow for significance assessment of the observed effects and extraction of half-maximal concentrations for most of the applied reagents. We quantitatively show that integrity of the F-actin cortex and microtubule network dominate cell deformation on millisecond timescales probed with RT-DC. Drug-induced alterations in the nuclear chromatin structure were not found to consistently affect cell deformation. The sensitivity of the high-throughput cell mechanical measurements to the cytoskeletal modifications we present in this study opens up new possibilities for label-free dose-response assays of cytoskeletal modifications. © 2017 The Authors Cytoskeleton Published by Wiley Periodicals, Inc.

  14. Sum rate maximization in the uplink of multi-cell OFDMA networks

    KAUST Repository

    Tabassum, Hina

    2012-10-03

    Resource allocation in orthogonal frequency division multiple access (OFDMA) networks plays an imperative role to guarantee the system performance. However, most of the known resource allocation schemes are focused on maximizing the local throughput of each cell, while ignoring the significant effect of inter-cell interference. This paper investigates the problem of resource allocation (i.e., subcarriers and powers) in the uplink of a multi-cell OFDMA network. The problem has a non-convex combinatorial structure and is known to be NP hard. Firstly, we investigate the upper and lower bounds to the average network throughput due to the inherent complexity of implementing the optimal solution. Later, a centralized sub-optimal resource allocation scheme is developed. We further develop less complex centralized and distributed schemes that are well-suited for practical scenarios. The computational complexity of all schemes has been analyzed and the performance is compared through numerical simulations. Simulation results demonstrate that the distributed scheme achieves comparable performance to the centralized resource allocation scheme in various scenarios. © 2011 IEEE.

  15. High throughput solar cell ablation system

    Science.gov (United States)

    Harley, Gabriel; Pass, Thomas; Cousins, Peter John; Viatella, John

    2012-09-11

    A solar cell is formed using a solar cell ablation system. The ablation system includes a single laser source and several laser scanners. The laser scanners include a master laser scanner, with the rest of the laser scanners being slaved to the master laser scanner. A laser beam from the laser source is split into several laser beams, with the laser beams being scanned onto corresponding wafers using the laser scanners in accordance with one or more patterns. The laser beams may be scanned on the wafers using the same or different power levels of the laser source.

  16. High-throughput ballistic injection nanorheology to measure cell mechanics

    Science.gov (United States)

    Wu, Pei-Hsun; Hale, Christopher M; Chen, Wei-Chiang; Lee, Jerry S H; Tseng, Yiider; Wirtz, Denis

    2015-01-01

    High-throughput ballistic injection nanorheology is a method for the quantitative study of cell mechanics. Cell mechanics are measured by ballistic injection of submicron particles into the cytoplasm of living cells and tracking the spontaneous displacement of the particles at high spatial resolution. The trajectories of the cytoplasm-embedded particles are transformed into mean-squared displacements, which are subsequently transformed into frequency-dependent viscoelastic moduli and time-dependent creep compliance of the cytoplasm. This method allows for the study of a wide range of cellular conditions, including cells inside a 3D matrix, cell subjected to shear flows and biochemical stimuli, and cells in a live animal. Ballistic injection lasts < 1 min and is followed by overnight incubation. Multiple particle tracking for one cell lasts < 1 min. Forty cells can be examined in < 1 h. PMID:22222790

  17. Resource allocation via sum-rate maximization in the uplink of multi-cell OFDMA networks

    KAUST Repository

    Tabassum, Hina

    2012-10-03

    In this paper, we consider maximizing the sum rate in the uplink of a multi-cell orthogonal frequency-division multiple access network. The problem has a non-convex combinatorial structure and is known to be NP-hard. Because of the inherent complexity of implementing the optimal solution, firstly, we derive an upper bound (UB) and a lower bound (LB) to the optimal average network throughput. Moreover, we investigate the performance of a near-optimal single cell resource allocation scheme in the presence of inter-cell interference, which leads to another easily computable LB. We then develop a centralized sub-optimal scheme that is composed of a geometric programming-based power control phase in conjunction with an iterative subcarrier allocation phase. Although the scheme is computationally complex, it provides an effective benchmark for low complexity schemes even without the power control phase. Finally, we propose less complex centralized and distributed schemes that are well suited for practical scenarios. The computational complexity of all schemes is analyzed, and the performance is compared through simulations. Simulation results demonstrate that the proposed low complexity schemes can achieve comparable performance with that of the centralized sub-optimal scheme in various scenarios. Moreover, comparisons with the UB and LB provide insight on the performance gap between the proposed schemes and the optimal solution. Copyright © 2011 John Wiley & Sons, Ltd.

  18. Mammogram segmentation using maximal cell strength updation in cellular automata.

    Science.gov (United States)

    Anitha, J; Peter, J Dinesh

    2015-08-01

    Breast cancer is the most frequently diagnosed type of cancer among women. Mammogram is one of the most effective tools for early detection of the breast cancer. Various computer-aided systems have been introduced to detect the breast cancer from mammogram images. In a computer-aided diagnosis system, detection and segmentation of breast masses from the background tissues is an important issue. In this paper, an automatic segmentation method is proposed to identify and segment the suspicious mass regions of mammogram using a modified transition rule named maximal cell strength updation in cellular automata (CA). In coarse-level segmentation, the proposed method performs an adaptive global thresholding based on the histogram peak analysis to obtain the rough region of interest. An automatic seed point selection is proposed using gray-level co-occurrence matrix-based sum average feature in the coarse segmented image. Finally, the method utilizes CA with the identified initial seed point and the modified transition rule to segment the mass region. The proposed approach is evaluated over the dataset of 70 mammograms with mass from mini-MIAS database. Experimental results show that the proposed approach yields promising results to segment the mass region in the mammograms with the sensitivity of 92.25% and accuracy of 93.48%.

  19. High-Throughput Cancer Cell Sphere Formation for 3D Cell Culture.

    Science.gov (United States)

    Chen, Yu-Chih; Yoon, Euisik

    2017-01-01

    Three-dimensional (3D) cell culture is critical in studying cancer pathology and drug response. Though 3D cancer sphere culture can be performed in low-adherent dishes or well plates, the unregulated cell aggregation may skew the results. On contrary, microfluidic 3D culture can allow precise control of cell microenvironments, and provide higher throughput by orders of magnitude. In this chapter, we will look into engineering innovations in a microfluidic platform for high-throughput cancer cell sphere formation and review the implementation methods in detail.

  20. High Throughput Single-cell and Multiple-cell Micro-encapsulation

    OpenAIRE

    Lagus, Todd P.; Edd, Jon F.

    2012-01-01

    Microfluidic encapsulation methods have been previously utilized to capture cells in picoliter-scale aqueous, monodisperse drops, providing confinement from a bulk fluid environment with applications in high throughput screening, cytometry, and mass spectrometry. We describe a method to not only encapsulate single cells, but to repeatedly capture a set number of cells (here we demonstrate one- and two-cell encapsulation) to study both isolation and the interactions between cells in groups of ...

  1. High throughput RNAi assay optimization using adherent cell cytometry

    Directory of Open Access Journals (Sweden)

    Pradhan Leena

    2011-04-01

    Full Text Available Abstract Background siRNA technology is a promising tool for gene therapy of vascular disease. Due to the multitude of reagents and cell types, RNAi experiment optimization can be time-consuming. In this study adherent cell cytometry was used to rapidly optimize siRNA transfection in human aortic vascular smooth muscle cells (AoSMC. Methods AoSMC were seeded at a density of 3000-8000 cells/well of a 96well plate. 24 hours later AoSMC were transfected with either non-targeting unlabeled siRNA (50 nM, or non-targeting labeled siRNA, siGLO Red (5 or 50 nM using no transfection reagent, HiPerfect or Lipofectamine RNAiMax. For counting cells, Hoechst nuclei stain or Cell Tracker green were used. For data analysis an adherent cell cytometer, Celigo® was used. Data was normalized to the transfection reagent alone group and expressed as red pixel count/cell. Results After 24 hours, none of the transfection conditions led to cell loss. Red fluorescence counts were normalized to the AoSMC count. RNAiMax was more potent compared to HiPerfect or no transfection reagent at 5 nM siGLO Red (4.12 +/-1.04 vs. 0.70 +/-0.26 vs. 0.15 +/-0.13 red pixel/cell and 50 nM siGLO Red (6.49 +/-1.81 vs. 2.52 +/-0.67 vs. 0.34 +/-0.19. Fluorescence expression results supported gene knockdown achieved by using MARCKS targeting siRNA in AoSMCs. Conclusion This study underscores that RNAi delivery depends heavily on the choice of delivery method. Adherent cell cytometry can be used as a high throughput-screening tool for the optimization of RNAi assays. This technology can accelerate in vitro cell assays and thus save costs.

  2. Underestimation of the Maximal Capacity of the Mitochondrial Electron Transport System in Oligomycin-Treated Cells.

    Directory of Open Access Journals (Sweden)

    Juliana S Ruas

    Full Text Available The maximal capacity of the mitochondrial electron transport system (ETS in intact cells is frequently estimated by promoting protonophore-induced maximal oxygen consumption preceded by inhibition of oxidative phosphorylation by oligomycin. In the present study, human glioma (T98G and U-87MG and prostate cancer (PC-3 cells were titrated with different concentrations of the protonophore CCCP to induce maximal oxygen consumption rate (OCR within respirometers in a conventional growth medium. The results demonstrate that the presence of oligomycin or its A-isomer leads to underestimation of maximal ETS capacity. In the presence of oligomycin, the spare respiratory capacity (SRC, i.e., the difference between the maximal and basal cellular OCR, was underestimated by 25 to 45%. The inhibitory effect of oligomycin on SRC was more pronounced in T98G cells and was observed in both suspended and attached cells. Underestimation of SRC also occurred when oxidative phosphorylation was fully inhibited by the ATP synthase inhibitor citreoviridin. Further experiments indicated that oligomycin cannot be replaced by the adenine nucleotide translocase inhibitors bongkrekic acid or carboxyatractyloside because, although these compounds have effects in permeabilized cells, they do not inhibit oxidative phosphorylation in intact cells. We replaced CCCP by FCCP, another potent protonophore and similar results were observed. Lower maximal OCR and SRC values were obtained with the weaker protonophore 2,4-dinitrophenol, and these parameters were not affected by the presence of oligomycin. In permeabilized cells or isolated brain mitochondria incubated with respiratory substrates, only a minor inhibitory effect of oligomycin on CCCP-induced maximal OCR was observed. We conclude that unless a previously validated protocol is employed, maximal ETS capacity in intact cells should be estimated without oligomycin. The inhibitory effect of an ATP synthase blocker on potent

  3. A cell-based high-throughput screening assay for radiation susceptibility using automated cell counting.

    Science.gov (United States)

    Hodzic, Jasmina; Dingjan, Ilse; Maas, Mariëlle Jp; van der Meulen-Muileman, Ida H; de Menezes, Renee X; Heukelom, Stan; Verheij, Marcel; Gerritsen, Winald R; Geldof, Albert A; van Triest, Baukelien; van Beusechem, Victor W

    2015-02-27

    Radiotherapy is one of the mainstays in the treatment for cancer, but its success can be limited due to inherent or acquired resistance. Mechanisms underlying radioresistance in various cancers are poorly understood and available radiosensitizers have shown only modest clinical benefit. There is thus a need to identify new targets and drugs for more effective sensitization of cancer cells to irradiation. Compound and RNA interference high-throughput screening technologies allow comprehensive enterprises to identify new agents and targets for radiosensitization. However, the gold standard assay to investigate radiosensitivity of cancer cells in vitro, the colony formation assay (CFA), is unsuitable for high-throughput screening. We developed a new high-throughput screening method for determining radiation susceptibility. Fast and uniform irradiation of batches up to 30 microplates was achieved using a Perspex container and a clinically employed linear accelerator. The readout was done by automated counting of fluorescently stained nuclei using the Acumen eX3 laser scanning cytometer. Assay performance was compared to that of the CFA and the CellTiter-Blue homogeneous uniform-well cell viability assay. The assay was validated in a whole-genome siRNA library screening setting using PC-3 prostate cancer cells. On 4 different cancer cell lines, the automated cell counting assay produced radiation dose response curves that followed a linear-quadratic equation and that exhibited a better correlation to the results of the CFA than did the cell viability assay. Moreover, the cell counting assay could be used to detect radiosensitization by silencing DNA-PKcs or by adding caffeine. In a high-throughput screening setting, using 4 Gy irradiated and control PC-3 cells, the effects of DNA-PKcs siRNA and non-targeting control siRNA could be clearly discriminated. We developed a simple assay for radiation susceptibility that can be used for high-throughput screening. This will

  4. Development of Droplet Microfluidics Enabling High-Throughput Single-Cell Analysis

    Directory of Open Access Journals (Sweden)

    Na Wen

    2016-07-01

    Full Text Available This article reviews recent developments in droplet microfluidics enabling high-throughput single-cell analysis. Five key aspects in this field are included in this review: (1 prototype demonstration of single-cell encapsulation in microfluidic droplets; (2 technical improvements of single-cell encapsulation in microfluidic droplets; (3 microfluidic droplets enabling single-cell proteomic analysis; (4 microfluidic droplets enabling single-cell genomic analysis; and (5 integrated microfluidic droplet systems enabling single-cell screening. We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on key performances of throughput, multifunctionality, and absolute quantification.

  5. An automated system for high-throughput single cell-based breeding

    Science.gov (United States)

    Yoshimoto, Nobuo; Kida, Akiko; Jie, Xu; Kurokawa, Masaya; Iijima, Masumi; Niimi, Tomoaki; Maturana, Andrés D.; Nikaido, Itoshi; Ueda, Hiroki R.; Tatematsu, Kenji; Tanizawa, Katsuyuki; Kondo, Akihiko; Fujii, Ikuo; Kuroda, Shun'ichi

    2013-01-01

    When establishing the most appropriate cells from the huge numbers of a cell library for practical use of cells in regenerative medicine and production of various biopharmaceuticals, cell heterogeneity often found in an isogenic cell population limits the refinement of clonal cell culture. Here, we demonstrated high-throughput screening of the most suitable cells in a cell library by an automated undisruptive single-cell analysis and isolation system, followed by expansion of isolated single cells. This system enabled establishment of the most suitable cells, such as embryonic stem cells with the highest expression of the pluripotency marker Rex1 and hybridomas with the highest antibody secretion, which could not be achieved by conventional high-throughput cell screening systems (e.g., a fluorescence-activated cell sorter). This single cell-based breeding system may be a powerful tool to analyze stochastic fluctuations and delineate their molecular mechanisms. PMID:23378922

  6. Microfluidic Impedance Flow Cytometry Enabling High-Throughput Single-Cell Electrical Property Characterization

    OpenAIRE

    Jian Chen; Chengcheng Xue; Yang Zhao; Deyong Chen; Min-Hsien Wu; Junbo Wang

    2015-01-01

    This article reviews recent developments in microfluidic impedance flow cytometry for high-throughput electrical property characterization of single cells. Four major perspectives of microfluidic impedance flow cytometry for single-cell characterization are included in this review: (1) early developments of microfluidic impedance flow cytometry for single-cell electrical property characterization; (2) microfluidic impedance flow cytometry with enhanced sensitivity; (3) microfluidic impedance ...

  7. Aging is associated with decreased maximal life span and accelerated senescence of bone marrow stromal cells

    DEFF Research Database (Denmark)

    Dokkedahl, Karin Stenderup; Justesen, Jeannette; Clausen, Christian

    2003-01-01

    maximal life span. Cell growth, markers of cellular senescence, and osteogenic and adipogenic potential were determined in early-passage and late-passage cells established from young and old donors. MSC from old donors exhibited a decreased maximal life span compared with cells from young donors (24...... +/- 11 population doublings [PD] vs 41 +/- 10 PD, P cells (0.05 +/- 0.02 PD/day) compared with young donor cells (0.09 +/- 0.02 PD/day) (P senescence-associated beta-galactosidase positive (SA beta......-gal+) cells and mean telomere length in early-passage cells obtained from young and old donors. However, MSC from old donors exhibited accelerated senescence evidenced by increased number of SA beta-gal+ cells per PD as compared with young (4% per PD vs 0.4% per PD, respectively). MSC from young and old...

  8. A high throughput screen identifies Nefopam as targeting cell proliferation in β-catenin driven neoplastic and reactive fibroproliferative disorders.

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    Raymond Poon

    Full Text Available Fibroproliferative disorders include neoplastic and reactive processes (e.g. desmoid tumor and hypertrophic scars. They are characterized by activation of β-catenin signaling, and effective pharmacologic approaches are lacking. Here we undertook a high throughput screen using human desmoid tumor cell cultures to identify agents that would inhibit cell viability in tumor cells but not normal fibroblasts. Agents were then tested in additional cell cultures for an effect on cell proliferation, apoptosis, and β-catenin protein level. Ultimately they were tested in Apc1638N mice, which develop desmoid tumors, as well as in wild type mice subjected to full thickness skin wounds. The screen identified Neofopam, as an agent that inhibited cell numbers to 42% of baseline in cell cultures from β-catenin driven fibroproliferative disorders. Nefopam decreased cell proliferation and β-catenin protein level to 50% of baseline in these same cell cultures. The half maximal effective concentration in-vitro was 0.5 uM and there was a plateau in the effect after 48 hours of treatment. Nefopam caused a 45% decline in tumor number, 33% decline in tumor volume, and a 40% decline in scar size when tested in mice. There was also a 50% decline in β-catenin level in-vivo. Nefopam targets β-catenin protein level in mesenchymal cells in-vitro and in-vivo, and may be an effective therapy for neoplastic and reactive processes driven by β-catenin mediated signaling.

  9. Optimization of total body irradiation: the match between (maximal) leukemic cell kill and (minimal) late effects

    NARCIS (Netherlands)

    Harteveld, M.L. van

    2007-01-01

    Optimization of total body irradiation: the match between (maximal) leukemic cell kill and (minimal) late effects: In this thesis, cataract formation and renal dysfunction as late effects of high-dose total body irradiation (TBI) as part of the conditioning before hematological stem cell

  10. High throughput single-cell and multiple-cell micro-encapsulation.

    Science.gov (United States)

    Lagus, Todd P; Edd, Jon F

    2012-06-15

    Microfluidic encapsulation methods have been previously utilized to capture cells in picoliter-scale aqueous, monodisperse drops, providing confinement from a bulk fluid environment with applications in high throughput screening, cytometry, and mass spectrometry. We describe a method to not only encapsulate single cells, but to repeatedly capture a set number of cells (here we demonstrate one- and two-cell encapsulation) to study both isolation and the interactions between cells in groups of controlled sizes. By combining drop generation techniques with cell and particle ordering, we demonstrate controlled encapsulation of cell-sized particles for efficient, continuous encapsulation. Using an aqueous particle suspension and immiscible fluorocarbon oil, we generate aqueous drops in oil with a flow focusing nozzle. The aqueous flow rate is sufficiently high to create ordering of particles which reach the nozzle at integer multiple frequencies of the drop generation frequency, encapsulating a controlled number of cells in each drop. For representative results, 9.9 μm polystyrene particles are used as cell surrogates. This study shows a single-particle encapsulation efficiency P(k=1) of 83.7% and a double-particle encapsulation efficiency P(k=2) of 79.5% as compared to their respective Poisson efficiencies of 39.3% and 33.3%, respectively. The effect of consistent cell and particle concentration is demonstrated to be of major importance for efficient encapsulation, and dripping to jetting transitions are also addressed. Continuous media aqueous cell suspensions share a common fluid environment which allows cells to interact in parallel and also homogenizes the effects of specific cells in measurements from the media. High-throughput encapsulation of cells into picoliter-scale drops confines the samples to protect drops from cross-contamination, enable a measure of cellular diversity within samples, prevent dilution of reagents and expressed biomarkers, and amplify

  11. Max-throughput interference avoidance mechanism for indoor self-organizing small cell networks

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    Kuang-Hsun Lin

    2017-09-01

    Full Text Available Since mobile traffic has been growing recently, the deployment of indoor small cells has become an attractive solution to enhance coverage. However, the increasing density of cells makes inter-cell interference more considerable. In this paper, we propose a max-throughput Interference Avoidance (MTIA centralized algorithm to improve the system’s throughput. Based on signaling and reports, a central controller connected to each base station can properly turn off base stations that may induce a relatively strong interference, and thus increase SINR. We implemented the MTIA algorithm in an LTE TDD network simulation and showed that MTIA effectively reduces inter-cell interference and improves the system’s throughput.

  12. Microfluidic cell microarray platform for high throughput analysis of particle-cell interactions.

    Science.gov (United States)

    Tong, Ziqiu; Rajeev, Gayathri; Guo, Keying; Ivask, Angela; McCormick, Scott; Lombi, Enzo; Priest, Craig; Voelcker, Nicolas H

    2018-03-02

    With the advances in nanotechnology, particles with various size, shape, surface chemistry and composition can be easily produced. Nano- and microparticles have been extensively explored in many industrial and clinical applications. Ensuring that the particles themselves are not possessing any toxic effects to the biological system is of paramount importance. This paper describes a proof of concept method in which a microfluidic system is used in conjunction with a cell microarray technique aiming to streamline the analysis of particle-cell interaction in a high throughput manner. Polymeric microparticles, with different particle surface functionalities, were firstly used to investigate the efficiency of particle-cell adhesion under dynamic flow. Silver nanoparticles (AgNPs,10 nm in diameter) perfused at different concentrations (0 to 20 μg/ml) in parallel streams over the cells in the microchannel exhibited higher toxicity compared to the static culture in the 96 well plate format. This developed microfluidic system can be easily scaled up to accommodate larger number of microchannels for high throughput analysis of potential toxicity of a wide range of particles in a single experiment.

  13. Patterning cell using Si-stencil for high-throughput assay

    KAUST Repository

    Wu, Jinbo

    2011-01-01

    In this communication, we report a newly developed cell pattering methodology by a silicon-based stencil, which exhibited advantages such as easy handling, reusability, hydrophilic surface and mature fabrication technologies. Cell arrays obtained by this method were used to investigate cell growth under a temperature gradient, which demonstrated the possibility of studying cell behavior in a high-throughput assay. This journal is © The Royal Society of Chemistry 2011.

  14. Label-free detection of neuronal differentiation in cell populations using high-throughput live-cell imaging of PC12 cells.

    Directory of Open Access Journals (Sweden)

    Sebastian Weber

    Full Text Available Detection of neuronal cell differentiation is essential to study cell fate decisions under various stimuli and/or environmental conditions. Many tools exist that quantify differentiation by neurite length measurements of single cells. However, quantification of differentiation in whole cell populations remains elusive so far. Because such populations can consist of both proliferating and differentiating cells, the task to assess the overall differentiation status is not trivial and requires a high-throughput, fully automated approach to analyze sufficient data for a statistically significant discrimination to determine cell differentiation. We address the problem of detecting differentiation in a mixed population of proliferating and differentiating cells over time by supervised classification. Using nerve growth factor induced differentiation of PC12 cells, we monitor the changes in cell morphology over 6 days by phase-contrast live-cell imaging. For general applicability, the classification procedure starts out with many features to identify those that maximize discrimination of differentiated and undifferentiated cells and to eliminate features sensitive to systematic measurement artifacts. The resulting image analysis determines the optimal post treatment day for training and achieves a near perfect classification of differentiation, which we confirmed in technically and biologically independent as well as differently designed experiments. Our approach allows to monitor neuronal cell populations repeatedly over days without any interference. It requires only an initial calibration and training step and is thereafter capable to discriminate further experiments. In conclusion, this enables long-term, large-scale studies of cell populations with minimized costs and efforts for detecting effects of external manipulation of neuronal cell differentiation.

  15. Estimation of immune cell densities in immune cell conglomerates: an approach for high-throughput quantification.

    Directory of Open Access Journals (Sweden)

    Niels Halama

    Full Text Available BACKGROUND: Determining the correct number of positive immune cells in immunohistological sections of colorectal cancer and other tumor entities is emerging as an important clinical predictor and therapy selector for an individual patient. This task is usually obstructed by cell conglomerates of various sizes. We here show that at least in colorectal cancer the inclusion of immune cell conglomerates is indispensable for estimating reliable patient cell counts. Integrating virtual microscopy and image processing principally allows the high-throughput evaluation of complete tissue slides. METHODOLOGY/PRINCIPAL FINDINGS: For such large-scale systems we demonstrate a robust quantitative image processing algorithm for the reproducible quantification of cell conglomerates on CD3 positive T cells in colorectal cancer. While isolated cells (28 to 80 microm(2 are counted directly, the number of cells contained in a conglomerate is estimated by dividing the area of the conglomerate in thin tissues sections (< or =6 microm by the median area covered by an isolated T cell which we determined as 58 microm(2. We applied our algorithm to large numbers of CD3 positive T cell conglomerates and compared the results to cell counts obtained manually by two independent observers. While especially for high cell counts, the manual counting showed a deviation of up to 400 cells/mm(2 (41% variation, algorithm-determined T cell numbers generally lay in between the manually observed cell numbers but with perfect reproducibility. CONCLUSION: In summary, we recommend our approach as an objective and robust strategy for quantifying immune cell densities in immunohistological sections which can be directly implemented into automated full slide image processing systems.

  16. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

    Science.gov (United States)

    2013-01-01

    The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

  17. Development of High-Throughput Quantitative Assays for Glucose Uptake in Cancer Cell Lines

    Science.gov (United States)

    Hassanein, Mohamed; Weidow, Brandy; Koehler, Elizabeth; Bakane, Naimish; Garbett, Shawn; Shyr, Yu; Quaranta, Vito

    2013-01-01

    Purpose Metabolism, and especially glucose uptake, is a key quantitative cell trait that is closely linked to cancer initiation and progression. Therefore, developing high-throughput assays for measuring glucose uptake in cancer cells would be enviable for simultaneous comparisons of multiple cell lines and microenvironmental conditions. This study was designed with two specific aims in mind: the first was to develop and validate a high-throughput screening method for quantitative assessment of glucose uptake in “normal” and tumor cells using the fluorescent 2-deoxyglucose analog 2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxyglucose (2-NBDG), and the second was to develop an image-based, quantitative, single-cell assay for measuring glucose uptake using the same probe to dissect the full spectrum of metabolic variability within populations of tumor cells in vitro in higher resolution. Procedure The kinetics of population-based glucose uptake was evaluated for MCF10A mammary epithelial and CA1d breast cancer cell lines, using 2-NBDG and a fluorometric microplate reader. Glucose uptake for the same cell lines was also examined at the single-cell level using high-content automated microscopy coupled with semi-automated cell-cytometric image analysis approaches. Statistical treatments were also implemented to analyze intra-population variability. Results Our results demonstrate that the high-throughput fluorometric assay using 2-NBDG is a reliable method to assess population-level kinetics of glucose uptake in cell lines in vitro. Similarly, single-cell image-based assays and analyses of 2-NBDG fluorescence proved an effective and accurate means for assessing glucose uptake, which revealed that breast tumor cell lines display intra-population variability that is modulated by growth conditions. Conclusions These studies indicate that 2-NBDG can be used to aid in the high-throughput analysis of the influence of chemotherapeutics on glucose uptake in cancer

  18. High-throughput microfluidic device for single cell analysis using multiple integrated soft lithographic pumps.

    Science.gov (United States)

    Patabadige, Damith E W; Mickleburgh, Tom; Ferris, Lorin; Brummer, Gage; Culbertson, Anne H; Culbertson, Christopher T

    2016-05-01

    The ability to accurately control fluid transport in microfluidic devices is key for developing high-throughput methods for single cell analysis. Making small, reproducible changes to flow rates, however, to optimize lysis and injection using pumps external to the microfluidic device are challenging and time-consuming. To improve the throughput and increase the number of cells analyzed, we have integrated previously reported micropumps into a microfluidic device that can increase the cell analysis rate to ∼1000 cells/h and operate for over an hour continuously. In order to increase the flow rates sufficiently to handle cells at a higher throughput, three sets of pumps were multiplexed. These pumps are simple, low-cost, durable, easy to fabricate, and biocompatible. They provide precise control of the flow rate up to 9.2 nL/s. These devices were used to automatically transport, lyse, and electrophoretically separate T-Lymphocyte cells loaded with Oregon green and 6-carboxyfluorescein. Peak overlap statistics predicted the number of fully resolved single-cell electropherograms seen. In addition, there was no change in the average fluorescent dye peak areas indicating that the cells remained intact and the dyes did not leak out of the cells over the 1 h analysis time. The cell lysate peak area distribution followed that expected of an asynchronous steady-state population of immortalized cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. The complete automation of cell culture: improvements for high-throughput and high-content screening.

    Science.gov (United States)

    Jain, Shushant; Sondervan, David; Rizzu, Patrizia; Bochdanovits, Zoltan; Caminada, Daniel; Heutink, Peter

    2011-09-01

    Genomic approaches provide enormous amounts of raw data with regard to genetic variation, the diversity of RNA species, and protein complement. High-throughput (HT) and high-content (HC) cellular screens are ideally suited to contextualize the information gathered from other "omic" approaches into networks and can be used for the identification of therapeutic targets. Current methods used for HT-HC screens are laborious, time-consuming, and prone to human error. The authors thus developed an automated high-throughput system with an integrated fluorescent imager for HC screens called the AI.CELLHOST. The implementation of user-defined culturing and assay plate setup parameters allows parallel operation of multiple screens in diverse mammalian cell types. The authors demonstrate that such a system is able to successfully maintain different cell lines in culture for extended periods of time as well as significantly increasing throughput, accuracy, and reproducibility of HT and HC screens.

  20. A high-throughput method for quantifying metabolically active yeast cells

    DEFF Research Database (Denmark)

    Nandy, Subir Kumar; Knudsen, Peter Boldsen; Rosenkjær, Alexander

    2015-01-01

    By redesigning the established methylene blue reduction test for bacteria and yeast, we present a cheap and efficient methodology for quantitative physiology of eukaryotic cells applicable for high-throughput systems. Validation of themethod in fermenters and highthroughput systems proved...... equivalent, displaying reduction curves that interrelated directly with CFU counts. For growth rate estimation, the methylene blue reduction test (MBRT) proved superior, since the discriminatory nature of the method allowed for the quantification of metabolically active cells only, excluding dead cells...

  1. Investigation of non-halogenated solvent mixtures for high throughput fabrication of polymerfullerene solar cells

    NARCIS (Netherlands)

    Schmidt-Hansberg, B.; Sanyal, M.; Grossiord, N.; Galagan, Y.O.; Baunach, M.; Klein, M.F.G.; Colsmann, A.; Scharfer, P.; Lemmer, U.; Dosch, H.; Michels, J.J; Barrena, E.; Schabel, W.

    2012-01-01

    The rapidly increasing power conversion efficiencies of organic solar cells are an important prerequisite towards low cost photovoltaic fabricated in high throughput. In this work we suggest indane as a non-halogenated replacement for the commonly used halogenated solvent o-dichlorobenzene. Indane

  2. Inertial-ordering-assisted droplet microfluidics for high-throughput single-cell RNA-sequencing.

    Science.gov (United States)

    Moon, Hui-Sung; Je, Kwanghwi; Min, Jae-Woong; Park, Donghyun; Han, Kyung-Yeon; Shin, Seung-Ho; Park, Woong-Yang; Yoo, Chang Eun; Kim, Shin-Hyun

    2018-02-27

    Single-cell RNA-seq reveals the cellular heterogeneity inherent in the population of cells, which is very important in many clinical and research applications. Recent advances in droplet microfluidics have achieved the automatic isolation, lysis, and labeling of single cells in droplet compartments without complex instrumentation. However, barcoding errors occurring in the cell encapsulation process because of the multiple-beads-in-droplet and insufficient throughput because of the low concentration of beads for avoiding multiple-beads-in-a-droplet remain important challenges for precise and efficient expression profiling of single cells. In this study, we developed a new droplet-based microfluidic platform that significantly improved the throughput while reducing barcoding errors through deterministic encapsulation of inertially ordered beads. Highly concentrated beads containing oligonucleotide barcodes were spontaneously ordered in a spiral channel by an inertial effect, which were in turn encapsulated in droplets one-by-one, while cells were simultaneously encapsulated in the droplets. The deterministic encapsulation of beads resulted in a high fraction of single-bead-in-a-droplet and rare multiple-beads-in-a-droplet although the bead concentration increased to 1000 μl -1 , which diminished barcoding errors and enabled accurate high-throughput barcoding. We successfully validated our device with single-cell RNA-seq. In addition, we found that multiple-beads-in-a-droplet, generated using a normal Drop-Seq device with a high concentration of beads, underestimated transcript numbers and overestimated cell numbers. This accurate high-throughput platform can expand the capability and practicality of Drop-Seq in single-cell analysis.

  3. High-throughput gene expression profiling of memory differentiation in primary human T cells

    Directory of Open Access Journals (Sweden)

    Russell Kate

    2008-08-01

    Full Text Available Abstract Background The differentiation of naive T and B cells into memory lymphocytes is essential for immunity to pathogens. Therapeutic manipulation of this cellular differentiation program could improve vaccine efficacy and the in vitro expansion of memory cells. However, chemical screens to identify compounds that induce memory differentiation have been limited by 1 the lack of reporter-gene or functional assays that can distinguish naive and memory-phenotype T cells at high throughput and 2 a suitable cell-line representative of naive T cells. Results Here, we describe a method for gene-expression based screening that allows primary naive and memory-phenotype lymphocytes to be discriminated based on complex genes signatures corresponding to these differentiation states. We used ligation-mediated amplification and a fluorescent, bead-based detection system to quantify simultaneously 55 transcripts representing naive and memory-phenotype signatures in purified populations of human T cells. The use of a multi-gene panel allowed better resolution than any constituent single gene. The method was precise, correlated well with Affymetrix microarray data, and could be easily scaled up for high-throughput. Conclusion This method provides a generic solution for high-throughput differentiation screens in primary human T cells where no single-gene or functional assay is available. This screening platform will allow the identification of small molecules, genes or soluble factors that direct memory differentiation in naive human lymphocytes.

  4. High-throughput single-cell PCR using microfluidic emulsions

    Science.gov (United States)

    Guo, Mira; Mazutis, Linas; Agresti, Jeremy; Sommer, Morten; Dantas, Gautam; Church, George; Turnbaugh, Peter; Weitz, David

    2012-02-01

    The human gut and other environmental samples contain large populations of diverse bacteria that are poorly characterized and unculturable, yet have many functions relevant to human health. Our goal is to identify exactly which species carry some gene of interest, such as a carbohydrate metabolism gene. Conventional metagenomic assays sequence DNA extracted in bulk from populations of mixed cell types, and are therefore unable to associate a gene of interest with a species-identifying 16S gene, to determine that the two genes originated from the same cell. We solve this problem by microfluidically encapsulating single bacteria cells in drops, using PCR to amplify the two genes inside any drop whose encapsulated cell contains both genes, and sequencing the DNA from those drops that contain both amplification products.

  5. Hydrogel Droplet Microfluidics for High-Throughput Single Molecule/Cell Analysis.

    Science.gov (United States)

    Zhu, Zhi; Yang, Chaoyong James

    2017-01-17

    Heterogeneity among individual molecules and cells has posed significant challenges to traditional bulk assays, due to the assumption of average behavior, which would lose important biological information in heterogeneity and result in a misleading interpretation. Single molecule/cell analysis has become an important and emerging field in biological and biomedical research for insights into heterogeneity between large populations at high resolution. Compared with the ensemble bulk method, single molecule/cell analysis explores the information on time trajectories, conformational states, and interactions of individual molecules/cells, all key factors in the study of chemical and biological reaction pathways. Various powerful techniques have been developed for single molecule/cell analysis, including flow cytometry, atomic force microscopy, optical and magnetic tweezers, single-molecule fluorescence spectroscopy, and so forth. However, some of them have the low-throughput issue that has to analyze single molecules/cells one by one. Flow cytometry is a widely used high-throughput technique for single cell analysis but lacks the ability for intercellular interaction study and local environment control. Droplet microfluidics becomes attractive for single molecule/cell manipulation because single molecules/cells can be individually encased in monodisperse microdroplets, allowing high-throughput analysis and manipulation with precise control of the local environment. Moreover, hydrogels, cross-linked polymer networks that swell in the presence of water, have been introduced into droplet microfluidic systems as hydrogel droplet microfluidics. By replacing an aqueous phase with a monomer or polymer solution, hydrogel droplets can be generated on microfluidic chips for encapsulation of single molecules/cells according to the Poisson distribution. The sol-gel transition property endows the hydrogel droplets with new functionalities and diversified applications in single

  6. Droplet microfluidic technology for single-cell high-throughput screening.

    Science.gov (United States)

    Brouzes, Eric; Medkova, Martina; Savenelli, Neal; Marran, Dave; Twardowski, Mariusz; Hutchison, J Brian; Rothberg, Jonathan M; Link, Darren R; Perrimon, Norbert; Samuels, Michael L

    2009-08-25

    We present a droplet-based microfluidic technology that enables high-throughput screening of single mammalian cells. This integrated platform allows for the encapsulation of single cells and reagents in independent aqueous microdroplets (1 pL to 10 nL volumes) dispersed in an immiscible carrier oil and enables the digital manipulation of these reactors at a very high-throughput. Here, we validate a full droplet screening workflow by conducting a droplet-based cytotoxicity screen. To perform this screen, we first developed a droplet viability assay that permits the quantitative scoring of cell viability and growth within intact droplets. Next, we demonstrated the high viability of encapsulated human monocytic U937 cells over a period of 4 days. Finally, we developed an optically-coded droplet library enabling the identification of the droplets composition during the assay read-out. Using the integrated droplet technology, we screened a drug library for its cytotoxic effect against U937 cells. Taken together our droplet microfluidic platform is modular, robust, uses no moving parts, and has a wide range of potential applications including high-throughput single-cell analyses, combinatorial screening, and facilitating small sample analyses.

  7. High-throughput physically based approach for mammalian cell encapsulation

    Science.gov (United States)

    Yu, Jiashing; Wu, Po-Chen; Huang, Chi-Hui; Yang, Chung-Yao; Cheng, Chao-Min

    2013-10-01

    Herein, we wish to tear down the traditional boundaries between physics and life sciences by demonstrating a physically based, flow-focusing method to encapsulate mammalian cells into alginate-based microspheres in a very short period of time. We paid particular attention to the physical properties of the alginate solution as it was critical to create a physiologically relevant environment within the alginate microspheres. The cells we cultured when re-culturing them on Petri dishes could still be maintained for at least 4 days after microsphere encapsulation. We believe that this study would provide interesting insight in biophysics, polymer physics, and applied physics.

  8. Evaluation of the Droplet-Microarray Platform for High-Throughput Screening of Suspension Cells.

    Science.gov (United States)

    Popova, Anna A; Depew, Claire; Permana, Katya Manuella; Trubitsyn, Alexander; Peravali, Ravindra; Ordiano, Jorge Ángel González; Reischl, Markus; Levkin, Pavel A

    2017-04-01

    Phenotypic cell-based high-throughput screenings play a central role in drug discovery and toxicology. The main tendency in cell screenings is the increase of the throughput and decrease of reaction volume in order to accelerate the experiments, reduce the costs, and enable screenings of rare cells. Conventionally, cell-based assays are performed in microtiter plates, which exist in 96- to 1536-wells formats and cannot be further miniaturized. In addition, performing screenings of suspension cells is associated with risk of losing cell content during the staining procedures and incompatibility with high-content microscopy. Here, we evaluate the Droplet-Microarray screening platform for culturing, screening, and imaging of suspension cells. We demonstrate pipetting-free cell seeding and proliferation of cells in individual droplets of 3-80 nL in volume. We developed a methodology to perform parallel treatment, staining, and fixation of suspension cells in individual droplets. Automated imaging of live suspension cells directly in the droplets combined with algorithms for pattern recognition for image analysis is demonstrated. We evaluated the developed methodology by performing a dose-response study with antineoplastic drugs. We believe that the DMA screening platform carries great potential to be adopted for broad spectrum of screenings of suspension cells.

  9. High throughput system for magnetic manipulation of cells, polymers, and biomaterials

    Science.gov (United States)

    Spero, Richard Chasen; Vicci, Leandra; Cribb, Jeremy; Bober, David; Swaminathan, Vinay; O’Brien, E. Timothy; Rogers, Stephen L.; Superfine, R.

    2008-01-01

    In the past decade, high throughput screening (HTS) has changed the way biochemical assays are performed, but manipulation and mechanical measurement of micro- and nanoscale systems have not benefited from this trend. Techniques using microbeads (particles ∼0.1–10 μm) show promise for enabling high throughput mechanical measurements of microscopic systems. We demonstrate instrumentation to magnetically drive microbeads in a biocompatible, multiwell magnetic force system. It is based on commercial HTS standards and is scalable to 96 wells. Cells can be cultured in this magnetic high throughput system (MHTS). The MHTS can apply independently controlled forces to 16 specimen wells. Force calibrations demonstrate forces in excess of 1 nN, predicted force saturation as a function of pole material, and powerlaw dependence of F∼r−2.7±0.1. We employ this system to measure the stiffness of SR2+ Drosophila cells. MHTS technology is a key step toward a high throughput screening system for micro- and nanoscale biophysical experiments. PMID:19044357

  10. Microfluidic Impedance Flow Cytometry Enabling High-Throughput Single-Cell Electrical Property Characterization

    Directory of Open Access Journals (Sweden)

    Jian Chen

    2015-04-01

    Full Text Available This article reviews recent developments in microfluidic impedance flow cytometry for high-throughput electrical property characterization of single cells. Four major perspectives of microfluidic impedance flow cytometry for single-cell characterization are included in this review: (1 early developments of microfluidic impedance flow cytometry for single-cell electrical property characterization; (2 microfluidic impedance flow cytometry with enhanced sensitivity; (3 microfluidic impedance and optical flow cytometry for single-cell analysis and (4 integrated point of care system based on microfluidic impedance flow cytometry. We examine the advantages and limitations of each technique and discuss future research opportunities from the perspectives of both technical innovation and clinical applications.

  11. Microfluidic impedance flow cytometry enabling high-throughput single-cell electrical property characterization.

    Science.gov (United States)

    Chen, Jian; Xue, Chengcheng; Zhao, Yang; Chen, Deyong; Wu, Min-Hsien; Wang, Junbo

    2015-04-29

    This article reviews recent developments in microfluidic impedance flow cytometry for high-throughput electrical property characterization of single cells. Four major perspectives of microfluidic impedance flow cytometry for single-cell characterization are included in this review: (1) early developments of microfluidic impedance flow cytometry for single-cell electrical property characterization; (2) microfluidic impedance flow cytometry with enhanced sensitivity; (3) microfluidic impedance and optical flow cytometry for single-cell analysis and (4) integrated point of care system based on microfluidic impedance flow cytometry. We examine the advantages and limitations of each technique and discuss future research opportunities from the perspectives of both technical innovation and clinical applications.

  12. Gateway-compatible vectors for high-throughput protein expression in pro- and eukaryotic cell-free systems.

    Science.gov (United States)

    Gagoski, Dejan; Mureev, Sergey; Giles, Nichole; Johnston, Wayne; Dahmer-Heath, Mareike; Škalamera, Dubravka; Gonda, Thomas J; Alexandrov, Kirill

    2015-02-10

    Although numerous techniques for protein expression and production are available the pace of genome sequencing outstrips our ability to analyze the encoded proteins. To address this bottleneck, we have established a system for parallelized cloning, DNA production and cell-free expression of large numbers of proteins. This system is based on a suite of pCellFree Gateway destination vectors that utilize a Species Independent Translation Initiation Sequence (SITS) that mediates recombinant protein expression in any in vitro translation system. These vectors introduce C or N terminal EGFP and mCherry fluorescent and affinity tags, enabling direct analysis and purification of the expressed proteins. To maximize throughput and minimize the cost of protein production we combined Gateway cloning with Rolling Circle DNA Amplification. We demonstrate that as little as 0.1 ng of plasmid DNA is sufficient for template amplification and production of recombinant human protein in Leishmania tarentolae and Escherichia coli cell-free expression systems. Our experiments indicate that this approach can be applied to large gene libraries as it can be reliably performed in multi-well plates. The resulting protein expression pipeline provides a valuable new tool for applications of the post genomic era. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria.

    Science.gov (United States)

    Bruno, Antonia; Sandionigi, Anna; Galimberti, Andrea; Siani, Eleonora; Labra, Massimo; Cocuzza, Clementina; Ferri, Emanuele; Casiraghi, Maurizio

    2017-02-01

    We propose an innovative, repeatable, and reliable experimental workflow to concentrate and detect environmental bacteria in drinking water using molecular techniques. We first concentrated bacteria in water samples using tangential flow filtration and then we evaluated two methods of environmental DNA extraction. We performed tests on both artificially contaminated water samples and real drinking water samples. The efficiency of the experimental workflow was measured through qPCR. The successful applicability of the high-throughput DNA sequencing (HTS) approach was demonstrated on drinking water samples. Our results demonstrate the feasibility of our approach in high-throughput-based studies, and we suggest incorporating it in monitoring strategies to have a better representation of the microbial community. In the recent years, HTS techniques have become key tools in the study of microbial communities. To make the leap from academic laboratories to the routine monitoring (e.g., water treatment plants laboratories), we here propose an experimental workflow suitable for the introduction of HTS as a standard method for detecting environmental bacteria. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  14. Simple-cell-like receptive fields maximize temporal coherence in natural video.

    Science.gov (United States)

    Hurri, Jarmo; Hyvärinen, Aapo

    2003-03-01

    Recently, statistical models of natural images have shown the emergence of several properties of the visual cortex. Most models have considered the nongaussian properties of static image patches, leading to sparse coding or independent component analysis. Here we consider the basic time dependencies of image sequences instead of their nongaussianity. We show that simple-cell-type receptive fields emerge when temporal response strength correlation is maximized for natural image sequences. Thus, temporal response strength correlation, which is a nonlinear measure of temporal coherence, provides an alternative to sparseness in modeling simple-cell receptive field properties. Our results also suggest an interpretation of simple cells in terms of invariant coding principles, which have previously been used to explain complex-cell receptive fields.

  15. Microengineering methods for cell-based microarrays and high-throughput drug-screening applications

    Energy Technology Data Exchange (ETDEWEB)

    Xu Feng; Wu Jinhui; Wang Shuqi; Gurkan, Umut Atakan; Demirci, Utkan [Department of Medicine, Demirci Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Biomedical Engineering, Brigham and Women' s Hospital, Harvard Medical School, Boston, MA (United States); Durmus, Naside Gozde, E-mail: udemirci@rics.bwh.harvard.edu [School of Engineering and Division of Biology and Medicine, Brown University, Providence, RI (United States)

    2011-09-15

    Screening for effective therapeutic agents from millions of drug candidates is costly, time consuming, and often faces concerns due to the extensive use of animals. To improve cost effectiveness, and to minimize animal testing in pharmaceutical research, in vitro monolayer cell microarrays with multiwell plate assays have been developed. Integration of cell microarrays with microfluidic systems has facilitated automated and controlled component loading, significantly reducing the consumption of the candidate compounds and the target cells. Even though these methods significantly increased the throughput compared to conventional in vitro testing systems and in vivo animal models, the cost associated with these platforms remains prohibitively high. Besides, there is a need for three-dimensional (3D) cell-based drug-screening models which can mimic the in vivo microenvironment and the functionality of the native tissues. Here, we present the state-of-the-art microengineering approaches that can be used to develop 3D cell-based drug-screening assays. We highlight the 3D in vitro cell culture systems with live cell-based arrays, microfluidic cell culture systems, and their application to high-throughput drug screening. We conclude that among the emerging microengineering approaches, bioprinting holds great potential to provide repeatable 3D cell-based constructs with high temporal, spatial control and versatility.

  16. A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing

    Science.gov (United States)

    Woodruff, Kristina; Maerkl, Sebastian J.

    2016-01-01

    Mammalian synthetic biology could be augmented through the development of high-throughput microfluidic systems that integrate cellular transfection, culturing, and imaging. We created a microfluidic chip that cultures cells and implements 280 independent transfections at up to 99% efficiency. The chip can perform co-transfections, in which the number of cells expressing each protein and the average protein expression level can be precisely tuned as a function of input DNA concentration and synthetic gene circuits can be optimized on chip. We co-transfected four plasmids to test a histidine kinase signaling pathway and mapped the dose dependence of this network on the level of one of its constituents. The chip is readily integrated with high-content imaging, enabling the evaluation of cellular behavior and protein expression dynamics over time. These features make the transfection chip applicable to high-throughput mammalian protein and synthetic biology studies. PMID:27030663

  17. Massively Parallel Rogue Cell Detection using Serial Time-Encoded Amplified Microscopy of Inertially Ordered Cells in High Throughput Flow

    Science.gov (United States)

    2013-06-01

    technology, and information technology. To show the system’s utility, we demonstrated high-throughput image-based screening of budding yeast and...circulating   tumor  cell  detection  from  blood  in  breast  cancer  patients.     Conclusion   In   summary,   we

  18. Massively Parrell Rogue Cell Detection Using Serial Time-Encoded Amplified Microscopy of Inertially Ordered Cells in High Throughput Flow

    Science.gov (United States)

    2012-08-01

    To show the utility of the STEAM flow analyzer, we used it to demonstrate high-throughput screening of Saccharomyces cerevisiae , commonly known as...efficiency and missing smaller MCF7 cells in the FPGA selection process) (Fig. 4C). Furthermore, our receiver operating characteristic (ROC) curve

  19. Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy?

    DEFF Research Database (Denmark)

    Lundegaard, Claus; Lund, Ole; Nielsen, Morten

    2012-01-01

    Prediction methods as well as experimental methods for T-cell epitope discovery have developed significantly in recent years. High-throughput experimental methods have made it possible to perform full-length protein scans for epitopes restricted to a limited number of MHC alleles. The high costs...... discovery. We expect prediction methods as well as experimental validation methods to continue to develop and that we will soon see clinical trials of products whose development has been guided by prediction methods....

  20. Quantitative high-throughput screening identifies inhibitors of anthrax-induced cell death.

    Science.gov (United States)

    Zhu, Ping Jun; Hobson, John P; Southall, Noel; Qiu, Cunping; Thomas, Craig J; Lu, Jiamo; Inglese, James; Zheng, Wei; Leppla, Stephen H; Bugge, Thomas H; Austin, Christopher P; Liu, Shihui

    2009-07-15

    Here, we report the results of a quantitative high-throughput screen (qHTS) measuring the endocytosis and translocation of a beta-lactamase-fused-lethal factor and the identification of small molecules capable of obstructing the process of anthrax toxin internalization. Several small molecules protect RAW264.7 macrophages and CHO cells from anthrax lethal toxin and protected cells from an LF-Pseudomonas exotoxin fusion protein and diphtheria toxin. Further efforts demonstrated that these compounds impaired the PA heptamer pre-pore to pore conversion in cells expressing the CMG2 receptor, but not the related TEM8 receptor, indicating that these compounds likely interfere with toxin internalization.

  1. Packet Throughput Analysis of Static and Dynamic TDD in Small Cell Networks

    OpenAIRE

    Yang, Howard H.; Geraci, Giovanni; Zhong, Yi; Quek, Tony Q. S.

    2017-01-01

    We develop an analytical framework for the perfor- mance comparison of small cell networks operating under static time division duplexing (S-TDD) and dynamic TDD (D-TDD). While in S-TDD downlink/uplink (DL/UL) cell transmissions are synchronized, in D-TDD each cell dynamically allocates resources to the most demanding direction. By leveraging stochastic geom- etry and queuing theory, we derive closed-form expressions for the UL and DL packet throughput, also capturing the impact of random tra...

  2. DESIGN OF LOW EPI AND HIGH THROUGHPUT CORDIC CELL TO IMPROVE THE PERFORMANCE OF MOBILE ROBOT

    Directory of Open Access Journals (Sweden)

    P. VELRAJKUMAR

    2014-04-01

    Full Text Available This paper mainly focuses on pass logic based design, which gives an low Energy Per Instruction (EPI and high throughput COrdinate Rotation Digital Computer (CORDIC cell for application of robotic exploration. The basic components of CORDIC cell namely register, multiplexer and proposed adder is designed using pass transistor logic (PTL design. The proposed adder is implemented in bit-parallel iterative CORDIC circuit whereas designed using DSCH2 VLSI CAD tool and their layouts are generated by Microwind 3 VLSI CAD tool. The propagation delay, area and power dissipation are calculated from the simulated results for proposed adder based CORDIC cell. The EPI, throughput and effect of temperature are calculated from generated layout. The output parameter of generated layout is analysed using BSIM4 advanced analyzer. The simulated result of the proposed adder based CORDIC circuit is compared with other adder based CORDIC circuits. From the analysis of these simulated results, it was found that the proposed adder based CORDIC circuit dissipates low power, gives faster response, low EPI and high throughput.

  3. Efficient production of a gene mutant cell line through integrating TALENs and high-throughput cell cloning.

    Science.gov (United States)

    Sun, Changhong; Fan, Yu; Li, Juan; Wang, Gancheng; Zhang, Hanshuo; Xi, Jianzhong Jeff

    2015-02-01

    Transcription activator-like effectors (TALEs) are becoming powerful DNA-targeting tools in a variety of mammalian cells and model organisms. However, generating a stable cell line with specific gene mutations in a simple and rapid manner remains a challenging task. Here, we report a new method to efficiently produce monoclonal cells using integrated TALE nuclease technology and a series of high-throughput cell cloning approaches. Following this method, we obtained three mTOR mutant 293T cell lines within 2 months, which included one homozygous mutant line. © 2014 Society for Laboratory Automation and Screening.

  4. High-throughput Biological Cell Classification Featuring Real-time Optical Data Compression

    CERN Document Server

    Jalali, Bahram; Chen, Claire L

    2015-01-01

    High throughput real-time instruments are needed to acquire large data sets for detection and classification of rare events. Enabled by the photonic time stretch digitizer, a new class of instruments with record throughputs have led to the discovery of optical rogue waves [1], detection of rare cancer cells [2], and the highest analog-to-digital conversion performance ever achieved [3]. Featuring continuous operation at 100 million frames per second and shutter speed of less than a nanosecond, the time stretch camera is ideally suited for screening of blood and other biological samples. It has enabled detection of breast cancer cells in blood with record, one-in-a-million, sensitivity [2]. Owing to their high real-time throughput, instruments produce a torrent of data - equivalent to several 4K movies per second - that overwhelm data acquisition, storage, and processing operations. This predicament calls for technologies that compress images in optical domain and in real-time. An example of this, based on war...

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

    Science.gov (United States)

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

    2017-03-01

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

  6. Profiling the main cell wall polysaccharides of grapevine leaves using high-throughput and fractionation methods.

    Science.gov (United States)

    Moore, John P; Nguema-Ona, Eric; Fangel, Jonatan U; Willats, William G T; Hugo, Annatjie; Vivier, Melané A

    2014-01-01

    Vitis species include Vitis vinifera, the domesticated grapevine, used for wine and grape agricultural production and considered the world's most important fruit crop. A cell wall preparation, isolated from fully expanded photosynthetically active leaves, was fractionated via chemical and enzymatic reagents; and the various extracts obtained were assayed using high-throughput cell wall profiling tools according to a previously optimized and validated workflow. The bulk of the homogalacturonan-rich pectin present was efficiently extracted using CDTA treatment, whereas over half of the grapevine leaf cell wall consisted of vascular veins, comprised of xylans and cellulose. The main hemicellulose component was found to be xyloglucan and an enzymatic oligosaccharide fingerprinting approach was used to analyze the grapevine leaf xyloglucan fraction. When Paenibacillus sp. xyloglucanase was applied the main subunits released were XXFG and XLFG; whereas the less-specific Trichoderma reesei EGII was also able to release the XXXG motif as well as other oligomers likely of mannan and xylan origin. This latter enzyme would thus be useful to screen for xyloglucan, xylan and mannan-linked cell wall alterations in laboratory and field grapevine populations. This methodology is well-suited for high-throughput cell wall profiling of grapevine mutant and transgenic plants for investigating the range of biological processes, specifically plant disease studies and plant-pathogen interactions, where the cell wall plays a crucial role. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. High-throughput mapping of cell-wall polymers within and between plants using novel microarrays

    DEFF Research Database (Denmark)

    Moller, Isabel Eva; Sørensen, Iben; Bernal Giraldo, Adriana Jimena

    2007-01-01

    We describe here a methodology that enables the occurrence of cell-wall glycans to be systematically mapped throughout plants in a semi-quantitative high-throughput fashion. The technique (comprehensive microarray polymer profiling, or CoMPP) integrates the sequential extraction of glycans from...... analysis of mutant and wild-type plants, as demonstrated here for the Arabidopsis thaliana mutants fra8, mur1 and mur3. CoMPP was also applied to Physcomitrella patens cell walls and was validated by carbohydrate linkage analysis. These data provide new insights into the structure and functions of plant...

  8. Immune Cell Activation and Co-X-irradiation Effect of Eleutherococcus senticosus Maxim Root

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Hyoung Cheol [Chonbuk National University, Jeonju (Korea, Republic of); Park, Jeong Seob [Iksan National College, Iksan (Korea, Republic of); Choi, Dong Seong [Woosuk University, Samrye (Korea, Republic of)

    2007-09-15

    Purpose: This study was performed to investigate the effects of immune cell activation and the antitumor effect for the combination of treatment with X-irradiation and Eleutherococcus senticosus Maxim Root (ESMR) on mouse tumor cells. Materials and Methods: ESMR (250g) was extracted with 80% methanol, concentrated under decompression and lyophilized. To determine whether ESMR is able to activate the immune cells or not, the proliferation of splenocytes in vitro and the number of B cells and T cells in splenic lymphocytes in ESMR-pretreated mice were evaluated. X-irradiation was given to the mouse fibrosarcoma tumor cells (FSa II) by 250 kv X-irradiation machine. The cytotoxicity of ESMR was evaluated from its ability to reduce the clonogenecity of FSa II cells. In X-irradiation alone group, each 2, 4, 6 and 8 Gy was given to FSa II cells. In X-irradiation with ESMR group, 0.2 mg/ml of ESMR was exposed to FSa II cells for 1 hour before X-irradiation. Results: The proliferation of cultured mouse splenocytes and thymocytes were enhanced by the addition of ESMR in vitro. The number of B cells and T cells in mouse splenic lymphocytes was significantly increased in ESMR pretreated mice in vivo. In FSa II cells that received a combination of 0.2 mg/ml of ESMR with X-irradiation exposure, the survival fraction with a dose of 2, 4 and 6 Gy was 0.39{+-}0.005, 0.22{+-}0.005 and 0.06{+-}0.007, respectively. For FSa II cells treated with X-irradiation alone, the survival fraction with a dose of 2, 4 and 6 Gy was 0.76{+-}0.02, 0.47{+-}0.008 and 0.37{+-}0.01. The difference in the survival fraction of the mouse FSa II cells treated with and without ESMR was statistically significant (p<0.05). Conclusion: Treatment with ESMR increased cell viability of mouse splenocytes in vitro and especially the subpopulation of B cells and T cells in splenocytes in ESMR-pretreated mice. However, treatment with ESMR did not increase the level of Th and Tc subpopulations in the thymocytes

  9. Serine phosphorylation of cortactin is required for maximal host cell invasion by Campylobacter jejuni.

    Science.gov (United States)

    Samuelson, Derrick R; Konkel, Michael E

    2013-11-04

    Campylobacter jejuni causes acute disease characterized by severe diarrhea containing blood and leukocytes, fever, and abdominal cramping. Disease caused by C. jejuni is dependent on numerous bacterial and host factors. C. jejuni invasion of the intestinal epithelial cells is seen in both clinical samples and animal models indicating that host cell invasion is, in part, necessary for disease. C. jejuni utilizes a flagellar Type III Secretion System (T3SS) to deliver the Campylobacter invasion antigens (Cia) to host cells. The Cia proteins modulate host cell signaling leading to actin cytoskeleton rearrangement necessary for C. jejuni host cell invasion, and are required for the development of disease. This study was based on the hypothesis that the C. jejuni CiaD effector protein mediates Erk 1/2 dependent cytoskeleton rearrangement. We showed that CiaD was required for the maximal phosphorylation of Erk 1/2 by performing an immunoblot with a p-Erk 1/2 specific antibody and that Erk 1/2 participates in C. jejuni invasion of host cells by performing the gentamicin protection assay in the presence and absence of the PD98059 (a potent inhibitor of Erk 1/2 activation). CiaD was also found to be required for the maximal phosphorylation of cortactin S405 and S418, as judged by immunoblot analysis. The response of human INT 407 epithelial cells to infection with C. jejuni was evaluated by confocal microscopy and scanning electron microscopy to determine the extent of membrane ruffling. This analysis revealed that CiaD, Erk 1/2, and cortactin participate in C. jejuni-induced membrane ruffling. Finally, cortactin and N-WASP were found to be involved in C. jejuni invasion of host cells using siRNA to N-WASP, and siRNA to cortactin, coupled with the gentamicin protection assay. We conclude that CiaD is involved in the activation of Erk 1/2 and that activated Erk 1/2 facilitates C. jejuni invasion by phosphorylation of cortactin on serine 405 and 418. This is the first time

  10. High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.

    Science.gov (United States)

    Sebé-Pedrós, Arnau; Peña, Marcia Ivonne; Capella-Gutiérrez, Salvador; Antó, Meritxell; Gabaldón, Toni; Ruiz-Trillo, Iñaki; Sabidó, Eduard

    2016-10-24

    Cell-specific regulation of protein levels and activity is essential for the distribution of functions among multiple cell types in animals. The finding that many genes involved in these regulatory processes have a premetazoan origin raises the intriguing possibility that the mechanisms required for spatially regulated cell differentiation evolved prior to the appearance of animals. Here, we use high-throughput proteomics in Capsaspora owczarzaki, a close unicellular relative of animals, to characterize the dynamic proteome and phosphoproteome profiles of three temporally distinct cell types in this premetazoan species. We show that life-cycle transitions are linked to extensive proteome and phosphoproteome remodeling and that they affect key genes involved in animal multicellularity, such as transcription factors and tyrosine kinases. The observation of shared features between Capsaspora and metazoans indicates that elaborate and conserved phosphosignaling and proteome regulation supported temporal cell-type differentiation in the unicellular ancestor of animals. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Two-step protocol for preparing adherent cells for high-throughput flow cytometry.

    Science.gov (United States)

    Kaur, Mandeep; Esau, Luke

    2015-09-01

    We have developed a simple, cost-effective, and labor-efficient two-step protocol for preparing adherent cells for high-throughput flow cytometry. Adherent cells were grown on microplates, detached with 2.9 mM EDTA (pH 6.14) added directly to wells containing cell culture medium, stained, and then analyzed on a flow cytometer. This protocol bypasses washing, centrifugation, and transfer between plates, reducing the cell loss that occurs in standard multistep protocols. The method has been validated using six adherent cell lines, four commercially available dyes, and two antibodies; the results have been confirmed using two different flow cytometry (FC) instruments. Our approach has been used for estimating apoptosis, mitochondrial membrane potential, reactive oxygen species, and autophagy in response to exposure to pure compounds as well as plant and bacterial extracts.

  12. Automated High-Throughput Damage Scoring of Zebrafish Lateral Line Hair Cells After Ototoxin Exposure.

    Science.gov (United States)

    Philip, Rohit C; Rodriguez, Jeffrey J; Niihori, Maki; Francis, Ross H; Mudery, Jordan A; Caskey, Justin S; Krupinski, Elizabeth; Jacob, Abraham

    2018-01-30

    Zebrafish have emerged as a powerful biological system for drug development against hearing loss. Zebrafish hair cells, contained within neuromasts along the lateral line, can be damaged with exposure to ototoxins, and therefore, pre-exposure to potentially otoprotective compounds can be a means of identifying promising new drug candidates. Unfortunately, anatomical assays of hair cell damage are typically low-throughput and labor intensive, requiring trained experts to manually score hair cell damage in fluorescence or confocal images. To enhance throughput and consistency, our group has developed an automated damage-scoring algorithm based on machine-learning techniques that produce accurate damage scores, eliminate potential operator bias, provide more fidelity in determining damage scores that are between two levels, and deliver consistent results in a fraction of the time required for manual analysis. The system has been validated against trained experts using linear regression, hypothesis testing, and the Pearson's correlation coefficient. Furthermore, performance has been quantified by measuring mean absolute error for each image and the time taken to automatically compute damage scores. Coupling automated analysis of zebrafish hair cell damage to behavioral assays for ototoxicity produces a novel drug discovery platform for rapid translation of candidate drugs into preclinical mammalian models of hearing loss.

  13. Carbon nanotubes for voltage reduction and throughput enhancement of electrical cell lysis on a lab-on-a-chip

    Science.gov (United States)

    Shahini, Mehdi; Yeow, John T. W.

    2011-08-01

    We report on the enhancement of electrical cell lysis using carbon nanotubes (CNTs). Electrical cell lysis systems are widely utilized in microchips as they are well suited to integration into lab-on-a-chip devices. However, cell lysis based on electrical mechanisms has high voltage requirements. Here, we demonstrate that by incorporating CNTs into microfluidic electrolysis systems, the required voltage for lysis is reduced by half and the lysis throughput at low voltages is improved by ten times, compared to non-CNT microchips. In our experiment, E. coli cells are lysed while passing through an electric field in a microchannel. Based on the lightning rod effect, the electric field strengthened at the tip of the CNTs enhances cell lysis at lower voltage and higher throughput. This approach enables easy integration of cell lysis with other on-chip high-throughput sample-preparation processes.

  14. Resonant waveguide grating imagers for single cell analysis and high throughput screening

    Science.gov (United States)

    Fang, Ye

    2015-08-01

    Resonant waveguide grating (RWG) systems illuminate an array of diffractive nanograting waveguide structures in microtiter plate to establish evanescent wave for measuring tiny changes in local refractive index arising from the dynamic mass redistribution of living cells upon stimulation. Whole-plate RWG imager enables high-throughput profiling and screening of drugs. Microfluidics RWG imager not only manifests distinct receptor signaling waves, but also differentiates long-acting agonism and antagonism. Spatially resolved RWG imager allows for single cell analysis including receptor signaling heterogeneity and the invasion of cancer cells in a spheroidal structure through 3-dimensional extracellular matrix. High frequency RWG imager permits real-time detection of drug-induced cardiotoxicity. The wide coverage in target, pathway, assay, and cell phenotype has made RWG systems powerful tool in both basic research and early drug discovery process.

  15. A high-throughput, homogeneous microplate assay for agents that kill mammalian tissue culture cells.

    Science.gov (United States)

    Pierce, Michael; Wang, Chunwei; Rebentisch, Matt; Endo, Mark; Stump, Mark; Kamb, Alexander

    2003-06-01

    Screens for cytostasis/cytoxicity have considerable value for the discovery of therapeutic agents and the investigation of the biology of apoptosis. For instance, genetic screens for proteins, protein fragments, peptides, RNAs, or chemicals that kill tissue culture cells may aid in identifying new cancer therapeutic targets. A microplate assay for cell death is needed to achieve throughputs sufficient to sift through thousands of agents from expression or chemical libraries. The authors describe a homogeneous assay for cell death in tissue culture cells compatible with 96- or 384-well plates. In combination with a previously described system for retroviral packaging and transduction, nearly 6000 expression library clones could be screened per week in a 96-well plate format. The screening system may also prove useful for chemical screens.

  16. A High-Throughput Small Molecule Screen for C. elegans Linker Cell Death Inhibitors.

    Science.gov (United States)

    Schwendeman, Andrew R; Shaham, Shai

    2016-01-01

    Programmed cell death is a ubiquitous process in metazoan development. Apoptosis, one cell death form, has been studied extensively. However, mutations inactivating key mammalian apoptosis regulators do not block most developmental cell culling, suggesting that other cell death pathways are likely important. Recent work in the nematode Caenorhabditis elegans identified a non-apoptotic cell death form mediating the demise of the male-specific linker cell. This cell death process (LCD, linker cell-type death) is morphologically conserved, and its molecular effectors also mediate axon degeneration in mammals and Drosophila. To develop reagents to manipulate LCD, we established a simple high-throughput screening protocol for interrogating the effects of small molecules on C. elegans linker cell death in vivo. From 23,797 compounds assayed, 11 reproducibly block linker cell death onset. Of these, five induce animal lethality, and six promote a reversible developmental delay. These results provide proof-of principle validation of our screening protocol, demonstrate that developmental progression is required for linker cell death, and suggest that larger scale screens may identify LCD-specific small-molecule regulators that target the LCD execution machinery.

  17. Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle.

    Science.gov (United States)

    Gibbs, David L; Shmulevich, Ilya

    2017-06-01

    The Influence Maximization Problem (IMP) aims to discover the set of nodes with the greatest influence on network dynamics. The problem has previously been applied in epidemiology and social network analysis. Here, we demonstrate the application to cell cycle regulatory network analysis for Saccharomyces cerevisiae. Fundamentally, gene regulation is linked to the flow of information. Therefore, our implementation of the IMP was framed as an information theoretic problem using network diffusion. Utilizing more than 26,000 regulatory edges from YeastMine, gene expression dynamics were encoded as edge weights using time lagged transfer entropy, a method for quantifying information transfer between variables. By picking a set of source nodes, a diffusion process covers a portion of the network. The size of the network cover relates to the influence of the source nodes. The set of nodes that maximizes influence is the solution to the IMP. By solving the IMP over different numbers of source nodes, an influence ranking on genes was produced. The influence ranking was compared to other metrics of network centrality. Although the top genes from each centrality ranking contained well-known cell cycle regulators, there was little agreement and no clear winner. However, it was found that influential genes tend to directly regulate or sit upstream of genes ranked by other centrality measures. The influential nodes act as critical sources of information flow, potentially having a large impact on the state of the network. Biological events that affect influential nodes and thereby affect information flow could have a strong effect on network dynamics, potentially leading to disease. Code and data can be found at: https://github.com/gibbsdavidl/miergolf.

  18. Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle.

    Directory of Open Access Journals (Sweden)

    David L Gibbs

    2017-06-01

    Full Text Available The Influence Maximization Problem (IMP aims to discover the set of nodes with the greatest influence on network dynamics. The problem has previously been applied in epidemiology and social network analysis. Here, we demonstrate the application to cell cycle regulatory network analysis for Saccharomyces cerevisiae. Fundamentally, gene regulation is linked to the flow of information. Therefore, our implementation of the IMP was framed as an information theoretic problem using network diffusion. Utilizing more than 26,000 regulatory edges from YeastMine, gene expression dynamics were encoded as edge weights using time lagged transfer entropy, a method for quantifying information transfer between variables. By picking a set of source nodes, a diffusion process covers a portion of the network. The size of the network cover relates to the influence of the source nodes. The set of nodes that maximizes influence is the solution to the IMP. By solving the IMP over different numbers of source nodes, an influence ranking on genes was produced. The influence ranking was compared to other metrics of network centrality. Although the top genes from each centrality ranking contained well-known cell cycle regulators, there was little agreement and no clear winner. However, it was found that influential genes tend to directly regulate or sit upstream of genes ranked by other centrality measures. The influential nodes act as critical sources of information flow, potentially having a large impact on the state of the network. Biological events that affect influential nodes and thereby affect information flow could have a strong effect on network dynamics, potentially leading to disease. Code and data can be found at: https://github.com/gibbsdavidl/miergolf.

  19. Continuous high throughput molecular adhesion based cell sorting using ridged microchannels

    Science.gov (United States)

    Tasadduq, Bushra; Wang, Gonghao; Alexeev, Alexander; Sarioglu, Ali Fatih; Sulchek, Todd

    2016-11-01

    Cell molecular interactions govern important physiological processes such as stem cell homing, inflammation and cancer metastasis. But due to a lack of effective separation technologies selective to these interactions it is challenging to specifically sort cells. Other label free separation techniques based on size, stiffness and shape do not provide enough specificity to cell type, and correlation to clinical condition. We propose a novel microfluidic device capable of high throughput molecule dependent separation of cells by flowing them through a microchannel decorated with molecule specific coated ridges. The unique aspect of this sorting design is the use of optimized gap size which is small enough to lightly squeeze the cells while flowing under the ridged part of the channel to increase the surface area for interaction between the ligand on cell surface and coated receptor molecule but large enough so that biomechanical markers, stiffness and viscoelasticity, do not dominate the cell separation mechanism. We are able to separate Jurkat cells based on its expression of PSGL-1ligand using ridged channel coated with P selectin at a flow rate of 0.045ml/min and achieve 2-fold and 5-fold enrichment of PSGL-1 positive and negative Jurkat cells respectively.

  20. Noninvasive High-Throughput Single-Cell Analysis of HIV Protease Activity Using Ratiometric Flow Cytometry

    Science.gov (United States)

    Gaber, Rok; Majerle, Andreja; Jerala, Roman; Benčina, Mojca

    2013-01-01

    To effectively fight against the human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) epidemic, ongoing development of novel HIV protease inhibitors is required. Inexpensive high-throughput screening assays are needed to quickly scan large sets of chemicals for potential inhibitors. We have developed a Förster resonance energy transfer (FRET)-based, HIV protease-sensitive sensor using a combination of a fluorescent protein pair, namely mCerulean and mCitrine. Through extensive in vitro characterization, we show that the FRET-HIV sensor can be used in HIV protease screening assays. Furthermore, we have used the FRET-HIV sensor for intracellular quantitative detection of HIV protease activity in living cells, which more closely resembles an actual viral infection than an in vitro assay. We have developed a high-throughput method that employs a ratiometric flow cytometry for analyzing large populations of cells that express the FRET-HIV sensor. The method enables FRET measurement of single cells with high sensitivity and speed and should be used when subpopulation-specific intracellular activity of HIV protease needs to be estimated. In addition, we have used a confocal microscopy sensitized emission FRET technique to evaluate the usefulness of the FRET-HIV sensor for spatiotemporal detection of intracellular HIV protease activity. PMID:24287545

  1. Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.

    Science.gov (United States)

    Kamentsky, Lee; Jones, Thouis R; Fraser, Adam; Bray, Mark-Anthony; Logan, David J; Madden, Katherine L; Ljosa, Vebjorn; Rueden, Curtis; Eliceiri, Kevin W; Carpenter, Anne E

    2011-04-15

    There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been engineered to meet the needs of its growing user base. It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work. ImageJ plugins can now be run within a CellProfiler pipeline. CellProfiler 2.0 is free and open source, available at http://www.cellprofiler.org under the GPL v. 2 license. It is available as a packaged application for Macintosh OS X and Microsoft Windows and can be compiled for Linux. anne@broadinstitute.org Supplementary data are available at Bioinformatics online.

  2. High-throughput linear optical stretcher for mechanical characterization of blood cells.

    Science.gov (United States)

    Roth, Kevin B; Neeves, Keith B; Squier, Jeff; Marr, David W M

    2016-04-01

    This study describes a linear optical stretcher as a high-throughput mechanical property cytometer. Custom, inexpensive, and scalable optics image a linear diode bar source into a microfluidic channel, where cells are hydrodynamically focused into the optical stretcher. Upon entering the stretching region, antipodal optical forces generated by the refraction of tightly focused laser light at the cell membrane deform each cell in flow. Each cell relaxes as it flows out of the trap and is compared to the stretched state to determine deformation. The deformation response of untreated red blood cells and neutrophils were compared to chemically treated cells. Statistically significant differences were observed between normal, diamide-treated, and glutaraldehyde-treated red blood cells, as well as between normal and cytochalasin D-treated neutrophils. Based on the behavior of the pure, untreated populations of red cells and neutrophils, a mixed population of these cells was tested and the discrete populations were identified by deformability. © 2015 International Society for Advancement of Cytometry. © 2015 International Society for Advancement of Cytometry.

  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 10 to 20 mAcm(2). 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 150 mAcm(2), respectively.

  4. Identification of fluorescent compounds with non-specific binding property via high throughput live cell microscopy.

    Directory of Open Access Journals (Sweden)

    Sangeeta Nath

    Full Text Available INTRODUCTION: Compounds exhibiting low non-specific intracellular binding or non-stickiness are concomitant with rapid clearing and in high demand for live-cell imaging assays because they allow for intracellular receptor localization with a high signal/noise ratio. The non-stickiness property is particularly important for imaging intracellular receptors due to the equilibria involved. METHOD: Three mammalian cell lines with diverse genetic backgrounds were used to screen a combinatorial fluorescence library via high throughput live cell microscopy for potential ligands with high in- and out-flux properties. The binding properties of ligands identified from the first screen were subsequently validated on plant root hair. A correlative analysis was then performed between each ligand and its corresponding physiochemical and structural properties. RESULTS: The non-stickiness property of each ligand was quantified as a function of the temporal uptake and retention on a cell-by-cell basis. Our data shows that (i mammalian systems can serve as a pre-screening tool for complex plant species that are not amenable to high-throughput imaging; (ii retention and spatial localization of chemical compounds vary within and between each cell line; and (iii the structural similarities of compounds can infer their non-specific binding properties. CONCLUSION: We have validated a protocol for identifying chemical compounds with non-specific binding properties that is testable across diverse species. Further analysis reveals an overlap between the non-stickiness property and the structural similarity of compounds. The net result is a more robust screening assay for identifying desirable ligands that can be used to monitor intracellular localization. Several new applications of the screening protocol and results are also presented.

  5. Do Multiwell Plate High Throughput Assays Measure Loss of Cell Viability Following Exposure to Genotoxic Agents?

    Directory of Open Access Journals (Sweden)

    Razmik Mirzayans

    2017-08-01

    Full Text Available Cell-based assays in multiwell plates are widely used for radiosensitivity and chemosensitivity assessment with different mammalian cell types. Despite their relative ease of performance, such assays lack specificity as they do not distinguish between the cytostatic (reversible/sustained growth arrest and cytotoxic (loss of viability effects of genotoxic agents. We recently reported studies with solid tumor-derived cell lines demonstrating that radiosensitivity as measured by multiwell plate colorimetric (e.g., XTT and fluorimetric (e.g., CellTiter-Blue assays reflects growth arrest but not loss of viability. Herein we report similar observations with cancer cell lines expressing wild-type p53 (A549 lung carcinoma or mutant p53 (MDA–MB-231 breast carcinoma after treatment with the chemotherapeutic drug cisplatin. Importantly, we show that treatment of cancer cells with concentrations of cisplatin that result in 50% effect (i.e., IC50 in multiwell plate assays trigger the emergence of growth arrested cells that exhibit highly enlarged morphology, remain viable and adherent to the culture dish, and metabolize the tetrazolium salt 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyl-tetrazolium bromide (MTT to its formazan derivative. The emergence of markedly enlarged viable cells complicates the interpretation of chemosensitivity data obtained with multiwell plate high throughput assays. Relying solely on IC50 values could be misleading.

  6. Optimisation of insect cell growth in deep-well blocks: development of a high-throughput insect cell expression screen.

    Science.gov (United States)

    Bahia, Daljit; Cheung, Robert; Buchs, Mirjam; Geisse, Sabine; Hunt, Ian

    2005-01-01

    This report describes a method to culture insects cells in 24 deep-well blocks for the routine small-scale optimisation of baculovirus-mediated protein expression experiments. Miniaturisation of this process provides the necessary reduction in terms of resource allocation, reagents, and labour to allow extensive and rapid optimisation of expression conditions, with the concomitant reduction in lead-time before commencement of large-scale bioreactor experiments. This therefore greatly simplifies the optimisation process and allows the use of liquid handling robotics in much of the initial optimisation stages of the process, thereby greatly increasing the throughput of the laboratory. We present several examples of the use of deep-well block expression studies in the optimisation of therapeutically relevant protein targets. We also discuss how the enhanced throughput offered by this approach can be adapted to robotic handling systems and the implications this has on the capacity to conduct multi-parallel protein expression studies.

  7. One-Step Seeding of Neural Stem Cells with Vitronectin-Supplemented Medium for High-Throughput Screening Assays.

    Science.gov (United States)

    Dai, Sheng; Li, Rong; Long, Yan; Titus, Steve; Zhao, Jinghua; Huang, Ruili; Xia, Menghang; Zheng, Wei

    2016-12-01

    Human neuronal cells differentiated from induced pluripotent cells have emerged as a new model system for the study of disease pathophysiology and evaluation of drug efficacy. Differentiated neuronal cells are more similar in genetics and biological content to human brain cells than other animal disease models. However, culture of neuronal cells in assay plates requires a labor-intensive procedure of plate precoating, hampering its applications in high-throughput screening (HTS). We developed a simplified method with one-step seeding of neural stem cells in assay plates by supplementing the medium with a recombinant human vitronectin (VTN), thus avoiding plate precoating. Robust results were obtained from cell viability, calcium response, and neurite outgrowth assays using this new method. Our data demonstrate that this approach greatly simplifies high-throughput assays using neuronal cells differentiated from human stem cells for translational research.

  8. A High-Throughput Mechanofluidic Screening Platform for Investigating Tumor Cell Adhesion During Metastasis†

    Science.gov (United States)

    Spencer, A.; Spruell, C.; Nandi, S.; Wong, M.; Crexiell, M.; Baker, A. B.

    2015-01-01

    The metastatic spread of cancer is a major barrier to effective and curative therapies for cancer. During metastasis, tumor cells intravasate into the vascular system, survive in the shear forces and immunological environment of the circulation, and then extravasate into secondary tumor sites. Biophysical forces are potent regulators of cancer biology and are key in many of the steps of metastasis. In particular, the adhesion of circulating cells is highly dependent upon competing forces between cell adhesion receptors and the shear stresses due to fluid flow. Conventional in vitro assays for drug development and the mechanistic study of metastasis are often carried out in the absence of fluidic forces and, consequently, are poorly representative of the true biology of metastasis. Here, we present a novel high-throughput approach to studying cell adhesion under flow that uses a multi-well, mechanofluidic flow system to interrogate adhesion of cancer cell to endothelial cells, extracellular matrix and platelets under physiological shear stresses. We use this system to identify pathways and compounds that can potentially be used to inhibit cancer adhesion under flow by screening anti-inflammatory compounds, integrin inhibitors and a kinase inhibitor library. In particular, we identify several small molecule inhibitors of FLT-3 and AKT that are potent inhibitors of cancer cell adhesion to endothelial cells and platelets under flow. In addition, we found that many kinase inhibitors lead to increased adhesion of cancer cells in flow-based but not static assays. This finding suggests that even compounds that reduce cell proliferation might also enhance cancer cell adhesion during metastasis. Overall, our results validate a novel platform for investigating the mechanisms of cell adhesion under biophysical flow conditions and identify several potential inhibitors of cancer cell adhesion during metastasis. PMID:26584160

  9. 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

  10. Electrofusion of cells on chip - From a static, parallel approach to a high-throughput, serial, microdroplet platform

    NARCIS (Netherlands)

    Kemna, Evelien

    2013-01-01

    In this thesis, the results of the development of two microfluidic devices (static and high-throughput) for efficient electrofucion of cells were described and evaulated. Electrofusion of cells is an important tool for generating antibody producing hybridomas. The hybridomas are the result of the

  11. High-throughput sorting of the highest producing cell via a transiently protein-anchored system.

    Directory of Open Access Journals (Sweden)

    Kuo-Hsiang Chuang

    Full Text Available Developing a high-throughput method for the effecient selection of the highest producing cell is very important for the production of recombinant protein drugs. Here, we developed a novel transiently protein-anchored system coupled with fluorescence activated cell sorting (FACS for the efficient selection of the highest producing cell. A furin cleavage peptide (RAKR was used to join a human anti-epithelial growth factor antibody (αEGFR Ab and the extracellular-transmembrane-cytosolic domains of the mouse B7-1 antigen (B7. The furin inhibitor can transiently switch secreted αEGFR Ab into a membrane-anchored form. After cell sorting, the level of membrane αEGFR Ab-RAKR-B7 is proportional to the amount of secreted αEGFR Ab in the medium. We further selected 23 αEGFR Ab expressing cells and demonstrated a high correlation (R2 = 0.9165 between the secretion level and surface expression levels of αEGFR Ab. These results suggested that the novel transiently protein-anchored system can easily and efficiently select the highest producing cells, reducing the cost for the production of biopharmaceuticals.

  12. Combinatorial approach toward high-throughput analysis of direct methanol fuel cells.

    Science.gov (United States)

    Jiang, Rongzhong; Rong, Charles; Chu, Deryn

    2005-01-01

    A 40-member array of direct methanol fuel cells (with stationary fuel and convective air supplies) was generated by electrically connecting the fuel cells in series. High-throughput analysis of these fuel cells was realized by fast screening of voltages between the two terminals of a fuel cell at constant current discharge. A large number of voltage-current curves (200) were obtained by screening the voltages through multiple small-current steps. Gaussian distribution was used to statistically analyze the large number of experimental data. The standard deviation (sigma) of voltages of these fuel cells increased linearly with discharge current. The voltage-current curves at various fuel concentrations were simulated with an empirical equation of voltage versus current and a linear equation of sigma versus current. The simulated voltage-current curves fitted the experimental data well. With increasing methanol concentration from 0.5 to 4.0 M, the Tafel slope of the voltage-current curves (at sigma=0.0), changed from 28 to 91 mV.dec-1, the cell resistance from 2.91 to 0.18 Omega, and the power output from 3 to 18 mW.cm-2.

  13. Quantitative Live-Cell Confocal Imaging of 3D Spheroids in a High-Throughput Format.

    Science.gov (United States)

    Leary, Elizabeth; Rhee, Claire; Wilks, Benjamin T; Morgan, Jeffrey R

    2018-02-01

    Accurately predicting the human response to new compounds is critical to a wide variety of industries. Standard screening pipelines (including both in vitro and in vivo models) often lack predictive power. Three-dimensional (3D) culture systems of human cells, a more physiologically relevant platform, could provide a high-throughput, automated means to test the efficacy and/or toxicity of novel substances. However, the challenge of obtaining high-magnification, confocal z stacks of 3D spheroids and understanding their respective quantitative limitations must be overcome first. To address this challenge, we developed a method to form spheroids of reproducible size at precise spatial locations across a 96-well plate. Spheroids of variable radii were labeled with four different fluorescent dyes and imaged with a high-throughput confocal microscope. 3D renderings of the spheroid had a complex bowl-like appearance. We systematically analyzed these confocal z stacks to determine the depth of imaging and the effect of spheroid size and dyes on quantitation. Furthermore, we have shown that this loss of fluorescence can be addressed through the use of ratio imaging. Overall, understanding both the limitations of confocal imaging and the tools to correct for these limits is critical for developing accurate quantitative assays using 3D spheroids.

  14. Use of flow cytometry for high-throughput cell population estimates in fixed brain tissue

    Directory of Open Access Journals (Sweden)

    Nicole A Young

    2012-07-01

    Full Text Available The numbers and types of cells in an area of cortex define its function. Therefore it is essential to characterize the numbers and distributions of total cells in areas of the cortex, as well as to identify numbers of subclasses of neurons and glial cells. To date, the large size of the primate brain and the lack of innovation in cell counting methods have been a roadblock to obtaining high-resolution maps of cell and neuron density across the cortex in humans and non-human primates. Stereological counting methods and the isotropic fractionator are valuable tools for estimating cell numbers, but are better suited to smaller, well-defined brain structures or to cortex as a whole. In the present study, we have extended our flow-cytometry based counting method, the flow fractionator (Collins et al., 2010a, to include high-throughput total cell population estimates in homogenized cortical samples. We demonstrate that our method produces consistent, accurate and repeatable cell estimates quickly. The estimates we report are in excellent agreement with estimates for the same samples obtained using a Neubauer chamber and a fluorescence microscope. We show that our flow cytometry-based method for total cell estimation in homogenized brain tissue is more efficient and more precise than manual counting methods. The addition of automated nuclei counting to our flow fractionator method allows for a fully automated, rapid characterization of total cells and neuronal and non-neuronal populations in human and non-human primate brains, providing valuable data to further our understanding of the functional organization of normal, aging and diseased brains.

  15. 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.

  16. High throughput, non-invasive and dynamic toxicity screening on adherent cells using respiratory measurements.

    Science.gov (United States)

    Beckers, Simone; Noor, Fozia; Müller-Vieira, Ursula; Mayer, Manuela; Strigun, Alexander; Heinzle, Elmar

    2010-03-01

    A dynamic respiration assay based on luminescence decay time detection of oxygen for high throughput toxicological assessment is presented. The method uses 24-well plates (OxoDishes) read with the help of a sensor dish reader placed in a humidified CO(2)-incubator. Adherent primary rat hepatocytes and the human hepatic cell line Hep G2 were exposed to known toxic compounds. Dissolved oxygen concentration, a measure of respiration, was measured with an oxygen sensor optode immobilized in the centre of each well. The cells were maintained in the dishes during the assay period and can afterwards be processed for further analyses. This dynamic, non-invasive measurement allowed calculation of 50% lethal concentrations (LC(50)) for any incubation time point giving concentration-time-dependent responses without further manipulation or removal of the cells from the incubator. Toxicokinetic profiles are compared with Sulforhodamine B assay, a common cytotoxicity assay. The novel assay is robust and flexible, very easy to carry out and provides continuous online respiration data reflecting dynamic toxicity responses. It can be adapted to any cell-based system and the calculated kinetics contributes to understanding of cell death mechanisms. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  17. Hepatic differentiation of human pluripotent stem cells in miniaturized format suitable for high-throughput screen

    Directory of Open Access Journals (Sweden)

    Arnaud Carpentier

    2016-05-01

    Full Text Available The establishment of protocols to differentiate human pluripotent stem cells (hPSCs including embryonic (ESC and induced pluripotent (iPSC stem cells into functional hepatocyte-like cells (HLCs creates new opportunities to study liver metabolism, genetic diseases and infection of hepatotropic viruses (hepatitis B and C viruses in the context of specific genetic background. While supporting efficient differentiation to HLCs, the published protocols are limited in terms of differentiation into fully mature hepatocytes and in a smaller-well format. This limitation handicaps the application of these cells to high-throughput assays. Here we describe a protocol allowing efficient and consistent hepatic differentiation of hPSCs in 384-well plates into functional hepatocyte-like cells, which remain differentiated for more than 3 weeks. This protocol affords the unique opportunity to miniaturize the hPSC-based differentiation technology and facilitates screening for molecules in modulating liver differentiation, metabolism, genetic network, and response to infection or other external stimuli.

  18. High-throughput miniaturized bioreactors for cell culture process development: reproducibility, scalability, and control.

    Science.gov (United States)

    Rameez, Shahid; Mostafa, Sigma S; Miller, Christopher; Shukla, Abhinav A

    2014-01-01

    Decreasing the timeframe for cell culture process development has been a key goal toward accelerating biopharmaceutical development. Advanced Microscale Bioreactors (ambr™) is an automated micro-bioreactor system with miniature single-use bioreactors with a 10-15 mL working volume controlled by an automated workstation. This system was compared to conventional bioreactor systems in terms of its performance for the production of a monoclonal antibody in a recombinant Chinese Hamster Ovary cell line. The miniaturized bioreactor system was found to produce cell culture profiles that matched across scales to 3 L, 15 L, and 200 L stirred tank bioreactors. The processes used in this article involve complex feed formulations, perturbations, and strict process control within the design space, which are in-line with processes used for commercial scale manufacturing of biopharmaceuticals. Changes to important process parameters in ambr™ resulted in predictable cell growth, viability and titer changes, which were in good agreement to data from the conventional larger scale bioreactors. ambr™ was found to successfully reproduce variations in temperature, dissolved oxygen (DO), and pH conditions similar to the larger bioreactor systems. Additionally, the miniature bioreactors were found to react well to perturbations in pH and DO through adjustments to the Proportional and Integral control loop. The data presented here demonstrates the utility of the ambr™ system as a high throughput system for cell culture process development. © 2014 American Institute of Chemical Engineers.

  19. Treatability studies on different refinery wastewater samples using high-throughput microbial electrolysis cells (MECs)

    KAUST Repository

    Ren, Lijiao

    2013-05-01

    High-throughput microbial electrolysis cells (MECs) were used to perform treatability studies on many different refinery wastewater samples all having appreciably different characteristics, which resulted in large differences in current generation. A de-oiled refinery wastewater sample from one site (DOW1) produced the best results, with 2.1±0.2A/m2 (maximum current density), 79% chemical oxygen demand removal, and 82% headspace biological oxygen demand removal. These results were similar to those obtained using domestic wastewater. Two other de-oiled refinery wastewater samples also showed good performance, with a de-oiled oily sewer sample producing less current. A stabilization lagoon sample and a stripped sour wastewater sample failed to produce appreciable current. Electricity production, organics removal, and startup time were improved when the anode was first acclimated to domestic wastewater. These results show mini-MECs are an effective method for evaluating treatability of different wastewaters. © 2013 Elsevier Ltd.

  20. Can Full Duplex Boost Throughput and Delay of 5G Ultra-Dense Small Cell Networks?

    DEFF Research Database (Denmark)

    Gatnau, Marta; Berardinelli, Gilberto; Mahmood, Nurul Huda

    2016-01-01

    Given the recent advances in system and antenna design, practical implementation of full duplex (FD) communication is becoming increasingly feasible. In this paper, the potential of FD in enhancing the performance of 5th generation (5G) ultra-dense small cell networks is investigated. The goal...... is to understand whether FD is able to boost the system performance from a throughput and delay perspective. The impact of having symmetric and asymmetric finite buffer traffic is studied for two types of FD: when only the base station is FD capable, and when both the user equipment and base station are FD nodes....... System level results indicate that there is a trade-off between multiple-input multiple-output (MIMO) spatial multiplexing and FD in achieving the optimal system performance. Moreover, results show that FD may be useful for asymmetric traffic applications where the lightly loaded link requires high level...

  1. Soft inertial microfluidics for high throughput separation of bacteria from human blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Zhigang; Willing, Ben; Bjerketorp, Joakim; Jansson, Janet K.; Hjort, Klas

    2009-01-05

    We developed a new approach to separate bacteria from human blood cells based on soft inertial force induced migration with flow defined curved and focused sample flow inside a microfluidic device. This approach relies on a combination of an asymmetrical sheath flow and proper channel geometry to generate a soft inertial force on the sample fluid in the curved and focused sample flow segment to deflect larger particles away while the smaller ones are kept on or near the original flow streamline. The curved and focused sample flow and inertial effect were visualized and verified using a fluorescent dye primed in the device. First the particle behavior was studied in detail using 9.9 and 1.0 {micro}m particles with a polymer-based prototype. The prototype device is compact with an active size of 3 mm{sup 2}. The soft inertial effect and deflection distance were proportional to the fluid Reynolds number (Re) and particle Reynolds number (Re{sub p}), respectively. We successfully demonstrated separation of bacteria (Escherichia coli) from human red blood cells at high cell concentrations (above 10{sup 8}/mL), using a sample flow rate of up to 18 {micro}L/min. This resulted in at least a 300-fold enrichment of bacteria at a wide range of flow rates with a controlled flow spreading. The separated cells were proven to be viable. Proteins from fractions before and after cell separation were analyzed by gel electrophoresis and staining to verify the removal of red blood cell proteins from the bacterial cell fraction. This novel microfluidic process is robust, reproducible, simple to perform, and has a high throughput compared to other cell sorting systems. Microfluidic systems based on these principles could easily be manufactured for clinical laboratory and biomedical applications.

  2. High-Throughput Cryopreservation of Plant Cell Cultures for Functional Genomics

    Science.gov (United States)

    Ogawa, Yoichi; Sakurai, Nozomu; Oikawa, Akira; Kai, Kosuke; Morishita, Yoshihiko; Mori, Kumiko; Moriya, Kanami; Fujii, Fumiko; Aoki, Koh; Suzuki, Hideyuki; Ohta, Daisaku; Saito, Kazuki; Shibata, Daisuke

    2012-01-01

    Suspension-cultured cell lines from plant species are useful for genetic engineering. However, maintenance of these lines is laborious, involves routine subculturing and hampers wider use of transgenic lines, especially when many lines are required for a high-throughput functional genomics application. Cryopreservation of these lines may reduce the need for subculturing. Here, we established a simple protocol for cryopreservation of cell lines from five commonly used plant species, Arabidopsis thaliana, Daucus carota, Lotus japonicus, Nicotiana tabacum and Oryza sativa. The LSP solution (2 M glycerol, 0.4 M sucrose and 86.9 mM proline) protected cells from damage during freezing and was only mildly toxic to cells kept at room temperature for at least 2 h. More than 100 samples were processed for freezing simultaneously. Initially, we determined the conditions for cryopreservation using a programmable freezer; we then developed a modified simple protocol that did not require a programmable freezer. In the simple protocol, a thick expanded polystyrene (EPS) container containing the vials with the cell–LSP solution mixtures was kept at −30°C for 6 h to cool the cells slowly (pre-freezing); samples from the EPS containers were then plunged into liquid nitrogen before long-term storage. Transgenic Arabidopsis cells were subjected to cryopreservation, thawed and then re-grown in culture; transcriptome and metabolome analyses indicated that there was no significant difference in gene expression or metabolism between cryopreserved cells and control cells. The simplicity of the protocol will accelerate the pace of research in functional plant genomics. PMID:22437846

  3. FIREWACh: High-throughput Functional Detection of Transcriptional Regulatory Modules in Mammalian Cells

    Science.gov (United States)

    Murtha, Matthew; Tokcaer-Keskin, Zeynep; Tang, Zuojian; Strino, Francesco; Chen, Xi; Wang, Yatong; Xi, Xiangmei; Basilico, Claudio; Brown, Stuart; Bonneau, Richard; Kluger, Yuval; Dailey, Lisa

    2014-01-01

    Promoters and enhancers establish precise gene transcription patterns. The development of functional approaches for their identification in mammalian cells has been complicated by the size of these genomes. Here we report a new method called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), a high-throughput functional assay for directly identifying active promoter and enhancer elements. FIREWACh simultaneously assessed over 80,000 DNA fragments derived from “nucleosome-free regions” within embryonic stem cell (ESC) chromatin to identify 6,364 new active regulatory elements. Many FIREWACh DNAs represent newly discovered ESC-specific enhancers and their analyses identified enriched binding site motifs for ESC transcription factors including SOX2, OCT4 (POU5f1), and KLF4. Thus FIREWACh identifies endogenous regulators of gene expression and can be used for the discovery of key cell-specific transcription factors. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics. PMID:24658142

  4. High-Throughput Screening of Myxoid Liposarcoma Cell Lines: Survivin Is Essential for Tumor Growth

    Directory of Open Access Journals (Sweden)

    Marieke A. de Graaff

    2017-08-01

    Full Text Available Myxoid liposarcoma (MLS is a soft tissue sarcoma characterized by a recurrent t(12;16 translocation. Although tumors are initially radio- and chemosensitive, the management of inoperable or metastatic MLS can be challenging. Therefore, our aim was to identify novel targets for systemic therapy. We performed an in vitro high-throughput drug screen using three MLS cell lines (402091, 1765092, DL-221, which were treated with 273 different drugs at four different concentrations. Cell lines and tissue microarrays were used for validation. As expected, all cell lines revealed a strong growth inhibition to conventional chemotherapeutic agents, such as anthracyclines and taxanes. A good response was observed to compounds interfering with Src and the mTOR pathway, which are known to be affected in these tumors. Moreover, BIRC5 was important for MLS survival because a strong inhibitory effect was seen at low concentration using the survivin inhibitor YM155, and siRNA for BIRC5 decreased cell viability. Immunohistochemistry revealed abundant expression of survivin restricted to the nucleus in all 32 tested primary tumor specimens. Inhibition of survivin in 402-91 and 1765-92 by YM155 increased the percentage S-phase but did not induce apoptosis, which warrants further investigation before application in the treatment of metastatic MLS. Thus, using a 273-compound drug screen, we confirmed previously identified targets (mTOR, Src in MLS and demonstrate survivin as essential for MLS survival.

  5. A Mammalian Retinal Ganglion Cell Implements a Neuronal Computation That Maximizes the SNR of Its Postsynaptic Currents.

    Science.gov (United States)

    Homann, Jan; Freed, Michael A

    2017-02-08

    Neurons perform computations by integrating excitatory and inhibitory synaptic inputs. Yet, it is rarely understood what computation is being performed, or how much excitation or inhibition this computation requires. Here we present evidence for a neuronal computation that maximizes the signal-to-noise power ratio (SNR). We recorded from OFF delta retinal ganglion cells in the guinea pig retina and monitored synaptic currents that were evoked by visual stimulation (flashing dark spots). These synaptic currents were mediated by a decrease in an outward current from inhibitory synapses (disinhibition) combined with an increase in an inward current from excitatory synapses. We found that the SNR of combined excitatory and disinhibitory currents was voltage sensitive, peaking at membrane potentials near resting potential. At the membrane potential for maximal SNR, the amplitude of each current, either excitatory or disinhibitory, was proportional to its SNR. Such proportionate scaling is the theoretically best strategy for combining excitatory and disinhibitory currents to maximize the SNR of their combined current. Moreover, as spot size or contrast changed, the amplitudes of excitatory and disinhibitory currents also changed but remained in proportion to their SNRs, indicating a dynamic rebalancing of excitatory and inhibitory currents to maximize SNR.SIGNIFICANCE STATEMENT We present evidence that the balance of excitatory and disinhibitory inputs to a type of retinal ganglion cell maximizes the signal-to-noise ratio power ratio (SNR) of its postsynaptic currents. This is significant because chemical synapses on a retinal ganglion cell require the probabilistic release of transmitter. Consequently, when the same visual stimulus is presented repeatedly, postsynaptic currents vary in amplitude. Thus, maximizing SNR may be a strategy for producing the most reliable signal possible given the inherent unreliability of synaptic transmission. Copyright © 2017 the authors

  6. A sandwiched microarray platform for benchtop cell-based high throughput screening.

    Science.gov (United States)

    Wu, Jinhui; Wheeldon, Ian; Guo, Yuqi; Lu, Tingli; Du, Yanan; Wang, Ben; He, Jiankang; Hu, Yiqiao; Khademhosseini, Ali

    2011-01-01

    The emergence of combinatorial chemistries and the increased discovery of natural compounds have led to the production of expansive libraries of drug candidates and vast numbers of compounds with potentially interesting biological activities. Despite broad interest in high throughput screening (HTS) across varied fields of biological research, there has not been an increase in accessible HTS technologies. Here, we present a simple microarray sandwich system suitable for screening chemical libraries in cell-based assays at the benchtop. The microarray platform delivers chemical compounds to isolated cell cultures by 'sandwiching' chemical-laden arrayed posts with cell-seeded microwells. In this way, an array of sealed cell-based assays was generated without cross-contamination between neighbouring assays. After chemical exposure, cell viability was analyzed by fluorescence detection of cell viability assays on a per microwell basis using a standard microarray scanner. We demonstrate the efficacy of the system by generating four hits from toxicology screens towards MCF-7 human breast cancer cells. Three of the hits were identified in a combinatorial screen of a library of natural compounds in combination with verapamil, a P-glycoprotein inhibitor. A fourth hit, 9-methoxy-camptothecin, was identified by screening the natural compound library in the absence of verapamil. The method developed here miniaturizes existing HTS systems and enables the screening of a wide array of individual or combinatorial libraries in a reproducible and scalable manner. We anticipate broad application of such a system as it is amenable to combinatorial drug screening in a simple, robust and portable platform. Copyright © 2010 Elsevier Ltd. All rights reserved.

  7. High-Throughput Separation of White Blood Cells From Whole Blood Using Inertial Microfluidics.

    Science.gov (United States)

    Zhang, Jun; Yuan, Dan; Sluyter, Ronald; Yan, Sheng; Zhao, Qianbin; Xia, Huanming; Tan, Say Hwa; Nguyen, Nam-Trung; Li, Weihua

    2017-08-29

    White blood cells (WBCs) constitute only about 0.1% of human blood cells, yet contain rich information about the immune status of the body; thus, separation of WBCs from the whole blood is an indispensable and critical sample preparation step in many scientific, clinical, and diagnostic applications. In this paper, we developed a continuous and high-throughput microfluidic WBC separation platform utilizing the differential inertial focusing of particles in serpentine microchannels. First, separation performance of the proposed method is characterized and evaluated using polystyrene beads in the serpentine channel. The purity of 10-μm polystyrene beads is increased from 0.1% to 80.3% after two cascaded processes, with an average enrichment ratio of 28 times. Next, we investigated focusing and separation properties of Jurkat cells spiked in the blood to mimic the presence of WBCs in whole blood. Finally, separation of WBCs from human whole blood was conducted and separation purity of WBCs was measured by the flow cytometry. The results show that the purity of WBCs can be increased to 48% after two consecutive processes, with an average enrichment ratio of ten times. Meanwhile, a parallelized inertial microfluidic device was designed to provide a high processing flow rate of 288 ml/h for the diluted (×1/20) whole blood. The proposed microfluidic device can potentially work as an upstream component for blood sample preparation and analysis in the integrated microfluidic systems.

  8. A method for high throughput bioelectrochemical research based on small scale microbial electrolysis cells

    KAUST Repository

    Call, Douglas F.

    2011-07-01

    There is great interest in studying exoelectrogenic microorganisms, but existing methods can require expensive electrochemical equipment and specialized reactors. We developed a simple system for conducting high throughput bioelectrochemical research using multiple inexpensive microbial electrolysis cells (MECs) built with commercially available materials and operated using a single power source. MECs were small crimp top serum bottles (5mL) with a graphite plate anode (92m 2/m 3) and a cathode of stainless steel (SS) mesh (86m 2/m 3), graphite plate, SS wire, or platinum wire. The highest volumetric current density (240A/m 3, applied potential of 0.7V) was obtained using a SS mesh cathode and a wastewater inoculum (acetate electron donor). Parallel operated MECs (single power source) did not lead to differences in performance compared to non-parallel operated MECs, which can allow for high throughput reactor operation (>1000 reactors) using a single power supply. The utility of this method for cultivating exoelectrogenic microorganisms was demonstrated through comparison of buffer effects on pure (Geobacter sulfurreducens and Geobacter metallireducens) and mixed cultures. Mixed cultures produced current densities equal to or higher than pure cultures in the different media, and current densities for all cultures were higher using a 50mM phosphate buffer than a 30mM bicarbonate buffer. Only the mixed culture was capable of sustained current generation with a 200mM phosphate buffer. These results demonstrate the usefulness of this inexpensive method for conducting in-depth examinations of pure and mixed exoelectrogenic cultures. © 2011 Elsevier B.V.

  9. Effects of eye drops of Buddleja officinalis Maxim. extract on lacrimal gland cell apoptosis in castrated rats with dry eye.

    Science.gov (United States)

    Peng, Qing-hua; Yao, Xiao-lei; Wu, Quan-long; Tan, Han-yu; Zhang, Jing-rong

    2010-03-01

    To explore the possible mechanism of eye drops of Buddleja officinalis extract in treating dry eye of castrated rats by analyzing the expressions of Bax and Bcl-2 proteins. Forty-five Wistar male rats were randomly divided into sham-operated group, untreated group and eye drops of Buddleja officinalis Maxim. extract (treatment) group. The dry eye model was established with orchiectomy in the untreated group and treatment group. Rats in the treatment group were treated with eye drops of Buddleja officinalis Maxim. extract, one drop once, three times daily. Eyes of rats in the sham-operated group and untreated group were instilled with normal saline. After one-, two-, or three-month treatment, five rats in each group were scarified respectively. Then samples were taken to detect related indices. Expressions of Bax and Bcl-2 of lacrimal gland were checked by immunohistochemical method and quantity of apoptotic cells was counted. After one-, two- or three-month treatment, the quantities of expressions of Bax in acinar epithelial cells and glandular tube cells were significantly lower, and those of Bcl-2 were significantly higher in the treatment group than in the untreated group, and the quantities of apoptotic cells of the treatment group were significantly lower than those of the untreated group (PBuddleja officinalis Maxim. are flavonoids, which can significantly inhibit cell apoptosis in lacrimal gland.

  10. NSC23925, identified in a high-throughput cell-based screen, reverses multidrug resistance.

    Directory of Open Access Journals (Sweden)

    Zhenfeng Duan

    2009-10-01

    Full Text Available Multidrug resistance (MDR is a major factor which contributes to the failure of cancer chemotherapy, and numerous efforts have been attempted to overcome MDR. To date, none of these attempts have yielded a tolerable and effective therapy to reverse MDR; thus, identification of new agents would be useful both clinically and scientifically.To identify small molecule compounds that can reverse chemoresistance, we developed a 96-well plate high-throughput cell-based screening assay in a paclitaxel resistant ovarian cancer cell line. Coincubating cells with a sublethal concentration of paclitaxel in combination with each of 2,000 small molecule compounds from the National Cancer Institute Diversity Set Library, we identified a previously uncharacterized molecule, NSC23925, that inhibits Pgp1 and reverses MDR1 (Pgp1 but does not inhibit MRP or BCRP-mediated MDR. The cytotoxic activity of NSC23925 was further evaluated using a panel of cancer cell lines expressing Pgp1, MRP, and BCRP. We found that at a concentration of >10 microM NSC23925 moderately inhibits the proliferation of both sensitive and resistant cell lines with almost equal activity, but its inhibitory effect was not altered by co-incubation with the Pgp1 inhibitor, verapamil, suggesting that NSC23925 itself is not a substrate of Pgp1. Additionally, NSC23925 increases the intracellular accumulation of Pgp1 substrates: calcein AM, Rhodamine-123, paclitaxel, mitoxantrone, and doxorubicin. Interestingly, we further observed that, although NSC23925 directly inhibits the function of Pgp1 in a dose-dependent manner without altering the total expression level of Pgp1, NSC23925 actually stimulates ATPase activity of Pgp, a phenomenon seen in other Pgp inhibitors.The ability of NSC23925 to restore sensitivity to the cytotoxic effects of chemotherapy or to prevent resistance could significantly benefit cancer patients.

  11. Development of a high-throughput microscale cell disruption platform for Pichia pastoris in rapid bioprocess design.

    Science.gov (United States)

    Bláha, Benjamin A F; Morris, Stephen A; Ogonah, Olotu W; Maucourant, Sophie; Crescente, Vincenzo; Rosenberg, William; Mukhopadhyay, Tarit K

    2017-09-07

    The time and cost benefits of miniaturized fermentation platforms can only be gained by employing complementary techniques facilitating high-throughput at small sample volumes. Microbial cell disruption is a major bottleneck in experimental throughput and is often restricted to large processing volumes. Moreover, for rigid yeast species, such as Pichia pastoris, no effective high-throughput disruption methods exist. The development of an automated, miniaturized, high-throughput, noncontact, scalable platform based on adaptive focused acoustics (AFA) to disrupt P. pastoris and recover intracellular heterologous protein is described. Augmented modes of AFA were established by investigating vessel designs and a novel enzymatic pretreatment step. Three different modes of AFA were studied and compared to the performance high-pressure homogenization. For each of these modes of cell disruption, response models were developed to account for five different performance criteria. Using multiple responses not only demonstrated that different operating parameters are required for different response optima, with highest product purity requiring suboptimal values for other criteria, but also allowed for AFA-based methods to mimic large-scale homogenization processes. These results demonstrate that AFA-mediated cell disruption can be used for a wide range of applications including buffer development, strain selection, fermentation process development, and whole bioprocess integration. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 2017. © 2017 American Institute of Chemical Engineers.

  12. Using a medium-throughput comet assay to evaluate the global DNA methylation status of single cells

    Science.gov (United States)

    Lewies, Angélique; Van Dyk, Etresia; Wentzel, Johannes F.; Pretorius, Pieter J.

    2014-01-01

    The comet assay is a simple and cost effective technique, commonly used to analyze and quantify DNA damage in individual cells. The versatility of the comet assay allows introduction of various modifications to the basic technique. The difference in the methylation sensitivity of the isoschizomeric restriction enzymes HpaII and MspI are used to demonstrate the ability of the comet assay to measure the global DNA methylation level of individual cells when using cell cultures. In the experiments described here, a medium-throughput comet assay and methylation sensitive comet assay are combined to produce a methylation sensitive medium-throughput comet assay to measure changes in the global DNA methylation pattern in individual cells under various growth conditions. PMID:25071840

  13. Using a medium-throughput comet assay to evaluate the global DNA methylation status of single cells

    Directory of Open Access Journals (Sweden)

    Angelique eLewies

    2014-07-01

    Full Text Available The comet assay is a simple and cost effective technique, commonly used to analyse and quantify DNA damage in individual cells. The versatility of the comet assay allows introduction of various modifications to the basic technique. The difference in the methylation sensitivity of the isoschizomeric restriction enzymes HpaII and MspI are used to demonstrate the ability of the comet assay to measure the global DNA methylation level of individual cells when using cell cultures. In the experiments described here, a medium-throughput comet assay and methylation sensitive comet assay are combined to produce a methylation sensitive medium-throughput comet assay to measure changes in the global DNA methylation pattern in individual cells under various growth conditions.

  14. Maximal ? -regularity

    NARCIS (Netherlands)

    Van Neerven, J.M.A.M.; Veraar, M.C.; Weis, L.

    2015-01-01

    In this paper, we prove maximal regularity estimates in “square function spaces” which are commonly used in harmonic analysis, spectral theory, and stochastic analysis. In particular, they lead to a new class of maximal regularity results for both deterministic and stochastic equations in L p

  15. Comparative Polygenic Analysis of Maximal Ethanol Accumulation Capacity and Tolerance to High Ethanol Levels of Cell Proliferation in Yeast

    Science.gov (United States)

    Pais, Thiago M.; Foulquié-Moreno, María R.; Hubmann, Georg; Duitama, Jorge; Swinnen, Steve; Goovaerts, Annelies; Yang, Yudi; Dumortier, Françoise; Thevelein, Johan M.

    2013-01-01

    The yeast Saccharomyces cerevisiae is able to accumulate ≥17% ethanol (v/v) by fermentation in the absence of cell proliferation. The genetic basis of this unique capacity is unknown. Up to now, all research has focused on tolerance of yeast cell proliferation to high ethanol levels. Comparison of maximal ethanol accumulation capacity and ethanol tolerance of cell proliferation in 68 yeast strains showed a poor correlation, but higher ethanol tolerance of cell proliferation clearly increased the likelihood of superior maximal ethanol accumulation capacity. We have applied pooled-segregant whole-genome sequence analysis to identify the polygenic basis of these two complex traits using segregants from a cross of a haploid derivative of the sake strain CBS1585 and the lab strain BY. From a total of 301 segregants, 22 superior segregants accumulating ≥17% ethanol in small-scale fermentations and 32 superior segregants growing in the presence of 18% ethanol, were separately pooled and sequenced. Plotting SNP variant frequency against chromosomal position revealed eleven and eight Quantitative Trait Loci (QTLs) for the two traits, respectively, and showed that the genetic basis of the two traits is partially different. Fine-mapping and Reciprocal Hemizygosity Analysis identified ADE1, URA3, and KIN3, encoding a protein kinase involved in DNA damage repair, as specific causative genes for maximal ethanol accumulation capacity. These genes, as well as the previously identified MKT1 gene, were not linked in this genetic background to tolerance of cell proliferation to high ethanol levels. The superior KIN3 allele contained two SNPs, which are absent in all yeast strains sequenced up to now. This work provides the first insight in the genetic basis of maximal ethanol accumulation capacity in yeast and reveals for the first time the importance of DNA damage repair in yeast ethanol tolerance. PMID:23754966

  16. Common fusion transcripts identified in colorectal cancer cell lines by high-throughput RNA sequencing.

    Science.gov (United States)

    Nome, Torfinn; Thomassen, Gard Os; Bruun, Jarle; Ahlquist, Terje; Bakken, Anne C; Hoff, Andreas M; Rognum, Torleiv; Nesbakken, Arild; Lorenz, Susanne; Sun, Jinchang; Barros-Silva, João Diogo; Lind, Guro E; Myklebost, Ola; Teixeira, Manuel R; Meza-Zepeda, Leonardo A; Lothe, Ragnhild A; Skotheim, Rolf I

    2013-01-01

    Colorectal cancer (CRC) is the third most common cancer disease in the Western world, and about 40% of the patients die from this disease. The cancer cells are commonly genetically unstable, but only a few low-frequency recurrent fusion genes have so far been reported for this disease. In this study, we present a thorough search for novel fusion transcripts in CRC using high-throughput RNA sequencing. From altogether 220 million paired-end sequence reads from seven CRC cell lines, we identified 3391 candidate fused transcripts. By stringent requirements, we nominated 11 candidate fusion transcripts for further experimental validation, of which 10 were positive by reverse transcription-polymerase chain reaction and Sanger sequencing. Six were intrachromosomal fusion transcripts, and interestingly, three of these, AKAP13-PDE8A, COMMD10-AP3S1, and CTB-35F21.1-PSD2, were present in, respectively, 18, 18, and 20 of 21 analyzed cell lines and in, respectively, 18, 61, and 48 (17%-58%) of 106 primary cancer tissues. These three fusion transcripts were also detected in 2 to 4 of 14 normal colonic mucosa samples (14%-28%). Whole-genome sequencing identified a specific genomic breakpoint in COMMD10-AP3S1 and further indicates that both the COMMD10-AP3S1 and AKAP13-PDE8A fusion transcripts are due to genomic duplications in specific cell lines. In conclusion, we have identified AKAP13-PDE8A, COMMD10-AP3S1, and CTB-35F21.1-PSD2 as novel intrachromosomal fusion transcripts and the most highly recurring chimeric transcripts described for CRC to date. The functional and clinical relevance of these chimeric RNA molecules remains to be elucidated.

  17. Common Fusion Transcripts Identified in Colorectal Cancer Cell Lines by High-Throughput RNA Sequencing12

    Science.gov (United States)

    Nome, Torfinn; Thomassen, Gard OS; Bruun, Jarle; Ahlquist, Terje; Bakken, Anne C; Hoff, Andreas M; Rognum, Torleiv; Nesbakken, Arild; Lorenz, Susanne; Sun, Jinchang; Barros-Silva, João Diogo; Lind, Guro E; Myklebost, Ola; Teixeira, Manuel R; Meza-Zepeda, Leonardo A; Lothe, Ragnhild A; Skotheim, Rolf I

    2013-01-01

    Colorectal cancer (CRC) is the third most common cancer disease in the Western world, and about 40% of the patients die from this disease. The cancer cells are commonly genetically unstable, but only a few low-frequency recurrent fusion genes have so far been reported for this disease. In this study, we present a thorough search for novel fusion transcripts in CRC using high-throughput RNA sequencing. From altogether 220 million paired-end sequence reads from seven CRC cell lines, we identified 3391 candidate fused transcripts. By stringent requirements, we nominated 11 candidate fusion transcripts for further experimental validation, of which 10 were positive by reverse transcription-polymerase chain reaction and Sanger sequencing. Six were intrachromosomal fusion transcripts, and interestingly, three of these, AKAP13-PDE8A, COMMD10-AP3S1, and CTB-35F21.1-PSD2, were present in, respectively, 18, 18, and 20 of 21 analyzed cell lines and in, respectively, 18, 61, and 48 (17%-58%) of 106 primary cancer tissues. These three fusion transcripts were also detected in 2 to 4 of 14 normal colonic mucosa samples (14%–28%). Whole-genome sequencing identified a specific genomic breakpoint in COMMD10-AP3S1 and further indicates that both the COMMD10-AP3S1 and AKAP13-PDE8A fusion transcripts are due to genomic duplications in specific cell lines. In conclusion, we have identified AKAP13-PDE8A, COMMD10-AP3S1, and CTB-35F21.1-PSD2 as novel intrachromosomal fusion transcripts and the most highly recurring chimeric transcripts described for CRC to date. The functional and clinical relevance of these chimeric RNA molecules remains to be elucidated. PMID:24151535

  18. Cell surface profiling using high-throughput flow cytometry: a platform for biomarker discovery and analysis of cellular heterogeneity.

    Directory of Open Access Journals (Sweden)

    Craig A Gedye

    Full Text Available Cell surface proteins have a wide range of biological functions, and are often used as lineage-specific markers. Antibodies that recognize cell surface antigens are widely used as research tools, diagnostic markers, and even therapeutic agents. The ability to obtain broad cell surface protein profiles would thus be of great value in a wide range of fields. There are however currently few available methods for high-throughput analysis of large numbers of cell surface proteins. We describe here a high-throughput flow cytometry (HT-FC platform for rapid analysis of 363 cell surface antigens. Here we demonstrate that HT-FC provides reproducible results, and use the platform to identify cell surface antigens that are influenced by common cell preparation methods. We show that multiple populations within complex samples such as primary tumors can be simultaneously analyzed by co-staining of cells with lineage-specific antibodies, allowing unprecedented depth of analysis of heterogeneous cell populations. Furthermore, standard informatics methods can be used to visualize, cluster and downsample HT-FC data to reveal novel signatures and biomarkers. We show that the cell surface profile provides sufficient molecular information to classify samples from different cancers and tissue types into biologically relevant clusters using unsupervised hierarchical clustering. Finally, we describe the identification of a candidate lineage marker and its subsequent validation. In summary, HT-FC combines the advantages of a high-throughput screen with a detection method that is sensitive, quantitative, highly reproducible, and allows in-depth analysis of heterogeneous samples. The use of commercially available antibodies means that high quality reagents are immediately available for follow-up studies. HT-FC has a wide range of applications, including biomarker discovery, molecular classification of cancers, or identification of novel lineage specific or stem cell

  19. Treatability studies on different refinery wastewater samples using high-throughput microbial electrolysis cells (MECs).

    Science.gov (United States)

    Ren, Lijiao; Siegert, Michael; Ivanov, Ivan; Pisciotta, John M; Logan, Bruce E

    2013-05-01

    High-throughput microbial electrolysis cells (MECs) were used to perform treatability studies on many different refinery wastewater samples all having appreciably different characteristics, which resulted in large differences in current generation. A de-oiled refinery wastewater sample from one site (DOW1) produced the best results, with 2.1±0.2 A/m(2) (maximum current density), 79% chemical oxygen demand removal, and 82% headspace biological oxygen demand removal. These results were similar to those obtained using domestic wastewater. Two other de-oiled refinery wastewater samples also showed good performance, with a de-oiled oily sewer sample producing less current. A stabilization lagoon sample and a stripped sour wastewater sample failed to produce appreciable current. Electricity production, organics removal, and startup time were improved when the anode was first acclimated to domestic wastewater. These results show mini-MECs are an effective method for evaluating treatability of different wastewaters. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. High Throughput Single-cell and Multiple-cell Micro-encapsulation

    National Research Council Canada - National Science Library

    Lagus, Todd P; Edd, Jon F

    2012-01-01

    Microfluidic encapsulation methods have been previously utilized to capture cells in picoliter-scale aqueous, monodisperse drops, providing confinement from a bulk fluid environment with applications...

  1. Weighted MMSE Beamforming Design for Weighted Sum-rate Maximization in Coordinated Multi-Cell MIMO Systems

    DEFF Research Database (Denmark)

    Sun, Fan; De Carvalho, Elisabeth

    2012-01-01

    This paper proposes a low-complexity design for the linear weighted MMSE (WMMSE) transmit filters of a coordinated multi-cell system with multiple users per cell. This design is based on a modified WMMSE approach applied to each transmitting base station individually incorporating the signals sent...... the linear transmit filter maximizing the weighted sum-rate of the multicell system. This algorithm is based on WMMSE where the MSE weights are optimally adjusted so that the WMMSE optimum coincides with the WSR optimum....

  2. Process development of human multipotent stromal cell microcarrier culture using an automated high‐throughput microbioreactor

    Science.gov (United States)

    Hanga, Mariana P.; Heathman, Thomas R. J.; Coopman, Karen; Nienow, Alvin W.; Williams, David J.; Hewitt, Christopher J.

    2017-01-01

    ABSTRACT Microbioreactors play a critical role in process development as they reduce reagent requirements and can facilitate high‐throughput screening of process parameters and culture conditions. Here, we have demonstrated and explained in detail, for the first time, the amenability of the automated ambr15 cell culture microbioreactor system for the development of scalable adherent human mesenchymal multipotent stromal/stem cell (hMSC) microcarrier culture processes. This was achieved by first improving suspension and mixing of the microcarriers and then improving cell attachment thereby reducing the initial growth lag phase. The latter was achieved by using only 50% of the final working volume of medium for the first 24 h and using an intermittent agitation strategy. These changes resulted in >150% increase in viable cell density after 24 h compared to the original process (no agitation for 24 h and 100% working volume). Using the same methodology as in the ambr15, similar improvements were obtained with larger scale spinner flask studies. Finally, this improved bioprocess methodology based on a serum‐based medium was applied to a serum‐free process in the ambr15, resulting in >250% increase in yield compared to the serum‐based process. At both scales, the agitation used during culture was the minimum required for microcarrier suspension, NJS. The use of the ambr15, with its improved control compared to the spinner flask, reduced the coefficient of variation on viable cell density in the serum containing medium from 7.65% to 4.08%, and the switch to serum free further reduced these to 1.06–0.54%, respectively. The combination of both serum‐free and automated processing improved the reproducibility more than 10‐fold compared to the serum‐based, manual spinner flask process. The findings of this study demonstrate that the ambr15 microbioreactor is an effective tool for bioprocess development of hMSC microcarrier cultures and that a combination

  3. 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.

  4. 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.

  5. High-throughput ultra high performance liquid chromatography combined with mass spectrometry approach for the rapid analysis and characterization of multiple constituents of the fruit of Acanthopanax senticosus (Rupr. et Maxim.) Harms.

    Science.gov (United States)

    Han, Yue; Zhang, Aihua; Sun, Hui; Zhang, Yingzhi; Meng, Xiangcai; Yan, Guangli; Liu, Liang; Wang, Xijun

    2017-05-01

    Acanthopanax senticosus (Rupr. et Maxim.) Harms, a traditional Chinese medicine, has been widely used to improve the function of skeleton, heart, spleen and kidney. This fruit is rich in nutrients, but the chemical constituents of Acanthopanax senticosus fruit are still unclear. A rapid method based on ultra high performance liquid chromatography with time-of-flight mass spectrometry was developed for the compound analysis of Acanthopanax senticosus fruit in vitro and in vivo. In this study, the Acanthopanax senticosus fruit could significantly increase the weight of immune organs, promote the proliferation of lymphatic T cells, regulate the lymphatic B cell function, and decrease the ability of natural killer cells. A total of 104 compounds of Acanthopanax senticosus fruit including lignans, flavones, triterpenoidsaponins, phenolic acids, and other constituents were identified. Among them, seven chemical compounds were reported for the first time in the Acanthopanax senticosus fruit. Compared with the serum sample of blank and dosed samples, 24 prototype compositions were characterized. The results of our experiment could be helpful to understand the complex compounds of Acanthopanax senticosus fruit in vitro and in vivo for further pharmacological activity studies. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. High-throughput microarray mapping of cell wall polymers in roots and tubers during the viscosity-reducing process

    DEFF Research Database (Denmark)

    Huang, Yuhong; Willats, William George Tycho; Lange, Lene

    2016-01-01

    the viscosity-reducing process are poorly characterized. Comprehensive microarray polymer profiling, which is a high-throughput microarray, was used for the first time to map changes in the cell wall polymers of sweet potato (Ipomoea batatas), cassava (Manihot esculenta), and Canna edulis Ker. over the entire...... of the sweet potato and the cassava was attributed to the degradation of homogalacturonan and the released 1,4-β-d-galactan and 1,5-α-l-arabinan....

  7. Development of droplets‐based microfluidic systems for single­‐cell high‐throughput screening

    DEFF Research Database (Denmark)

    Chen, Jun; Jensen, Thomas Glasdam; Godina, Alexei

    2014-01-01

    High-throughput screening (HTS) plays an important role in the development of microbial cell factories. One of the most popular approaches is to use microplates combined with the application of robotics, liquid handling and sophisticated detection methods. However, these workstations require large...... picoliter aqueous droplets surround by an immiscible fluorinated oil phase. Our aim is to use this system to facilitate the screening process for both the biotechnology and food industry....

  8. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism

    OpenAIRE

    Nemenman, Ilya; Escola, G. Sean; Hlavacek, William S.; Unkefer, Pat J.; Unkefer, Clifford J.; Wall, Michael E.

    2007-01-01

    We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For this, we generate synthetic metabolic profiles for benchmarking purposes based on a well-established model for red blood cell metabolism. A variety of data sets is generated, accounting for different properties of real metabolic networks, such as experimental noise, metabolite correlations, and t...

  9. Towards high throughput tissue engineering: development of chitosan-calcium phosphate scaffolds for engineering bone tissue from embryonic stem cells

    OpenAIRE

    Ko, Junghyuk; Kolehmainen, Kathleen; Ahmed, Farid; Jun, Martin BG; Willerth, Stephanie M.

    2011-01-01

    Tissue engineering strategies have shown promise for the repair of damaged organs, including bone. One of the major challenges associated with tissue engineering is how to scale up such processes for high throughput manufacturing of biomaterial scaffolds used to support stem cell culture. Generation of certain types of 3D biomaterial scaffolds, including chitosan-calcium phosphate blends, involves a slow fabrication process followed by a lengthy required freeze drying step. This work investig...

  10. High throughput sequencing identifies an imprinted gene, Grb10, associated with the pluripotency state in nuclear transfer embryonic stem cells.

    Science.gov (United States)

    Li, Hui; Gao, Shuai; Huang, Hua; Liu, Wenqiang; Huang, Huanwei; Liu, Xiaoyu; Gao, Yawei; Le, Rongrong; Kou, Xiaochen; Zhao, Yanhong; Kou, Zhaohui; Li, Jia; Wang, Hong; Zhang, Yu; Wang, Hailin; Cai, Tao; Sun, Qingyuan; Gao, Shaorong; Han, Zhiming

    2017-07-18

    Somatic cell nuclear transfer and transcription factor mediated reprogramming are two widely used techniques for somatic cell reprogramming. Both fully reprogrammed nuclear transfer embryonic stem cells and induced pluripotent stem cells hold potential for regenerative medicine, and evaluation of the stem cell pluripotency state is crucial for these applications. Previous reports have shown that the Dlk1-Dio3 region is associated with pluripotency in induced pluripotent stem cells and the incomplete somatic cell reprogramming causes abnormally elevated levels of genomic 5-methylcytosine in induced pluripotent stem cells compared to nuclear transfer embryonic stem cells and embryonic stem cells. In this study, we compared pluripotency associated genes Rian and Gtl2 in the Dlk1-Dio3 region in exactly syngeneic nuclear transfer embryonic stem cells and induced pluripotent stem cells with same genomic insertion. We also assessed 5-methylcytosine and 5-hydroxymethylcytosine levels and performed high-throughput sequencing in these cells. Our results showed that Rian and Gtl2 in the Dlk1-Dio3 region related to pluripotency in induced pluripotent stem cells did not correlate with the genes in nuclear transfer embryonic stem cells, and no significant difference in 5-methylcytosine and 5-hydroxymethylcytosine levels were observed between fully and partially reprogrammed nuclear transfer embryonic stem cells and induced pluripotent stem cells. Through syngeneic comparison, our study identifies for the first time that Grb10 is associated with the pluripotency state in nuclear transfer embryonic stem cells.

  11. Strategies to Maximize the Potential of Marine Biomaterials as a Platform for Cell Therapy

    Science.gov (United States)

    Kim, Hyeongmin; Lee, Jaehwi

    2016-01-01

    Marine biopolymers have been explored as a promising cell therapy system for efficient cell delivery and tissue engineering. However, the marine biomaterial-based systems themselves have exhibited limited performance in terms of maintenance of cell viability and functions, promotion of cell proliferation and differentiation as well as cell delivery efficiency. Thus, numerous novel strategies have been devised to improve cell therapy outcomes. The strategies include optimization of physical and biochemical properties, provision of stimuli-responsive functions, and design of platforms for efficient cell delivery and tissue engineering. These approaches have demonstrated substantial improvement of therapeutic outcomes in a variety of research settings. In this review, therefore, research progress made with marine biomaterials as a platform for cell therapy is reported along with current research directions to further advance cell therapies as a tool to cure incurable diseases. PMID:26821034

  12. A high-throughput fluorescence resonance energy transfer (FRET)-based endothelial cell apoptosis assay and its application for screening vascular disrupting agents

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Xiaoming; Fu, Afu [Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University (Singapore); Luo, Kathy Qian, E-mail: kluo@ntu.edu.sg [Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University (Singapore)

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer An endothelial cell apoptosis assay using FRET-based biosensor was developed. Black-Right-Pointing-Pointer The fluorescence of the cells changed from green to blue during apoptosis. Black-Right-Pointing-Pointer This method was developed into a high-throughput assay in 96-well plates. Black-Right-Pointing-Pointer This assay was applied to screen vascular disrupting agents. -- Abstract: In this study, we developed a high-throughput endothelial cell apoptosis assay using a fluorescence resonance energy transfer (FRET)-based biosensor. After exposure to apoptotic inducer UV-irradiation or anticancer drugs such as paclitaxel, the fluorescence of the cells changed from green to blue. We developed this method into a high-throughput assay in 96-well plates by measuring the emission ratio of yellow fluorescent protein (YFP) to cyan fluorescent protein (CFP) to monitor the activation of a key protease, caspase-3, during apoptosis. The Z Prime factor for this assay was above 0.5 which indicates that this assay is suitable for a high-throughput analysis. Finally, we applied this functional high-throughput assay for screening vascular disrupting agents (VDA) which could induce endothelial cell apoptosis from our in-house compounds library and dioscin was identified as a hit. As this assay allows real time and sensitive detection of cell apoptosis, it will be a useful tool for monitoring endothelial cell apoptosis in living cell situation and for identifying new VDA candidates via a high-throughput screening.

  13. High-throughput assay for the identification of compounds regulating osteogenic differentiation of human mesenchymal stromal cells.

    Directory of Open Access Journals (Sweden)

    Hugo Alves

    Full Text Available Human mesenchymal stromal cells are regarded as the golden standard for cell-based therapies. They present multilineage differentiation potential and trophic and immunosuppressive abilities, making them the best candidate for clinical applications. Several molecules have been described to increase bone formation and were mainly discovered by candidate approaches towards known signaling pathways controlling osteogenesis. However, their bone forming potential is still limited, making the search for novel molecules a necessity. High-throughput screening (HTS not only allows the screening of a large number of diverse chemical compounds, but also allows the discovery of unexpected signaling pathways and molecular mechanisms for a certain application, even without the prior knowledge of the full molecular pathway. Typically HTS is performed in cell lines, however, in this manuscript we have performed a phenotypical screen on more clinically relevant human mesenchymal stromal cells, as a proof of principle that HTS can be performed in those cells and can be used to find small molecules that impact stem cell fate. From a library of pharmacologically active small molecules, we were able to identify novel compounds with increased osteogenic activity. These compounds allowed achieving levels of bone-specific alkaline phosphatase higher than any other combination previously known. By combining biochemical techniques, we were able to demonstrate that a medium to high-throughput phenotypic assay can be performed in academic research laboratories allowing the discovery of novel molecules able to enhance stem cell differentiation.

  14. An Analytic Approach for Optimal Geometrical Design of GaAs Nanowires for Maximal Light Harvesting in Photovoltaic Cells

    Science.gov (United States)

    Wu, Dan; Tang, Xiaohong; Wang, Kai; Li, Xianqiang

    2017-04-01

    Semiconductor nanowires(NWs) with subwavelength scale diameters have demonstrated superior light trapping features, which unravel a new pathway for low cost and high efficiency future generation solar cells. Unlike other published work, a fully analytic design is for the first time proposed for optimal geometrical parameters of vertically-aligned GaAs NW arrays for maximal energy harvesting. Using photocurrent density as the light absorbing evaluation standard, 2 μm length NW arrays whose multiple diameters and periodicity are quantitatively identified achieving the maximal value of 29.88 mA/cm2 under solar illumination. It also turns out that our method has wide suitability for single, double and four different diameters of NW arrays for highest photon energy harvesting. To validate this analytical method, intensive numerical three-dimensional finite-difference time-domain simulations of the NWs’ light harvesting are also carried out. Compared with the simulation results, the predicted maximal photocurrent densities lie within 1.5% tolerance for all cases. Along with the high accuracy, through directly disclosing the exact geometrical dimensions of NW arrays, this method provides an effective and efficient route for high performance photovoltaic design.

  15. Maximizing Benefits from Maintenance Pemetrexed with Stereotactic Ablative Radiotherapy in Oligoprogressive Non-Squamous Non-Small Cell Lung Cancer

    Directory of Open Access Journals (Sweden)

    Shao-Lun Lu

    2016-08-01

    Full Text Available Maintenance pemetrexed offers survival benefit with well-tolerated toxicities for advanced non-squamous non-small cell lung cancer (NSCLC. We present 3 consecutively enrolled patients with advanced non-squamous NSCLC, receiving stereotactic ablative radiotherapy (SABR for oligoprogressive disease during maintenance pemetrexed. All of them had sustained local control of thoracic oligoprogression after the SABR, while maintenance pemetrexed were kept for additionally long progression-free interval. SABR targeting oligoprogression with continued pemetrexed is an effective and safe approach to extend exposure of maintenance pemetrexed, thus maximizing the benefit from it.

  16. Towards high throughput tissue engineering: development of chitosan-calcium phosphate scaffolds for engineering bone tissue from embryonic stem cells.

    Science.gov (United States)

    Ko, Junghyuk; Kolehmainen, Kathleen; Ahmed, Farid; Jun, Martin Bg; Willerth, Stephanie M

    2012-01-01

    Tissue engineering strategies have shown promise for the repair of damaged organs, including bone. One of the major challenges associated with tissue engineering is how to scale up such processes for high throughput manufacturing of biomaterial scaffolds used to support stem cell culture. Generation of certain types of 3D biomaterial scaffolds, including chitosan-calcium phosphate blends, involves a slow fabrication process followed by a lengthy required freeze drying step. This work investigates the use of automated microwave vacuum drying technology as an alternative to traditional freeze drying as a method of fabricating chitosan-calcium phosphate scaffolds for supporting embryonic stem cell cultures. Scaffolds produced using both drying techniques possess similar properties when characterized using scanning electron microscopy and this paper is the first to report that both types of these scaffolds support undifferentiated embryonic stem cell culture as well as promote stem cell differentiation into osteogenic lineages when treated with the appropriate factors. Compared to existing scaffold manufacturing processes using freeze drying, the use of microwave vacuum drying will lead to faster production times while reducing the costs, enabling high-throughput manufacturing of biomaterial scaffolds for stem cell applications.

  17. High-throughput genotoxicity assay identifies antioxidants as inducers of DNA damage response and cell death

    Science.gov (United States)

    Human ATAD5 is an excellent biomarker for identifying genotoxic compounds because ATADS protein levels increase post-transcriptionally following exposure to a variety of DNA damaging agents. Here we report a novel quantitative high-throughput ATAD5-Iuciferase assay that can moni...

  18. The Complete Automation of Cell Culture: Improvements for High-Throughput and High-Content Screening

    NARCIS (Netherlands)

    Jain, S.; Sondervan, D.; Rizzu, P.; Bochdanovits, Z.; Caminada, D.; Heutink, P.

    2011-01-01

    Genomic approaches provide enormous amounts of raw data with regard to genetic variation, the diversity of RNA species, and protein complement. high-throughput (HT) and high-content (HC) cellular screens are ideally suited to contextualize the information gathered from other "omic" approaches into

  19. Human IL-12 p40 as a reporter gene for high-throughput screening of engineered mouse embryonic stem cells

    Directory of Open Access Journals (Sweden)

    Shaffer Benjamin

    2008-06-01

    Full Text Available Abstract Background Establishing a suitable level of exogenous gene expression in mammalian cells in general, and embryonic stem (ES cells in particular, is an important aspect of understanding pathways of cell differentiation, signal transduction and cell physiology. Despite its importance, this process remains challenging because of the poor correlation between the presence of introduced exogenous DNA and its transcription. Consequently, many transfected cells must be screened to identify those with an appropriate level of expression. To improve the screening process, we investigated the utility of the human interleukin 12 (IL-12 p40 cDNA as a reporter gene for studies of mammalian gene expression and for high-throughput screening of engineered mouse embryonic stem cells. Results A series of expression plasmids were used to study the utility of IL-12 p40 as an accurate reporter of gene activity. These studies included a characterization of the IL-12 p40 expression system in terms of: (i a time course of IL-12 p40 accumulation in the medium of transfected cells; (ii the dose-response relationship between the input DNA and IL-12 p40 mRNA levels and IL-12 p40 protein secretion; (iii the utility of IL-12 p40 as a reporter gene for analyzing the activity of cis-acting genetic elements; (iv expression of the IL-12 p40 reporter protein driven by an IRES element in a bicistronic mRNA; (v utility of IL-12 p40 as a reporter gene in a high-throughput screening strategy to identify successful transformed mouse embryonic stem cells; (vi demonstration of pluripotency of IL-12 p40 expressing ES cells in vitro and in vivo; and (vii germline transmission of the IL-12 p40 reporter gene. Conclusion IL-12 p40 showed several advantages as a reporter gene in terms of sensitivity and ease of the detection procedure. The IL-12 p40 assay was rapid and simple, in as much as the reporter protein secreted from the transfected cells was accurately measured by ELISA using

  20. Experimental and theoretical study of hydrodynamic cell lysing of cancer cells in a high-throughput Circular Multi-Channel Microfiltration device

    KAUST Repository

    Ma, W.

    2013-04-01

    Microfiltration is an important microfluidic technique suitable for enrichment and isolation of cells. However, cell lysing could occur due to hydrodynamic damage that may be detrimental for medical diagnostics. Therefore, we conducted a systematic study of hydrodynamic cell lysing in a high-throughput Circular Multi-Channel Microfiltration (CMCM) device integrated with a polycarbonate membrane. HeLa cells (cervical cancer cells) were driven into the CMCM at different flow rates. The viability of the cells in the CMCM was examined by fluorescence microscopy using Acridine Orange (AO)/Ethidium Bromide (EB) as a marker for viable/dead cells. A simple analytical cell viability model was derived and a 3D numerical model was constructed to examine the correlation of between cell lysing and applied shear stress under varying flow rate and Reynolds number. The measured cell viability as a function of the shear stress was consistent with theoretical and numerical predictions when accounting for cell size distribution. © 2013 IEEE.

  1. Laser-Induced Fluorescence Detection in High-Throughput Screening of Heterogeneous Catalysts and Single Cells Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Su, Hui [Iowa State Univ., Ames, IA (United States)

    2001-01-01

    Laser-induced fluorescence detection is one of the most sensitive detection techniques and it has found enormous applications in various areas. The purpose of this research was to develop detection approaches based on laser-induced fluorescence detection in two different areas, heterogeneous catalysts screening and single cell study. First, we introduced laser-induced imaging (LIFI) as a high-throughput screening technique for heterogeneous catalysts to explore the use of this high-throughput screening technique in discovery and study of various heterogeneous catalyst systems. This scheme is based on the fact that the creation or the destruction of chemical bonds alters the fluorescence properties of suitably designed molecules. By irradiating the region immediately above the catalytic surface with a laser, the fluorescence intensity of a selected product or reactant can be imaged by a charge-coupled device (CCD) camera to follow the catalytic activity as a function of time and space. By screening the catalytic activity of vanadium pentoxide catalysts in oxidation of naphthalene, we demonstrated LIFI has good detection performance and the spatial and temporal resolution needed for high-throughput screening of heterogeneous catalysts. The sample packing density can reach up to 250 x 250 subunits/cm2 for 40-μm wells. This experimental set-up also can screen solid catalysts via near infrared thermography detection.

  2. High-throughput evaluation of synthetic metabolic pathways.

    Science.gov (United States)

    Klesmith, Justin R; Whitehead, Timothy A

    2016-03-01

    A central challenge in the field of metabolic engineering is the efficient identification of a metabolic pathway genotype that maximizes specific productivity over a robust range of process conditions. Here we review current methods for optimizing specific productivity of metabolic pathways in living cells. New tools for library generation, computational analysis of pathway sequence-flux space, and high-throughput screening and selection techniques are discussed.

  3. Semi-fuel cell studies for powering underwater devices: integrated design for maximized net power output

    Science.gov (United States)

    Cardenas-Valencia, Andres M.; Short, R. Timothy; Adornato, Lori; Langebrake, Larry

    2010-04-01

    Use of sensor systems in water bodies has applications that range from environmental and oceanographic research to port and homeland security. Power sources are often the limiting component for further reduction of sensor system size and weight. We present recent investigations of metal-anode water-activated galvanic cells, specifically water-activated Alcells using inorganic alkali peroxides and solid organic oxidizers (heterocyclic halamines), in a semi-fuel cell configuration (i.e., with cathode species generated in situ and flow-through cells). The oxidizers utilized are inexpensive solid materials that are generally (1) safer to handle than liquid solutions or gases, (2) have inherently higher current and energy capacity (as they are not dissolved), and, (3) if appropriately packaged, will not degrade over time. The specific energy (S.E.) of Al-alkali peroxide was found to be 230 Wh/kg (460 Wh/kg, considering only active materials) in a seven-gram cell. Interestingly, when the cell size was increased (making more area of the catalytic cathode electrode available), the results from a single addition of water in an Al-organic oxidizer cell (weighing ~18 grams) showed an S.E. of about 200 Wh/kg. This scalability characteristic suggests that values in excess of 400 Wh/kg could be obtained in a semi-fuel-cell-like system. In this paper, we also present design considerations that take into account the energy requirements of the pumping devices and show that the proposed oxidizers, and the possible control of the chemical equilibrium of these cathodes in solution, may help reduce this power requirement and hence enhance the overall energetic balance.

  4. Reduced fitness and abnormal cardiopulmonary responses to maximal exercise testing in children and young adults with sickle cell anemia

    Science.gov (United States)

    Liem, Robert I; Reddy, Madhuri; Pelligra, Stephanie A; Savant, Adrienne P; Fernhall, Bo; Rodeghier, Mark; Thompson, Alexis A

    2015-01-01

    Physiologic contributors to reduced exercise capacity in individuals with sickle cell anemia (SCA) are not well understood. The objective of this study was to characterize the cardiopulmonary response to maximal cardiopulmonary exercise testing (CPET) and determine factors associated with reduced exercise capacity among children and young adults with SCA. A cross-sectional cohort of 60 children and young adults (mean 15.1 ± 3.4 years) with hemoglobin SS or S/β0 thalassemia and 30 matched controls (mean 14.6 ± 3.5 years) without SCA or sickle cell trait underwent maximal CPET by a graded, symptom-limited cycle ergometry protocol with breath-by-breath, gas exchange analysis. Compared to controls without SCA, subjects with SCA demonstrated significantly lower peak VO2 (26.9 ± 6.9 vs. 37.0 ± 9.2 mL/kg/min, P < 0.001). Subjects demonstrated slower oxygen uptake (ΔVO2/ΔWR, 9 ± 2 vs. 12 ± 2 mL/min/watt, P < 0.001) and lower oxygen pulse (ΔVO2/ΔHR, 12 ± 4 vs. 20 ± 7 mL/beat, P < 0.001) as well as reduced oxygen uptake efficiency (ΔVE/ΔVO2, 42 ± 8 vs. 32 ± 5, P < 0.001) and ventilation efficiency (ΔVE/ΔVCO2, 30.3 ± 3.7 vs. 27.3 ± 2.5, P < 0.001) during CPET. Peak VO2 remained significantly lower in subjects with SCA after adjusting for age, sex, body mass index (BMI), and hemoglobin, which were independent predictors of peak VO2 for subjects with SCA. In the largest study to date using maximal CPET in SCA, we demonstrate that children and young adults with SCA have reduced exercise capacity attributable to factors independent of anemia. Complex derangements in gas exchange and oxygen uptake during maximal exercise are common in this population. PMID:25847915

  5. Towards maximizing the haze effect of electrodes for high efficiency hybrid tandem solar cell

    Science.gov (United States)

    Vincent, Premkumar; Song, Dong-Seok; Kwon, Hyeok Bin; Kim, Do-Kyung; Jung, Ji-Hoon; Kwon, Jin-Hyuk; Choe, Eunji; Kim, Young-Rae; Kim, Hyeok; Bae, Jin-Hyuk

    2018-02-01

    In this study, we executed optical simulations to compute the optimum power conversion efficiency (PCE) of a-Si:H/organic photovoltaic (OPV) hybrid tandem solar cell. The maximum ideal short circuit current density (Jsc,max) of the tandem solar cell is initially obtained by optimizing the thickness of the active layer of the OPV subcell for varying thickness of the a-Si:H bottom subcell. To investigate the effect of Haze parameter on the ideal short-circuit current density (Jsc,ideal) of the solar cells, we have varied the haze ratio for the TCO electrode of the a-Si:H subcell in the tandem structure. The haze ratio was obtained for various root mean square (RMS) roughness of the TCO of the front cell. The effect of haze ratio on the Jsc,ideal on the tandem structured solar cell was studied, and the highest Jsc,ideal was obtained at a haze of 55.5% when the thickness of the OPV subcell was 150 nm and that of the a-Si:H subcell was 500 nm.

  6. γδ T Cells Are Required for Maximal Expression of Allergic Conjunctivitis

    Science.gov (United States)

    Reyes, Nancy J.; Mayhew, Elizabeth; Chen, Peter W.

    2011-01-01

    Purpose. To determine the function of γδ T cells in early- and late-phase responses in allergic conjunctivitis. Methods. Wild-type (WT) C57BL/6 and γδ T cell–deficient (TCR-δ−/−) mice were immunized intraperitoneally and challenged topically for 7 consecutive days with short ragweed pollen. Natural killer T (NKT) and γδ T cell–double-deficient mice were generated by treating TCR-δ−/− mice with anti-CD1d antibody. Allergic conjunctivitis was evaluated clinically, and the late-phase response was assessed by histopathology. Cytokine profiles were evaluated by ELISA. The afferent and efferent arms of allergic conjunctivitis were assessed by adoptive transfer of CD4+ T cells from WT or TCR-δ−/− mice into naive TCR-δ−/− or WT mice. Results. TCR-δ−/− mice had decreased clinical manifestations of allergic conjunctivitis compared with WT mice. TCR-δ−/− mice had decreased eosinophilic infiltration compared with WT mice. TCR-δ−/− mice produced less Th2-associated cytokines interleukin (IL)-4, -5, and -13 compared with WT mice. Clinical manifestations of allergic conjunctivitis were lowest in NKT cell–depleted TCR-δ−/− mice. However, late-phase allergic conjunctivitis in NKT cell–depleted, TCR-δ−/− mice was the same as TCR-δ−/− mice. Adoptive transfer of CD4+ T cells revealed that γδ T cells are needed for the afferent and efferent arms of allergic conjunctivitis. Conclusions. γδ T cells are needed for full expression of both the clinical manifestations and the late phase of allergic conjunctivitis. Thus, γδ T cells have an important impact in the expression of allergic conjunctivitis and are a potential therapeutic target in the management of allergic diseases of the ocular surface. PMID:21212171

  7. Cytotoxicity Test Based on Human Cells Labeled with Fluorescent Proteins: Fluorimetry, Photography, and Scanning for High-Throughput Assay.

    Science.gov (United States)

    Kalinina, Marina A; Skvortsov, Dmitry A; Rubtsova, Maria P; Komarova, Ekaterina S; Dontsova, Olga A

    2017-12-21

    High- and medium-throughput assays are now routine methods for drug screening and toxicology investigations on mammalian cells. However, a simple and cost-effective analysis of cytotoxicity that can be carried out with commonly used laboratory equipment is still required. The developed cytotoxicity assays are based on human cell lines stably expressing eGFP, tdTomato, mCherry, or Katushka2S fluorescent proteins. Red fluorescent proteins exhibit a higher signal-to-noise ratio, due to less interference by medium autofluorescence, in comparison to green fluorescent protein. Measurements have been performed on a fluorescence scanner, a plate fluorimeter, and a camera photodocumentation system. For a 96-well plate assay, the sensitivity per well and the measurement duration were 250 cells and 15 min for the scanner, 500 cells and 2 min for the plate fluorimeter, and 1000 cells and less than 1 min for the camera detection. These sensitivities are similar to commonly used MTT (tetrazolium dye) assays. The used scanner and the camera had not been previously applied for cytotoxicity evaluation. An image processing scheme for the high-resolution scanner is proposed that significantly diminishes the number of control wells, even for a library containing fluorescent substances. The suggested cytotoxicity assay has been verified by measurements of the cytotoxicity of several well-known cytotoxic drugs and further applied to test a set of novel bacteriotoxic compounds in a medium-throughput format. The fluorescent signal of living cells is detected without disturbing them and adding any reagents, thus allowing to investigate time-dependent cytotoxicity effects on the same sample of cells. A fast, simple and cost-effective assay is suggested for cytotoxicity evaluation based on mammalian cells expressing fluorescent proteins and commonly used laboratory equipment.

  8. High-throughput cell-based screening reveals a role for ZNF131 as a repressor of ERalpha signaling

    Directory of Open Access Journals (Sweden)

    Du Peige

    2008-10-01

    Full Text Available Abstract Background Estrogen receptor α (ERα is a transcription factor whose activity is affected by multiple regulatory cofactors. In an effort to identify the human genes involved in the regulation of ERα, we constructed a high-throughput, cell-based, functional screening platform by linking a response element (ERE with a reporter gene. This allowed the cellular activity of ERα, in cells cotransfected with the candidate gene, to be quantified in the presence or absence of its cognate ligand E2. Results From a library of 570 human cDNA clones, we identified zinc finger protein 131 (ZNF131 as a repressor of ERα mediated transactivation. ZNF131 is a typical member of the BTB/POZ family of transcription factors, and shows both ubiquitous expression and a high degree of sequence conservation. The luciferase reporter gene assay revealed that ZNF131 inhibits ligand-dependent transactivation by ERα in a dose-dependent manner. Electrophoretic mobility shift assay clearly demonstrated that the interaction between ZNF131 and ERα interrupts or prevents ERα binding to the estrogen response element (ERE. In addition, ZNF131 was able to suppress the expression of pS2, an ERα target gene. Conclusion We suggest that the functional screening platform we constructed can be applied for high-throughput genomic screening candidate ERα-related genes. This in turn may provide new insights into the underlying molecular mechanisms of ERα regulation in mammalian cells.

  9. High-Throughput Accurate Single-Cell Screening of Euglena gracilis with Fluorescence-Assisted Optofluidic Time-Stretch Microscopy.

    Science.gov (United States)

    Guo, Baoshan; Lei, Cheng; Ito, Takuro; Jiang, Yiyue; Ozeki, Yasuyuki; Goda, Keisuke

    2016-01-01

    The development of reliable, sustainable, and economical sources of alternative fuels is an important, but challenging goal for the world. As an alternative to liquid fossil fuels, algal biofuel is expected to play a key role in alleviating global warming since algae absorb atmospheric CO2 via photosynthesis. Among various algae for fuel production, Euglena gracilis is an attractive microalgal species as it is known to produce wax ester (good for biodiesel and aviation fuel) within lipid droplets. To date, while there exist many techniques for inducing microalgal cells to produce and accumulate lipid with high efficiency, few analytical methods are available for characterizing a population of such lipid-accumulated microalgae including E. gracilis with high throughout, high accuracy, and single-cell resolution simultaneously. Here we demonstrate high-throughput, high-accuracy, single-cell screening of E. gracilis with fluorescence-assisted optofluidic time-stretch microscopy-a method that combines the strengths of microfluidic cell focusing, optical time-stretch microscopy, and fluorescence detection used in conventional flow cytometry. Specifically, our fluorescence-assisted optofluidic time-stretch microscope consists of an optical time-stretch microscope and a fluorescence analyzer on top of a hydrodynamically focusing microfluidic device and can detect fluorescence from every E. gracilis cell in a population and simultaneously obtain its image with a high throughput of 10,000 cells/s. With the multi-dimensional information acquired by the system, we classify nitrogen-sufficient (ordinary) and nitrogen-deficient (lipid-accumulated) E. gracilis cells with a low false positive rate of 1.0%. This method holds promise for evaluating cultivation techniques and selective breeding for microalgae-based biofuel production.

  10. High-Throughput Accurate Single-Cell Screening of Euglena gracilis with Fluorescence-Assisted Optofluidic Time-Stretch Microscopy.

    Directory of Open Access Journals (Sweden)

    Baoshan Guo

    Full Text Available The development of reliable, sustainable, and economical sources of alternative fuels is an important, but challenging goal for the world. As an alternative to liquid fossil fuels, algal biofuel is expected to play a key role in alleviating global warming since algae absorb atmospheric CO2 via photosynthesis. Among various algae for fuel production, Euglena gracilis is an attractive microalgal species as it is known to produce wax ester (good for biodiesel and aviation fuel within lipid droplets. To date, while there exist many techniques for inducing microalgal cells to produce and accumulate lipid with high efficiency, few analytical methods are available for characterizing a population of such lipid-accumulated microalgae including E. gracilis with high throughout, high accuracy, and single-cell resolution simultaneously. Here we demonstrate high-throughput, high-accuracy, single-cell screening of E. gracilis with fluorescence-assisted optofluidic time-stretch microscopy-a method that combines the strengths of microfluidic cell focusing, optical time-stretch microscopy, and fluorescence detection used in conventional flow cytometry. Specifically, our fluorescence-assisted optofluidic time-stretch microscope consists of an optical time-stretch microscope and a fluorescence analyzer on top of a hydrodynamically focusing microfluidic device and can detect fluorescence from every E. gracilis cell in a population and simultaneously obtain its image with a high throughput of 10,000 cells/s. With the multi-dimensional information acquired by the system, we classify nitrogen-sufficient (ordinary and nitrogen-deficient (lipid-accumulated E. gracilis cells with a low false positive rate of 1.0%. This method holds promise for evaluating cultivation techniques and selective breeding for microalgae-based biofuel production.

  11. Laser-Induced Fluorescence Detection in High-Throughput Screening of Heterogeneous Catalysts and Single Cells Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Su, Hui [Iowa State Univ., Ames, IA (United States)

    2001-01-01

    Laser-induced fluorescence detection is one of the most sensitive detection techniques and it has found enormous applications in various areas. The purpose of this research was to develop detection approaches based on laser-induced fluorescence detection in two different areas, heterogeneous catalysts screening and single cell study. First, the author introduced laser-induced imaging (LIFI) as a high-throughput screening technique for heterogeneous catalysts to explore the use of this high-throughput screening technique in discovery and study of various heterogeneous catalyst systems. This scheme is based on the fact that the creation or the destruction of chemical bonds alters the fluorescence properties of suitably designed molecules. By irradiating the region immediately above the catalytic surface with a laser, the fluorescence intensity of a selected product or reactant can be imaged by a charge-coupled device (CCD) camera to follow the catalytic activity as a function of time and space. By screening the catalytic activity of vanadium pentoxide catalysts in oxidation of naphthalene, they demonstrated LIFI has good detection performance and the spatial and temporal resolution needed for high-throughput screening of heterogeneous catalysts. The sample packing density can reach up to 250 x 250 subunits/cm2 for 40-μm wells. This experimental set-up also can screen solid catalysts via near infrared thermography detection. In the second part of this dissertation, the author used laser-induced native fluorescence coupled with capillary electrophoresis (LINF-CE) and microscope imaging to study the single cell degranulation. On the basis of good temporal correlation with events observed through an optical microscope, they have identified individual peaks in the fluorescence electropherograms as serotonin released from the granular core on contact with the surrounding fluid.

  12. Metabolic regulation and maximal reaction optimization in the central metabolism of a yeast cell

    Science.gov (United States)

    Kasbawati, Gunawan, A. Y.; Hertadi, R.; Sidarto, K. A.

    2015-03-01

    Regulation of fluxes in a metabolic system aims to enhance the production rates of biotechnologically important compounds. Regulation is held via modification the cellular activities of a metabolic system. In this study, we present a metabolic analysis of ethanol fermentation process of a yeast cell in terms of continuous culture scheme. The metabolic regulation is based on the kinetic formulation in combination with metabolic control analysis to indicate the key enzymes which can be modified to enhance ethanol production. The model is used to calculate the intracellular fluxes in the central metabolism of the yeast cell. Optimal control is then applied to the kinetic model to find the optimal regulation for the fermentation system. The sensitivity results show that there are external and internal control parameters which are adjusted in enhancing ethanol production. As an external control parameter, glucose supply should be chosen in appropriate way such that the optimal ethanol production can be achieved. For the internal control parameter, we find three enzymes as regulation targets namely acetaldehyde dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase which reside in the acetaldehyde branch. Among the three enzymes, however, only acetaldehyde dehydrogenase has a significant effect to obtain optimal ethanol production efficiently.

  13. Design of a high-throughput human neural crest cell migration assay to indicate potential developmental toxicants.

    Science.gov (United States)

    Nyffeler, Johanna; Karreman, Christiaan; Leisner, Heidrun; Kim, Yong Jun; Lee, Gabsang; Waldmann, Tanja; Leist, Marcel

    2017-01-01

    Migration of neural crest cells (NCCs) is one of the pivotal processes of human fetal development. Malformations arise if NCC migration and differentiation are impaired genetically or by toxicants. In the currently available test systems for migration inhibition of NCC (MINC), the manual generation of a cell-free space results in extreme operator dependencies, and limits throughput. Here a new test format was established. The assay avoids scratching by plating cells around a commercially available circular stopper. Removal of the stopper barrier after cell attachment initiates migration. This microwell-based circular migration zone NCC function assay (cMINC) was further optimized for toxicological testing of human pluripotent stem cell (hPSC)-derived NCCs. The challenge of obtaining data on viability and migration by automated image processing was addressed by developing a freeware. Data on cell proliferation were obtained by labelling replicating cells, and by careful assessment of cell viability for each experimental sample. The role of cell proliferation as an experimental confounder was tested experimentally by performing the cMINC in the presence of the proliferation-inhibiting drug cytosine arabinoside (AraC), and by a careful evaluation of mitotic events over time. Data from these studies led to an adaptation of the test protocol, so that toxicant exposure was limited to 24 h. Under these conditions, a prediction model was developed that allows classification of toxicants as either inactive, leading to unspecific cytotoxicity, or specifically inhibiting NC migration at non-cytotoxic concentrations.

  14. High-Throughput Single-Cell Labeling (Hi-SCL for RNA-Seq Using Drop-Based Microfluidics.

    Directory of Open Access Journals (Sweden)

    Assaf Rotem

    Full Text Available The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High-throughput Single-Cell Labeling (Hi-SCL in drops is a novel method that uses drop-based libraries of oligonucleotide barcodes to index individual cells in a population. The use of drops as containers, and a microfluidics platform to manipulate them en-masse, yields a highly scalable methodological framework. Once tagged, labeled molecules from different cells may be mixed without losing the cell-of-origin information. Here we demonstrate an application of the method for generating RNA-sequencing data for multiple individual cells within a population. Barcoded oligonucleotides are used to prime cDNA synthesis within drops. Barcoded cDNAs are then combined and subjected to second generation sequencing. The data are deconvoluted based on the barcodes, yielding single-cell mRNA expression data. In a proof-of-concept set of experiments we show that this method yields data comparable to other existing methods, but with unique potential for assaying very large numbers of cells.

  15. High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies

    Science.gov (United States)

    Liao, Hua-Xin; Levesque, Marc C.; Nagel, Ashleigh; Dixon, Ashlyn; Zhang, Ruijun; Walter, Emmanuel; Parks, Robert; Whitesides, John; Marshall, Dawn J.; Hwang, Kwan-Ki; Yang, Yi; Chen, Xi; Gao, Feng; Munshaw, Supriya; Kepler, Thomas B.; Denny, Thomas; Moody, M. Anthony; Haynes, Barton F.

    2009-01-01

    Defining human B cell repertoires to viral pathogens is critical for design of vaccines that induce broadly protective antibodies to infections such as HIV-1 and influenza. Single B cell sorting and cloning of immunoglobulin (Ig) heavy- and light-chain variable regions (VH and VL) is a powerful technology for defining anti-viral B cell repertoires. However, the Ig-cloning step is time-consuming and prevents high-throughput analysis of the B cell repertoire. Novel linear Ig heavy- and light-chain gene expression cassettes were designed to express Ig VH and VL genes isolated from sorted single B cells as IgG1 antibody without a cloning step. The cassettes contain all essential elements for transcriptional and translational regulation, including CMV promoter, Ig leader sequences, constant region of IgG1 heavy- or Ig light-chain, poly(A) tail and substitutable VH or VL genes. The utility of these Ig gene expression cassettes was established using synthetic VH or VL genes from an anti-HIV-1 gp41 mAb 2F5 as a model system, and validated further using VH and VL genes isolated from cloned EBV-transformed antibody-producing cell lines. Finally, this strategy was successfully used for rapid production of recombinant influenza mAbs from sorted single human plasmablasts after influenza vaccination. These Ig gene expression cassettes constitute a highly efficient strategy for rapid expression of Ig genes for high-throughput screening and analysis without cloning. PMID:19428587

  16. Studies on Cytotoxic Activity against HepG-2 Cells of Naphthoquinones from Green Walnut Husks of Juglans mandshurica Maxim

    Directory of Open Access Journals (Sweden)

    Yuanyuan Zhou

    2015-08-01

    Full Text Available Twenty-seven naphthoquinones and their derivatives, including four new naphthalenyl glucosides and twenty-three known compounds, were isolated from green walnut husks, which came from Juglans mandshurica Maxim. The structures of four new naphthalenyl glucosides were elucidated based on extensive spectroscopic analyses. All of these compounds were evaluated for their cytotoxic activities against the growth of human cancer cells lines HepG-2 by MTT [3-(4,5-dimethylthiazo l-2-yl-2,5 diphenyl tetrazolium bromide] assay. The results were shown that most naphthoquinones in an aglycone form exhibited better cytotoxicity in vitro than naphthalenyl glucosides with IC50 values in the range of 7.33–88.23 μM. Meanwhile, preliminary structure-activity relationships for these compounds were discussed.

  17. Cathode Assessment for Maximizing Current Generation in Microbial Fuel Cells Utilizing Bioethanol Effluent as Substrate

    DEFF Research Database (Denmark)

    Sun, Guotao; Thygesen, Anders; Meyer, Anne S.

    2016-01-01

    Implementation of microbial fuel cells (MFCs) for electricity production requires effective current generation from waste products via robust cathode reduction. Three cathode types using dissolved oxygen cathodes (DOCs), ferricyanide cathodes (FeCs) and air cathodes (AiCs) were therefore assessed...... responses to substrate loading rates and external resistance. At the lowest external resistance of 27 and highest substrate loading rate of 2 g chemical oxygen demand (COD) per Lday, FeC-MFC generated highest average current density (1630 mA/m(2)) followed by AiC-MFC (802 mA/m(2)) and DOC-MFC (184 mA/m(2......)). Electrochemical impedance spectroscopy (EIS) was used to determine the impedance of the cathodes. It was thereby confirmed that the FeC-MFC produced the highest current density with the lowest internal resistance for the cathode. However, in a setup using bioethanol effluent, the AiC-MFC was concluded...

  18. Identification of novel compounds inhibiting chikungunya virus-induced cell death by high throughput screening of a kinase inhibitor library.

    Directory of Open Access Journals (Sweden)

    Deu John M Cruz

    Full Text Available Chikungunya virus (CHIKV is a mosquito-borne arthrogenic alphavirus that causes acute febrile illness in humans accompanied by joint pains and in many cases, persistent arthralgia lasting weeks to years. The re-emergence of CHIKV has resulted in numerous outbreaks in the eastern hemisphere, and threatens to expand in the foreseeable future. Unfortunately, no effective treatment is currently available. The present study reports the use of resazurin in a cell-based high-throughput assay, and an image-based high-content assay to identify and characterize inhibitors of CHIKV-infection in vitro. CHIKV is a highly cytopathic virus that rapidly kills infected cells. Thus, cell viability of HuH-7 cells infected with CHIKV in the presence of compounds was determined by measuring metabolic reduction of resazurin to identify inhibitors of CHIKV-associated cell death. A kinase inhibitor library of 4,000 compounds was screened against CHIKV infection of HuH-7 cells using the resazurin reduction assay, and the cell toxicity was also measured in non-infected cells. Seventy-two compounds showing ≥50% inhibition property against CHIKV at 10 µM were selected as primary hits. Four compounds having a benzofuran core scaffold (CND0335, CND0364, CND0366 and CND0415, one pyrrolopyridine (CND0545 and one thiazol-carboxamide (CND3514 inhibited CHIKV-associated cell death in a dose-dependent manner, with EC50 values between 2.2 µM and 7.1 µM. Based on image analysis, these 6 hit compounds did not inhibit CHIKV replication in the host cell. However, CHIKV-infected cells manifested less prominent apoptotic blebs typical of CHIKV cytopathic effect compared with the control infection. Moreover, treatment with these compounds reduced viral titers in the medium of CHIKV-infected cells by up to 100-fold. In conclusion, this cell-based high-throughput screening assay using resazurin, combined with the image-based high content assay approach identified compounds against

  19. Combination of multifaceted strategies to maximize the therapeutic benefits of neural stem cell transplantation for spinal cord repair.

    Science.gov (United States)

    Hwang, Dong H; Kim, Hyuk M; Kang, Young M; Joo, In S; Cho, Chong-Su; Yoon, Byung-Woo; Kim, Seung U; Kim, Byung G

    2011-01-01

    Neural stem cells (NSCs) possess therapeutic potentials to reverse complex pathological processes following spinal cord injury (SCI), but many obstacles remain that could not be fully overcome by NSC transplantation alone. Combining complementary strategies might be required to advance NSC-based treatments to the clinical stage. The present study was undertaken to examine whether combination of NSCs, polymer scaffolds, neurotrophin-3 (NT3), and chondroitinase, which cleaves chondroitin sulfate proteoglycans at the interface between spinal cord and implanted scaffold, could provide additive therapeutic benefits. In a rat hemisection model, poly(ɛ-caprolactone) (PCL) was used as a bridging scaffold and as a vehicle for NSC delivery. The PCL scaffolds seeded with F3 NSCs or NT3 overexpressing F3 cells (F3.NT3) were implanted into hemisected cavities. F3.NT3 showed better survival and migration, and more frequently differentiated into neurons and oligodendrocytes than F3 cells. Animals with PCL scaffold containing F3.NT3 cells showed the best locomotor recovery, and motor evoked potentials (MEPs) following transcranial magnetic stimulation were recorded only in PCL-F3.NT3 group in contralateral, but not ipsilateral, hindlimbs. Implantation of PCL scaffold with F3.NT3 cells increased NT3 levels, promoted neuroplasticity, and enhanced remyelination of contralateral white matter. Combining chondroitinase treatment after PCL-F3.NT3 implantation further enhanced cell migration and promoted axonal remodeling, and this was accompanied by augmented locomotor recovery and restoration of MEPs in ipsilateral hindlimbs. We demonstrate that combining multifaceted strategies can maximize the therapeutic benefits of NSC transplantation for SCI. Our results may have important clinical implications for the design of future NSC-based strategies.

  20. High-throughput, cell-free, liposome-based approach for assessing in vitro activity of lipid kinases.

    Science.gov (United States)

    Demian, Douglas J; Clugston, Susan L; Foster, Meta M; Rameh, Lucia; Sarkes, Deborah; Townson, Sharon A; Yang, Lily; Zhang, Melvin; Charlton, Maura E

    2009-08-01

    Lipid kinases are central players in lipid signaling pathways involved in inflammation, tumorigenesis, and metabolic syndrome. A number of these kinase targets have proven difficult to investigate in higher throughput cell-free assay systems. This challenge is partially due to specific substrate interaction requirements for several of the lipid kinase family members and the resulting incompatibility of these substrates with most established, homogeneous assay formats. Traditional, cell-free in vitro investigational methods for members of the lipid kinase family typically involve substrate incorporation of [gamma-32P] and resolution of signal by thin-layer chromatography (TLC) and autoradiograph densitometry. This approach, although highly sensitive, does not lend itself to high-throughput testing of large numbers of small molecules (100 s to 1 MM+). The authors present the development and implementation of a fully synthetic, liposome-based assay for assessing in vitro activity of phosphatidylinositol-5-phosphate-4-kinase isoforms (PIP4KIIbeta and alpha) in 2 commonly used homogeneous technologies. They have validated these assays through compound testing in both traditional TLC and radioactive filterplate approaches as well as binding validation using isothermic calorimetry. A directed library representing known kinase pharmacophores was screened against type IIbeta phosphatidylinositol-phosphate kinase (PIPK) to identify small-molecule inhibitors. This assay system can be applied to other types and isoforms of PIPKs as well as a variety of other lipid kinase targets.

  1. Two-loop controller for maximizing performance of a grid-connected photovoltaic - fuel cell hybrid power plant

    Science.gov (United States)

    Ro, Kyoungsoo

    The study started with the requirement that a photovoltaic (PV) power source should be integrated with other supplementary power sources whether it operates in a stand-alone or grid-connected mode. First, fuel cells for a backup of varying PV power were compared in detail with batteries and were found to have more operational benefits. Next, maximizing performance of a grid-connected PV-fuel cell hybrid system by use of a two-loop controller was discussed. One loop is a neural network controller for maximum power point tracking, which extracts maximum available solar power from PV arrays under varying conditions of insolation, temperature, and system load. A real/reactive power controller (RRPC) is the other loop. The RRPC meets the system's requirement for real and reactive powers by controlling incoming fuel to fuel cell stacks as well as switching control signals to a power conditioning subsystem. The RRPC is able to achieve more versatile control of real/reactive powers than the conventional power sources since the hybrid power plant does not contain any rotating mass. Results of time-domain simulations prove not only effectiveness of the proposed computer models of the two-loop controller, but also their applicability for use in transient stability analysis of the hybrid power plant. Finally, environmental evaluation of the proposed hybrid plant was made in terms of plant's land requirement and lifetime COsb2 emissions, and then compared with that of the conventional fossil-fuel power generating forms.

  2. A new cell line for high throughput HIV-specific antibody-dependent cellular cytotoxicity (ADCC) and cell-to-cell virus transmission studies.

    Science.gov (United States)

    Orlandi, Chiara; Flinko, Robin; Lewis, George K

    2016-06-01

    Several lines of evidence indicate that antibody-dependent cellular cytotoxicity (Wren et al., 2013) is important in the pathogenesis of HIV-1 infection. Namely, ADCC is induced during natural HIV-1 infection or in HIV-1 vaccine studies, the latter demonstrated by the RV144 vaccine trial. To expedite the assessment of ADCC in studies of HIV, we have developed a high throughput assay. We have optimized the rapid fluorometric antibody-mediated cytotoxicity assay (RFADCC) by transfecting the EGFP-CEM-NKr cell line to constitutively express SNAP-tagged CCR5. This cell line can then serve as a source of HIV-specific targets when coated with monomeric gp120, spinoculated with inactivated intact virions, infected by cell-free viral diffusion or infected by cell-to-cell transmission of virus. The optimized strategy has two significant advantages over the original RFADCC method: First, the preparation of detectable target cells is less labor intensive and faster as it does not rely on multiple staining and washing steps for target cells. Second, because the target cell markers GFP and SNAP are constitutively expressed, the assay provides highly reproducible data. These strengths make the optimized RFADCC assay suitable not only for studies of HIV-1 specific cytotoxicity but also for studies of cell-cell transmission of virus. In conclusion, this assay provides a new generation T cell line that can expedite large clinical studies as well as research studies in humans or non-human primates. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Heterogeneous batch structures in throughput scheduling

    NARCIS (Netherlands)

    Weeda, P.J.; Weeda, P.J.

    1993-01-01

    Recently a few papers appeared on throughput scheduling, dealing with the relationship between batch structure and process structure in discrete batch production, while maximizing time-constrained throughput. Results have been concentrated on the class of homogeneous batch structures, i.e. batch

  4. Clinical validation of an ultra high-throughput spiral microfluidics for the detection and enrichment of viable circulating tumor cells.

    Directory of Open Access Journals (Sweden)

    Bee Luan Khoo

    Full Text Available Circulating tumor cells (CTCs are cancer cells that can be isolated via liquid biopsy from blood and can be phenotypically and genetically characterized to provide critical information for guiding cancer treatment. Current analysis of CTCs is hindered by the throughput, selectivity and specificity of devices or assays used in CTC detection and isolation.Here, we enriched and characterized putative CTCs from blood samples of patients with both advanced stage metastatic breast and lung cancers using a novel multiplexed spiral microfluidic chip. This system detected putative CTCs under high sensitivity (100%, n = 56 (Breast cancer samples: 12-1275 CTCs/ml; Lung cancer samples: 10-1535 CTCs/ml rapidly from clinically relevant blood volumes (7.5 ml under 5 min. Blood samples were completely separated into plasma, CTCs and PBMCs components and each fraction were characterized with immunophenotyping (Pan-cytokeratin/CD45, CD44/CD24, EpCAM, fluorescence in-situ hybridization (FISH (EML4-ALK or targeted somatic mutation analysis. We used an ultra-sensitive mass spectrometry based system to highlight the presence of an EGFR-activating mutation in both isolated CTCs and plasma cell-free DNA (cf-DNA, and demonstrate concordance with the original tumor-biopsy samples.We have clinically validated our multiplexed microfluidic chip for the ultra high-throughput, low-cost and label-free enrichment of CTCs. Retrieved cells were unlabeled and viable, enabling potential propagation and real-time downstream analysis using next generation sequencing (NGS or proteomic analysis.

  5. Corydalis edulis Maxim. Promotes Insulin Secretion via the Activation of Protein Kinase Cs (PKCs) in Mice and Pancreatic β Cells.

    Science.gov (United States)

    Zheng, Jiao; Zhao, Yunfang; Lun, Qixing; Song, Yuelin; Shi, Shepo; Gu, Xiaopan; Pan, Bo; Qu, Changhai; Li, Jun; Tu, Pengfei

    2017-01-16

    Corydalis edulis Maxim., a widely grown plant in China, had been proposed for the treatment for type 2 diabetes mellitus. In this study, we found that C. edulis extract (CE) is protective against diabetes in mice. The treatment of hyperglycemic and hyperlipidemic apolipoprotein E (ApoE)-/- mice with a high dose of CE reduced serum glucose by 28.84% and serum total cholesterol by 17.34% and increased insulin release. We also found that CE significantly enhanced insulin secretion in a glucose-independent manner in hamster pancreatic β cell (HIT-T15). Further investigation revealed that CE stimulated insulin exocytosis by a protein kinase C (PKC)-dependent signaling pathway and that CE selectively activated novel protein kinase Cs (nPKCs) and atypical PKCs (aPKCs) but not conventional PKCs (cPKCs) in HIT-T15 cells. To the best of our knowledge, our study is the first to identify the PKC pathway as a direct target and one of the major mechanisms underlying the antidiabetic effect of CE. Given the good insulinotropic effect of this herbal medicine, CE is a promising agent for the development of new drugs for treating diabetes.

  6. Automated Patch Clamp Meets High-Throughput Screening: 384 Cells Recorded in Parallel on a Planar Patch Clamp Module.

    Science.gov (United States)

    Obergrussberger, Alison; Brüggemann, Andrea; Goetze, Tom A; Rapedius, Markus; Haarmann, Claudia; Rinke, Ilka; Becker, Nadine; Oka, Takayuki; Ohtsuki, Atsushi; Stengel, Timo; Vogel, Marius; Steindl, Juergen; Mueller, Max; Stiehler, Johannes; George, Michael; Fertig, Niels

    2016-12-01

    We have developed an automated patch clamp module for high-throughput ion channel screening, recording from 384 cells simultaneously. The module is incorporated into a laboratory pipetting robot and uses a 384-channel pipettor head for application of cells and compounds. The module contains 384 amplifier channels for fully parallel recordings using a digital amplifier. Success rates for completed experiments (1- to 4-point concentration-response curves for cells satisfying defined quality control parameters) of greater than 85% have been routinely achieved with, for example, HEK, CHO, and RBL cell lines expressing hNaV1.7, hERG, Kir2.1, GABA, or glutamate receptors. Pharmacology experiments are recorded and analyzed using specialized software, and the pharmacology of hNaV1.7 and hERG is described. Fast external solution exchange rates of robot to minimize exposure of the ligand on the receptor. This ensures that ligand-gated ion channels, for example, GABA and glutamate described in this report, can be reproducibly recorded. Stem cell-derived cardiomyocytes have also been used with success rates of 52% for cells that have a seal resistance of >200 MΩ, and recordings of voltage-gated Na+ and Ca2+ are shown. © 2015 Society for Laboratory Automation and Screening.

  7. 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.

  8. Potential of dynamically harmonized Fourier transform ion cyclotron resonance cell for high-throughput metabolomics fingerprinting: control of data quality.

    Science.gov (United States)

    Habchi, Baninia; Alves, Sandra; Jouan-Rimbaud Bouveresse, Delphine; Appenzeller, Brice; Paris, Alain; Rutledge, Douglas N; Rathahao-Paris, Estelle

    2018-01-01

    Due to the presence of pollutants in the environment and food, the assessment of human exposure is required. This necessitates high-throughput approaches enabling large-scale analysis and, as a consequence, the use of high-performance analytical instruments to obtain highly informative metabolomic profiles. In this study, direct introduction mass spectrometry (DIMS) was performed using a Fourier transform ion cyclotron resonance (FT-ICR) instrument equipped with a dynamically harmonized cell. Data quality was evaluated based on mass resolving power (RP), mass measurement accuracy, and ion intensity drifts from the repeated injections of quality control sample (QC) along the analytical process. The large DIMS data size entails the use of bioinformatic tools for the automatic selection of common ions found in all QC injections and for robustness assessment and correction of eventual technical drifts. RP values greater than 106 and mass measurement accuracy of lower than 1 ppm were obtained using broadband mode resulting in the detection of isotopic fine structure. Hence, a very accurate relative isotopic mass defect (RΔm) value was calculated. This reduces significantly the number of elemental composition (EC) candidates and greatly improves compound annotation. A very satisfactory estimate of repeatability of both peak intensity and mass measurement was demonstrated. Although, a non negligible ion intensity drift was observed for negative ion mode data, a normalization procedure was easily applied to correct this phenomenon. This study illustrates the performance and robustness of the dynamically harmonized FT-ICR cell to perform large-scale high-throughput metabolomic analyses in routine conditions. Graphical abstract Analytical performance of FT-ICR instrument equipped with a dynamically harmonized cell.

  9. Yeast Replicator: A High-Throughput Multiplexed Microfluidics Platform for Automated Measurements of Single-Cell Aging

    Directory of Open Access Journals (Sweden)

    Ping Liu

    2015-10-01

    Full Text Available The yeast Saccharomyces cerevisiae is a model organism for replicative aging studies; however, conventional lifespan measurement platforms have several limitations. Here, we present a microfluidics platform that facilitates simultaneous lifespan and gene expression measurements of aging yeast cells. Our multiplexed high-throughput platform offers the capability to perform independent lifespan experiments using different yeast strains or growth media. Using this platform in minimal media environments containing glucose, we measured the full lifespan of individual yeast cells in wild-type and canonical gene deletion backgrounds. Compared to glucose, in galactose we observed a 16.8% decrease in replicative lifespan accompanied by an ∼2-fold increase in single-cell oxidative stress levels reported by PSOD1-mCherry. Using PGAL1-YFP to measure the activity of the bistable galactose network, we saw that OFF and ON cells are similar in their lifespan. Our work shows that aging cells are committed to a single phenotypic state throughout their lifespan.

  10. High-throughput microarray mapping of cell wall polymers in roots and tubers during the viscosity-reducing process.

    Science.gov (United States)

    Huang, Yuhong; Willats, William G; Lange, Lene; Jin, Yanling; Fang, Yang; Salmeán, Armando A; Pedersen, Henriette L; Busk, Peter Kamp; Zhao, Hai

    2016-01-01

    Viscosity reduction has a great impact on the efficiency of ethanol production when using roots and tubers as feedstock. Plant cell wall-degrading enzymes have been successfully applied to overcome the challenges posed by high viscosity. However, the changes in cell wall polymers during the viscosity-reducing process are poorly characterized. Comprehensive microarray polymer profiling, which is a high-throughput microarray, was used for the first time to map changes in the cell wall polymers of sweet potato (Ipomoea batatas), cassava (Manihot esculenta), and Canna edulis Ker. over the entire viscosity-reducing process. The results indicated that the composition of cell wall polymers among these three roots and tubers was markedly different. The gel-like matrix and glycoprotein network in the C. edulis Ker. cell wall caused difficulty in viscosity reduction. The obvious viscosity reduction of the sweet potato and the cassava was attributed to the degradation of homogalacturonan and the released 1,4-β-d-galactan and 1,5-α-l-arabinan. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

  11. Rapid preparation and single-cell analysis of concentrated blood smears using a high-throughput blood cell separator and a microfabricated grid film.

    Science.gov (United States)

    You, Dongwon; Oh, Sein; Kim, Byeongyeon; Hahn, Young Ki; Choi, Sungyoung

    2017-07-21

    Cytological examination of peripheral white blood cells inhomogeneously distributed on a blood smear is currently limited by the low abundance and random sampling of the target cells. To address the challenges, we present a new approach to prepare and analyze concentrated blood smears by rapidly enriching white blood cells up to 32-fold with 92% recovery on average at a high throughput (1mL/min) using a deterministic migration-based separator and by systematically analyzing a large number of the cells distributed over a blood slide using a microfabricated grid film. We anticipate that our approach will improve the clinical utility of blood smear tests, while offering the capability to detect rare cell populations. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Studies on Cytotoxic Constituents from the Leaves of Elaeagnus oldhamii Maxim. in Non-Small Cell Lung Cancer A549 Cells

    Directory of Open Access Journals (Sweden)

    Chi-Ren Liao

    2014-07-01

    Full Text Available Elaeagnus oldhamii Maxim. is a commonly used traditional herbal medicine. In Taiwan the leaves of E. oldhamii Maxim. are mainly used for treating lung disorders. Twenty five compounds were isolated from the leaves of E. oldhamii Maxim. in the present study. These included oleanolic acid (1, 3-O-(Z-coumaroyl oleanolic acid (2, 3-O-(E-coumaroyl oleanolic acid (3, 3-O-caffeoyl oleanolic acid (4, ursolic acid (5, 3-O-(Z-coumaroyl ursolic acid (6, 3-O-(E-coumaroyl ursolic acid (7, 3-O-caffeoyl ursolic acid (8, 3β, 13β-dihydroxyolean-11-en-28-oic acid (9, 3β, 13β-dihydroxyurs-11-en-28-oic acid (10, uvaol (11, betulin (12, lupeol (13, kaempferol (14, aromadendrin (15, epigallocatechin (16, cis-tiliroside (17, trans-tiliroside (18, isoamericanol B (19, trans-p-coumaric acid (20, protocatechuic acid (21, salicylic acid (22, trans-ferulic acid (23, syringic acid (24 and 3-O-methylgallic acid (25. Of the 25 isolated compounds, 21 compounds were identified for the first time in E. oldhamii Maxim. These included compounds 1, 4, 5 and 8–25. These 25 compounds were evaluated for their inhibitory activity against the growth of non-small cell lung cancer A549 cells by the MTT assay, and the corresponding structure-activity relationships were discussed. Among these 25 compounds, compound 6 displayed the best activity against the A549 cell line in vitro (CC50 = 8.56 ± 0.57 μg/mL, at 48 h of MTT asssay. Furthermore, compound 2, 4, 8 and 18 exhibited in vitro cytotoxicity against the A549 cell line with the CC50 values of less than 20 μg/mL at 48 h of MTT asssay. These five compounds 2, 4, 6, 8 and 18 exhibited better cytotoxic activity compared with cisplatin (positive control, CC50 value of 14.87 ± 1.94 μg/mL, at 48 h of MTT asssay. The result suggested that the five compounds might be responsible for its clinical anti-lung cancer effect.

  13. Studies on cytotoxic constituents from the leaves of Elaeagnus oldhamii Maxim. in non-small cell lung cancer A549 cells.

    Science.gov (United States)

    Liao, Chi-Ren; Kuo, Yueh-Hsiung; Ho, Yu-Ling; Wang, Ching-Ying; Yang, Chang-Syun; Lin, Cheng-Wen; Chang, Yuan-Shiun

    2014-07-04

    Elaeagnus oldhamii Maxim. is a commonly used traditional herbal medicine. In Taiwan the leaves of E. oldhamii Maxim. are mainly used for treating lung disorders. Twenty five compounds were isolated from the leaves of E. oldhamii Maxim. in the present study. These included oleanolic acid (1), 3-O-(Z)-coumaroyl oleanolic acid (2), 3-O-(E)-coumaroyl oleanolic acid (3), 3-O-caffeoyl oleanolic acid (4), ursolic acid (5), 3-O-(Z)-coumaroyl ursolic acid (6), 3-O-(E)-coumaroyl ursolic acid (7), 3-O-caffeoyl ursolic acid (8), 3β, 13β-dihydroxyolean-11-en-28-oic acid (9), 3β, 13β-dihydroxyurs-11-en-28-oic acid (10), uvaol (11), betulin (12), lupeol (13), kaempferol (14), aromadendrin (15), epigallocatechin (16), cis-tiliroside (17), trans-tiliroside (18), isoamericanol B (19), trans-p-coumaric acid (20), protocatechuic acid (21), salicylic acid (22), trans-ferulic acid (23), syringic acid (24) and 3-O-methylgallic acid (25). Of the 25 isolated compounds, 21 compounds were identified for the first time in E. oldhamii Maxim. These included compounds 1, 4, 5 and 8-25. These 25 compounds were evaluated for their inhibitory activity against the growth of non-small cell lung cancer A549 cells by the MTT assay, and the corresponding structure-activity relationships were discussed. Among these 25 compounds, compound 6 displayed the best activity against the A549 cell line in vitro (CC50=8.56±0.57 μg/mL, at 48 h of MTT asssay). Furthermore, compound 2, 4, 8 and 18 exhibited in vitro cytotoxicity against the A549 cell line with the CC50 values of less than 20 μg/mL at 48 h of MTT asssay. These five compounds 2, 4, 6, 8 and 18 exhibited better cytotoxic activity compared with cisplatin (positive control, CC50 value of 14.87±1.94 μg/mL, at 48 h of MTT asssay). The result suggested that the five compounds might be responsible for its clinical anti-lung cancer effect.

  14. High-throughput screening of high-capacity electrodes for hybrid Li-ion-Li-O₂ cells.

    Science.gov (United States)

    Kirklin, S; Chan, M K Y; Trahey, L; Thackeray, M M; Wolverton, C

    2014-10-28

    Recent experiments have shown that lithium and oxygen can be electrochemically removed from Li5FeO4 (5Li2O·Fe2O3) and re-accommodated during discharge, creating the possibility of its use as a high-capacity electrode in a hybrid Li-ion/Li-O2 electrochemical cell. Taking this novel chemistry as a model, we use density functional theory (DFT) within a high-throughput framework to screen for analogous reactions in other materials. We search for candidate materials possessing high capacity, voltages compatible with existing electrolytes, and reasonable electrical conductivity. We identify several promising candidate materials that may operate by a similar reaction mechanism and are worthy of investigation, such as Li6MnO4, Li6CoO4, Li4MoO5 and Li8IrO6. This work paves the way for accelerated exploration of this intriguing new battery chemistry.

  15. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism.

    Science.gov (United States)

    Nemenman, Ilya; Escola, G Sean; Hlavacek, William S; Unkefer, Pat J; Unkefer, Clifford J; Wall, Michael E

    2007-12-01

    We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For benchmarking purposes, we generate synthetic metabolic profiles based on a well-established model for red blood cell metabolism. A variety of data sets are generated, accounting for different properties of real metabolic networks, such as experimental noise, metabolite correlations, and temporal dynamics. These data sets are made available online. We use ARACNE, a mainstream algorithm for reverse engineering of transcriptional regulatory networks from gene expression data, to predict metabolic interactions from these data sets. We find that the performance of ARACNE on metabolic data is comparable to that on gene expression data.

  16. Ultra-high-throughput screening of an in vitro-synthesized horseradish peroxidase displayed on microbeads using cell sorter.

    Directory of Open Access Journals (Sweden)

    Bo Zhu

    Full Text Available The C1a isoenzyme of horseradish peroxidase (HRP is an industrially important heme-containing enzyme that utilizes hydrogen peroxide to oxidize a wide variety of inorganic and organic compounds for practical applications, including synthesis of fine chemicals, medical diagnostics, and bioremediation. To develop a ultra-high-throughput screening system for HRP, we successfully produced active HRP in an Escherichia coli cell-free protein synthesis system, by adding disulfide bond isomerase DsbC and optimizing the concentrations of hemin and calcium ions and the temperature. The biosynthesized HRP was fused with a single-chain Cro (scCro DNA-binding tag at its N-terminal and C-terminal sites. The addition of the scCro-tag at both ends increased the solubility of the protein. Next, HRP and its fusion proteins were successfully synthesized in a water droplet emulsion by using hexadecane as the oil phase and SunSoft No. 818SK as the surfactant. HRP fusion proteins were displayed on microbeads attached with double-stranded DNA (containing the scCro binding sequence via scCro-DNA interactions. The activities of the immobilized HRP fusion proteins were detected with a tyramide-based fluorogenic assay using flow cytometry. Moreover, a model microbead library containing wild type hrp (WT and inactive mutant (MUT genes was screened using fluorescence-activated cell-sorting, thus efficiently enriching the WT gene from the 1:100 (WT:MUT library. The technique described here could serve as a novel platform for the ultra-high-throughput discovery of more useful HRP mutants and other heme-containing peroxidases.

  17. Cytotoxicity of Triterpenes from Green Walnut Husks of Juglans mandshurica Maxim in HepG-2 Cancer Cells.

    Science.gov (United States)

    Zhou, Yuanyuan; Yang, Bingyou; Liu, Zhaoxi; Jiang, Yanqiu; Liu, Yuxin; Fu, Lei; Wang, Xiaoli; Kuang, Haixue

    2015-10-22

    Among the classes of identified natural products, triterpenoids, one of the largest families, have been studied extensively for their diverse structures and variety of biological activities, including antitumor effects. In the present study, a phytochemical study of the green walnut husks of Juglans mandshurica Maxim led to the isolation of a new dammarane triterpene, 12β, 20(R), 24(R)-trihydroxydammar-25-en-3-one (6), together with sixteen known compounds, chiefly from chloroform and ethyl acetate extracts. According to their structural characteristics, these compounds were divided into dammarane-type, oleanane- and ursane-type. Dammarane-type triterpenoids were isolated for the first time from the Juglans genus. As part of our continuing search for biologically active compounds from this plant, all of these compounds were also evaluated for their cytotoxic activities against the growth of human cancer cells lines HepG-2 by the MTT assay. The results were shown that 20(S)-protopanaxadiol, 2α,3β,23-trihydroxyolean-12-en-28-oic acid and 2α,3β,23-trihydroxyurs-12-en-28-oic acid exhibited better cytotoxicity in vitro with IC50 values of 10.32±1.13, 16.13±3.83, 15.97±2.47 μM, respectively. Preliminary structure-activity relationships for these compounds were discussed.

  18. High-content live cell imaging with RNA probes: advancements in high-throughput antimalarial drug discovery

    Directory of Open Access Journals (Sweden)

    Cervantes Serena

    2009-06-01

    Full Text Available Abstract Background Malaria, a major public health issue in developing nations, is responsible for more than one million deaths a year. The most lethal species, Plasmodium falciparum, causes up to 90% of fatalities. Drug resistant strains to common therapies have emerged worldwide and recent artemisinin-based combination therapy failures hasten the need for new antimalarial drugs. Discovering novel compounds to be used as antimalarials is expedited by the use of a high-throughput screen (HTS to detect parasite growth and proliferation. Fluorescent dyes that bind to DNA have replaced expensive traditional radioisotope incorporation for HTS growth assays, but do not give additional information regarding the parasite stage affected by the drug and a better indication of the drug's mode of action. Live cell imaging with RNA dyes, which correlates with cell growth and proliferation, has been limited by the availability of successful commercial dyes. Results After screening a library of newly synthesized stryrl dyes, we discovered three RNA binding dyes that provide morphological details of live parasites. Utilizing an inverted confocal imaging platform, live cell imaging of parasites increases parasite detection, improves the spatial and temporal resolution of the parasite under drug treatments, and can resolve morphological changes in individual cells. Conclusion This simple one-step technique is suitable for automation in a microplate format for novel antimalarial compound HTS. We have developed a new P. falciparum RNA high-content imaging growth inhibition assay that is robust with time and energy efficiency.

  19. High-content live cell imaging with RNA probes: advancements in high-throughput antimalarial drug discovery

    Science.gov (United States)

    Cervantes, Serena; Prudhomme, Jacques; Carter, David; Gopi, Krishna G; Li, Qian; Chang, Young-Tae; Le Roch, Karine G

    2009-01-01

    Background Malaria, a major public health issue in developing nations, is responsible for more than one million deaths a year. The most lethal species, Plasmodium falciparum, causes up to 90% of fatalities. Drug resistant strains to common therapies have emerged worldwide and recent artemisinin-based combination therapy failures hasten the need for new antimalarial drugs. Discovering novel compounds to be used as antimalarials is expedited by the use of a high-throughput screen (HTS) to detect parasite growth and proliferation. Fluorescent dyes that bind to DNA have replaced expensive traditional radioisotope incorporation for HTS growth assays, but do not give additional information regarding the parasite stage affected by the drug and a better indication of the drug's mode of action. Live cell imaging with RNA dyes, which correlates with cell growth and proliferation, has been limited by the availability of successful commercial dyes. Results After screening a library of newly synthesized stryrl dyes, we discovered three RNA binding dyes that provide morphological details of live parasites. Utilizing an inverted confocal imaging platform, live cell imaging of parasites increases parasite detection, improves the spatial and temporal resolution of the parasite under drug treatments, and can resolve morphological changes in individual cells. Conclusion This simple one-step technique is suitable for automation in a microplate format for novel antimalarial compound HTS. We have developed a new P. falciparum RNA high-content imaging growth inhibition assay that is robust with time and energy efficiency. PMID:19515257

  20. A High-Throughput, Flow Cytometry-Based Method to Quantify DNA-End Resection in Mammalian Cells

    Science.gov (United States)

    Forment, Josep V; Walker, Rachael V; Jackson, Stephen P

    2012-01-01

    Replication protein A (RPA) is an essential trimeric protein complex that binds to single-stranded DNA (ssDNA) in eukaryotic cells and is involved in various aspects of cellular DNA metabolism, including replication and repair. Although RPA is ubiquitously expressed throughout the cell cycle, it localizes to DNA replication forks during S phase, and is recruited to sites of DNA damage when regions of ssDNA are exposed. During DNA double-strand break (DSB) repair by homologous recombination (HR), RPA recruitment to DNA damage sites depends on a process termed DNA-end resection. Consequently, RPA recruitment to sub-nuclear regions bearing DSBs has been used as readout for resection and for ongoing HR. Quantification of RPA recruitment by immunofluorescence-based microscopy techniques is time consuming and requires extensive image analysis of relatively small populations of cells. Here, we present a high-throughput flow-cytometry method that allows the use of RPA staining to measure cell proliferation and DNA-damage repair by HR in an unprecedented, unbiased and quantitative manner. © 2012 International Society for Advancement of Cytometry PMID:22893507

  1. Studying host cell protein interactions with monoclonal antibodies using high throughput protein A chromatography.

    Science.gov (United States)

    Sisodiya, Vikram N; Lequieu, Joshua; Rodriguez, Maricel; McDonald, Paul; Lazzareschi, Kathlyn P

    2012-10-01

    Protein A chromatography is typically used as the initial capture step in the purification of monoclonal antibodies produced in Chinese hamster ovary (CHO) cells. Although exploiting an affinity interaction for purification, the level of host cell proteins in the protein A eluent varies significantly with different feedstocks. Using a batch binding chromatography method, we performed a controlled study to assess host cell protein clearance across both MabSelect Sure and Prosep vA resins. We individually spiked 21 purified antibodies into null cell culture fluid generated with a non-producing cell line, creating mock cell culture fluids for each antibody with an identical composition of host cell proteins and antibody concentration. We demonstrated that antibody-host cell protein interactions are primarily responsible for the variable levels of host cell proteins in the protein A eluent for both resins when antibody is present. Using the additives guanidine HCl and sodium chloride, we demonstrated that antibody-host cell protein interactions may be disrupted, reducing the level of host cell proteins present after purification on both resins. The reduction in the level of host cell proteins differed between antibodies suggesting that the interaction likely varies between individual antibodies but encompasses both an electrostatic and hydrophobic component. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Identification and use of fluorescent dyes for plant cell wall imaging using high-throughput screening.

    Science.gov (United States)

    Anderson, Charles T; Carroll, Andrew

    2014-01-01

    Plant cell walls define cell shape during development and are composed of interlaced carbohydrate and protein networks. Fluorescent dyes have long been used to label plant cell walls, enabling optical microscopy-based interrogation of cell wall structure and composition. However, the specific cell wall components to which these dyes bind are often poorly defined. The availability of fluorescent compound libraries provides the potential to screen for and identify new fluorescent compounds that interact with specific plant cell wall components, enabling the study of cell wall architecture in intact, living tissues. Here, we describe a technique for screening fluorescent compound libraries for enhanced fluorescence upon interaction with plant cell walls, a secondary screening method to identify which cell wall components interact with a given dye, and a protocol for staining and observing Arabidopsis seedlings using a fluorescent cell wall-labeling dye. These methods have the potential to be applied to screening for differences in cell wall structure and composition among genetically diverse plant varieties or species.

  3. Development of a high-throughput cell-based reporter assay for screening of JAK3 inhibitors.

    Science.gov (United States)

    Yin, Chang-Hong; Bach, Erika A; Baeg, Gyeong-Hun

    2011-04-01

    JAK3 is an ideal target for the treatment of immune-related diseases and the prevention of organ allograft rejection. Several JAK3 inhibitors have been identified by biochemical enzymatic assays, but the majority display significant off-target effects on JAK2. Therefore, there is a need to develop new experimental approaches to identify compounds that specifically inhibit JAK3. Here, we show that in 32D/IL-2Rβ cells, STAT5 becomes phosphorylated by an IL-3/JAK2- or IL-2/JAK3-dependent pathway. Importantly, the selective JAK3 inhibitor CP-690,550 blocked the phosphorylation and the nuclear translocation of STAT5 following treatment of cells with IL-2 but not with IL-3. In an attempt to use the cells for large-scale chemical screens to identify JAK3 inhibitors, we established a cell line, 32D/IL-2Rβ/6xSTAT5, stably expressing a STAT5 reporter gene. Treatment of this cell line with IL-2 or IL-3 dramatically increased the reporter activity in a high-throughput format. As expected, CP-690,550 selectively inhibited the activity of the 6xSTAT5 reporter following treatment with IL-2. By contrast, the pan-JAK inhibitor curcumin inhibited the activity of this reporter following treatment with either IL-2 or IL-3. Thus, this study indicates that the STAT5 reporter cell line can be used as an efficacious cellular model for chemical screens to identify selective JAK3 inhibitors.

  4. Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes.

    Directory of Open Access Journals (Sweden)

    Ditte Hededam Welner

    Full Text Available Molecular characterization of plant cell wall glycosyltransferases is a critical step towards understanding the biosynthesis of the complex plant cell wall, and ultimately for efficient engineering of biofuel and agricultural crops. The majority of these enzymes have proven very difficult to obtain in the needed amount and purity for such molecular studies, and recombinant cell wall glycosyltransferase production efforts have largely failed. A daunting number of strategies can be employed to overcome this challenge, including optimization of DNA and protein sequences, choice of expression organism, expression conditions, co-expression partners, purification methods, and optimization of protein solubility and stability. Hence researchers are presented with thousands of potential conditions to test. Ultimately, the subset of conditions that will be sampled depends on practical considerations and prior knowledge of the enzyme(s being studied. We have developed a rational approach to this process. We devise a pipeline comprising in silico selection of targets and construct design, and high-throughput expression screening, target enrichment, and hit identification. We have applied this pipeline to a test set of Arabidopsis thaliana cell wall glycosyltransferases known to be challenging to obtain in soluble form, as well as to a library of cell wall glycosyltransferases from other plants including agricultural and biofuel crops. The screening results suggest that recombinant cell wall glycosyltransferases in general have a very low soluble:insoluble ratio in lysates from heterologous expression cultures, and that co-expression of chaperones as well as lysis buffer optimization can increase this ratio. We have applied the identified preferred conditions to Reversibly Glycosylated Polypeptide 1 from Arabidopsis thaliana, and processed this enzyme to near-purity in unprecedented milligram amounts. The obtained preparation of Reversibly Glycosylated

  5. Androgen receptor functional analyses by high throughput imaging: determination of ligand, cell cycle, and mutation-specific effects.

    Directory of Open Access Journals (Sweden)

    Adam T Szafran

    Full Text Available Understanding how androgen receptor (AR function is modulated by exposure to steroids, growth factors or small molecules can have important mechanistic implications for AR-related disease therapies (e.g., prostate cancer, androgen insensitivity syndrome, AIS, and in the analysis of environmental endocrine disruptors.We report the development of a high throughput (HT image-based assay that quantifies AR subcellular and subnuclear distribution, and transcriptional reporter gene activity on a cell-by-cell basis. Furthermore, simultaneous analysis of DNA content allowed determination of cell cycle position and permitted the analysis of cell cycle dependent changes in AR function in unsynchronized cell populations. Assay quality for EC50 coefficients of variation were 5-24%, with Z' values reaching 0.91. This was achieved by the selective analysis of cells expressing physiological levels of AR, important because minor over-expression resulted in elevated nuclear speckling and decreased transcriptional reporter gene activity. A small screen of AR-binding ligands, including known agonists, antagonists, and endocrine disruptors, demonstrated that nuclear translocation and nuclear "speckling" were linked with transcriptional output, and specific ligands were noted to differentially affect measurements for wild type versus mutant AR, suggesting differing mechanisms of action. HT imaging of patient-derived AIS mutations demonstrated a proof-of-principle personalized medicine approach to rapidly identify ligands capable of restoring multiple AR functions.HT imaging-based multiplex screening will provide a rapid, systems-level analysis of compounds/RNAi that may differentially affect wild type AR or clinically relevant AR mutations.

  6. Identification of novel Mycobacterium tuberculosis CD4 T-cell antigens via high throughput proteome screening

    OpenAIRE

    Nayak, Kaustuv; Jing, Lichen; Russell, Ronnie M.; Davies, D. Huw; Hermanson, Gary; Molina, Douglas M.; Liang, Xiaowu; Sherman, David R.; Kwok, William W.; Yang, Junbao; Kenneth, John; Ahamed, Syed F.; Chandele, Anmol; Kaja, Murali-Krishna; Koelle, David M.

    2015-01-01

    Elicitation of CD4 IFN-gamma T cell responses to Mycobacterium tuberculosis (MTB) is a rational vaccine strategy to prevent clinical tuberculosis. Diagnosis of MTB infection is based on T-cell immune memory to MTB antigens. The MTB proteome contains over four thousand open reading frames (ORFs). We conducted a pilot antigen identification study using 164 MTB proteins and MTB-specific T-cells expanded in vitro from 12 persons with latent MTB infection. Enrichment of MTB-reactive T-cells from P...

  7. Serial isoelectric focusing as an effective and economic way to obtain maximal resolution and high-throughput in 2D-based comparative proteomics of scarce samples: proof-of-principle.

    Science.gov (United States)

    Farhoud, Murtada H; Wessels, Hans J C T; Wevers, Ron A; van Engelen, Baziel G; van den Heuvel, Lambert P; Smeitink, Jan A

    2005-01-01

    In 2D-based comparative proteomics of scarce samples, such as limited patient material, established methods for prefractionation and subsequent use of different narrow range IPG strips to increase overall resolution are difficult to apply. Also, a high number of samples, a prerequisite for drawing meaningful conclusions when pathological and control samples are considered, will increase the associated amount of work almost exponentially. Here, we introduce a novel, effective, and economic method designed to obtain maximum 2D resolution while maintaining the high throughput necessary to perform large-scale comparative proteomics studies. The method is based on connecting different IPG strips serially head-to-tail so that a complete line of different IPG strips with sequential pH regions can be focused in the same experiment. We show that when 3 IPG strips (covering together the pH range of 3-11) are connected head-to-tail an optimal resolution is achieved along the whole pH range. Sample consumption, time required, and associated costs are reduced by almost 70%, and the workload is reduced significantly.

  8. Use of flow cytometry for high-throughput cell population estimates in brain tissue

    Science.gov (United States)

    Young, Nicole A.; Flaherty, David K.; Airey, David C.; Varlan, Peter; Aworunse, Feyi; Kaas, Jon H.; Collins, Christine E.

    2012-01-01

    The large size of primate brains is an impediment to obtaining high-resolution cell number maps of the cortex in humans and non-human primates. We present a rapid, flow cytometry-based cell counting method that can be used to estimate cell numbers from homogenized brain tissue samples comprising the entire cortical sheet. The new method, called the flow fractionator, is based on the isotropic fractionator (IF) method (Herculano-Houzel and Lent, 2005), but substitutes flow cytometry analysis for manual, microscope analysis using a Neubauer counting chamber. We show that our flow cytometry-based method for total cell estimation in homogenized brain tissue provides comparable data to that obtained using a counting chamber on a microscope. The advantages of the flow fractionator over existing methods are improved precision of cell number estimates and improved speed of analysis. PMID:22798947

  9. Microfluidic Concentric Gradient Generator Design for High-Throughput Cell-Based Studies.

    Science.gov (United States)

    Ezra Tsur, Elishai; Zimerman, Michal; Maor, Idan; Elrich, Avner; Nahmias, Yaakov

    2017-01-01

    Gradients of diffusible signaling molecules play important role in various processes, ranging from cell differentiation to toxicological evaluation. Microfluidic technology provides an accurate control of tempospatial conditions. However, current microfluidic platforms are not designed to handle multiple gradients and cell populations simultaneously. Here, we demonstrate a rapidly adaptable microfluidic design able to expose multiple cell populations to an array of chemical gradients. Our design is based on pressure-equilibrated concentric channels and a pressure-dissipating control layer, facilitating the seeding of multiple cell populations in a single device. The design was numerically evaluated and experimentally validated. The device consists of 8 radiating stimuli channels and 12 circular cell culture channels, creating an array of 96 different continuous gradients that can be simultaneously monitored over time.

  10. A near-infrared fluorescent voltage-sensitive dye allows for moderate-throughput electrophysiological analyses of human induced pluripotent stem cell-derived cardiomyocytes

    Science.gov (United States)

    Lopez-Izquierdo, Angelica; Warren, Mark; Riedel, Michael; Cho, Scott; Lai, Shuping; Lux, Robert L.; Spitzer, Kenneth W.; Benjamin, Ivor J.; Jou, Chuanchau J.

    2014-01-01

    Human induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM)-based assays are emerging as a promising tool for the in vitro preclinical screening of QT interval-prolonging side effects of drugs in development. A major impediment to the widespread use of human iPSC-CM assays is the low throughput of the currently available electrophysiological tools. To test the precision and applicability of the near-infrared fluorescent voltage-sensitive dye 1-(4-sulfanatobutyl)-4-{β[2-(di-n-butylamino)-6-naphthyl]butadienyl}quinolinium betaine (di-4-ANBDQBS) for moderate-throughput electrophysiological analyses, we compared simultaneous transmembrane voltage and optical action potential (AP) recordings in human iPSC-CM loaded with di-4-ANBDQBS. Optical AP recordings tracked transmembrane voltage with high precision, generating nearly identical values for AP duration (AP durations at 10%, 50%, and 90% repolarization). Human iPSC-CMs tolerated repeated laser exposure, with stable optical AP parameters recorded over a 30-min study period. Optical AP recordings appropriately tracked changes in repolarization induced by pharmacological manipulation. Finally, di-4-ANBDQBS allowed for moderate-throughput analyses, increasing throughput >10-fold over the traditional patch-clamp technique. We conclude that the voltage-sensitive dye di-4-ANBDQBS allows for high-precision optical AP measurements that markedly increase the throughput for electrophysiological characterization of human iPSC-CMs. PMID:25172899

  11. A whole-cell assay for the high throughput screening of calmodulin antagonists.

    Science.gov (United States)

    Dikici, Emre; Deo, Sapna K; Daunert, Sylvia

    2008-04-01

    Cell-based screening systems for pharmaceuticals are desired over molecular biosensing systems because of the information they provide on toxicity and bioavailability. However, the majority of sensing systems developed are molecular biosensing type screening systems and cannot be easily adapted to cell-based screening. In this study, we demonstrate that protein-based molecular sensing systems that employ a fluorescent protein as a signal transducer are amenable to cell-based sensing by expressing the protein molecular sensing system in the cell and employing these cells for screening of desired molecules. To achieve this, we expressed a molecular sensing system based on the fusion protein of calmodulin (CaM) and enhanced green fluorescent protein (EGFP) in bacterial cells, and utilized these cells for the screening of CaM antagonists. In the presence of Ca(2+), CaM undergoes a conformational change exposing a hydrophobic pocket that interacts with CaM-binding proteins, peptides, and drugs. This conformational change induced in CaM leads to a change in the microenvironment of EGFP, resulting in a change in its fluorescence intensity. The observed change in fluorescence intensity of EGFP can be correlated to the concentration of the analyte present in the sample. Dose-response curves for various tricyclic antidepressants were generated using cells containing CaM-EGFP fusion protein. Additionally, we demonstrate the versatility of our system for studying protein-protein interactions by using cells to study the binding of a peptide to CaM. The study showed that the CaM-EGFP fusion protein within the intact cells responds similarly to that of the isolated fusion protein, hence eliminating the need for any isolation and purification steps. We have demonstrated that this system can be used for the rapid screening of various CaM antagonists that are potential antipsychotic drugs.

  12. High-throughput generation of spheroids using magnetic nanoparticles for three-dimensional cell culture.

    Science.gov (United States)

    Kim, Jeong Ah; Choi, Jong-Ho; Kim, Minsoo; Rhee, Won Jong; Son, Boram; Jung, Hyun-Kyo; Park, Tai Hyun

    2013-11-01

    Various attempts have been made to develop three-dimensional (3-D) cell culture methods because 3-D cells mimic the structures and functional properties of real tissue compared with those of monolayer cultures. Here, we report on a highly simple and efficient 3-D spheroid generation method based on a magnetic pin-array system to concentrate magnetic nanoparticle-incorporated cells in a focal direction. This system was comprised only of external magnets and magnetically induced iron pins to generate a concentrated magnetic field for attracting cells in a focused direction. 3-D spheroid generation was achieved simply by adding magnetic nanoparticle-incorporated cells into a well and covering the plate with a magnetic lid. Cell clustering occurred rapidly within 5 min and created more compact cells with time through the focused magnetic force. This system ensured not only reproducible and size-controlled generation of spheroids but also versatile types of spheroids such as random mixed, core-shell, and fused spheroids, providing a very useful tool for various biological applications. © 2013 Elsevier Ltd. All rights reserved.

  13. A Robust High Throughput Platform to Generate Functional Recombinant Monoclonal Antibodies Using Rabbit B Cells from Peripheral Blood

    Science.gov (United States)

    Seeber, Stefan; Ros, Francesca; Thorey, Irmgard; Tiefenthaler, Georg; Kaluza, Klaus; Lifke, Valeria; Fischer, Jens André Alexander; Klostermann, Stefan; Endl, Josef; Kopetzki, Erhard; Pashine, Achal; Siewe, Basile; Kaluza, Brigitte; Platzer, Josef; Offner, Sonja

    2014-01-01

    We have developed a robust platform to generate and functionally characterize rabbit-derived antibodies using B cells from peripheral blood. The rapid high throughput procedure generates a diverse set of antibodies, yet requires only few animals to be immunized without the need to sacrifice them. The workflow includes (i) the identification and isolation of single B cells from rabbit blood expressing IgG antibodies, (ii) an elaborate short term B-cell cultivation to produce sufficient monoclonal antigen specific IgG for comprehensive phenotype screens, (iii) the isolation of VH and VL coding regions via PCR from B-cell clones producing antigen specific and functional antibodies followed by the sequence determination, and (iv) the recombinant expression and purification of IgG antibodies. The fully integrated and to a large degree automated platform (demonstrated in this paper using IL1RL1 immunized rabbits) yielded clonal and very diverse IL1RL1-specific and functional IL1RL1-inhibiting rabbit antibodies. These functional IgGs from individual animals were obtained at a short time range after immunization and could be identified already during primary screening, thus substantially lowering the workload for the subsequent B-cell PCR workflow. Early availability of sequence information permits one to select early-on function- and sequence-diverse antibodies for further characterization. In summary, this powerful technology platform has proven to be an efficient and robust method for the rapid generation of antigen specific and functional monoclonal rabbit antibodies without sacrificing the immunized animal. PMID:24503933

  14. BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires

    Science.gov (United States)

    Lee, Donald W.; Khavrutskii, Ilja V.; Wallqvist, Anders; Bavari, Sina; Cooper, Christopher L.; Chaudhury, Sidhartha

    2017-01-01

    The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate

  15. BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires.

    Science.gov (United States)

    Lee, Donald W; Khavrutskii, Ilja V; Wallqvist, Anders; Bavari, Sina; Cooper, Christopher L; Chaudhury, Sidhartha

    2016-01-01

    The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate BRILIA

  16. 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.

  17. Combinatorial Biomolecular Nanopatterning for High-Throughput Screening of Stem-Cell Behavior.

    Science.gov (United States)

    Amin, Yacoub Y I; Runager, Kasper; Simoes, Fabio; Celiz, Adam; Taresco, Vincenzo; Rossi, Roberto; Enghild, Jan J; Abildtrup, Lisbeth A; Kraft, David C E; Sutherland, Duncan S; Alexander, Morgan R; Foss, Morten; Ogaki, Ryosuke

    2016-02-17

    A novel combinatorial biomolecular nanopatterning method is reported, in which multiple biomolecular ligands can be patterned in multiple nanoscale dimensions on a single surface. The applicability of the combinatorial platform toward cell-biology applications is demonstrated by screening the adhesion behavior of a population of human dental pulp stem cell (hDPSC) on 64 combinations of nanopatterned extracellular matrix (ECM) proteins in parallel. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis

    Directory of Open Access Journals (Sweden)

    Ludovico eSilvestri

    2015-05-01

    Full Text Available Characterizing the cytoarchitecture of mammalian central nervous system on a brain-wide scale is becoming a compelling need in neuroscience. For example, realistic modeling of brain activity requires the definition of quantitative features of large neuronal populations in the whole brain. Quantitative anatomical maps will also be crucial to classify the cytoarchtitectonic abnormalities associated with neuronal pathologies in a high reproducible and reliable manner. In this paper, we apply recent advances in optical microscopy and image analysis to characterize the spatial distribution of Purkinje cells across the whole cerebellum. Light sheet microscopy was used to image with micron-scale resolution a fixed and cleared cerebellum of an L7-GFP transgenic mouse, in which all Purkinje cells are fluorescently labeled. A fast and scalable algorithm for fully automated cell identification was applied on the image to extract the position of all the fluorescent Purkinje cells. This vectorized representation of the cell population allows a thorough characterization of the complex three-dimensional distribution of the neurons, highlighting the presence of gaps inside the lamellar organization of Purkinje cells, whose density is believed to play a significant role in autism spectrum disorders. Furthermore, clustering analysis of the localized somata permits dividing the whole cerebellum in groups of Purkinje cells with high spatial correlation, suggesting new possibilities of anatomical partition. The quantitative approach presented here can be extended to study the distribution of different types of cell in many brain regions and across the whole encephalon, providing a robust base for building realistic computational models of the brain, and for unbiased morphological tissue screening in presence of pathologies and/or drug treatments.

  19. Pt skin on AuCu intermetallic substrate: a strategy to maximize Pt utilization for fuel cells.

    Science.gov (United States)

    Wang, Gongwei; Huang, Bing; Xiao, Li; Ren, Zhandong; Chen, Hao; Wang, Deli; Abruña, Héctor D; Lu, Juntao; Zhuang, Lin

    2014-07-09

    The dependence on Pt catalysts has been a major issue of proton-exchange membrane (PEM) fuel cells. Strategies to maximize the Pt utilization in catalysts include two main approaches: to put Pt atoms only at the catalyst surface and to further enhance the surface-specific catalytic activity (SA) of Pt. Thus far there has been no practical design that combines these two features into one single catalyst. Here we report a combined computational and experimental study on the design and implementation of Pt-skin catalysts with significantly improved SA toward the oxygen reduction reaction (ORR). Through screening, using density functional theory (DFT) calculations, a Pt-skin structure on AuCu(111) substrate, consisting of 1.5 monolayers of Pt, is found to have an appropriately weakened oxygen affinity, in comparison to that on Pt(111), which would be ideal for ORR catalysis. Such a structure is then realized by substituting the Cu atoms in three surface layers of AuCu intermetallic nanoparticles (AuCu iNPs) with Pt. The resulting Pt-skinned catalyst (denoted as Pt(S)AuCu iNPs) has been characterized in depth using synchrotron XRD, XPS, HRTEM, and HAADF-STEM/EDX, such that the Pt-skin structure is unambiguously identified. The thickness of the Pt skin was determined to be less than two atomic layers. Finally the catalytic activity of Pt(S)AuCu iNPs toward the ORR was measured via rotating disk electrode (RDE) voltammetry through which it was established that the SA was more than 2 times that of a commercial Pt/C catalyst. Taking into account the ultralow Pt loading in Pt(S)AuCu iNPs, the mass-specific catalytic activity (MA) was determined to be 0.56 A/mg(Pt)@0.9 V, a value that is well beyond the DOE 2017 target for ORR catalysts (0.44 A/mg(Pt)@0.9 V). These findings provide a strategic design and a realizable approach to high-performance and Pt-efficient catalysts for fuel cells.

  20. Optimal Thawing of Cryopreserved Peripheral Blood Mononuclear Cells for Use in High-Throughput Human Immune Monitoring Studies

    Directory of Open Access Journals (Sweden)

    Ramu A. Subbramanian

    2012-07-01

    Full Text Available Cryopreserved peripheral blood mononuclear cells (PBMC constitute an important component of immune monitoring studies as they allow for efficient batch- testing of samples as well as for the validation and extension of original studies in the future. In this study, we systematically test the permutations of PBMC thawing practices commonly employed in the field and identify conditions that are high and low risk for the viability of PBMC and their functionality in downstream ELISPOT assays. The study identifies the addition of ice-chilled washing media to thawed cells at the same temperature as being a high risk practice, as it yields significantly lower viability and functionality of recovered PBMC when compared to warming the cryovials to 37 °C and adding a warm washing medium. We found thawed PBMC in cryovials could be kept up to 30 minutes at 37 °C in the presence of DMSO before commencement of washing, which surprisingly identifies exposure to DMSO as a low risk step during the thawing process. This latter finding is of considerable practical relevance since it permits batch-thawing of PBMC in high-throughput immune monitoring environments.

  1. PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics.

    Science.gov (United States)

    Möller, Birgit; Poeschl, Yvonne; Plötner, Romina; Bürstenbinder, Katharina

    2017-11-01

    Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets. © 2017 American Society of Plant Biologists. All Rights Reserved.

  2. Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments.

    Science.gov (United States)

    Sachs, Christian Carsten; Grünberger, Alexander; Helfrich, Stefan; Probst, Christopher; Wiechert, Wolfgang; Kohlheyer, Dietrich; Nöh, Katharina

    Microfluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool. We present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks. Presented is the software molyso, a ready-to-use open source software (BSD-licensed) for the unsupervised analysis of MM time-lapse image stacks. molyso source code and user manual are available at https://github.com/modsim/molyso.

  3. Large-scale tracking and classification for automatic analysis of cell migration and proliferation, and experimental optimization of high-throughput screens of neuroblastoma cells.

    Science.gov (United States)

    Harder, Nathalie; Batra, Richa; Diessl, Nicolle; Gogolin, Sina; Eils, Roland; Westermann, Frank; König, Rainer; Rohr, Karl

    2015-06-01

    Computational approaches for automatic analysis of image-based high-throughput and high-content screens are gaining increased importance to cope with the large amounts of data generated by automated microscopy systems. Typically, automatic image analysis is used to extract phenotypic information once all images of a screen have been acquired. However, also in earlier stages of large-scale experiments image analysis is important, in particular, to support and accelerate the tedious and time-consuming optimization of the experimental conditions and technical settings. We here present a novel approach for automatic, large-scale analysis and experimental optimization with application to a screen on neuroblastoma cell lines. Our approach consists of cell segmentation, tracking, feature extraction, classification, and model-based error correction. The approach can be used for experimental optimization by extracting quantitative information which allows experimentalists to optimally choose and to verify the experimental parameters. This involves systematically studying the global cell movement and proliferation behavior. Moreover, we performed a comprehensive phenotypic analysis of a large-scale neuroblastoma screen including the detection of rare division events such as multi-polar divisions. Major challenges of the analyzed high-throughput data are the relatively low spatio-temporal resolution in conjunction with densely growing cells as well as the high variability of the data. To account for the data variability we optimized feature extraction and classification, and introduced a gray value normalization technique as well as a novel approach for automatic model-based correction of classification errors. In total, we analyzed 4,400 real image sequences, covering observation periods of around 120 h each. We performed an extensive quantitative evaluation, which showed that our approach yields high accuracies of 92.2% for segmentation, 98.2% for tracking, and 86.5% for

  4. The cooperative action of bacterial fibronectin-binding proteins and secreted proteins promote maximal Campylobacter jejuni invasion of host cells by stimulating membrane ruffling.

    Science.gov (United States)

    Eucker, Tyson P; Konkel, Michael E

    2012-02-01

    This study was performed to elucidate the host cell scaffolding and signalling molecules that Campylobacter jejuni utilizes to invade epithelial cells. We hypothesized that the C. jejuni fibronectin-binding proteins and secreted proteins are required for cell signalling and maximal invasion of host cells. C. jejuni binding to host cells via the CadF and FlpA fibronectin-binding proteins activated the epidermal growth factor (EGF) pathway, as evidenced by inhibitor studies and immunoprecipitation coupled with immunoblot analysis using antibodies reactive against total and active EGF receptor. Inhibitor studies revealed maximal C. jejuni host cell invasion was dependent upon PI3-Kinase, c-Src and focal adhesion kinase (FAK), all of which are known to participate in cytoskeletal rearrangements. Knockdown of endogenous Dock180, which is a Rac1-specific guanine nucleotide exchange factor, using siRNA revealed that C. jejuni invasion was significantly reduced compared with cells treated with scrambled siRNA. We further demonstrated that the C. jejuni Cia proteins are, in part, responsible for Rho GTPase Rac1 recruitment and activation, as judged by immunofluorescence microscopy and Rac1 activation. Based on these data, we present a model that illustrates that C. jejuni utilizes a coordinated mechanism involving both adhesins and secreted proteins to promote membrane ruffling and host cell invasion. © 2011 Blackwell Publishing Ltd.

  5. High-throughput analysis reveals novel maternal germline RNAs crucial for primordial germ cell preservation and proper migration.

    Science.gov (United States)

    Owens, Dawn A; Butler, Amanda M; Aguero, Tristan H; Newman, Karen M; Van Booven, Derek; King, Mary Lou

    2017-01-15

    During oogenesis, hundreds of maternal RNAs are selectively localized to the animal or vegetal pole, including determinants of somatic and germline fates. Although microarray analysis has identified localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high-throughput RNA-sequencing analysis to comprehensively interrogate animal and vegetal pole RNAs in the fully grown Xenopus laevis oocyte. We identified 411 (198 annotated) and 27 (15 annotated) enriched mRNAs at the vegetal and animal pole, respectively. Ninety were novel mRNAs over 4-fold enriched at the vegetal pole and six were over 10-fold enriched at the animal pole. Unlike mRNAs, microRNAs were not asymmetrically distributed. Whole-mount in situ hybridization confirmed that all 17 selected mRNAs were localized. Biological function and network analysis of vegetally enriched transcripts identified protein-modifying enzymes, receptors, ligands, RNA-binding proteins, transcription factors and co-factors with five defining hubs linking 47 genes in a network. Initial functional studies of maternal vegetally localized mRNAs show that sox7 plays a novel and important role in primordial germ cell (PGC) development and that ephrinB1 (efnb1) is required for proper PGC migration. We propose potential pathways operating at the vegetal pole that highlight where future investigations might be most fruitful. © 2017. Published by The Company of Biologists Ltd.

  6. Estimation of bisphenol A-Human toxicity by 3D cell culture arrays, high throughput alternatives to animal tests.

    Science.gov (United States)

    Lee, Dong Woo; Oh, Woo-Yeon; Yi, Sang Hyun; Ku, Bosung; Lee, Moo-Yeal; Cho, Yoon Hee; Yang, Mihi

    2016-09-30

    Bisphenol A (BPA) has been widely used for manufacturing polycarbonate plastics and epoxy resins and has been extensively tested in animals to predict human toxicity. In order to reduce the use of animals for toxicity assessment and provide further accurate information on BPA toxicity in humans, we encapsulated Hep3B human hepatoma cells in alginate and cultured them in three dimensions (3D) on a micropillar chip coupled to a panel of metabolic enzymes on a microwell chip. As a result, we were able to assess the toxicity of BPA under various metabolic enzyme conditions using a high-throughput and micro assay; sample volumes were nearly 2,000 times less than that required for a 96-well plate. We applied a total of 28 different enzymes to each chip, including 10 cytochrome P450s (CYP450s), 10 UDP-glycosyltransferases (UGTs), 3 sulfotransferases (SULTs), alcohol dehydrogenase (ADH), and aldehyde dehydrogenase 2 (ALDH2). Phase I enzyme mixtures, phase II enzyme mixtures, and a combination of phase I and phase II enzymes were also applied to the chip. BPA toxicity was higher in samples containing CYP2E1 than controls, which contained no enzymes (IC50, 184±16μM and 270±25.8μM, respectively, palternative to animal testing for estimating BPA toxicity via human metabolic systems. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. High-throughput screens in mammalian cells using the CRISPR-Cas9 system.

    Science.gov (United States)

    Peng, Jingyu; Zhou, Yuexin; Zhu, Shiyou; Wei, Wensheng

    2015-06-01

    As a powerful genome-editing tool, the clustered regularly interspaced short palindromic repeats (CRISPR)-clustered regularly interspaced short palindromic repeats-associated protein 9 (Cas9) system has been quickly developed into a large-scale function-based screening strategy in mammalian cells. This new type of genetic library is constructed through the lentiviral delivery of single-guide RNA collections that direct Cas9 or inactive dead Cas9 fused with effectors to interrogate gene function or regulate gene transcription in targeted cells. Compared with RNA interference screening, the CRISPR-Cas9 system demonstrates much higher levels of effectiveness and reliability with respect to both loss-of-function and gain-of-function screening. Unlike the RNA interference strategy, a CRISPR-Cas9 library can target both protein-coding sequences and regulatory elements, including promoters, enhancers and elements transcribing microRNAs and long noncoding RNAs. This powerful genetic tool will undoubtedly accelerate the mechanistic discovery of various biological processes. In this mini review, we summarize the general procedure of CRISPR-Cas9 library mediated functional screening, system optimization strategies and applications of this new genetic toolkit. © 2015 FEBS.

  8. Development and qualification of a high sensitivity, high throughput Q-PCR assay for quantitation of residual host cell DNA in purification process intermediate and drug substance samples.

    Science.gov (United States)

    Zhang, Wei; Wu, Meng; Menesale, Emily; Lu, Tongjun; Magliola, Aeona; Bergelson, Svetlana

    2014-11-01

    Methods of high sensitivity, accuracy and throughput are needed for quantitation of low level residual host cell DNA in purification process intermediates and drug substances of therapeutic proteins. In this study, we designed primer/probe sets targeting repetitive Alu repeats or Alu-equivalent sequences in the human, Chinese hamster and murine genomes. When used in quantitative polymerase chain reactions (Q-PCRs), these primer/probe sets showed high species specificity and gave significantly higher sensitivity compared to those targeting the low copy number GAPDH gene. This allowed for detection of residual host cell DNA of much lower concentrations and, for some samples, eliminated the need for DNA extraction. By combining the high sensitivity Alu Q-PCR with high throughput automated DNA extraction using an automated MagMAX magnetic particle processor, we successfully developed and qualified a highly accurate, specific, sensitive and efficient method for the quantitation of residual host cell DNA in process intermediates and drug substances of multiple therapeutic proteins purified from cells of multiple species. Compared to the previous method using manual DNA extraction and primer/probe sets targeting the GAPDH gene, this new method increased our DNA extraction throughput by over sevenfold, and lowered the lower limit of quantitation by up to eightfold. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Polymer surface functionalities that control human embryoid body cell adhesion revealed by high throughput surface characterization of combinatorial material microarrays

    OpenAIRE

    Yang, Jing; Mei, Ying; Hook, Andrew L.; Taylor, Michael; Urquhart, Andrew J.; Bogatyrev, Said R.; Langer, Robert; Anderson, Daniel G.; Davies, Martyn C.; Alexander, Morgan R.

    2010-01-01

    High throughput materials discovery using combinatorial polymer microarrays to screen for new biomaterials with new and improved function is established as a powerful strategy. Here we combine this screening approach with high throughput surface characterisation (HT-SC) to identify surface structure-function relationships. We explore how this combination can help to identify surface chemical moieties that control protein adsorption and subsequent cellular response. The adhesion of human embry...

  10. High-throughput sequencing of microRNAs in peripheral blood mononuclear cells: identification of potential weight loss biomarkers.

    Directory of Open Access Journals (Sweden)

    Fermín I Milagro

    Full Text Available INTRODUCTION: MicroRNAs (miRNAs are being increasingly studied in relation to energy metabolism and body composition homeostasis. Indeed, the quantitative analysis of miRNAs expression in different adiposity conditions may contribute to understand the intimate mechanisms participating in body weight control and to find new biomarkers with diagnostic or prognostic value in obesity management. OBJECTIVE: The aim of this study was the search for miRNAs in blood cells whose expression could be used as prognostic biomarkers of weight loss. METHODS: Ten Caucasian obese women were selected among the participants in a weight-loss trial that consisted in following an energy-restricted treatment. Weight loss was considered unsuccessful when 5% (responders. At baseline, total miRNA isolated from peripheral blood mononuclear cells (PBMC was sequenced with SOLiD v4. The miRNA sequencing data were validated by RT-PCR. RESULTS: Differential baseline expression of several miRNAs was found between responders and non-responders. Two miRNAs were up-regulated in the non-responder group (mir-935 and mir-4772 and three others were down-regulated (mir-223, mir-224 and mir-376b. Both mir-935 and mir-4772 showed relevant associations with the magnitude of weight loss, although the expression of other transcripts (mir-874, mir-199b, mir-766, mir-589 and mir-148b also correlated with weight loss. CONCLUSIONS: This research addresses the use of high-throughput sequencing technologies in the search for miRNA expression biomarkers in obesity, by determining the miRNA transcriptome of PBMC. Basal expression of different miRNAs, particularly mir-935 and mir-4772, could be prognostic biomarkers and may forecast the response to a hypocaloric diet.

  11. High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis.

    Science.gov (United States)

    Tani, Akio; Sahin, Nurettin; Matsuyama, Yumiko; Enomoto, Takashi; Nishimura, Naoki; Yokota, Akira; Kimbara, Kazuhide

    2012-01-01

    Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing.

  12. High-throughput identification and screening of novel Methylobacterium species using whole-cell MALDI-TOF/MS analysis.

    Directory of Open Access Journals (Sweden)

    Akio Tani

    Full Text Available Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics. Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing.

  13. [High throughput-targeted sequencing panel for exploring radiosensitivity associated genes in esophageal squamous cell carcinoma].

    Science.gov (United States)

    Qiao, Y; Hu, C X; Song, D A; Li, S Q; Zhou, L H; Jiang, X D

    2017-08-23

    Objective: To explore radiosensitivity-associated genes in esophageal squamous cell carcinoma by targeted sequencing panel. Methods: The peripheral blood from 22 esophageal squamous cell carcinoma (ESCC) patients received radiotherapy alone were collected, respectively. The genomic DNA (gDNA) of peripheral blood was extracted and used to create a library of gDNA restriction fragments. The gDNA restriction fragments were hybridized to the HaloPlex probe capture library, which comprises 356 cancer genes selected from the Catalogue of Somatic Mutations in Cancer (Cosmic) database of 2011 updated edition. The sequencing data were aligned by the Genome Analysis Toolkit GATK (version 3.0) and Picar. The single nucleotide polymorphism and inserted-deletion (SNP/InDel) variations were annotated by online database. The pathway enrichment was analyzed by Ingenuity Pathway analysis (IPA). Moreover, according to the short-period curative effect, 22 patients were divided into two groups: the radiation- sensitivity group (CR+ PR) and the radiation-resistant group (PD+ SD). The nonsynonymous mutation sites were statistically analyzed and the genes associated with radiosensitivity of ESCC were screened. Results: More than 97% sequencing reads were aligned to human genome reference sequence and more than 90% sequencing reads were the target sequences. SNP/InDel database annotation results showed that the mutations of 22 cases mainly distributed in exons, and the mutant types were mainly missense and synonymous single nucleotide variant (SNV). There were 23 genes of high-frequency mutation associated with esophageal cancer. Pathway enrichment by IPA showed that 3 pathways were associated with the development of esophageal cancer, which were roles of BRCA1 in DNA damage response pathway, DNA double-strand break repair by non-homologous end joining pathway and ATM signaling pathway. According to the curative effect, five genes including mismatch repair system component (PMS1

  14. Enabling systematic interrogation of protein-protein interactions in live cells with a versatile ultra-high-throughput biosensor platform | Office of Cancer Genomics

    Science.gov (United States)

    The vast datasets generated by next generation gene sequencing and expression profiling have transformed biological and translational research. However, technologies to produce large-scale functional genomics datasets, such as high-throughput detection of protein-protein interactions (PPIs), are still in early development. While a number of powerful technologies have been employed to detect PPIs, a singular PPI biosensor platform featured with both high sensitivity and robustness in a mammalian cell environment remains to be established.

  15. High-throughput multiplex single-nucleotide polymorphism analysis for red cell and platelet antigen genotypes.

    Science.gov (United States)

    Denomme, G A; Van Oene, M

    2005-05-01

    Transfusion recipients who become alloimmunized to red cell or platelet (PLT) antigens require antigen-negative blood to limit adverse transfusion reactions. Blood collection facilities use regulated and unregulated antibodies to phenotype blood, the cost of which can be prohibitive depending on the antisera and demand. An alternative strategy is to screen blood for these antigens with genomic DNA and the associated single-nucleotide polymorphisms (SNPs). A multiplex polymerase chain reaction (PCR)-oligonucleotide extension assay was developed with genomic DNA and a SNP genotyping platform (GenomeLab SNPstream, Beckman Coulter) to identify SNPs related to D, C/c, E, S/s, K/k, Kp(a/b), Fy(a/b), FY0 (-33 promoter silencing polymorphism), Jk(a/b), Di(a/b), and human PLT antigen (HPA)-1a/1b. A total of 372 samples were analyzed for 12 SNPs. The genotypes were compared to the blood group and PLT antigen phenotypes. Individual sample results varied from 98 to 100 percent for 11 of 12 SNPs. D was correctly identified in 292 of 296 (98.6%) D+ donors. The RHCE exon 5 E/e SNP analysis had the lowest concordance (89.5%). Thirty-three R(1)R(1) and 1 r"r were correctly identified. PCR-restriction fragment length polymorphism (RFLP) on selected samples confirmed the presence of the FY0 silencing polymorphism in nine donors. Homozygous HPA-1b/1b was identified in four donors, which was confirmed by PCR-RFLP (n = 4) and anti-HPA-1a serology (n = 2). The two HPA-1a-negative donors were recruited into the plateletpheresis program. The platform has the capacity to genotype thousands of samples per day. The suite of SNPs provides genotype data for all blood donors within 36 hours of the start of testing.

  16. Profit maximization mitigates competition

    DEFF Research Database (Denmark)

    Dierker, Egbert; Grodal, Birgit

    1996-01-01

    competition than utility maximization. Since profit maximization tends to raise prices, it may be regarded as beneficial for the owners as a whole. Moreover, if profit maximization is a good proxy for utility maximization, then there is no need for a general equilibrium analysis that takes the distribution...

  17. High-Throughput Phenotyping of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes and Neurons Using Electric Field Stimulation and High-Speed Fluorescence Imaging.

    Science.gov (United States)

    Daily, Neil J; Du, Zhong-Wei; Wakatsuki, Tetsuro

    Electrophysiology of excitable cells, including muscle cells and neurons, has been measured by making direct contact with a single cell using a micropipette electrode. To increase the assay throughput, optical devices such as microscopes and microplate readers have been used to analyze electrophysiology of multiple cells. We have established a high-throughput (HTP) analysis of action potentials (APs) in highly enriched motor neurons and cardiomyocytes (CMs) that are differentiated from human induced pluripotent stem cells (iPSCs). A multichannel electric field stimulation (EFS) device enabled the ability to electrically stimulate cells and measure dynamic changes in APs of excitable cells ultra-rapidly (>100 data points per second) by imaging entire 96-well plates. We found that the activities of both neurons and CMs and their response to EFS and chemicals are readily discerned by our fluorescence imaging-based HTP phenotyping assay. The latest generation of calcium (Ca(2+)) indicator dyes, FLIPR Calcium 6 and Cal-520, with the HTP device enables physiological analysis of human iPSC-derived samples highlighting its potential application for understanding disease mechanisms and discovering new therapeutic treatments.

  18. On the Achievable Throughput Over TVWS Sensor Networks.

    Science.gov (United States)

    Caleffi, Marcello; Cacciapuoti, Angela Sara

    2016-03-30

    In this letter, we study the throughput achievable by an unlicensed sensor network operating over TV white space spectrum in presence of coexistence interference. Through the letter, we first analytically derive the achievable throughput as a function of the channel ordering. Then, we show that the problem of deriving the maximum expected throughput through exhaustive search is computationally unfeasible. Finally, we derive a computational-efficient algorithm characterized by polynomial-time complexity to compute the channel set maximizing the expected throughput and, stemming from this, we derive a closed-form expression of the maximum expected throughput. Numerical simulations validate the theoretical analysis.

  19. High-content, high-throughput screening for the identification of cytotoxic compounds based on cell morphology and cell proliferation markers.

    Directory of Open Access Journals (Sweden)

    Heather L Martin

    Full Text Available Toxicity is a major cause of failure in drug discovery and development, and whilst robust toxicological testing occurs, efficiency could be improved if compounds with cytotoxic characteristics were identified during primary compound screening. The use of high-content imaging in primary screening is becoming more widespread, and by utilising phenotypic approaches it should be possible to incorporate cytotoxicity counter-screens into primary screens. Here we present a novel phenotypic assay that can be used as a counter-screen to identify compounds with adverse cellular effects. This assay has been developed using U2OS cells, the PerkinElmer Operetta high-content/high-throughput imaging system and Columbus image analysis software. In Columbus, algorithms were devised to identify changes in nuclear morphology, cell shape and proliferation using DAPI, TOTO-3 and phosphohistone H3 staining, respectively. The algorithms were developed and tested on cells treated with doxorubicin, taxol and nocodazole. The assay was then used to screen a novel, chemical library, rich in natural product-like molecules of over 300 compounds, 13.6% of which were identified as having adverse cellular effects. This assay provides a relatively cheap and rapid approach for identifying compounds with adverse cellular effects during screening assays, potentially reducing compound rejection due to toxicity in subsequent in vitro and in vivo assays.

  20. Label-free high-throughput detection and quantification of circulating melanoma tumor cell clusters by linear-array-based photoacoustic tomography

    Science.gov (United States)

    Hai, Pengfei; Zhou, Yong; Zhang, Ruiying; Ma, Jun; Li, Yang; Shao, Jin-Yu; Wang, Lihong V.

    2017-04-01

    Circulating tumor cell (CTC) clusters, arising from multicellular groupings in a primary tumor, greatly elevate the metastatic potential of cancer compared with single CTCs. High-throughput detection and quantification of CTC clusters are important for understanding the tumor metastatic process and improving cancer therapy. Here, we applied a linear-array-based photoacoustic tomography (LA-PAT) system and improved the image reconstruction for label-free high-throughput CTC cluster detection and quantification in vivo. The feasibility was first demonstrated by imaging CTC cluster ex vivo. The relationship between the contrast-to-noise ratios (CNRs) and the number of cells in melanoma tumor cell clusters was investigated and verified. Melanoma CTC clusters with a minimum of four cells could be detected, and the number of cells could be computed from the CNR. Finally, we demonstrated imaging of injected melanoma CTC clusters in rats in vivo. Similarly, the number of cells in the melanoma CTC clusters could be quantified. The data showed that larger CTC clusters had faster clearance rates in the bloodstream, which agreed with the literature. The results demonstrated the capability of LA-PAT to detect and quantify melanoma CTC clusters in vivo and showed its potential for tumor metastasis study and cancer therapy.

  1. High-throughput quantitation of Fc-containing recombinant proteins in cell culture supernatant by fluorescence polarization spectroscopy.

    Science.gov (United States)

    Thompson, Ben; Clifford, Jerry; Jenns, Mike; Smith, Andrew; Field, Ray; Nayyar, Kalpana; James, David C

    2017-10-01

    Measurement of recombinant protein product titer critically underpins all biopharmaceutical manufacturing process development, as well as diverse research and discovery activity. Here, we describe a simple rapid (quantitation of recombinant immunoglobulin G and Fc-containing IgG derivatives in mammalian cell culture supernatant over a wide dynamic range of 2.5-80 mg/L, using microplate fluorescence polarization (FP) spectroscopy. The solution-phase FP assay is based on the detection of immunoglobulin Fc domain containing analyte binding to FITC-conjugated recombinant Protein G ligand to measure analyte concentration dependent changes in emitted FP. For ease of use and maximal shelf life, we showed that air-dried assay microplates containing pre-formulated ligand that is re-solubilized on addition of analyte containing solution did not affect assay performance, typically yielding an across plate coefficient of variation of Protein A HPLC and bio-interferometry) yielded a coefficient of determination >0.99 in each case. Copyright © 2017. Published by Elsevier Inc.

  2. High-Throughput Cancer Cell Sphere Formation for Characterizing the Efficacy of Photo Dynamic Therapy in 3D Cell Cultures

    Science.gov (United States)

    Chen, Yu-Chih; Lou, Xia; Zhang, Zhixiong; Ingram, Patrick; Yoon, Euisik

    2015-07-01

    Photodynamic therapy (PDT), wherein light sensitive non-toxic agents are locally and selectively activated using light, has emerged as an appealing alternative to traditional cancer chemotherapy. Yet to date, PDT efficacy has been mostly characterized using 2D cultures. Compared to 2D cultures, 3D sphere culture generates unique spatial distributions of nutrients and oxygen for the cells that better mimics the in-vivo conditions. Using a novel polyHEMA (non-adherent polymer) fabrication process, we developed a microfluidic sphere formation platform that can (1) generate 1,024 uniform (size variation cancer spheres within a 2 cm by 2 cm core area, (2) culture spheres for more than 2 weeks, and (3) allow the retrieval of spheres. Using the presented platform, we have successfully characterized the different responses in 2D and 3D cell culture to PDT. Furthermore, we investigated the treatment resistance effect in cancer cells induced by tumor associated fibroblasts (CAF). Although the CAFs can enhance the resistance to traditional chemotherapy agents, no significant difference in PDT was observed. The preliminary results suggest that the PDT can be an attractive alternative cancer therapy, which is less affected by the therapeutic resistance induced by cancer associated cells.

  3. Multiplexing spheroid volume, resazurin and acid phosphatase viability assays for high-throughput screening of tumour spheroids and stem cell neurospheres.

    Directory of Open Access Journals (Sweden)

    Delyan P Ivanov

    Full Text Available Three-dimensional cell culture has many advantages over monolayer cultures, and spheroids have been hailed as the best current representation of small avascular tumours in vitro. However their adoption in regular screening programs has been hindered by uneven culture growth, poor reproducibility and lack of high-throughput analysis methods for 3D. The objective of this study was to develop a method for a quick and reliable anticancer drug screen in 3D for tumour and human foetal brain tissue in order to investigate drug effectiveness and selective cytotoxic effects. Commercially available ultra-low attachment 96-well round-bottom plates were employed to culture spheroids in a rapid, reproducible manner amenable to automation. A set of three mechanistically different methods for spheroid health assessment (Spheroid volume, metabolic activity and acid phosphatase enzyme activity were validated against cell numbers in healthy and drug-treated spheroids. An automated open-source ImageJ macro was developed to enable high-throughput volume measurements. Although spheroid volume determination was superior to the other assays, multiplexing it with resazurin reduction and phosphatase activity produced a richer picture of spheroid condition. The ability to distinguish between effects on malignant and the proliferating component of normal brain was tested using etoposide on UW228-3 medulloblastoma cell line and human neural stem cells. At levels below 10 µM etoposide exhibited higher toxicity towards proliferating stem cells, whereas at concentrations above 10 µM the tumour spheroids were affected to a greater extent. The high-throughput assay procedures use ready-made plates, open-source software and are compatible with standard plate readers, therefore offering high predictive power with substantial savings in time and money.

  4. Multiplexing Spheroid Volume, Resazurin and Acid Phosphatase Viability Assays for High-Throughput Screening of Tumour Spheroids and Stem Cell Neurospheres

    Science.gov (United States)

    Ivanov, Delyan P.; Parker, Terry L.; Walker, David A.; Alexander, Cameron; Ashford, Marianne B.; Gellert, Paul R.; Garnett, Martin C.

    2014-01-01

    Three-dimensional cell culture has many advantages over monolayer cultures, and spheroids have been hailed as the best current representation of small avascular tumours in vitro. However their adoption in regular screening programs has been hindered by uneven culture growth, poor reproducibility and lack of high-throughput analysis methods for 3D. The objective of this study was to develop a method for a quick and reliable anticancer drug screen in 3D for tumour and human foetal brain tissue in order to investigate drug effectiveness and selective cytotoxic effects. Commercially available ultra-low attachment 96-well round-bottom plates were employed to culture spheroids in a rapid, reproducible manner amenable to automation. A set of three mechanistically different methods for spheroid health assessment (Spheroid volume, metabolic activity and acid phosphatase enzyme activity) were validated against cell numbers in healthy and drug-treated spheroids. An automated open-source ImageJ macro was developed to enable high-throughput volume measurements. Although spheroid volume determination was superior to the other assays, multiplexing it with resazurin reduction and phosphatase activity produced a richer picture of spheroid condition. The ability to distinguish between effects on malignant and the proliferating component of normal brain was tested using etoposide on UW228-3 medulloblastoma cell line and human neural stem cells. At levels below 10 µM etoposide exhibited higher toxicity towards proliferating stem cells, whereas at concentrations above 10 µM the tumour spheroids were affected to a greater extent. The high-throughput assay procedures use ready-made plates, open-source software and are compatible with standard plate readers, therefore offering high predictive power with substantial savings in time and money. PMID:25119185

  5. Multidisciplinary insight into clonal expansion of HTLV-1-infected cells in adult T-cell leukemia via modeling by deterministic finite automata coupled with high-throughput sequencing.

    Science.gov (United States)

    Farmanbar, Amir; Firouzi, Sanaz; Park, Sung-Joon; Nakai, Kenta; Uchimaru, Kaoru; Watanabe, Toshiki

    2017-01-31

    Clonal expansion of leukemic cells leads to onset of adult T-cell leukemia (ATL), an aggressive lymphoid malignancy with a very poor prognosis. Infection with human T-cell leukemia virus type-1 (HTLV-1) is the direct cause of ATL onset, and integration of HTLV-1 into the human genome is essential for clonal expansion of leukemic cells. Therefore, monitoring clonal expansion of HTLV-1-infected cells via isolation of integration sites assists in analyzing infected individuals from early infection to the final stage of ATL development. However, because of the complex nature of clonal expansion, the underlying mechanisms have yet to be clarified. Combining computational/mathematical modeling with experimental and clinical data of integration site-based clonality analysis derived from next generation sequencing technologies provides an appropriate strategy to achieve a better understanding of ATL development. As a comprehensively interdisciplinary project, this study combined three main aspects: wet laboratory experiments, in silico analysis and empirical modeling. We analyzed clinical samples from HTLV-1-infected individuals with a broad range of proviral loads using a high-throughput methodology that enables isolation of HTLV-1 integration sites and accurate measurement of the size of infected clones. We categorized clones into four size groups, "very small", "small", "big", and "very big", based on the patterns of clonal growth and observed clone sizes. We propose an empirical formal model based on deterministic finite state automata (DFA) analysis of real clinical samples to illustrate patterns of clonal expansion. Through the developed model, we have translated biological data of clonal expansion into the formal language of mathematics and represented the observed clonality data with DFA. Our data suggest that combining experimental data (absolute size of clones) with DFA can describe the clonality status of patients. This kind of modeling provides a basic

  6. Discovery of Novel Small Molecule Inhibitors of VEGF Expression in Tumor Cells Using a Cell-Based High Throughput Screening Platform.

    Directory of Open Access Journals (Sweden)

    Liangxian Cao

    Full Text Available Current anti-VEGF (Vascular Endothelial Growth Factor A therapies to treat various cancers indiscriminately block VEGF function in the patient resulting in the global loss of VEGF signaling which has been linked to dose-limiting toxicities as well as treatment failures due to acquired resistance. Accumulating evidence suggests that this resistance is at least partially due to increased production of compensatory tumor angiogenic factors/cytokines. VEGF protein production is differentially controlled depending on whether cells are in the normal "homeostatic" state or in a stressed state, such as hypoxia, by post-transcriptional regulation imparted by elements in the 5' and 3' untranslated regions (UTR of the VEGF mRNA. Using the Gene Expression Modulation by Small molecules (GEMS™ phenotypic assay system, we performed a high throughput screen to identify low molecular weight compounds that target the VEGF mRNA UTR-mediated regulation of stress-induced VEGF production in tumor cells. We identified a number of compounds that potently and selectively reduce endogenous VEGF production under hypoxia in HeLa cells. Medicinal chemistry efforts improved the potency and pharmaceutical properties of one series of compounds resulting in the discovery of PTC-510 which inhibits hypoxia-induced VEGF expression in HeLa cells at low nanomolar concentration. In mouse xenograft studies, oral administration of PTC-510 results in marked reduction of intratumor VEGF production and single agent control of tumor growth without any evident toxicity. Here, we show that selective suppression of stress-induced VEGF production within tumor cells effectively controls tumor growth. Therefore, this approach may minimize the liabilities of current global anti-VEGF therapies.

  7. Sensitivity of neuroprogenitor cells to chemical-induced apoptosis using a multiplexed assay suitable for high-throughput screening*

    Science.gov (United States)

    AbstractHigh-throughput methods are useful for rapidly screening large numbers of chemicals for biological activity, including the perturbation of pathways that may lead to adverse cellular effects. In vitro assays for the key events of neurodevelopment, including apoptosis, may ...

  8. Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes

    DEFF Research Database (Denmark)

    Welner, Ditte Hededam; Shin, David; Tomaleri, Giovani P.

    2017-01-01

    knowledge of the enzyme(s) being studied. We have developed a rational approach to this process. We devise a pipeline comprising in silico selection of targets and construct design, and high-throughput expression screening, target enrichment, and hit identification. We have applied this pipeline to a test...

  9. A cell-free fluorometric high-throughput screen for inhibitors of Rtt109-catalyzed histone acetylation.

    Directory of Open Access Journals (Sweden)

    Jayme L Dahlin

    Full Text Available The lysine acetyltransferase (KAT Rtt109 forms a complex with Vps75 and catalyzes the acetylation of histone H3 lysine 56 (H3K56ac in the Asf1-H3-H4 complex. Rtt109 and H3K56ac are vital for replication-coupled nucleosome assembly and genotoxic resistance in yeast and pathogenic fungal species such as Candida albicans. Remarkably, sequence homologs of Rtt109 are absent in humans. Therefore, inhibitors of Rtt109 are hypothesized as potential and minimally toxic antifungal agents. Herein, we report the development and optimization of a cell-free fluorometric high-throughput screen (HTS for small-molecule inhibitors of Rtt109-catalyzed histone acetylation. The KAT component of the assay consists of the yeast Rtt109-Vps75 complex, while the histone substrate complex consists of full-length Drosophila histone H3-H4 bound to yeast Asf1. Duplicated assay runs of the LOPAC demonstrated day-to-day and plate-to-plate reproducibility. Approximately 225,000 compounds were assayed in a 384-well plate format with an average Z' factor of 0.71. Based on a 3σ cut-off criterion, 1,587 actives (0.7% were identified in the primary screen. The assay method is capable of identifying previously reported KAT inhibitors such as garcinol. We also observed several prominent active classes of pan-assay interference compounds such as Mannich bases, catechols and p-hydroxyarylsulfonamides. The majority of the primary active compounds showed assay signal interference, though most assay artifacts can be efficiently removed by a series of straightforward counter-screens and orthogonal assays. Post-HTS triage demonstrated a comparatively small number of confirmed actives with IC50 values in the low micromolar range. This assay, which utilizes five label-free proteins involved in H3K56 acetylation in vivo, can in principle identify compounds that inhibit Rtt109-catalyzed H3K56 acetylation via different mechanisms. Compounds discovered via this assay or adaptations thereof could

  10. Fluorescence-based high throughput screening for noble metal-free and platinum-poor anode catalysts for the direct methanol fuel cell.

    Science.gov (United States)

    Welsch, F G; Stöwe, K; Maier, W F

    2011-09-12

    We describe here the results of a high throughput screening study for direct methanol fuel cell (DMFC) anode catalysts consisting of new elemental combinations with an optical high-throughput screening method, which allows the quantitative evaluation of the electrochemical activity of catalysts. The method is based on the fluorescence of protonated quinine generated during electrooxidation of methanol. The high-throughput screening included noble-metal free binary and ternary mixed oxides of the elements Al, Co, Cr, Cu, Fe, Mn, Mo, Nb, Ni, Ta, Ti, Zn, and Zr in the oxidized form as well as after prior reduction in hydrogen. In addition 318 ternary and quaternary Pt-containing materials composed out of the mixed oxides of Bi, Ce, Co, Cr, Cu, Fe, Ga, Ge, In, La, Mn, Mo, Nb, Nd, Ni, Pr, Sb, Sn, Ta, Te, Ti, V, Zn, and Zr with a molar Pt-ratio of 10% and 30% were screened. Validation and long time experiments of the hits were performed by cyclovoltammetry (CV). The microstructural stability of the electrode preparations of the lead compositions was studied by X-ray diffraction (XRD) pattern analysis.

  11. Maximally incompatible quantum observables

    Energy Technology Data Exchange (ETDEWEB)

    Heinosaari, Teiko, E-mail: teiko.heinosaari@utu.fi [Turku Centre for Quantum Physics, Department of Physics and Astronomy, University of Turku, FI-20014 Turku (Finland); Schultz, Jussi, E-mail: jussi.schultz@gmail.com [Dipartimento di Matematica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); Toigo, Alessandro, E-mail: alessandro.toigo@polimi.it [Dipartimento di Matematica, Politecnico di Milano, Piazza Leonardo da Vinci 32, I-20133 Milano (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Milano, Via Celoria 16, I-20133 Milano (Italy); Ziman, Mario, E-mail: ziman@savba.sk [RCQI, Institute of Physics, Slovak Academy of Sciences, Dúbravská cesta 9, 84511 Bratislava (Slovakia); Faculty of Informatics, Masaryk University, Botanická 68a, 60200 Brno (Czech Republic)

    2014-05-01

    The existence of maximally incompatible quantum observables in the sense of a minimal joint measurability region is investigated. Employing the universal quantum cloning device it is argued that only infinite dimensional quantum systems can accommodate maximal incompatibility. It is then shown that two of the most common pairs of complementary observables (position and momentum; number and phase) are maximally incompatible.

  12. High-throughput, label-free, single-cell, microalgal lipid screening by machine-learning-equipped optofluidic time-stretch quantitative phase microscopy.

    Science.gov (United States)

    Guo, Baoshan; Lei, Cheng; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Jiang, Yiyue; Tanaka, Yo; Ozeki, Yasuyuki; Goda, Keisuke

    2017-05-01

    The development of reliable, sustainable, and economical sources of alternative fuels to petroleum is required to tackle the global energy crisis. One such alternative is microalgal biofuel, which is expected to play a key role in reducing the detrimental effects of global warming as microalgae absorb atmospheric CO 2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid amounts and fail to characterize a diverse population of microalgal cells with single-cell resolution in a non-invasive and interference-free manner. Here high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy was demonstrated. In particular, Euglena gracilis, an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement), within lipid droplets was investigated. The optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch quantitative phase microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase maps of every single cell at a high throughput of 10,000 cells/s, enabling accurate cell classification without the need for fluorescent staining. Specifically, the dataset was used to characterize heterogeneous populations of E. gracilis cells under two different culture conditions (nitrogen-sufficient and nitrogen-deficient) and achieve the cell classification with an error rate of only 2.15%. The method holds promise as an effective analytical tool for microalgae-based biofuel production. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

  13. Quantification of rapid Myosin regulatory light chain phosphorylation using high-throughput in-cell Western assays: comparison to Western immunoblots.

    Directory of Open Access Journals (Sweden)

    Hector N Aguilar

    2010-04-01

    Full Text Available Quantification of phospho-proteins (PPs is crucial when studying cellular signaling pathways. Western immunoblotting (WB is commonly used for the measurement of relative levels of signaling intermediates in experimental samples. However, WB is in general a labour-intensive and low-throughput technique. Because of variability in protein yield and phospho-signal preservation during protein harvesting, and potential loss of antigen during protein transfer, WB provides only semi-quantitative data. By comparison, the "in-cell western" (ICW technique has high-throughput capacity and requires less extensive sample preparation. Thus, we compared the ICW technique to WB for measuring phosphorylated myosin regulatory light chain (PMLC(20 in primary cultures of uterine myocytes to assess their relative specificity, sensitivity, precision, and quantification of biologically relevant responses.ICWs are cell-based microplate assays for quantification of protein targets in their cellular context. ICWs utilize a two-channel infrared (IR scanner (Odyssey(R to quantify signals arising from near-infrared (NIR fluorophores conjugated to secondary antibodies. One channel is dedicated to measuring the protein of interest and the second is used for data normalization of the signal in each well of the microplate. Using uterine myocytes, we assessed oxytocin (OT-stimulated MLC(20 phosphorylation measured by ICW and WB, both using NIR fluorescence. ICW and WB data were comparable regarding signal linearity, signal specificity, and time course of phosphorylation response to OT.ICW and WB yield comparable biological data. The advantages of ICW over WB are its high-throughput capacity, improved precision, and reduced sample preparation requirements. ICW might provide better sensitivity and precision with low-quantity samples or for protocols requiring large numbers of samples. These features make the ICW technique an excellent tool for the study of phosphorylation endpoints

  14. High-throughput analysis reveals novel maternal germline RNAs crucial for primordial germ cell preservation and proper migration

    OpenAIRE

    Owens, Dawn A.; Butler, Amanda M.; Aguero, Tristan H.; Newman, Karen M.; Van Booven, Derek; King, Mary Lou

    2017-01-01

    During oogenesis, hundreds of maternal RNAs are selectively localized to the animal or vegetal pole, including determinants of somatic and germline fates. Although microarray analysis has identified localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high-throughput RNA-sequencing analysis to comprehensively interrogate animal and vegetal pole RNAs in the fully grown Xenopus laevis oocyte. We identified 411 (198 annotated) and 27 (15 annotate...

  15. A holistic high-throughput screening framework for biofuel feedstock assessment that characterises variations in soluble sugars and cell wall composition in Sorghum bicolor.

    Science.gov (United States)

    Martin, Antony P; Palmer, William M; Byrt, Caitlin S; Furbank, Robert T; Grof, Christopher Pl

    2013-12-23

    A major hindrance to the development of high yielding biofuel feedstocks is the ability to rapidly assess large populations for fermentable sugar yields. Whilst recent advances have outlined methods for the rapid assessment of biomass saccharification efficiency, none take into account the total biomass, or the soluble sugar fraction of the plant. Here we present a holistic high-throughput methodology for assessing sweet Sorghum bicolor feedstocks at 10 days post-anthesis for total fermentable sugar yields including stalk biomass, soluble sugar concentrations, and cell wall saccharification efficiency. A mathematical method for assessing whole S. bicolor stalks using the fourth internode from the base of the plant proved to be an effective high-throughput strategy for assessing stalk biomass, soluble sugar concentrations, and cell wall composition and allowed calculation of total stalk fermentable sugars. A high-throughput method for measuring soluble sucrose, glucose, and fructose using partial least squares (PLS) modelling of juice Fourier transform infrared (FTIR) spectra was developed. The PLS prediction was shown to be highly accurate with each sugar attaining a coefficient of determination (R2) of 0.99 with a root mean squared error of prediction (RMSEP) of 11.93, 5.52, and 3.23 mM for sucrose, glucose, and fructose, respectively, which constitutes an error of <4% in each case. The sugar PLS model correlated well with gas chromatography-mass spectrometry (GC-MS) and brix measures. Similarly, a high-throughput method for predicting enzymatic cell wall digestibility using PLS modelling of FTIR spectra obtained from S. bicolor bagasse was developed. The PLS prediction was shown to be accurate with an R2 of 0.94 and RMSEP of 0.64 μg.mgDW-1.h-1. This methodology has been demonstrated as an efficient and effective way to screen large biofuel feedstock populations for biomass, soluble sugar concentrations, and cell wall digestibility simultaneously allowing a

  16. Label-free high-throughput detection and quantification of circulating melanoma tumor cell clusters by linear-array-based photoacoustic tomography.

    Science.gov (United States)

    Hai, Pengfei; Zhou, Yong; Zhang, Ruiying; Ma, Jun; Li, Yang; Shao, Jin-Yu; Wang, Lihong V

    2017-04-01

    Circulating tumor cell (CTC) clusters, arising from multicellular groupings in a primary tumor, greatly elevate the metastatic potential of cancer compared with single CTCs. High-throughput detection and quantification of CTC clusters are important for understanding the tumor metastatic process and improving cancer therapy. Here, we applied a linear-array-based photoacoustic tomography (LA-PAT) system and improved the image reconstruction for label-free high-throughput CTC cluster detection and quantification cluster clusters was investigated and verified. Melanoma CTC clusters with a minimum of four cells could be detected, and the number of cells could be computed from the CNR. Finally, we demonstrated imaging of injected melanoma CTC clusters in rats clusters could be quantified. The data showed that larger CTC clusters had faster clearance rates in the bloodstream, which agreed with the literature. The results demonstrated the capability of LA-PAT to detect and quantify melanoma CTC clusters

  17. MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.

    Science.gov (United States)

    Gupta, Surya; De Puysseleyr, Veronic; Van der Heyden, José; Maddelein, Davy; Lemmens, Irma; Lievens, Sam; Degroeve, Sven; Tavernier, Jan; Martens, Lennart

    2017-05-01

    Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments. MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT. jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be. Supplementary data are available at Bioinformatics online.

  18. JA, a new type of polyunsaturated fatty acid isolated from Juglans mandshurica Maxim, limits the survival and induces apoptosis of heptocarcinoma cells.

    Science.gov (United States)

    Gao, Xiu-Li; Lin, Hua; Zhao, Wei; Hou, Ya-Qin; Bao, Yong-Li; Song, Zhen-Bo; Sun, Lu-Guo; Tian, Shang-Yi; Liu, Biao; Li, Yu-Xin

    2016-03-01

    Juglans mandshurica Maxim (Juglandaceae) is a famous folk medicine for cancer treatment and some natural compounds isolated from it have been studied extensively. Previously we isolated a type of ω-9 polyunsaturated fatty acid (JA) from the bark of J. mandshurica, however little is known about its activity and the underlying mechanisms. In this study, we studied anti-tumor activity of JA on several human cancer cell lines. Results showed that JA is cytotoxic to HepG2, MDA-MB-231, SGC-7901, A549 and Huh7 cells at a concentration exerting minimal toxic effects on L02 cells. The selective toxicity of JA was better than other classical anti-cancer drugs. Further investigation indicated that JA could induce cell apoptosis, characterized by chromatin condensation, DNA fragmentation and activation of the apoptosis-associated proteins such as Caspase-3 and PARP-1. Moreover, we investigated the cellular apoptosis pathway involved in the apoptosis process in HepG2 cells. We found that proteins involved in mitochondrion (cleaved-Caspase-9, Apaf-1, HtrA2/Omi, Bax, and Mitochondrial Bax) and endocytoplasmic reticulum (XBP-1s, GRP78, cleaved-Caspase-7 and cleaved-Caspase-12) apoptotic pathways were up-regulated when cells were treated by JA. In addition, a morphological change in the mitochondrion was detected. Furthermore, we found that JA could inhibit DNA synthesis and induce G2/M cell cycle arrest. The expression of G2-to-M transition related proteins, such as CyclinB1 and phosphorylated-CDK1, were reduced. In contrast, the G2-to-M inhibitor p21 was increased in JA-treated cells. Overall, our results suggest that JA can induce mitochondrion- and endocytoplasmic reticulum-mediated apoptosis, and G2/M phase arrest in HepG2 cells, making it a promising therapeutic agent against hepatoma.

  19. Uplink SDMA with Limited Feedback: Throughput Scaling

    Directory of Open Access Journals (Sweden)

    Jeffrey G. Andrews

    2008-01-01

    Full Text Available Combined space division multiple access (SDMA and scheduling exploit both spatial multiplexing and multiuser diversity, increasing throughput significantly. Both SDMA and scheduling require feedback of multiuser channel sate information (CSI. This paper focuses on uplink SDMA with limited feedback, which refers to efficient techniques for CSI quantization and feedback. To quantify the throughput of uplink SDMA and derive design guidelines, the throughput scaling with system parameters is analyzed. The specific parameters considered include the numbers of users, antennas, and feedback bits. Furthermore, different SNR regimes and beamforming methods are considered. The derived throughput scaling laws are observed to change for different SNR regimes. For instance, the throughput scales logarithmically with the number of users in the high SNR regime but double logarithmically in the low SNR regime. The analysis of throughput scaling suggests guidelines for scheduling in uplink SDMA. For example, to maximize throughput scaling, scheduling should use the criterion of minimum quantization errors for the high SNR regime and maximum channel power for the low SNR regime.

  20. The significance of the initiation process parameters and reactor design for maximizing the efficiency of microbial fuel cells

    DEFF Research Database (Denmark)

    Sun, Guotao; Thygesen, Anders; Ale, Marcel Tutor

    2014-01-01

    Microbial fuel cells (MFCs) can be used for electricity generation via bioconversion of wastewater and organic waste substrates. MFCs also hold potential for production of certain chemicals, such as H2 and H2O2. The studies of electricity generation in MFCs have mainly focused on the microbial...... the initiation process, including inoculum, substrate, and reactor configuration. The key messages are that optimal performance of MFCs for electricity production requires (1) understanding of the electrogenic bacterial biofilm formation, (2) proper substrates at the initiation stage, (3) focus on operational...

  1. Anti-proliferative effect of Juglone from Juglans mandshurica Maxim on human leukemia cell HL-60 by inducing apoptosis through the mitochondria-dependent pathway.

    Science.gov (United States)

    Xu, Hua-Li; Yu, Xiao-Feng; Qu, Shao-Chun; Zhang, Rui; Qu, Xiang-Ru; Chen, Yan-Ping; Ma, Xing-Yuan; Sui, Da-Yuan

    2010-10-25

    Induction of apoptosis in tumor cells has become the major focus of anti-tumor therapeutics development. Juglone, a major chemical constituent of Juglans mandshurica Maxim, possesses several bioactivities including anti-tumor. Here, for the first time, we studied the molecular mechanism of Juglone-induced apoptosis in human leukemia HL-60 cells. In the present study, HL-60 cells were incubated with Juglone at various concentrations. Occurrence of apoptosis was detected by Hoechst 33342 staining and flow cytometry. Expression of Bcl-2 and Bax mRNA was determined by quantitative polymerase chain reaction (qPCR). The results showed that Juglone inhibits the growth of human leukemia HL-60 cells in dose- and time-dependent manner. Topical morphological changes of apoptotic body formation after Juglone treatment were observed by Hoechst 33342 staining. The percentages of Annexin V-FITC-positive/PI negative cells were 7.81%, 35.46%, 49.11% and 66.02% with the concentrations of Juglone (0, 0.5, 1.0 and 1.5 microg/ml). Juglone could induce the mitochondrial membrane potential (DeltaPsim) loss, which preceded release of cytochrome c (Cyt c), Smac and apoptosis inducing factor (AIF) to cell cytoplasm. A marked increased of Bax mRNA and protein appeared with Juglone treatment, while an evidently decreased of Bcl-2 mRNA and protein appeared at the same time. These events paralleled with activation of caspase-9, -3 and PARP cleavage. And the apoptosis induced by Juglone was blocked by z-LEHD-fmk, a caspase-9 inhibitor. Those results of our studies demonstrated that Juglone-induced mitochondrial dysfunction in HL-60 cells trigger events responsible for mitochondrial-dependent apoptosis pathways and the elevated ratio of Bax/Bcl-2 was also probably involved in this effect. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. From microbial fuel cell (MFC) to microbial electrochemical snorkel (MES): maximizing chemical oxygen demand (COD) removal from wastewater.

    Science.gov (United States)

    Erable, Benjamin; Etcheverry, Luc; Bergel, Alain

    2011-03-01

    The paper introduces the concept of the microbial electrochemical snorkel (MES), a simplified design of a "short-circuited" microbial fuel cell (MFC). The MES cannot provide current but it is optimized for wastewater treatment. An electrochemically active biofilm (EAB) was grown on graphite felt under constant polarization in an urban wastewater. Controlling the electrode potential and inoculating the bioreactor with a suspension of an established EAB improved the performance and the reproducibility of the anodes. Anodes, colonized by an EAB were tested for the chemical oxygen demand (COD) removal from urban wastewater using a variety of bio-electrochemical processes (microbial electrolysis, MFC, MES). The MES technology, as well as a short-circuited MFC, led to a COD removal 57% higher than a 1000 Ω-connected MFC, confirming the potential for wastewater treatment.

  3. Maxims for Mentoring.

    Science.gov (United States)

    Kirk, James J.

    This paper describes five maxims for an effective faculty mentoring program developed at Western Carolina University (North Carolina) designed to increase retention of new faculty. The first maxim, "ask what the program will do for the school," emphasizes that a program should not be undertaken until this question has been specifically…

  4. A High-Throughput Cell-Based Screen Identified a 2-[(E)-2-Phenylvinyl]-8-Quinolinol Core Structure That Activates p53.

    Science.gov (United States)

    Bechill, John; Zhong, Rong; Zhang, Chen; Solomaha, Elena; Spiotto, Michael T

    2016-01-01

    p53 function is frequently inhibited in cancer either through mutations or by increased degradation via MDM2 and/or E6AP E3-ubiquitin ligases. Most agents that restore p53 expression act by binding MDM2 or E6AP to prevent p53 degradation. However, fewer compounds directly bind to and activate p53. Here, we identified compounds that shared a core structure that bound p53, caused nuclear localization of p53 and caused cell death. To identify these compounds, we developed a novel cell-based screen to redirect p53 degradation to the Skip-Cullin-F-box (SCF) ubiquitin ligase complex in cells expressing high levels of p53. In a multiplexed assay, we coupled p53 targeted degradation with Rb1 targeted degradation in order to identify compounds that prevented p53 degradation while not inhibiting degradation through the SCF complex or other proteolytic machinery. High-throughput screening identified several leads that shared a common 2-[(E)-2-phenylvinyl]-8-quinolinol core structure that stabilized p53. Surface plasmon resonance analysis indicated that these compounds bound p53 with a KD of 200 ± 52 nM. Furthermore, these compounds increased p53 nuclear localization and transcription of the p53 target genes PUMA, BAX, p21 and FAS in cancer cells. Although p53-null cells had a 2.5±0.5-fold greater viability compared to p53 wild type cells after treatment with core compounds, loss of p53 did not completely rescue cell viability suggesting that compounds may target both p53-dependent and p53-independent pathways to inhibit cell proliferation. Thus, we present a novel, cell-based high-throughput screen to identify a 2-[(E)-2-phenylvinyl]-8-quinolinol core structure that bound to p53 and increased p53 activity in cancer cells. These compounds may serve as anti-neoplastic agents in part by targeting p53 as well as other potential pathways.

  5. Maximizers versus satisficers

    Directory of Open Access Journals (Sweden)

    Andrew M. Parker

    2007-12-01

    Full Text Available Our previous research suggests that people reporting a stronger desire to maximize obtain worse life outcomes (Bruine de Bruin et al., 2007. Here, we examine whether this finding may be explained by the decision-making styles of self-reported maximizers. Expanding on Schwartz et al. (2002, we find that self-reported maximizers are more likely to show problematic decision-making styles, as evidenced by self-reports of less behavioral coping, greater dependence on others when making decisions, more avoidance of decision making, and greater tendency to experience regret. Contrary to predictions, self-reported maximizers were more likely to report spontaneous decision making. However, the relationship between self-reported maximizing and worse life outcomes is largely unaffected by controls for measures of other decision-making styles, decision-making competence, and demographic variables.

  6. Maximization of cell growth and lipid production of freshwater microalga Chlorella vulgaris by enrichment technique for biodiesel production.

    Science.gov (United States)

    Wong, Y K; Ho, Y H; Ho, K C; Leung, H M; Yung, K K L

    2017-04-01

    Chlorella vulgaris was cultivated under limitation and starvation and under controlled conditions using different concentrations of nitrate (NaNO3) and phosphate (K2HPO4 and KH2PO4) chemicals in modified Bold basal medium (BBM). The biomass and lipid production responses to different media were examined in terms of optical density, cell density, dry biomass, and lipid productivity. In the 12-day batch culture period, the highest biomass productivity obtained was 72.083 mg L-1 day-1 under BBM - NcontrolPlimited condition. The highest lipid content, lipid concentration, and lipid productivity obtained were 53.202 %, 287.291 mg/L, and 23.449 mg L-1 day-1 under BBM - NControlPDeprivation condition, respectively. Nitrogen had a major effect in the biomass concentration of C. vulgaris, while no significant effect was found for phosphorus. Nitrogen and phosphorus starvation was found to be the strategy affecting the lipid accumulation and affected the lipid composition of C. vulgaris cultures.

  7. Mitochondria-specific antioxidant supplementation does not influence endurance exercise training-induced adaptations in circulating angiogenic cells, skeletal muscle oxidative capacity or maximal oxygen uptake.

    Science.gov (United States)

    Shill, Daniel D; Southern, W Michael; Willingham, T Bradley; Lansford, Kasey A; McCully, Kevin K; Jenkins, Nathan T

    2016-12-01

    Reducing excessive oxidative stress, through chronic exercise or antioxidants, can decrease the negative effects induced by excessive amounts of oxidative stress. Transient increases in oxidative stress produced during acute exercise facilitate beneficial vascular training adaptations, but the effects of non-specific antioxidants on exercise training-induced vascular adaptations remain elusive. Circulating angiogenic cells (CACs) are an exercise-inducible subset of white blood cells that maintain vascular integrity. We investigated whether mitochondria-specific antioxidant (MitoQ) supplementation would affect the response to 3 weeks of endurance exercise training in CACs, muscle mitochondrial capacity and maximal oxygen uptake in young healthy men. We show that endurance exercise training increases multiple CAC types, an adaptation that is not altered by MitoQ supplementation. Additionally, MitoQ does not affect skeletal muscle or whole-body aerobic adaptations to exercise training. These results indicate that MitoQ supplementation neither enhances nor attenuates endurance training adaptations in young healthy men. Antioxidants have been shown to improve endothelial function and cardiovascular outcomes. However, the effects of antioxidants on exercise training-induced vascular adaptations remain elusive. General acting antioxidants combined with exercise have not impacted circulating angiogenic cells (CACs). We investigated whether mitochondria-specific antioxidant (MitoQ) supplementation would affect the response to 3 weeks of endurance exercise training on CD3+ , CD3+ /CD31+ , CD14+ /CD31+ , CD31+ , CD34+ /VEGFR2+ and CD62E+ peripheral blood mononuclear cells (PBMCs), muscle mitochondrial capacity, and maximal oxygen uptake (VO2 max ) in healthy men aged 22.1 ± 0.7 years, with a body mass index of 26.9 ± 0.9 kg m-2 , and 24.8 ± 1.3% body fat. Analysis of main effects revealed that training induced 33, 105 and 285% increases in CD14+ /CD31+ , CD62E

  8. Engineered optical properties of silver-aluminum alloy nanoparticles embedded in SiON matrix for maximizing light confinement in plasmonic silicon solar cells.

    Science.gov (United States)

    Parashar, Piyush K; Komarala, Vamsi K

    2017-10-02

    Self-assembled silver-aluminum (Ag-Al) alloy nanoparticles (NPs) embedded in SiO 2 , Si 3 N 4, and SiON dielectric thin film matrices explored as a hybrid plasmonic structure for silicon solar cells to maximize light confinement. The Ag 2 Al NPs prepared by ex-vacuo solid-state dewetting, and alloy formation confirmed by X-ray diffraction and photoelectron spectroscopy analysis. Nanoindentation by atomic force microscopy revealed better surface adhesion of alloy NPs on silicon surface than Ag NPs due to the Al presence. The SiON spacer layer/Ag 2 Al NPs reduced silicon average reflectance from 22.7% to 9.2% due to surface plasmonic and antireflection effects. The SiON capping layer on NPs reduced silicon reflectance from 9.2% to 3.6% in wavelength region 300-1150 nm with preferential forward light scattering due to uniform Coulombic restoring force on NPs' surface. Minimum reflectance and parasitic absorptance from 35 nm SiON/Ag 2 Al NPs/25 nm SiON structure reflected in plasmonic cell's photocurrent enhancement from 26.27 mA/cm 2 (of bare cell) to 34.61 mA/cm 2 due to the better photon management. Quantum efficiency analysis also showed photocurrent enhancement of cell in surface plasmon resonance and off-resonance regions of NPs. We also quantified dielectric thin film antireflection and alloy NPs plasmonic effects separately in cell photocurrent enhancement apart from hybrid plasmonic structure role.

  9. Use of high throughput qPCR screening to rapidly clone low frequency tumour specific T-cells from peripheral blood for adoptive immunotherapy

    Directory of Open Access Journals (Sweden)

    Serrano Oscar K

    2008-10-01

    Full Text Available Abstract Background The adoptive transfer of autologous tumor reactive lymphocytes can mediate significant tumor regression in some patients with refractory metastatic cancer. However, a significant obstacle for this promising therapy has been the availability of highly efficient methods to rapidly isolate and expand a variety of potentially rare tumor reactive lymphocytes from the natural repertoire of cancer patients. Methods We developed a novel in vitro T cell cloning methodology using high throughput quantitative RT-PCR (qPCR assay as a rapid functional screen to detect and facilitate the limiting dilution cloning of a variety of low frequency T cells from bulk PBMC. In preclinical studies, this strategy was applied to the isolation and expansion of gp100 specific CD8+ T cell clones from the peripheral blood of melanoma patients. Results In optimization studies, the qPCR assay could detect the reactivity of 1 antigen specific T cell in 100,000 background cells. When applied to short term sensitized PBMC microcultures, this assay could detect T cell reactivity against a variety of known melanoma tumor epitopes. This screening was combined with early limiting dilution cloning to rapidly isolate gp100154–162 reactive CD8+ T cell clones. These clones were highly avid against peptide pulsed targets and melanoma tumor lines. They had an effector memory phenotype and showed significant proliferative capacity to reach cell numbers appropriate for adoptive transfer trials (~1010 cells. Conclusion This report describes a novel high efficiency strategy to clone tumor reactive T cells from peripheral blood for use in adoptive immunotherapy.

  10. Asynchronous progression through the lytic cascade and variations in intracellular viral loads revealed by high-throughput single-cell analysis of Kaposi's sarcoma-associated herpesvirus infection.

    Science.gov (United States)

    Adang, Laura A; Parsons, Christopher H; Kedes, Dean H

    2006-10-01

    Kaposi's sarcoma-associated herpesvirus (KSHV or human herpesvirus-8) is frequently tumorigenic in immunocompromised patients. The average intracellular viral copy number within infected cells, however, varies markedly by tumor type. Since the KSHV-encoded latency-associated nuclear antigen (LANA) tethers viral episomes to host heterochromatin and displays a punctate pattern by fluorescence microscopy, we investigated whether accurate quantification of individual LANA dots is predictive of intracellular viral genome load. Using a novel technology that integrates single-cell imaging with flow cytometry, we found that both the number and the summed immunofluorescence of individual LANA dots are directly proportional to the amount of intracellular viral DNA. Moreover, combining viral (immediate early lytic replication and transcription activator [RTA] and late lytic K8.1) and cellular (syndecan-1) staining with image-based flow cytometry, we were also able to rapidly and simultaneously distinguish among cells supporting latent, immediate early lytic, early lytic, late lytic, and a potential fourth "delayed late" category of lytic replication. Applying image-based flow cytometry to KSHV culture models, we found that de novo infection results in highly varied levels of intracellular viral load and that lytic induction of latently infected cells likewise leads to a heterogeneous population at various stages of reactivation. These findings additionally underscore the potential advantages of studying KSHV biology with high-throughput analysis of individual cells.

  11. Throughput for steel pipes manufacturing process design

    Directory of Open Access Journals (Sweden)

    N. Fafandjel

    2008-10-01

    Full Text Available Conventional approach to pipe manufacturing process design is using capacity to satisfy maximal load for each process. In the new approach, throughput is suggested as a basic determinant aiming at finding dynamic balance among following and previous process phases. Throughput is defined by the interval of time between product exiting from the preceding process phase and its entry to the next one. Interval of time for the product delivery from the preceding phase must be less or equal as the amount of time necessary for activating the next phase. Knowing the performances of the next phase one can impact to the characteristics of the preceding phase. Throughput can be also used as a more precise way for observed process productivity measurement. Such approach is suggested and for other complex technological processes.

  12. Establishment of IL-7 Expression Reporter Human Cell Lines, and Their Feasibility for High-Throughput Screening of IL-7-Upregulating Chemicals.

    Science.gov (United States)

    Cho, Yeon Sook; Kim, Byung Soo; Sim, Chan Kyu; Kim, Inki; Lee, Myeong Sup

    2016-01-01

    Interleukin-7 (IL-7) is a cytokine essential for T cell homeostasis, and is clinically important. However, the regulatory mechanism of IL-7 gene expression is not well known, and a systematic approach to screen chemicals that regulate IL-7 expression has not yet been developed. In this study, we attempted to develop human reporter cell lines using CRISPR/Cas9-mediated genome editing technology. For this purpose, we designed donor DNA that contains an enhanced green fluorescent protein (eGFP) gene, drug selection cassette, and modified homologous arms which are considered to enhance the translation of the eGFP reporter transcript, and also a highly efficient single-guide RNA with a minimal off-target effect to target the IL-7 start codon region. By applying this system, we established IL-7 eGFP reporter cell lines that could report IL-7 gene transcription based on the eGFP protein signal. Furthermore, we utilized the cells to run a pilot screen campaign for IL-7-upregulating chemicals in a high-throughput format, and identified a chemical that can up-regulate IL-7 gene transcription. Collectively, these results suggest that our IL-7 reporter system can be utilized in large-scale chemical library screening to reveal novel IL-7 regulatory pathways and to identify potential drugs for development of new treatments in immunodeficiency disease.

  13. Silicon photonic crystal microarrays for high throughput label-free detection of lung cancer cell line lysates with sensitivity and specificity

    Science.gov (United States)

    Chakravarty, Swapnajit; Lai, Wei-Cheng; Zou, Yi; Gemmill, Robert M.; Chen, Ray T.

    2013-03-01

    Detection of biomolecules on microarrays based on label-free on-chip optical biosensors is very attractive since this format avoids complex chemistries caused by steric hindrance of labels. Application areas include the detection of cancers and allergens, and food-borne pathogens to name a few. We have demonstrated photonic crystal microcavity biosensors with high sensitivity down to 1pM concentrations (67pg/ml). High sensitivities were achieved by slow light engineering which reduced the radiation loss and increased the stored energy in the photonic crystal microcavity resonance mode. Resonances with high quality factor Q~26,760 in liquid ambient, coupled with larger optical mode volumes allowed enhanced interaction with the analyte biomolecules which resulted in sensitivities down to 10 cells per micro-liter to lung cancer cell lysates. The specificity of detection was ensured by multiplexed detections from multiple photonic crystal microcavities arrayed on the arms of a multimode interference power splitter. Specific binding interactions and control experiments were performed simultaneously at the same instant of time with the same 60 microliter sample volume. Specificity is further ensured by sandwich assay methods in the multiplexed experiment. Sandwich assay based amplification increased the sensitivity further resulting in the detection of lung cancer cell lysates down to concentrations of 2 cells per micro-liter. The miniaturization enabled by photonic crystal biosensors coupled with waveguide interconnected layout thus offers the potential of high throughput proteomics with high sensitivity and specificity.

  14. A NOVEL LOW THERMAL BUDGET THIN-FILM POLYSILICON FABRICATION PROCESS FOR LARGE-AREA, HIGH-THROUGHPUT SOLAR CELL PRODUCTION

    Energy Technology Data Exchange (ETDEWEB)

    Yue Kuo

    2010-08-15

    A novel thin-film poly-Si fabrication process has been demonstrated. This low thermal budget process transforms the single- and multi-layer amorphous silicon thin films into a poly-Si structure in one simple step over a pulsed rapid thermal annealing process with the enhancement of an ultrathin Ni layer. The complete poly-Si solar cell was fabricated in a short period of time without deteriorating the underneath glass substrate. The unique vertical crystallization process including the mechanism is discussed. Influences of the dopant type and process parameters on crystal structure will be revealed. The poly-Si film structure has been proved using TEM, XRD, Raman, and XPS methods. The poly-Si solar cell structure and the performance have been examined. In principle, the new process is potentially applicable to produce large-area thin-film poly-Si solar cells at a high throughput and low cost. A critical issue in this process is to prevent the excessive dopant diffusion during crystallization. Process parameters and the cell structure have to be optimized to achieve the production goal.

  15. Dependence of cancer cell adhesion kinetics on integrin ligand surface density measured by a high-throughput label-free resonant waveguide grating biosensor

    Science.gov (United States)

    Orgovan, Norbert; Peter, Beatrix; Bősze, Szilvia; Ramsden, Jeremy J.; Szabó, Bálint; Horvath, Robert

    2014-02-01

    A novel high-throughput label-free resonant waveguide grating (RWG) imager biosensor, the Epic® BenchTop (BT), was utilized to determine the dependence of cell spreading kinetics on the average surface density (vRGD) of integrin ligand RGD-motifs. vRGD was tuned over four orders of magnitude by co-adsorbing the biologically inactive PLL-g-PEG and the RGD-functionalized PLL-g-PEG-RGD synthetic copolymers from their mixed solutions onto the sensor surface. Using highly adherent human cervical tumor (HeLa) cells as a model system, cell adhesion kinetic data of unprecedented quality were obtained. Spreading kinetics were fitted with the logistic equation to obtain the spreading rate constant (r) and the maximum biosensor response (Δλmax), which is assumed to be directly proportional to the maximum spread contact area (Amax). r was found to be independent of the surface density of integrin ligands. In contrast, Δλmax increased with increasing RGD surface density until saturation at high densities. Interpreting the latter behavior with a simple kinetic mass action model, a 2D dissociation constant of 1753 +/- 243 μm-2 (corresponding to a 3D dissociation constant of ~30 μM) was obtained for the binding between RGD-specific integrins embedded in the cell membrane and PLL-g-PEG-RGD. All of these results were obtained completely noninvasively without using any labels.

  16. Designer Self-Assemble Peptides Maximize the Therapeutic Benefits of Neural Stem Cell Transplantation for Alzheimer's Disease via Enhancing Neuron Differentiation and Paracrine Action.

    Science.gov (United States)

    Cui, Guo-hong; Shao, Shui-jin; Yang, Jia-jun; Liu, Jian-ren; Guo, Hai-dong

    2016-03-01

    maximize the therapeutic benefits of NSC transplantation for AD through improving the survival and differentiation of transplanted stem cells and promoting the effects of neuroprotection, anti-neuroinflammatory and paracrine action. Our results may have important clinical implications for the design of future NSC-based strategies using the biomaterials for various neurodegenerative diseases including AD.

  17. High-throughput de novo screening of receptor agonists with an automated single-cell analysis and isolation system.

    Science.gov (United States)

    Yoshimoto, Nobuo; Tatematsu, Kenji; Iijima, Masumi; Niimi, Tomoaki; Maturana, Andrés D; Fujii, Ikuo; Kondo, Akihiko; Tanizawa, Katsuyuki; Kuroda, Shun'ichi

    2014-02-28

    Reconstitution of signaling pathways involving single mammalian transmembrane receptors has not been accomplished in yeast cells. In this study, intact EGF receptor (EGFR) and a cell wall-anchored form of EGF were co-expressed on the yeast cell surface, which led to autophosphorylation of the EGFR in an EGF-dependent autocrine manner. After changing from EGF to a conformationally constrained peptide library, cells were fluorescently labeled with an anti-phospho-EGFR antibody. Each cell was subjected to an automated single-cell analysis and isolation system that analyzed the fluorescent intensity of each cell and automatically retrieved each cell with the highest fluorescence. In ~3.2 × 10(6) peptide library, we isolated six novel peptides with agonistic activity of the EGFR in human squamous carcinoma A431 cells. The combination of yeast cells expressing mammalian receptors, a cell wall-anchored peptide library, and an automated single-cell analysis and isolation system might facilitate a rational approach for de novo drug screening.

  18. High-throughput deterministic single-cell encapsulation and droplet pairing, fusion, and shrinkage in a single microfluidic device

    NARCIS (Netherlands)

    Schoeman, R.M.; Kemna, Evelien; Wolbers, F.; van den Berg, Albert

    In this article, we present a microfluidic device capable of successive high-yield single-cell encapsulation in droplets, with additional droplet pairing, fusion, and shrinkage. Deterministic single-cell encapsulation is realized using Dean-coupled inertial ordering of cells in a Yin-Yang-shaped

  19. High Throughput Facility

    Data.gov (United States)

    Federal Laboratory Consortium — Argonne?s high throughput facility provides highly automated and parallel approaches to material and materials chemistry development. The facility allows scientists...

  20. A cell-based high-throughput protocol to screen entry inhibitors of highly pathogenic viruses with Traditional Chinese Medicines.

    Science.gov (United States)

    Yang, Yong; Cheng, Han; Yan, Hui; Wang, Peng-Zhan; Rong, Rong; Zhang, Ying-Ying; Zhang, Cheng-Bo; Du, Rui-Kun; Rong, Li-Jun

    2017-05-01

    Emerging viruses such as Ebola virus (EBOV), Lassa virus (LASV), and avian influenza virus H5N1 (AIV) are global health concerns. Since there is very limited options (either vaccine or specific therapy) approved for humans against these viruses, there is an urgent need to develop prophylactic and therapeutic treatments. Previously we reported a high-throughput screening (HTS) protocol to identify entry inhibitors for three highly pathogenic viruses (EBOV, LASV, and AIV) using a human immunodeficiency virus-based pseudotyping platform which allows us to perform the screening in a BSL-2 facility. In this report, we have adopted this screening protocol to evaluate traditional Chinese Medicines (TCMs) in an effort to discover entry inhibitors against these viruses. Here we show that extracts of the following Chinese medicinal herbs exhibit potent anti-Ebola viral activities: Gardenia jasminoides Ellis, Citrus aurantium L., Viola yedoensis Makino, Prunella vulgaris L., Coix lacryma-jobi L. var. mayuen (Roman.) Stapf, Pinellia ternata (Thunb.) Breit., and Morus alba L. This study represents a proof-of-principle investigation supporting the suitability of this assay for rapid screening TCMs and identifying putative entry inhibitors for these viruses. J. Med. Virol. 89:908-916, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  1. High-throughput deterministic single-cell encapsulation and droplet pairing, fusion, and shrinkage in a single microfluidic device.

    Science.gov (United States)

    Schoeman, Rogier M; Kemna, Evelien W M; Wolbers, Floor; van den Berg, Albert

    2014-02-01

    In this article, we present a microfluidic device capable of successive high-yield single-cell encapsulation in droplets, with additional droplet pairing, fusion, and shrinkage. Deterministic single-cell encapsulation is realized using Dean-coupled inertial ordering of cells in a Yin-Yang-shaped curved microchannel using a double T-junction, with a frequency over 2000 Hz, followed by controlled droplet pairing with a 100% success rate. Subsequently, droplet fusion is realized using electrical actuation resulting in electro-coalescence of two droplets, each containing a single HL60 cell, with 95% efficiency. Finally, volume reduction of the fused droplet up to 75% is achieved by a triple pitchfork structure. This droplet volume reduction is necessary to obtain close cell-cell membrane contact necessary for final cell electrofusion, leading to hybridoma formation, which is the ultimate aim of this research. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. High-throughput Characterization of HIV-1 Reservoir Reactivation Using a Single-Cell-in-Droplet PCR Assay

    Directory of Open Access Journals (Sweden)

    Robert W. Yucha

    2017-06-01

    Full Text Available Reactivation of latent viral reservoirs is on the forefront of HIV-1 eradication research. However, it is unknown if latency reversing agents (LRAs increase the level of viral transcription from cells producing HIV RNA or harboring transcriptionally-inactive (latent infection. We therefore developed a microfluidic single-cell-in-droplet (scdPCR assay to directly measure the number of CD4+ T cells that produce unspliced (usRNA and multiply spliced (msRNA following ex vivo latency reversal with either an histone deacetylase inhibitor (romidepsin or T cell receptor (TCR stimulation. Detection of HIV-1 transcriptional activity can also be performed on hundreds of thousands of CD4+ T-cells in a single experiment. The scdPCR method was then applied to CD4+ T cells obtained from HIV-1-infected individuals on antiretroviral therapy. Overall, our results suggest that effects of LRAs on HIV-1 reactivation may be heterogeneous—increasing transcription from active cells in some cases and increasing the number of transcriptionally active cells in others. Genomic DNA and human mRNA isolated from HIV-1 reactivated cells could also be detected and quantified from individual cells. As a result, our assay has the potential to provide needed insight into various reservoir eradication strategies.

  3. Relationship between length of longitudinal extension and maximal depth of transmural invasion in roentgenographically occult squamous cell carcinoma of the bronchus (nonpolypoid type).

    Science.gov (United States)

    Nagamoto, N; Saito, Y; Suda, H; Imai, T; Sato, M; Ohta, S; Kanma, K; Sagawa, M; Takahashi, S; Usuda, K

    1989-01-01

    This study was designed to verify our hypothesis that there are two different growth types in roentgenographically occult squamous cell carcinoma of the bronchus. Serial blocks prepared from the entire bronchial tree of 83 resected specimens of occult carcinoma were used for the evaluation of the relationship between the length of longitudinal extension and the maximal depth of transmural invasion. We prepared a length-depth diagram of 92 lesions, including multifocal carcinomas, which confirmed that there are at least two types: Most of these lesions are of the creeping type, which shows a marked superficial growth; the minority are of the penetrating type, which shows a marked downward growth. The diagram suggests that occult carcinoma has a propensity either for longitudinal growth along the bronchial lumen or for transmural growth into the bronchial wall at the time of occurrence. It is likely that the penetrating type grows rapidly and becomes advanced in a short time. Identification of longer lesions of the creeping type is occasionally problematical both at bronchoscopy and at surgical treatment. The stump is usually positive for carcinoma unless frozen sections or imprint specimens of the margin of resection are examined, because it is frequently difficult to identify the proximal end of extension by bronchoscopy.

  4. A 3D in vitro model of differentiated HepG2 cell spheroids with improved liver-like properties for repeated dose high-throughput toxicity studies.

    Science.gov (United States)

    Ramaiahgari, Sreenivasa C; den Braver, Michiel W; Herpers, Bram; Terpstra, Valeska; Commandeur, Jan N M; van de Water, Bob; Price, Leo S

    2014-05-01

    Immortalized hepatocyte cell lines show only a weak resemblance to primary hepatocytes in terms of gene expression and function, limiting their value in predicting drug-induced liver injury (DILI). Furthermore, primary hepatocytes cultured on two-dimensional tissue culture plastic surfaces rapidly dedifferentiate losing their hepatocyte functions and metabolic competence. We have developed a three-dimensional in vitro model using extracellular matrix-based hydrogel for long-term culture of the human hepatoma cell line HepG2. HepG2 cells cultured in this model stop proliferating, self-organize and differentiate to form multiple polarized spheroids. These spheroids re-acquire lost hepatocyte functions such as storage of glycogen, transport of bile salts and the formation of structures resembling bile canaliculi. HepG2 spheroids also show increased expression of albumin, urea, xenobiotic transcription factors, phase I and II drug metabolism enzymes and transporters. Consistent with this, cytochrome P450-mediated metabolism is significantly higher in HepG2 spheroids compared to monolayer cultures. This highly differentiated phenotype can be maintained in 384-well microtiter plates for at least 28 days. Toxicity assessment studies with this model showed an increased sensitivity in identifying hepatotoxic compounds with repeated dosing regimens. This simple and robust high-throughput-compatible methodology may have potential for use in toxicity screening assays and mechanistic studies and may represent an alternative to animal models for studying DILI.

  5. Cell-Based High-Throughput Luciferase Reporter Gene Assays for Identifying and Profiling Chemical Modulators of Endoplasmic Reticulum Signaling Protein, IRE1.

    Science.gov (United States)

    Rong, Juan; Pass, Ian; Diaz, Paul W; Ngo, Tram A; Sauer, Michelle; Magnuson, Gavin; Zeng, Fu-Yue; Hassig, Christian A; Jackson, Michael R; Cosford, Nicholas D P; Matsuzawa, Shu-Ichi; Reed, John C

    2015-12-01

    Endoplasmic reticulum (ER) stress activates three distinct signal transducers on the ER membrane. Inositol-requiring protein 1 (IRE1), the most conserved signal transducer, plays a key role in ER stress-mediated signaling. During ER stress, IRE1 initiates two discrete signaling cascades: the "adaptive" signaling cascade mediated by the XBP1 pathway and the "alarm" signaling cascade mediated by stress-activated protein kinase pathways. Fine-tuning of the balance between the adaptive and alarm signals contributes significantly to cellular fate under ER stress. Thus, we propose that the design of high-throughput screening (HTS) assays to selectively monitor IRE1 mediated-signaling would be desirable for drug discovery. To this end, we report the generation of stable human neural cell lines and development of cell-based HTS luciferase (Luc) reporter gene assays for the identification of pathway-specific chemical modulators of IRE1. We implemented a cell-based Luc assay using a chimeric CHOP-Gal4 transcription factor in 384-well format for monitoring IRE1 kinase-mediated p38MAPK activation and an unfolded response pathway element (URPE)-Luc cell-based assay in 1536-well format for monitoring IRE1's RNase-mediated activation of XBP1. Chemical library screening was successfully conducted with both the CHOP/Gal4-Luc cells and UPRE-Luc engineered cells. The studies demonstrate the feasibility of using these HTS assays for discovery of pathway-selective modulators of IRE1. © 2015 Society for Laboratory Automation and Screening.

  6. High-Throughput Assay Development for Cystine-Glutamate Antiporter (xc- Highlights Faster Cystine Uptake than Glutamate Release in Glioma Cells.

    Directory of Open Access Journals (Sweden)

    Ajit G Thomas

    Full Text Available The cystine-glutamate antiporter (system xc- is a Na+-independent amino acid transporter that exchanges extracellular cystine for intracellular glutamate. It is thought to play a critical role in cellular redox processes through regulation of intracellular glutathione synthesis via cystine uptake. In gliomas, system xc- expression is universally up-regulated while that of glutamate transporters down-regulated, leading to a progressive accumulation of extracellular glutamate and excitotoxic cell death of the surrounding non-tumorous tissue. Additionally, up-regulation of system xc- in activated microglia has been implicated in the pathogenesis of several neurodegenerative disorders mediated by excess glutamate. Consequently, system xc- is a new drug target for brain cancer and neuroinflammatory diseases associated with excess extracellular glutamate. Unfortunately no potent and selective small molecule system xc- inhibitors exist and to our knowledge, no high throughput screening (HTS assay has been developed to identify new scaffolds for inhibitor design. To develop such an assay, various neuronal and non-neuronal human cells were evaluated as sources of system xc-. Human glioma cells were chosen based on their high system xc- activity. Using these cells, [14C]-cystine uptake and cystine-induced glutamate release assays were characterized and optimized with respect to cystine and protein concentrations and time of incubation. A pilot screen of the LOPAC/NINDS libraries using glutamate release demonstrated that the logistics of the assay were in place but unfortunately, did not yield meaningful pharmacophores. A larger, HTS campaign using the 384-well cystine-induced glutamate release as primary assay and the 96-well 14C-cystine uptake as confirmatory assay is currently underway. Unexpectedly, we observed that the rate of cystine uptake was significantly faster than the rate of glutamate release in human glioma cells. This was in contrast to the

  7. High-Throughput Platform for Patient-Derived, Small Cell Number, Three-Dimensional Ovarian Cancer Spheroids

    Science.gov (United States)

    2014-09-01

    649-654. 56. Lee KH, No da Y, Kim SH, Ryoo JH, Wong SF, Lee SH. Diffusion-mediated in situ alginate encapsulation of cell spheroids using microscale...OVCAR3 dsRED spheroids generated with 10-50 cells. 17 Spheroids were harvested, encapsulated in agarose, imaged with a confocal microscope and the z

  8. Guinea pig maximization test

    DEFF Research Database (Denmark)

    Andersen, Klaus Ejner

    1985-01-01

    Guinea pig maximization tests (GPMT) with chlorocresol were performed to ascertain whether the sensitization rate was affected by minor changes in the Freund's complete adjuvant (FCA) emulsion used. Three types of emulsion were evaluated: the oil phase was mixed with propylene glycol, saline...

  9. Microscopy-based Assays for High-throughput Screening of Host Factors Involved in Brucella Infection of Hela Cells.

    Science.gov (United States)

    Casanova, Alain; Low, Shyan H; Emmenlauer, Mario; Conde-Alvarez, Raquel; Salcedo, Suzana P; Gorvel, Jean-Pierre; Dehio, Christoph

    2016-08-05

    Brucella species are facultative intracellular pathogens that infect animals as their natural hosts. Transmission to humans is most commonly caused by direct contact with infected animals or by ingestion of contaminated food and can lead to severe chronic infections. Brucella can invade professional and non-professional phagocytic cells and replicates within endoplasmic reticulum (ER)-derived vacuoles. The host factors required for Brucella entry into host cells, avoidance of lysosomal degradation, and replication in the ER-like compartment remain largely unknown. Here we describe two assays to identify host factors involved in Brucella entry and replication in HeLa cells. The protocols describe the use of RNA interference, while alternative screening methods could be applied. The assays are based on the detection of fluorescently labeled bacteria in fluorescently labeled host cells using automated wide-field microscopy. The fluorescent images are analyzed using a standardized image analysis pipeline in CellProfiler which allows single cell-based infection scoring. In the endpoint assay, intracellular replication is measured two days after infection. This allows bacteria to traffic to their replicative niche where proliferation is initiated around 12 hr after bacterial entry. Brucella which have successfully established an intracellular niche will thus have strongly proliferated inside host cells. Since intracellular bacteria will greatly outnumber individual extracellular or intracellular non-replicative bacteria, a strain constitutively expressing GFP can be used. The strong GFP signal is then used to identify infected cells. In contrast, for the entry assay it is essential to differentiate between intracellular and extracellular bacteria. Here, a strain encoding for a tetracycline-inducible GFP is used. Induction of GFP with simultaneous inactivation of extracellular bacteria by gentamicin enables the differentiation between intracellular and extracellular

  10. Ultra-Sensitive, High-Resolution Liquid Chromatography Methods for the High-Throughput Quantitative Analysis of Bacterial Cell Wall Chemistry and Structure.

    Science.gov (United States)

    Alvarez, Laura; Hernandez, Sara B; de Pedro, Miguel A; Cava, Felipe

    2016-01-01

    High-performance liquid chromatography (HPLC) analysis has been critical for determining the structural and chemical complexity of the cell wall. However this method is very time consuming in terms of sample preparation and chromatographic separation. Here we describe (1) optimized methods for peptidoglycan isolation from both Gram-negative and Gram-positive bacteria that dramatically reduce the sample preparation time, and (2) the application of the fast and highly efficient ultra-performance liquid chromatography (UPLC) technology to muropeptide separation and quantification. The advances in both analytical instrumentation and stationary-phase chemistry have allowed for evolved protocols which cut run time from hours (2-3 h) to minutes (10-20 min), and sample demands by at least one order of magnitude. Furthermore, development of methods based on organic solvents permits in-line mass spectrometry (MS) of the UPLC-resolved muropeptides. Application of these technologies to high-throughput analysis will expedite the better understanding of the cell wall biology.

  11. PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics1[OPEN

    Science.gov (United States)

    Poeschl, Yvonne; Plötner, Romina

    2017-01-01

    Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets. PMID:28931626

  12. Principles of maximally classical and maximally realistic quantum ...

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics; Volume 59; Issue 2. Principles of maximally classical and maximally realistic quantum mechanics. S M Roy. Volume 59 Issue 2 August ... Keywords. Maximally realistic quantum theory; phase space Bell inequalities; maximally classical trajectories in realistic quantum theory.

  13. High-Throughput Sequencing of MicroRNAs in Adenovirus Type 3 Infected Human Laryngeal Epithelial Cells

    Directory of Open Access Journals (Sweden)

    Yuhua Qi

    2010-01-01

    Full Text Available Adenovirus infection can cause various illnesses depending on the infecting serotype, such as gastroenteritis, conjunctivitis, cystitis, and rash illness, but the infection mechanism is still unknown. MicroRNAs (miRNA have been reported to play essential roles in cell proliferation, cell differentiation, and pathogenesis of human diseases including viral infections. We analyzed the miRNA expression profiles from adenovirus type 3 (AD3 infected Human laryngeal epithelial (Hep2 cells using a SOLiD deep sequencing. 492 precursor miRNAs were identified in the AD3 infected Hep2 cells, and 540 precursor miRNAs were identified in the control. A total of 44 miRNAs demonstrated high expression and 36 miRNAs showed lower expression in the AD3 infected cells than control. The biogenesis of miRNAs has been analyzed, and some of the SOLiD results were confirmed by Quantitative PCR analysis. The present studies may provide a useful clue for the biological function research into AD3 infection.

  14. Linear-array-based photoacoustic tomography for label-free high-throughput detection and quantification of circulating melanoma tumor cell clusters

    Science.gov (United States)

    Hai, Pengfei; Zhou, Yong; Zhang, Ruiying; Ma, Jun; Li, Yang; Wang, Lihong V.

    2017-03-01

    Circulating tumor cell (CTC) clusters arise from multicellular grouping in the primary tumor and elevate the metastatic potential by 23 to 50 fold compared to single CTCs. High throughout detection and quantification of CTC clusters is critical for understanding the tumor metastasis process and improving cancer therapy. In this work, we report a linear-array-based photoacoustic tomography (LA-PAT) system capable of label-free high-throughput CTC cluster detection and quantification in vivo. LA-PAT detects CTC clusters and quantifies the number of cells in them based on the contrast-to-noise ratios (CNRs) of photoacoustic signals. The feasibility of LA-PAT was first demonstrated by imaging CTC clusters ex vivo. LA-PAT detected CTC clusters in the blood-filled microtubes and computed the number of cells in the clusters. The size distribution of the CTC clusters measured by LA-PAT agreed well with that obtained by optical microscopy. We demonstrated the ability of LA-PAT to detect and quantify CTC clusters in vivo by imaging injected CTC clusters in rat tail veins. LA-PAT detected CTC clusters immediately after injection as well as when they were circulating in the rat bloodstreams. Similarly, the numbers of cells in the clusters were computed based on the CNRs of the photoacoustic signals. The data showed that larger CTC clusters disappear faster than the smaller ones. The results prove the potential of LA-PAT as a promising tool for both preclinical tumor metastasis studies and clinical cancer therapy evaluation.

  15. High-throughput discovery of T cell epitopes in type 1 diabetes using DNA barcode labelledpeptide-MHC multimers

    DEFF Research Database (Denmark)

    Lyngaa, Rikke Birgitte; Bentzen, Amalie Kai; Overgaard, A. Julie

    2016-01-01

    Type 1 diabetes (T1D) is characterized by a CD8+ lymphocyte-mediated selective destruction of theinsulin-producing β-cells causing clinical diabetes. Several autoantigens including glutamic acid decarboxylase 65kDa (GAD65), insulin, protein tyrosine phosphatase (IA-2) and zinc transporter 8 (ZnT8...... as T cell targets in other autoimmune diseases. We used netMHC prediction algorithm to identify 764 epitopes from Insulin, GAD65, IA-2 and ZnT8 restricted to HLA-A2, A24, B8 and B15. Among these 91 peptide sequences were susceptible for citrullination. We evaluate the MHC-affinity of both...

  16. High Throughput Screening of Natural Phenolic Compounds Against Migration of Metastatic Triple-Negative Breast Cancer (TNBC) Cells

    OpenAIRE

    Nasrollahi, Samila

    2013-01-01

    In this report, we hypothesize that natural phenolic compounds may present a new class of chemotherapeutics against migration of metastatic triple-negative breast cancers (TNBC). In this project we will screen a small library of phenolic compounds to test this hypothesis, identify compounds that show efficacy against TNBC cell migration, and elucidate underlying molecular mechanisms.

  17. Maximally Atomic Languages

    Directory of Open Access Journals (Sweden)

    Janusz Brzozowski

    2014-05-01

    Full Text Available The atoms of a regular language are non-empty intersections of complemented and uncomplemented quotients of the language. Tight upper bounds on the number of atoms of a language and on the quotient complexities of atoms are known. We introduce a new class of regular languages, called the maximally atomic languages, consisting of all languages meeting these bounds. We prove the following result: If L is a regular language of quotient complexity n and G is the subgroup of permutations in the transition semigroup T of the minimal DFA of L, then L is maximally atomic if and only if G is transitive on k-subsets of 1,...,n for 0 <= k <= n and T contains a transformation of rank n-1.

  18. Integrated High Throughput Analysis Identifies GSK3 as a Crucial Determinant of p53-Mediated Apoptosis in Lung Cancer Cells.

    Science.gov (United States)

    Zhang, Yu; Zhu, Chenyang; Sun, Bangyao; Lv, Jiawei; Liu, Zhonghua; Liu, Shengwang; Li, Hai

    2017-01-01

    p53 dysfunction is frequently observed in lung cancer. Although restoring the tumour suppressor function of p53 is recently approved as a putative strategy for combating cancers, the lack of understanding of the molecular mechanism underlying p53-mediated lung cancer suppression has limited the application of p53-based therapies in lung cancer. Using RNA sequencing, we determined the transcriptional profile of human non-small cell lung carcinoma A549 cells after treatment with two p53-activating chemical compounds, nutlin and RITA, which could induce A549 cell cycle arrest and apoptosis, respectively. Bioinformatics analysis of genome-wide gene expression data showed that distinct transcription profiles were induced by nutlin and RITA and 66 pathways were differentially regulated by these two compounds. However, only two of these pathways, 'Adherens junction' and 'Axon guidance', were found to be synthetic lethal with p53 re-activation, as determined via integrated analysis of genome-wide gene expression profile and short hairpin RNA (shRNA) screening. Further functional protein association analysis of significantly regulated genes associated with these two synthetic lethal pathways indicated that GSK3 played a key role in p53-mediated A549 cell apoptosis, and then gene function study was performed, which revealed that GSK3 inhibition promoted p53-mediated A549 cell apoptosis in a p53 post-translational activity-dependent manner. Our findings provide us with new insights regarding the mechanism by which p53 mediates A549 apoptosis and may cast light on the development of more efficient p53-based strategies for treating lung cancer. © 201 The Author(s). Published by S. Karger AG, Basel.

  19. Quantum-Inspired Maximizer

    Science.gov (United States)

    Zak, Michail

    2008-01-01

    A report discusses an algorithm for a new kind of dynamics based on a quantum- classical hybrid-quantum-inspired maximizer. The model is represented by a modified Madelung equation in which the quantum potential is replaced by different, specially chosen 'computational' potential. As a result, the dynamics attains both quantum and classical properties: it preserves superposition and entanglement of random solutions, while allowing one to measure its state variables, using classical methods. Such optimal combination of characteristics is a perfect match for quantum-inspired computing. As an application, an algorithm for global maximum of an arbitrary integrable function is proposed. The idea of the proposed algorithm is very simple: based upon the Quantum-inspired Maximizer (QIM), introduce a positive function to be maximized as the probability density to which the solution is attracted. Then the larger value of this function will have the higher probability to appear. Special attention is paid to simulation of integer programming and NP-complete problems. It is demonstrated that the problem of global maximum of an integrable function can be found in polynomial time by using the proposed quantum- classical hybrid. The result is extended to a constrained maximum with applications to integer programming and TSP (Traveling Salesman Problem).

  20. High-Throughput Screening to Identify Compounds That Increase Fragile X Mental Retardation Protein Expression in Neural Stem Cells Differentiated From Fragile X Syndrome Patient-Derived Induced Pluripotent Stem Cells.

    Science.gov (United States)

    Kumari, Daman; Swaroop, Manju; Southall, Noel; Huang, Wenwei; Zheng, Wei; Usdin, Karen

    2015-07-01

    : Fragile X syndrome (FXS), the most common form of inherited cognitive disability, is caused by a deficiency of the fragile X mental retardation protein (FMRP). In most patients, the absence of FMRP is due to an aberrant transcriptional silencing of the fragile X mental retardation 1 (FMR1) gene. FXS has no cure, and the available treatments only provide symptomatic relief. Given that FMR1 gene silencing in FXS patient cells can be partially reversed by treatment with compounds that target repressive epigenetic marks, restoring FMRP expression could be one approach for the treatment of FXS. We describe a homogeneous and highly sensitive time-resolved fluorescence resonance energy transfer assay for FMRP detection in a 1,536-well plate format. Using neural stem cells differentiated from an FXS patient-derived induced pluripotent stem cell (iPSC) line that does not express any FMRP, we screened a collection of approximately 5,000 known tool compounds and approved drugs using this FMRP assay and identified 6 compounds that modestly increase FMR1 gene expression in FXS patient cells. Although none of these compounds resulted in clinically relevant levels of FMR1 mRNA, our data provide proof of principle that this assay combined with FXS patient-derived neural stem cells can be used in a high-throughput format to identify better lead compounds for FXS drug development. In this study, a specific and sensitive fluorescence resonance energy transfer-based assay for fragile X mental retardation protein detection was developed and optimized for high-throughput screening (HTS) of compound libraries using fragile X syndrome (FXS) patient-derived neural stem cells. The data suggest that this HTS format will be useful for the identification of better lead compounds for developing new therapeutics for FXS. This assay can also be adapted for FMRP detection in clinical and research settings. ©AlphaMed Press.

  1. A High Throughput Screening Assay for Anti-Mycobacterial Small Molecules Based on Adenylate Kinase Release as a Reporter of Cell Lysis.

    Directory of Open Access Journals (Sweden)

    Lauren Forbes

    Full Text Available Mycobacterium tuberculosis (Mtb is well-established to be one of the most important bacterial pathogens for which new antimicrobial therapies are needed. Herein, we describe the development of a high throughput screening assay for the identification of molecules that are bactericidal against Mycobacteria. The assay utilizes the release of the intracellular enzyme adenylate kinase into the culture medium as a reporter of mycobacterial cell death. We demonstrate that the assay is selective for mycobactericidal molecules and detects anti-mycobacterial activity at concentrations below the minimum inhibitory concentration of many molecules. Thus, the AK assay is more sensitive than traditional growth assays. We have validated the AK assay in the HTS setting using the Mtb surrogate organism M. smegmatis and libraries of FDA approved drugs as well as a commercially available Diversity set. The screen of the FDA-approved library demonstrated that the AK assay is able to identify the vast majority of drugs with known mycobactericidal activity. Importantly, our screen of the Diversity set revealed that the increased sensitivity of the AK assay increases the ability of M. smegmatis-based screens to detect molecules with relatively poor activity against M. smegmatis but good to excellent activity against Mtb.

  2. A high-throughput 2D-analytical technique to obtain single protein parameters from complex cell lysates for in silico process development of ion exchange chromatography.

    Science.gov (United States)

    Kröner, Frieder; Elsäßer, Dennis; Hubbuch, Jürgen

    2013-11-29

    The accelerating growth of the market for biopharmaceutical proteins, the market entry of biosimilars and the growing interest in new, more complex molecules constantly pose new challenges for bioseparation process development. In the presented work we demonstrate the application of a multidimensional, analytical separation approach to obtain the relevant physicochemical parameters of single proteins in a complex mixture for in silico chromatographic process development. A complete cell lysate containing a low titre target protein was first fractionated by multiple linear salt gradient anion exchange chromatography (AEC) with varying gradient length. The collected fractions were subsequently analysed by high-throughput capillary gel electrophoresis (HT-CGE) after being desalted and concentrated. From the obtained data of the 2D-separation the retention-volumes and the concentration of the single proteins were determined. The retention-volumes of the single proteins were used to calculate the related steric-mass action model parameters. In a final evaluation experiment the received parameters were successfully applied to predict the retention behaviour of the single proteins in salt gradient AEC. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. High-throughput roll-to-roll X-ray characterization of polymer solar cell active layers

    DEFF Research Database (Denmark)

    Böttiger, Arvid P.L.; Jørgensen, Mikkel; Menzel, Andreas

    2012-01-01

    Synchrotron-based X-rays were used to probe active materials for polymer solar cells on flexible polyester foil. The active material was coated onto a flexible 130 micron thick polyester foil using roll-to-roll differentially pumped slot-die coating and presented variation in composition, thickness...... be possible with dedicated laboratory instruments. We found that poly(3-hexyl)thiophene (P3HT) only crystallizes at a ratio above 1 : 2 with phenyl-C61-butyric acid methyl ester (PCBM) and that an optimum addition of 2 vol% chloronaphthalene (CN) as a processing additive significantly improves polymer...

  4. Social group utility maximization

    CERN Document Server

    Gong, Xiaowen; Yang, Lei; Zhang, Junshan

    2014-01-01

    This SpringerBrief explains how to leverage mobile users' social relationships to improve the interactions of mobile devices in mobile networks. It develops a social group utility maximization (SGUM) framework that captures diverse social ties of mobile users and diverse physical coupling of mobile devices. Key topics include random access control, power control, spectrum access, and location privacy.This brief also investigates SGUM-based power control game and random access control game, for which it establishes the socially-aware Nash equilibrium (SNE). It then examines the critical SGUM-b

  5. A high-throughput, cell-based screening method for siRNA and small molecule inhibitors of mTORC1 signaling using the In Cell Western technique.

    Science.gov (United States)

    Hoffman, Gregory R; Moerke, Nathan J; Hsia, Max; Shamu, Caroline E; Blenis, John

    2010-04-01

    The mTORC1 pathway is a central regulator of cell growth, and defective mTORC1 regulation plays a causative role in a variety of human diseases, including cancer, tumor syndromes such as the tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM), and metabolic diseases such as diabetes and obesity. Given the importance of mTORC1 signaling in these diseases, there has been significant interest in developing screening methods suitable for identifying inhibitors of mTORC1 activation. To this end, we have developed a high-throughput, cell-based assay for the detection of rpS6-phosphorylation as a measure of mTORC1 signaling. This assay takes advantage of the "In Cell Western" (ICW) technique using the Aerius infrared imaging system (LI-COR Biosciences). The ICW procedure involves fixation and immunostaining of cells in a manner similar to standard immunofluorescence methods but takes advantage of secondary antibodies conjugated to infrared-excitable fluorophores for quantitative detection by the Aerius scanner. In addition, the cells are stained with an infrared-excitable succinimidyl ester dye, which covalently modifies free amine groups in fixed cells and provides a quantitative measure of cell number. We present validation data and pilot screens in a 384-well format demonstrating that this assay provides a statistically robust method for both small molecule and siRNA screening approaches designed to identify inhibitors of mTORC1 signaling.

  6. Identification of candidate agents active against N. ceranae infection in honey bees: establishment of a medium throughput screening assay based on N. ceranae infected cultured cells.

    Science.gov (United States)

    Gisder, Sebastian; Genersch, Elke

    2015-01-01

    Many flowering plants in both natural ecosytems and agriculture are dependent on insect pollination for fruit set and seed production. Managed honey bees (Apis mellifera) and wild bees are key pollinators providing this indispensable eco- and agrosystem service. Like all other organisms, bees are attacked by numerous pathogens and parasites. Nosema apis is a honey bee pathogenic microsporidium which is widely distributed in honey bee populations without causing much harm. Its congener Nosema ceranae was originally described as pathogen of the Eastern honey bee (Apis cerana) but jumped host from A. cerana to A. mellifera about 20 years ago and spilled over from A. mellifera to Bombus spp. quite recently. N. ceranae is now considered a deadly emerging parasite of both Western honey bees and bumblebees. Hence, novel and sustainable treatment strategies against N. ceranae are urgently needed to protect honey and wild bees. We here present the development of an in vitro medium throughput screening assay for the identification of candidate agents active against N. ceranae infections. This novel assay is based on our recently developed cell culture model for N. ceranae and coupled with an RT-PCR-ELISA protocol for quantification of N. ceranae in infected cells. The assay has been adapted to the 96-well microplate format to allow automated analysis. Several substances with known (fumagillin) or presumed (surfactin) or no (paromomycin) activity against N. ceranae were tested as well as substances for which no data concerning N. ceranae inhibition existed. While fumagillin and two nitroimidazoles (metronidazole, tinidazole) totally inhibited N. ceranae proliferation, all other test substances were inactive. In summary, the assay proved suitable for substance screening and demonstrated the activity of two synthetic antibiotics against N. ceranae.

  7. Identification of Candidate Agents Active against N. ceranae Infection in Honey Bees: Establishment of a Medium Throughput Screening Assay Based on N. ceranae Infected Cultured Cells

    Science.gov (United States)

    Gisder, Sebastian; Genersch, Elke

    2015-01-01

    Many flowering plants in both natural ecosytems and agriculture are dependent on insect pollination for fruit set and seed production. Managed honey bees (Apis mellifera) and wild bees are key pollinators providing this indispensable eco- and agrosystem service. Like all other organisms, bees are attacked by numerous pathogens and parasites. Nosema apis is a honey bee pathogenic microsporidium which is widely distributed in honey bee populations without causing much harm. Its congener Nosema ceranae was originally described as pathogen of the Eastern honey bee (Apis cerana) but jumped host from A. cerana to A. mellifera about 20 years ago and spilled over from A. mellifera to Bombus spp. quite recently. N. ceranae is now considered a deadly emerging parasite of both Western honey bees and bumblebees. Hence, novel and sustainable treatment strategies against N. ceranae are urgently needed to protect honey and wild bees. We here present the development of an in vitro medium throughput screening assay for the identification of candidate agents active against N. ceranae infections. This novel assay is based on our recently developed cell culture model for N. ceranae and coupled with an RT-PCR-ELISA protocol for quantification of N. ceranae in infected cells. The assay has been adapted to the 96-well microplate format to allow automated analysis. Several substances with known (fumagillin) or presumed (surfactin) or no (paromomycin) activity against N. ceranae were tested as well as substances for which no data concerning N. ceranae inhibition existed. While fumagillin and two nitroimidazoles (metronidazole, tinidazole) totally inhibited N. ceranae proliferation, all other test substances were inactive. In summary, the assay proved suitable for substance screening and demonstrated the activity of two synthetic antibiotics against N. ceranae. PMID:25658121

  8. Identification of candidate agents active against N. ceranae infection in honey bees: establishment of a medium throughput screening assay based on N. ceranae infected cultured cells.

    Directory of Open Access Journals (Sweden)

    Sebastian Gisder

    Full Text Available Many flowering plants in both natural ecosytems and agriculture are dependent on insect pollination for fruit set and seed production. Managed honey bees (Apis mellifera and wild bees are key pollinators providing this indispensable eco- and agrosystem service. Like all other organisms, bees are attacked by numerous pathogens and parasites. Nosema apis is a honey bee pathogenic microsporidium which is widely distributed in honey bee populations without causing much harm. Its congener Nosema ceranae was originally described as pathogen of the Eastern honey bee (Apis cerana but jumped host from A. cerana to A. mellifera about 20 years ago and spilled over from A. mellifera to Bombus spp. quite recently. N. ceranae is now considered a deadly emerging parasite of both Western honey bees and bumblebees. Hence, novel and sustainable treatment strategies against N. ceranae are urgently needed to protect honey and wild bees. We here present the development of an in vitro medium throughput screening assay for the identification of candidate agents active against N. ceranae infections. This novel assay is based on our recently developed cell culture model for N. ceranae and coupled with an RT-PCR-ELISA protocol for quantification of N. ceranae in infected cells. The assay has been adapted to the 96-well microplate format to allow automated analysis. Several substances with known (fumagillin or presumed (surfactin or no (paromomycin activity against N. ceranae were tested as well as substances for which no data concerning N. ceranae inhibition existed. While fumagillin and two nitroimidazoles (metronidazole, tinidazole totally inhibited N. ceranae proliferation, all other test substances were inactive. In summary, the assay proved suitable for substance screening and demonstrated the activity of two synthetic antibiotics against N. ceranae.

  9. Spheroid arrays for high-throughput single-cell analysis of spatial patterns and biomarker expression in 3D.

    Science.gov (United States)

    Ivanov, Delyan P; Grabowska, Anna M

    2017-01-30

    We describe and share a device, methodology and image analysis algorithms, which allow up to 66 spheroids to be arranged into a gel-based array directly from a culture plate for downstream processing and analysis. Compared to processing individual samples, the technique uses 11-fold less reagents, saves time and enables automated imaging. To illustrate the power of the technology, we showcase applications of the methodology for investigating 3D spheroid morphology and marker expression and for in vitro safety and efficacy screens. First, spheroid arrays of 11 cell-lines were rapidly assessed for differences in spheroid morphology. Second, highly-positive (SOX-2), moderately-positive (Ki-67) and weakly-positive (βIII-tubulin) protein targets were detected and quantified. Third, the arrays enabled screening of ten media compositions for inducing differentiation in human neurospheres. Last, the application of spheroid microarrays for spheroid-based drug screens was demonstrated by quantifying the dose-dependent drop in proliferation and increase in differentiation in etoposide-treated neurospheres.

  10. Chemometric Optimization Studies in Catalysis Employing High-Throughput Experimentation

    NARCIS (Netherlands)

    Pereira, S.R.M.

    2008-01-01

    The main topic of this thesis is the investigation of the synergies between High-Throughput Experimentation (HTE) and Chemometric Optimization methodologies in Catalysis research and of the use of such methodologies to maximize the advantages of using HTE methods. Several case studies were analysed

  11. High throughput protein production screening

    Science.gov (United States)

    Beernink, Peter T [Walnut Creek, CA; Coleman, Matthew A [Oakland, CA; Segelke, Brent W [San Ramon, CA

    2009-09-08

    Methods, compositions, and kits for the cell-free production and analysis of proteins are provided. The invention allows for the production of proteins from prokaryotic sequences or eukaryotic sequences, including human cDNAs using PCR and IVT methods and detecting the proteins through fluorescence or immunoblot techniques. This invention can be used to identify optimized PCR and WT conditions, codon usages and mutations. The methods are readily automated and can be used for high throughput analysis of protein expression levels, interactions, and functional states.

  12. Maximizing band gaps in plate structures

    DEFF Research Database (Denmark)

    Halkjær, Søren; Sigmund, Ole; Jensen, Jakob Søndergaard

    2006-01-01

    periodic plate using Bloch theory, which conveniently reduces the maximization problem to that of a single base cell. Secondly, we construct a finite periodic plate using a number of the optimized base cells in a postprocessed version. The dynamic properties of the finite plate are investigated......Band gaps, i.e., frequency ranges in which waves cannot propagate, can be found in elastic structures for which there is a certain periodic modulation of the material properties or structure. In this paper, we maximize the band gap size for bending waves in a Mindlin plate. We analyze an infinite...

  13. The GLP-1 analogue liraglutide improves first-phase insulin secretion and maximal beta-cell secretory capacity over 14 weeks of therapy in subjects with Type 2 diabetes

    DEFF Research Database (Denmark)

    Madsbad, Sten; Vilsbøll, Tina; Brock, Birgitte

    modified frequently sampled intravenous glucose tolerance test (FSIGTT), to test maximal- and first-phase insulin secretion, respectively, before and after 14 weeks’ liraglutide (0.65, 1.25 or 1.9 mg/day) or placebo treatment. Twelve healthy, untreated matched subjects were also tested. Results: Compared...... with placebo, the 1.25 and 1.9 mg/day doses of liraglutide increased maximal beta-cell secretory capacity with 6.3 pM (95% CI: 2.9–9.6) B114%, and 7.2 pM (95% CI: 3.3–11.0) B97%, respectively. These doses also increased first-phase insulin secretion relative to placebo by 11.0 pMh (95% CI: 6.6–15.4) B124...... group. Conclusion: In subjects with Type 2 diabetes, 14 weeks’ once-daily liraglutide (1.25 and 1.9 mg/day) markedly improves beta-cell function, significantly increases first-phase insulin secretion and maximal beta-cell secretory capacity....

  14. Detection and Tracking of NY-ESO-1-Specific CD8+ T Cells by High-Throughput T Cell Receptor β (TCRB Gene Rearrangements Sequencing in a Peptide-Vaccinated Patient.

    Directory of Open Access Journals (Sweden)

    Manami Miyai

    Full Text Available Comprehensive immunological evaluation is crucial for monitoring patients undergoing antigen-specific cancer immunotherapy. The identification and quantification of T cell responses is most important for the further development of such therapies. Using well-characterized clinical samples from a high responder patient (TK-f01 in an NY-ESO-1f peptide vaccine study, we performed high-throughput T cell receptor β-chain (TCRB gene next generation sequencing (NGS to monitor the frequency of NY-ESO-1-specific CD8+ T cells. We compared these results with those of conventional immunological assays, such as IFN-γ capture, tetramer binding and limiting dilution clonality assays. We sequenced human TCRB complementarity-determining region 3 (CDR3 rearrangements of two NY-ESO-1f-specific CD8+ T cell clones, 6-8L and 2F6, as well as PBMCs over the course of peptide vaccination. Clone 6-8L possessed the TCRB CDR3 gene TCRBV11-03*01 and BJ02-01*01 with amino acid sequence CASSLRGNEQFF, whereas 2F6 possessed TCRBV05-08*01 and BJ02-04*01 (CASSLVGTNIQYF. Using these two sequences as models, we evaluated the frequency of NY-ESO-1-specific CD8+ T cells in PBMCs ex vivo. The 6-8L CDR3 sequence was the second most frequent in PBMC and was present at high frequency (0.7133% even prior to vaccination, and sustained over the course of vaccination. Despite a marked expansion of NY-ESO-1-specific CD8+ T cells detected from the first through 6th vaccination by tetramer staining and IFN-γ capture assays, as evaluated by CDR3 sequencing the frequency did not increase with increasing rounds of peptide vaccination. By clonal analysis using 12 day in vitro stimulation, the frequency of B*52:01-restricted NY-ESO-1f peptide-specific CD8+ T cells in PBMCs was estimated as only 0.0023%, far below the 0.7133% by NGS sequencing. Thus, assays requiring in vitro stimulation might be underestimating the frequency of clones with lower proliferation potential. High-throughput TCRB

  15. Detection and Tracking of NY-ESO-1-Specific CD8+ T Cells by High-Throughput T Cell Receptor β (TCRB) Gene Rearrangements Sequencing in a Peptide-Vaccinated Patient.

    Science.gov (United States)

    Miyai, Manami; Eikawa, Shingo; Hosoi, Akihiro; Iino, Tamaki; Matsushita, Hirokazu; Isobe, Midori; Uenaka, Akiko; Udono, Heiichiro; Nakajima, Jun; Nakayama, Eiichi; Kakimi, Kazuhiro

    2015-01-01

    Comprehensive immunological evaluation is crucial for monitoring patients undergoing antigen-specific cancer immunotherapy. The identification and quantification of T cell responses is most important for the further development of such therapies. Using well-characterized clinical samples from a high responder patient (TK-f01) in an NY-ESO-1f peptide vaccine study, we performed high-throughput T cell receptor β-chain (TCRB) gene next generation sequencing (NGS) to monitor the frequency of NY-ESO-1-specific CD8+ T cells. We compared these results with those of conventional immunological assays, such as IFN-γ capture, tetramer binding and limiting dilution clonality assays. We sequenced human TCRB complementarity-determining region 3 (CDR3) rearrangements of two NY-ESO-1f-specific CD8+ T cell clones, 6-8L and 2F6, as well as PBMCs over the course of peptide vaccination. Clone 6-8L possessed the TCRB CDR3 gene TCRBV11-03*01 and BJ02-01*01 with amino acid sequence CASSLRGNEQFF, whereas 2F6 possessed TCRBV05-08*01 and BJ02-04*01 (CASSLVGTNIQYF). Using these two sequences as models, we evaluated the frequency of NY-ESO-1-specific CD8+ T cells in PBMCs ex vivo. The 6-8L CDR3 sequence was the second most frequent in PBMC and was present at high frequency (0.7133%) even prior to vaccination, and sustained over the course of vaccination. Despite a marked expansion of NY-ESO-1-specific CD8+ T cells detected from the first through 6th vaccination by tetramer staining and IFN-γ capture assays, as evaluated by CDR3 sequencing the frequency did not increase with increasing rounds of peptide vaccination. By clonal analysis using 12 day in vitro stimulation, the frequency of B*52:01-restricted NY-ESO-1f peptide-specific CD8+ T cells in PBMCs was estimated as only 0.0023%, far below the 0.7133% by NGS sequencing. Thus, assays requiring in vitro stimulation might be underestimating the frequency of clones with lower proliferation potential. High-throughput TCRB sequencing using NGS

  16. High-throughput sequencing reveals miRNA effects on the primary and secondary production properties in long-term subcultured Taxus cells

    Directory of Open Access Journals (Sweden)

    Meng eZhang

    2015-08-01

    Full Text Available Plant-cell culture technology is a promising alternative for production of high-value secondary metabolites but is limited by the decreased metabolite production after long-term subculture. The goal of this study was to determine the effects of miRNAs on altered gene expression profiles during long-term subculture. Two Taxus cell lines, CA (subcultured for 10 years and NA (subcultured for 6 months, were high-throughput sequenced at the mRNA and miRNA levels. A total of 265 known (78.87% of 336 and 221 novel (79.78% of 277 miRNAs were differentially expressed. Furthermore, 67.17% of the known differentially expressed (DE miRNAs (178 and 60.63% of the novel DE-miRNAs (134 were upregulated in NA. A total of 275 inverse-related miRNA/mRNA modules were identified by target prediction analysis. Functional annotation of the targets revealed that the high-ranking miRNA targets were those implicated in primary metabolism and abiotic or biotic signal transduction. For example, various genes for starch metabolism and oxidative phosphorylation were inversely related to the miRNA levels, thereby indicating that miRNAs have important roles in these pathways. Interestingly, only a few genes for secondary metabolism were inversely related to miRNA, thereby indicating that factors other than miRNA are present in the regulatory system. Moreover, miR8154 and miR5298b were upregulated miRNAs that targeted a mass of DE genes. The overexpression of these miRNAs in CA increased the genes of taxol, phenylpropanoid, and flavonoid biosynthesis, thereby suggesting their function as crucial factors that regulate the entire metabolic network during long-term subculture. Our current studies indicated that a positive conversion of production properties from secondary metabolism to primary metabolism occurred in long-term subcultured cells. miRNAs are important regulators in the upregulation of primary metabolism.

  17. A high throughput spectral image microscopy system

    Science.gov (United States)

    Gesley, M.; Puri, R.

    2018-01-01

    A high throughput spectral image microscopy system is configured for rapid detection of rare cells in large populations. To overcome flow cytometry rates and use of fluorophore tags, a system architecture integrates sample mechanical handling, signal processors, and optics in a non-confocal version of light absorption and scattering spectroscopic microscopy. Spectral images with native contrast do not require the use of exogeneous stain to render cells with submicron resolution. Structure may be characterized without restriction to cell clusters of differentiation.

  18. MAXIMS VIOLATIONS IN LITERARY WORK

    Directory of Open Access Journals (Sweden)

    Widya Hanum Sari Pertiwi

    2015-12-01

    Full Text Available This study was qualitative research action that focuses to find out the flouting of Gricean maxims and the functions of the flouting in the tales which are included in collection of children literature entitled My Giant Treasury of Stories and Rhymes. The objective of the study is generally to identify the violation of maxims of quantity, quality, relevance, and manner in the data sources and also to analyze the use of the flouting in the tales which are included in the book. Qualitative design using categorizing strategies, specifically coding strategy, was applied. Thus, the researcher as the instrument in this investigation was selecting the tales, reading them, and gathering every item which reflects the violation of Gricean maxims based on some conditions of flouting maxims. On the basis of the data analysis, it was found that the some utterances in the tales, both narration and conversation, flouting the four maxims of conversation, namely maxim of quality, maxim of quantity, maxim of relevance, and maxim of manner. The researcher has also found that the flouting of maxims has one basic function that is to encourage the readers’ imagination toward the tales. This one basic function is developed by six others functions: (1 generating specific situation, (2 developing the plot, (3 enlivening the characters’ utterance, (4 implicating message, (5 indirectly characterizing characters, and (6 creating ambiguous setting. Keywords: children literature, tales, flouting maxims

  19. High throughput study of fuel cell proton exchange membranes: Poly(vinylidene fluoride)/acrylic polyelectrolyte blends and nanocomposites with zirconium

    Science.gov (United States)

    Zapata B., Pedro Jose

    Sustainability is perhaps one of the most heard buzzwords in the post-20 th century society; nevertheless, it is not without a reason. Our present practices for energy supply are largely unsustainable if we consider their environmental and social impact. In view of this unfavorable panorama, alternative sustainable energy sources and conversion approaches have acquired noteworthy significance in recent years. Among these, proton exchange membrane fuel cells (PEMFCs) are being considered as a pivotal building block in the transition towards a sustainable energy economy in the 21st century. The polyelectrolyte membrane or proton exchange membrane (PEM) is a vital component, as well as a performance-limiting factor, of the PEMFC. Consequently, the development of high-performance PEM materials is of utmost importance for the advance of the PEMFC field. In this work, alternative PEM materials based on semi-interpenetrated networks from blends of poly(vinyledene fluoride) (PVDF) (inert phase) and sulfonated crosslinked acrylic polyelectrolytes (PE) (proton-conducting phase), as well as tri-phase PVDF/PE/zirconium-based composites, are studied. To alleviate the burden resulting from the vast number of possible combinations of the different precursors utilized in the preparation of the membranes (PVDF: 5x, PE: 2x, Nanoparticle: 3x), custom high-throughput (HT) screening systems have been developed for their characterization. By coupling the data spaces obtained via these systems with the appropriate statistical and data analysis tools it was found that, despite not being directly involved in the proton transport process, the inert PVDF phase plays a major role on proton conductivity. Particularly, a univocal inverse correlation between the PVDF crystalline characteristics (i.e., crystallinity and crystallite size) and melt viscosity, and membrane proton conductivity was discovered. Membranes based on highly crystalline and viscous PVDF homopolymers exhibited reduced proton

  20. Genome-wide association mapping in winter barley for grain yield and culm cell wall polymer content using the high-throughput CoMPP technique.

    Directory of Open Access Journals (Sweden)

    Andrea Bellucci

    Full Text Available A collection of 112 winter barley varieties (Hordeum vulgare L. was grown in the field for two years (2008/09 and 2009/10 in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0.09 and higher in 2010 (0.29. Cell wall polymers in culms were quantified by means of the monoclonal antibodies LM6, LM11, JIM13 and BS-400-3 and the carbohydrate-binding module CBM3a using the high-throughput CoMPP technique. Of these, LM6, which detects arabinan components, showed a relatively high GD in both years and a significantly negative correlation with grain yield (GYLD. Overall, heritability (H2 was calculated for GYLD, LM6 and JIM and resulted to be 0.42, 0.32 and 0.20, respectively. A total of 4,976 SNPs from the 9K iSelect array were used in the study for the analysis of population structure, linkage disequilibrium (LD and genome-wide association study (GWAS. Marker-trait associations (MTA were analyzed for grain yield and cell wall determination by LM6 and JIM13 as these were the traits showing significant correlations between the years. A single QTL for GYLD containing three MTAs was found on chromosome 3H located close to the Hv-eIF4E gene, which is known to regulate resistance to BaYMV. Subsequently the QTL was shown to be tightly linked to rym4, a locus for resistance to the virus. GWAs on arabinans quantified by LM6 resulted in the identification of major QTLs closely located on 3H and hypotheses regarding putative candidate genes were formulated through the study of gene expression levels based on bioinformatics tools.

  1. Maximizing relationship possibilities: relational maximization in romantic relationships.

    Science.gov (United States)

    Mikkelson, Alan C; Pauley, Perry M

    2013-01-01

    Using Rusbult's (1980) investment model and Schwartz's (2000) conceptualization of decision maximization, we sought to understand how an individual's propensity to maximize his or her decisions factored into investment, satisfaction, and awareness of alternatives in romantic relationships. In study one, 275 participants currently involved in romantic relationships completed measures of maximization, satisfaction, investment size, quality of alternatives, and commitment. In study two, 343 participants were surveyed as part of the creation of a scale of relational maximization. Results from both studies revealed that the tendency to maximize (in general and in relationships specifically) was negatively correlated with satisfaction, investment, and commitment, and positively correlated with quality of alternatives. Furthermore, we found that satisfaction and investments mediated the relationship between maximization and relationship commitment.

  2. High Throughput Plasma Water Treatment

    Science.gov (United States)

    Mujovic, Selman; Foster, John

    2016-10-01

    The troublesome emergence of new classes of micro-pollutants, such as pharmaceuticals and endocrine disruptors, poses challenges for conventional water treatment systems. In an effort to address these contaminants and to support water reuse in drought stricken regions, new technologies must be introduced. The interaction of water with plasma rapidly mineralizes organics by inducing advanced oxidation in addition to other chemical, physical and radiative processes. The primary barrier to the implementation of plasma-based water treatment is process volume scale up. In this work, we investigate a potentially scalable, high throughput plasma water reactor that utilizes a packed bed dielectric barrier-like geometry to maximize the plasma-water interface. Here, the water serves as the dielectric medium. High-speed imaging and emission spectroscopy are used to characterize the reactor discharges. Changes in methylene blue concentration and basic water parameters are mapped as a function of plasma treatment time. Experimental results are compared to electrostatic and plasma chemistry computations, which will provide insight into the reactor's operation so that efficiency can be assessed. Supported by NSF (CBET 1336375).

  3. Inhibitory effect of desoxyrhaponticin and rhaponticin, two natural stilbene glycosides from the Tibetan nutritional food Rheum tanguticum Maxim. ex Balf., on fatty acid synthase and human breast cancer cells.

    Science.gov (United States)

    Li, Ping; Tian, Weixi; Wang, Xiaoyan; Ma, Xiaofeng

    2014-02-01

    Fatty acid synthase (FAS) has attracted more and more attention as a potential target for cancer treatment. Natural FAS inhibitors are emerging as potential therapeutic agents to treat cancer. Rheum tanguticum Maxim. ex Balf. (rhubarb) is a traditional Chinese nutritional food and has been reported to possess a variety of biological activities, including the ability to induce the apoptosis of cancer cells. This study indicates that desoxyrhaponticin (DC) and rhaponticin (RC), two stilbene glycosides from rhubarb, could be considered as promising FAS inhibitors. We found that both DC and RC could inhibit intracellular FAS activity and downregulate FAS expression in human breast cancer MCF-7 cells. In addition, the apoptotic effect of DC on human cancer cells was announced for the first time. Since FAS plays a key role in the biosynthesis pathway of fatty acids in cancer cells, these findings suggest that DC has potential applications in the prevention and treatment of cancer.

  4. High-Throughput Screening of Compounds for Anti-Transmissible Spongiform Encephalopathy Activity Using Cell-Culture and Cell-Free Models and Infected Animals

    National Research Council Canada - National Science Library

    Caughey, Byron

    2006-01-01

    .... One therapeutic approach is the inhibitors of PrPSc accumulation indeed many inhibitors of PrPSc accumulation in scrapie-infected cells also have anti-scrapie activity in rodents During This year...

  5. High throughput measurement of high temperature strength of ceramics in controlled atmosphere and its use on solid oxide fuel cell anode supports

    DEFF Research Database (Denmark)

    Frandsen, Henrik Lund; Curran, Declan; Rasmussen, Steffen

    2014-01-01

    for testing multiple samples at operational conditions providing a high throughput and thus the possibility achieve high reliability. Optical methods are used to measure deformations contactless, frictionless load measuring is achieved, and multiple samples are handled in one heat up. The methodology...

  6. Maximally Symmetric Composite Higgs Models

    Science.gov (United States)

    Csáki, Csaba; Ma, Teng; Shu, Jing

    2017-09-01

    Maximal symmetry is a novel tool for composite pseudo Goldstone boson Higgs models: it is a remnant of an enhanced global symmetry of the composite fermion sector involving a twisting with the Higgs field. Maximal symmetry has far-reaching consequences: it ensures that the Higgs potential is finite and fully calculable, and also minimizes the tuning. We present a detailed analysis of the maximally symmetric S O (5 )/S O (4 ) model and comment on its observational consequences.

  7. Term Amniotic membrane is a high throughput source for multipotent Mesenchymal Stem Cells with the ability to differentiate into endothelial cells in vitro

    DEFF Research Database (Denmark)

    Alviano, Francesco; Fossati, Valentina; Marchionni, Cosetta

    2007-01-01

    BACKGROUND: Term Amniotic membrane (AM) is a very attractive source of Mesenchymal Stem Cells (MSCs) due to the fact that this fetal tissue is usually discarded without ethical conflicts, leading to high efficiency in MSC recovery with no intrusive procedures. Here we confirmed that term AM...... profile, i.e., positive for CD105, CD73, CD29, CD44, CD166 and negative for CD14, CD34, CD45, consistent with that reported for bone marrow-derived MSCs. In addition, amniotic membrane-isolated cells underwent in vitro osteogenic (von Kossa stain), adipogenic (Oil Red-O stain), chondrogenic (collagen type...

  8. Term amniotic membrane is a high throughput source for multipotent mesenchymal stem cells with the ability to differentiate into endothelial cells in vitro

    Directory of Open Access Journals (Sweden)

    Pasquinelli Gianandrea

    2007-02-01

    Full Text Available Abstract Background Term Amniotic membrane (AM is a very attractive source of Mesenchymal Stem Cells (MSCs due to the fact that this fetal tissue is usually discarded without ethical conflicts, leading to high efficiency in MSC recovery with no intrusive procedures. Here we confirmed that term AM, as previously reported in the literature, is an abundant source of hMSCs; in particular we further investigated the AM differentiation potential by assessing whether these cells may also be committed to the angiogenic fate. In agreement with the recommendation of the International Society for Cellular Therapy, the mesenchymal cells herein investigated were named Amniotic Membrane-human Mesenchymal Stromal Cells (AM-hMSC. Results The recovery of hMSCs and their in vitro expansion potential were greater in amniotic membrane than in bone marrow stroma. At flow cytometry analysis AM-hMSCs showed an immunophenotypical profile, i.e., positive for CD105, CD73, CD29, CD44, CD166 and negative for CD14, CD34, CD45, consistent with that reported for bone marrow-derived MSCs. In addition, amniotic membrane-isolated cells underwent in vitro osteogenic (von Kossa stain, adipogenic (Oil Red-O stain, chondrogenic (collagen type II immunohistochemichal detection and myogenic (RT-PCR MyoD and Myogenin expression as well as desmin immunohistochemical detection differentiation. In angiogenic experiments, a spontaneous differentiation into endothelial cells was detected by in vitro matrigel assay and this behaviour has been enhanced through Vascular Endothelial Growth Factor (VEGF induction. According to these findings, VEGF receptor 1 and 2 (FLT-1 and KDR were basally expressed in AM-hMSCs and the expression of endothelial-specific markers like FLT-1 KDR, ICAM-1 increased after exposure to VEGF together with the occurrence of CD34 and von Willebrand Factor positive cells. Conclusion The current study suggests that AM-hMSCs may emerge as a remarkable tool for the cell

  9. Maximal cuts in arbitrary dimension

    Science.gov (United States)

    Bosma, Jorrit; Sogaard, Mads; Zhang, Yang

    2017-08-01

    We develop a systematic procedure for computing maximal unitarity cuts of multiloop Feynman integrals in arbitrary dimension. Our approach is based on the Baikov representation in which the structure of the cuts is particularly simple. We examine several planar and nonplanar integral topologies and demonstrate that the maximal cut inherits IBPs and dimension shift identities satisfied by the uncut integral. Furthermore, for the examples we calculated, we find that the maximal cut functions from different allowed regions, form the Wronskian matrix of the differential equations on the maximal cut.

  10. Stimulation with lysates of Aspergillus terreus, Candida krusei and Rhizopus oryzae maximizes cross-reactivity of anti-fungal T cells.

    Science.gov (United States)

    Deo, Shivashni S; Virassamy, Balaji; Halliday, Catriona; Clancy, Leighton; Chen, Sharon; Meyer, Wieland; Sorrell, Tania C; Gottlieb, David J

    2016-01-01

    Invasive fungal diseases caused by filamentous fungi and yeasts are significant causes of morbidity and mortality in immunosuppressed hematology patients. We previously published a method to expand Aspergillus fumigatus-specific T cells for clinical cell therapy. In the present study, we investigated expansion of T cells specific for other fungal pathogens and creation of a broadly reactive panfungal T-cell product. Fungal strains selected were those frequently observed in the clinical hematology setting and included Aspergillus, Candida, Fusarium, Rhizopus and Lomentospora/Scedosporium. Four T-cell cultures specific to each fungus were established. We selected lysates of Aspergillus terreus, Candida krusei and Rhizopus oryzae to expand panfungal T cells. Allelic restriction of anti-fungal activity was determined through the use of specific major histocompatibility complex class II-blocking antibodies. Individual T-cell cultures specific to each fungus could be expanded in vitro, generating predominantly CD4(+) T cells of which 8% to 20% were fungus-specific. We successfully expanded panfungal T cells from the peripheral blood (n = 8) and granulocyte-colony-stimulating factor-primed stem cell products (n = 3) of normal donors by using a combination of lysates from Aspergillus terreus, Candida krusei and Rhizopus oryzae. Anti-fungal activity was mediated through human leukocyte antigen (HLA)-DR alleles and was maintained when antigen-presenting cells from partially HLA-DRB1-matched donors were used to stimulate T cells. We demonstrate a method to manufacture panfungal T-cell products with specificity against a range of clinical fungal pathogens by use of the blood and stem cells of healthy donors as the starting material. The safety and efficacy of these products will need to be tested clinically. Copyright © 2015 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

  11. A Non-imaging High Throughput Approach to Chemical Library Screening at the Unmodified Adenosine-A3 Receptor in Living Cells

    Directory of Open Access Journals (Sweden)

    Maria Augusta Arruda

    2017-12-01

    Full Text Available Recent advances in fluorescent ligand technology have enabled the study of G protein-coupled receptors in their native environment without the need for genetic modification such as addition of N-terminal fluorescent or bioluminescent tags. Here, we have used a non-imaging plate reader (PHERAstar FS to monitor the binding of fluorescent ligands to the human adenosine-A3 receptor (A3AR; CA200645 and AV039, stably expressed in CHO-K1 cells. To verify that this method was suitable for the study of other GPCRs, assays at the human adenosine-A1 receptor, and β1 and β2 adrenoceptors (β1AR and β2AR; BODIPY-TMR-CGP-12177 were also carried out. Affinity values determined for the binding of the fluorescent ligands CA200645 and AV039 to A3AR for a range of classical adenosine receptor antagonists were consistent with A3AR pharmacology and correlated well (R2 = 0.94 with equivalent data obtained using a confocal imaging plate reader (ImageXpress Ultra. The binding of BODIPY-TMR-CGP-12177 to the β1AR was potently inhibited by low concentrations of the β1-selective antagonist CGP 20712A (pKi 9.68 but not by the β2-selective antagonist ICI 118551(pKi 7.40. Furthermore, in experiments conducted in CHO K1 cells expressing the β2AR this affinity order was reversed with ICI 118551 showing the highest affinity (pKi 8.73 and CGP20712A (pKi 5.68 the lowest affinity. To determine whether the faster data acquisition of the non-imaging plate reader (~3 min per 96-well plate was suitable for high throughput screening (HTS, we screened the LOPAC library for inhibitors of the binding of CA200645 to the A3AR. From the initial 1,263 compounds evaluated, 67 hits (defined as those that inhibited the total binding of 25 nM CA200645 by ≥40% were identified. All compounds within the library that had medium to high affinity for the A3AR (pKi ≥6 were successfully identified. We found three novel compounds in the library that displayed unexpected sub-micromolar affinity

  12. High-throughput targeted screening in triple-negative breast cancer cells identifies Wnt-inhibiting activities in Pacific brittle stars

    OpenAIRE

    Blagodatski, Artem; Cherepanov, Vsevolod; Koval, Alexey; Kharlamenko, Vladimir I.; Khotimchenko, Yuri S.; Katanaev, Vladimir L.

    2017-01-01

    Pro-proliferative oncogenic signaling is one of the hallmarks of cancer. Specific targeting of such signaling pathways is one of the main approaches to modern anti-cancer drug discovery, as opposed to more traditional search for general cytotoxic agents. Natural products, especially from marine sources, represent a largely untapped source of chemical diversity, which so far have mostly been screened for cytotoxicity. Here we present a pioneering pipeline of high-throughput screening of marine...

  13. A novel cell-based high-throughput screen for inhibitors of HIV-1 gene expression and budding identifies the cardiac glycosides.

    Science.gov (United States)

    Laird, Gregory M; Eisele, Evelyn E; Rabi, S Alireza; Nikolaeva, Daria; Siliciano, Robert F

    2014-04-01

    Highly active antiretroviral therapy (HAART) is the mainstay of treatment for HIV-1 infection. While current HAART regimens have been extremely effective, issues of associated toxicity, cost and resistance remain and there is a need for novel antiretroviral compounds to complement the existing therapy. We sought to develop a novel high-throughput method for identifying compounds that block later steps in the life cycle not targeted by current therapy. We designed a high-throughput screen to identify inhibitors of post-integration steps in the HIV-1 life cycle. The screening method was applied to a library of compounds that included numerous FDA-approved small molecules. Among the small molecules that inhibited late stages in HIV-1 replication were members of the cardiac glycoside family. We demonstrate that cardiac glycosides potently inhibit HIV-1 gene expression, thereby reducing the production of infectious HIV-1. We demonstrate that this inhibition is dependent upon the human Na(+)/K(+)-ATPase, but independent of cardiac glycoside-induced increases in intracellular Ca(2+). We have validated a novel high-throughput screen to identify small molecule inhibitors of HIV-1 gene expression, virion assembly and budding. Using this screen, we have demonstrated that a number of FDA-approved compounds developed for other purposes potently inhibit HIV-1 replication, including the cardiac glycosides. Our work indicates that the entire cardiac glycoside family of drugs shows potential for antiretroviral drug development.

  14. Characterisation of cell cycle arrest and terminal differentiation in a maximally proliferative human epithelial tissue: Lessons from the human hair follicle matrix.

    Science.gov (United States)

    Purba, Talveen S; Brunken, Lars; Peake, Michael; Shahmalak, Asim; Chaves, Asuncion; Poblet, Enrique; Ceballos, Laura; Gandarillas, Alberto; Paus, Ralf

    2017-09-01

    Human hair follicle (HF) growth and hair shaft formation require terminal differentiation-associated cell cycle arrest of highly proliferative matrix keratinocytes. However, the regulation of this complex event remains unknown. CIP/KIP family member proteins (p21(CIP1), p27(KIP1) and p57(KIP2)) regulate cell cycle progression/arrest, endoreplication, differentiation and apoptosis. Since they have not yet been adequately characterized in the human HF, we asked whether and where CIP/KIP proteins localise in the human hair matrix and pre-cortex in relation to cell cycle activity and HF-specific epithelial cell differentiation that is marked by keratin 85 (K85) protein expression. K85 expression coincided with loss or reduction in cell cycle activity markers, including in situ DNA synthesis (EdU incorporation), Ki-67, phospho-histone H3 and cyclins A and B1, affirming a post-mitotic state of pre-cortical HF keratinocytes. Expression of CIP/KIP proteins was found abundantly within the proliferative hair matrix, concomitant with a role in cell cycle checkpoint control. p21(CIP1), p27(KIP1) and cyclin E persisted within post-mitotic keratinocytes of the pre-cortex, whereas p57(KIP2) protein decreased but became nuclear. These data imply a supportive role for CIP/KIP proteins in maintaining proliferative arrest, differentiation and anti-apoptotic pathways, promoting continuous hair bulb growth and hair shaft formation in anagen VI. Moreover, post-mitotic hair matrix regions contained cells with enlarged nuclei, and DNA in situ hybridisation showed cells that were >2N in the pre-cortex. This suggests that CIP/KIP proteins might counterbalance cyclin E to control further rounds of DNA replication in a cell population that has a propensity to become tetraploid. These data shed new light on the in situ-biography of human hair matrix keratinocytes on their path of active cell cycling, arrest and terminal differentiation, and showcase the human HF as an excellent, clinically

  15. Maximizing and customer loyalty: Are maximizers less loyal?

    Directory of Open Access Journals (Sweden)

    Linda Lai

    2011-06-01

    Full Text Available Despite their efforts to choose the best of all available solutions, maximizers seem to be more inclined than satisficers to regret their choices and to experience post-decisional dissonance. Maximizers may therefore be expected to change their decisions more frequently and hence exhibit lower customer loyalty to providers of products and services compared to satisficers. Findings from the study reported here (N = 1978 support this prediction. Maximizers reported significantly higher intentions to switch to another service provider (television provider than satisficers. Maximizers' intentions to switch appear to be intensified and mediated by higher proneness to regret, increased desire to discuss relevant choices with others, higher levels of perceived knowledge of alternatives, and higher ego involvement in the end product, compared to satisficers. Opportunities for future research are suggested.

  16. Juglanthraquinone C, a novel natural compound derived from Juglans mandshurica Maxim, induces S phase arrest and apoptosis in HepG2 cells.

    Science.gov (United States)

    Yao, Yao; Zhang, Yu-Wei; Sun, Lu-Guo; Liu, Biao; Bao, Yong-Li; Lin, Hua; Zhang, Yu; Zheng, Li-Hua; Sun, Ying; Yu, Chun-Lei; Wu, Yin; Wang, Guan-Nan; Li, Yu-Xin

    2012-08-01

    Juglanthraquinone C (1,5-dihydroxy-9,10-anthraquinone-3-carboxylic acid, JC), a naturally occurring anthraquinone isolated from the stem bark of Juglans mandshurica, shows strong cytotoxicity in various human cancer cells in vitro. Here, we first performed a structure-activity relationship study of six anthraquinone compounds (JC, rhein, emodin, aloe-emodin, physcion and chrysophanol) to exploit the relationship between their structural features and activity. The results showed that JC exhibited the strongest cytotoxicity of all compounds evaluated. Next, we used JC to treat several human cancer cell lines and found that JC showed an inhibitory effect on cell viability in dose-dependent (2.5-10 μg/ml JC) and time-dependent (24-48 h) manners. Importantly, the inhibitory effect of JC on HepG2 (human hepatocellular carcinoma) cells was more significant as shown by an IC(50) value of 9 ± 1.4 μg/ml, and 36 ± 1.2 μg/ml in L02 (human normal liver) cells. Further study suggested that JC-induced inhibition HepG2 cell proliferation was associated with S phase arrest, decreased protein expression of proliferation marker Ki67, cyclin A and cyclin-dependent kinase (CDK) 2, and increased expression of cyclin E and CDK inhibitory protein Cip1/p21. In addition, JC significantly triggered apoptosis in HepG2 cells, which was characterized by increased chromatin condensation and DNA fragmentation, activation of caspase-9 and -3, and induction of a higher Bax/Bcl2 ratio. Collectively, our study demonstrated that JC can efficiently inhibit proliferation and induce apoptosis in HepG2 cells.

  17. Throughput Optimization of Continuous Biopharmaceutical Manufacturing Facilities.

    Science.gov (United States)

    Garcia, Fernando A; Vandiver, Michael W

    2017-01-01

    In order to operate profitably under different product demand scenarios, biopharmaceutical companies must design their facilities with mass output flexibility in mind. Traditional biologics manufacturing technologies pose operational challenges in this regard due to their high costs and slow equipment turnaround times, restricting the types of products and mass quantities that can be processed. Modern plant design, however, has facilitated the development of lean and efficient bioprocessing facilities through footprint reduction and adoption of disposable and continuous manufacturing technologies. These development efforts have proven to be crucial in seeking to drastically reduce the high costs typically associated with the manufacturing of recombinant proteins. In this work, mathematical modeling is used to optimize annual production schedules for a single-product commercial facility operating with a continuous upstream and discrete batch downstream platform. Utilizing cell culture duration and volumetric productivity as process variables in the model, and annual plant throughput as the optimization objective, 3-D surface plots are created to understand the effect of process and facility design on expected mass output. The model shows that once a plant has been fully debottlenecked it is capable of processing well over a metric ton of product per year. Moreover, the analysis helped to uncover a major limiting constraint on plant performance, the stability of the neutralized viral inactivated pool, which may indicate that this should be a focus of attention during future process development efforts. LAY ABSTRACT: Biopharmaceutical process modeling can be used to design and optimize manufacturing facilities and help companies achieve a predetermined set of goals. One way to perform optimization is by making the most efficient use of process equipment in order to minimize the expenditure of capital, labor and plant resources. To that end, this paper introduces a

  18. Jeffamine derivatized TentaGel beads and poly(dimethylsiloxane) microbead cassettes for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound combinatorial small molecule libraries.

    Science.gov (United States)

    Townsend, Jared B; Shaheen, Farzana; Liu, Ruiwu; Lam, Kit S

    2010-09-13

    A method to efficiently immobilize and partition large quantities of microbeads in an array format in microfabricated poly(dimethylsiloxane) (PDMS) cassette for ultrahigh-throughput in situ releasable solution-phase cell-based screening of one-bead-one-compound (OBOC) combinatorial libraries is described. Commercially available Jeffamine triamine T-403 (∼440 Da) was derivatized such that two of its amino groups were protected by Fmoc and the remaining amino group capped with succinic anhydride to generate a carboxyl group. This resulting trifunctional hydrophilic polymer was then sequentially coupled two times to the outer layer of topologically segregated bilayer TentaGel (TG) beads with solid phase peptide synthesis chemistry resulting in beads with increased loading capacity, hydrophilicity, and porosity at the outer layer. We have found that such bead configuration can facilitate ultrahigh-throughput in situ releasable solution-phase screening of OBOC libraries. An encoded releasable OBOC small molecule library was constructed on Jeffamine derivatized TG beads with library compounds tethered to the outer layer via a disulfide linker and coding tags in the interior of the beads. Compound-beads could be efficiently loaded (5-10 min) into a 5 cm diameter Petri dish containing a 10,000-well PDMS microbead cassette, such that over 90% of the microwells were each filled with only one compound-bead. Jurkat T-lymphoid cancer cells suspended in Matrigel were then layered over the microbead cassette to immobilize the compound-beads. After 24 h of incubation at 37 °C, dithiothreitol was added to trigger the release of library compounds. Forty-eight hours later, MTT reporter assay was used to identify regions of reduced cell viability surrounding each positive bead. From a total of about 20,000 beads screened, 3 positive beads were detected and physically isolated for decoding. A strong consensus motif was identified for these three positive compounds. These compounds

  19. Maximizing power generation from dark fermentation effluents in microbial fuel cell by selective enrichment of exoelectrogens and optimization of anodic operational parameters.

    Science.gov (United States)

    Varanasi, Jhansi L; Sinha, Pallavi; Das, Debabrata

    2017-05-01

    To selectively enrich an electrogenic mixed consortium capable of utilizing dark fermentative effluents as substrates in microbial fuel cells and to further enhance the power outputs by optimization of influential anodic operational parameters. A maximum power density of 1.4 W/m 3 was obtained by an enriched mixed electrogenic consortium in microbial fuel cells using acetate as substrate. This was further increased to 5.43 W/m 3 by optimization of influential anodic parameters. By utilizing dark fermentative effluents as substrates, the maximum power densities ranged from 5.2 to 6.2 W/m 3 with an average COD removal efficiency of 75% and a columbic efficiency of 10.6%. A simple strategy is provided for selective enrichment of electrogenic bacteria that can be used in microbial fuel cells for generating power from various dark fermentative effluents.

  20. High-throughput screening techniques for rapid PEG-based precipitation of IgG4 mAb from clarified cell culture supernatant.

    Science.gov (United States)

    Knevelman, Carol; Davies, Jim; Allen, Lee; Titchener-Hooker, Nigel J

    2010-01-01

    Locating optimal protein precipitation conditions for complex biological feed materials is problematic. This article describes the application of a series of high-throughput platforms for the rapid identification and selection of conditions for the precipitation of an IgG(4) monoclonal antibody (mAb) from a complex feedstock using only microliter quantities of material. The approach uses 96-microwell filter plates combined with high-throughput analytical methods and a method for well volume determination for product quantification. The low material, time and resource requirements facilitated the use of a full factorial Design of Experiments (DoE) for the rapid investigation into how critical parameters impact the IgG(4) precipitation. To aid the DoE, a set of preliminary range-finding studies were conducted first. Data collected through this approach describing Polyethylene Glycol (PEG) precipitation of the IgG(4) as a function of mAb concentration, precipitant concentration, and pH are presented. Response surface diagrams were used to explore interactions between parameters and to inform selection of the most favorable conditions for maximum yield and purification. PEG concentrations required for maximum yield and purity were dependant on the IgG(4) concentration; however, concentrations of 14 to 20% w/v, pH 6.5, gave optimal levels of yield and purity. Application of the high-throughput approach enabled 1,155 conditions to be examined with less than 1 g of material. The level of insights gained over such a short time frame is indicative of the power of microwell experimentation in allowing the rapid identification of appropriate processing conditions for key bioprocess operations. Copyright 2009 American Institute of Chemical Engineers

  1. Maximization

    Directory of Open Access Journals (Sweden)

    A. Garmroodi Asil

    2017-09-01

    To further reduce the sulfur dioxide emission of the entire refining process, two scenarios of acid gas or air preheats are investigated when either of them is used simultaneously with the third enrichment scheme. The maximum overall sulfur recovery efficiency and highest combustion chamber temperature is slightly higher for acid gas preheats but air preheat is more favorable because it is more benign. To the best of our knowledge, optimization of the entire GTU + enrichment section and SRU processes has not been addressed previously.

  2. Opportunistic scheduling policies for improved throughput guarantees in wireless networks

    Directory of Open Access Journals (Sweden)

    Hassel Vegard

    2011-01-01

    Full Text Available Abstract Offering throughput guarantees for cellular wireless networks, carrying real-time traffic, is of interest to both the network operators and the customers. In this article, we formulate an optimization problem which aims at maximizing the throughput that can be guaranteed to the mobile users. By building on results obtained by Borst and Whiting and by assuming that the distributions of the users' carrier-to-noise ratios are known, we find the solution to this problem for users with different channel quality distributions, for both the scenario where all the users have the same throughput guarantees, and the scenario where all the users have different throughput guarantees. Based on these solutions, we also propose two simple and low complexity adaptive scheduling algorithms that perform significantly better than other well-known scheduling algorithms. We further develop an expression for the approximate throughput guarantee violation probability for users in time-slotted networks with the given cumulants of the distribution of bit-rate in a time-slot, and a given distribution for the number of time-slots allocated within a time-window.

  3. Influence Maximization in Ising Networks

    Science.gov (United States)

    Lynn, Christopher; Lee, Daniel

    In the analysis of social networks, a fundamental problem is influence maximization: Which individuals should be influenced to maximally impact the collective opinions of an entire population? Traditionally, influence maximization has been studied in the context of contagion models and irreversible processes. However, by including stochastic noise in the opinion formation process, repeated interactions between individuals give rise to complex macroscopic patterns that are observed, for example, in the formation of political opinions. Here we map influence maximization in the presence of stochastic noise onto the Ising model, and the resulting problem has a natural physical interpretation as maximizing the magnetization given a budget of external magnetic field. Using the susceptibility matrix, we provide a gradient ascent algorithm for calculating optimal external fields in real-world social networks. Remarkably, we find that the optimal external field solutions undergo a phase transition from intuitively focusing on high-degree individuals at high temperatures to counterintuitively focusing on low-degree individuals at low temperatures, a feature previously neglected under the viral paradigm. We acknowledge support from the U.S. National Science Foundation, the Air Force Office of Scientific Research, and the Department of Transportation.

  4. Applications of High Throughput Sequencing for Immunology and Clinical Diagnostics

    OpenAIRE

    Kim, Hyunsung John

    2014-01-01

    High throughput sequencing methods have fundamentally shifted the manner in which biological experiments are performed. In this dissertation, conventional and novel high throughput sequencing and bioinformatics methods are applied to immunology and diagnostics. In order to study rare subsets of cells, an RNA sequencing method was first optimized for use with minimal levels of RNA and cellular input. The optimized RNA sequencing method was then applied to study the transcriptional differences ...

  5. High throughput CIGS solar cell fabrication via ultra-thin absorber layer with optical confinement and (Cd, CBD)-free heterojunction partner

    Energy Technology Data Exchange (ETDEWEB)

    Marsillac, Sylvain [Old Dominion Univ., Norfolk, VA (United States)

    2015-11-30

    The main objective of this proposal was to use several pathways to reduce the production cost of Cu(In,Ga)Se2 (CIGS) PV modules and therefore the levelized cost of energy (LCOE) associated with this technology. Three high cost drivers were identified, nominally: 1) Materials cost and availability; 2) Large scale uniformity; 3) Improved throughput These three cost drivers were targeted using the following pathways: 1) Reducing the thickness of the CIGS layer while enhancing materials quality; 2) Developing and applying enhanced in-situ metrology via real time spectroscopic ellipsometry; 3) Looking into alternative heterojunction partner, back contact and anti-reflection (AR) coating Eleven main Tasks were then defined to achieve these goals (5 in Phase 1 and 6 in Phase 2), with 11 Milestones and 2 Go/No-go decision points at the end of Phase 1. The key results are summarized below

  6. Near-infrared triggered co-delivery of doxorubicin and quercetin by using gold nanocages with tetradecanol to maximize anti-tumor effects on MCF-7/ADR cells.

    Science.gov (United States)

    Zhang, Zhipeng; Xu, Shaohui; Wang, Yun; Yu, Yanna; Li, Fangzhou; Zhu, Hao; Shen, Yuanyuan; Huang, Shengtang; Guo, Shengrong

    2018-01-01

    Previously, combination chemotherapy of doxorubicin (DOX) and quercetin (QUR) was developed to improve antitumor effects and reverse multidrug resistance and several biocompatible nanocarriers, such as liposomes and micelles, were validated for their targeted delivery. In this study, we report a near-infrared (NIR)-responsive drug delivery system based on DOX and QUR co-loaded gold nanocages (AuNCs) with biotin modification. The system was simply fabricated by filling the hollow interiors of AuNCs with tetradecanol (TD), a phase-change material with a melting point of 39°C, to control the drug release. The main cause of multidrug resistance (MDR) of DOX is the overexpression of P-glycoprotein (P-gp), which can be inhibited by QUR. Thus the combination chemotherapy of DOX and QUR may provide a promising strategy for MDR. The in vitro cytotoxicity of DOX and QUR at several fixed mass ratios was carried out and showed that the combination index (CI) was the smallest at the ratio of 1:0.2, indicating that the best synergistic effect was achieved. The resultant nanocomplex (abbreviated as BPQD-AuNCs) exhibited fast release (80% released in 20min) and strong cytotoxicity against MCF-7/ADR cells (IC50, 1.5μg/mL) under NIR irradiation. Additionally, BPQD-AuNCs were found to generate a large amount of reactive oxygen species (ROS), to inhibit P-gp expression and ATP activity. Taken together, the results show that BPQD-AuNC is a prospective nano-delivery system for overcoming multidrug-resistant cancer. Copyright © 2017. Published by Elsevier Inc.

  7. A high-throughput media design approach for high performance mammalian fed-batch cultures.

    Science.gov (United States)

    Rouiller, Yolande; Périlleux, Arnaud; Collet, Natacha; Jordan, Martin; Stettler, Matthieu; Broly, Hervé

    2013-01-01

    An innovative high-throughput medium development method based on media blending was successfully used to improve the performance of a Chinese hamster ovary fed-batch medium in shaking 96-deepwell plates. Starting from a proprietary chemically-defined medium, 16 formulations testing 43 of 47 components at 3 different levels were designed. Media blending was performed following a custom-made mixture design of experiments considering binary blends, resulting in 376 different blends that were tested during both cell expansion and fed-batch production phases in one single experiment. Three approaches were chosen to provide the best output of the large amount of data obtained. A simple ranking of conditions was first used as a quick approach to select new formulations with promising features. Then, prediction of the best mixes was done to maximize both growth and titer using the Design Expert software. Finally, a multivariate analysis enabled identification of individual potential critical components for further optimization. Applying this high-throughput method on a fed-batch, rather than on a simple batch, process opens new perspectives for medium and feed development that enables identification of an optimized process in a short time frame.

  8. Finding Maximal Quasiperiodicities in Strings

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Pedersen, Christian N. S.

    2000-01-01

    of length n in time O(n log n) and space O(n). Our algorithm uses the suffix tree as the fundamental data structure combined with efficient methods for merging and performing multiple searches in search trees. Besides finding all maximal quasiperiodic substrings, our algorithm also marks the nodes...... in the suffix tree that have a superprimitive path-label....

  9. Performance Modeling of Maximal Sharing

    NARCIS (Netherlands)

    M.J. Steindorfer (Michael); J.J. Vinju (Jurgen)

    2016-01-01

    textabstractIt is noticeably hard to predict the effect of optimization strategies in Java without implementing them. "Maximal sharing" (a.k.a. "hash-consing") is one of these strategies that may have great benefit in terms of time and space, or may have detrimental overhead. It all depends on the

  10. Principles of maximally classical and maximally realistic quantum ...

    Indian Academy of Sciences (India)

    While these equations hold att =0 by definition, in general we expect them to break down at nonzero time since classical motion may not ensure agreement with quantum marginal conditions. Instead we define maximal classicality to mean that h h cl is just a sum of a function of (x t) and a function of (p t), and λ(t) is as close ...

  11. Investigation of Gene Expression Profile of A549 Cells after Overexpression of GPC5 
by High Throughput Transcriptome Sequencing

    Directory of Open Access Journals (Sweden)

    Haitian ZHANG

    2016-08-01

    Full Text Available Background and objective Glypican-5 (GPC5 is an important tumor suppressor, while little is known about the impact of GPC5 on proliferation ability and gene expression in lung adenocarcinoma cell lines. Here, we stably overexpressed GPC5 in A549 cells and investigated the impact of cell proliferation ability and gene expression. Methods A549 cells that stably overexpressed GPC5 were constructed by lentivirus. Cell counter kit 8 (CCK8, colony formation, EdU assay were conducted to analyze cell proliferation ability, and transcriptome sequencing was utilized to investigate gene expression profile. Results CCK8 assay showed that compared with empty vector, overexpression of GPC5 significantly inhibited cell proliferation rate in A549 cells and the number of colony was also decreased (181±17 vs 278±23. EdU assay also confirmed the percentage of positive staining cells decreased after GPC5 overexpression. Transcriptome sequencing revealed that 2,108 genes were differentially expressed after GPC5 overexpression. Among these differentially expressed genes, 47 genes of the Gene Ontology item “positive regulation of cell proliferation” were downregulated. Conclusion Overexpression of GPC5 inhibited proliferation ability in lung adenocarcinoma A549 cells and genes with the function of “positive regulation of cell proliferation” were downregulated.

  12. High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

    NARCIS (Netherlands)

    Moller, I.; Marcus, S.E.; Haeger, A.; Verhertbruggen, Y.; Verhoef, R.P.; Schols, H.A.; Ulvskov, P.; Mikkelsen, J.D.; Knox, J.P.; Willats, W.G.T.

    2008-01-01

    Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall

  13. High-Throughput Flow Cytometry Screening Reveals a Role for Junctional Adhesion Molecule A as a Cancer Stem Cell Maintenance Factor

    DEFF Research Database (Denmark)

    Lathia, Justin D; Li, Meizhang; Sinyuk, Maksim

    2014-01-01

    Stem cells reside in niches that regulate the balance between self-renewal and differentiation. The identity of a stem cell is linked with the ability to interact with its niche through adhesion mechanisms. To identify targets that disrupt cancer stem cell (CSC) adhesion, we performed a flow cyto...

  14. Achieving High Throughput for Data Transfer over ATM Networks

    Science.gov (United States)

    Johnson, Marjory J.; Townsend, Jeffrey N.

    1996-01-01

    File-transfer rates for ftp are often reported to be relatively slow, compared to the raw bandwidth available in emerging gigabit networks. While a major bottleneck is disk I/O, protocol issues impact performance as well. Ftp was developed and optimized for use over the TCP/IP protocol stack of the Internet. However, TCP has been shown to run inefficiently over ATM. In an effort to maximize network throughput, data-transfer protocols can be developed to run over UDP or directly over IP, rather than over TCP. If error-free transmission is required, techniques for achieving reliable transmission can be included as part of the transfer protocol. However, selected image-processing applications can tolerate a low level of errors in images that are transmitted over a network. In this paper we report on experimental work to develop a high-throughput protocol for unreliable data transfer over ATM networks. We attempt to maximize throughput by keeping the communications pipe full, but still keep packet loss under five percent. We use the Bay Area Gigabit Network Testbed as our experimental platform.

  15. Strategy to maximize maintenance operation

    OpenAIRE

    Espinoza, Michael

    2005-01-01

    This project presents a strategic analysis to maximize maintenance operations in Alcan Kitimat Works in British Columbia. The project studies the role of maintenance in improving its overall maintenance performance. It provides strategic alternatives and specific recommendations addressing Kitimat Works key strategic issues and problems. A comprehensive industry and competitive analysis identifies the industry structure and its competitive forces. In the mature aluminium industry, the bargain...

  16. Maximization, learning, and economic behavior.

    Science.gov (United States)

    Erev, Ido; Roth, Alvin E

    2014-07-22

    The rationality assumption that underlies mainstream economic theory has proved to be a useful approximation, despite the fact that systematic violations to its predictions can be found. That is, the assumption of rational behavior is useful in understanding the ways in which many successful economic institutions function, although it is also true that actual human behavior falls systematically short of perfect rationality. We consider a possible explanation of this apparent inconsistency, suggesting that mechanisms that rest on the rationality assumption are likely to be successful when they create an environment in which the behavior they try to facilitate leads to the best payoff for all agents on average, and most of the time. Review of basic learning research suggests that, under these conditions, people quickly learn to maximize expected return. This review also shows that there are many situations in which experience does not increase maximization. In many cases, experience leads people to underweight rare events. In addition, the current paper suggests that it is convenient to distinguish between two behavioral approaches to improve economic analyses. The first, and more conventional approach among behavioral economists and psychologists interested in judgment and decision making, highlights violations of the rational model and proposes descriptive models that capture these violations. The second approach studies human learning to clarify the conditions under which people quickly learn to maximize expected return. The current review highlights one set of conditions of this type and shows how the understanding of these conditions can facilitate market design.

  17. Maximization, learning, and economic behavior

    Science.gov (United States)

    Erev, Ido; Roth, Alvin E.

    2014-01-01

    The rationality assumption that underlies mainstream economic theory has proved to be a useful approximation, despite the fact that systematic violations to its predictions can be found. That is, the assumption of rational behavior is useful in understanding the ways in which many successful economic institutions function, although it is also true that actual human behavior falls systematically short of perfect rationality. We consider a possible explanation of this apparent inconsistency, suggesting that mechanisms that rest on the rationality assumption are likely to be successful when they create an environment in which the behavior they try to facilitate leads to the best payoff for all agents on average, and most of the time. Review of basic learning research suggests that, under these conditions, people quickly learn to maximize expected return. This review also shows that there are many situations in which experience does not increase maximization. In many cases, experience leads people to underweight rare events. In addition, the current paper suggests that it is convenient to distinguish between two behavioral approaches to improve economic analyses. The first, and more conventional approach among behavioral economists and psychologists interested in judgment and decision making, highlights violations of the rational model and proposes descriptive models that capture these violations. The second approach studies human learning to clarify the conditions under which people quickly learn to maximize expected return. The current review highlights one set of conditions of this type and shows how the understanding of these conditions can facilitate market design. PMID:25024182

  18. Transcriptomic profiling and quantitative high-throughput (qHTS) drug screening of CDH1 deficient hereditary diffuse gastric cancer (HDGC) cells identify treatment leads for familial gastric cancer.

    Science.gov (United States)

    Chen, Ina; Mathews-Greiner, Lesley; Li, Dandan; Abisoye-Ogunniyan, Abisola; Ray, Satyajit; Bian, Yansong; Shukla, Vivek; Zhang, Xiaohu; Guha, Raj; Thomas, Craig; Gryder, Berkley; Zacharia, Athina; Beane, Joal D; Ravichandran, Sarangan; Ferrer, Marc; Rudloff, Udo

    2017-05-01

    Patients with hereditary diffuse gastric cancer (HDGC), a cancer predisposition syndrome associated with germline mutations of the CDH1 (E-cadherin) gene, have few effective treatment options. Despite marked differences in natural history, histopathology, and genetic profile to patients afflicted by sporadic gastric cancer, patients with HDGC receive, in large, identical systemic regimens. The lack of a robust preclinical in vitro system suitable for effective drug screening has been one of the obstacles to date which has hampered therapeutic advances in this rare disease. In order to identify therapeutic leads selective for the HDGC subtype of gastric cancer, we compared gene expression profiles and drug phenotype derived from an oncology library of 1912 compounds between gastric cancer cells established from a patient with metastatic HDGC harboring a c.1380delA CDH1 germline variant and sporadic gastric cancer cells. Unsupervised hierarchical cluster analysis shows select gene expression alterations in c.1380delA CDH1 SB.mhdgc-1 cells compared to a panel of sporadic gastric cancer cell lines with enrichment of ERK1-ERK2 (extracellular signal regulated kinase) and IP3 (inositol trisphosphate)/DAG (diacylglycerol) signaling as the top networks in c.1380delA SB.mhdgc-1 cells. Intracellular phosphatidylinositol intermediaries were increased upon direct measure in c.1380delA CDH1 SB.mhdgc-1 cells. Differential high-throughput drug screening of c.1380delA CDH1 SB.mhdgc-1 versus sporadic gastric cancer cells identified several compound classes with enriched activity in c.1380 CDH1 SB.mhdgc-1 cells including mTOR (Mammalian Target Of Rapamycin), MEK (Mitogen-Activated Protein Kinase), c-Src kinase, FAK (Focal Adhesion Kinase), PKC (Protein Kinase C), or TOPO2 (Topoisomerase II) inhibitors. Upon additional drug response testing, dual PI3K (Phosphatidylinositol 3-Kinase)/mTOR and topoisomerase 2A inhibitors displayed up to >100-fold increased activity in hereditary c.1380

  19. High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

    DEFF Research Database (Denmark)

    Moller, Isabel Eva; Marcus, Susan E.; Haeger, Ash

    2008-01-01

    Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall...... investigated using subsequent immunochemical and biochemical analyses and two novel mAbs are described in detail. mAb LM13 binds to an arabinanase-sensitive pectic epitope and mAb LM14, binds to an epitope occurring on arabinogalactan-proteins. Both mAbs display novel patterns of recognition of cell walls...... in plant materials...

  20. Phase I lead-in and subsequent randomized trial assessing safety and modulation of regulatory T cell numbers following a maximally tolerated dose doxorubicin and metronomic dose cyclophosphamide combination chemotherapy protocol in tumour-bearing dogs.

    Science.gov (United States)

    Rasmussen, R M; Kurzman, I D; Biller, B J; Guth, A; Vail, D M

    2017-06-01

    Maximally tolerated dose (MTD) and metronomic dose chemotherapeutic approaches alter the immune system and the angiogenic process in different yet potentially complementary ways. A combination of MTD doxorubicin (MTD-DOX) and metronomic cyclophosphamide (mCTX) protocol was evaluated for safety and effect on circulating regulatory T (Treg) cells. We found that mCTX can be safely administered with MTD-DOX in tumour-bearing dogs. Both combination DOX/mCTX and single-agent DOX resulted in significant depletions of circulating lymphocytes throughout the chemotherapy cycle without apparent selectivity for Tregs. The indiscriminant lymphocyte depletions were similar between dogs randomized to receive DOX and dogs randomized to receive DOX/mCTX, suggesting this effect is because of DOX alone. These findings may have implications as to the therapeutic benefit (or lack thereof) of concurrent combination MTD and metronomic protocols. Future investigations are required to determine the effects and indeed the efficacy of concurrent versus sequential applications of MTD and metronomic chemotherapy protocols. © 2015 John Wiley & Sons Ltd.

  1. High throughput laser processing

    Energy Technology Data Exchange (ETDEWEB)

    Harley, Gabriel; Pass, Thomas; Cousins, Peter John; Viatella, John

    2016-12-27

    A solar cell is formed using a solar cell ablation system. The ablation system includes a single laser source and several laser scanners. The laser scanners include a master laser scanner, with the rest of the laser scanners being slaved to the master laser scanner. A laser beam from the laser source is split into several laser beams, with the laser beams being scanned onto corresponding wafers using the laser scanners in accordance with one or more patterns. The laser beams may be scanned on the wafers using the same or different power levels of the laser source.

  2. Maximizing entropy over Markov processes

    DEFF Research Database (Denmark)

    Biondi, Fabrizio; Legay, Axel; Nielsen, Bo Friis

    2014-01-01

    computation reduces to finding a model of a specification with highest entropy. Entropy maximization for probabilistic process specifications has not been studied before, even though it is well known in Bayesian inference for discrete distributions. We give a characterization of global entropy of a process...... to use Interval Markov Chains to model abstractions of deterministic systems with confidential data, and use the above results to compute their channel capacity. These results are a foundation for ongoing work on computing channel capacity for abstractions of programs derived from code. © 2014 Elsevier...

  3. Performance Evaluation of Throughput Maximization in MC-CDMA for 4G Standard

    OpenAIRE

    Hema Kale; C.G. Dethe; M.M. Mushrif

    2012-01-01

    Efficient resource allocation is the major issue in the development of fourth generation mobile communication systems. A very high data rate is needed for advanced multimedia applications and internet. This paper evaluates the performance of improved algorithm for the future Long Term Evolution(LTE) advanced standards-the 3GPP candidate for 4G. For the analysis auto regressive model of correlated Rayleigh fading processes is used. Simulation results shows that for down link transmission a ver...

  4. Towards a Maximal Mass Model

    CERN Document Server

    Kadyshevskij, V G; Rodionov, R N; Sorin, A S

    2007-01-01

    We investigate the possibility to construct a generalization of the Standard Model, which we call the Maximal Mass Model because it contains a limiting mass $M$ for its fundamental constituents. The parameter $M$ is considered as a new universal physical constant of Nature and therefore is called the fundamental mass. It is introduced in a purely geometrical way, like the velocity of light as a maximal velocity in the special relativity. If one chooses the Euclidean formulation of quantum field theory, the adequate realization of the limiting mass hypothesis is reduced to the choice of the de Sitter geometry as the geometry of the 4-momentum space. All fields, defined in de Sitter p-space in configurational space obey five dimensional Klein-Gordon type equation with fundamental mass $M$ as a mass parameter. The role of dynamical field variables is played by the Cauchy initial conditions given at $x_5 = 0$, guarantying the locality and gauge invariance principles. The corresponding to the geometrical requireme...

  5. High-Throughput Flow Cytometry Screening Reveals a Role for Junctional Adhesion Molecule A as a Cancer Stem Cell Maintenance Factor

    Directory of Open Access Journals (Sweden)

    Justin D. Lathia

    2014-01-01

    Full Text Available Stem cells reside in niches that regulate the balance between self-renewal and differentiation. The identity of a stem cell is linked with the ability to interact with its niche through adhesion mechanisms. To identify targets that disrupt cancer stem cell (CSC adhesion, we performed a flow cytometry screen on patient-derived glioblastoma (GBM cells and identified junctional adhesion molecule A (JAM-A as a CSC adhesion mechanism essential for self-renewal and tumor growth. JAM-A was dispensable for normal neural stem/progenitor cell (NPC function, and JAM-A expression was reduced in normal brain versus GBM. Targeting JAM-A compromised the self-renewal of CSCs. JAM-A expression negatively correlated to GBM patient prognosis. Our results demonstrate that GBM-targeting strategies can be identified through screening adhesion receptors and JAM-A represents a mechanism for niche-driven CSC maintenance.

  6. High Throughput Transcriptomics @ USEPA (Toxicology ...

    Science.gov (United States)

    The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest. Responses should ideally be translated into tissue-, organ-, and organism-level effects. It must be economical and scalable. Using a High Throughput Transcriptomics platform within US EPA provides broader coverage of biological activity space and toxicological MOAs and helps fill the toxicological data gap. Slide presentation at the 2016 ToxForum on using High Throughput Transcriptomics at US EPA for broader coverage biological activity space and toxicological MOAs.

  7. The Development of Novel Small Molecule Inhibitors of the Phosphoinositide- 3-Kinase Pathway through High-Throughput Cell-Based Screens

    Science.gov (United States)

    2007-02-01

    intracellular Ca2 levels or inhibiting CaM leadsin the environment might be mediated through CRM1 binding to inactivation of Akt in PC12 cells ( Egea et al., 2001...manner ( Egea et al., 2001; Yang et al.,might act as a protector of the cell. 2000). Together, these suggest the presence of a CaM-depen-The utility of...skeletal muscle FKBP12/calcium channel complex from Ianthella Egea , J., Espinet, C., Soler, R.M., Dolcet, X., Yuste, V.J., Encinas, M., Iglesias, basta

  8. Human Pluripotent Stem Cell-derived Cortical Neurons for High Throughput Medication Screening in Autism: A Proof of Concept Study in SHANK3 Haploinsufficiency Syndrome

    Directory of Open Access Journals (Sweden)

    Hélène Darville

    2016-07-01

    Full Text Available Autism spectrum disorders affect millions of individuals worldwide, but their heterogeneity complicates therapeutic intervention that is essentially symptomatic. A versatile yet relevant model to rationally screen among hundreds of therapeutic options would help improving clinical practice. Here we investigated whether neurons differentiated from pluripotent stem cells can provide such a tool using SHANK3 haploinsufficiency as a proof of principle. A library of compounds was screened for potential to increase SHANK3 mRNA content in neurons differentiated from control human embryonic stem cells. Using induced pluripotent stem cell technology, active compounds were then evaluated for efficacy in correcting dysfunctional networks of neurons differentiated from individuals with deleterious point mutations of SHANK3. Among 202 compounds tested, lithium and valproic acid showed the best efficacy at corrected SHANK3 haploinsufficiency associated phenotypes in cellulo. Lithium pharmacotherapy was subsequently provided to one patient and, after one year, an encouraging decrease in autism severity was observed. This demonstrated that pluripotent stem cell-derived neurons provide a novel cellular paradigm exploitable in the search for specific disease-modifying treatments.

  9. Human Pluripotent Stem Cell-derived Cortical Neurons for High Throughput Medication Screening in Autism: A Proof of Concept Study in SHANK3 Haploinsufficiency Syndrome.

    Science.gov (United States)

    Darville, Hélène; Poulet, Aurélie; Rodet-Amsellem, Frédérique; Chatrousse, Laure; Pernelle, Julie; Boissart, Claire; Héron, Delphine; Nava, Caroline; Perrier, Anselme; Jarrige, Margot; Cogé, Francis; Millan, Mark J; Bourgeron, Thomas; Peschanski, Marc; Delorme, Richard; Benchoua, Alexandra

    2016-07-01

    Autism spectrum disorders affect millions of individuals worldwide, but their heterogeneity complicates therapeutic intervention that is essentially symptomatic. A versatile yet relevant model to rationally screen among hundreds of therapeutic options would help improving clinical practice. Here we investigated whether neurons differentiated from pluripotent stem cells can provide such a tool using SHANK3 haploinsufficiency as a proof of principle. A library of compounds was screened for potential to increase SHANK3 mRNA content in neurons differentiated from control human embryonic stem cells. Using induced pluripotent stem cell technology, active compounds were then evaluated for efficacy in correcting dysfunctional networks of neurons differentiated from individuals with deleterious point mutations of SHANK3. Among 202 compounds tested, lithium and valproic acid showed the best efficacy at corrected SHANK3 haploinsufficiency associated phenotypes in cellulo. Lithium pharmacotherapy was subsequently provided to one patient and, after one year, an encouraging decrease in autism severity was observed. This demonstrated that pluripotent stem cell-derived neurons provide a novel cellular paradigm exploitable in the search for specific disease-modifying treatments. Copyright © 2016. Published by Elsevier B.V.

  10. The Development of Novel Small Molecule Inhibitors of the Phosphoinositide-3-Kinase Pathway Through High-Throughput Cell-Based Screens

    Science.gov (United States)

    2005-02-01

    times and staining with Alexa Fluor 594 goat CANCER CELL: DECEMBER 2003 473 anti-mouse antibody (Molecular Probes) and Hoechst 33258 (Sigma). Both...lead to greater efficacy hypocalcemia was seen at high doses in another.’ 24 In the with lower toxicity. initial phase I trials, several patients with

  11. On the optimal frequency selectivity to maximize multiuser diversity in an OFDMA scheduling system

    CERN Document Server

    Seong-Ho,; Rao, Bhaskar D; Rim, Min-Joong; Zeidler, James R

    2011-01-01

    We consider an orthogonal frequency division multiple access (OFDMA) scheduling system. A scheduling unit block consists of contiguous multiple subcarriers. Users are scheduled based on their block average throughput in a proportional fair way. The multiuser diversity gain increases with the degree and dynamic range of channel fluctuations. %Lack of diversity in a limited frequency selective channel may decrease the sum rate. However, a decrease of the block average throughput in a too much selective channel may lessen the sum rate as well. In this paper, we first study optimal channel selectivity in view of maximizing the maximum of the block average throughput of an arbitrary user. Based on this study, we then propose a method to determine a per-user optimal cyclic delay when cyclic delay diversity (CDD) is used to enhance the sum rate by increasing channel selectivity for a limited fluctuating channel. We show that the proposed technique achieves better performance than a conventional fixed cyclic delay sc...

  12. High-throughput optical screening of cellular mechanotransduction

    OpenAIRE

    Compton, JL; Luo, JC; Ma, H.; Botvinick, E; Venugopalan, V

    2014-01-01

    We introduce an optical platform for rapid, high-throughput screening of exogenous molecules that affect cellular mechanotransduction. Our method initiates mechanotransduction in adherent cells using single laser-microbeam generated microcavitation bubbles without requiring flow chambers or microfluidics. These microcavitation bubbles expose adherent cells to a microtsunami, a transient microscale burst of hydrodynamic shear stress, which stimulates cells over areas approaching 1 mm2. We demo...

  13. Adaptive Subgradient Methods for Online AUC Maximization

    OpenAIRE

    Ding, Yi; Zhao, Peilin; Hoi, Steven C. H.; Ong, Yew-Soon

    2016-01-01

    Learning for maximizing AUC performance is an important research problem in Machine Learning and Artificial Intelligence. Unlike traditional batch learning methods for maximizing AUC which often suffer from poor scalability, recent years have witnessed some emerging studies that attempt to maximize AUC by single-pass online learning approaches. Despite their encouraging results reported, the existing online AUC maximization algorithms often adopt simple online gradient descent approaches that...

  14. Asynchronous Progression through the Lytic Cascade and Variations in Intracellular Viral Loads Revealed by High-Throughput Single-Cell Analysis of Kaposi's Sarcoma-Associated Herpesvirus Infection

    OpenAIRE

    Adang, Laura A.; Parsons, Christopher H.; Kedes, Dean H.

    2006-01-01

    Kaposi's sarcoma-associated herpesvirus (KSHV or human herpesvirus-8) is frequently tumorigenic in immunocompromised patients. The average intracellular viral copy number within infected cells, however, varies markedly by tumor type. Since the KSHV-encoded latency-associated nuclear antigen (LANA) tethers viral episomes to host heterochromatin and displays a punctate pattern by fluorescence microscopy, we investigated whether accurate quantification of individual LANA dots is predictive of in...

  15. Identification of Novel Myelin-Associated CD4+ T cell Autoantigens Targeted in MS Using a High-Throughput Gene Synthesis Technology

    Science.gov (United States)

    2013-10-01

    Werner. 2009. Myelin proteomics: molecular anatomy of an insulating sheath . Mol. Neurobiol. 40: 55-72. 4. Derfuss, T., K. Parikh, S. Velhin, M...AD______________ Award Number: W81XWH-12-1-0227 TITLE: Identification of Novel Myelin -Associated...4 . TITLE AND SUBTITLE Identification of Novel Myelin -Associated CD4+ T cell Autoantigens Targeted in MS 5a. CONTRACT NUMBER Using a High

  16. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

    Directory of Open Access Journals (Sweden)

    Adam C. Wilkinson

    2013-10-01

    Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2−/− Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

  17. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses.

    Science.gov (United States)

    Wilkinson, Adam C; Goode, Debbie K; Cheng, Yi-Han; Dickel, Diane E; Foster, Sam; Sendall, Tim; Tijssen, Marloes R; Sanchez, Maria-Jose; Pennacchio, Len A; Kirkpatrick, Aileen M; Göttgens, Berthold

    2013-01-01

    Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2(-/-) Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

  18. Decentralized Utility Maximization in Heterogeneous Multicell Scenarios with Interference Limited and Orthogonal Air Interfaces

    Directory of Open Access Journals (Sweden)

    Karla Ingo

    2009-01-01

    Full Text Available Overlapping coverage of multiple radio access technologies provides new multiple degrees of freedom for tuning the fairness-throughput tradeoff in heterogeneous communication systems through proper resource allocation. This paper treats the problem of resource allocation in terms of optimum air interface and cell selection in cellular multi-air interface scenarios. We find a close to optimum allocation for a given set of voice users with minimum QoS requirements and a set of best-effort users which guarantees service for the voice users and maximizes the sum utility of the best-effort users. Our model applies to arbitrary heterogeneous scenarios where the air interfaces belong to the class of interference limited systems like UMTS or to a class with orthogonal resource assignment such as TDMA-based GSM or WLAN. We present a convex formulation of the problem and by using structural properties thereof deduce two algorithms for static and dynamic scenarios, respectively. Both procedures rely on simple information exchange protocols and can be operated in a completely decentralized way. The performance of the dynamic algorithm is then evaluated for a heterogeneous UMTS/GSM scenario showing high-performance gains in comparison to standard load-balancing solutions.

  19. High-Throughput Selection, Enumeration, Electrokinetic Manipulation, and Molecular Profiling of Low-Abundance Circulating Tumor Cells Using a Microfluidic System

    Science.gov (United States)

    Dharmasiri, Udara; Njoroge, Samuel K.; Witek, Mazgorzata A.; Adebiyi, Morayo G.; Kamande, Joyce W.; Hupert, Mateusz L.; Barany, Francis; Soper, Steven A.

    2015-01-01

    A circulating tumor cell (CTC) selection microfluidic device was integrated to an electrokinetic enrichment device for preconcentrating CTCs directly from whole blood to allow for the detection of mutations contained within the genomic DNA of the CTCs. Molecular profiling of CTCs can provide important clinical information that cannot be garnered simply by enumerating the selected CTCs. We evaluated our approach using SW620 and HT29 cells (colorectal cancer cell lines) seeded into whole blood as a model system. Because SW620 and HT29 cells overexpress the integral membrane protein EpCAM, they could be immunospecifically selected using a microfluidic device containing anti-EpCAM antibodies immobilized to the walls of a selection bed. The microfluidic device was operated at an optimized flow rate of 2 mm s−1, which allowed for the ability to process 1 mL of whole blood in <40 min. The selected CTCs were then enzymatically released from the antibody selection surface and hydrodynamically transported through a pair of Pt electrodes for conductivity-based enumeration. The efficiency of CTC selection was found to be 96% ± 4%. Following enumeration, the CTCs were hydrodynamically transported at a flow rate of 1 μL min−1 to an on-chip electromanipulation unit, where they were electrophoretically withdrawn from the bulk hydrodynamic flow and directed into a receiving reservoir. Using an electric field of 100 V cm−1, the negatively charged CTCs were enriched into an anodic receiving reservoir to a final volume of 2 μL, providing an enrichment factor of 500. The collected CTCs could then be searched for point mutations using a PCR/LDR/capillary electrophoresis assay. The DNA extracted from the CTCs was subjected to a primary polymerase chain reaction (PCR) with the amplicons used for a ligase detection reaction (LDR) to probe for KRAS oncogenic point mutations. Point mutations in codon 12 of the KRAS gene were successfully detected in the SW620 CTCs for samples

  20. High-Throughput Microfluidics for the Screening of Yeast Libraries.

    Science.gov (United States)

    Huang, Mingtao; Joensson, Haakan N; Nielsen, Jens

    2018-01-01

    Cell factory development is critically important for efficient biological production of chemicals, biofuels, and pharmaceuticals. Many rounds of the Design-Build-Test-Learn cycles may be required before an engineered strain meeting specific metrics required for industrial application. The bioindustry prefer products in secreted form (secreted products or extracellular metabolites) as it can lower the cost of downstream processing, reduce metabolic burden to cell hosts, and allow necessary modification on the final products , such as biopharmaceuticals. Yet, products in secreted form result in the disconnection of phenotype from genotype, which may have limited throughput in the Test step for identification of desired variants from large libraries of mutant strains. In droplet microfluidic screening, single cells are encapsulated in individual droplet and enable high-throughput processing and sorting of single cells or clones. Encapsulation in droplets allows this technology to overcome the throughput limitations present in traditional methods for screening by extracellular phenotypes. In this chapter, we describe a protocol/guideline for high-throughput droplet microfluidics screening of yeast libraries for higher protein secretion . This protocol can be adapted to screening by a range of other extracellular products from yeast or other hosts.

  1. High-throughput sequencing reveals key genes and immune homeostatic pathways activated in myeloid dendritic cells by Porphyromonas gingivalis 381 and its fimbrial mutants.

    Science.gov (United States)

    Arjunan, P; El-Awady, A; Dannebaum, R O; Kunde-Ramamoorthy, G; Cutler, C W

    2016-02-01

    The human microbiome consists of highly diverse microbial communities that colonize our skin and mucosal surfaces, aiding in maintenance of immune homeostasis. The keystone pathogen Porphyromonas gingivalis induces a dysbiosis and disrupts immune homeostasis through as yet unclear mechanisms. The fimbrial adhesins of P. gingivalis facilitate biofilm formation, invasion of and dissemination by blood dendritic cells; hence, fimbriae may be key factors in disruption of immune homeostasis. In this study we employed RNA-sequencing transcriptome profiling to identify differentially expressed genes (DEGs) in human monocyte-derived dendritic cells (MoDCs) in response to in vitro infection/exposure by Pg381 or its isogenic mutant strains that solely express minor-Mfa1 fimbriae (DPG3), major-FimA fimbriae (MFI) or are deficient in both fimbriae (MFB) relative to uninfected control. Our results yielded a total of 479 DEGs that were at least two-fold upregulated and downregulated in MoDCs significantly (P ≤ 0.05) by all four strains and certain DEGs that were strain-specific. Interestingly, the gene ontology biological and functional analysis shows that the upregulated genes in DPG3-induced MoDCs were more significant than other strains and associated with inflammation, immune response, anti-apoptosis, cell proliferation, and other homeostatic functions. Both transcriptome and quantitative polymerase chain reaction results show that DPG3, which solely expresses Mfa1, increased ZNF366, CD209, LOX1, IDO1, IL-10, CCL2, SOCS3, STAT3 and FOXO1 gene expression. In conclusion, we have identified key DC-mediated immune homeostatic pathways that could contribute to dysbiosis in periodontal infection with P. gingivalis. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Proliferation extent of CD34+ cells as a key parameter to maximize megakaryocytic differentiation of umbilical cord blood-derived hematopoietic stem/progenitor cells in a two-stage culture protocol.

    Science.gov (United States)

    Hatami, Javad; Andrade, Pedro Z; Bacalhau, Denise; Cirurgião, Fernando; Ferreira, Frederico Castelo; Cabral, Joaquim M S; da Silva, Cláudia L

    2014-12-01

    Co-infusion of ex-vivo generated megakaryocytic progenitors with hematopoietic stem/progenitor cells (HSC/HPC) may contribute to a faster platelet recovery upon umbilical cord blood (UCB) transplantation. A two stage protocol containing cell expansion and megakaryocyte (Mk) differentiation was established using human UCB CD34+-enriched cells. The expansion stage used a pre-established protocol supported by a human bone marrow mesenchymal stem cells (MSC) feeder layer and the differentiation stage used TPO (100 ng/mL) and IL-3 (10 ng/mL). 18% of culture-derived Mks had higher DNA content (>4 N) and were able to produce platelet-like particles. The proliferation extent of CD34+ cells obtained in the expansion stage (FI-CD34+), rather than expansion duration, determined as a key parameter for efficient megakaryocytic differentiation. A maximum efficiency yield (EY) of 48 ± 7.7 Mks/input CD34+ cells was obtained for a FI-CD34+ of 17 ± 2.5, where a higher FI-CD34+ of 42 ± 13 resulted in a less efficient megakaryocytic differentiation (EY of 22 ± 6.7 and 19 ± 4.6 %CD41).

  3. Hierarchical Model of Container Ports Throughput

    Directory of Open Access Journals (Sweden)

    Monika Rozmarynowska

    2015-12-01

    Full Text Available In this article the attempt has been made to construct hierarchical model of container ports throughput development. The presented hierarchical approach uses the relationships of development of global economy and container flows at different geographical levels: global (container throughput in all seaport on the world, regional (container throughput in the Baltic seaports and national (container throughput in Polish seaports. Model have been evaluated for their fit and usefulness for predictive purposes.

  4. A Maximally Supersymmetric Kondo Model

    Energy Technology Data Exchange (ETDEWEB)

    Harrison, Sarah; Kachru, Shamit; Torroba, Gonzalo; /Stanford U., Phys. Dept. /SLAC

    2012-02-17

    We study the maximally supersymmetric Kondo model obtained by adding a fermionic impurity to N = 4 supersymmetric Yang-Mills theory. While the original Kondo problem describes a defect interacting with a free Fermi liquid of itinerant electrons, here the ambient theory is an interacting CFT, and this introduces qualitatively new features into the system. The model arises in string theory by considering the intersection of a stack of M D5-branes with a stack of N D3-branes, at a point in the D3 worldvolume. We analyze the theory holographically, and propose a dictionary between the Kondo problem and antisymmetric Wilson loops in N = 4 SYM. We perform an explicit calculation of the D5 fluctuations in the D3 geometry and determine the spectrum of defect operators. This establishes the stability of the Kondo fixed point together with its basic thermodynamic properties. Known supergravity solutions for Wilson loops allow us to go beyond the probe approximation: the D5s disappear and are replaced by three-form flux piercing a new topologically non-trivial S3 in the corrected geometry. This describes the Kondo model in terms of a geometric transition. A dual matrix model reflects the basic properties of the corrected gravity solution in its eigenvalue distribution.

  5. Conormal Geometry of Maximal Minors

    CERN Document Server

    Kleiman, S L

    1997-01-01

    Let A be a Noetherian local domain, N be a finitely generated torsion- free module, and M a proper submodule that is generically equal to N. Let A[N] be an arbitrary graded overdomain of A generated as an A-algebra by N placed in degree 1. Let A[M] be the subalgebra generated by M. Set C:=Proj(A[M]) and r:=dim C. Form the (closed) subset W of Spec(A) of primes p where A[N]_p is not a finitely generated module over A[M]_p, and denote the preimage of W in C by E. We prove this: (1) dim E=r-1 if either (a) N is free and A[N] is the symmetric algebra, or (b) W is nonempty and A is universally catenary, and (2) E is equidimensional if (a) holds and A is universally catenary. Our proof was inspired by some recent work of Gaffney and Massey, which we sketch; they proved (2) when A is the ring of germs of a complex- analytic variety, and applied it to perfect a characterization of Thom's A_f-condition in equisingularity theory. From (1), we recover, with new proofs, the usual height inequality for maximal minors and ...

  6. Modeling Steroidogenesis Disruption Using High-Throughput ...

    Science.gov (United States)

    Environmental chemicals can elicit endocrine disruption by altering steroid hormone biosynthesis and metabolism (steroidogenesis) causing adverse reproductive and developmental effects. Historically, a lack of assays resulted in few chemicals having been evaluated for effects on steroidogenesis. The steroidogenic pathway is a series of hydroxylation and dehydrogenation steps carried out by CYP450 and hydroxysteroid dehydrogenase enzymes, yet the only enzyme in the pathway for which a high-throughput screening (HTS) assay has been developed is aromatase (CYP19A1), responsible for the aromatization of androgens to estrogens. Recently, the ToxCast HTS program adapted the OECD validated H295R steroidogenesis assay using human adrenocortical carcinoma cells into a high-throughput model to quantitatively assess the concentration-dependent (0.003-100 µM) effects of chemicals on 10 steroid hormones including progestagens, androgens, estrogens and glucocorticoids. These results, in combination with two CYP19A1 inhibition assays, comprise a large dataset amenable to clustering approaches supporting the identification and characterization of putative mechanisms of action (pMOA) for steroidogenesis disruption. In total, 514 chemicals were tested in all CYP19A1 and steroidogenesis assays. 216 chemicals were identified as CYP19A1 inhibitors in at least one CYP19A1 assay. 208 of these chemicals also altered hormone levels in the H295R assay, suggesting 96% sensitivity in the

  7. Throughput optimization for dual collaborative spectrum sensing with dynamic scheduling

    Science.gov (United States)

    Cui, Cuimei; Yang, Dezhi

    2017-07-01

    Cognitive radio technology is envisaged to alleviate both spectrum inefficiency and spectrum scarcity problems by exploiting the existing licensed spectrum opportunistically. However, cognitive radio ad hoc networks (CRAHNs) impose unique challenges due to the high dynamic scheduling in the available spectrum, diverse quality of service (QOS) requirements, as well as hidden terminals and shadow fading issues in a harsh radio environment. To solve these problems, this paper proposes a dynamic and variable time-division multiple-access scheduling mechanism (DV-TDMA) incorporated with dual collaborative spectrum sensing scheme for CRAHNs. This study involves the cross-layered cooperation between the Physical (PHY) layer and Medium Access Control (MAC) layer under the consideration of average sensing time, sensing accuracy and the average throughput of cognitive radio users (CRs). Moreover, multiple-objective optimization algorithm is proposed to maximize the average throughput of CRs while still meeting QOS requirements on sensing time and detection error. Finally, performance evaluation is conducted through simulations, and the simulation results reveal that this optimization algorithm can significantly improve throughput and sensing accuracy and reduce average sensing time.

  8. Identification of strain-specific B-cell epitopes in Trypanosoma cruzi using genome-scale epitope prediction and high-throughput immunoscreening with peptide arrays.

    Science.gov (United States)

    Mendes, Tiago Antônio de Oliveira; Reis Cunha, João Luís; de Almeida Lourdes, Rodrigo; Rodrigues Luiz, Gabriela Flávia; Lemos, Lucas Dhom; dos Santos, Ana Rita Rocha; da Câmara, Antônia Cláudia Jácome; Galvão, Lúcia Maria da Cunha; Bern, Caryn; Gilman, Robert H; Fujiwara, Ricardo Toshio; Gazzinelli, Ricardo Tostes; Bartholomeu, Daniella Castanheira

    2013-01-01

    The factors influencing variation in the clinical forms of Chagas disease have not been elucidated; however, it is likely that the genetics of both the host and the parasite are involved. Several studies have attempted to correlate the T. cruzi strains involved in infection with the clinical forms of the disease by using hemoculture and/or PCR-based genotyping of parasites from infected human tissues. However, both techniques have limitations that hamper the analysis of large numbers of samples. The goal of this work was to identify conserved and polymorphic linear B-cell epitopes of T. cruzi that could be used for serodiagnosis and serotyping of Chagas disease using ELISA. By performing B-cell epitope prediction on proteins derived from pair of alleles of the hybrid CL Brener genome, we have identified conserved and polymorphic epitopes in the two CL Brener haplotypes. The rationale underlying this strategy is that, because CL Brener is a recent hybrid between the TcII and TcIII DTUs (discrete typing units), it is likely that polymorphic epitopes in pairs of alleles could also be polymorphic in the parental genotypes. We excluded sequences that are also present in the Leishmania major, L. infantum, L. braziliensis and T. brucei genomes to minimize the chance of cross-reactivity. A peptide array containing 150 peptides was covalently linked to a cellulose membrane, and the reactivity of the peptides was tested using sera from C57BL/6 mice chronically infected with the Colombiana (TcI) and CL Brener (TcVI) clones and Y (TcII) strain. A total of 36 peptides were considered reactive, and the cross-reactivity among the strains is in agreement with the evolutionary origin of the different T. cruzi DTUs. Four peptides were tested against a panel of chagasic patients using ELISA. A conserved peptide showed 95.8% sensitivity, 88.5% specificity, and 92.7% accuracy for the identification of T. cruzi in patients infected with different strains of the parasite. Therefore, this

  9. Identification of the new gene Zrsr1 to associate with the pluripotency state in induced pluripotent stem cells (iPSCs using high throughput sequencing technology

    Directory of Open Access Journals (Sweden)

    Shuai Gao

    2014-12-01

    Full Text Available Finding the markers to predict the quality of induced pluripotent stem cells (iPSCs will accelerate its practical application. The fully pluripotent iPSCs has been determined as viable all-iPSC mice can be generated through tetraploid (4N complementation. The activation of the imprinted Dlk1-Dio3 gene cluster was reported to correlate with the pluripotency of iPSCs. However, recent studies demonstrated that the loss of imprinting at the Dlk1-Dio3 locus does not strictly correlate with the reduced pluripotency of iPSCs. In our study (ref [1], iPSC lines with the same genetic background and proviral integration sites were established, and the pluripotency state of each iPSC line was well characterized using tetraploid (4N complementation assay. The gene expression and global epigenetic modifications of “4N-ON” and the corresponding “4N-OFF” iPSC lines were compared through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4me3, H3K27me3 and H3K4me2 and DNA methylation. Very few differences were detected in the iPSC lines that were investigated. However, an imprinted gene, Zrsr1 was disrupted in the “4N-OFF” iPSC lines. Here we provide more detail about the dataset and the R script with additional data for others to repeat the finding.

  10. Does mental exertion alter maximal muscle activation?

    Directory of Open Access Journals (Sweden)

    Vianney eRozand

    2014-09-01

    Full Text Available Mental exertion is known to impair endurance performance, but its effects on neuromuscular function remain unclear. The purpose of this study was to test the hypothesis that mental exertion reduces torque and muscle activation during intermittent maximal voluntary contractions of the knee extensors. Ten subjects performed in a randomized order three separate mental exertion conditions lasting 27 minutes each: i high mental exertion (incongruent Stroop task, ii moderate mental exertion (congruent Stroop task, iii low mental exertion (watching a movie. In each condition, mental exertion was combined with ten intermittent maximal voluntary contractions of the knee extensor muscles (one maximal voluntary contraction every 3 minutes. Neuromuscular function was assessed using electrical nerve stimulation. Maximal voluntary torque, maximal muscle activation and other neuromuscular parameters were similar across mental exertion conditions and did not change over time. These findings suggest that mental exertion does not affect neuromuscular function during intermittent maximal voluntary contractions of the knee extensors.

  11. Maximal Inequalities for Dependent Random Variables

    DEFF Research Database (Denmark)

    Hoffmann-Jorgensen, Jorgen

    2016-01-01

    Maximal inequalities play a crucial role in many probabilistic limit theorem; for instance, the law of large numbers, the law of the iterated logarithm, the martingale limit theorem and the central limit theorem. Let X-1, X-2,... be random variables with partial sums S-k = X-1 + ... + X......-k. Then a maximal inequality gives conditions ensuring that the maximal partial sum M-n = max(1) (...

  12. Maximizing Barber's bipartite modularity is also hard

    OpenAIRE

    Miyauchi, Atsushi; Sukegawa, Noriyoshi

    2013-01-01

    Modularity introduced by Newman and Girvan [Phys. Rev. E 69, 026113 (2004)] is a quality function for community detection. Numerous methods for modularity maximization have been developed so far. In 2007, Barber [Phys. Rev. E 76, 066102 (2007)] introduced a variant of modularity called bipartite modularity which is appropriate for bipartite networks. Although maximizing the standard modularity is known to be NP-hard, the computational complexity of maximizing bipartite modularity has yet to b...

  13. Lessons from high-throughput protein crystallization screening: 10 years of practical experience

    Science.gov (United States)

    JR, Luft; EH, Snell; GT, DeTitta

    2011-01-01

    Introduction X-ray crystallography provides the majority of our structural biological knowledge at a molecular level and in terms of pharmaceutical design is a valuable tool to accelerate discovery. It is the premier technique in the field, but its usefulness is significantly limited by the need to grow well-diffracting crystals. It is for this reason that high-throughput crystallization has become a key technology that has matured over the past 10 years through the field of structural genomics. Areas covered The authors describe their experiences in high-throughput crystallization screening in the context of structural genomics and the general biomedical community. They focus on the lessons learnt from the operation of a high-throughput crystallization screening laboratory, which to date has screened over 12,500 biological macromolecules. They also describe the approaches taken to maximize the success while minimizing the effort. Through this, the authors hope that the reader will gain an insight into the efficient design of a laboratory and protocols to accomplish high-throughput crystallization on a single-, multiuser-laboratory or industrial scale. Expert Opinion High-throughput crystallization screening is readily available but, despite the power of the crystallographic technique, getting crystals is still not a solved problem. High-throughput approaches can help when used skillfully; however, they still require human input in the detailed analysis and interpretation of results to be more successful. PMID:22646073

  14. Optimal Throughput and Energy Efficiency for Wireless Sensor Networks: Multiple Access and Multipacket Reception

    Directory of Open Access Journals (Sweden)

    Li Wenjun

    2005-01-01

    Full Text Available We investigate two important aspects in sensor network design—the throughput and the energy efficiency. We consider the uplink reachback problem where the receiver is equipped with multiple antennas and linear multiuser detectors. We first assume Rayleigh flat-fading, and analyze two MAC schemes: round-robin and slotted-ALOHA. We optimize the average number of transmissions per slot and the transmission power for two purposes: maximizing the throughput, or minimizing the effective energy (defined as the average energy consumption per successfully received packet subject to a throughput constraint. For each MAC scheme with a given linear detector, we derive the maximum asymptotic throughput as the signal-to-noise ratio goes to infinity. It is shown that the minimum effective energy grows rapidly as the throughput constraint approaches the maximum asymptotic throughput. By comparing the optimal performance of different MAC schemes equipped with different detectors, we draw important tradeoffs involved in the sensor network design. Finally, we show that multiuser scheduling greatly enhances system performance in a shadow fading environment.

  15. Nearly maximally predictive features and their dimensions

    Science.gov (United States)

    Marzen, Sarah E.; Crutchfield, James P.

    2017-05-01

    Scientific explanation often requires inferring maximally predictive features from a given data set. Unfortunately, the collection of minimal maximally predictive features for most stochastic processes is uncountably infinite. In such cases, one compromises and instead seeks nearly maximally predictive features. Here, we derive upper bounds on the rates at which the number and the coding cost of nearly maximally predictive features scale with desired predictive power. The rates are determined by the fractal dimensions of a process' mixed-state distribution. These results, in turn, show how widely used finite-order Markov models can fail as predictors and that mixed-state predictive features can offer a substantial improvement.

  16. Comparison analysis of microRNAs in response to EV71 and CA16 infection in human bronchial epithelial cells by high-throughput sequencing to reveal differential infective mechanisms.

    Science.gov (United States)

    Hu, Yajie; Song, Jie; Liu, Longding; Li, Jing; Tang, Beibei; Zhang, Ying; Wang, Jingjing; Wang, Lichun; Fan, Shengtao; Feng, Ming; Li, Qihan

    2017-01-15

    Hand, foot, and mouth disease (HFMD) mainly caused by Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) infections which presented significantly different clinical manifestations. Nevertheless, the factors underlying these differences remain unclear. Recently, the functions of microRNAs (miRNAs) in pathogen-host interactions have been highlighted. Here, we performed comprehensive miRNA profiling in EV71- and CA16-infected human bronchial epithelial (16HBE) cells at multiple time points using high-throughput sequencing. The results showed that 154 known and 47 novel miRNAs exhibited remarkable differences in expression. Of these, 65 miRNAs, including 58 known and 7 novel miRNAs, presented opposite trends in EV71- and CA16-infected samples. Subsequently, we mainly focused on the 56 known differentially expressed miRNAs by further screening for targets prediction. GO and pathway analysis of these targets demonstrated that 18 biological processes, 7 molecular functions, 1 cellular component and 123 pathways were enriched. Among these pathways, Cadherin signalling pathway, Wnt signalling pathway and angiogenesis showed significant alterations. The regulatory networks of these miRNAs with predicted targets, GOs, pathways and transcription factors were determined, which suggested that miRNAs displayed intricate regulatory mechanisms during the infection phase. Consequently, we specifically analysed the hierarchical GO categories of the predicted targets involved in adhesion. The results indicated that the distinct changes induced by EV71 and CA16 infection may be partly linked to airway epithelial barrier function. Taken together, our data provide useful insights that help elucidate the different host-pathogen interactions following EV71 and CA16 infection and might offer novel therapeutic targets for these infections. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  17. High throughput assays for analyzing transcription factors.

    Science.gov (United States)

    Li, Xianqiang; Jiang, Xin; Yaoi, Takuro

    2006-06-01

    Transcription factors are a group of proteins that modulate the expression of genes involved in many biological processes, such as cell growth and differentiation. Alterations in transcription factor function are associated with many human diseases, and therefore these proteins are attractive potential drug targets. A key issue in the development of such therapeutics is the generation of effective tools that can be used for high throughput discovery of the critical transcription factors involved in human diseases, and the measurement of their activities in a variety of disease or compound-treated samples. Here, a number of innovative arrays and 96-well format assays for profiling and measuring the activities of transcription factors will be discussed.

  18. High-throughput hyperdimensional vertebrate phenotyping.

    Science.gov (United States)

    Pardo-Martin, Carlos; Allalou, Amin; Medina, Jaime; Eimon, Peter M; Wählby, Carolina; Fatih Yanik, Mehmet

    2013-01-01

    Most gene mutations and biologically active molecules cause complex responses in animals that cannot be predicted by cell culture models. Yet animal studies remain too slow and their analyses are often limited to only a few readouts. Here we demonstrate high-throughput optical projection tomography with micrometre resolution and hyperdimensional screening of entire vertebrates in tens of seconds using a simple fluidic system. Hundreds of independent morphological features and complex phenotypes are automatically captured in three dimensions with unprecedented speed and detail in semitransparent zebrafish larvae. By clustering quantitative phenotypic signatures, we can detect and classify even subtle alterations in many biological processes simultaneously. We term our approach hyperdimensional in vivo phenotyping. To illustrate the power of hyperdimensional in vivo phenotyping, we have analysed the effects of several classes of teratogens on cartilage formation using 200 independent morphological measurements, and identified similarities and differences that correlate well with their known mechanisms of actions in mammals.

  19. High-Throughput Process Development for Biopharmaceuticals.

    Science.gov (United States)

    Shukla, Abhinav A; Rameez, Shahid; Wolfe, Leslie S; Oien, Nathan

    2017-11-14

    The ability to conduct multiple experiments in parallel significantly reduces the time that it takes to develop a manufacturing process for a biopharmaceutical. This is particularly significant before clinical entry, because process development and manufacturing are on the "critical path" for a drug candidate to enter clinical development. High-throughput process development (HTPD) methodologies can be similarly impactful during late-stage development, both for developing the final commercial process as well as for process characterization and scale-down validation activities that form a key component of the licensure filing package. This review examines the current state of the art for HTPD methodologies as they apply to cell culture, downstream purification, and analytical techniques. In addition, we provide a vision of how HTPD activities across all of these spaces can integrate to create a rapid process development engine that can accelerate biopharmaceutical drug development. Graphical Abstract.

  20. Applications of High Throughput Nucleotide Sequencing

    DEFF Research Database (Denmark)

    Waage, Johannes Eichler

    The recent advent of high throughput sequencing of nucleic acids (RNA and DNA) has vastly expanded research into the functional and structural biology of the genome of all living organisms (and even a few dead ones). With this enormous and exponential growth in biological data generation come...... equally large demands in data handling, analysis and interpretation, perhaps defining the modern challenge of the computational biologist of the post-genomic era. The first part of this thesis consists of a general introduction to the history, common terms and challenges of next generation sequencing......). For the second flavor, DNA-seq, a study presenting genome wide profiling of transcription factor CEBP/A in liver cells undergoing regeneration after partial hepatectomy (article IV) is included....

  1. An image-based algorithm for precise and accurate high throughput assessment of drug activity against the human parasite Trypanosoma cruzi.

    Directory of Open Access Journals (Sweden)

    Seunghyun Moon

    Full Text Available We present a customized high content (image-based and high throughput screening algorithm for the quantification of Trypanosoma cruzi infection in host cells. Based solely on DNA staining and single-channel images, the algorithm precisely segments and identifies the nuclei and cytoplasm of mammalian host cells as well as the intracellular parasites infecting the cells. The algorithm outputs statistical parameters including the total number of cells, number of infected cells and the total number of parasites per image, the average number of parasites per infected cell, and the infection ratio (defined as the number of infected cells divided by the total number of cells. Accurate and precise estimation of these parameters allow for both quantification of compound activity against parasites, as well as the compound cytotoxicity, thus eliminating the need for an additional toxicity-assay, hereby reducing screening costs significantly. We validate the performance of the algorithm using two known drugs against T.cruzi: Benznidazole and Nifurtimox. Also, we have checked the performance of the cell detection with manual inspection of the images. Finally, from the titration of the two compounds, we confirm that the algorithm provides the expected half maximal effective concentration (EC50 of the anti-T. cruzi activity.

  2. An image-based algorithm for precise and accurate high throughput assessment of drug activity against the human parasite Trypanosoma cruzi.

    Science.gov (United States)

    Moon, Seunghyun; Siqueira-Neto, Jair L; Moraes, Carolina Borsoi; Yang, Gyongseon; Kang, Myungjoo; Freitas-Junior, Lucio H; Hansen, Michael A E

    2014-01-01

    We present a customized high content (image-based) and high throughput screening algorithm for the quantification of Trypanosoma cruzi infection in host cells. Based solely on DNA staining and single-channel images, the algorithm precisely segments and identifies the nuclei and cytoplasm of mammalian host cells as well as the intracellular parasites infecting the cells. The algorithm outputs statistical parameters including the total number of cells, number of infected cells and the total number of parasites per image, the average number of parasites per infected cell, and the infection ratio (defined as the number of infected cells divided by the total number of cells). Accurate and precise estimation of these parameters allow for both quantification of compound activity against parasites, as well as the compound cytotoxicity, thus eliminating the need for an additional toxicity-assay, hereby reducing screening costs significantly. We validate the performance of the algorithm using two known drugs against T.cruzi: Benznidazole and Nifurtimox. Also, we have checked the performance of the cell detection with manual inspection of the images. Finally, from the titration of the two compounds, we confirm that the algorithm provides the expected half maximal effective concentration (EC50) of the anti-T. cruzi activity.

  3. Financial Management Practices, Wealth Maximization Criterion and ...

    African Journals Online (AJOL)

    In the field of financial management, shareholders wealth maximization is often seen as the desirable goal not only from the shareholders perspective but for the society at large; with the firm's primary goal aimed mainly at maximizing the wealth of its shareholders. This study thus aimed at determining the impact of the core ...

  4. Corporate Social Responsibility and Profit Maximizing Behaviour

    OpenAIRE

    Becchetti, Leonardo; Giallonardo, Luisa; Tessitore, Maria Elisabetta

    2005-01-01

    We examine the behavior of a profit maximizing monopolist in a horizontal differentiation model in which consumers differ in their degree of social responsibility (SR) and consumers SR is dynamically influenced by habit persistence. The model outlines parametric conditions under which (consumer driven) corporate social responsibility is an optimal choice compatible with profit maximizing behavior.

  5. Maximal Entanglement in High Energy Physics

    NARCIS (Netherlands)

    Cervera-Lierta, Alba; Latorre, José I.; Rojo, Juan; Rottoli, Luca

    2017-01-01

    We analyze how maximal entanglement is generated at the fundamental level in QED by studying correlations between helicity states in tree-level scattering processes at high energy. We demonstrate that two mechanisms for the generation of maximal entanglement are at work: i) $s$-channel processes

  6. Alternative trailer configurations for maximizing payloads

    Science.gov (United States)

    Jason D. Thompson; Dana Mitchell; John Klepac

    2017-01-01

    In order for harvesting contractors to stay ahead of increasing costs, it is imperative that they employ all options to maximize productivity and efficiency. Transportation can account for half the cost to deliver wood to a mill. Contractors seek to maximize truck payload to increase productivity. The Forest Operations Research Unit, Southern Research Station, USDA...

  7. Purification of Gaussian maximally mixed states

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kabgyun [Center for Macroscopic Quantum Control, Department of Physics and Astronomy, Seoul National University, Seoul 08826 (Korea, Republic of); School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455 (Korea, Republic of); Lim, Youngrong, E-mail: sshaep@gmail.com [Center for Macroscopic Quantum Control, Department of Physics and Astronomy, Seoul National University, Seoul 08826 (Korea, Republic of)

    2016-10-23

    We find that the purifications of several Gaussian maximally mixed states (GMMSs) correspond to some Gaussian maximally entangled states (GMESs) in the continuous-variable regime. Here, we consider a two-mode squeezed vacuum (TMSV) state as a purification of the thermal state and construct a general formalism of the Gaussian purification process. Moreover, we introduce other kind of GMESs via the process. All of our purified states of the GMMSs exhibit Gaussian profiles; thus, the states show maximal quantum entanglement in the Gaussian regime. - Highlights: • Candidates of Gaussian maximally mixed state are proposed. • Obtaining Gaussian maximally entangled states using the purification process. • The suggested states can be applicable for the test of capacity problem in Gaussian regime.

  8. Maximal Entanglement in High Energy Physics

    Directory of Open Access Journals (Sweden)

    Alba Cervera-Lierta, José I. Latorre, Juan Rojo, Luca Rottoli

    2017-11-01

    Full Text Available We analyze how maximal entanglement is generated at the fundamental level in QED by studying correlations between helicity states in tree-level scattering processes at high energy. We demonstrate that two mechanisms for the generation of maximal entanglement are at work: i $s$-channel processes where the virtual photon carries equal overlaps of the helicities of the final state particles, and ii the indistinguishable superposition between $t$- and $u$-channels. We then study whether requiring maximal entanglement constrains the coupling structure of QED and the weak interactions. In the case of photon-electron interactions unconstrained by gauge symmetry, we show how this requirement allows reproducing QED. For $Z$-mediated weak scattering, the maximal entanglement principle leads to non-trivial predictions for the value of the weak mixing angle $\\theta_W$. Our results are a first step towards understanding the connections between maximal entanglement and the fundamental symmetries of high-energy physics.

  9. Power Control for Maximum Throughput in Spectrum Underlay Cognitive Radio Networks

    CERN Document Server

    Tadrous, John; Nafie, Mohammed; El-Keyi, Amr

    2010-01-01

    We investigate power allocation for users in a spectrum underlay cognitive network. Our objective is to find a power control scheme that allocates transmit power for both primary and secondary users so that the overall network throughput is maximized while maintaining the quality of service (QoS) of the primary users greater than a certain minimum limit. Since an optimum solution to our problem is computationally intractable, as the optimization problem is non-convex, we propose an iterative algorithm based on sequential geometric programming, that is proved to converge to at least a local optimum solution. We use the proposed algorithm to show how a spectrum underlay network would achieve higher throughput with secondary users operation than with primary users operating alone. Also, we show via simulations that the loss in primary throughput due to the admission of the secondary users is accompanied by a reduction in the total primary transmit power.

  10. High-throughput system-wide engineering and screening for microbial biotechnology.

    Science.gov (United States)

    Vervoort, Yannick; Linares, Alicia Gutiérrez; Roncoroni, Miguel; Liu, Chengxun; Steensels, Jan; Verstrepen, Kevin J

    2017-08-01

    Genetic engineering and screening of large number of cells or populations is a crucial bottleneck in today's systems biology and applied (micro)biology. Instead of using standard methods in bottles, flasks or 96-well plates, scientists are increasingly relying on high-throughput strategies that miniaturize their experiments to the nanoliter and picoliter scale and the single-cell level. In this review, we summarize different high-throughput system-wide genome engineering and screening strategies for microbes. More specifically, we will emphasize the use of multiplex automated genome evolution (MAGE) and CRISPR/Cas systems for high-throughput genome engineering and the application of (lab-on-chip) nanoreactors for high-throughput single-cell or population screening. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. Maximizing binding capacity for protein A chromatography.

    Science.gov (United States)

    Ghose, Sanchayita; Zhang, Jennifer; Conley, Lynn; Caple, Ryan; Williams, Kevin P; Cecchini, Douglas

    2014-01-01

    Advances in cell culture expression levels in the last two decades have resulted in monoclonal antibody titers of ≥10 g/L to be purified downstream. A high capacity capture step is crucial to prevent purification from being the bottleneck in the manufacturing process. Despite its high cost and other disadvantages, Protein A chromatography still remains the optimal choice for antibody capture due to the excellent selectivity provided by this step. A dual flow loading strategy was used in conjunction with a new generation high capacity Protein A resin to maximize binding capacity without significantly increasing processing time. Optimum conditions were established using a simple empirical Design of Experiment (DOE) based model and verified with a wide panel of antibodies. Dynamic binding capacities of >65 g/L could be achieved under these new conditions, significantly higher by more than one and half times the values that have been typically achieved with Protein A in the past. Furthermore, comparable process performance and product quality was demonstrated for the Protein A step at the increased loading. © 2014 American Institute of Chemical Engineers.

  12. Analytical Model of IPsec Process Throughput

    Directory of Open Access Journals (Sweden)

    Adam Tisovsky

    2012-01-01

    Full Text Available The paper concerns with a throughput of securing process which cannot be described neither by a constant value of bits per second nor by a constant value of packets per second over the range of packet sizes. We propose general throughput model of IPsec process based on characteristic parameters that are independent on the packet size. These parameters might be used for comprehensive definition of throughput on any security system. Further, a method for obtaining characteristic parameters is proposed. Usage of the method can significantly decrease count of throughput measurements required for modelling the system.

  13. Throughput and Delay Analysis of HARQ with Code Combining over Double Rayleigh Fading Channels

    KAUST Repository

    Chelli, Ali

    2018-01-15

    This paper proposes the use of hybrid automatic repeat request (HARQ) with code combining (HARQ-CC) to offer reliable communications over double Rayleigh channels. The double Rayleigh fading channel is of particular interest to vehicle-to-vehicle communication systems as well as amplify-and-forward relaying and keyhole channels. This work studies the performance of HARQ-CC over double Rayleigh channels from an information theoretic perspective. Analytical approximations are derived for the $\\\\epsilon$-outage capacity, the average number of transmissions, and the throughput of HARQ-CC. Moreover, we evaluate the delay experienced by Poisson arriving packets for HARQ-CC. We provide analytical expressions for the average waiting time, the packets sojourn time, the average consumed power, and the energy efficiency. In our investigation, we take into account the impact of imperfect feedback on different performance metrics. Additionally, we explore the tradeoff between energy efficiency and the throughput. The proposed scheme is shown to maintain the outage probability below a specified threshold $\\\\epsilon$ which ensures the link reliability. Meanwhile, HARQ-CC adapts implicitly the transmission rate to the channel conditions such that the throughput is maximized. Our results demonstrate that HARQ-CC allows improving the achievable communication rate compared to fixed time diversity schemes. To maximize the throughput of HARQ-CC, the rate per HARQ round should be less than the rate required to meet the outage constraint. Our investigation of the performance of HARQ-CC over Rayleigh and double Rayleigh channels shows that double Rayleigh channels have a higher severity of fading and result in a larger degradation of the throughput. Our analysis reveals that HARQ with incremental redundancy (HARQ-IR) achieves a larger throughput compared to HARQ-CC, while HARQ-CC is simpler to implement, has a lower decoding

  14. Light Microscopy at Maximal Precision

    Science.gov (United States)

    Bierbaum, Matthew; Leahy, Brian D.; Alemi, Alexander A.; Cohen, Itai; Sethna, James P.

    2017-10-01

    Microscopy is the workhorse of the physical and life sciences, producing crisp images of everything from atoms to cells well beyond the capabilities of the human eye. However, the analysis of these images is frequently little more accurate than manual marking. Here, we revolutionize the analysis of microscopy images, extracting all the useful information theoretically contained in a complex microscope image. Using a generic, methodological approach, we extract the information by fitting experimental images with a detailed optical model of the microscope, a method we call parameter extraction from reconstructing images (PERI). As a proof of principle, we demonstrate this approach with a confocal image of colloidal spheres, improving measurements of particle positions and radii by 10-100 times over current methods and attaining the maximum possible accuracy. With this unprecedented accuracy, we measure nanometer-scale colloidal interactions in dense suspensions solely with light microscopy, a previously impossible feat. Our approach is generic and applicable to imaging methods from brightfield to electron microscopy, where we expect accuracies of 1 nm and 0.1 pm, respectively.

  15. The development and implementation of high-throughput tools for discovery and characterization of proton exchange membranes

    Science.gov (United States)

    Reed, Keith Gregory

    supplied by Arkema, Inc. Although mass transport values were generally lower than reported literature values, pervaporation experiments showed that HT-MTA could be used to effectively screen and optimize relative water transport characteristics in PEMs. To further demonstrate the utility of HT-MTA, the instrument was incorporated into the lab's current high-throughput characterization toolset and used to investigate the mechanisms and effects of rapid free radical degradation of NafionRTM membranes based on various concentrations of H2O2 and Fe2+. The results showed that changes in Nafion'sRTM mechanical, conductive, and water transport properties were strong functions of H2O 2, and that maximal degradation could be achieved around 50 ppm Fe 2+. Furthermore, by including chemical composition analysis techniques in the characterization toolset, the dominating free radical degradation pathways could be deduced. These results are promising for later correlating rapidly aged degradation experiments to in situ fuel cell lifetime testing which is both time-intensive and costly. The high-throughput toolset was also used to develop a novel optimized blend consisting of polyetherimide (PEI), a low-cost high performance resin, and sulfonated PEI (S-PEI) made using a relatively mild post sulfonation reaction with trimethylsilyl chlorosulfonate. The effects of blend composition and thermal annealing on film performance were evaluated and the polymer system was shown to have optimal mechanical and ion-conducting properties between 20--30 wt% S-PEI in the unannealed state. Although the properties of the proposed PEI-based polymer system were below PEMFC performance standards, a PEI film with superior mechanical properties was discovered and should prove to be useful in other applications. In general, this work shows promising results for efficiently developing advanced polymer materials using high-throughput screening techniques.

  16. High-throughput screening for modulators of cellular contractile force

    CERN Document Server

    Park, Chan Young; Tambe, Dhananjay; Chen, Bohao; Lavoie, Tera; Dowell, Maria; Simeonov, Anton; Maloney, David J; Marinkovic, Aleksandar; Tschumperlin, Daniel J; Burger, Stephanie; Frykenberg, Matthew; Butler, James P; Stamer, W Daniel; Johnson, Mark; Solway, Julian; Fredberg, Jeffrey J; Krishnan, Ramaswamy

    2014-01-01

    When cellular contractile forces are central to pathophysiology, these forces comprise a logical target of therapy. Nevertheless, existing high-throughput screens are limited to upstream signaling intermediates with poorly defined relationship to such a physiological endpoint. Using cellular force as the target, here we screened libraries to identify novel drug candidates in the case of human airway smooth muscle cells in the context of asthma, and also in the case of Schlemm's canal endothelial cells in the context of glaucoma. This approach identified several drug candidates for both asthma and glaucoma. We attained rates of 1000 compounds per screening day, thus establishing a force-based cellular platform for high-throughput drug discovery.

  17. Combination therapy design for maximizing sensitivity and minimizing toxicity.

    Science.gov (United States)

    Matlock, Kevin; Berlow, Noah; Keller, Charles; Pal, Ranadip

    2017-03-22

    Design of personalized targeted therapies involve modeling of patient sensitivity to various drugs and drug combinations. Majority of studies evaluate the sensitivity of tumor cells to targeted drugs without modeling the effect of the drugs on normal cells. In this article, we consider the individual modeling of drug responses to tumor and normal cells and utilize them to design targeted combination therapies that maximize sensitivity over tumor cells and minimize toxicity over normal cells. The problem is formulated as maximizing sensitivity over tumor cell models while maintaining sensitivity below a threshold over normal cell models. We utilize the constrained structure of tumor proliferation models to design an accelerated lexicographic search algorithm for generating the optimal solution. For comparison purposes, we also designed two suboptimal search algorithms based on evolutionary algorithms and hill-climbing based techniques. Results over synthetic models and models generated from Genomics of Drug Sensitivity in Cancer database shows the ability of the proposed algorithms to arrive at optimal or close to optimal solutions in significantly lower number of steps as compared to exhaustive search. We also present the theoretical analysis of the expected number of comparisons required for the proposed Lexicographic search that compare favorably with the observed number of computations. The proposed algorithms provide a framework for design of combination therapy that tackles tumor heterogeneity while satisfying toxicity constraints.

  18. HEALTH INSURANCE: CONTRIBUTIONS AND REIMBURSEMENT MAXIMAL

    CERN Multimedia

    HR Division

    2000-01-01

    Affected by both the salary adjustment index on 1.1.2000 and the evolution of the staff members and fellows population, the average reference salary, which is used as an index for fixed contributions and reimbursement maximal, has changed significantly. An adjustment of the amounts of the reimbursement maximal and the fixed contributions is therefore necessary, as from 1 January 2000.Reimbursement maximalThe revised reimbursement maximal will appear on the leaflet summarising the benefits for the year 2000, which will soon be available from the divisional secretariats and from the AUSTRIA office at CERN.Fixed contributionsThe fixed contributions, applicable to some categories of voluntarily insured persons, are set as follows (amounts in CHF for monthly contributions):voluntarily insured member of the personnel, with complete coverage:815,- (was 803,- in 1999)voluntarily insured member of the personnel, with reduced coverage:407,- (was 402,- in 1999)voluntarily insured no longer dependent child:326,- (was 321...

  19. Independent Component Analysis by Entropy Maximization (INFOMAX)

    National Research Council Canada - National Science Library

    Garvey, Jennie H

    2007-01-01

    ... (BSS). The Infomax method separates unknown source signals from a number of signal mixtures by maximizing the entropy of a transformed set of signal mixtures and is accomplished by performing gradient ascent in MATLAB...

  20. Insulin resistance and maximal oxygen uptake

    DEFF Research Database (Denmark)

    Seibaek, Marie; Vestergaard, Henrik; Burchardt, Hans

    2003-01-01

    BACKGROUND: Type 2 diabetes, coronary atherosclerosis, and physical fitness all correlate with insulin resistance, but the relative importance of each component is unknown. HYPOTHESIS: This study was undertaken to determine the relationship between insulin resistance, maximal oxygen uptake......, and the presence of either diabetes or ischemic heart disease. METHODS: The study population comprised 33 patients with and without diabetes and ischemic heart disease. Insulin resistance was measured by a hyperinsulinemic euglycemic clamp; maximal oxygen uptake was measured during a bicycle exercise test. RESULTS......: There was a strong correlation between maximal oxygen uptake and insulin-stimulated glucose uptake (r = 0.7, p = 0.001), and maximal oxygen uptake was the only factor of importance for determining insulin sensitivity in a model, which also included the presence of diabetes and ischemic heart disease. CONCLUSION...

  1. High-Throughput Automation in Chemical Process Development.

    Science.gov (United States)

    Selekman, Joshua A; Qiu, Jun; Tran, Kristy; Stevens, Jason; Rosso, Victor; Simmons, Eric; Xiao, Yi; Janey, Jacob

    2017-06-07

    High-throughput (HT) techniques built upon laboratory automation technology and coupled to statistical experimental design and parallel experimentation have enabled the acceleration of chemical process development across multiple industries. HT technologies are often applied to interrogate wide, often multidimensional experimental spaces to inform the design and optimization of any number of unit operations that chemical engineers use in process development. In this review, we outline the evolution of HT technology and provide a comprehensive overview of how HT automation is used throughout different industries, with a particular focus on chemical and pharmaceutical process development. In addition, we highlight the common strategies of how HT automation is incorporated into routine development activities to maximize its impact in various academic and industrial settings.

  2. Maximizing biogas production from the anaerobic digestion

    OpenAIRE

    Ghouali, A.; Sari, T.; Harmand, J.

    2015-01-01

    This paper presents an optimal control law policy for maximizing biogas production of anaerobic digesters. In particular, using a simple model of the anaerobic digestion process, we derive a control law to maximize the biogas production over a period T using the dilution rate as the control variable. Depending on initial conditions and constraints on the actuator (the dilution rate D(·)), the search for a solution to the optimal control problem reveals very different levels of difficulty. In ...

  3. Maximizing biogas production from the anaerobic digestion

    OpenAIRE

    Ghouali, Amel; Sari, Tewfik; Harmand, Jérôme

    2015-01-01

    Sous presse; International audience; This paper presents an optimal control law policy for maximizing biogas pro-duction of anaerobic digesters. In particular, using a simple model of the anaerobicdigestion process, we derive a control law to maximize the biogas production overa period T using the dilution rate as the control variable. Depending on initialconditions and constraints on the actuator (the dilution rate D(:)), the search fora solution to the optimal control problem reveals very d...

  4. Adaptive Influence Maximization in Dynamic Social Networks

    OpenAIRE

    Tong, Guangmo; Wu, Weili; Tang, Shaojie; Du, Ding-Zhu

    2015-01-01

    For the purpose of propagating information and ideas through a social network, a seeding strategy aims to find a small set of seed users that are able to maximize the spread of the influence, which is termed as influence maximization problem. Despite a large number of works have studied this problem, the existing seeding strategies are limited to the static social networks. In fact, due to the high speed data transmission and the large population of participants, the diffusion processes in re...

  5. Design and Performance Analysis of Multi-tier Heterogeneous Network through Coverage, Throughput and Energy Efficiency

    Directory of Open Access Journals (Sweden)

    A. Shabbir,

    2017-12-01

    Full Text Available The unprecedented acceleration in wireless industry strongly compels wireless operators to increase their data network throughput, capacity and coverage on emergent basis. In upcoming 5G heterogeneous networks inclusion of low power nodes (LPNs like pico cells and femto cells for increasing network’s throughput, capacity and coverage are getting momentum. Addition of LPNs in such a massive level will eventually make a network populated in terms of base stations (BSs.The dense deployments of BSs will leads towards high operating expenditures (Op-Ex, capital expenditure (Cap-Ex and most importantly high energy consumption in future generation networks. Recognizing theses networks issues this research work investigates data throughput and energy efficiency of 5G multi-tier heterogeneous network. The network is modeled using tools from stochastic geometry. Monte Carlo results confirmed that rational deployment of LPNs can contribute towards increased throughput along with better energy efficiency of overall network.

  6. An image analysis toolbox for high-throughput C. elegans assays.

    Science.gov (United States)

    Wählby, Carolina; Kamentsky, Lee; Liu, Zihan H; Riklin-Raviv, Tammy; Conery, Annie L; O'Rourke, Eyleen J; Sokolnicki, Katherine L; Visvikis, Orane; Ljosa, Vebjorn; Irazoqui, Javier E; Golland, Polina; Ruvkun, Gary; Ausubel, Frederick M; Carpenter, Anne E

    2012-04-22

    We present a toolbox for high-throughput screening of image-based Caenorhabditis elegans phenotypes. The image analysis algorithms measure morphological phenotypes in individual worms and are effective for a variety of assays and imaging systems. This WormToolbox is available through the open-source CellProfiler project and enables objective scoring of whole-worm high-throughput image-based assays of C. elegans for the study of diverse biological pathways that are relevant to human disease.

  7. A new tetrahydrofuran lignan diglycoside from Viola tianshanica Maxim.

    Science.gov (United States)

    Qin, Yan; Yin, Chengle; Cheng, Zhihong

    2013-11-04

    A new lignan glycoside, tianshanoside A (1), together with a known phenylpropanoid glycoside, syringin (2) and two known lignan glycosides, picraquassioside C (3), and aketrilignoside B (4), were isolated from the whole plant of Viola tianshanica Maxim. The structure of the new compound was elucidated by extensive NMR (1H, 13C, COSY, HSQC, HMBC and ROESY) and high resolution mass spectrometry analysis. The three lignans 1, 3, and 4 did not exhibit significant cytotoxicity against human gastric cancer Ags cells or HepG2 liver cancer cells. This is the first report of the isolation of a lignan skeleton from the genus Viola L.

  8. A New Tetrahydrofuran Lignan Diglycoside from Viola tianshanica Maxim

    Directory of Open Access Journals (Sweden)

    Yan Qin

    2013-11-01

    Full Text Available A new lignan glycoside, tianshanoside A (1, together with a known phenylpropanoid glycoside, syringin (2 and two known lignan glycosides, picraquassioside C (3, and aketrilignoside B (4, were isolated from the whole plant of Viola tianshanica Maxim. The structure of the new compound was elucidated by extensive NMR (1H, 13C, COSY, HSQC, HMBC and ROESY and high resolution mass spectrometry analysis. The three lignans 1, 3, and 4 did not exhibit significant cytotoxicity against human gastric cancer Ags cells or HepG2 liver cancer cells. This is the first report of the isolation of a lignan skeleton from the genus Viola L.

  9. Computational analysis of high-throughput flow cytometry data.

    Science.gov (United States)

    Robinson, J Paul; Rajwa, Bartek; Patsekin, Valery; Davisson, Vincent Jo

    2012-08-01

    Flow cytometry has been around for over 40 years, but only recently has the opportunity arisen to move into the high-throughput domain. The technology is now available and is highly competitive with imaging tools under the right conditions. Flow cytometry has, however, been a technology that has focused on its unique ability to study single cells and appropriate analytical tools are readily available to handle this traditional role of the technology. Expansion of flow cytometry to a high-throughput (HT) and high-content technology requires both advances in hardware and analytical tools. The historical perspective of flow cytometry operation as well as how the field has changed and what the key changes have been discussed. The authors provide a background and compelling arguments for moving toward HT flow, where there are many innovative opportunities. With alternative approaches now available for flow cytometry, there will be a considerable number of new applications. These opportunities show strong capability for drug screening and functional studies with cells in suspension. There is no doubt that HT flow is a rich technology awaiting acceptance by the pharmaceutical community. It can provide a powerful phenotypic analytical toolset that has the capacity to change many current approaches to HT screening. The previous restrictions on the technology, based on its reduced capacity for sample throughput, are no longer a major issue. Overcoming this barrier has transformed a mature technology into one that can focus on systems biology questions not previously considered possible.

  10. Computational analysis of high-throughput flow cytometry data

    Science.gov (United States)

    Robinson, J Paul; Rajwa, Bartek; Patsekin, Valery; Davisson, Vincent Jo

    2015-01-01

    Introduction Flow cytometry has been around for over 40 years, but only recently has the opportunity arisen to move into the high-throughput domain. The technology is now available and is highly competitive with imaging tools under the right conditions. Flow cytometry has, however, been a technology that has focused on its unique ability to study single cells and appropriate analytical tools are readily available to handle this traditional role of the technology. Areas covered Expansion of flow cytometry to a high-throughput (HT) and high-content technology requires both advances in hardware and analytical tools. The historical perspective of flow cytometry operation as well as how the field has changed and what the key changes have been discussed. The authors provide a background and compelling arguments for moving toward HT flow, where there are many innovative opportunities. With alternative approaches now available for flow cytometry, there will be a considerable number of new applications. These opportunities show strong capability for drug screening and functional studies with cells in suspension. Expert opinion There is no doubt that HT flow is a rich technology awaiting acceptance by the pharmaceutical community. It can provide a powerful phenotypic analytical toolset that has the capacity to change many current approaches to HT screening. The previous restrictions on the technology, based on its reduced capacity for sample throughput, are no longer a major issue. Overcoming this barrier has transformed a mature technology into one that can focus on systems biology questions not previously considered possible. PMID:22708834

  11. High-throughput theoretical design of lithium battery materials

    Science.gov (United States)

    Shi-Gang, Ling; Jian, Gao; Rui-Juan, Xiao; Li-Quan, Chen

    2016-01-01

    The rapid evolution of high-throughput theoretical design schemes to discover new lithium battery materials is reviewed, including high-capacity cathodes, low-strain cathodes, anodes, solid state electrolytes, and electrolyte additives. With the development of efficient theoretical methods and inexpensive computers, high-throughput theoretical calculations have played an increasingly important role in the discovery of new materials. With the help of automatic simulation flow, many types of materials can be screened, optimized and designed from a structural database according to specific search criteria. In advanced cell technology, new materials for next generation lithium batteries are of great significance to achieve performance, and some representative criteria are: higher energy density, better safety, and faster charge/discharge speed. Project supported by the National Natural Science Foundation of China (Grant Nos. 11234013 and 51172274) and the National High Technology Research and Development Program of China (Grant No. 2015AA034201).

  12. [Chemical constituents from Salvia przewalskii Maxim].

    Science.gov (United States)

    Yang, Li-Xin; Li, Xing-Cui; Liu, Chao; Xiao, Lei; Qin, De-Hua; Chen, Ruo-Yun

    2011-07-01

    The investigation on Salvia przewalskii Maxim was carried out to find the relationship of the constituents and their pharmacological activities. The isolation and purification were performed by various chromatographies such as silica gel, Sephadex LH-20, RP-C18 column chromatography, etc. Further investigation on the fraction of the 95% ethanol extract of Salvia przewalskii Maxim yielded przewalskin Y-1 (1), anhydride of tanshinone-II A (2), sugiol (3), epicryptoacetalide (4), cryptoacetalide (5), arucadiol (6), 1-dehydromiltirone (7), miltirone (8), cryptotanshinone (9), tanshinone II A (10) and isotanshinone-I (11). Their structures were elucidated by the spectral analysis such as NMR (Nuclear Magnetic Resonance) and MS (Mass Spectrometry). Compound 1 is a new compound. Compounds 4 and 5 are mirror isomers (1 : 3). Compounds 4, 5, 6, 8, 11 were isolated from Salvia przewalskii Maxim for the first time.

  13. Finding all maximal cliques in dynamic graphs

    OpenAIRE

    Stix, Volker

    2002-01-01

    Clustering applications dealing with perception based or biased data lead to models with non-disjunct clusters. There, objects to be clustered are allowed to belong to several clusters at the same time which results in a fuzzy clustering. It can be shown that this is equivalent to searching all maximal cliques in dynamic graphs like G_t=(V,E_t), where E_(t-1) in E_t, t=1,... ,T; E_0=(). In this article algorithms are provided to track all maximal cliques in a fully dynamic graph. It is natura...

  14. Fluorescent foci quantitation for high-throughput analysis

    Directory of Open Access Journals (Sweden)

    Elena Ledesma-Fernández

    2015-06-01

    Full Text Available A number of cellular proteins localize to discrete foci within cells, for example DNA repair proteins, microtubule organizing centers, P bodies or kinetochores. It is often possible to measure the fluorescence emission from tagged proteins within these foci as a surrogate for the concentration of that specific protein. We wished to develop tools that would allow quantitation of fluorescence foci intensities in high-throughput studies. As proof of principle we have examined the kinetochore, a large multi-subunit complex that is critical for the accurate segregation of chromosomes during cell division. Kinetochore perturbations lead to aneuploidy, which is a hallmark of cancer cells. Hence, understanding kinetochore homeostasis and regulation are important for a global understanding of cell division and genome integrity. The 16 budding yeast kinetochores colocalize within the nucleus to form a single focus. Here we have created a set of freely-available tools to allow high-throughput quantitation of kinetochore foci fluorescence. We use this ‘FociQuant’ tool to compare methods of kinetochore quantitation and we show proof of principle that FociQuant can be used to identify changes in kinetochore protein levels in a mutant that affects kinetochore function. This analysis can be applied to any protein that forms discrete foci in cells.

  15. High Throughput Direct Detection Doppler Lidar Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Lite Cycles, Inc. (LCI) proposes to develop a direct-detection Doppler lidar (D3L) technology called ELITE that improves the system optical throughput by more than...

  16. Maximizing the Spectacle of Water Fountains

    Science.gov (United States)

    Simoson, Andrew J.

    2009-01-01

    For a given initial speed of water from a spigot or jet, what angle of the jet will maximize the visual impact of the water spray in the fountain? This paper focuses on fountains whose spigots are arranged in circular fashion, and couches the measurement of the visual impact in terms of the surface area and the volume under the fountain's natural…

  17. An ethical justification of profit maximization

    DEFF Research Database (Denmark)

    Koch, Carsten Allan

    2010-01-01

    behaviour. It is argued that some form of consequential ethics must be applied, and that both profit seeking and profit maximization can be defended from a rule-consequential point of view. It is noted, however, that the result does not apply unconditionally, but requires that certain form of profit (and...

  18. Maximization of eigenvalues using topology optimization

    DEFF Research Database (Denmark)

    Pedersen, Niels Leergaard

    2000-01-01

    to localized modes in low density areas. The topology optimization problem is formulated using the SIMP method. Special attention is paid to a numerical method for removing localized eigenmodes in low density areas. The method is applied to numerical examples of maximizing the first eigenfrequency, One example...

  19. Robust Utility Maximization Under Convex Portfolio Constraints

    Energy Technology Data Exchange (ETDEWEB)

    Matoussi, Anis, E-mail: anis.matoussi@univ-lemans.fr [Université du Maine, Risk and Insurance institut of Le Mans Laboratoire Manceau de Mathématiques (France); Mezghani, Hanen, E-mail: hanen.mezghani@lamsin.rnu.tn; Mnif, Mohamed, E-mail: mohamed.mnif@enit.rnu.tn [University of Tunis El Manar, Laboratoire de Modélisation Mathématique et Numérique dans les Sciences de l’Ingénieur, ENIT (Tunisia)

    2015-04-15

    We study a robust maximization problem from terminal wealth and consumption under a convex constraints on the portfolio. We state the existence and the uniqueness of the consumption–investment strategy by studying the associated quadratic backward stochastic differential equation. We characterize the optimal control by using the duality method and deriving a dynamic maximum principle.

  20. How to Generate Good Profit Maximization Problems

    Science.gov (United States)

    Davis, Lewis

    2014-01-01

    In this article, the author considers the merits of two classes of profit maximization problems: those involving perfectly competitive firms with quadratic and cubic cost functions. While relatively easy to develop and solve, problems based on quadratic cost functions are too simple to address a number of important issues, such as the use of…

  1. Maximizing scientific knowledge from randomized clinical trials

    DEFF Research Database (Denmark)

    Gustafsson, Finn; Atar, Dan; Pitt, Bertram

    2010-01-01

    Trialists have an ethical and financial responsibility to plan and conduct clinical trials in a manner that will maximize the scientific knowledge gained from the trial. However, the amount of scientific information generated by randomized clinical trials in cardiovascular medicine is highly...

  2. Definable maximal discrete sets in forcing extensions

    DEFF Research Database (Denmark)

    Törnquist, Asger Dag; Schrittesser, David

    2017-01-01

    that in the Sacks and Miller extensions there is a Π11 maximal orthogonal family ("mof") of Borel probability measures on Cantor space. A similar result is also obtained for Π11 mad families. By contrast, we show that if there is a Mathias real over L then there are no Σ12 mofs....

  3. Maximizing Learning Potential in the Communicative Classroom.

    Science.gov (United States)

    Kumaravadivelu, B.

    1993-01-01

    A classroom observational study is presented to assess whether a macrostrategies framework will help communicative language teaching teachers to maximize learner potential in the classroom. Analysis of two classroom episodes revealed that one episode was evidently more communicative than the other. (seven references) (VWL)

  4. Maximizing Resource Utilization in Video Streaming Systems

    Science.gov (United States)

    Alsmirat, Mohammad Abdullah

    2013-01-01

    Video streaming has recently grown dramatically in popularity over the Internet, Cable TV, and wire-less networks. Because of the resource demanding nature of video streaming applications, maximizing resource utilization in any video streaming system is a key factor to increase the scalability and decrease the cost of the system. Resources to…

  5. A THEORY OF MAXIMIZING SENSORY INFORMATION

    NARCIS (Netherlands)

    Hateren, J.H. van

    1992-01-01

    A theory is developed on the assumption that early sensory processing aims at maximizing the information rate in the channels connecting the sensory system to more central parts of the brain, where it is assumed that these channels are noisy and have a limited dynamic range. Given a stimulus power

  6. Ehrenfest's Lottery--Time and Entropy Maximization

    Science.gov (United States)

    Ashbaugh, Henry S.

    2010-01-01

    Successful teaching of the Second Law of Thermodynamics suffers from limited simple examples linking equilibrium to entropy maximization. I describe a thought experiment connecting entropy to a lottery that mixes marbles amongst a collection of urns. This mixing obeys diffusion-like dynamics. Equilibrium is achieved when the marble distribution is…

  7. Relationship between maximal exercise parameters and individual ...

    African Journals Online (AJOL)

    ... predicted 83% of the variance when performance was measured as 20km average watts and was the only significant variable, amongst all VT and maximal variables, included in the stepwise multiple regression model. These results suggest that the self-selected exercise intensity of cyclists with physical disabilities during ...

  8. Singularity Structure of Maximally Supersymmetric Scattering Amplitudes

    DEFF Research Database (Denmark)

    Arkani-Hamed, Nima; Bourjaily, Jacob L.; Cachazo, Freddy

    2014-01-01

    We present evidence that loop amplitudes in maximally supersymmetric (N=4) Yang-Mills theory (SYM) beyond the planar limit share some of the remarkable structures of the planar theory. In particular, we show that through two loops, the four-particle amplitude in full N=4 SYM has only logarithmic ...

  9. High-throughput computational and experimental techniques in structural genomics.

    Science.gov (United States)

    Chance, Mark R; Fiser, Andras; Sali, Andrej; Pieper, Ursula; Eswar, Narayanan; Xu, Guiping; Fajardo, J Eduardo; Radhakannan, Thirumuruhan; Marinkovic, Nebojsa

    2004-10-01

    Structural genomics has as its goal the provision of structural information for all possible ORF sequences through a combination of experimental and computational approaches. The access to genome sequences and cloning resources from an ever-widening array of organisms is driving high-throughput structural studies by the New York Structural Genomics Research Consortium. In this report, we outline the progress of the Consortium in establishing its pipeline for structural genomics, and some of the experimental and bioinformatics efforts leading to structural annotation of proteins. The Consortium has established a pipeline for structural biology studies, automated modeling of ORF sequences using solved (template) structures, and a novel high-throughput approach (metallomics) to examining the metal binding to purified protein targets. The Consortium has so far produced 493 purified proteins from >1077 expression vectors. A total of 95 have resulted in crystal structures, and 81 are deposited in the Protein Data Bank (PDB). Comparative modeling of these structures has generated >40,000 structural models. We also initiated a high-throughput metal analysis of the purified proteins; this has determined that 10%-15% of the targets contain a stoichiometric structural or catalytic transition metal atom. The progress of the structural genomics centers in the U.S. and around the world suggests that the goal of providing useful structural information on most all ORF domains will be realized. This projected resource will provide structural biology information important to understanding the function of most proteins of the cell.

  10. A Self-Driven and Adaptive Adjusting Teaching Learning Method for Optimizing Optical Multicast Network Throughput

    Science.gov (United States)

    Liu, Huanlin; Xu, Yifan; Chen, Yong; Zhang, Mingjia

    2016-09-01

    With the development of one point to multiple point applications, network resources become scarcer and wavelength channels become more crowded in optical networks. To improve the bandwidth utilization, the multicast routing algorithm based on network coding can greatly increase the resource utilization, but it is most difficult to maximize the network throughput owing to ignoring the differences between the multicast receiving nodes. For making full use of the destination nodes' receives ability to maximize optical multicast's network throughput, a new optical multicast routing algorithm based on teaching-learning-based optimization (MR-iTLBO) is proposed in the paper. In order to increase the diversity of learning, a self-driven learning method is adopted in MR-iTLBO algorithm, and the mutation operator of genetic algorithm is introduced to prevent the algorithm into a local optimum. For increasing learner's learning efficiency, an adaptive learning factor is designed to adjust the learning process. Moreover, the reconfiguration scheme based on probability vector is devised to expand its global search capability in MR-iTLBO algorithm. The simulation results show that performance in terms of network throughput and convergence rate has been improved significantly with respect to the TLBO and the variant TLBO.

  11. High throughput generated micro-aggregates of chondrocytes stimulate cartilage formation in vitro and in vivo

    NARCIS (Netherlands)

    Moreira Teixeira, Liliana; Leijten, Jeroen Christianus Hermanus; Sobral, J.; Jin, R.; van Apeldoorn, Aart A.; Feijen, Jan; van Blitterswijk, Clemens; Dijkstra, Pieter J.; Karperien, Hermanus Bernardus Johannes

    2012-01-01

    Cell-based cartilage repair strategies such as matrix-induced autologous chondrocyte implantation (MACI) could be improved by enhancing cell performance. We hypothesised that micro-aggregates of chondrocytes generated in high-throughput prior to implantation in a defect could stimulate cartilaginous

  12. Understanding Violations of Gricean Maxims in Preschoolers and Adults

    Directory of Open Access Journals (Sweden)

    Mako eOkanda

    2015-07-01

    Full Text Available This study used a revised Conversational Violations Test to examine Gricean maxim violations in 4- to 6-year-old Japanese children and adults. Participants’ understanding of the following maxims was assessed: be informative (first maxim of quantity, avoid redundancy (second maxim of quantity, be truthful (maxim of quality, be relevant (maxim of relation, avoid ambiguity (second maxim of manner, and be polite (maxim of politeness. Sensitivity to violations of Gricean maxims increased with age: 4-year-olds’ understanding of maxims was near chance, 5-year-olds understood some maxims (first maxim of quantity and maxims of quality, relation, and manner, and 6-year-olds and adults understood all maxims. Preschoolers acquired the maxim of relation first and had the greatest difficulty understanding the second maxim of quantity. Children and adults differed in their comprehension of the maxim of politeness. The development of the pragmatic understanding of Gricean maxims and implications for the construction of developmental tasks from early childhood to adulthood are discussed.

  13. Understanding violations of Gricean maxims in preschoolers and adults.

    Science.gov (United States)

    Okanda, Mako; Asada, Kosuke; Moriguchi, Yusuke; Itakura, Shoji

    2015-01-01

    This study used a revised Conversational Violations Test to examine Gricean maxim violations in 4- to 6-year-old Japanese children and adults. Participants' understanding of the following maxims was assessed: be informative (first maxim of quantity), avoid redundancy (second maxim of quantity), be truthful (maxim of quality), be relevant (maxim of relation), avoid ambiguity (second maxim of manner), and be polite (maxim of politeness). Sensitivity to violations of Gricean maxims increased with age: 4-year-olds' understanding of maxims was near chance, 5-year-olds understood some maxims (first maxim of quantity and maxims of quality, relation, and manner), and 6-year-olds and adults understood all maxims. Preschoolers acquired the maxim of relation first and had the greatest difficulty understanding the second maxim of quantity. Children and adults differed in their comprehension of the maxim of politeness. The development of the pragmatic understanding of Gricean maxims and implications for the construction of developmental tasks from early childhood to adulthood are discussed.

  14. A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays

    Science.gov (United States)

    Khan, Zia; Bloom, Joshua S.; Kruglyak, Leonid; Singh, Mona

    2009-01-01

    Motivation: High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anchor points for genome–genome comparisons. Results: We introduce a new algorithm for finding MEMs. The algorithm leverages a sparse suffix array (SA), a text index that stores every K-th position of the text. In contrast to a full text index that stores every position of the text, a sparse SA occupies much less memory. Even though we use a sparse index, the output of our algorithm is the same as a full text index algorithm as long as the space between the indexed suffixes is not greater than a minimum length of a MEM. By relying on partial matches and additional text scanning between indexed positions, the algorithm trades memory for extra computation. The reduced memory usage makes it possible to determine MEMs between significantly longer sequences. Availability: Source code for the algorithm is available under a BSD open source license at http://compbio.cs.princeton.edu/mems. The implementation can serve as a drop-in replacement for the MEMs algorithm in MUMmer 3. Contact: zkhan@cs.princeton.edu;mona@cs.princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19389736

  15. A Fully Automated High-Throughput Zebrafish Behavioral Ototoxicity Assay.

    Science.gov (United States)

    Todd, Douglas W; Philip, Rohit C; Niihori, Maki; Ringle, Ryan A; Coyle, Kelsey R; Zehri, Sobia F; Zabala, Leanne; Mudery, Jordan A; Francis, Ross H; Rodriguez, Jeffrey J; Jacob, Abraham

    2017-08-01

    Zebrafish animal models lend themselves to behavioral assays that can facilitate rapid screening of ototoxic, otoprotective, and otoregenerative drugs. Structurally similar to human inner ear hair cells, the mechanosensory hair cells on their lateral line allow the zebrafish to sense water flow and orient head-to-current in a behavior called rheotaxis. This rheotaxis behavior deteriorates in a dose-dependent manner with increased exposure to the ototoxin cisplatin, thereby establishing itself as an excellent biomarker for anatomic damage to lateral line hair cells. Building on work by our group and others, we have built a new, fully automated high-throughput behavioral assay system that uses automated image analysis techniques to quantify rheotaxis behavior. This novel system consists of a custom-designed swimming apparatus and imaging system consisting of network-controlled Raspberry Pi microcomputers capturing infrared video. Automated analysis techniques detect individual zebrafish, compute their orientation, and quantify the rheotaxis behavior of a zebrafish test population, producing a powerful, high-throughput behavioral assay. Using our fully automated biological assay to test a standardized ototoxic dose of cisplatin against varying doses of compounds that protect or regenerate hair cells may facilitate rapid translation of candidate drugs into preclinical mammalian models of hearing loss.

  16. Numerical Model of Streaming DEP for Stem Cell Sorting

    Directory of Open Access Journals (Sweden)

    Rucha Natu

    2016-11-01

    Full Text Available Neural stem cells are of special interest due to their potential in neurogenesis to treat spinal cord injuries and other nervous disorders. Flow cytometry, a common technique used for cell sorting, is limited due to the lack of antigens and labels that are specific enough to stem cells of interest. Dielectrophoresis (DEP is a label-free separation technique that has been recently demonstrated for the enrichment of neural stem/progenitor cells. Here we use numerical simulation to investigate the use of streaming DEP for the continuous sorting of neural stem/progenitor cells. Streaming DEP refers to the focusing of cells into streams by equilibrating the dielectrophoresis and drag forces acting on them. The width of the stream should be maximized to increase throughput while the separation between streams must be widened to increase efficiency during retrieval. The aim is to understand how device geometry and experimental variables affect the throughput and efficiency of continuous sorting of SC27 stem cells, a neurogenic progenitor, from SC23 cells, an astrogenic progenitor. We define efficiency as the ratio between the number of SC27 cells over total number of cells retrieved in the streams, and throughput as the number of SC27 cells retrieved in the streams compared to their total number introduced to the device. The use of cylindrical electrodes as tall as the channel yields streams featuring >98% of SC27 cells and width up to 80 µm when using a flow rate of 10 µL/min and sample cell concentration up to 105 cells/mL.

  17. High-throughput antibody development and retrospective epitope mapping

    DEFF Research Database (Denmark)

    Rydahl, Maja Gro

    Plant cell walls are composed of an interlinked network of polysaccharides, glycoproteins and phenolic polymers. When addressing the diverse polysaccharides in green plants, including land plants and the ancestral green algae, there are significant overlaps in the cell wall structures. Yet......, there are noteworthy differences in the less evolved species of algae as compared to land plants. The dynamic process orchestrating the deposition of these biopolymers both in algae and higher plants, is complex and highly heterogeneous, yet immensely important for the development and differentiation of the cell...... of green algae, during the development into land plants. Hence, there is a pressing need for rethinking the glycomic toolbox, by developing new and high-throughput (HTP) technology, in order to acquire information of the location and relative abundance of diverse cell wall polymers. In this dissertation...

  18. [Chemical constituents of Trichosanthes kirilowii Maxim].

    Science.gov (United States)

    Sun, Xiao-Ye; Wu, Hong-Hua; Fu, Ai-Zhen; Zhang, Peng

    2012-07-01

    To study the chemical constituents of Trichosanthes kirilowii Maxim., chromatographic methods such as D101 macroporous resin, silica gel column chromatographic technology, Sephadex LH-20, octadecylsilyl (ODS) column chromatographic technique and preparative HPLC were used and nine compounds were isolated from a 95% (v/v) ethanol extract of the plant. By using spectroscopic techniques including 1H NMR, 13C NMR, 1H-1H COSY, HSQC and HMBC, these compounds were identified as 5-ethoxymethyl-1-carboxyl propyl-1H-pyrrole-2-carbaldehyde (1), 5-hydroxymethyl-2-furfural (2), chrysoeriol (3), 4'-hydroxyscutellarin (4), vanillic acid (5), alpha-spinasterol (6), beta-D-glucopyranosyl-a-spinasterol (7), stigmast-7-en-3beta-ol (8), and adenosine (9), separately. Among them, compound 1 is a new compound, and compounds 3, 4 and 5 are isolated from the genus Trichosanthes kirilowii Maxim. for the first time.

  19. Maximal temperature in a simple thermodynamical system

    Science.gov (United States)

    Dai, De-Chang; Stojkovic, Dejan

    2016-06-01

    Temperature in a simple thermodynamical system is not limited from above. It is also widely believed that it does not make sense talking about temperatures higher than the Planck temperature in the absence of the full theory of quantum gravity. Here, we demonstrate that there exist a maximal achievable temperature in a system where particles obey the laws of quantum mechanics and classical gravity before we reach the realm of quantum gravity. Namely, if two particles with a given center of mass energy come at the distance shorter than the Schwarzschild diameter apart, according to classical gravity they will form a black hole. It is possible to calculate that a simple thermodynamical system will be dominated by black holes at a critical temperature which is about three times lower than the Planck temperature. That represents the maximal achievable temperature in a simple thermodynamical system.

  20. Modularity maximization using completely positive programming

    Science.gov (United States)

    Yazdanparast, Sakineh; Havens, Timothy C.

    2017-04-01

    Community detection is one of the most prominent problems of social network analysis. In this paper, a novel method for Modularity Maximization (MM) for community detection is presented which exploits the Alternating Direction Augmented Lagrangian (ADAL) method for maximizing a generalized form of Newman's modularity function. We first transform Newman's modularity function into a quadratic program and then use Completely Positive Programming (CPP) to map the quadratic program to a linear program, which provides the globally optimal maximum modularity partition. In order to solve the proposed CPP problem, a closed form solution using the ADAL merged with a rank minimization approach is proposed. The performance of the proposed method is evaluated on several real-world data sets used for benchmarks community detection. Simulation results shows the proposed technique provides outstanding results in terms of modularity value for crisp partitions.

  1. High throughput electrophysiology: new perspectives for ion channel drug discovery

    DEFF Research Database (Denmark)

    Willumsen, Niels J; Bech, Morten; Olesen, Søren-Peter

    2003-01-01

    Proper function of ion channels is crucial for all living cells. Ion channel dysfunction may lead to a number of diseases, so-called channelopathies, and a number of common diseases, including epilepsy, arrhythmia, and type II diabetes, are primarily treated by drugs that modulate ion channels...... channel targets accessible for drug screening. Specifically, genuine HTS parallel processing techniques based on arrays of planar silicon chips are being developed, but also lower throughput sequential techniques may be of value in compound screening, lead optimization, and safety screening....... The introduction of new powerful HTS electrophysiological techniques is predicted to cause a revolution in ion channel drug discovery....

  2. Spectrophotometric Enzyme Assays for High-Throughput Screening

    Directory of Open Access Journals (Sweden)

    Jean-Louis Reymond

    2004-01-01

    Full Text Available This paper reviews high-throughput screening enzyme assays developed in our laboratory over the last ten years. These enzyme assays were initially developed for the purpose of discovering catalytic antibodies by screening cell culture supernatants, but have proved generally useful for testing enzyme activities. Examples include TLC-based screening using acridone-labeled substrates, fluorogenic assays based on the β-elimination of umbelliferone or nitrophenol, and indirect assays such as the back-titration method with adrenaline and the copper-calcein fluorescence assay for aminoacids.

  3. Coulomb's law in maximally symmetric spaces

    OpenAIRE

    Vakili, B.; Gorji, M. A.

    2012-01-01

    We study the modifications to the Coulomb's law when the background geometry is a $n$-dimensional maximally symmetric space, by using of the $n$-dimensional version of the Gauss' theorem. It is shown that some extra terms are added to the usual expression of the Coulomb electric field due to the curvature of the background space. Also, we consider the problem of existence of magnetic monopoles in such spaces and present analytical expressions for the corresponding magnetic fields and vector p...

  4. Distributed Maximality based CTL Model Checking

    OpenAIRE

    Djamel Eddine Saidouni; Zine EL Abidine Bouneb

    2010-01-01

    In this paper we investigate an approach to perform a distributed CTL Model checker algorithm on a network of workstations using Kleen three value logic, the state spaces is partitioned among the network nodes, We represent the incomplete state spaces as a Maximality labeled Transition System MLTS which are able to express true concurrency. we execute in parallel the same algorithm in each node, for a certain property on an incomplete MLTS , this last compute the set of states which satisfy o...

  5. Quantum stochastic calculus with maximal operator domains

    OpenAIRE

    Lindsay, J. Martin; Attal, Stéphane

    2004-01-01

    Quantum stochastic calculus is extended in a new formulation in which its stochastic integrals achieve their natural and maximal domains. Operator adaptedness, conditional expectations and stochastic integrals are all defined simply in terms of the orthogonal projections of the time filtration of Fock space, together with sections of the adapted gradient operator. Free from exponential vector domains, our stochastic integrals may be satisfactorily composed yielding quantum Itô formulas for op...

  6. High Throughput and Acceptance Ratio Multipath Routing Algorithm in Cognitive Wireless Mesh Network

    Directory of Open Access Journals (Sweden)

    Zhufang Kuang

    2017-11-01

    Full Text Available The link failure due to the secondary users exiting the licensed channels when primary users reoccupy the licensed channels is very important in cognitive wireless mesh networks (CWMNs. A multipath routing and spectrum allocation algorithm based on channel interference and reusability with Quality of Service (QoS constraints in CWMNs (MRIR was proposed. Maximizing the throughput and the acceptance ratio of the wireless service is the objective of the MRIR. First, a primary path of resource conservation with QoS constraints was constructed, then, a resource conservation backup path based on channel interference and reusability with QoS constraints was constructed. The MRIR algorithm contains the primary path routing and spectrum allocation algorithm, and the backup path routing and spectrum allocation algorithm. The simulation results showed that the MRIR algorithm could achieve the expected goals and could achieve a higher throughput and acceptance ratio.

  7. Measurement of Mobile Switching Centres Throughput in GSM Network Integrating Sliding Window Algorithm with a Single Server Finite Queuing Model

    Directory of Open Access Journals (Sweden)

    Dinaker Babu Bollini

    2016-01-01

    Full Text Available The sliding window algorithm proposed for determining an optimal sliding window does not consider the waiting times of call setup requests of a mobile station in queue at a Mobile Switching Centre (MSC in the Global System for Mobile (GSM Communication Network. This study proposes a model integrating the sliding window algorithm with a single server finite queuing model, referred to as integrated model for measurement of realistic throughput of a MSC considering the waiting times of call setup requests. It assumes that a MSC can process one call setup request at a time. It is useful in determining an optimal sliding window size that maximizes the realistic throughput of a MSC. Though the model assumes that a MSC can process one call setup request at a time, its scope can be extended for measuring the realistic throughput of a MSC that can process multiple call setup requests at a time.

  8. High throughput inclusion body sizing: Nano particle tracking analysis.

    Science.gov (United States)

    Reichelt, Wieland N; Kaineder, Andreas; Brillmann, Markus; Neutsch, Lukas; Taschauer, Alexander; Lohninger, Hans; Herwig, Christoph

    2017-06-01

    The expression of pharmaceutical relevant proteins in Escherichia coli frequently triggers inclusion body (IB) formation caused by protein aggregation. In the scientific literature, substantial effort has been devoted to the quantification of IB size. However, particle-based methods used up to this point to analyze the physical properties of representative numbers of IBs lack sensitivity and/or orthogonal verification. Using high pressure freezing and automated freeze substitution for transmission electron microscopy (TEM) the cytosolic inclusion body structure was preserved within the cells. TEM imaging in combination with manual grey scale image segmentation allowed the quantification of relative areas covered by the inclusion body within the cytosol. As a high throughput method nano particle tracking analysis (NTA) enables one to derive the diameter of inclusion bodies in cell homogenate based on a measurement of the Brownian motion. The NTA analysis of fixated (glutaraldehyde) and non-fixated IBs suggests that high pressure homogenization annihilates the native physiological shape of IBs. Nevertheless, the ratio of particle counts of non-fixated and fixated samples could potentially serve as factor for particle stickiness. In this contribution, we establish image segmentation of TEM pictures as an orthogonal method to size biologic particles in the cytosol of cells. More importantly, NTA has been established as a particle-based, fast and high throughput method (1000-3000 particles), thus constituting a much more accurate and representative analysis than currently available methods. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. High-throughput microcavitation bubble induced cellular mechanotransduction

    Science.gov (United States)

    Compton, Jonathan Lee

    Focused pulsed laser irradiation allows for the deposition of energy with high spatial and temporal resolution. These attributes provide an optimal tool for non-contact manipulation in cellular biology such as laser microsurgery, cell membrane permeabilization, as well as targeted cell death. In this thesis we investigate the direct physical effects produced by laser- generated microcavitation bubbles in adherent cell cultures. We examine how variation in pulse durations (180 ps - 6ns) and pulse energy (0.5 - 40 mu;J) affect microcavitation bubble (mu;CB) generated cell lysis, necrosis, and molecular delivery. To compare the effects of pulse duration we employ classical fluid dynamics modeling to quantify the perturbation caused on cell populations from mu;CB generated microTsunamis (a transient microscale burst of hydrodynamic shear stress). Through time-resolved imaging we capture the mu;CB dynamics at various energies and pulse durations. Moreover, the mathematical modeling provides information regarding the cellular exposure to time varying shear stress and impulse as a function of radial location from the mu;CB center. We demonstrate that the resultant cellular effect can be predicted based on the total impulse across a two order of magnitude span of pulse duration and pulse energy. We also examine the region of cells beyond the zone of molecular delivery to investigate possible cellular reactions to mu;Tsunami exposure. Our studies have shown that cellular mechanotransduction occurs within cell populations spanning an area of up to 1 mm2 surrounding the mu;CB. Visualization of mechanotransduction is achieved through the visualization of intracellular calcium signaling via fluorescence microscopy that occurs due to the ability of the muTsunami generated shear stresses to stimulate G-protein coupled receptors at the apical cell surface. Moreover, we have shown that the observed signaling can be attenuated in a dose-dependent manner using 2-APB which is a known

  10. Compound Cytotoxicity Profiling Using Quantitative High-Throughput Screening

    Science.gov (United States)

    Xia, Menghang; Huang, Ruili; Witt, Kristine L.; Southall, Noel; Fostel, Jennifer; Cho, Ming-Hsuang; Jadhav, Ajit; Smith, Cynthia S.; Inglese, James; Portier, Christopher J.; Tice, Raymond R.; Austin, Christopher P.

    2008-01-01

    Background The propensity of compounds to produce adverse health effects in humans is generally evaluated using animal-based test methods. Such methods can be relatively expensive, low-throughput, and associated with pain suffered by the treated animals. In addition, differences in species biology may confound extrapolation to human health effects. Objective The National Toxicology Program and the National Institutes of Health Chemical Genomics Center are collaborating to identify a battery of cell-based screens to prioritize compounds for further toxicologic evaluation. Methods A collection of 1,408 compounds previously tested in one or more traditional toxicologic assays were profiled for cytotoxicity using quantitative high-throughput screening (qHTS) in 13 human and rodent cell types derived from six common targets of xenobiotic toxicity (liver, blood, kidney, nerve, lung, skin). Selected cytotoxicants were further tested to define response kinetics. Results qHTS of these compounds produced robust and reproducible results, which allowed cross-compound, cross-cell type, and cross-species comparisons. Some compounds were cytotoxic to all cell types at similar concentrations, whereas others exhibited species- or cell type–specific cytotoxicity. Closely related cell types and analogous cell types in human and rodent frequently showed different patterns of cytotoxicity. Some compounds inducing similar levels of cytotoxicity showed distinct time dependence in kinetic studies, consistent with known mechanisms of toxicity. Conclusions The generation of high-quality cytotoxicity data on this large library of known compounds using qHTS demonstrates the potential of this methodology to profile a much broader array of assays and compounds, which, in aggregate, may be valuable for prioritizing compounds for further toxicologic evaluation, identifying compounds with particular mechanisms of action, and potentially predicting in vivo biological response. PMID:18335092

  11. Cardiorespiratory Coordination in Repeated Maximal Exercise

    Directory of Open Access Journals (Sweden)

    Sergi Garcia-Retortillo

    2017-06-01

    Full Text Available Increases in cardiorespiratory coordination (CRC after training with no differences in performance and physiological variables have recently been reported using a principal component analysis approach. However, no research has yet evaluated the short-term effects of exercise on CRC. The aim of this study was to delineate the behavior of CRC under different physiological initial conditions produced by repeated maximal exercises. Fifteen participants performed 2 consecutive graded and maximal cycling tests. Test 1 was performed without any previous exercise, and Test 2 6 min after Test 1. Both tests started at 0 W and the workload was increased by 25 W/min in males and 20 W/min in females, until they were not able to maintain the prescribed cycling frequency of 70 rpm for more than 5 consecutive seconds. A principal component (PC analysis of selected cardiovascular and cardiorespiratory variables (expired fraction of O2, expired fraction of CO2, ventilation, systolic blood pressure, diastolic blood pressure, and heart rate was performed to evaluate the CRC defined by the number of PCs in both tests. In order to quantify the degree of coordination, the information entropy was calculated and the eigenvalues of the first PC (PC1 were compared between tests. Although no significant differences were found between the tests with respect to the performed maximal workload (Wmax, maximal oxygen consumption (VO2 max, or ventilatory threshold (VT, an increase in the number of PCs and/or a decrease of eigenvalues of PC1 (t = 2.95; p = 0.01; d = 1.08 was found in Test 2 compared to Test 1. Moreover, entropy was significantly higher (Z = 2.33; p = 0.02; d = 1.43 in the last test. In conclusion, despite the fact that no significant differences were observed in the conventionally explored maximal performance and physiological variables (Wmax, VO2 max, and VT between tests, a reduction of CRC was observed in Test 2. These results emphasize the interest of CRC

  12. Antiproliferative Activity of Phenylpropanoids Isolated from Lagotis brevituba Maxim.

    Science.gov (United States)

    Xiang, Yuan; Jing, Zhao; Haixia, Wang; Ruitao, Yu; Huaixiu, Wen; Zenggen, Liu; Lijuan, Mei; Yiping, Wang; Yanduo, Tao

    2017-10-01

    The aim of the present study was to evaluate the antiproliferative effect of phenylpropanoids isolated from the n-BuOH-soluble fraction of an ethanolic extract of Lagotis brevituba Maxim. The phenylpropanoids were identified as echinacoside, lagotioside, glucopyranosyl(1-6)martynoside, plantamoside, and verbascoside. Three of the compounds, lagotioside, glucopyranosyl(1-6)martynoside, and plantamoside, were isolated from L. brevituba for the first time. The antiproliferative activity of the isolates was evaluated in human gastric carcinoma (MGC-803), human colorectal carcinoma (HCT116), human hepatocellar carcinoma (HepG2), and human lung cancer (HCT116) cells using an 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Plantamoside showed promising activity against MGC-803 cells, with a half maximal inhibitory concentration value of 37.09 μM. The mechanism of the pro-apoptosis effect of plantamoside was then evaluated in MGC-803 cells. Changes in cell morphology, including disorganization of the architecture of actin microfilaments and formation of apoptotic bodies, together with cell cycle arrest in G2/M phases, were observed after treatment of plantamoside. The antiproliferative and pro-apoptotic effects were associated with a decrease in the ratio of Bcl-2/Bax and reduced mitochondrial membrane potential, which was accompanied by the release of reactive oxygen species and Ca(2+) into the cytoplasm. Taken together, the results indicated that plantamoside promotes apoptosis via a mitochondria-dependent mechanism. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  13. Process automation toward ultra-high-throughput screening of combinatorial one-bead-one-compound (OBOC) peptide libraries.

    Science.gov (United States)

    Cha, Junhoe; Lim, Jaehong; Zheng, Yiran; Tan, Sylvia; Ang, Yi Li; Oon, Jessica; Ang, Mei Wei; Ling, Jingjing; Bode, Marcus; Lee, Su Seong

    2012-06-01

    With an aim to develop peptide-based protein capture agents that can replace antibodies for in vitro diagnosis, an ultra-high-throughput screening strategy has been investigated by automating labor-intensive, time-consuming processes that are the construction of peptide libraries, sorting of positive beads, and peptide sequencing through analysis of tandem mass spectrometry data. Although instruments for automation, such as peptide synthesizers and automatic bead sorters, have been used in some groups, the overall process has not been well optimized to minimize time, cost, and efforts, as well as to maximize product quality and performance. Herein we suggest and explore several solutions to the existing problems with the automation of the key processes. The overall process optimization has been done successfully in orchestration with the technologies such as rapid cleavage of peptides from beads and semiautomatic peptide sequencing that we have developed previously. This optimization allowed one-round screening, from peptide library construction to peptide sequencing, to be completed within 4 to 5 days. We also successfully identified a 6-mer ligand for carcinoembryonic antigen-cell adhesion molecule 5 (CEACAM 5) through three-round screenings, including one-round screening of a focused library.

  14. Modeling data throughput on communication networks

    Energy Technology Data Exchange (ETDEWEB)

    Eldridge, J.M.

    1993-11-01

    New challenges in high performance computing and communications are driving the need for fast, geographically distributed networks. Applications such as modeling physical phenomena, interactive visualization, large data set transfers, and distributed supercomputing require high performance networking [St89][Ra92][Ca92]. One measure of a communication network`s performance is the time it takes to complete a task -- such as transferring a data file or displaying a graphics image on a remote monitor. Throughput, defined as the ratio of the number of useful data bits transmitted per the time required to transmit those bits, is a useful gauge of how well a communication system meets this performance measure. This paper develops and describes an analytical model of throughput. The model is a tool network designers can use to predict network throughput. It also provides insight into those parts of the network that act as a performance bottleneck.

  15. Goodput Maximization in Cooperative Networks with ARQ

    CERN Document Server

    Chen, Qing

    2010-01-01

    In this paper, the average successful throughput, i.e., goodput, of a coded 3-node cooperative network is studied in a Rayleigh fading environment. It is assumed that a simple automatic repeat request (ARQ) technique is employed in the network so that erroneously received codeword is retransmitted until successful delivery. The relay is assumed to operate in either amplify-and-forward (AF) or decode-and-forward (DF) mode. Under these assumptions, retransmission mechanisms and protocols are described, and the average time required to send information successfully is determined. Subsequently, the goodput for both AF and DF relaying is formulated. The tradeoffs and interactions between the goodput, transmission rates, and relay location are investigated and optimal strategies are identified.

  16. Reverse Phase Protein Arrays for High-throughput Toxicity Screening

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    RNAs with known killing effects as a model system to demonstrate that RPPA-based protein quantification can serve as substitute readout of cell viability, hereby reliably reflecting toxicity. In terms of automation, cell exposure, protein harvest, serial dilution and sample reformatting were performed using...... beneficially in automated high-throughput toxicity testing. An advantage of using RPPAs is that, in addition to the baseline toxicity readout, they allow testing of multiple markers of toxicity, such as inflammatory responses, which do not necessarily cumulate in cell death. We used transfection of si...... a robotic screening platform. Furthermore, we automated sample tracking and data analysis by developing a bundled bioinformatics tool named “MIRACLE”. Automation and RPPA-based viability/toxicity readouts enable rapid testing of large sample numbers, while granting the possibility for flexible consecutive...

  17. Oleanane-type triterpenoid saponins from Lysimachia fortunei Maxim.

    Science.gov (United States)

    Zhang, Shu-Lin; Yang, Zi-Ni; He, Cui; Liao, Hai-Bing; Wang, Heng-Shan; Chen, Zhen-Feng; Liang, Dong

    2018-03-01

    Six previously undescribed oleanane-type triterpenoid saponins, fortunosides A-F, together with six known ones, were isolated from the aerial parts of Lysimachia fortunei Maxim. Their structures were established by spectroscopic data analyses (1D, 2D-NMR and HRESIMS) and chemical methods. All isolated triterpenoid saponins were evaluated for their cytotoxicity against four human liver cancer cell lines (SMMC-7721, Hep3B, HuH7, and SK-Hep-1). Three saponins with the aglycone protoprimulagenin A exhibited moderate cytotoxicity against all of the tested human cancer cell lines, with IC 50 values ranging from 4.76 to 15.12 μM. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Heterocyst placement strategies to maximize growth of cyanobacterial filaments

    CERN Document Server

    Brown, Aidan I

    2012-01-01

    Under conditions of limited fixed-nitrogen, some filamentous cyanobacteria develop a regular pattern of heterocyst cells that fix nitrogen for the remaining vegetative cells. We examine three different heterocyst placement strategies by quantitatively modelling filament growth while varying both external fixed-nitrogen and leakage from the filament. We find that there is an optimum heterocyst frequency which maximizes the growth rate of the filament; the optimum frequency decreases as the external fixed-nitrogen concentration increases but increases as the leakage increases. In the presence of leakage, filaments implementing a local heterocyst placement strategy grow significantly faster than filaments implementing random heterocyst placement strategies. With no extracellular fixed-nitrogen, consistent with recent experimental studies of Anabaena sp. PCC 7120, the modelled heterocyst spacing distribution using our local heterocyst placement strategy is qualitatively similar to experimentally observed patterns...

  19. Changes of maximal muscle torque and maximal power output of lower extremities in male judoists during training

    OpenAIRE

    Buśko, Krzysztof; Nowak, Anna

    2008-01-01

    Purpose. The aim of the study was to follow changes of the maximal muscle torque and maximal power output of lower extremities in male judoists during pre-competition training (PCT). The original hypothesis assumed that different training loads would cause changes of the maximal muscle torque and maximal power output of legs in male judoists during pre-competition training, but not changes of the topography of the maximal muscle torque in all muscle groups. Basic procedures. The study sample ...

  20. Maximal unbordered factors of random strings

    DEFF Research Database (Denmark)

    Cording, Patrick Hagge; Knudsen, Mathias Bæk Tejs

    2016-01-01

    A border of a string is a non-empty prefix of the string that is also a suffix of the string, and a string is unbordered if it has no border. Loptev, Kucherov, and Starikovskaya [CPM 2015] conjectured the following: If we pick a string of length n from a fixed alphabet uniformly at random......, then the expected length of the maximal unbordered factor is n − O(1). We prove that this conjecture is true by proving that the expected value is in fact n − Θ(σ−1), where σ is the size of the alphabet. We discuss some of the consequences of this theorem....

  1. Using molecular biology to maximize concurrent training.

    Science.gov (United States)

    Baar, Keith

    2014-11-01

    Very few sports use only endurance or strength. Outside of running long distances on a flat surface and power-lifting, practically all sports require some combination of endurance and strength. Endurance and strength can be developed simultaneously to some degree. However, the development of a high level of endurance seems to prohibit the development or maintenance of muscle mass and strength. This interaction between endurance and strength is called the concurrent training effect. This review specifically defines the concurrent training effect, discusses the potential molecular mechanisms underlying this effect, and proposes strategies to maximize strength and endurance in the high-level athlete.

  2. Process Improvement for Maximized Therapeutic Innovation Outcome.

    Science.gov (United States)

    Waldman, Scott A; Terzic, Andre

    2018-01-01

    Deconvoluting key biological mechanisms forms the framework for therapeutic discovery. Strategies that enable effective translation of those insights along the development and regulatory path ultimately drive validated clinical application in patients and populations. Accordingly, parity in What vs. How we transform novel mechanistic insights into therapeutic paradigms is essential in achieving success. Aligning molecular discovery with innovations in structures and processes along the discovery-development-regulation-utilization continuum maximizes the return on public and private investments for next-generation solutions in managing health and disease. © 2017 ASCPT.

  3. Relaxation dynamics of maximally clustered networks

    Science.gov (United States)

    Klaise, Janis; Johnson, Samuel

    2018-01-01

    We study the relaxation dynamics of fully clustered networks (maximal number of triangles) to an unclustered state under two different edge dynamics—the double-edge swap, corresponding to degree-preserving randomization of the configuration model, and single edge replacement, corresponding to full randomization of the Erdős-Rényi random graph. We derive expressions for the time evolution of the degree distribution, edge multiplicity distribution and clustering coefficient. We show that under both dynamics networks undergo a continuous phase transition in which a giant connected component is formed. We calculate the position of the phase transition analytically using the Erdős-Rényi phenomenology.

  4. Dynamic robust duality in utility maximization

    OpenAIRE

    Øksendal, Bernt; Sulem, Agnès

    2013-01-01

    A celebrated financial application of convex duality theory gives an explicit relation between the following two quantities: (i) The optimal terminal wealth X^*(T) : = X_{\\varphi ^*}(T) of the problem to maximize the expected U-utility of the terminal wealth X_{\\varphi }(T) generated by admissible portfolios \\varphi (t); 0 \\le t \\le T in a market with the risky asset price process modeled as a semimartingale; (ii) The optimal scenario \\frac{dQ^*}{dP} of the dual problem to minimize the ...

  5. Intraoperative MRI and Maximizing Extent of Resection.

    Science.gov (United States)

    Rao, Ganesh

    2017-10-01

    Intraoperative MRI (iMRI) is a neurosurgical adjunct used to maximize the removal of glioma, the most common primary brain tumor. Increased extent of resection of gliomas has been shown to correlate with longer survival times. iMRI units are variable in design and magnet strength, which can affect patient selection and image quality. Multiple studies have shown that surgical resection of gliomas using iMRI results in increased extent of resection and survival time. Level II evidence supports the use of iMRI in the surgical treatment of glioma. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Maximizing versus satisficing: happiness is a matter of choice.

    Science.gov (United States)

    Schwartz, Barry; Ward, Andrew; Monterosso, John; Lyubomirsky, Sonja; White, Katherine; Lehman, Darrin R

    2002-11-01

    Can people feel worse off as the options they face increase? The present studies suggest that some people--maximizers--can. Study 1 reported a Maximization Scale, which measures individual differences in desire to maximize. Seven samples revealed negative correlations between maximization and happiness, optimism, self-esteem, and life satisfaction, and positive correlations between maximization and depression, perfectionism, and regret. Study 2 found maximizers less satisfied than nonmaximizers (satisficers) with consumer decisions, and more likely to engage in social comparison. Study 3 found maximizers more adversely affected by upward social comparison. Study 4 found maximizers more sensitive to regret and less satisfied in an ultimatum bargaining game. The interaction between maximizing and choice is discussed in terms of regret, adaptation, and self-blame.

  7. An Updated Protocol for High Throughput Plant Tissue Sectioning

    Directory of Open Access Journals (Sweden)

    Jonathan A. Atkinson

    2017-10-01

    Full Text Available Quantification of the tissue and cellular structure of plant material is essential for the study of a variety of plant sciences applications. Currently, many methods for sectioning plant material are either low throughput or involve free-hand sectioning which requires a significant amount of practice. Here, we present an updated method to provide rapid and high-quality cross sections, primarily of root tissue but which can also be readily applied to other tissues such as leaves or stems. To increase the throughput of traditional agarose embedding and sectioning, custom designed 3D printed molds were utilized to embed 5–15 roots in a block for sectioning in a single cut. A single fluorescent stain in combination with laser scanning confocal microscopy was used to obtain high quality images of thick sections. The provided CAD files allow production of the embedding molds described here from a number of online 3D printing services. Although originally developed for roots, this method provides rapid, high quality cross sections of many plant tissue types, making it suitable for use in forward genetic screens for differences in specific cell structures or developmental changes. To demonstrate the utility of the technique, the two parent lines of the wheat (Triticum aestivum Chinese Spring × Paragon doubled haploid mapping population were phenotyped for root anatomical differences. Significant differences in adventitious cross section area, stele area, xylem, phloem, metaxylem, and cortical cell file count were found.

  8. Maximal lactate steady state in Judo.

    Science.gov (United States)

    de Azevedo, Paulo Henrique Silva Marques; Pithon-Curi, Tania; Zagatto, Alessandro Moura; Oliveira, João; Perez, Sérgio

    2014-04-01

    the purpose of this study was to verify the validity of respiratory compensation threshold (RCT) measured during a new single judo specific incremental test (JSIT) for aerobic demand evaluation. to test the validity of the new test, the JSIT was compared with Maximal Lactate Steady State (MLSS), which is the gold standard procedure for aerobic demand measuring. Eight well-trained male competitive judo players (24.3 ± 7.9 years; height of 169.3 ± 6.7cm; fat mass of 12.7 ± 3.9%) performed a maximal incremental specific test for judo to assess the RCT and performed on 30-minute MLSS test, where both tests were performed mimicking the UchiKomi drills. the intensity at RCT measured on JSIT was not significantly different compared to MLSS (p=0.40). In addition, it was observed high and significant correlation between MLSS and RCT (r=0.90, p=0.002), as well as a high agreement. RCT measured during JSIT is a valid procedure to measure the aerobic demand, respecting the ecological validity of Judo.

  9. Breaking the Ceiling of Human Maximal Lifespan.

    Science.gov (United States)

    Ben-Haim, Moshe Shay; Kanfi, Yariv; Mitchel, Sarah J; Maoz, Noam; Vaughan, Kelli; Amariglio, Ninette; Lerrer, Batia; de Cabo, Rafael; Rechavi, Gideon; Cohen, Haim Y

    2017-11-07

    While average human life expectancy has increased dramatically in the last century, the maximum lifespan has only modestly increased. These observations prompted the notion that human lifespan might have reached its maximal natural limit of ~115 years. To evaluate this hypothesis, we conducted a systematic analysis of all-cause human mortality throughout the 20 th century. Our analyses revealed that, once cause of death is accounted for, there is a proportional increase in both median age of death and maximum lifespan. To examine whether pathway targeted aging interventions affected both median and maximum lifespan, we analyzed hundreds of interventions performed in multiple organisms (yeast, worms, flies, and rodents). Three criteria: median, maximum, and last survivor lifespans were all significantly extended, and to a similar extent. Altogether, these findings suggest that targeting the biological/genetic causes of aging can allow breaking the currently observed ceiling of human maximal lifespan. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. Spiders Tune Glue Viscosity to Maximize Adhesion.

    Science.gov (United States)

    Amarpuri, Gaurav; Zhang, Ci; Diaz, Candido; Opell, Brent D; Blackledge, Todd A; Dhinojwala, Ali

    2015-11-24

    Adhesion in humid conditions is a fundamental challenge to both natural and synthetic adhesives. Yet, glue from most spider species becomes stickier as humidity increases. We find the adhesion of spider glue, from five diverse spider species, maximizes at very different humidities that matches their foraging habitats. By using high-speed imaging and spreading power law, we find that the glue viscosity varies over 5 orders of magnitude with humidity for each species, yet the viscosity at maximal adhesion for each species is nearly identical, 10(5)-10(6) cP. Many natural systems take advantage of viscosity to improve functional response, but spider glue's humidity responsiveness is a novel adaptation that makes the glue stickiest in each species' preferred habitat. This tuning is achieved by a combination of proteins and hygroscopic organic salts that determines water uptake in the glue. We therefore anticipate that manipulation of polymer-salts interaction to control viscosity can provide a simple mechanism to design humidity responsive smart adhesives.

  11. Throughput analysis of ALOHA with cooperative diversity

    OpenAIRE

    Göktürk, Sarper Muharrem; Gokturk, Sarper Muharrem; Erçetin, Özgür; Ercetin, Ozgur; Gürbüz, Özgür; Gurbuz, Ozgur

    2008-01-01

    Cooperative transmissions emulate multi-antenna systems and can improve the quality of signal reception. In this paper, we propose and analyze a cross layer random access scheme, C-ALOHA, that enables cooperative transmissions in the context of ALOHA system. Our analysis shows that over a fading channel C-ALOHA can improve the throughput by 30%, as compared to standard ALOHA protocol.

  12. High-throughput scoring of seed germination

    NARCIS (Netherlands)

    Ligterink, Wilco; Hilhorst, Henk W.M.

    2017-01-01

    High-throughput analysis of seed germination for phenotyping large genetic populations or mutant collections is very labor intensive and would highly benefit from an automated setup. Although very often used, the total germination percentage after a nominated period of time is not very

  13. Data Transfer Throughput Research Over Mobile Networks

    Directory of Open Access Journals (Sweden)

    Karolis Žvinys

    2013-05-01

    Full Text Available This work analyses communication channel settings of UMTS technology, which are related with a data transfer throughput. The paper describes the measurement equipment that is suitable for measuring parameters of a mobile network channel. Besides, it analyses the suitability of this equipment and issue of parameter values that are associated with data throughput. Further, the study includes the selection of the most specific parameters, which are crucial for data speed. Using these parameters, models were developed for prediction of data transfer throughput. To build the model, the linear and nonlinear forecasting methods were used. The linear prediction was made by using linear regression, nonlinear — neural networks. Using the linear prediction model, 77.83% forecast accuracy was achieved, while the accuracy of forecasted nonlinear transmission rate amounted to 76.19%. The accuracy of prediction models was obtained using eight parameters of the communication channel. Finally, the paper presents the data throughput prediction models that allow predicting data speed with the help of channel parameters presented by a standard terminal. The list of these channel parameters is derived from five UE‘s of different manufacturers. The expected most accurate data transfer rate can be predicted using a set of parameters issued by Nokia device.Article in Lithuanian

  14. THROUGHPUT ANALYSIS OF EXTENDED ARQ SCHEMES

    African Journals Online (AJOL)

    PUBLICATIONS1

    formation transmitted in digital communication systems. Such schemes ... Department of Electronics and Telecommunications Engineering,. University of Dar es ...... (2): 165-176. Kundaeli, H. N. (2013). Throughput-Delay. Analysis of the SR-ST-GBN ARQ Scheme. Mediterranean Journal of Electronics and. Communication.

  15. Phenolic compounds from Glycyrrhiza pallidiflora Maxim. and their cytotoxic activity.

    Science.gov (United States)

    Shults, Elvira E; Shakirov, Makhmut M; Pokrovsky, Mikhail A; Petrova, Tatijana N; Pokrovsky, Andrey G; Gorovoy, Petr G

    2017-02-01

    Twenty-one phenolic compounds (1-21) including dihydrocinnamic acid, isoflavonoids, flavonoids, coumestans, pterocarpans, chalcones, isoflavan and isoflaven, were isolated from the roots of Glycyrrhiza pallidiflora Maxim. Phloretinic acid (1), chrysin (6), 9-methoxycoumestan (8), isoglycyrol (9), 6″-O-acetylanonin (19) and 6″-O-acetylwistin (21) were isolated from G. pallidiflora for the first time. Isoflavonoid acetylglycosides 19, 21 might be artefacts that could be produced during the EtOAc fractionation process of whole extract. Compounds 2-4, 10, 11, 19 and 21 were evaluated for their cytotoxic activity with respect to model cancer cell lines (CEM-13, MT-4, U-937) using the conventional MTT assays. Isoflavonoid calycosin (4) showed the best potency against human T-cell leukaemia cells MT-4 (CTD50, 2.9 μM). Pterocarpans medicarpin (10) and homopterocarpin (11) exhibit anticancer activity in micromolar range with selectivity on the human monocyte cells U-937. The isoflavan (3R)-vestitol (16) was highly selective on the lymphoblastoid leukaemia cells CEM-13 and was more active than the drug doxorubicin.

  16. Reverse Phase Protein Arrays for High-Throughput Protein Measurements in Mammospheres

    DEFF Research Database (Denmark)

    Pedersen, Marlene Lemvig; Block, Ines; List, Markus

    Protein Array (RPPA)-based readout format integrated into robotic siRNA screening. This technique would allow post-screening high-throughput quantification of protein changes. Recently, breast cancer stem cells (BCSCs) have attracted much attention, as a tumor- and metastasis-driving subpopulation...

  17. Functional characterisation of human glycine receptors in a fluorescence-based high throughput screening assay

    DEFF Research Database (Denmark)

    Jensen, Anders A.

    2005-01-01

    receptors in this assay were found to be in good agreement with those from electrophysiology studies of the receptors expressed in Xenopus oocytes or mammalian cell lines. Hence, this high throughput screening assay will be of great use in future pharmacological studies of glycine receptors, particular...

  18. Energy Efficiency vs. Throughput Trade-Off in an LTE-A Scenario

    DEFF Research Database (Denmark)

    Mihaylov, Mihail Rumenov; Mihovska, Albena D.; Prasad, Ramjee

    2014-01-01

    The growing demand of throughput, coverage and capacity has motivated the deployment of small cells as a cheaper option to macro base stations. Such heterogeneous scenario has also introduced novel advanced resource allocation and load balancing mechanisms for increased system performance. This p...

  19. High-throughput siRNA screening applied to the ubiquitin-proteasome system

    DEFF Research Database (Denmark)

    Poulsen, Esben Guldahl; Nielsen, Sofie V.; Pietras, Elin J.

    2016-01-01

    that are not genetically tractable as, for instance, a yeast model system. Here, we describe a method relying on high-throughput cellular imaging of cells transfected with a targeted siRNA library to screen for components involved in degradation of a protein of interest. This method is a rapid and cost-effective tool...

  20. High-throughput tri-colour flow cytometry technique to assess Plasmodium falciparum parasitaemia in bioassays

    DEFF Research Database (Denmark)

    Tiendrebeogo, Regis W; Adu, Bright; Singh, Susheel K

    2014-01-01

    distinction of early ring stages of Plasmodium falciparum from uninfected red blood cells (uRBC) remains a challenge. METHODS: Here, a high-throughput, three-parameter (tri-colour) flow cytometry technique based on mitotracker red dye, the nucleic acid dye coriphosphine O (CPO) and the leucocyte marker CD45...

  1. High-throughput screening for industrial enzyme production hosts by droplet microfluidics

    DEFF Research Database (Denmark)

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

    2014-01-01

    A high-throughput method for single cell screening by microfluidic droplet sorting is applied to a whole-genome mutated yeast cell library yielding improved production hosts of secreted industrial enzymes. The sorting method is validated by enriching a yeast strain 14 times based on its α......-amylase production, close to the theoretical maximum enrichment. Furthermore, a 105 member yeast cell library is screened yielding a clone with a more than 2-fold increase in α-amylase production. The increase in enzyme production results from an improvement of the cellular functions of the production host......) with the genotype (contained in the cell) inside a droplet enables selection of single cells with improved enzyme production capacity by droplet sorting. The platform has a throughput over 300 times higher than that of the current industry standard, an automated microtiter plate screening system. At the same time...

  2. A high throughput mechanical screening device for cartilage tissue engineering.

    Science.gov (United States)

    Mohanraj, Bhavana; Hou, Chieh; Meloni, Gregory R; Cosgrove, Brian D; Dodge, George R; Mauck, Robert L

    2014-06-27

    Articular cartilage enables efficient and near-frictionless load transmission, but suffers from poor inherent healing capacity. As such, cartilage tissue engineering strategies have focused on mimicking both compositional and mechanical properties of native tissue in order to provide effective repair materials for the treatment of damaged or degenerated joint surfaces. However, given the large number design parameters available (e.g. cell sources, scaffold designs, and growth factors), it is difficult to conduct combinatorial experiments of engineered cartilage. This is particularly exacerbated when mechanical properties are a primary outcome, given the long time required for testing of individual samples. High throughput screening is utilized widely in the pharmaceutical industry to rapidly and cost-effectively assess the effects of thousands of compounds for therapeutic discovery. Here we adapted this approach to develop a high throughput mechanical screening (HTMS) system capable of measuring the mechanical properties of up to 48 materials simultaneously. The HTMS device was validated by testing various biomaterials and engineered cartilage constructs and by comparing the HTMS results to those derived from conventional single sample compression tests. Further evaluation showed that the HTMS system was capable of distinguishing and identifying 'hits', or factors that influence the degree of tissue maturation. Future iterations of this device will focus on reducing data variability, increasing force sensitivity and range, as well as scaling-up to even larger (96-well) formats. This HTMS device provides a novel tool for cartilage tissue engineering, freeing experimental design from the limitations of mechanical testing throughput. © 2013 Published by Elsevier Ltd.

  3. A pocket device for high-throughput optofluidic holographic microscopy

    Science.gov (United States)

    Mandracchia, B.; Bianco, V.; Wang, Z.; Paturzo, M.; Bramanti, A.; Pioggia, G.; Ferraro, P.

    2017-06-01

    Here we introduce a compact holographic microscope embedded onboard a Lab-on-a-Chip (LoC) platform. A wavefront division interferometer is realized by writing a polymer grating onto the channel to extract a reference wave from the object wave impinging the LoC. A portion of the beam reaches the samples flowing along the channel path, carrying their information content to the recording device, while one of the diffraction orders from the grating acts as an off-axis reference wave. Polymeric micro-lenses are delivered forward the chip by Pyro-ElectroHydroDynamic (Pyro-EHD) inkjet printing techniques. Thus, all the required optical components are embedded onboard a pocket device, and fast, non-iterative, reconstruction algorithms can be used. We use our device in combination with a novel high-throughput technique, named Space-Time Digital Holography (STDH). STDH exploits the samples motion inside microfluidic channels to obtain a synthetic hologram, mapped in a hybrid space-time domain, and with intrinsic useful features. Indeed, a single Linear Sensor Array (LSA) is sufficient to build up a synthetic representation of the entire experiment (i.e. the STDH) with unlimited Field of View (FoV) along the scanning direction, independently from the magnification factor. The throughput of the imaging system is dramatically increased as STDH provides unlimited FoV, refocusable imaging of samples inside the liquid volume with no need for hologram stitching. To test our embedded STDH microscopy module, we counted, imaged and tracked in 3D with high-throughput red blood cells moving inside the channel volume under non ideal flow conditions.

  4. High Throughput PBTK: Open-Source Data and Tools for ...

    Science.gov (United States)

    Presentation on High Throughput PBTK at the PBK Modelling in Risk Assessment meeting in Ispra, Italy Presentation on High Throughput PBTK at the PBK Modelling in Risk Assessment meeting in Ispra, Italy

  5. Understanding the factors that effect maximal fat oxidation.

    Science.gov (United States)

    Purdom, Troy; Kravitz, Len; Dokladny, Karol; Mermier, Christine

    2018-01-01

    Lipids as a fuel source for energy supply during submaximal exercise originate from subcutaneous adipose tissue derived fatty acids (FA), intramuscular triacylglycerides (IMTG), cholesterol and dietary fat. These sources of fat contribute to fatty acid oxidation (FAox) in various ways. The regulation and utilization of FAs in a maximal capacity occur primarily at exercise intensities between 45 and 65% VO2max, is known as maximal fat oxidation (MFO), and is measured in g/min. Fatty acid oxidation occurs during submaximal exercise intensities, but is also complimentary to carbohydrate oxidation (CHOox). Due to limitations within FA transport across the cell and mitochondrial membranes, FAox is limited at higher exercise intensities. The point at which FAox reaches maximum and begins to decline is referred to as the crossover point. Exercise intensities that exceed the crossover point (~65% VO2max) utilize CHO as the predominant fuel source for energy supply. Training status, exercise intensity, exercise duration, sex differences, and nutrition have all been shown to affect cellular expression responsible for FAox rate. Each stimulus affects the process of FAox differently, resulting in specific adaptions that influence endurance exercise performance. Endurance training, specifically long duration (>2 h) facilitate adaptations that alter both the origin of FAs and FAox rate. Additionally, the influence of sex and nutrition on FAox are discussed. Finally, the role of FAox in the improvement of performance during endurance training is discussed.

  6. High-Throughput 3D Tumor Culture in a Recyclable Microfluidic Platform.

    Science.gov (United States)

    Liu, Wenming; Wang, Jinyi

    2017-01-01

    Three-dimensional (3D) tumor culture miniaturized platforms are of importance to biomimetic model construction and pathophysiological studies. Controllable and high-throughput production of 3D tumors is desirable to make cell-based manipulation dynamic and efficient at micro-scale. Moreover, the 3D culture platform being reusable is convenient to research scholars. In this chapter, we describe a dynamically controlled 3D tumor manipulation and culture method using pneumatic microstructure-based microfluidics, which has potential applications in the fields of tissue engineering, tumor biology, and clinical medicine in a high-throughput way.

  7. Primordial two-component maximally symmetric inflation

    Science.gov (United States)

    Enqvist, K.; Nanopoulos, D. V.; Quirós, M.; Kounnas, C.

    1985-12-01

    We propose a two-component inflation model, based on maximally symmetric supergravity, where the scales of reheating and the inflation potential at the origin are decoupled. This is possible because of the second-order phase transition from SU(5) to SU(3)×SU(2)×U(1) that takes place when φ≅φcinflation at the global minimum, and leads to a reheating temperature TR≅(1015-1016) GeV. This makes it possible to generate baryon asymmetry in the conventional way without any conflict with experimental data on proton lifetime. The mass of the gravitinos is m3/2≅1012 GeV, thus avoiding the gravitino problem. Monopoles are diluted by residual inflation in the broken phase below the cosmological bounds if φcUSA.

  8. Holographic equipartition and the maximization of entropy

    Science.gov (United States)

    Krishna, P. B.; Mathew, Titus K.

    2017-09-01

    The accelerated expansion of the Universe can be interpreted as a tendency to satisfy holographic equipartition. It can be expressed by a simple law, Δ V =Δ t (Nsurf-ɛ Nbulk) , where V is the Hubble volume in Planck units, t is the cosmic time in Planck units, and Nsurf /bulk is the number of degrees of freedom on the horizon/bulk of the Universe. We show that this holographic equipartition law effectively implies the maximization of entropy. In the cosmological context, a system that obeys the holographic equipartition law behaves as an ordinary macroscopic system that proceeds to an equilibrium state of maximum entropy. We consider the standard Λ CDM model of the Universe and show that it is consistent with the holographic equipartition law. Analyzing the entropy evolution, we find that it also proceeds to an equilibrium state of maximum entropy.

  9. MAXIMIZING THE BENEFITS OF ERP SYSTEMS

    Directory of Open Access Journals (Sweden)

    Paulo André da Conceição Menezes

    2010-04-01

    Full Text Available The ERP (Enterprise Resource Planning systems have been consolidated in companies with different sizes and sectors, allowing their real benefits to be definitively evaluated. In this study, several interactions have been studied in different phases, such as the strategic priorities and strategic planning defined as ERP Strategy; business processes review and the ERP selection in the pre-implementation phase, the project management and ERP adaptation in the implementation phase, as well as the ERP revision and integration efforts in the post-implementation phase. Through rigorous use of case study methodology, this research led to developing and to testing a framework for maximizing the benefits of the ERP systems, and seeks to contribute for the generation of ERP initiatives to optimize their performance.

  10. Maximal mydriasis evaluation in cataract surgery

    Directory of Open Access Journals (Sweden)

    Ho Tony

    1992-01-01

    Full Text Available We propose the Maximal Mydriasis Test (MMT as a simple and safe means to provide the cataract surgeon with objective and dependable pre-operative information on the idiosyncratic mydriatic response of the pupil. The MMT results of a consecutive series of 165 eyes from 100 adults referred for cataract evaluation are presented to illustrate its practical applications and value. The results of the MMT allows the surgeon to anticipate problem eyes pre-operatively so that he can plan his surgical strategy more appropriately and effectively. Conversely, the surgeon can also appropriately and confidently plan surgical procedures where wide pupillary dilation is important. The MMT has also helped improve our cost-effectiveness by cutting down unnecessary delays in the operating room and enabling better utilisation of restricted costly resources.

  11. The maximal family of exactly solvable chaos

    CERN Document Server

    Umeno, K

    1996-01-01

    A new two-parameter family of ergordic transformations with non-uniform invariant measures on the unit interval (I=[0,1]) is found here. The family has a special property that their invariant measures can be explicitly written in terms of algebraic functions of parameters and a dynamical variable. Furthermore, it is also proven here that this family is the most generalized class of exactly solvable chaos on (I) including the Ulam=Neumann map (y=4x(1-x)). Unpredictably, by choosing certain parameters, the maximal class of exactly solvable chaos is found to describe the asymmetric shape of the experimentally obtained first return maps of the Beloussof-Zhabotinski chemical reaction.

  12. Maximizing policy learning in international committees

    DEFF Research Database (Denmark)

    Nedergaard, Peter

    2007-01-01

    , this article demonstrates that valuable lessons can be learned about policy learning, in practice and theoretically, by analysing the cooperation in the OMC committees. Using the Advocacy Coalition Framework as the starting point of analysis, 15 hypotheses on policy learning are tested. Among other things......In the voluminous literature on the European Union's open method of coordination (OMC), no one has hitherto analysed on the basis of scholarly examination the question of what contributes to the learning processes in the OMC committees. On the basis of a questionnaire sent to all participants......, it is concluded that in order to maximize policy learning in international committees, empirical data should be made available to committees and provided by sources close to the participants (i.e. the Commission). In addition, the work in the committees should be made prestigious in order to attract well...

  13. Maximal lattice free bodies, test sets and the Frobenius problem

    DEFF Research Database (Denmark)

    Jensen, Anders Nedergaard; Lauritzen, Niels; Roune, Bjarke Hammersholt

    Maximal lattice free bodies are maximal polytopes without interior integral points. Scarf initiated the study of maximal lattice free bodies relative to the facet normals in a fixed matrix. In this paper we give an efficient algorithm for computing the maximal lattice free bodies of an integral...... method is inspired by the novel algorithm by Einstein, Lichtblau, Strzebonski and Wagon and the Groebner basis approach by Roune....

  14. Anaerobic contribution during maximal anaerobic running test: correlation with maximal accumulated oxygen deficit.

    Science.gov (United States)

    Zagatto, A; Redkva, P; Loures, J; Kalva Filho, C; Franco, V; Kaminagakura, E; Papoti, M

    2011-12-01

    The aims of this study were: (i) to measure energy system contributions in maximal anaerobic running test (MART); and (ii) to verify any correlation between MART and maximal accumulated oxygen deficit (MAOD). Eleven members of the armed forces were recruited for this study. Participants performed MART and MAOD, both accomplished on a treadmill. MART consisted of intermittent exercise, 20 s effort with 100 s recovery, after each spell of effort exercise. Energy system contributions by MART were also determined by excess post-exercise oxygen consumption, lactate response, and oxygen uptake measurements. MAOD was determined by five submaximal intensities and one supramaximal intensity exercises corresponding to 120% at maximal oxygen uptake intensity. Energy system contributions were 65.4±1.1% to aerobic; 29.5±1.1% to anaerobic a-lactic; and 5.1±0.5% to anaerobic lactic system throughout the whole test, while only during effort periods the anaerobic contribution corresponded to 73.5±1.0%. Maximal power found in MART corresponded to 111.25±1.33 mL/kg/min but did not significantly correlate with MAOD (4.69±0.30 L and 70.85±4.73 mL/kg). We concluded that the anaerobic a-lactic system is the main energy system in MART efforts and this test did not significantly correlate to MAOD. © 2011 John Wiley & Sons A/S.

  15. From entropy-maximization to equality-maximization: Gauss, Laplace, Pareto, and Subbotin

    Science.gov (United States)

    Eliazar, Iddo

    2014-12-01

    The entropy-maximization paradigm of statistical physics is well known to generate the omnipresent Gauss law. In this paper we establish an analogous socioeconomic model which maximizes social equality, rather than physical disorder, in the context of the distributions of income and wealth in human societies. We show that-on a logarithmic scale-the Laplace law is the socioeconomic equality-maximizing counterpart of the physical entropy-maximizing Gauss law, and that this law manifests an optimized balance between two opposing forces: (i) the rich and powerful, striving to amass ever more wealth, and thus to increase social inequality; and (ii) the masses, struggling to form more egalitarian societies, and thus to increase social equality. Our results lead from log-Gauss statistics to log-Laplace statistics, yield Paretian power-law tails of income and wealth distributions, and show how the emergence of a middle-class depends on the underlying levels of socioeconomic inequality and variability. Also, in the context of asset-prices with Laplace-distributed returns, our results imply that financial markets generate an optimized balance between risk and predictability.

  16. A High Performance Target Tracing Transmission Model Oriented to Lifecycle Maximization

    Directory of Open Access Journals (Sweden)

    Zhong-Nan Zhao

    2016-01-01

    Full Text Available For the high speed sensor networks applications such as Internet of Things, multimedia transmission, the realization of high-rate transmission under limited resources has become a problem to be solved. A high speed transmission and energy optimization model oriented to lifecycle maximization is proposed in this paper. Based on information-directed mechanism, the energy threshold set and the relay node distance selection will be done in the process of target tracing, as a result, retaining a balance between transmission rate and energy consumption. Meanwhile, multiagent coevolution is adopted to achieve the maximum of network lifecycle. Comparing with the relevant methods, indexes for network such as hops, throughput, and number of active nodes, standard deviation of remaining energy, and the network lifecycle are considered, and the simulated experiments show that the proposed method will promote the transmission rate effectively, prolong the network lifecycle, and improve network performance as a whole.

  17. Fusion genes and their discovery using high throughput sequencing.

    Science.gov (United States)

    Annala, M J; Parker, B C; Zhang, W; Nykter, M

    2013-11-01

    Fusion genes are hybrid genes that combine parts of two or more original genes. They can form as a result of chromosomal rearrangements or abnormal transcription, and have been shown to act as drivers of malignant transformation and progression in many human cancers. The biological significance of fusion genes together with their specificity to cancer cells has made them into excellent targets for molecular therapy. Fusion genes are also used as diagnostic and prognostic markers to confirm cancer diagnosis and monitor response to molecular therapies. High-throughput sequencing has enabled the systematic discovery of fusion genes in a wide variety of cancer types. In this review, we describe the history of fusion genes in cancer and the ways in which fusion genes form and affect cellular function. We also describe computational methodologies for detecting fusion genes from high-throughput sequencing experiments, and the most common sources of error that lead to false discovery of fusion genes. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. TCP throughput adaptation in WiMax networks using replicator dynamics.

    Science.gov (United States)

    Anastasopoulos, Markos P; Petraki, Dionysia K; Kannan, Rajgopal; Vasilakos, Athanasios V

    2010-06-01

    The high-frequency segment (10-66 GHz) of the IEEE 802.16 standard seems promising for the implementation of wireless backhaul networks carrying large volumes of Internet traffic. In contrast to wireline backbone networks, where channel errors seldom occur, the TCP protocol in IEEE 802.16 Worldwide Interoperability for Microwave Access networks is conditioned exclusively by wireless channel impairments rather than by congestion. This renders a cross-layer design approach between the transport and physical layers more appropriate during fading periods. In this paper, an adaptive coding and modulation (ACM) scheme for TCP throughput maximization is presented. In the current approach, Internet traffic is modulated and coded employing an adaptive scheme that is mathematically equivalent to the replicator dynamics model. The stability of the proposed ACM scheme is proven, and the dependence of the speed of convergence on various physical-layer parameters is investigated. It is also shown that convergence to the strategy that maximizes TCP throughput may be further accelerated by increasing the amount of information from the physical layer.

  19. High-throughput DNA Stretching in Continuous Elongational Flow for Genome Sequence Scanning

    Science.gov (United States)

    Meltzer, Robert; Griffis, Joshua; Safranovitch, Mikhail; Malkin, Gene; Cameron, Douglas

    2014-03-01

    Genome Sequence Scanning (GSS) identifies and compares bacterial genomes by stretching long (60 - 300 kb) genomic DNA restriction fragments and scanning for site-selective fluorescent probes. Practical application of GSS requires: 1) high throughput data acquisition, 2) efficient DNA stretching, 3) reproducible DNA elasticity in the presence of intercalating fluorescent dyes. GSS utilizes a pseudo-two-dimensional micron-scale funnel with convergent sheathing flows to stretch one molecule at a time in continuous elongational flow and center the DNA stream over diffraction-limited confocal laser excitation spots. Funnel geometry has been optimized to maximize throughput of DNA within the desired length range (>10 million nucleobases per second). A constant-strain detection channel maximizes stretching efficiency by applying a constant parabolic tension profile to each molecule, minimizing relaxation and flow-induced tumbling. The effect of intercalator on DNA elasticity is experimentally controlled by reacting one molecule of DNA at a time in convergent sheathing flows of the dye. Derivations of accelerating flow and non-linear tension distribution permit alignment of detected fluorescence traces to theoretical templates derived from whole-genome sequence data.

  20. Cross-Layer Throughput Optimization in Cognitive Radio Networks with SINR Constraints

    Directory of Open Access Journals (Sweden)

    Miao Ma

    2010-01-01

    Full Text Available Recently, there have been some research works in the design of cross-layer protocols for cognitive radio (CR networks, where the Protocol Model is used to model the radio interference. In this paper we consider a multihop multi-channel CR network. We use a more realistic Signal-to-Interference-plus-Noise Ratio (SINR model for radio interference and study the following cross-layer throughput optimization problem: (1 Given a set of secondary users with random but fixed location, and a set of traffic flows, what is the max-min achievable throughput? (2 To achieve the optimum, how to choose the set of active links, how to assign the channels to each active link, and how to route the flows? To the end, we present a formal mathematical formulation with the objective of maximizing the minimum end-to-end flow throughput. Since the formulation is in the forms of mixed integer nonlinear programming (MINLP, which is generally a hard problem, we develop a heuristic method by solving a relaxation of the original problem, followed by rounding and simple local optimization. Simulation results show that the heuristic approach performs very well, that is, the solutions obtained by the heuristic are very close to the global optimum obtained via LINGO.