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Sample records for measuring single-cell oxygen

  1. Single-cell measurement of red blood cell oxygen affinity

    PubMed Central

    Di Caprio, Giuseppe; Stokes, Chris; Higgins, John M.; Schonbrun, Ethan

    2015-01-01

    Oxygen is transported throughout the body by hemoglobin (Hb) in red blood cells (RBCs). Although the oxygen affinity of blood is well-understood and routinely assessed in patients by pulse oximetry, variability at the single-cell level has not been previously measured. In contrast, single-cell measurements of RBC volume and Hb concentration are taken millions of times per day by clinical hematology analyzers, and they are important factors in determining the health of the hematologic system. To better understand the variability and determinants of oxygen affinity on a cellular level, we have developed a system that quantifies the oxygen saturation, cell volume, and Hb concentration for individual RBCs in high throughput. We find that the variability in single-cell saturation peaks at an oxygen partial pressure of 2.9%, which corresponds to the maximum slope of the oxygen–Hb dissociation curve. In addition, single-cell oxygen affinity is positively correlated with Hb concentration but independent of osmolarity, which suggests variation in the Hb to 2,3-diphosphoglycerate (2–3 DPG) ratio on a cellular level. By quantifying the functional behavior of a cellular population, our system adds a dimension to blood cell analysis and other measurements of single-cell variability. PMID:26216973

  2. Metabolic oxygen consumption measurement with a single-cell biosensor after particle microbeam irradiation.

    PubMed

    Xu, Yanping; Zhang, Bo; Messerli, Mark; Randers-Pehrson, Gerhard; Hei, Tom K; Brenner, David J

    2015-03-01

    A noninvasive, self-referencing biosensor/probe system has been integrated into the Columbia University Radiological Research Accelerator Facility Microbeam II end station. A single-cell oxygen consumption measurement has been conducted with this type of oxygen probe in 37° C Krebs-Ringer Bicarbonate buffer immediately before and after a single-cell microbeam irradiation. It is the first such measurement made for a microbeam irradiation, and a six fold increment of oxygen flux induced during a 15-s period of time has been observed following radiation exposure. The experimental procedure and the results are discussed. PMID:25335641

  3. Metabolic oxygen consumption measurement with a single-cell biosensor after particle microbeam irradiation

    PubMed Central

    Zhang, Bo; Messerli, Mark; Randers-Pehrson, Gerhard; Hei, Tom K.; Brenner, David J.

    2015-01-01

    A noninvasive, self-referencing biosensor/probe system has been integrated into the Columbia University Radiological Research Accelerator Facility Microbeam II end station. A single-cell oxygen consumption measurement has been conducted with this type of oxygen probe in 37°C Krebs–Ringer Bicarbonate buffer immediately before and after a single-cell microbeam irradiation. It is the first such measurement made for a microbeam irradiation, and a six fold increment of oxygen flux induced during a 15-s period of time has been observed following radiation exposure. The experimental procedure and the results are discussed. PMID:25335641

  4. A microwell array device capable of measuring single-cell oxygen consumption rates

    PubMed Central

    Molter, Timothy W.; McQuaide, Sarah C.; Suchorolski, Martin T.; Strovas, Tim J.; Burgess, Lloyd W.; Meldrum, Deirdre R.; Lidstrom, Mary E.

    2009-01-01

    Due to interest in cell population heterogeneity, the development of new technology and methodologies for studying single cells has dramatically increased in recent years. The ideal single cell measurement system would be high throughput for statistical relevance, would measure the most important cellular parameters, and minimize disruption of normal cell function. We have developed a microwell array device capable of measuring single cell oxygen consumption rates (OCR). This OCR device is able to diffusionally isolate single cells and enables the quantitative measurement of oxygen consumed by a single cell with fmol/min resolution in a non-invasive and relatively high throughput manner. A glass microwell array format containing fixed luminescent sensors allows for future incorporation of additional cellular parameter sensing capabilities. To demonstrate the utility of the OCR device, we determined the oxygen consumption rates of a small group of single cells (12 to 18) for three different cells lines: murine macrophage cell line RAW264.7, human epithelial lung cancer cell line A549, and human Barrett’s esophagus cell line CP-D. PMID:20084089

  5. A New Approach for Measuring Single-Cell Oxygen Consumption Rates

    PubMed Central

    Molter, Timothy W.; McQuaide, Sarah C.; Holl, Mark R.; Meldrum, Deirdre R.; Dragavon, Joseph M.; Anderson, Judith B.; Young, A. Cody; Burgess, Lloyd W.; Lidstrom, Mary E.

    2010-01-01

    A novel system that has enabled the measurement of single-cell oxygen consumption rates is presented. The experimental apparatus includes a temperature controlled environmental chamber, an array of microwells etched in glass, and a lid actuator used to seal cells in the microwells. Each microwell contains an oxygen sensitive platinum phosphor sensor used to monitor the cellular metabolic rates. Custom automation software controls the digital image data collection for oxygen sensor measurements, which are analyzed using an image-processing program to yield the oxygen concentration within each microwell versus time. Two proof-of-concept experiments produced oxygen consumption rate measurements for A549 human epithelial lung cancer cells of 5.39 and 5.27 fmol/min/cell, closely matching published oxygen consumption rates for bulk A549 populations. PMID:21057593

  6. Propellant production on Mars - Single cell oxygen production test bed

    NASA Technical Reports Server (NTRS)

    Colvin, James; Schallhorn, Paul; Ramohalli, Kumar

    1991-01-01

    A study focusing on oxygen production using resources indigenous to Mars is presented. A bank of solid zirconia electrolytic cells that will electrochemically separate oxygen from a high temperature stream of carbon dioxide is at the center of the oxygen production system. The experimental data are discussed with attention given to the cell operating temperature, the carbon dioxide flow rate, and the voltage applied across the cell.

  7. Development of Nano/Micro Probes for Femtoliter Volume and Single Cell Measurements

    NASA Astrophysics Data System (ADS)

    Gao, Yang

    Single cell analysis has recently emerged as an important field of biomedical re- search. It is now clear that heterogeneity of cell metabolism functions in complex biological systems is correlated to changes in biological function and disease processes. A variety of nano/micro probes were developed to enable investigation of cells properties such as membrane stiffness, pH value. However, very few designs were focused on single cell metabolic function studies. There is a critical need for technologies that provide analysis of heterogeneity of cell metabolic functions, especially on metabolism. Nevertheless, the few existing approaches suffer from fundamental defects and need to be improved. This work focused on developing nano/micro probes that are suitable for single cell functionality investigation. Both types of probes are designed to measure cell-to-cell/time-to-time heterogeneity in metabolic functions over a long period of time. Lab-made carbon nanoprobes were developed especially for electro-physiological measurement. The unique structure of the carbon nanoprobes makes them suitable for important intracellular applications like trans-membrane potential measurements and various electrochemical measurement for cell function studies. While it is important of have ability to carry out intracellular measure, there are also occasions where the information of a cell as a whole is collected. One of the most important indicator of a cells metabolic functions is cell respiration rate/oxygen consumption rate. A micro-perfusion based multi-functional single cell sensing probe was the developed to carry out measurements on cell as a whole. Formed by a double-barrel theta pipette, the perfusion flow enables the direct measurement of the metabolic flux for example oxygen consumption rate. In conclusion, this work developed nano/micro-probes as novel single cell investigation tools. The data acquired from these tools could provide valuable assistance on applications

  8. A photoacoustic technique to measure the properties of single cells

    NASA Astrophysics Data System (ADS)

    Strohm, Eric M.; Berndl, Elizabeth S. L.; Kolios, Michael C.

    2013-03-01

    We demonstrate a new technique to non-invasively determine the diameter and sound speed of single cells using a combined ultrasonic and photoacoustic technique. Two cell lines, B16-F1 melanoma cells and MCF7 breast cancer cells were examined using this technique. Using a 200 MHz transducer, the ultrasound backscatter from a single cell in suspension was recorded. Immediately following, the cell was irradiated with a 532 nm laser and the resulting photoacoustic wave recorded by the same transducer. The melanoma cells contain optically absorbing melanin particles, which facilitated photoacoustic wave generation. MCF7 cells have negligible optical absorption at 532 nm; the cells were permeabilized and stained with trypan blue prior to measurements. The measured ultrasound and photoacoustic power spectra were compared to theoretical equations with the cell diameter and sound speed as variables (Anderson scattering model for ultrasound, and a thermoelastic expansion model for photoacoustics). The diameter and sound speed were extracted from the models where the spectral shape matched the measured signals. However the photoacoustic spectrum for the melanoma cell did not match theory, which is likely because melanin particles are located around the cytoplasm, and not within the nucleus. Therefore a photoacoustic finite element model of a cell was developed where the central region was not used to generate a photoacoustic wave. The resulting power spectrum was in better agreement with the measured signal than the thermoelastic expansion model. The MCF7 cell diameter obtained using the spectral matching method was 17.5 μm, similar to the optical measurement of 16 μm, while the melanoma cell diameter obtained was 22 μm, similar to the optical measurement of 21 μm. The sound speed measured from the MCF7 and melanoma cell was 1573 and 1560 m/s, respectively, which is within acceptable values that have been published in literature.

  9. Using measures of single-cell physiology and physiological state to understand organismic aging.

    PubMed

    Mendenhall, Alexander; Driscoll, Monica; Brent, Roger

    2016-02-01

    Genetically identical organisms in homogeneous environments have different lifespans and healthspans. These differences are often attributed to stochastic events, such as mutations and 'epimutations', changes in DNA methylation and chromatin that change gene function and expression. But work in the last 10 years has revealed differences in lifespan- and health-related phenotypes that are not caused by lasting changes in DNA or identified by modifications to DNA or chromatin. This work has demonstrated persistent differences in single-cell and whole-organism physiological states operationally defined by values of reporter gene signals in living cells. While some single-cell states, for example, responses to oxygen deprivation, were defined previously, others, such as a generally heightened ability to make proteins, were, revealed by direct experiment only recently, and are not well understood. Here, we review technical progress that promises to greatly increase the number of these measurable single-cell physiological variables and measureable states. We discuss concepts that facilitate use of single-cell measurements to provide insight into physiological states and state transitions. We assert that researchers will use this information to relate cell level physiological readouts to whole-organism outcomes, to stratify aging populations into groups based on different physiologies, to define biomarkers predictive of outcomes, and to shed light on the molecular processes that bring about different individual physiologies. For these reasons, quantitative study of single-cell physiological variables and state transitions should provide a valuable complement to genetic and molecular explanations of how organisms age. PMID:26616110

  10. High Throughput Micropatterning of Optical Oxygen Sensor for Single Cell Analysis

    PubMed Central

    Zhu, Haixin; Tian, Yanqing; Bhushan, Shivani; Su, Fengyu; Meldrum, Deirdre R.

    2012-01-01

    In this paper, we present our results from process development and characterization of optical oxygen sensors that are patterned by traditional UV lithography. An oxygen sensitive luminescent probe, platinum octaethylporphyrin (PtOEP), was encapsulated in commercially purchased photoresist (AZ5214) to form uniform thin sensor films on fused silica substrates. Plasticizer ethoxylated trimethylolpropane triacrylate (SR454) was added to the dye-photoresist sensor mixtures to improve the oxygen sensitivity. The optimum sensor mixture composition that can be patterned with maximum sensitivity was identified. The microfabrication process conditions, cell adherence and oxygen sensitivity results from patterned structures were characterized in detail. Down to 3 µm features have been fabricated on fused silica substrates using the developed techniques. The result implies the developed methods can provide a feasible way to miniaturize the optical sensor system for single cell analysis with precise control of sensor volume and response PMID:23066352

  11. Reactive oxygen species production in single cells following laser irradiation (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Duquette, Michelle L.; Kim, Justine; Shi, Linda Z.; Berns, Michael W.

    2015-08-01

    Region specific DNA breaks can be created in single cells using laser light that damages DNA but does not directly generate reactive oxygen species (ROS). We have examined the cellular response to directly generated DNA breaks in single cells. Using a combination of ROS specific dyes and oxidase inhibitors we have found that the oxidase and chromatin remodeling protein Lysine demethylase I (LSD1) generates detectable ROS as a byproduct of its chromatin remodeling activity during the initial DNA damage response. ROS is produced at detectable amounts primarily within the first 3 minutes post irradiation. LSD1 activity has been previously associated with transcriptional regulation therefore these findings have implications for regulation of gene expression following DNA damage particularly in cells with altered redox states.

  12. Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells

    PubMed Central

    Darmanis, Spyros; Gallant, Caroline Julie; Marinescu, Voichita Dana; Niklasson, Mia; Segerman, Anna; Flamourakis, Georgios; Fredriksson, Simon; Assarsson, Erika; Lundberg, Martin; Nelander, Sven; Westermark, Bengt; Landegren, Ulf

    2015-01-01

    Summary Significant advances have been made in methods to analyze genomes and transcriptomes of single cells, but to fully define cell states, proteins must also be accessed as central actors defining a cell’s phenotype. Methods currently used to analyze endogenous protein expression in single cells are limited in specificity, throughput, or multiplex capability. Here, we present an approach to simultaneously and specifically interrogate large sets of protein and RNA targets in lysates from individual cells, enabling investigations of cell functions and responses. We applied our method to investigate the effects of BMP4, an experimental therapeutic agent, on early-passage glioblastoma cell cultures. We uncovered significant heterogeneity in responses to treatment at levels of RNA and protein, with a subset of cells reacting in a distinct manner to BMP4. Moreover, we found overall poor correlation between protein and RNA at the level of single cells, with proteins more accurately defining responses to treatment. PMID:26748716

  13. A combined electrochemical and optical trapping platform for measuring single cell respiration rates at electrode interfaces

    SciTech Connect

    Gross, Benjamin J.; El-Naggar, Mohamed Y.

    2015-06-15

    Metal-reducing bacteria gain energy by extracellular electron transfer to external solids, such as naturally abundant minerals, which substitute for oxygen or the other common soluble electron acceptors of respiration. This process is one of the earliest forms of respiration on earth and has significant environmental and technological implications. By performing electron transfer to electrodes instead of minerals, these microbes can be used as biocatalysts for conversion of diverse chemical fuels to electricity. Understanding such a complex biotic-abiotic interaction necessitates the development of tools capable of probing extracellular electron transfer down to the level of single cells. Here, we describe an experimental platform for single cell respiration measurements. The design integrates an infrared optical trap, perfusion chamber, and lithographically fabricated electrochemical chips containing potentiostatically controlled transparent indium tin oxide microelectrodes. Individual bacteria are manipulated using the optical trap and placed on the microelectrodes, which are biased at a suitable oxidizing potential in the absence of any chemical electron acceptor. The potentiostat is used to detect the respiration current correlated with cell-electrode contact. We demonstrate the system with single cell measurements of the dissimilatory-metal reducing bacterium Shewanella oneidensis MR-1, which resulted in respiration currents ranging from 15 fA to 100 fA per cell under our measurement conditions. Mutants lacking the outer-membrane cytochromes necessary for extracellular respiration did not result in any measurable current output upon contact. In addition to the application for extracellular electron transfer studies, the ability to electronically measure cell-specific respiration rates may provide answers for a variety of fundamental microbial physiology questions.

  14. A combined electrochemical and optical trapping platform for measuring single cell respiration rates at electrode interfaces

    NASA Astrophysics Data System (ADS)

    Gross, Benjamin J.; El-Naggar, Mohamed Y.

    2015-06-01

    Metal-reducing bacteria gain energy by extracellular electron transfer to external solids, such as naturally abundant minerals, which substitute for oxygen or the other common soluble electron acceptors of respiration. This process is one of the earliest forms of respiration on earth and has significant environmental and technological implications. By performing electron transfer to electrodes instead of minerals, these microbes can be used as biocatalysts for conversion of diverse chemical fuels to electricity. Understanding such a complex biotic-abiotic interaction necessitates the development of tools capable of probing extracellular electron transfer down to the level of single cells. Here, we describe an experimental platform for single cell respiration measurements. The design integrates an infrared optical trap, perfusion chamber, and lithographically fabricated electrochemical chips containing potentiostatically controlled transparent indium tin oxide microelectrodes. Individual bacteria are manipulated using the optical trap and placed on the microelectrodes, which are biased at a suitable oxidizing potential in the absence of any chemical electron acceptor. The potentiostat is used to detect the respiration current correlated with cell-electrode contact. We demonstrate the system with single cell measurements of the dissimilatory-metal reducing bacterium Shewanella oneidensis MR-1, which resulted in respiration currents ranging from 15 fA to 100 fA per cell under our measurement conditions. Mutants lacking the outer-membrane cytochromes necessary for extracellular respiration did not result in any measurable current output upon contact. In addition to the application for extracellular electron transfer studies, the ability to electronically measure cell-specific respiration rates may provide answers for a variety of fundamental microbial physiology questions.

  15. A combined electrochemical and optical trapping platform for measuring single cell respiration rates at electrode interfaces.

    PubMed

    Gross, Benjamin J; El-Naggar, Mohamed Y

    2015-06-01

    Metal-reducing bacteria gain energy by extracellular electron transfer to external solids, such as naturally abundant minerals, which substitute for oxygen or the other common soluble electron acceptors of respiration. This process is one of the earliest forms of respiration on earth and has significant environmental and technological implications. By performing electron transfer to electrodes instead of minerals, these microbes can be used as biocatalysts for conversion of diverse chemical fuels to electricity. Understanding such a complex biotic-abiotic interaction necessitates the development of tools capable of probing extracellular electron transfer down to the level of single cells. Here, we describe an experimental platform for single cell respiration measurements. The design integrates an infrared optical trap, perfusion chamber, and lithographically fabricated electrochemical chips containing potentiostatically controlled transparent indium tin oxide microelectrodes. Individual bacteria are manipulated using the optical trap and placed on the microelectrodes, which are biased at a suitable oxidizing potential in the absence of any chemical electron acceptor. The potentiostat is used to detect the respiration current correlated with cell-electrode contact. We demonstrate the system with single cell measurements of the dissimilatory-metal reducing bacterium Shewanella oneidensis MR-1, which resulted in respiration currents ranging from 15 fA to 100 fA per cell under our measurement conditions. Mutants lacking the outer-membrane cytochromes necessary for extracellular respiration did not result in any measurable current output upon contact. In addition to the application for extracellular electron transfer studies, the ability to electronically measure cell-specific respiration rates may provide answers for a variety of fundamental microbial physiology questions. PMID:26133851

  16. Low-pressure airlift fermenter for single cell protein production. I. Design and oxygen transfer studies

    SciTech Connect

    Chen, N.Y.; Kondis, E.F.; Srinivasan, S.

    1987-03-01

    The energy consumption of a fermenter constitutes a major part of the operating expense of a single cell protein process. A low-pressure airlift fermenter was designed to reduce this cost. In this new design, the fermenter broth is kept below 120 cm in depth, and air alone is employed to fulfil the need of supplying oxygen, and cooling and agitating the broth. The use of low-pressure air from air blowers instead of air compressors lowers the capital cost of air delivery and reduces the energy consumption in the fermenter section to below 1 kWh/kg protein, a saving of over 70% as compared to a conventional stirred tank fermenter. It also eliminates the investment of mechanical agitators, heat exchangers, and air compressors. Sulfite oxidation studies confirmed the design concepts. 30 references.

  17. A fast solution switching system with temperature control for single cell measurements

    PubMed Central

    Koh, Duk-Su; Chen, Liangyi; Ufret-Vincenty, Carmen A.; Jung, Seung-Ryoung

    2011-01-01

    This article describes a perfusion system for biophysical single cell experiments at the physiological temperature. Our system regulates temperature of test solutions using a small heat exchanger that includes several capillaries. Water circulating inside the heat exchanger warms or cools test solutions flowing inside the capillaries. Temperature-controlled solutions are delivered directly to a single cell(s) through a multibarreled manifold that switches solutions bathing a cell in less than 1 s. This solution exchange is optimal for patch clamp, single-cell microamperometry, and microfluorometry experiments. Using this system, we demonstrate that exocytosis from pancreatic β cells and activation of TRPV1 channels are temperature sensitive. We also discuss how to measure local temperature near a single cell under investigation. PMID:21536068

  18. Single Cell Mass Measurement Using Drag Force Inside Lab-on-Chip Microfluidics System.

    PubMed

    Rahman, Md Habibur; Ahmad, Mohd Ridzuan; Takeuchi, Masaru; Nakajima, Masahiro; Hasegawa, Yasuhisa; Fukuda, Toshio

    2015-12-01

    Single cell mass (SCM) is an intrinsic property of single cell, it arouses a great interest among scientists as cell mass depends on the synthesis of proteins, DNA replication, cell wall stiffness, cell cytoplasm density, cell growth, ribosome, and other analogous of organisms. To date, several great strides have been taken to the advancements of SCM measurement techniques. Nevertheless, more works are required to enable the technology to push frontier in deep analysis of SCM measurement, hence to elucidate intracellular properties. In this paper, we present a lab-on-chip microfluidics system for SCM measurement, related with the force required to drag a single cell and Newton's law of motion inside microfluidics channel. Drag force on the cell was generated by a pressure driven syringe micropump and the motion of the cell was measured using optical observation under an inverted microscope. This approach of measuring SCM was calibrated using known mass (77.3 pg) of a polystyrene particle of 5.2 μm diameter. Furthermore, we used Saccharomyces cerevisiae baker's yeast cells of different sizes ([Formula: see text] diameter) for SCM measurement. Mass of 4.4 μm diameter of single yeast cell was measured as 2.12 pg which is in the range of previously reported single yeast cell mass (2-3 pg). In addition, we also studied the relation between SCM and single cell size. Results showed that single yeast cell mass increases exponentially with the increasing of single cell size. PMID:26761952

  19. Kinetics of small molecule interactions with membrane proteins in single cells measured with mechanical amplification

    PubMed Central

    Guan, Yan; Shan, Xiaonan; Zhang, Fenni; Wang, Shaopeng; Chen, Hong-Yuan; Tao, Nongjian

    2015-01-01

    Measuring small molecule interactions with membrane proteins in single cells is critical for understanding many cellular processes and for screening drugs. However, developing such a capability has been a difficult challenge. We show that molecular interactions with membrane proteins induce a mechanical deformation in the cellular membrane, and real-time monitoring of the deformation with subnanometer resolution allows quantitative analysis of small molecule–membrane protein interaction kinetics in single cells. This new strategy provides mechanical amplification of small binding signals, making it possible to detect small molecule interactions with membrane proteins. This capability, together with spatial resolution, also allows the study of the heterogeneous nature of cells by analyzing the interaction kinetics variability between different cells and between different regions of a single cell. PMID:26601298

  20. Single Cell Spectroscopy: Noninvasive Measures of Small-Scale Structure and Function

    PubMed Central

    Mousoulis, Charilaos; Xu, Xin; Reiter, David A.; Neu, Corey P.

    2013-01-01

    The advancement of spectroscopy methods attained through increases in sensitivity, and often with the coupling of complementary techniques, has enabled real-time structure and function measurements of single cells. The purpose of this review is to illustrate, in light of advances, the strengths and the weaknesses of these methods. Included also is an assessment of the impact of the experimental setup and conditions of each method on cellular function and integrity. A particular emphasis is placed on noninvasive and nondestructive techniques for achieving single cell detection, including nuclear magnetic resonance, in addition to physical, optical, and vibrational methods. PMID:23886910

  1. A microchip integrating cell array positioning with in situ single-cell impedance measurement.

    PubMed

    Guo, Xiaoliang; Zhu, Rong; Zong, Xianli

    2015-10-01

    This paper presents a novel microarray chip integrating cell positioning with in situ, real-time and long-time impedance measurement on a single cell. The microchip integrates a plurality of quadrupole-electrode units (termed positioning electrodes) patterned into an array with pairs of planar electrodes (termed measuring electrodes) located at the centers of each quadrupole-electrode unit. The positioning electrodes are utilized to trap and position living cells onto the measuring electrodes based on negative dielectrophoresis (nDEP), while the measuring electrodes are used to measure impedances of the trapped single cells. Each measuring electrode has a small footprint area of 7 × 7 μm(2) to ensure inhabiting only one single cell on it. However, the electrode with a small surface area has a low double-layer capacitance when it is immersed in a liquid solution, thus generating a large double-layer impedance, which reduces the sensitivity for impedance measurement on the single cell. To enlarge the effective surface areas of the measuring electrodes, a novel surface-modification process is proposed to controllably construct gold nanostructures on the surfaces of the measuring electrodes while the positioning electrodes are unstained. The double layer capacitances of the modified electrodes are increased by about one order after surface-modification. The developed microchip is used to monitor the adhering behavior of a single HeLa cell by measuring its impedance spectra in real time. The measured impedance is analyzed and used to extract cellular electrical parameters, which demonstrated that the cell compresses the electrical double layer in the process of adherence and adheres onto the measuring electrodes after 4-5 hours. PMID:26282920

  2. Nanofork for single cells adhesion measurement via ESEM-nanomanipulator system.

    PubMed

    Ahmad, Mohd Ridzuan; Nakajima, Masahiro; Kojima, Masaru; Kojima, Seiji; Homma, Michio; Fukuda, Toshio

    2012-03-01

    In this paper, single cells adhesion force was measured using a nanofork. The nanofork was used to pick up a single cell on a line array substrate inside an environmental scanning electron microscope (ESEM). The line array substrate was used to provide small gaps between the single cells and the substrate. Therefore, the nanofork could be inserted through these gaps in order to successfully pick up a single cell. Adhesion force was measured during the cell pick-up process from the deflection of the cantilever beam. The nanofork was fabricated using focused ion beam (FIB) etching process while the line array substrate was fabricated using nanoimprinting technology. As to investigate the effect of contact area on the strength of the adhesion force, two sizes of gap distance of line array substrate were used, i.e., 1 μm and 2 μm. Results showed that cells attached on the 1 μm gap line array substrate required more force to be released as compared to the cells attached on the 1 μm gap line array substrate. PMID:22275723

  3. Measurement of nitric oxide in single cells and tissue using a porphyrinic microsensor.

    PubMed

    Malinski, T; Huk, I

    2001-05-01

    This unit describes the preparation and applications of porphyrinic sensors for quantitative measurement of nitric oxide (NO) in single cells and in tissues. The determination of NO is based on the electrochemical oxidation of NO on a carbon fiber electrode covered with a thin layer of a conducting polymeric metalloporphyrin catalyst, overlaid with another thin film of Nafion, a cation exchange material. The electric current generated during NO oxidation on the surface of the polymeric porphyrin is linearly proportional to the concentration of NO, so this current is used as an analytical signal which can be measured in either the amperometric or the voltammetric mode. Both methods provide a quantitative signal. This unit describes the electrochemical setup for measurement of NO in single cells and tissue. Support protocols describe porphyrin synthesis, sensor preparation, and sensor calibration. PMID:18428525

  4. Measuring tissue oxygenation

    NASA Technical Reports Server (NTRS)

    Soyemi, Olusola O. (Inventor); Soller, Babs R. (Inventor); Yang, Ye (Inventor)

    2009-01-01

    Methods and systems for calculating tissue oxygenation, e.g., oxygen saturation, in a target tissue are disclosed. In some embodiments, the methods include: (a) directing incident radiation to a target tissue and determining reflectance spectra of the target tissue by measuring intensities of reflected radiation from the target tissue at a plurality of radiation wavelengths; (b) correcting the measured intensities of the reflectance spectra to reduce contributions thereto from skin and fat layers through which the incident radiation propagates; (c) determining oxygen saturation in the target tissue based on the corrected reflectance spectra; and (d) outputting the determined value of oxygen saturation.

  5. Evaluating quantitative methods for measuring plasmid copy numbers in single cells

    PubMed Central

    Tal, Shay; Paulsson, Johan

    2013-01-01

    The life of plasmids is a constant battle against fluctuations: failing to correct copy number fluctuations can increase the plasmid loss rate by many orders of magnitude, as can a failure to more evenly divide the copies between daughters at cell division. Plasmids are therefore long-standing model systems for stochastic processes in cells, much thanks to the efforts of Kurt Nordström to whose memory this issue is dedicated. Here we analyze a range of experimental methods for measuring plasmid copy numbers in single cells, focusing on challenges, trade-offs and necessary experimental controls. In particular we analyze published and unpublished strategies to infer copy numbers from expression of plasmid-encoded reporters, direct labeling of plasmids with fluorescent probes or DNA binding proteins fused to fluorescent reporters, PCR based methods applied to single cell lysates, and plasmid-specific replication arrest. We conclude that no method currently exists to measure plasmid copy numbers in single cells, and that most methods instead inadvertently measure various types of experimental noise. We also discuss how accurate methods can be developed. PMID:22305922

  6. Quantitative single-cell gene expression measurements of multiple genes in response to hypoxia treatment.

    PubMed

    Zeng, Jia; Wang, Jiangxin; Gao, Weimin; Mohammadreza, Aida; Kelbauskas, Laimonas; Zhang, Weiwen; Johnson, Roger H; Meldrum, Deirdre R

    2011-07-01

    Cell-to-cell heterogeneity in gene transcription plays a central role in a variety of vital cell processes. To quantify gene expression heterogeneity patterns among cells and to determine their biological significance, methods to measure gene expression levels at the single-cell level are highly needed. We report an experimental technique based on the DNA-intercalating fluorescent dye SYBR green for quantitative expression level analysis of up to ten selected genes in single mammalian cells. The method features a two-step procedure consisting of a step to isolate RNA from a single mammalian cell, synthesize cDNA from it, and a qPCR step. We applied the method to cell populations exposed to hypoxia, quantifying expression levels of seven different genes spanning a wide dynamic range of expression in randomly picked single cells. In the experiment, 72 single Barrett's esophageal epithelial (CP-A) cells, 36 grown under normal physiological conditions (controls) and 36 exposed to hypoxia for 30 min, were randomly collected and used for measuring the expression levels of 28S rRNA, PRKAA1, GAPDH, Angptl4, MT3, PTGES, and VEGFA genes. The results demonstrate that the method is sensitive enough to measure alterations in gene expression at the single-cell level, clearly showing heterogeneity within a cell population. We present technical details of the method development and implementation, and experimental results obtained by use of the procedure. We expect the advantages of this technique will facilitate further developments and advances in the field of single-cell gene expression profiling on a nanotechnological scale, and eventually as a tool for future point-of-care medical applications. PMID:21614642

  7. Frequency measurement of the prototype storage ring stainless steel single cell cavity

    SciTech Connect

    Reisinger, E.A.

    1992-07-29

    Frequency measurements were made on the stainless steel single cell cavity after prototype storage ring at the Advanced Photon Source with various port terminations, using two small loops. The cavity contains six larger ports. The top and bottom ports have a diameter of 144 mm, the front and back ports (beam ports) have a diameter of 140 mm, and the two side ports have a diameter of 120 mm. The cavity also have four smaller ports of diameter 34.8 mm, which contain an E-probe, a H-loop, and two field probes.

  8. Sensitive thermal microsensor with pn junction for heat measurement of a single cell

    NASA Astrophysics Data System (ADS)

    Yamada, Taito; Inomata, Naoki; Ono, Takahito

    2016-02-01

    A sensitive thermal microsensor based on a pn junction diode for heat measurements of biological single cells is developed and evaluated. Using a fabricated device, we demonstrated the heat measurement of a single brown fat cell. The principle of the sensor relies on the temperature dependence of the pn junction diode resistance. This method has a capability of the highly thermal sensitivity by downsizing and the advantage of a simple experimental setup using electrical circuits without any special equipment. To achieve highly sensitive heat measurement of single cells, downsizing of the sensor is necessary to reduce the heat capacity of the sensor itself. The sensor with the pn junction diode can be downsized by microfabrication. A bridge beam structure with the pn junction diode as a thermal sensor is placed in vacuum using a microfludic chip to decrease the heat loss to the surroundings. A temperature coefficient of resistance of 1.4%/K was achieved. The temperature and thermal resolutions of the fabricated device are 1.1 mK and 73.6 nW, respectively. The heat measurements of norepinephrine stimulated and nonstimulated single brown fat cells were demonstrated, and different behaviors in heat generation were observed.

  9. Robust organelle size extractions from elastic scattering measurements of single cells (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Cannaday, Ashley E.; Draham, Robert; Berger, Andrew J.

    2016-04-01

    The goal of this project is to estimate non-nuclear organelle size distributions in single cells by measuring angular scattering patterns and fitting them with Mie theory. Simulations have indicated that the large relative size distribution of organelles (mean:width≈2) leads to unstable Mie fits unless scattering is collected at polar angles less than 20 degrees. Our optical system has therefore been modified to collect angles down to 10 degrees. Initial validations will be performed on polystyrene bead populations whose size distributions resemble those of cell organelles. Unlike with the narrow bead distributions that are often used for calibration, we expect to see an order-of-magnitude improvement in the stability of the size estimates as the minimum angle decreases from 20 to 10 degrees. Scattering patterns will then be acquired and analyzed from single cells (EMT6 mouse cancer cells), both fixed and live, at multiple time points. Fixed cells, with no changes in organelle sizes over time, will be measured to determine the fluctuation level in estimated size distribution due to measurement imperfections alone. Subsequent measurements on live cells will determine whether there is a higher level of fluctuation that could be attributed to dynamic changes in organelle size. Studies on unperturbed cells are precursors to ones in which the effects of exogenous agents are monitored over time.

  10. Apparatus and method for measuring single cell and sub-cellular photosynthetic efficiency

    DOEpatents

    Davis, Ryan Wesley; Singh, Seema; Wu, Huawen

    2013-07-09

    Devices for measuring single cell changes in photosynthetic efficiency in algal aquaculture are disclosed that include a combination of modulated LED trans-illumination of different intensities with synchronized through objective laser illumination and confocal detection. Synchronization and intensity modulation of a dual illumination scheme were provided using a custom microcontroller for a laser beam block and constant current LED driver. Therefore, single whole cell photosynthetic efficiency, and subcellular (diffraction limited) photosynthetic efficiency measurement modes are permitted. Wide field rapid light scanning actinic illumination is provided for both by an intensity modulated 470 nm LED. For the whole cell photosynthetic efficiency measurement, the same LED provides saturating pulses for generating photosynthetic induction curves. For the subcellular photosynthetic efficiency measurement, a switched through objective 488 nm laser provides saturating pulses for generating photosynthetic induction curves. A second near IR LED is employed to generate dark adapted states in the system under study.

  11. Measuring single cell mass, volume, and density with dual suspended microchannel resonators.

    PubMed

    Bryan, Andrea K; Hecht, Vivian C; Shen, Wenjiang; Payer, Kristofor; Grover, William H; Manalis, Scott R

    2014-02-01

    Cell size, measured as either volume or mass, is a fundamental indicator of cell state. Far more tightly regulated than size is density, the ratio between mass and volume, which can be used to distinguish between cell populations even when volume and mass appear to remain constant. Here we expand upon a previous method for measuring cell density involving a suspended microchannel resonator (SMR). We introduce a new device, the dual SMR, as a high-precision instrument for measuring single-cell mass, volume, and density using two resonators connected by a serpentine fluidic channel. The dual SMR designs considered herein demonstrate the critical role of channel geometry in ensuring proper mixing and damping of pressure fluctuations in microfluidic systems designed for precision measurement. We use the dual SMR to compare the physical properties of two well-known cancer cell lines: human lung cancer cell H1650 and mouse lymphoblastic leukemia cell line L1210. PMID:24296901

  12. Measurement of Protein Tyrosine Phosphatase Activity in Single Cells by Capillary Electrophoresis

    PubMed Central

    Phillips, Ryan M.; Bair, Eric; Lawrence, David S.; Sims, Christopher E.; Allbritton, Nancy L.

    2013-01-01

    A fluorescent peptide substrate was used to measure dephosphorylation by protein tyrosine phosphatases (PTP) in cell lysates, and single cells and to investigate the effect of environmental toxins on PTP activity in these systems. Dephosphorylation of the substrate by PTPN1 and PTPN2 obeyed Michaelis-Menten kinetics, with KM values of 770 ± 250 nM and 290 ± 54 nM, respectively. Dose-response curves and IC50 values were determined for the inhibition of these two enzymes by the environmental toxins Zn2+ and 1,2-naphthoquinone, as well as pervanadate. In A431 cell lysates, the reporter was a poor substrate for peptidases (degradation rate of 100 ± 8.2 fmol min−1 mg−1) but an excellent substrate for phosphatases (dephosphorylation rate of 1.4 ± 0.3 nmol min−1 mg−1). Zn2+, 1,2-naphthoquinone and pervanadate inhibited dephosphorylation of the reporter in cell lysates with IC50 values of 470 nM, 35 μM, and 100 nM, respectively. Dephosphorylation of the reporter following loading into living single cells occurred at rates of at least 2 pmol min−1 mg−1. When single cells were exposed to 1,2-naphthoquinone (50 μM), Zn2+ (100 μM), and pervandate (1 mM), dephosphorylation was inhibited with median values and first and third quartile values of 41 (Q1 = 0%, Q3 = 96%), 50 (Q1 = 46%, Q3 = 74%), and 53% (Q1 = 36%, Q3 = 77%), respectively, demonstrating both the impact of these toxic exposures on cell signaling and the heterogeneity of response between cells. This approach will provide a valuable tool for the study of PTP dynamics, particularly in small, heterogeneous populations such as human biopsy specimens. PMID:23682679

  13. ATP Consumption of Eukaryotic Flagella Measured at a Single-Cell Level.

    PubMed

    Chen, Daniel T N; Heymann, Michael; Fraden, Seth; Nicastro, Daniela; Dogic, Zvonimir

    2015-12-15

    The motility of cilia and flagella is driven by thousands of dynein motors that hydrolyze adenosine triphosphate (ATP). Despite decades of genetic, biochemical, structural, and biophysical studies, some aspects of ciliary motility remain elusive, such as the regulation of beating patterns and the energetic efficiency of these nanomachines. In this study, we introduce an experimental method to measure ATP consumption of actively beating axonemes on a single-cell level. We encapsulated individual sea urchin sperm with demembranated flagellum inside water-in-oil emulsion droplets and measured the axoneme's ATP consumption by monitoring fluorescence intensity of a fluorophore-coupled reporter system for ATP turnover in the droplet. Concomitant phase contrast imaging allowed us to extract a linear dependence between the ATP consumption rate and the flagellar beating frequency, with ∼2.3 × 10(5) ATP molecules consumed per beat of a demembranated flagellum. Increasing the viscosity of the aqueous medium led to modified beating waveforms of the axonemes and to higher energy consumption per beat cycle. Our single-cell experimental platform provides both new insights, to our knowledge, into the beating mechanism of flagella and a powerful tool for future studies. PMID:26682814

  14. ATP Consumption of Eukaryotic Flagella Measured at a Single-Cell Level

    NASA Astrophysics Data System (ADS)

    Chen, Daniel T. N.; Heymann, Michael; Fraden, Seth; Nicastro, Daniela; Dogic, Zvonimir

    2015-12-01

    The motility of cilia and flagella is driven by thousands of dynein motors that hydrolyze adenosine triphosphate (ATP). Despite decades of genetic, biochemical, structural and biophysical studies, some aspects of ciliary motility remain elusive, such as the regulation of beating patterns and the energetic efficiency of these nanomachines. Here, we introduce an experimental method to measure ATP consumption of actively beating axonemes on a single-cell level. We encapsulated individual sea urchin sperm with demembranated flagellum inside water-in-oil emulsion droplets and measured the axonemes ATP consumption by monitoring fluorescence intensity of a fluorophore-coupled reporter system for ATP turnover in the droplet. Concomitant phase contrast imaging allowed us to extract a linear dependence between the ATP consumption rate and the flagellar beating frequency, with ~2.3e5 ATP molecules consumed per beat of a demembranated flagellum. Increasing the viscosity of the aqueous medium led to modified beating waveforms of the axonemes and to higher energy consumption per beat cycle. Our single-cell experimental platform provides both new insights into the beating mechanism of flagella and a powerful tool for future studies.

  15. Ultrasonic Scattering Measurements of a Live Single Cell at 86 MHz

    PubMed Central

    Lee, Changyang; Jung, Hayong; Lam, Kwok Ho; Yoon, Changhan; Shung, K. Kirk

    2016-01-01

    Cell separation and sorting techniques have been employed biomedical applications such as cancer diagnosis and cell gene expression analysis. The capability to accurately measure ultrasonic scattering properties from cells is crucial in making an ultrasonic cell sorter a reality if ultrasound scattering is to be used as the sensing mechanism as well. To assess the performance of sensing and identifying live single cells with high-frequency ultrasound, an 86-MHz lithium niobate press-focused single-element acoustic transducer was used in a high-frequency ultrasound scattering measurement system that was custom designed and developed for minimizing noise and allowing better mobility. Peak-to-peak echo amplitude, integrated backscatter (IB) coefficient, spectral parameters including spectral slope and intercept, and midband fit from spectral analysis of the backscattered echoes were measured and calculated from a live single cell of two different types on an agar surface: leukemia cells (K562 cells) and red blood cells (RBCs). The amplitudes of echo signals from K562 cells and RBCs were 48.25 ± 11.98 mVpp and 56.97 ± 7.53 mVpp, respectively. The IB coefficient was −89.39 ± 2.44 dB for K562 cells and −89.00 ± 1.19 dB for RBCs. The spectral slope and intercept were 0.30 ± 0.19 dB/MHz and −56.07 ± 17.17 dB, respectively, for K562 cells and 0.78 ± 0.092 dB/MHz and −98.18 ± 8.80 dB, respectively, for RBCs. Midband fits of K562 cells and RBCs were −31.02 ± 3.04 dB and −33.51 ± 1.55 dB, respectively. Acoustic cellular discrimination via these parameters was tested by Student’s t-test. Their values, except for the IB value, showed statistically significant difference (p < 0.001). This paper reports for the first time that ultrasonic scattering measurements can be made on a live single cell with a highly focused high-frequency ultrasound microbeam at 86 MHz. These results also suggest the feasibility of ultrasonic scattering as a sensing mechanism in

  16. Quantitative photoacoustics to measure single cell melanin production and nanoparticle attachment

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, Kiran; Eshein, Adam; Chandrasekhar, Anand; Viator, John A.

    2015-04-01

    Photoacoustics can be used as a label-free spectroscopic method of identifying pigmented proteins and characterizing their intracellular concentration over time in a single living cell. The authors use a microscopic laser irradiation system with a 5 ns, Q-switched laser focused onto single cells in order to collect photoacoustic responses of melanoma cells from the HS936 cell line and gold nanoparticle labeled breast cancer cells from the T47D cell line. The volume averaged intracellular concentration of melanin is found to range from 29-270 mM for single melanoma cells and the number of gold nanoparticles (AuNP) is shown to range from 850-5900 AuNPs/cell. Additionally, the melanin production response to UV-A light stimulus is measured in four melanoma cells to find a mass production rate of 5.7 pg of melanin every 15 min.

  17. Quantitative photoacoustics to measure single cell melanin production and nanoparticle attachment

    PubMed Central

    Bhattacharyya, Kiran; Eshein, Adam; Chandrasekhar, Anand; Viator, John A.

    2015-01-01

    Photoacoustics can be used as a label-free spectroscopic method of identifying pigmented proteins and characterizing their intracellular concentration over time in a single living cell. The authors use a microscopic laser irradiation system with a 5 ns, Q-switched laser focused onto single cells in order to collect photoacoustic responses of melanoma cells from the HS936 cell line and gold nanoparticle labeled breast cancer cells from the T47D cell line. The volume averaged intracellular concentration of melanin is found to range from 29–270mM for single melanoma cells and the number of gold nanoparticles (AuNP) is shown to range from 850–5900 AuNPs/cell. Additionally, the melanin production response to UV-A light stimulus is measured in four melanoma cells to find a mass production rate of 5.7 pg of melanin every 15 minutes. PMID:25803095

  18. PolyMUMPs MEMS device to measure mechanical stiffness of single cells in aqueous media

    NASA Astrophysics Data System (ADS)

    Warnat, S.; King, H.; Forbrigger, C.; Hubbard, T.

    2015-02-01

    A method of experimentally determining the mechanical stiffness of single cells by using differential displacement measurements in a two stage spring system is presented. The spring system consists of a known MEMS reference spring and an unknown cellular stiffness: the ratio of displacements is related to the ratio of stiffness. A polyMUMPs implementation for aqueous media is presented and displacement measurements made from optical microphotographs using a FFT based displacement method with a repeatability of ~20 nm. The approach was first validated on a MEMS two stage spring system of known stiffness. The measured stiffness ratios of control structures (i) MEMS spring systems and (ii) polystyrene microspheres were found to agree with theoretical values. Mechanical tests were then performed on Saccharomyces cerevisiae (Baker’s yeast) in aqueous media. Cells were placed (using a micropipette) inside MEMS measuring structures and compressed between two jaws using an electrostatic actuator and displacements measured. Tested cells showed stiffness values between 5.4 and 8.4 N m-1 with an uncertainty of 11%. In addition, non-viable cells were tested by exposing viable cells to methanol. The resultant mean cell stiffness dropped by factor of 3 × and an explicit discrimination between viable and non-viable cells based on mechanical stiffness was seen.

  19. The physical origins of transit time measurements for rapid, single cell mechanotyping.

    PubMed

    Nyberg, Kendra D; Scott, Michael B; Bruce, Samuel L; Gopinath, Ajay B; Bikos, Dimitri; Mason, Thomas G; Kim, Jin Woong; Choi, Hong Sung; Rowat, Amy C

    2016-08-16

    The mechanical phenotype or 'mechanotype' of cells is emerging as a potential biomarker for cell types ranging from pluripotent stem cells to cancer cells. Using a microfluidic device, cell mechanotype can be rapidly analyzed by measuring the time required for cells to deform as they flow through constricted channels. While cells typically exhibit deformation timescales, or transit times, on the order of milliseconds to tens of seconds, transit times can span several orders of magnitude and vary from day to day within a population of single cells; this makes it challenging to characterize different cell samples based on transit time data. Here we investigate how variability in transit time measurements depends on both experimental factors and heterogeneity in physical properties across a population of single cells. We find that simultaneous transit events that occur across neighboring constrictions can alter transit time, but only significantly when more than 65% of channels in the parallel array are occluded. Variability in transit time measurements is also affected by the age of the device following plasma treatment, which could be attributed to changes in channel surface properties. We additionally investigate the role of variability in cell physical properties. Transit time depends on cell size; by binning transit time data for cells of similar diameters, we reduce measurement variability by 20%. To gain further insight into the effects of cell-to-cell differences in physical properties, we fabricate a panel of gel particles and oil droplets with tunable mechanical properties. We demonstrate that particles with homogeneous composition exhibit a marked reduction in transit time variability, suggesting that the width of transit time distributions reflects the degree of heterogeneity in subcellular structure and mechanical properties within a cell population. Our results also provide fundamental insight into the physical underpinnings of transit measurements

  20. Measuring activity in the ubiquitin-proteasome system: From large scale discoveries to single cells analysis

    PubMed Central

    Melvin, Adam T.; Woss, Gregery S.; Park, Jessica H.; Waters, Marcey L.; Allbritton, Nancy L.

    2013-01-01

    The ubiquitin proteasome system (UPS) is the primary pathway responsible for the recognition and degradation of misfolded, damaged, or tightly regulated proteins in addition to performing essential roles in DNA repair, cell cycle regulation, cell migration, and the immune response. While traditional biochemical techniques have proven useful in the identification of key proteins involved in this pathway, the implementation of novel reporters responsible for measuring enzymatic activity of the UPS have provided valuable insight into the effectiveness of therapeutics and role of the UPS in various human diseases such as multiple myeloma and Huntington’s disease. These reporters, usually consisting of a recognition sequences fused to an analytical handle, are designed to specifically evaluate enzymatic activity of certain members of the UPS including the proteasome, E3 ubiquitin ligases, and deubiquitinating enzymes (DUBs). This review highlights the more commonly used reporters employed in a variety of scenarios ranging from high-throughput screening of novel inhibitors to single cell microscopy techniques measuring E3 ligase or proteasome activity. Finally, recent work is presented highlighting the development of novel degron-based substrate designed to overcome the limitations of current reporting techniques in measuring E3 ligase and proteasome activity in patient samples. PMID:23686610

  1. Oxygen pressure measurement using singlet oxygen emission

    SciTech Connect

    Khalil, Gamal E.; Chang, Alvin; Gouterman, Martin; Callis, James B.; Dalton, Larry R.; Turro, Nicholas J.; Jockusch, Steffen

    2005-05-15

    Pressure sensitive paint (PSP) provides a visualization of two-dimensional pressure distributions on airfoil and model automobile surfaces. One type of PSP utilizes platinum tetra(pentafluorophenyl)porphine (PtTFPP) dissolved in a fluoro-polymer film. Since the intense 650 nm triplet emission of PtTFPP is quenched by ground state oxygen, it is possible to measure two-dimensional oxygen concentration from the 650 nm emission intensity using a Stern-Volmer-type relationship. This article reports an alternative luminescence method to measure oxygen concentration based on the porphyrin-sensitized 1270 nm singlet oxygen emission, which can be imaged with an InGaAs near infrared camera. This direct measurement of oxygen emission complements and further validates the oxygen measurement based on PtTFPP phosphorescence quenching. Initial success at obtaining a negative correlation between the 650 nm PtTFPP emission and the 1270 nm O{sub 2} emission in solution led us to additional two-dimensional film studies using surfaces coated with PtTFPP, MgTFPP, and H{sub 2}TFPP in polymers in a pressure and temperature controlled chamber.

  2. Parallel measurement of dynamic changes in translation rates in single cells

    PubMed Central

    Han, Kyuho; Jaimovich, Ariel; Dey, Gautam; Ruggero, Davide; Meyuhas, Oded; Sonenberg, Nahum; Meyer, Tobias

    2014-01-01

    Protein concentrations are often regulated by dynamic changes in translation rates. Nevertheless, it has been challenging to directly monitor changes in translation in living cells. We have developed a reporter system to measure real-time changes of translation rates in human or mouse individual cells by conjugating translation regulatory motifs to sequences encoding a nuclear targeted fluorescent protein and a controllable destabilization domain. Application of the method showed that individual cells undergo marked fluctuations in the translation rate of mRNAs whose 5′ terminal oligopyrimidine (5′ TOP) motif regulates the synthesis of ribosomal proteins. Furthermore, we show that small reductions in amino acid levels signal through different mTOR-dependent pathways to control TOP mRNA translation, whereas larger reductions in amino acid levels control translation through eIF2A. Our study demonstrates that dynamic measurements of single-cell activities of translation regulatory motifs can be used to identify and investigate fundamental principles of translation. PMID:24213167

  3. Single Cell Mass Cytometry Adapted to Measurements of the Cell Cycle1

    PubMed Central

    Behbehani, Gregory K.; Bendall, Sean C.; Clutter, Matthew R.; Fantl, Wendy J.; Nolan, Garry P.

    2013-01-01

    Mass cytometry is a recently introduced technology that utilizes transition element isotope-tagged antibodies for protein detection on a single-cell basis. By circumventing the limitations of emission spectral overlap associated with fluorochromes utilized in traditional flow cytometry, mass cytometry currently allows measurement of up to 40 parameters per cell. Recently a comprehensive mass cytometry analysis was described for the hematopoietic differentiation program in human bone marrow from a healthy donor. The present study describes approaches to delineate cell cycle stages utilizing iododeoxyuridine (IdU) to mark cells in S phase, simultaneously with antibodies against cyclin B1, cyclin A, and phosphorylated histone H3 (S28) that characterize the other cell cycle phases. Protocols were developed in which an antibody against phosphorylated retinoblastoma protein (Rb) at serines 807 and 811 was used to separate cells in G0 and G1 phases of the cell cycle. This mass cytometry method yielded cell cycle distributions of both normal and cancer cell populations that were equivalent to those obtained by traditional fluorescence cytometry techniques. We applied this to map the cell cycle phases of cells spanning the hematopoietic hierarchy in healthy human bone marrow as a prelude to later studies with cancers and other disorders of this lineage. PMID:22693166

  4. SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression.

    PubMed

    Nakamura, Tomonori; Yabuta, Yukihiro; Okamoto, Ikuhiro; Aramaki, Shinya; Yokobayashi, Shihori; Kurimoto, Kazuki; Sekiguchi, Kiyotoshi; Nakagawa, Masato; Yamamoto, Takuya; Saitou, Mitinori

    2015-05-19

    Single-cell mRNA sequencing (RNA-seq) methods have undergone rapid development in recent years, and transcriptome analysis of relevant cell populations at single-cell resolution has become a key research area of biomedical sciences. We here present single-cell mRNA 3-prime end sequencing (SC3-seq), a practical methodology based on PCR amplification followed by 3-prime-end enrichment for highly quantitative, parallel and cost-effective measurement of gene expression in single cells. The SC3-seq allows excellent quantitative measurement of mRNAs ranging from the 10,000-cell to 1-cell level, and accordingly, allows an accurate estimate of the transcript levels by a regression of the read counts of spike-in RNAs with defined copy numbers. The SC3-seq has clear advantages over other typical single-cell RNA-seq methodologies for the quantitative measurement of transcript levels and at a sequence depth required for the saturation of transcript detection. The SC3-seq distinguishes four distinct cell types in the peri-implantation mouse blastocysts. Furthermore, the SC3-seq reveals the heterogeneity in human-induced pluripotent stem cells (hiPSCs) cultured under on-feeder as well as feeder-free conditions, demonstrating a more homogeneous property of the feeder-free hiPSCs. We propose that SC3-seq might be used as a powerful strategy for single-cell transcriptome analysis in a broad range of investigations in biomedical sciences. PMID:25722368

  5. SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression

    PubMed Central

    Nakamura, Tomonori; Yabuta, Yukihiro; Okamoto, Ikuhiro; Aramaki, Shinya; Yokobayashi, Shihori; Kurimoto, Kazuki; Sekiguchi, Kiyotoshi; Nakagawa, Masato; Yamamoto, Takuya; Saitou, Mitinori

    2015-01-01

    Single-cell mRNA sequencing (RNA-seq) methods have undergone rapid development in recent years, and transcriptome analysis of relevant cell populations at single-cell resolution has become a key research area of biomedical sciences. We here present single-cell mRNA 3-prime end sequencing (SC3-seq), a practical methodology based on PCR amplification followed by 3-prime-end enrichment for highly quantitative, parallel and cost-effective measurement of gene expression in single cells. The SC3-seq allows excellent quantitative measurement of mRNAs ranging from the 10,000-cell to 1-cell level, and accordingly, allows an accurate estimate of the transcript levels by a regression of the read counts of spike-in RNAs with defined copy numbers. The SC3-seq has clear advantages over other typical single-cell RNA-seq methodologies for the quantitative measurement of transcript levels and at a sequence depth required for the saturation of transcript detection. The SC3-seq distinguishes four distinct cell types in the peri-implantation mouse blastocysts. Furthermore, the SC3-seq reveals the heterogeneity in human-induced pluripotent stem cells (hiPSCs) cultured under on-feeder as well as feeder-free conditions, demonstrating a more homogeneous property of the feeder-free hiPSCs. We propose that SC3-seq might be used as a powerful strategy for single-cell transcriptome analysis in a broad range of investigations in biomedical sciences. PMID:25722368

  6. Single cell measurement of telomerase expression and splicing using microfluidic emulsion cultures

    PubMed Central

    Novak, Richard; Hart, Kristina; Mathies, Richard A.

    2015-01-01

    Telomerase is a reverse transcriptase that maintains telomeres on the ends of chromosomes, allowing rapidly dividing cells to proliferate while avoiding senescence and apoptosis. Understanding telomerase gene expression and splicing at the single cell level could yield insights into the roles of telomerase during normal cell growth as well as cancer development. Here we use droplet-based single cell culture followed by single cell or colony transcript abundance analysis to investigate the relationship between cell growth and transcript abundance of the telomerase genes encoding the RNA component (hTR) and protein component (hTERT) as well as hTERT splicing. Jurkat and K562 cells were examined under normal cell culture conditions and during exposure to curcumin, a natural compound with anti-carcinogenic and telomerase activity-reducing properties. Individual cells predominantly express single hTERT splice variants, with the α+/β− variant exhibiting significant transcript abundance bimodality that is sustained through cell division. Sub-lethal curcumin exposure results in reduced bimodality of all hTERT splice variants and significant upregulation of alpha splicing, suggesting a possible role in cellular stress response. The single cell culture and transcript abundance analysis method presented here provides the tools necessary for multiparameter single cell analysis which will be critical for understanding phenotypes of heterogeneous cell populations, disease cell populations and their drug response. PMID:26202962

  7. Nanowell-Based Immunoassays for Measuring Single-Cell Secretion: Characterization of Transport and Surface Binding

    PubMed Central

    2015-01-01

    Arrays of subnanoliter wells (nanowells) provide a useful system to isolate single cells and analyze their secreted proteins. Two general approaches have emerged: one that uses open arrays and local capture of secreted proteins, and a second (called microengraving) that relies on closed arrays to capture secreted proteins on a solid substrate, which is subsequently removed from the array. However, the design and operating parameters for efficient capture from these two approaches to analyze single-cell secretion have not been extensively considered. Using numerical simulations, we analyzed the operational envelope for both open and closed formats, as a function of the spatial distribution of capture ligands, their affinities for the protein, and the rates of single-cell secretion. Based on these analyses, we present a modified approach to capture secreted proteins in-well for highly active secreting cells. This simple method for in-well detection should facilitate rapid identification of cell lines with high specific productivities. PMID:25347613

  8. Direct Measurement of Aluminum Uptake and Distribution in Single Cells of Chara corallina1

    PubMed Central

    Taylor, Gregory J.; McDonald-Stephens, Julie L.; Hunter, Douglas B.; Bertsch, Paul M.; Elmore, David; Rengel, Zdenko; Reid, Robert J.

    2000-01-01

    Quantitative information on the uptake and distribution of Al at the cellular level is required to understand mechanisms of Al toxicity, but direct measurement of uptake across the plasma membrane has remained elusive. We measured rates of Al transport across membranes in single cells of Chara corallina using the rare 26Al isotope, an emerging technology (accelerator mass spectrometry), and a surgical technique for isolating subcellular compartments. Accumulation of Al in the cell wall dominated total uptake (71–318 μg m−2 min−1), although transport across the plasma membrane was detectable (71–540 ng m−2 min−1) within 30 min of exposure. Transport across the tonoplast was initially negligible, but accelerated to rates approximating uptake across the plasma membrane. The avacuolate protoplasm showed signs of saturation after 60 min, but continued movement across the plasma membrane was supported by sequestration in the vacuole. Saturation of all compartments was observed after 12 to 24 h. Accumulation of Al in the cell wall reflected variation in {Al3+} induced by changes in Al supply or complexing ligands, but was unaffected by pH. In contrast, transport across the plasma membrane peaked at pH 4.3 and increased when {Al3+} was reduced by complexing ligands. Cold temperature (4°C) reduced accumulation in the cell wall and protoplasm, whereas 2,4-dinitrophenol and m-chlorocarbonylcyanidephenyl hydrazone increased membrane transport by 12- to 13-fold. Our data suggest that the cell wall is the major site of Al accumulation. Nonetheless, membrane transport occurs within minutes of exposure and is supported by subsequent sequestration in the vacuole. The rapid delivery of Al to the protoplasm suggests that intracellular lesions may be possible. PMID:10889247

  9. Measurement of free cytosolic calcium in single cells: method and application.

    PubMed

    Raue, F; Zink, A

    1992-05-01

    Intracellular calcium [Ca2+]i acts as an important intracellular messenger system for secretion and synthesis, cell growth and differentiation. In order to demonstrate definitively that a change in [Ca2+]i is responsible for a physiological event, one has to measure [Ca2+]i directly within intact cells and correlate the time course of any [Ca2+]i changes with the biological response. Measurement of [Ca2+]i was done in a single cell preloaded with fluorescent Ca indicator fura2 using a fluorescent unit (lonoquant) consisting of an inverted microscope (Zeiss IM 35) equipped with a mercury lamp and a rotating filter wheel containing filters at wavelengths of 340 and 380 nm. Cells were alternately excited and emission signals of fura 2-loaded cells were collected by a photomultiplier and recorded on-line on a computer screen. As a model system, the rat C-cell carcinoma cell line rMTC 6-23 secreting calcitonin was used. An acute elevation of extracellular calcium resulted in an increase in [Ca2+]i within 5 sec and rapid release of preformed calcitonin. This tight linkage between extracellular calcium and [Ca2+]i is mediated via Ca influx through voltage-dependent Ca channels. These channels are modulated by intracellular cAMP, yielding a rhythmic oscillation of [Ca2+]i, as well as by extracellular somatostatin blocking the Ca channel and the increase of [Ca2+]i via a pertussis toxin sensitive Gi protein. The change in [Ca2+]i is associated with changes in calcitonin secretion, confirming the stimulus secretion coupling via voltage-dependent Ca channels in C-cells. PMID:1354776

  10. Single Cell Multiplex Protein Measurements through Rare Earth Element Immunolabeling, Laser Capture Microdissection and Inductively Coupled Mass Spectrometry

    PubMed Central

    Liba, Amir; Wanagat, Jonathan

    2016-01-01

    Complex diseases such as heart disease, stroke, cancer, and aging are the primary causes of death in the US. These diseases cause heterogeneous conditions among cells, conditions that cannot be measured in tissue homogenates and require single cell approaches. Understanding protein levels within tissues is currently assayed using various molecular biology techniques (e.g., Western blots) that rely on milligram to gram quantities of tissue homogenates or immunofluorescent (IF) techniques that are limited by spectral overlap. Tissue homogenate studies lack references to tissue structure and mask signals from individual or rare cellular events. Novel techniques are required to bring protein measurement sensitivity to the single cell level and offer spatiotemporal resolution and scalability. We are developing a novel approach to protein quantification by exploiting the inherently low concentration of rare earth elements (REE) in biological systems. By coupling REE-antibody immunolabeling of cells with laser capture microdissection (LCM) and ICP-QQQ, we are achieving multiplexed protein measurement in histological sections of single cells. This approach will add to evolving single cell techniques and our ability to understand cellular heterogeneity in complex biological systems and diseases.

  11. Electroporation followed by electrochemical measurement of quantal transmitter release from single cells using a patterned microelectrode

    PubMed Central

    Ghosh, Jaya; Liu, Xin; Gillis, Kevin D.

    2013-01-01

    An electrochemical microelectrode located immediately adjacent to a single neuroendocrine cell can record spikes of amperometric current that result from exocytosis of oxidizable transmitter from individual vesicles, i.e., quantal exocytosis. Here, we report the development of an efficient method where the same electrochemical microelectrode is used to electropermeabilize an adjacent chromaffin cell and then measure the consequent quantal catecholamine release using amperometry. Trains of voltage pulses, 5–7 V in amplitude and 0.1–0.2 ms in duration, were used to reliably trigger release from cells using gold electrodes. Amperometric spikes induced by electropermeabilization had similar areas, peak heights and durations as amperometric spikes elicited by depolarizing high K+ solutions, therefore release occurs from individual secretory granules. Uptake of trypan blue stain into cells demonstrated that the plasma membrane is permeabilized by the voltage stimulus. Voltage pulses did not degrade the electrochemical sensitivity of the electrodes assayed using a test analyte. Surprisingly, robust quantal release was elicited upon electroporation in the absence of Ca2+ in the bath solution (0 Ca2+/5 mM EGTA). In contrast, electropermeabilization-induced transmitter release required Cl− in the bath solution in that bracketed experiments demonstrated a steep dependence of the rate of electropermeabilization-induced transmitter release on [Cl−] between 2 and 32 mM. Using the same electrochemical electrode to electroporate and record quantal release of catecholamines from an individual chromaffin cell allows precise timing of the stimulus, stimulation of a single cell at a time, and can be used to load membrane-impermeant substances into a cell. PMID:23598689

  12. Single cell adhesion force measurement for cell viability identification using an AFM cantilever-based micro putter

    NASA Astrophysics Data System (ADS)

    Shen, Yajing; Nakajima, Masahiro; Kojima, Seiji; Homma, Michio; Kojima, Masaru; Fukuda, Toshio

    2011-11-01

    Fast and sensitive cell viability identification is a key point for single cell analysis. To address this issue, this paper reports a novel single cell viability identification method based on the measurement of single cell shear adhesion force using an atomic force microscopy (AFM) cantilever-based micro putter. Viable and nonviable yeast cells are prepared and put onto three kinds of substrate surfaces, i.e. tungsten probe, gold and ITO substrate surfaces. A micro putter is fabricated from the AFM cantilever by focused ion beam etching technique. The spring constant of the micro putter is calibrated using the nanomanipulation approach. The shear adhesion force between the single viable or nonviable cell and each substrate is measured using the micro putter based on the nanorobotic manipulation system inside an environmental scanning electron microscope. The adhesion force is calculated based on the deflection of the micro putter beam. The results show that the adhesion force of the viable cell to the substrate is much larger than that of the nonviable cell. This identification method is label free, fast, sensitive and can give quantitative results at the single cell level.

  13. An automatic measure for classifying clusters of suspected spikes into single cells versus multiunits

    NASA Astrophysics Data System (ADS)

    Tankus, Ariel; Yeshurun, Yehezkel; Fried, Itzhak

    2009-10-01

    While automatic spike sorting has been investigated for decades, little attention has been allotted to consistent evaluation criteria that will automatically determine whether a cluster of spikes represents the activity of a single cell or a multiunit. Consequently, the main tool for evaluation has remained visual inspection by a human. This paper quantifies the visual inspection process. The results are well-defined criteria for evaluation, which are mainly based on visual features of the spike waveform, and an automatic adaptive algorithm that learns the classification by a given human and can apply similar visual characteristics for classification of new data. To evaluate the suggested criteria, we recorded the activity of 1652 units (single cells and multiunits) from the cerebrum of 12 human patients undergoing evaluation for epilepsy surgery requiring implantation of chronic intracranial depth electrodes. The proposed method performed similar to human classifiers and obtained significantly higher accuracy than two existing methods (three variants of each). Evaluation on two synthetic datasets is also provided. The criteria are suggested as a standard for evaluation of the quality of separation that will allow comparison between different studies. The proposed algorithm is suitable for real-time operation and as such may allow brain-computer interfaces to treat single cells differently than multiunits.

  14. An automatic measure for classifying clusters of suspected spikes into single cells versus multiunits

    PubMed Central

    Tankus, Ariel; Yeshurun, Yehezkel; Fried, Itzhak

    2010-01-01

    While automatic spike sorting has been investigated for decades, little attention has been allotted to consistent evaluation criteria that will automatically determine whether a cluster of spikes represents the activity of a single cell or a multiunit. Consequently, the main tool for evaluation has remained visual inspection by a human. This paper quantifies the visual inspection process. The results are well-defined criteria for evaluation, which are mainly based on visual features of the spike waveform, and an automatic adaptive algorithm that learns the classification by a given human and can apply similar visual characteristics for classification of new data. To evaluate the suggested criteria, we recorded the activity of 1652 units (single cells and multiunits) from the cerebrum of 12 human patients undergoing evaluation for epilepsy surgery requiring implantation of chronic intracranial depth electrodes. The proposed method performed similar to human classifiers and obtained significantly higher accuracy than two existing methods (three variants of each). Evaluation on two synthetic datasets is also provided. The criteria are suggested as a standard for evaluation of the quality of separation that will allow comparison between different studies. The proposed algorithm is suitable for real-time operation and as such may allow brain–computer interfaces to treat single cells differently than multiunits. PMID:19667458

  15. Single cell studies of mouse embryonic stem cell (mESC) differentiation by electrical impedance measurements in a microfluidic device.

    PubMed

    Zhou, Ying; Basu, Srinjan; Laue, Ernest; Seshia, Ashwin A

    2016-07-15

    Biological populations of cells show considerable cell-to-cell variability. Study of single cells and analysis of cell heterogeneity are considered to be critical in understanding biological processes such as stem cell differentiation and cancer development. Recent advances in lab-on-a-chip techniques have allowed single-cell capture in microfluidic channels with the possibility of precise environmental control and high throughput of experiments with minimal usage of samples and reagents. In recent years, label-free techniques such as electrical impedance spectroscopy have emerged as a non-invasive approach to studying cell properties. In this study, we have designed and fabricated a microfluidic device that combines hydrodynamic trapping of single cells in pre-defined locations with the capability of running electrical impedance measurements within the same device. We have measured mouse embryonic stem cells (mESCs) at different states during differentiation (t=0h, 24h and 48h) and quantitatively analysed the changes in electrical parameters of cells during differentiation. A marked increase in the magnitude of the cell impedance is found during cell differentiation, which can be attributed to an increase in cell size. The analysis of the measurements shows that the nucleus-to-cytoplasm ratio decreases during this process. The degree of cell heterogeneity is observed to be the highest when the cells are at the transition state (24h), compare with cells at undifferentiated (0h) and fully differentiated (48h) states. The device enables highly efficient single cell trapping and provides sensitive, label-free electrical impedance measurements of individual cells, enabling the possibility of quantitatively analysing their physical state as well as studying the associated heterogeneity of a cell population. PMID:26963790

  16. Single cell studies of mouse embryonic stem cell (mESC) differentiation by electrical impedance measurements in a microfluidic device

    PubMed Central

    Zhou, Ying; Basu, Srinjan; Laue, Ernest; Seshia, Ashwin A.

    2016-01-01

    Biological populations of cells show considerable cell-to-cell variability. Study of single cells and analysis of cell heterogeneity are considered to be critical in understanding biological processes such as stem cell differentiation and cancer development. Recent advances in lab-on-a-chip techniques have allowed single-cell capture in microfluidic channels with the possibility of precise environmental control and high throughput of experiments with minimal usage of samples and reagents. In recent years, label-free techniques such as electrical impedance spectroscopy have emerged as a non-invasive approach to studying cell properties. In this study, we have designed and fabricated a microfluidic device that combines hydrodynamic trapping of single cells in pre-defined locations with the capability of running electrical impedance measurements within the same device. We have measured mouse embryonic stem cells (mESCs) at different states during differentiation (t=0 h, 24 h and 48 h) and quantitatively analysed the changes in electrical parameters of cells during differentiation. A marked increase in the magnitude of the cell impedance is found during cell differentiation, which can be attributed to an increase in cell size. The analysis of the measurements shows that the nucleus-to-cytoplasm ratio decreases during this process. The degree of cell heterogeneity is observed to be the highest when the cells are at the transition state (24 h), compare with cells at undifferentiated (0 h) and fully differentiated (48 h) states. The device enables highly efficient single cell trapping and provides sensitive, label-free electrical impedance measurements of individual cells, enabling the possibility of quantitatively analysing their physical state as well as studying the associated heterogeneity of a cell population. PMID:26963790

  17. Measurement of enzyme activity in single cells by voltammetry using a microcell with a positionable dual electrode.

    PubMed

    Gao, Ning; Zhao, Minghui; Zhang, Xiaoli; Jin, Wenrui

    2006-01-01

    The electrochemical single-cell analysis for enzyme activity was developed using microcells on a microcell array coupled with a positionable dual microelectrode. The microcell array with the nanoliter-scale microcells was constructed using simple chemical etching without photolithographic techniques. The positionable dual microelectrodes consisted of the nanometer-to-micrometer-radius Au disk working electrode and a approximately 80-microm-radius Ag/AgCl reference electrode. Peroxidase was chosen as the model enzyme. Factors that concern electrochemical single-cell analysis in microcells such as solution evaporation, interference of soluble oxygen, electrode size, solution volume, and electrode fouling were investigated and discussed. The 20 or 100 nL of detection volume was found to be suitable for peroxidase determination in single neutrophils or single acute promyelocytic leukemia cells without interference from intracellular macromolecules and electrode fouling, when the dual electrode with a 10-microm-radius Au disk working electrode was used. Cells were perforated with digitonin before transferring them into the microcells, to lyse cells easily. The perforated cells were transferred into the microcells by pushing a microscope slide on a drop of the cell suspension on the microcell array. After a single cell in the microcell was lysed using a freeze-thawing technique and allowed to dry, physiological buffer saline containing 2.0 x 10(-3) mol/L hydroquinone and 2.0 x 10(-3) mol/L H2O2 as the substrates of the enzyme-catalyzed reaction was added. The microcell array was positioned in a constant-humidity chamber to prevent evaporation. Then the dual electrode was inserted into the microcell by means of a scanning electrochemical microscope and the product benzoquinone of the enzyme-catalyzed reaction was voltammetrically detected. Peroxidase activity could be quantified using the steady-state current on the voltammogram after subtracting the blank and using the

  18. Comparison between steady-state and dynamic I-V measurements from a single-cell thermionic fuel element

    SciTech Connect

    Wernsman, B.

    1997-01-01

    A comparison between steady-state and dynamic I-V measurements from a single-cell thermionic fuel element (TFE) is made. The single-cell TFE used in this study is the prototype for the 40kW{sub e} space nuclear power system that is similar to the 6kW{sub e} TOPAZ-II. The steady-state I-V measurements influence the emitter temperature due to electron cooling. Therefore, to eliminate the steady-state I-V measurement influence on the TFE and provide a better understanding of the behavior of the thermionic energy converter and TFE characteristics, dynamic I-V measurements are made. The dynamic I-V measurements are made at various input power levels, cesium pressures, collector temperatures, and steady-state current levels. From these measurements, it is shown that the dynamic I-V{close_quote}s do not change the TFE characteristics at a given operating point. Also, the evaluation of the collector work function from the dynamic I-V measurements shows that the collector optimization is not due to a minimum in the collector work function but due to an emission optimization. Since the dynamic I-V measurements do not influence the TFE characteristics, it is believed that these measurements can be done at a system level to understand the influence of TFE placement in the reactor as a function of the core thermal distribution. {copyright} {ital 1997 American Institute of Physics.}

  19. Comparison between steady-state and dynamic I-V measurements from a single-cell thermionic fuel element

    SciTech Connect

    Wernsman, Bernard

    1997-01-10

    A comparison between steady-state and dynamic I-V measurements from a single-cell thermionic fuel element (TFE) is made. The single-cell TFE used in this study is the prototype for the 40 kW{sub e} space nuclear power system that is similar to the 6 kW{sub e} TOPAZ-II. The steady-state I-V measurements influence the emitter temperature due to electron cooling. Therefore, to eliminate the steady-state I-V measurement influence on the TFE and provide a better understanding of the behavior of the thermionic energy converter and TFE characteristics, dynamic I-V measurements are made. The dynamic I-V measurements are made at various input power levels, cesium pressures, collector temperatures, and steady-state current levels. From these measurements, it is shown that the dynamic I-V's do not change the TFE characteristics at a given operating point. Also, the evaluation of the collector work function from the dynamic I-V measurements shows that the collector optimization is not due to a minimum in the collector work function but due to an emission optimization. Since the dynamic I-V measurements do not influence the TFE characteristics, it is believed that these measurements can be done at a system level to understand the influence of TFE placement in the reactor as a function of the core thermal distribution.

  20. Tissue oxygen measurement system

    NASA Technical Reports Server (NTRS)

    Soller, Babs R. (Inventor)

    2004-01-01

    A device and method in accordance with the invention for determining the oxygen partial pressure (PO.sub.2) of a tissue by irradiating the tissue with optical radiation such that the light is emitted from the tissue, and by collecting the reflected or transmitted light from the tissue to form an optical spectrum. A spectral processor determines the PO.sub.2 level in tissue by processing this spectrum with a previously-constructed spectral calibration model. The tissue may, for example, be disposed underneath a covering tissue, such as skin, of a patient, and the tissue illuminated and light collected through the skin. Alternatively, direct tissue illumination and collection may be effected with a hand-held or endoscopic probe. A preferred system also determines pH from the same spectrum, and the processor may determine critical conditions and issue warnings based on parameter values.

  1. Single-Cell Measurements of IgE-Mediated FcεRI Signaling Using an Integrated Microfluidic Platform

    SciTech Connect

    Liu, Yanli; Barua, Dipak; Liu, Peng; Wilson, Bridget S.; Oliver, Janet M.; Hlavacek, William S.; Singh, Anup K.

    2013-03-27

    Heterogeneity in responses of cells to a stimulus, such as a pathogen or allergen, can potentially play an important role in deciding the fate of the responding cell population and the overall systemic response. Measuring heterogeneous responses requires tools capable of interrogating individual cells. Cell signaling studies commonly do not have single-cell resolution because of the limitations of techniques used such as Westerns, ELISAs, mass spectrometry, and DNA microarrays. Microfluidics devices are increasingly being used to overcome these limitations. In this paper, we report on a microfluidic platform for cell signaling analysis that combines two orthogonal single-cell measurement technologies: on-chip flow cytometry and optical imaging. The device seamlessly integrates cell culture, stimulation, and preparation with downstream measurements permitting hands-free, automated analysis to minimize experimental variability. The platform was used to interrogate IgE receptor (FcεRI) signaling, which is responsible for triggering allergic reactions, in RBL-2H3 cells. Following on-chip crosslinking of IgE-FcεRI complexes by multivalent antigen, we monitored signaling events including protein phosphorylation, calcium mobilization and the release of inflammatory mediators. The results demonstrate the ability of our platform to produce quantitative measurements on a cell-by-cell basis from just a few hundred cells. Finally, model-based analysis of the Syk phosphorylation data suggests that heterogeneity in Syk phosphorylation can be attributed to protein copy number variations, with the level of Syk phosphorylation being particularly sensitive to the copy number of Lyn.

  2. Single-Cell Measurements of IgE-Mediated FcεRI Signaling Using an Integrated Microfluidic Platform

    DOE PAGESBeta

    Liu, Yanli; Barua, Dipak; Liu, Peng; Wilson, Bridget S.; Oliver, Janet M.; Hlavacek, William S.; Singh, Anup K.

    2013-03-27

    Heterogeneity in responses of cells to a stimulus, such as a pathogen or allergen, can potentially play an important role in deciding the fate of the responding cell population and the overall systemic response. Measuring heterogeneous responses requires tools capable of interrogating individual cells. Cell signaling studies commonly do not have single-cell resolution because of the limitations of techniques used such as Westerns, ELISAs, mass spectrometry, and DNA microarrays. Microfluidics devices are increasingly being used to overcome these limitations. In this paper, we report on a microfluidic platform for cell signaling analysis that combines two orthogonal single-cell measurement technologies: on-chipmore » flow cytometry and optical imaging. The device seamlessly integrates cell culture, stimulation, and preparation with downstream measurements permitting hands-free, automated analysis to minimize experimental variability. The platform was used to interrogate IgE receptor (FcεRI) signaling, which is responsible for triggering allergic reactions, in RBL-2H3 cells. Following on-chip crosslinking of IgE-FcεRI complexes by multivalent antigen, we monitored signaling events including protein phosphorylation, calcium mobilization and the release of inflammatory mediators. The results demonstrate the ability of our platform to produce quantitative measurements on a cell-by-cell basis from just a few hundred cells. Finally, model-based analysis of the Syk phosphorylation data suggests that heterogeneity in Syk phosphorylation can be attributed to protein copy number variations, with the level of Syk phosphorylation being particularly sensitive to the copy number of Lyn.« less

  3. Reversible coupling of individual phycobiliprotein isoforms during state transitions in the cyanobacterium Trichodesmium analysed by single-cell fluorescence kinetic measurements.

    PubMed

    Küpper, Hendrik; Andresen, Elisa; Wiegert, Susanna; Simek, Miloslav; Leitenmaier, Barbara; Setlík, Ivan

    2009-03-01

    In the non-heterocyst, marine cyanobacterium Trichodesmium nitrogen fixation is confined to the photoperiod and occurs coevally with oxygenic photosynthesis although nitrogenase is irreversibly inactivated by oxygen. In previous studies it was found that regulation of photosynthesis for nitrogen fixation involves Mehler reaction and various activity states with reversible coupling of photosynthetic components. We now investigated these activity states in more detail. Spectrally resolved fluorescence kinetic measurements of single cells revealed that they were related to alternate uncoupling and coupling of phycobilisomes from and to the photosystems, changing the effective cross-section of PSII. Therefore, we isolated and purified the phycobiliproteins of Trichodesmium via ion exchange chromatography and recorded their UV/VIS absorption, fluorescence excitation and fluorescence emission spectra. After describing these spectra by mathematical equations via the Gauss-Peak-Spectra method, we used them to deconvolute the in vivo fluorescence spectra of Trichodesmium cells. This revealed that the contribution of different parts of the phycobilisome antenna to fluorescence quenching changed during the daily activity cycle, and that individual phycobiliproteins can be reversibly coupled to the photosystems, while the expression levels of these proteins did not change much during the daily activity cycle. Thus we propose that variable phycobilisome coupling plays a key role in the regulation of photosynthesis for nitrogen fixation in Trichodesmium. PMID:19186173

  4. Measuring bacterial adhesion at environmental interfaces with single-cell and single-molecule techniques

    NASA Astrophysics Data System (ADS)

    Camesano, Terri A.; Liu, Yatao; Datta, Meera

    2007-06-01

    A synopsis is provided of techniques currently used to quantify the interactions between bacterial cells and surfaces. Focus is placed on techniques which allow for direct probing of nano, pico, or femto-scale interaction forces between bacteria and surfaces of relevance for environmental science and engineering. We focus on bacterial adhesion measurements and surface characterizations via techniques that measure forces on individual bacterial cells or cellular macromolecules, particularly atomic force microscopy (AFM) and related force spectroscopy. However, we also include overviews of other techniques useful for evaluating cellular forces, such as optical tweezers, evanescent wave scattering-based techniques (i.e. total internal reflection microscopy (TIRM) and total internal reflection aqueous fluorescence (TIRAF) microscopy) and the quartz crystal microbalance (QCM). These latter techniques, while most are not providing direct measurements of forces of adhesion, can be used to explain adhesion and interaction forces in bacterial systems. We review the operating principles, advantages and limitations of each technique, and key bacterial adhesion studies from each area are presented. Qualitative and quantitative methodologies for relating force measurements to bacterial attachment, particularly to bacterial retention in porous media, are discussed.

  5. Single Cell Measurement of Dopamine Release with Simultaneous Voltage-clamp and Amperometry

    PubMed Central

    Saha, Kaustuv; Swant, Jarod; Khoshbouei, Habibeh

    2012-01-01

    After its release into the synaptic cleft, dopamine exerts its biological properties via its pre- and post-synaptic targets1. The dopamine signal is terminated by diffusion2-3, extracellular enzymes4, and membrane transporters5. The dopamine transporter, located in the peri-synaptic cleft of dopamine neurons clears the released amines through an inward dopamine flux (uptake). The dopamine transporter can also work in reverse direction to release amines from inside to outside in a process called outward transport or efflux of dopamine5. More than 20 years ago Sulzer et al. reported the dopamine transporter can operate in two modes of activity: forward (uptake) and reverse (efflux)5. The neurotransmitter released via efflux through the transporter can move a large amount of dopamine to the extracellular space, and has been shown to play a major regulatory role in extracellular dopamine homeostasis6. Here we describe how simultaneous patch clamp and amperometry recording can be used to measure released dopamine via the efflux mechanism with millisecond time resolution when the membrane potential is controlled. For this, whole-cell current and oxidative (amperometric) signals are measured simultaneously using an Axopatch 200B amplifier (Molecular Devices, with a low-pass Bessel filter set at 1,000 Hz for whole-cell current recording). For amperometry recording a carbon fiber electrode is connected to a second amplifier (Axopatch 200B) and is placed adjacent to the plasma membrane and held at +700 mV. The whole-cell and oxidative (amperometric) currents can be recorded and the current-voltage relationship can be generated using a voltage step protocol. Unlike the usual amperometric calibration, which requires conversion to concentration, the current is reported directly without considering the effective volume7. Thus, the resulting data represent a lower limit to dopamine efflux because some transmitter is lost to the bulk solution. PMID:23207721

  6. Spatiotemporal activity patterns detected from single cell measurements from behaving animals

    NASA Astrophysics Data System (ADS)

    Villa, Alessandro E. P.; Tetko, Igor V.

    1999-03-01

    Precise temporal patterning of activity within and between neurons has been predicted on theoretical grounds, and found in the spike trains of neurons recorded from anesthetized and conscious animals, in association with sensor stimuli and particular phases of task performance. However, the functional significance of such patterning in the generation of behavior has not been confirmed. We recorded from multiple single neurons in regions of rat auditory cortex during the waiting period of a Go/NoGo task. During this time the animal waited for an auditory signal with high cognitive load. Of note is the fact that neural activity during the period analyzed was essentially stationary, with no event related variability in firing. Detected patterns therefore provide a measure of brain state that could not be addressed by standard methods relying on analysis of changes in mean discharge rate. The possibility is discussed that some patterns might reflect a preset bias to a particular response, formed in the waiting period. Others patterns might reflect a state of prior preparation of appropriate neural assemblies for analyzing a signal that is expected but of unknown behavioral valence.

  7. Multiphoton photochemical crosslinking-based fabrication of protein micropatterns with controllable mechanical properties for single cell traction force measurements.

    PubMed

    Tong, Ming Hui; Huang, Nan; Zhang, Wei; Zhou, Zhuo Long; Ngan, Alfonso Hing Wan; Du, Yanan; Chan, Barbara Pui

    2016-01-01

    Engineering 3D microstructures with predetermined properties is critical for stem cell niche studies. We have developed a multiphoton femtosecond laser-based 3D printing platform, which generates complex protein microstructures in minutes. Here, we used the platform to test a series of fabrication and reagent parameters in precisely controlling the mechanical properties of protein micropillars. Atomic force microscopy was utilized to measure the reduced elastic modulus of the micropillars, and transmission electron microscopy was used to visualize the porosity of the structures. The reduced elastic modulus of the micropillars associated positively and linearly with the scanning power. On the other hand, the porosity and pore size of the micropillars associated inversely and linearly with the scanning power and reagent concentrations. While keeping the elastic modulus constant, the stiffness of the micropillars was controlled by varying their height. Subsequently, the single cell traction forces of rabbit chondrocytes, human dermal fibroblasts, human mesenchymal stem cells, and bovine nucleus pulposus cells (bNPCs) were successfully measured by culturing the cells on micropillar arrays of different stiffness. Our results showed that the traction forces of all groups showed positive relationship with stiffness, and that the chondrocytes and bNPCs generated the highest and lowest traction forces, respectively. PMID:26817674

  8. Multiphoton photochemical crosslinking-based fabrication of protein micropatterns with controllable mechanical properties for single cell traction force measurements

    PubMed Central

    Tong, Ming Hui; Huang, Nan; Zhang, Wei; Zhou, Zhuo Long; Ngan, Alfonso Hing Wan; Du, Yanan; Chan, Barbara Pui

    2016-01-01

    Engineering 3D microstructures with predetermined properties is critical for stem cell niche studies. We have developed a multiphoton femtosecond laser-based 3D printing platform, which generates complex protein microstructures in minutes. Here, we used the platform to test a series of fabrication and reagent parameters in precisely controlling the mechanical properties of protein micropillars. Atomic force microscopy was utilized to measure the reduced elastic modulus of the micropillars, and transmission electron microscopy was used to visualize the porosity of the structures. The reduced elastic modulus of the micropillars associated positively and linearly with the scanning power. On the other hand, the porosity and pore size of the micropillars associated inversely and linearly with the scanning power and reagent concentrations. While keeping the elastic modulus constant, the stiffness of the micropillars was controlled by varying their height. Subsequently, the single cell traction forces of rabbit chondrocytes, human dermal fibroblasts, human mesenchymal stem cells, and bovine nucleus pulposus cells (bNPCs) were successfully measured by culturing the cells on micropillar arrays of different stiffness. Our results showed that the traction forces of all groups showed positive relationship with stiffness, and that the chondrocytes and bNPCs generated the highest and lowest traction forces, respectively. PMID:26817674

  9. Quantification of the specific membrane capacitance of single cells using a microfluidic device and impedance spectroscopy measurement.

    PubMed

    Tan, Qingyuan; Ferrier, Graham A; Chen, Brandon K; Wang, Chen; Sun, Yu

    2012-09-01

    The specific membrane capacitance (SMC) is an electrical parameter that correlates with both the electrical activity and morphology of the plasma membrane, which are physiological markers for cellular phenotype and health. We have developed a microfluidic device that enables impedance spectroscopy measurements of the SMC of single biological cells. Impedance spectra induced by single cells aspirated into the device are captured over a moderate frequency range (5 kHz-1 MHz). Maximum impedance sensitivity is achieved using a tapered microfluidic channel, which effectively routes electric fields across the cell membranes. The SMC is extracted by curve-fitting impedance spectra to an equivalent circuit model. From our measurement, acute myeloid leukemia (AML) cells are found to exhibit larger SMC values in hypertonic solutions as compared with those in isotonic solutions. In addition, AML cell phenotypes (AML2 and NB4) exhibiting varying metastatic potential yield distinct SMC values (AML2: 16.9 ± 1.9 mF/m(2) (n = 23); NB4: 22.5 ± 4.7 mF/m(2) (n = 23)). Three-dimensional finite element simulations of the microfluidic device confirm the feasibility of this approach. PMID:23940502

  10. Multiphoton photochemical crosslinking-based fabrication of protein micropatterns with controllable mechanical properties for single cell traction force measurements

    NASA Astrophysics Data System (ADS)

    Tong, Ming Hui; Huang, Nan; Zhang, Wei; Zhou, Zhuo Long; Ngan, Alfonso Hing Wan; Du, Yanan; Chan, Barbara Pui

    2016-01-01

    Engineering 3D microstructures with predetermined properties is critical for stem cell niche studies. We have developed a multiphoton femtosecond laser-based 3D printing platform, which generates complex protein microstructures in minutes. Here, we used the platform to test a series of fabrication and reagent parameters in precisely controlling the mechanical properties of protein micropillars. Atomic force microscopy was utilized to measure the reduced elastic modulus of the micropillars, and transmission electron microscopy was used to visualize the porosity of the structures. The reduced elastic modulus of the micropillars associated positively and linearly with the scanning power. On the other hand, the porosity and pore size of the micropillars associated inversely and linearly with the scanning power and reagent concentrations. While keeping the elastic modulus constant, the stiffness of the micropillars was controlled by varying their height. Subsequently, the single cell traction forces of rabbit chondrocytes, human dermal fibroblasts, human mesenchymal stem cells, and bovine nucleus pulposus cells (bNPCs) were successfully measured by culturing the cells on micropillar arrays of different stiffness. Our results showed that the traction forces of all groups showed positive relationship with stiffness, and that the chondrocytes and bNPCs generated the highest and lowest traction forces, respectively.

  11. Measuring Oxygen Isotopes with COSIMA

    NASA Astrophysics Data System (ADS)

    Paquette, J. A.; Engrand, C.; Stenzel, O.; Hilchenbach, M.

    2014-12-01

    Oxygen isotopes in a variety of solar system solids show non-mass-dependent fractionation, i.e. are fractionated along a slope = 1 line in a three isotope plot, rather than the equilibrium fractionation line whose slope is close to 0.5 (Clayton, 1973). Many models have been put forward to explain this observation, such as galactic chemical evolution (Clayton, 1988), photochemical self-shielding (Thiemens and Jackson, 1987; Clayton, 2002; Yurimoto and Kuramoto, 2004; Lyons and Young, 2005), quantum chemical explanations (Hathorn and Marcus, 1999, 2000; Gao and Marcus, 2002; Marcus, 2004), the processing of solids via nebular lightning (Nuth et al, 2011), and others. Some of the models were invalidated when the Genesis results showed that the oxygen isotopic fractionation of solar wind (and hence of the Sun) was relatively much richer in 16O than such bodies as the Earth or the Moon. Whatever the process that produced non-mass-dependent fractionation in some chondrules and calcium aluminum inclusions, its signature may also be detectable in other solar system solids. If at least some cometary dust was produced in the inner nebula and only later transported outward to be incorporated into comets, then such dust may also show some degree of non-mass-dependent fractionation. The COSIMA instrument on the Rosetta spacecraft (Kissel et al 2009) is a secondary ion mass spectrometer designed to measure the composition of cometary dust. Using calibration data from the COSIMA reference model and flight data if possible, measurement all three isotopes of oxygen will be attempted, and the results compared to other solar system bodies.

  12. Dielectrophoretic Microfluidic Chip Enables Single-Cell Measurements for Multidrug Resistance in Heterogeneous Acute Myeloid Leukemia Patient Samples.

    PubMed

    Khamenehfar, Avid; Gandhi, Maher K; Chen, Yuchun; Hogge, Donna E; Li, Paul C H

    2016-06-01

    The front-line treatment for adult acute myeloid leukemia (AML) is anthracycline-based combination chemotherapy. However, treatment outcomes remain suboptimal with relapses frequently observed. Among the mechanisms of treatment failure is multidrug resistance (MDR) mediated by the ABCB1, ABCC1, and ABCG2 drug-efflux transporters. Although genetic and phenotypic heterogeneity between leukemic blast cells is a well-recognized phenomenon, there remains minimal data on differences in MDR activity at the individual cell level. Specifically, functional assays that can distinguish the variability in MDR activity between individual leukemic blasts are lacking. Here, we outline a new dielectrophoretic (DEP) chip-based assay. This assay permits measurement of drug accumulation in single cells, termed same-single-cell analysis in the accumulation mode (SASCA-A). Initially, the assay was optimized in pretherapy samples from 20 adults with AML whose leukemic blasts had MDR activity against the anthracyline daunorubicin (DNR) tested using multiple MDR inhibitors. Parameters tested were initial drug accumulation, time to achieve signal saturation, fold-increase of DNR accumulation with MDR inhibition, ease of cell trapping, and ease of maintaining the trapped cells stationary. This enabled categorization into leukemic blast cells with MDR activity (MDR(+)) and leukemic blast cells without MDR activity (MDR(-ve)). Leukemic blasts could also be distinguished from benign white blood cells (notably these also lacked MDR activity). MDR(-ve) blasts were observed to be enriched in samples taken from patients who went on to enter complete remission (CR), whereas MDR(+) blasts were frequently observed in patients who failed to achieve CR following front-line chemotherapy. However, pronounced variability in functional MDR activity between leukemic blasts was observed, with MDR(+) cells not infrequently seen in some patients that went on to achieve CR. Next, we tested MDR activity in two

  13. Cell-specific localization of alkaloids in Catharanthus roseus stem tissue measured with Imaging MS and Single-cell MS.

    PubMed

    Yamamoto, Kotaro; Takahashi, Katsutoshi; Mizuno, Hajime; Anegawa, Aya; Ishizaki, Kimitsune; Fukaki, Hidehiro; Ohnishi, Miwa; Yamazaki, Mami; Masujima, Tsutomu; Mimura, Tetsuro

    2016-04-01

    Catharanthus roseus (L.) G. Don is a medicinal plant well known for producing antitumor drugs such as vinblastine and vincristine, which are classified as terpenoid indole alkaloids (TIAs). The TIA metabolic pathway in C. roseus has been extensively studied. However, the localization of TIA intermediates at the cellular level has not been demonstrated directly. In the present study, the metabolic pathway of TIA in C. roseus was studied with two forefront metabolomic techniques, that is, Imaging mass spectrometry (MS) and live Single-cell MS, to elucidate cell-specific TIA localization in the stem tissue. Imaging MS indicated that most TIAs localize in the idioblast and laticifer cells, which emit blue fluorescence under UV excitation. Single-cell MS was applied to four different kinds of cells [idioblast (specialized parenchyma cell), laticifer, parenchyma, and epidermal cells] in the stem longitudinal section. Principal component analysis of Imaging MS and Single-cell MS spectra of these cells showed that similar alkaloids accumulate in both idioblast cell and laticifer cell. From MS/MS analysis of Single-cell MS spectra, catharanthine, ajmalicine, and strictosidine were found in both cell types in C. roseus stem tissue, where serpentine was also accumulated. Based on these data, we discuss the significance of TIA synthesis and accumulation in the idioblast and laticifer cells of C. roseus stem tissue. PMID:27001858

  14. The Measurement of Dissolved Oxygen

    ERIC Educational Resources Information Center

    Thistlethwayte, D.; And Others

    1974-01-01

    Describes an experiment in environmental chemistry which serves to determine the dissolved oxygen concentration in both fresh and saline water. Applications of the method at the undergraduate and secondary school levels are recommended. (CC)

  15. Measuring tissue oxygen saturation using NIR spectroscopy

    NASA Astrophysics Data System (ADS)

    Sircan-Kucuksayan, Aslinur; Uyuklu, Mehmet; Canpolat, Murat

    2014-05-01

    Tissue oxygen saturation (StO2) is known quite useful parameter for medical applications. A spectroscopic method has been developed to diagnose pathologic tissues due to lack of normal blood circulation by measuring tissue oxygen saturation. In the study, human blood samples with different level of oxygen saturations have been prepared and spectra were taken using an optical fiber probe to investigate correlation between the oxygen saturations and the spectra. The experimental set up for the spectroscopic measurements was consists of a miniature NIR light spectrometer, an optical fiber probe, a halogen-tungsten light source and a laptop. A linear correlation between the oxygen saturation of the blood samples and the ratio of the light of wavelengths 660 nm to 790 nm has been found from the spectra. Then, oxygen saturations of the blood samples were estimated from the spectroscopic measurements within an error of 2.9%. Furthermore, it has been shown that the linear dependence between the ratio and the oxygen saturation of the blood samples was valid for the blood samples with different hematocrits. Tissue oxygen saturation has been estimated from the spectroscopic measurements were taken from the fingers of healthy volunteers using the correlation between the spectra and blood oxygen saturation. The tissue StO2 measured was 80% as expected. The technique developed to measure tissue oxygen saturation has potential to diagnose premalignant tissues, follow up prognosis of cancerous tissues, and evaluation of ischemia reperfusion tissues.

  16. Single-cell western blotting

    PubMed Central

    Hughes, Alex J.; Spelke, Dawn P.; Xu, Zhuchen; Kang, Chi-Chih; Schaffer, David V.; Herr, Amy E.

    2014-01-01

    To measure cell-to-cell variation in protein-mediated functions — a hallmark of biological processes — we developed an approach to conduct ~103 concurrent single-cell western blots (scWesterns) in ~4 hours. A microscope slide supporting a 30 µm-thick photoactive polyacrylamide gel enables western blotting comprised of: settling of single cells into microwells, lysis in situ, gel electrophoresis, photoinitiated blotting to immobilize proteins, and antibody probing. We apply this scWestern to monitor single rat neural stem cell differentiation and responses to mitogen stimulation. The scWestern quantifies target proteins even with off-target antibody binding, multiplexes to 11 protein targets per single cell with detection thresholds of <30,000 molecules, and supports analyses of low starting cell numbers (~200) when integrated with fluorescence activated cell sorting. The scWestern thus overcomes limitations in single-cell protein analysis (i.e., antibody fidelity, sensitivity, and starting cell number) and constitutes a versatile tool for the study of complex cell populations at single-cell resolution. PMID:24880876

  17. Measurements Of Singlet Oxygen In Photodynamic Therapy

    NASA Astrophysics Data System (ADS)

    Profio, A. E.; Shu, Kuang-Hsien

    1989-06-01

    Photochemical reactions are used in photodynamic therapy of cancer and other disease. The cytotoxic agent in photochemotherapy is usually singlet oxygen. Thus measurements of singlet oxygen production or concentration may allow prediction of the biological response. The decrease in fluorescence of L-tryptophan because of reaction with singlet oxygen, the decrease in absorbance of a dye such as RNO subject to secondary oxidation by singlet oxygen, and the decrease in fluorescence of the most common photosensitizer, dihematoporphyrin ether/ester (DHE) because of photobleaching, have been investigated in solutions in vitro. The most promising method for dosimetry and prediction of biological response appears to be the photobleaching of DHE.

  18. A new toolbox for assessing single cells.

    PubMed

    Tsioris, Konstantinos; Torres, Alexis J; Douce, Thomas B; Love, J Christopher

    2014-01-01

    Unprecedented access to the biology of single cells is now feasible, enabled by recent technological advancements that allow us to manipulate and measure sparse samples and achieve a new level of resolution in space and time. This review focuses on advances in tools to study single cells for specific areas of biology. We examine both mature and nascent techniques to study single cells at the genomics, transcriptomics, and proteomics level. In addition, we provide an overview of tools that are well suited for following biological responses to defined perturbations with single-cell resolution. Techniques to analyze and manipulate single cells through soluble and chemical ligands, the microenvironment, and cell-cell interactions are provided. For each of these topics, we highlight the biological motivation, applications, methods, recent advances, and opportunities for improvement. The toolbox presented in this review can function as a starting point for the design of single-cell experiments. PMID:24910919

  19. Single-cell irradiation from [211At] astatine-labeled C215 monoclonal antibody: improved estimates of radiosensitivity from measurements on cellular uptake and retention.

    PubMed

    Palm, Stig; Bäck, Tom; Claesson, Ingela; Delle, Ulla; Hultborn, Ragnar; Lindegren, Sture; Jacobsson, Lars

    2003-01-01

    New data on the biological effect of 211At-C215 monoclonal antibody in a slowly rotating, widely dispersed single-cell suspension of the human cancer cell line Colo-205 is presented. Cell growth curves of each experiment were used to calculate an apparent cell survival after irradiation. Uptake measurements provided the data needed to calculate the average number of 211At decays per cell in the cell suspension. The results from each experiment were then fit to a mono-exponential function. From the exponential fit, an average of 35 +/- 2 (SD) astatine-211 decays per cell are required for 37% apparent cell survival (D0). PMID:12820374

  20. Oxygen measurements in thin ribbon silicon

    NASA Astrophysics Data System (ADS)

    Hyland, S. L.; Ast, D. G.; Baghdadi, A.

    1987-03-01

    The oxygen content of thin silicon ribbons grown by the dendritic web technique was measured using a modification of the ASTM method based on Fourier transform infrared spectroscopy. Web silicon was found to have a high oxygen content, ranging from 13 to 19 ppma, calculated from the absorption peak associated with interstitial oxygen and using the new ASTM conversion coefficient. The oxygen concentration changed by about 10 percent along the growth direction of the ribbon. In some samples, a shoulder was detected on the absorption peak. A similar shoulder in Czochralski grown material has been variously interpreted in the literature as due to a complex of silicon, oxygen, and vacancies, or to a phase of SiO2 developed along dislocations in the material. In the case of web silicon, it is not clear which is the correct interpretation.

  1. SINGLE CELL GENOME SEQUENCING

    PubMed Central

    Yilmaz, Suzan; Singh, Anup K.

    2011-01-01

    Whole genome amplification and next-generation sequencing of single cells has become a powerful approach for studying uncultivated microorganisms that represent 90–99 % of all environmental microbes. Single cell sequencing enables not only the identification of microbes but also linking of functions to species, a feat not achievable by metagenomic techniques. Moreover, it allows the analysis of low abundance species that may be missed in community-based analyses. It has also proved very useful in complementing metagenomics in the assembly and binning of single genomes. With the advent of drastically cheaper and higher throughput sequencing technologies, it is expected that single cell sequencing will become a standard tool in studying the genome and transcriptome of microbial communities. PMID:22154471

  2. Single Cell Oncogenesis

    NASA Astrophysics Data System (ADS)

    Lu, Xin

    It is believed that cancer originates from a single cell that has gone through generations of evolution of genetic and epigenetic changes that associate with the hallmarks of cancer. In some cancers such as various types of leukemia, cancer is clonal. Yet in other cancers like glioblastoma (GBM), there is tremendous tumor heterogeneity that is likely to be caused by simultaneous evolution of multiple subclones within the same tissue. It is obvious that understanding how a single cell develops into a clonal tumor upon genetic alterations, at molecular and cellular levels, holds the key to the real appreciation of tumor etiology and ultimate solution for therapeutics. Surprisingly very little is known about the process of spontaneous tumorigenesis from single cells in human or vertebrate animal models. The main reason is the lack of technology to track the natural process of single cell changes from a homeostatic state to a progressively cancerous state. Recently, we developed a patented compound, photoactivatable (''caged'') tamoxifen analogue 4-OHC and associated technique called optochemogenetic switch (OCG switch), which we believe opens the opportunity to address this urgent biological as well as clinical question about cancer. We propose to combine OCG switch with genetically engineered mouse models of head and neck squamous cell carcinoma and high grade astrocytoma (including GBM) to study how single cells, when transformed through acute loss of tumor suppressor genes PTEN and TP53 and gain of oncogenic KRAS, can develop into tumor colonies with cellular and molecular heterogeneity in these tissues. The abstract is for my invited talk in session ``Beyond Darwin: Evolution in Single Cells'' 3/18/2016 11:15 AM.

  3. Single-Cell Measurements of Enzyme Levels as a Predictive Tool for Cellular Fates during Organic Acid Production

    PubMed Central

    Zdraljevic, Stefan; Wagner, Drew; Cheng, Kevin; Ruohonen, Laura; Jäntti, Jussi; Penttilä, Merja; Resnekov, Orna

    2013-01-01

    Organic acids derived from engineered microbes can replace fossil-derived chemicals in many applications. Fungal hosts are preferred for organic acid production because they tolerate lignocellulosic hydrolysates and low pH, allowing economic production and recovery of the free acid. However, cell death caused by cytosolic acidification constrains productivity. Cytosolic acidification affects cells asynchronously, suggesting that there is an underlying cell-to-cell heterogeneity in acid productivity and/or in resistance to toxicity. We used fluorescence microscopy to investigate the relationship between enzyme concentration, cytosolic pH, and viability at the single-cell level in Saccharomyces cerevisiae engineered to synthesize xylonic acid. We found that cultures producing xylonic acid accumulate cells with cytosolic pH below 5 (referred to here as “acidified”). Using live-cell time courses, we found that the probability of acidification was related to the initial levels of xylose dehydrogenase and sharply increased from 0.2 to 0.8 with just a 60% increase in enzyme abundance (Hill coefficient, >6). This “switch-like” relationship likely results from an enzyme level threshold above which the produced acid overwhelms the cell's pH buffering capacity. Consistent with this hypothesis, we showed that expression of xylose dehydrogenase from a chromosomal locus yields ∼20 times fewer acidified cells and ∼2-fold more xylonic acid relative to expression of the enzyme from a plasmid with variable copy number. These results suggest that strategies that further reduce cell-to-cell heterogeneity in enzyme levels could result in additional gains in xylonic acid productivity. Our results demonstrate a generalizable approach that takes advantage of the cell-to-cell variation of a clonal population to uncover causal relationships in the toxicity of engineered pathways. PMID:24038690

  4. Single-cell measurements of enzyme levels as a predictive tool for cellular fates during organic acid production.

    PubMed

    Zdraljevic, Stefan; Wagner, Drew; Cheng, Kevin; Ruohonen, Laura; Jäntti, Jussi; Penttilä, Merja; Resnekov, Orna; Pesce, C Gustavo

    2013-12-01

    Organic acids derived from engineered microbes can replace fossil-derived chemicals in many applications. Fungal hosts are preferred for organic acid production because they tolerate lignocellulosic hydrolysates and low pH, allowing economic production and recovery of the free acid. However, cell death caused by cytosolic acidification constrains productivity. Cytosolic acidification affects cells asynchronously, suggesting that there is an underlying cell-to-cell heterogeneity in acid productivity and/or in resistance to toxicity. We used fluorescence microscopy to investigate the relationship between enzyme concentration, cytosolic pH, and viability at the single-cell level in Saccharomyces cerevisiae engineered to synthesize xylonic acid. We found that cultures producing xylonic acid accumulate cells with cytosolic pH below 5 (referred to here as "acidified"). Using live-cell time courses, we found that the probability of acidification was related to the initial levels of xylose dehydrogenase and sharply increased from 0.2 to 0.8 with just a 60% increase in enzyme abundance (Hill coefficient, >6). This "switch-like" relationship likely results from an enzyme level threshold above which the produced acid overwhelms the cell's pH buffering capacity. Consistent with this hypothesis, we showed that expression of xylose dehydrogenase from a chromosomal locus yields ∼20 times fewer acidified cells and ∼2-fold more xylonic acid relative to expression of the enzyme from a plasmid with variable copy number. These results suggest that strategies that further reduce cell-to-cell heterogeneity in enzyme levels could result in additional gains in xylonic acid productivity. Our results demonstrate a generalizable approach that takes advantage of the cell-to-cell variation of a clonal population to uncover causal relationships in the toxicity of engineered pathways. PMID:24038690

  5. A New Radio Frequency Plasma Oxygen Primary Ion Source on Nano Secondary Ion Mass Spectrometry for Improved Lateral Resolution and Detection of Electropositive Elements at Single Cell Level.

    PubMed

    Malherbe, Julien; Penen, Florent; Isaure, Marie-Pierre; Frank, Julia; Hause, Gerd; Dobritzsch, Dirk; Gontier, Etienne; Horréard, François; Hillion, François; Schaumlöffel, Dirk

    2016-07-19

    An important application field of secondary ion mass spectrometry at the nanometer scale (NanoSIMS) is the detection of chemical elements and, in particular, metals at the subcellular level in biological samples. The detection of many trace metals requires an oxygen primary ion source to allow the generation of positive secondary ions with high yield in the NanoSIMS. The duoplasmatron oxygen source is commonly used in this ion microprobe but cannot achieve the same quality of images as the cesium primary ion source used to produce negative secondary ions (C(-), CN(-), S(-), P(-)) due to a larger primary ion beam size. In this paper, a new type of an oxygen ion source using a rf plasma is fitted and characterized on a NanoSIMS50L. The performances of this primary ion source in terms of current density and achievable lateral resolution have been characterized and compared to the conventional duoplasmatron and cesium sources. The new rf plasma oxygen source offered a net improvement in terms of primary beam current density compared to the commonly used duoplasmatron source, which resulted in higher ultimate lateral resolutions down to 37 nm and which provided a 5-45 times higher apparent sensitivity for electropositive elements. Other advantages include a better long-term stability and reduced maintenance. This new rf plasma oxygen primary ion source has been applied to the localization of essential macroelements and trace metals at basal levels in two biological models, cells of Chlamydomonas reinhardtii and Arabidopsis thaliana. PMID:27291826

  6. Oxygen fugacities directly measured in magmatic gases

    USGS Publications Warehouse

    Sato, M.; Wright, T.L.

    1966-01-01

    An electrochemical device was used to measure the fugacity of oxygen (fO2) in holes drilled through the crust of Makaopuhi lava lake, Kilauea Volcano, Hawaii. Results obtained within 6 months of the lake formation show that log fO2 normally varies linearly with the reciprocal of the absolute temperature, and that chemical changes occurring in the cooling tholeiitic basalt are reflected in the fO2 values measured in the holes.

  7. A Method for Detecting Circulating Tumor Cells Based on the Measurement of Single-Cell Metabolism in Droplet-Based Microfluidics.

    PubMed

    Del Ben, Fabio; Turetta, Matteo; Celetti, Giorgia; Piruska, Aigars; Bulfoni, Michela; Cesselli, Daniela; Huck, Wilhelm T S; Scoles, Giacinto

    2016-07-18

    The number of circulating tumor cells (CTCs) in blood is strongly correlated with the progress of metastatic cancer. Current methods to detect CTCs are based on immunostaining or discrimination of physical properties. Herein, a label-free method is presented exploiting the abnormal metabolic behavior of cancer cells. A single-cell analysis technique is used to measure the secretion of acid from individual living tumor cells compartmentalized in microfluidically prepared, monodisperse, picoliter (pL) droplets. As few as 10 tumor cells can be detected in a background of 200 000 white blood cells and proof-of-concept data is shown on the detection of CTCs in the blood of metastatic patients. PMID:27247024

  8. Quantitative measurement of oxygen in microgravity combustion

    NASA Technical Reports Server (NTRS)

    Silver, Joel A.

    1995-01-01

    This research combines two innovations in an experimental system which should result in a new capability for quantitative, nonintrusive measurement of major combustion species. Using a newly available vertical cavity surface-emitting diode laser (VCSEL) and an improved spatial scanning method, we plan to measure the temporal and spatial profiles of the concentrations and temperatures of molecular oxygen in a candle flame and in a solid fuel (cellulose sheet) system. The required sensitivity for detecting oxygen is achieved by the use of high frequency wavelength modulation spectroscopy (WMS). Measurements will be performed in the NASA Lewis 2.2-second Drop Tower Facility. The objective of this research is twofold. First, we want to develop a better understanding of the relative roles of diffusion and reaction of oxygen in microgravity combustion. As the primary oxidizer species, oxygen plays a major role in controlling the observed properties of flames, including flame front speed (in solid or liquid flames), extinguishment characteristics, flame size, and flame temperature. The second objective is to develop better diagnostics based on diode laser absorption which can be of real value in microgravity combustion research. We will also demonstrate diode lasers' potential usefulness for compact, intrinsically-safe monitoring sensors aboard spacecraft. Such sensors could be used to monitor any of the major cabin gases as well as important pollutants.

  9. Single-cell proteins

    SciTech Connect

    Litchfield, J.H.

    1983-02-11

    Both photosynthetic and nonphotosynthetic microorganisms, grown on various carbon and energy sources, are used in fermentation processes for the production of single-cell proteins. Commercial-scale production has been limited to two algal processes, one bacterial process, and several yeast and fungal processes. High capital and operating costs and the need for extensive nutritional and toxicological assessments have limited the development and commercialization of new processes. Any increase in commercial-scale production appears to be limited to those regions of the world where low-cost carbon and energy sources are available and conventional animal feedstuff proteins, such as soybean meal or fish meal, are in short supply. (Refs. 59).

  10. Single cell wound repair

    PubMed Central

    Abreu-Blanco, Maria Teresa; Verboon, Jeffrey M

    2011-01-01

    Cell wounding is a common event in the life of many cell types, and the capacity of the cell to repair day-to-day wear-and-tear injuries, as well as traumatic ones, is fundamental for maintaining tissue integrity. Cell wounding is most frequent in tissues exposed to high levels of stress. Survival of such plasma membrane disruptions requires rapid resealing to prevent the loss of cytosolic components, to block Ca2+ influx and to avoid cell death. In addition to patching the torn membrane, plasma membrane and cortical cytoskeleton remodeling are required to restore cell function. Although a general understanding of the cell wound repair process is in place, the underlying mechanisms of each step of this response are not yet known. We have developed a model to study single cell wound repair using the early Drosophila embryo. Our system combines genetics and live imaging tools, allowing us to dissect in vivo the dynamics of the single cell wound response. We have shown that cell wound repair in Drosophila requires the coordinated activities of plasma membrane and cytoskeleton components. Furthermore, we identified an unexpected role for E-cadherin as a link between the contractile actomyosin ring and the newly formed plasma membrane plug. PMID:21922041

  11. [New Method of Measuring Arterial Oxygen Saturation].

    PubMed

    Li, Gang; Bao, Lei; Zhou, Mei; Lin, Ling; Liu, Rui; Zhao, Chun-jie

    2016-01-01

    The traditional method of measuring arterial oxygen saturation is that R value, the ratio of alternating component of the logarithmic photoplethysmography, is firstly computed and then the linear regression model is established by experiment. The R value computation is a dimension reduction process based on Lambert-beer law, which aims at eliminating the influence of optical path and minimizing the impact of individual differences. When taking scattering into consideration, the dimension reduction process loses information, introduces the system error and limits the precision of measurement. In order to reduce the measurement error resulting from the scattering effects, this paper presents a new method that the peak and valley values of dual-wavelength logarithmic photoplethysmography waves are used as the independent variables to develop a linear regression model to predict the arterial oxygen saturation. During the experiment, the in-vivo measurements were carried out on 23 healthy volunteer and 133 samples of photoplethysmography waves and the reference value of oxygen saturation were recorded. To compare the predictive performance between the new method and the R value method, 90 samples were randomly selected as modeling sets and the remaining 43 samples were used as prediction sets. Random selection of modeling sets and prediction are executed 10 times. The average related coefficients of the prediction sets of the new method and the R value method are 0.890 6 and 0.846 8, and the average root mean square errors are 0.889 6% and 1.037 3% respectively. Results indicate that the performance of the new method is better than the one of the R value method, and the predictivemodel based on 4 parameters can improve the stability and accuracy of measurement. And the new method has guiding significance to the measurement of human body's blood physiological information based on limited wavelength spectrum data. PMID:27228767

  12. Single Cell Physiology

    NASA Astrophysics Data System (ADS)

    Neveu, Pierre; Sinha, Deepak Kumar; Kettunen, Petronella; Vriz, Sophie; Jullien, Ludovic; Bensimon, David

    The possibility to control at specific times and specific places the activity of biomolecules (enzymes, transcription factors, RNA, hormones, etc.) is opening up new opportunities in the study of physiological processes at the single cell level in a live organism. Most existing gene expression systems allow for tissue specific induction upon feeding the organism with exogenous inducers (e.g., tetracycline). Local genetic control has earlier been achieved by micro-injection of the relevant inducer/repressor molecule, but this is an invasive and possibly traumatic technique. In this chapter, we present the requirements for a noninvasive optical control of the activity of biomolecules and review the recent advances in this new field of research.

  13. Single cell optical transfection.

    PubMed

    Stevenson, David J; Gunn-Moore, Frank J; Campbell, Paul; Dholakia, Kishan

    2010-06-01

    The plasma membrane of a eukaryotic cell is impermeable to most hydrophilic substances, yet the insertion of these materials into cells is an extremely important and universal requirement for the cell biologist. To address this need, many transfection techniques have been developed including viral, lipoplex, polyplex, capillary microinjection, gene gun and electroporation. The current discussion explores a procedure called optical injection, where a laser field transiently increases the membrane permeability to allow species to be internalized. If the internalized substance is a nucleic acid, such as DNA, RNA or small interfering RNA (siRNA), then the process is called optical transfection. This contactless, aseptic, single cell transfection method provides a key nanosurgical tool to the microscopist-the intracellular delivery of reagents and single nanoscopic objects. The experimental possibilities enabled by this technology are only beginning to be realized. A review of optical transfection is presented, along with a forecast of future applications of this rapidly developing and exciting technology. PMID:20064901

  14. Voltage clamp measurements of the hyperpolarization-activated inward current I(f) in single cells from rabbit sino-atrial node.

    PubMed Central

    van Ginneken, A C; Giles, W

    1991-01-01

    1. The kinetics and ion transfer characteristics of the hyperpolarization-activated inward current, I(f), have been studied in single cells obtained by enzymatic dispersion from the rabbit sino-atrial (S-A) node. These experiments were done to assess the role of I(f) in the generation of the pacemaker depolarization in the S-A node. 2. The activation and the deactivation of I(f) in these single cells are accompanied by significant conductance increases and decreases respectively, confirming earlier findings from multicellular man-made strips of rabbit S-A node, and from mammalian Purkinje fibres. 3. The steady-state activation of I(f) lies between -40 and -120 mV, and its voltage dependence can be described by a Boltzmann relation with the half-activation point at approximately -70 mV. 4. The delay or sigmoidicity in both the onset of I(f) and the deactivation of the tail currents can be accounted for semi-quantitatively by using a second-order Hodgkin-Huxley kinetic scheme. 5. The reversal potential for I(f) is -24 +/- 2 mV (mean +/- S.E.M., n = 6). It does not change significantly as a function of the amount of I(f) which is activated, indicating that ion accumulation or depletion phenomena are not important variables controlling the time course of I(f), or its selectivity. 6. The fully-activated current-voltage relationship for I(f) is approximately linear with a slope conductance of 12.0 +/- 0.88 nS per cell (mean +/- S.E.M., n = 6). 7. A simple mathematical model based on the measured values of maximum conductance, reversal potential, and kinetics of I(f) has been developed to simulate the size and time course of I(f) during typical spontaneous pacemaker activity in rabbit sino-atrial node cells. The calculations show that I(f) can change significantly during pacing and suggest that this current change is, at least in part, responsible for the pacemaker depolarization. Images Fig. 1 PMID:1708824

  15. EVALUATING AN INNOVATIVE OXYGEN SENSOR FOR REMOTE SUBSURFACE OXYGEN MEASUREMENTS

    SciTech Connect

    Millings, M; Brian Riha, B; Warren Hyde, W; Karen Vangelas, K; Brian02 Looney, B

    2006-10-12

    Oxygen is a primary indicator of whether anaerobic reductive dechlorination and similar redox based processes contribute to natural attenuation remedies at chlorinated solvent contaminated sites. Thus, oxygen is a viable indicator parameter for documenting that a system is being sustained in an anaerobic condition. A team of researchers investigated the adaptation of an optical sensor that was developed for oceanographic applications. The optical sensor, because of its design and operating principle, has potential for extended deployment and sensitivity at the low oxygen levels relevant to natural attenuation. The results of the research indicate this tool will be useful for in situ long-term monitoring applications, but that the traditional characterization tools continue to be appropriate for characterization activities.

  16. A New Generation of FRET Sensors for Robust Measurement of Gαi1, Gαi2 and Gαi3 Activation Kinetics in Single Cells

    PubMed Central

    van Unen, Jakobus; Stumpf, Anette D.; Schmid, Benedikt; Reinhard, Nathalie R.; Hordijk, Peter L.; Hoffmann, Carsten; Gadella, Theodorus W. J.; Goedhart, Joachim

    2016-01-01

    G-protein coupled receptors (GPCRs) can activate a heterotrimeric G-protein complex with subsecond kinetics. Genetically encoded biosensors based on Förster resonance energy transfer (FRET) are ideally suited for the study of such fast signaling events in single living cells. Here we report on the construction and characterization of three FRET biosensors for the measurement of Gαi1, Gαi2 and Gαi3 activation. To enable quantitative long-term imaging of FRET biosensors with high dynamic range, fluorescent proteins with enhanced photophysical properties are required. Therefore, we use the currently brightest and most photostable CFP variant, mTurquoise2, as donor fused to Gαi subunit, and cp173Venus fused to the Gγ2 subunit as acceptor. The Gαi FRET biosensors constructs are expressed together with Gβ1 from a single plasmid, providing preferred relative expression levels with reduced variation in mammalian cells. The Gαi FRET sensors showed a robust response to activation of endogenous or over-expressed alpha-2A-adrenergic receptors, which was inhibited by pertussis toxin. Moreover, we observed activation of the Gαi FRET sensor in single cells upon stimulation of several GPCRs, including the LPA2, M3 and BK2 receptor. Furthermore, we show that the sensors are well suited to extract kinetic parameters from fast measurements in the millisecond time range. This new generation of FRET biosensors for Gαi1, Gαi2 and Gαi3 activation will be valuable for live-cell measurements that probe Gαi activation. PMID:26799488

  17. A New Generation of FRET Sensors for Robust Measurement of Gαi1, Gαi2 and Gαi3 Activation Kinetics in Single Cells.

    PubMed

    van Unen, Jakobus; Stumpf, Anette D; Schmid, Benedikt; Reinhard, Nathalie R; Hordijk, Peter L; Hoffmann, Carsten; Gadella, Theodorus W J; Goedhart, Joachim

    2016-01-01

    G-protein coupled receptors (GPCRs) can activate a heterotrimeric G-protein complex with subsecond kinetics. Genetically encoded biosensors based on Förster resonance energy transfer (FRET) are ideally suited for the study of such fast signaling events in single living cells. Here we report on the construction and characterization of three FRET biosensors for the measurement of Gαi1, Gαi2 and Gαi3 activation. To enable quantitative long-term imaging of FRET biosensors with high dynamic range, fluorescent proteins with enhanced photophysical properties are required. Therefore, we use the currently brightest and most photostable CFP variant, mTurquoise2, as donor fused to Gαi subunit, and cp173Venus fused to the Gγ2 subunit as acceptor. The Gαi FRET biosensors constructs are expressed together with Gβ1 from a single plasmid, providing preferred relative expression levels with reduced variation in mammalian cells. The Gαi FRET sensors showed a robust response to activation of endogenous or over-expressed alpha-2A-adrenergic receptors, which was inhibited by pertussis toxin. Moreover, we observed activation of the Gαi FRET sensor in single cells upon stimulation of several GPCRs, including the LPA2, M3 and BK2 receptor. Furthermore, we show that the sensors are well suited to extract kinetic parameters from fast measurements in the millisecond time range. This new generation of FRET biosensors for Gαi1, Gαi2 and Gαi3 activation will be valuable for live-cell measurements that probe Gαi activation. PMID:26799488

  18. BENZO[A]PYRENE AND ITS K-REGION DIOL INDUCE DNA DAMAGE IN C3H10T1/2C18 CELLS AS MEASURED BY THE ALKALINE SINGLE CELL GEL (COMET) ASSAY

    EPA Science Inventory


    160. Benzo[a]pyrene and its K-region diol induce DNA damage in C3HlOTl/2Cl8 cells as measured by the alkaline single cell gel (Comet) assay

    In a continuing series of studies on the genotoxicity ofK-region dihydrodiols of polycyclic aromatic hydrocarbons, we have repo...

  19. Measuring tissue oxygen tension: a review.

    PubMed

    Sheffield, P J

    1998-01-01

    Because of technological advances in tissue oximetry, clinicians and scientists have a better understanding of the role of oxygen in wound healing. In wound care and hyperbaric medicine applications, an oximeter is principally used with vascular assessment to help determine amputation level and to estimate healing potential. With the current emphasis on cost savings in the managed care setting, transcutaneous oximetry (PtcO2) has gained importance as a tool for predicting potential candidates for hyperbaric oxygen (HBO2) therapy. It is used to identify the presence of hypoxia in wounded tissue, to predict the responders to hyperoxia and in some instances to determine when HBO2 treatment is complete. This literature review describes the principal current methods for measuring tissue O2 and the values obtained in normal and wounded tissue under both normobaric and hyperbaric conditions. The review includes the Jefferson C. Davis Wound Care and Hyperbaric Medicine Center protocol for PtcO2 assessment of potential HBO2 candidates and suggestions for obtaining reproducible PtcO2 data. PMID:9789339

  20. Chemical Analysis of Single Cells

    NASA Astrophysics Data System (ADS)

    Borland, Laura M.; Kottegoda, Sumith; Phillips, K. Scott; Allbritton, Nancy L.

    2008-07-01

    Chemical analysis of single cells requires methods for quickly and quantitatively detecting a diverse array of analytes from extremely small volumes (femtoliters to nanoliters) with very high sensitivity and selectivity. Microelectrophoretic separations, using both traditional capillary electrophoresis and emerging microfluidic methods, are well suited for handling the unique size of single cells and limited numbers of intracellular molecules. Numerous analytes, ranging from small molecules such as amino acids and neurotransmitters to large proteins and subcellular organelles, have been quantified in single cells using microelectrophoretic separation techniques. Microseparation techniques, coupled to varying detection schemes including absorbance and fluorescence detection, electrochemical detection, and mass spectrometry, have allowed researchers to examine a number of processes inside single cells. This review also touches on a promising direction in single cell cytometry: the development of microfluidics for integrated cellular manipulation, chemical processing, and separation of cellular contents.

  1. Quantification noise in single cell experiments

    PubMed Central

    Reiter, M.; Kirchner, B.; Müller, H.; Holzhauer, C.; Mann, W.; Pfaffl, M. W.

    2011-01-01

    In quantitative single-cell studies, the critical part is the low amount of nucleic acids present and the resulting experimental variations. In addition biological data obtained from heterogeneous tissue are not reflecting the expression behaviour of every single-cell. These variations can be derived from natural biological variance or can be introduced externally. Both have negative effects on the quantification result. The aim of this study is to make quantitative single-cell studies more transparent and reliable in order to fulfil the MIQE guidelines at the single-cell level. The technical variability introduced by RT, pre-amplification, evaporation, biological material and qPCR itself was evaluated by using RNA or DNA standards. Secondly, the biological expression variances of GAPDH, TNFα, IL-1β, TLR4 were measured by mRNA profiling experiment in single lymphocytes. The used quantification setup was sensitive enough to detect single standard copies and transcripts out of one solitary cell. Most variability was introduced by RT, followed by evaporation, and pre-amplification. The qPCR analysis and the biological matrix introduced only minor variability. Both conducted studies impressively demonstrate the heterogeneity of expression patterns in individual cells and showed clearly today's limitation in quantitative single-cell expression analysis. PMID:21745823

  2. Quantitative Measurement of Oxygen in Microgravity Combustion

    NASA Technical Reports Server (NTRS)

    Silver, Joel A.

    1997-01-01

    A low-gravity environment, in space or in ground-based facilities such as drop towers, provides a unique setting for studying combustion mechanisms. Understanding the physical phenomena controlling the ignition and spread of flames in microgravity has importance for space safety as well as for better characterization of dynamical and chemical combustion processes which are normally masked by buoyancy and other gravity-related effects. Due to restrictions associated with performing measurements in reduced gravity, diagnostic methods which have been applied to microgravity combustion studies have generally been limited to capture of flame emissions on film or video, laser Schlieren imaging and (intrusive) temperature measurements using thermocouples. Given the development of detailed theoretical models, more sophisticated diagnostic methods are needed to provide the kind of quantitative data necessary to characterize the properties of microgravity combustion processes as well as provide accurate feedback to improve the predictive capabilities of the models. When the demands of space flight are considered, the need for improved diagnostic systems which are rugged, compact, reliable, and operate at low power becomes apparent. The objective of this research is twofold. First, we want to develop a better understanding of the relative roles of diffusion and reaction of oxygen in microgravity combustion. As the primary oxidizer species, oxygen plays a major role in controlling the observed properties of flames, including flame front speed (in solid or liquid flames), extinguishment characteristics, flame size and flame temperature. The second objective is to develop better diagnostics based on diode laser absorption which can be of real value in both microgravity combustion research and as a sensor on-board Spacelab as either an air quality monitor or as part of a fire detection system. In our prior microgravity work, an eight line-of-sight fiber optic system measured

  3. Capillary Electrophoretic Technologies for Single Cell Metabolomics

    ERIC Educational Resources Information Center

    Lapainis, Theodore E.

    2009-01-01

    Understanding the functioning of the brain is hindered by a lack of knowledge of the full complement of neurotransmitters and neuromodulatory compounds. Single cell measurements aid in the discovery of neurotransmitters used by small subsets of neurons that would be diluted below detection limits or masked by ubiquitous compounds when working with…

  4. PHASE I SINGLE CELL ELECTROLYZER TEST RESULTS

    SciTech Connect

    Steimke, J; Timothy Steeper, T

    2008-08-05

    This document reports the results of Phase I Single Cell testing of an SO{sub 2}-Depolarized Water Electrolyzer. Testing was performed primarily during the first quarter of FY 2008 at the Savannah River National Laboratory (SRNL) using an electrolyzer cell designed and built at SRNL. Other facility hardware were also designed and built at SRNL. This test further advances this technology for which work began at SRNL in 2005. This research is valuable in achieving the ultimate goal of an economical hydrogen production process based on the Hybrid Sulfur (HyS) Cycle. The focus of this work was to conduct single cell electrolyzer tests to further develop the technology of SO{sub 2}-depolarized electrolysis as part of the HyS Cycle. The HyS Cycle is a hybrid thermochemical cycle that may be used in conjunction with advanced nuclear reactors or centralized solar receivers to produce hydrogen by water-splitting. Like all other sulfur-based cycles, HyS utilizes the high temperature thermal decomposition of sulfuric acid to produce oxygen and regenerate sulfur dioxide. The unique aspect of HyS is the generation of hydrogen in a water electrolyzer that is operated under conditions where dissolved sulfur dioxide depolarizes the anodic reaction, resulting in substantial voltage reduction. Low cell voltage is essential for both thermodynamic efficiency and hydrogen cost. Sulfur dioxide is oxidized at the anode, producing sulfuric acid that is sent to the high temperature acid decomposition portion of the cycle. The electrolyzer cell uses the membrane electrode assembly (MEA) concept. The anode and cathode are formed by spraying platinum containing catalyst on both sides of a Proton Exchange Membrane (PEM). In most testing the material of the PEM was NafionR. The electrolyzer cell active area can be as large as 54.8 cm{sup 2}. Feed to the anode of the electrolyzer is a sulfuric acid solution containing sulfur dioxide. The partial pressure of sulfur dioxide could be varied in the

  5. Aquatic Respiration Rate Measurements at Low Oxygen Concentrations

    PubMed Central

    Holtappels, Moritz; Tiano, Laura; Kalvelage, Tim; Lavik, Gaute; Revsbech, Niels Peter; Kuypers, Marcel M. M.

    2014-01-01

    Despite its huge ecological importance, microbial oxygen respiration in pelagic waters is little studied, primarily due to methodological difficulties. Respiration measurements are challenging because of the required high resolution of oxygen concentration measurements. Recent improvements in oxygen sensing techniques bear great potential to overcome these limitations. Here we compare 3 different methods to measure oxygen consumption rates at low oxygen concentrations, utilizing amperometric Clark type sensors (STOX), optical sensors (optodes), and mass spectrometry in combination with 18-18O2 labeling. Oxygen concentrations and consumption rates agreed well between the different methods when applied in the same experimental setting. Oxygen consumption rates between 30 and 400 nmol L−1 h−1 were measured with high precision and relative standard errors of less than 3%. Rate detection limits in the range of 1 nmol L−1 h−1 were suitable for rate determinations in open ocean water and were lowest at the lowest applied O2 concentration. PMID:24586724

  6. Optoacoustic measurements of human placenta and umbilical blood oxygenation

    NASA Astrophysics Data System (ADS)

    Nanovskaya, T. N.; Petrov, I. Y.; Petrov, Y.; Patrikeeva, S. L.; Ahmed, M. S.; Hankins, G. D. V.; Prough, D. S.; Esenaliev, R. O.

    2016-03-01

    Adequate oxygenation is essential for normal embryogenesis and fetal growth. Perturbations in the intrauterine oxidative environment during pregnancy are associated with several pathophysiological disorders such as pregnancy loss, preeclampsia, and intrauterine growth restriction. We proposed to use optoacoustic technology for monitoring placental and fetal umbilical blood oxygenation. In this work, we studied optoacoustic monitoring of oxygenation in placenta and umbilical cord blood ex vivo using technique of placenta perfusion. We used a medical grade, nearinfrared, tunable, optoacoustic system developed and built for oxygenation monitoring in blood vessels and in tissues. First, we calibrated the system for cord blood oxygenation measurements by using a CO-Oximeter (gold standard). Then we performed validation in cord blood circulating through the catheters localized on the fetal side of an isolated placental lobule. Finally, the oxygenation measurements were performed in the perfused placental tissue. To increase or decrease blood oxygenation, we used infusion of a gas mixture of 95% O2 + 5% CO2 and 95% N2 + 5% CO2, respectively. In placental tissue, up to four cycles of changes in oxygenation were performed. The optoacoustically measured oxygenation in circulating cord blood and in placental lobule closely correlated with the actual oxygenation data measured by CO-Oximeter. We plan to further test the placental and cord blood oxygenation monitoring with optoacoustics in animal and clinical studies.

  7. Oxygen saturation resolution influences regularity measurements.

    PubMed

    Garde, Ainara; Karlen, Walter; Dehkordi, Parastoo; Ansermino, J Mark; Dumont, Guy A

    2014-01-01

    The measurement of regularity in the oxygen saturation (SpO(2)) signal has been suggested for use in identifying subjects with sleep disordered breathing (SDB). Previous work has shown that children with SDB have lower SpO(2) regularity than subjects without SDB (NonSDB). Regularity was measured using non-linear methods like approximate entropy (ApEn), sample entropy (SamEn) and Lempel-Ziv (LZ) complexity. Different manufacturer's pulse oximeters provide SpO(2) at various resolutions and the effect of this resolution difference on SpO(2) regularity, has not been studied. To investigate this effect, we used the SpO(2) signal of children with and without SDB, recorded from the Phone Oximeter (0.1% resolution) and the same SpO(2) signal rounded to the nearest integer (artificial 1% resolution). To further validate the effect of rounding, we also used the SpO(2) signal (1% resolution) recorded simultaneously from polysomnography (PSG), as a control signal. We estimated SpO(2) regularity by computing the ApEn, SamEn and LZ complexity, using a 5-min sliding window and showed that different resolutions provided significantly different results. The regularity calculated using 0.1% SpO(2) resolution provided no significant differences between SDB and NonSDB. However, the artificial 1% resolution SpO(2) provided significant differences between SDB and NonSDB, showing a more random SpO(2) pattern (lower SpO(2) regularity) in SDB children, as suggested in the past. Similar results were obtained with the SpO(2) recorded from PSG (1% resolution), which further validated that this SpO(2) regularity change was due to the rounding effect. Therefore, the SpO(2) resolution has a great influence in regularity measurements like ApEn, SamEn and LZ complexity that should be considered when studying the SpO(2) pattern in children with SDB. PMID:25570437

  8. Device for measuring the total concentration of oxygen in gases

    DOEpatents

    Isaacs, Hugh S.; Romano, Anthony J.

    1977-01-01

    This invention provides a CO equilibrium in a device for measuring the total concentration of oxygen impurities in a fluid stream. To this end, the CO equilibrium is produced in an electrochemical measuring cell by the interaction of a carbon element in the cell with the chemically combined and uncombined oxygen in the fluid stream at an elevated temperature.

  9. Single Cell Electrical Characterization Techniques

    PubMed Central

    Mansor, Muhammad Asraf; Ahmad, Mohd Ridzuan

    2015-01-01

    Electrical properties of living cells have been proven to play significant roles in understanding of various biological activities including disease progression both at the cellular and molecular levels. Since two decades ago, many researchers have developed tools to analyze the cell’s electrical states especially in single cell analysis (SCA). In depth analysis and more fully described activities of cell differentiation and cancer can only be accomplished with single cell analysis. This growing interest was supported by the emergence of various microfluidic techniques to fulfill high precisions screening, reduced equipment cost and low analysis time for characterization of the single cell’s electrical properties, as compared to classical bulky technique. This paper presents a historical review of single cell electrical properties analysis development from classical techniques to recent advances in microfluidic techniques. Technical details of the different microfluidic techniques are highlighted, and the advantages and limitations of various microfluidic devices are discussed. PMID:26053399

  10. Non-invasive measurement of blood oxygen levels.

    PubMed

    Beyerl, D

    1982-05-01

    Comparison of transcutaneous (TC) monitoring of blood oxygen levels to arterial blood gas analyses was made on patients at rest with room air, during exercise, and at rest with oxygen. Three different transcutaneous monitors were evaluated: Novametrix TC O2 Mette, Biochem Sensomat, and Radiometer TC M1. The Hewlett-Packard ear oximeter for measuring oxygen saturation was also compared to oxygen saturation values calculated on the Severinghaus slide rule. Using at least one measured PO2 as a baseline, either TC monitoring or ear oximetry were valuable tools in monitoring pulmonary function. PMID:7102718

  11. Mass Cytometry: Single Cells, Many Features.

    PubMed

    Spitzer, Matthew H; Nolan, Garry P

    2016-05-01

    Technology development in biological research often aims to either increase the number of cellular features that can be surveyed simultaneously or enhance the resolution at which such observations are possible. For decades, flow cytometry has balanced these goals to fill a critical need by enabling the measurement of multiple features in single cells, commonly to examine complex or hierarchical cellular systems. Recently, a format for flow cytometry has been developed that leverages the precision of mass spectrometry. This fusion of the two technologies, termed mass cytometry, provides measurement of over 40 simultaneous cellular parameters at single-cell resolution, significantly augmenting the ability of cytometry to evaluate complex cellular systems and processes. In this Primer, we review the current state of mass cytometry, providing an overview of the instrumentation, its present capabilities, and methods of data analysis, as well as thoughts on future developments and applications. PMID:27153492

  12. Visible light optical coherence tomography measures retinal oxygen metabolic response to systemic oxygenation

    PubMed Central

    Yi, Ji; Liu, Wenzhong; Chen, Siyu; Backman, Vadim; Sheibani, Nader; Sorenson, Christine M.; Fawzi, Amani A.; Linsenmeier, Robert A.; Zhang, Hao F.

    2015-01-01

    The lack of capability to quantify oxygen metabolism noninvasively impedes both fundamental investigation and clinical diagnosis of a wide spectrum of diseases including all the major blinding diseases such as age-related macular degeneration, diabetic retinopathy, and glaucoma. Using visible light optical coherence tomography (vis-OCT), we demonstrated accurate and robust measurement of retinal oxygen metabolic rate (rMRO2) noninvasively in rat eyes. We continuously monitored the regulatory response of oxygen consumption to a progressive hypoxic challenge. We found that both oxygen delivery, and rMRO2 increased from the highly regulated retinal circulation (RC) under hypoxia, by 0.28 ± 0.08 μL min−1 (p < 0.001), and 0.20 ± 0.04 μL min−1 (p < 0.001) per 100 mmHg systemic pO2 reduction, respectively. The increased oxygen extraction compensated for the deficient oxygen supply from the poorly regulated choroidal circulation. Results from an oxygen diffusion model based on previous oxygen electrode measurements corroborated our in vivo observations. We believe that vis-OCT has the potential to reveal the fundamental role of oxygen metabolism in various retinal diseases. PMID:26658555

  13. ASRDI oxygen technology survey. Volume 6: Flow measurement instrumentation

    NASA Technical Reports Server (NTRS)

    Mann, D. B.

    1974-01-01

    A summary is provided of information available on liquid and gaseous oxygen flowmetering including an evaluation of commercial meters. The instrument types, physical principles of measurement, and performance characteristics are described. Problems concerning flow measurements of less than plus or minus two percent uncertainty are reviewed. Recommendations concerning work on flow reference systems, the use of surrogate fluids, and standard tests for oxygen flow measurements are also presented.

  14. ASRDI oxygen technology survey. Volume 8: Pressure measurement

    NASA Technical Reports Server (NTRS)

    Arvidson, J. M.; Brennan, J. A.

    1975-01-01

    Pressure transducers and their current uses with gaseous or liquid oxygen are reviewed. All transducer types such as strain gage, capacitance, potentiometric, piezoelectric, etc., are included. Topics covered include: cryogenic pressure measurement; material compatibility with gaseous and liquid oxygen; cleaning procedures; pressure tap connections; transducer types and descriptions; and calibration techniques.

  15. Visible light optical coherence tomography measure retinal oxygen metabolic response to systemic oxygenation (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Yi, Ji; Liu, Wenzhong; Chen, Siyu; Backman, Vadim; Sheibani, Nader; Sorenson, Christine M.; Fawzi, Amani A.; Linsenmeier, Robert A.; Zhang, Hao F.

    2016-03-01

    The lack of capability to quantify oxygen metabolism noninvasively impedes both fundamental investigation and clinical diagnosis of a wide spectrum of diseases including all the major blinding diseases such as age-related macular degeneration, diabetic retinopathy, and glaucoma. Using visible light optical coherence tomography (vis-OCT), we demonstrated accurate and robust measurement of retinal oxygen metabolic rate (rMRO2) noninvasively in rat eyes. The rMRO2 was calculated by concurrent measurement of blood flow and blood oxygen saturation (sO2). Blood flow was calculated by the principle of Doppler optical coherence tomography, where the phase shift between two closely spaced A-lines measures the axial velocity. The distinct optical absorption spectra of oxy- and deoxy-hemoglobin provided the contrast for sO2 measurement, combined with the spectroscopic analysis of vis-OCT signal within the blood vessels. We continuously monitored the regulatory response of oxygen consumption to a progressive hypoxic challenge. We found that both oxygen delivery, and rMRO2 increased from the highly regulated retinal circulation (RC) under hypoxia, by 0.28+/-0.08 μL/min (p<0.001), and 0.20+/-0.04 μL/min (p<0.001) per 100 mmHg systemic pO2 reduction, respectively. The increased oxygen extraction compensated for the deficient oxygen supply from the poorly regulated choroidal circulation (CC).

  16. Automated micropipette aspiration of single cells.

    PubMed

    Shojaei-Baghini, Ehsan; Zheng, Yi; Sun, Yu

    2013-06-01

    This paper presents a system for mechanically characterizing single cells using automated micropipette aspiration. Using vision-based control and position control, the system controls a micromanipulator, a motorized translation stage, and a custom-built pressure system to position a micropipette (4 μm opening) to approach a cell, form a seal, and aspirate the cell into the micropipette for quantifying the cell's elastic and viscoelastic parameters as well as viscosity. Image processing algorithms were developed to provide controllers with real-time visual feedback and to accurately measure cell deformation behavior on line. Experiments on both solid-like and liquid-like cells demonstrated that the system is capable of efficiently performing single-cell micropipette aspiration and has low operator skill requirements. PMID:23508635

  17. Method measuring oxygen tension and transport within subcutaneous devices

    PubMed Central

    Weidling, John; Sameni, Sara; Lakey, Jonathan R. T.; Botvinick, Elliot

    2014-01-01

    Abstract. Cellular therapies hold promise to replace the implantation of whole organs in the treatment of disease. For most cell types, in vivo viability depends on oxygen delivery to avoid the toxic effects of hypoxia. A promising approach is the in situ vascularization of implantable devices which can mediate hypoxia and improve both the lifetime and utility of implanted cells and tissues. Although mathematical models and bulk measurements of oxygenation in surrounding tissue have been used to estimate oxygenation within devices, such estimates are insufficient in determining if supplied oxygen is sufficient for the entire thickness of the implanted cells and tissues. We have developed a technique in which oxygen-sensitive microparticles (OSMs) are incorporated into the volume of subcutaneously implantable devices. Oxygen partial pressure within these devices can be measured directly in vivo by an optical probe placed on the skin surface. As validation, OSMs have been incorporated into alginate beads, commonly used as immunoisolation devices to encapsulate pancreatic islet cells. Alginate beads were implanted into the subcutaneous space of Sprague–Dawley rats. Oxygen transport through beads was characterized from dynamic OSM signals in response to changes in inhaled oxygen. Changes in oxygen dynamics over days demonstrate the utility of our technology. PMID:25162910

  18. Single cell-resolution western blotting.

    PubMed

    Kang, Chi-Chih; Yamauchi, Kevin A; Vlassakis, Julea; Sinkala, Elly; Duncombe, Todd A; Herr, Amy E

    2016-08-01

    This protocol describes how to perform western blotting on individual cells to measure cell-to-cell variation in protein expression levels and protein state. Like conventional western blotting, single-cell western blotting (scWB) is particularly useful for protein targets that lack selective antibodies (e.g., isoforms) and in cases in which background signal from intact cells is confounding. scWB is performed on a microdevice that comprises an array of microwells molded in a thin layer of a polyacrylamide gel (PAG). The gel layer functions as both a molecular sieving matrix during PAGE and a blotting scaffold during immunoprobing. scWB involves five main stages: (i) gravity settling of cells into microwells; (ii) chemical lysis of cells in each microwell; (iii) PAGE of each single-cell lysate; (iv) exposure of the gel to UV light to blot (immobilize) proteins to the gel matrix; and (v) in-gel immunoprobing of immobilized proteins. Multiplexing can be achieved by probing with antibody cocktails and using antibody stripping/reprobing techniques, enabling detection of 10+ proteins in each cell. We also describe microdevice fabrication for both uniform and pore-gradient microgels. To extend in-gel immunoprobing to gels of small pore size, we describe an optional gel de-cross-linking protocol for more effective introduction of antibodies into the gel layer. Once the microdevice has been fabricated, the assay can be completed in 4-6 h by microfluidic novices and it generates high-selectivity, multiplexed data from single cells. The technique is relevant when direct measurement of proteins in single cells is needed, with applications spanning the fundamental biosciences to applied biomedicine. PMID:27466711

  19. Herschel Measurements of Molecular Oxygen in Orion

    NASA Astrophysics Data System (ADS)

    Goldsmith, Paul F.; Liseau, René; Bell, Tom A.; Black, John H.; Chen, Jo-Hsin; Hollenbach, David; Kaufman, Michael J.; Li, Di; Lis, Dariusz C.; Melnick, Gary; Neufeld, David; Pagani, Laurent; Snell, Ronald; Benz, Arnold O.; Bergin, Edwin; Bruderer, Simon; Caselli, Paola; Caux, Emmanuel; Encrenaz, Pierre; Falgarone, Edith; Gerin, Maryvonne; Goicoechea, Javier R.; Hjalmarson, Åke; Larsson, Bengt; Le Bourlot, Jacques; Le Petit, Franck; De Luca, Massimo; Nagy, Zsofia; Roueff, Evelyne; Sandqvist, Aage; van der Tak, Floris; van Dishoeck, Ewine F.; Vastel, Charlotte; Viti, Serena; Yıldız, Umut

    2011-08-01

    We report observations of three rotational transitions of molecular oxygen (O2) in emission from the H2 Peak 1 position of vibrationally excited molecular hydrogen in Orion. We observed the 487 GHz, 774 GHz, and 1121 GHz lines using the Heterodyne Instrument for the Far Infrared on the Herschel Space Observatory, having velocities of 11 km s-1 to 12 km s-1 and widths of 3 km s-1. The beam-averaged column density is N(O2) = 6.5 × 1016 cm-2, and assuming that the source has an equal beam-filling factor for all transitions (beam widths 44, 28, and 19''), the relative line intensities imply a kinetic temperature between 65 K and 120 K. The fractional abundance of O2 relative to H2 is (0.3-7.3) × 10-6. The unusual velocity suggests an association with a ~5'' diameter source, denoted Peak A, the Western Clump, or MF4. The mass of this source is ~10 M sun and the dust temperature is >=150 K. Our preferred explanation of the enhanced O2 abundance is that dust grains in this region are sufficiently warm (T >= 100 K) to desorb water ice and thus keep a significant fraction of elemental oxygen in the gas phase, with a significant fraction as O2. For this small source, the line ratios require a temperature >=180 K. The inferred O2 column density sime5 × 1018 cm-2 can be produced in Peak A, having N(H2) ~= 4 × 1024 cm-2. An alternative mechanism is a low-velocity (10-15 km s-1) C-shock, which can produce N(O2) up to 1017 cm-2. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

  20. Outcome measures for palliative oxygen therapy: relevance and practical utility.

    PubMed

    Antoniu, Sabina; Mihaltan, Florin

    2014-06-01

    Dyspnea is a common symptom in many advanced malignant and non-malignant diseases and often is refractory to the usual therapies. In such circumstances palliative care approaches are necessary and among them palliative care oxygen therapy can be applied although currently its effectiveness is rather uncertain. Palliative oxygen therapy can be given on either continuous basis or on demand. Often the continuous palliative oxygen therapy is seen as long-term oxygen therapy although their aims are rather different. Palliative oxygen therapy was evaluated in populations with mixed underlying diseases, with outcome measures not only the most appropriate for the setting and therefore these limitations might have influenced the overall perceived therapeutic benefit. Therefore an evaluation of this method in subsets defined based on the etiology and pathogenic mechanisms and with appropriate outcome measures would help to better define the criteria for its indication and would increase its acceptability. PMID:24741999

  1. FIELD MEASUREMENT OF DISSOLVED OXYGEN: A COMPARISON OF TECHNIQUES

    EPA Science Inventory

    The measurement and interpretation of geochemical redox parameters are key components of ground water remedial investigations. Dissolved oxygen (DO) is perhaps the most robust geochemical parameter in redox characterization; however, recent work has indicated a need for proper da...

  2. Oxygen partial pressure measurement in the HVOF gun tail flame

    SciTech Connect

    Korpiola, K.; Hirvonen, J.P.; Jalkanen, H.; Laas, L.; Rossi, F.

    1995-12-31

    An important aspect of the HVOF thermal spray process is the turbulent mixing of the spray jet with the surrounding air. The air mixing into the jet causes undesirable oxidation of the sprayed coating. In this paper a low cost and accurate method to determine the degree of air mixing is presented. This method was used to measure for the first time the partial pressure of oxygen in the thermal spray flame. The measuring method is based on electrochemical determination of oxygen potential in the tail flame using a solid electrolyte cell. The oxygen partial pressure in the HVOF-gun tail flame was measured with the fuel-to-oxygen ratio, the fuel flow rate and the stand-off distance as variables. The oxygen content of the tail flame was measured and found to vary between 4 to 17% depending on fuel to oxygen ratios and stand-off distances. Such high oxygen contents are several magnitudes too high if serious oxidation in the coating is to be avoided.

  3. Measuring Intracellular Ca2+ Changes in Human Sperm using Four Techniques: Conventional Fluorometry, Stopped Flow Fluorometry, Flow Cytometry and Single Cell Imaging

    PubMed Central

    Mata-Martínez, Esperanza; José, Omar; Torres-Rodríguez, Paulina; Solís-López, Alejandra; Sánchez-Tusie, Ana A.; Sánchez-Guevara, Yoloxochitl; Treviño, Marcela B.; Treviño, Claudia L.

    2013-01-01

    Spermatozoa are male reproductive cells especially designed to reach, recognize and fuse with the egg. To perform these tasks, sperm cells must be prepared to face a constantly changing environment and to overcome several physical barriers. Being in essence transcriptionally and translationally silent, these motile cells rely profoundly on diverse signaling mechanisms to orient themselves and swim in a directed fashion, and to contend with challenging environmental conditions during their journey to find the egg. In particular, Ca2+-mediated signaling is pivotal for several sperm functions: activation of motility, capacitation (a complex process that prepares sperm for the acrosome reaction) and the acrosome reaction (an exocytotic event that allows sperm-egg fusion). The use of fluorescent dyes to track intracellular fluctuations of this ion is of remarkable importance due to their ease of application, sensitivity, and versatility of detection. Using one single dye-loading protocol we utilize four different fluorometric techniques to monitor sperm Ca2+ dynamics. Each technique provides distinct information that enables spatial and/or temporal resolution, generating data both at single cell and cell population levels. PMID:23728309

  4. A review on recent upper atmosphere atomic oxygen measurements

    NASA Astrophysics Data System (ADS)

    Kaufmann, Martin; Ern, Manfred; Riese, Martin; Zhu, Yajun

    2016-07-01

    Atomic oxygen is a key player in the upper mesosphere lower and thermosphere chemistry, energy balance, and dynamics. In recent years, a few new global datasets of this species have been presented. They are based on airglow measurements from low earth satellites. Surprisingly, the atomic oxygen abundance differs by 30-50% for similar atmospheric conditions. This paper gives an overview on the various atomic oxygen datasets available so far and presents most recent results obtained from measurements of the SCIAMACHY instrument on Envisat. Differences between the datasets are discussed.

  5. Surface pressure measurement by oxygen quenching of luminescence

    NASA Technical Reports Server (NTRS)

    Gouterman, Martin P. (Inventor); Kavandi, Janet L. (Inventor); Gallery, Jean (Inventor); Callis, James B. (Inventor)

    1994-01-01

    Methods and compositions for measuring the pressure of an oxygen-containing gas on an aerodynamic surface, by oxygen-quenching of luminescence of molecular sensors is disclosed. Objects are coated with luminescent films containing a first sensor and at least one of two additional sensors, each of the sensors having luminescences that have different dependencies on temperature and oxygen pressure. Methods and compositions are also provided for improving pressure measurements (qualitative or quantitive) on surfaces coated with a film having one or more types of sensor.

  6. Surface pressure measurement by oxygen quenching of luminescence

    NASA Technical Reports Server (NTRS)

    Gouterman, Martin P. (Inventor); Kavandi, Janet L. (Inventor); Gallery, Jean (Inventor); Callis, James B. (Inventor)

    1993-01-01

    Methods and compositions for measuring the pressure of an oxygen-containing gas on an aerodynamic surface, by oxygen-quenching of luminescence of molecular sensors is disclosed. Objects are coated with luminescent films containing a first sensor and at least one of two additional sensors, each of the sensors having luminescences that have different dependencies on temperature and oxygen pressure. Methods and compositions are also provided for improving pressure measurements (qualitative or quantitive) on surfaces coated with a film having one or more types of sensor.

  7. Dissolved-oxygen quenching of in-situ fluorescence measurements

    NASA Astrophysics Data System (ADS)

    Chudyk, Wayne; Tonaszuck, David; Pohlig, Kenneth

    1993-04-01

    In-situ fluorescence measurements of aromatic organic ground water contaminants do not always agree with gas chromatographic methods. Dissolved oxygen quenching of fluorescence may be an interferant in field measurements. Two standard fluorescent aromatics, quinine sulfate and naphthalene, were evaluated in this study. Over the range of dissolved oxygen concentrations expected to be encountered in the field, no effects of oxygen quenching on fluorescence of these compounds was observed. Quenching of quinine sulfate fluorescence by sodium chloride was observed using this system. Sodium chloride quenching was shown to follow the Stern-Volmer relation.

  8. HERSCHEL MEASUREMENTS OF MOLECULAR OXYGEN IN ORION

    SciTech Connect

    Goldsmith, Paul F.; Chen, Jo-Hsin; Li Di; Liseau, Rene; Black, John H.; Bell, Tom A.; Hollenbach, David; Kaufman, Michael J.; Lis, Dariusz C.; Melnick, Gary; Neufeld, David; Pagani, Laurent; Encrenaz, Pierre; Snell, Ronald; Benz, Arnold O.; Bruderer, Simon; Bergin, Edwin; Caselli, Paola; Caux, Emmanuel; Falgarone, Edith

    2011-08-20

    We report observations of three rotational transitions of molecular oxygen (O{sub 2}) in emission from the H{sub 2} Peak 1 position of vibrationally excited molecular hydrogen in Orion. We observed the 487 GHz, 774 GHz, and 1121 GHz lines using the Heterodyne Instrument for the Far Infrared on the Herschel Space Observatory, having velocities of 11 km s{sup -1} to 12 km s{sup -1} and widths of 3 km s{sup -1}. The beam-averaged column density is N(O{sub 2}) = 6.5 x 10{sup 16} cm{sup -2}, and assuming that the source has an equal beam-filling factor for all transitions (beam widths 44, 28, and 19''), the relative line intensities imply a kinetic temperature between 65 K and 120 K. The fractional abundance of O{sub 2} relative to H{sub 2} is (0.3-7.3) x 10{sup -6}. The unusual velocity suggests an association with a {approx}5'' diameter source, denoted Peak A, the Western Clump, or MF4. The mass of this source is {approx}10 M{sub sun} and the dust temperature is {>=}150 K. Our preferred explanation of the enhanced O{sub 2} abundance is that dust grains in this region are sufficiently warm (T {>=} 100 K) to desorb water ice and thus keep a significant fraction of elemental oxygen in the gas phase, with a significant fraction as O{sub 2}. For this small source, the line ratios require a temperature {>=}180 K. The inferred O{sub 2} column density {approx_equal}5 x 10{sup 18} cm{sup -2} can be produced in Peak A, having N(H{sub 2}) {approx_equal} 4 x 10{sup 24} cm{sup -2}. An alternative mechanism is a low-velocity (10-15 km s{sup -1}) C-shock, which can produce N(O{sub 2}) up to 10{sup 17} cm{sup -2}.

  9. Ultra High Precision Laser Monitor for Oxygen Eddy Flux Measurements

    NASA Astrophysics Data System (ADS)

    Nelson, David; Herndon, Scott; McManus, Barry; Roscioli, Rob; Jervis, Dylan; Zahniser, Mark

    2016-04-01

    Atmospheric oxygen provides one of the most powerful tracers to study the carbon cycle through its close interaction with carbon dioxide. Keeling and co-workers demonstrated this at the global scale by using small variations in atmospheric oxygen content to disentangle oceanic and terrestrial carbon sinks. It would be very exciting to apply similar ideas at the ecosystem level to improve our understanding of biosphere-atmosphere exchange and our ability to predict the response of the biosphere and atmosphere to climate change. The eddy covariance technique is perhaps the most effective approach available to quantify the exchange of gases between these spheres. Therefore, eddy covariance flux measurements of oxygen would be extremely valuable. However, this requires a fast response (0.1 seconds), high relative precision (0.001% or 10 per meg) oxygen sensor. We report recent progress in developing such a sensor using a high resolution visible laser to probe the oxygen A-band electronic transition. We have demonstrated precision of 1 ppmv or 5 per meg for a 100 second measurement duration. This sensor will enable oxygen flux measurements using eddy covariance. In addition, we will incorporate a second laser in this instrument to simultaneously determine the fluxes of oxygen, carbon dioxide and water vapor within the same sampling cell. This will provide a direct, real time measurement of the ratio of the flux of oxygen to that of carbon dioxide. This ratio is expected to vary on short time scales and small spatial scales due to the differing stoichiometry of processes producing and consuming carbon dioxide. Thus measuring the variations in the ratio of oxygen and carbon dioxide fluxes will provide mechanistic information to improve our understanding of the crucial exchange of carbon between the atmosphere and biosphere.

  10. A tandem mass spectrometric method for singlet oxygen measurement.

    PubMed

    Karonen, Maarit; Mattila, Heta; Huang, Ping; Mamedov, Fikret; Styring, Stenbjörn; Tyystjärvi, Esa

    2014-01-01

    Singlet oxygen, a harmful reactive oxygen species, can be quantified with the substance 2,2,6,6-tetramethylpiperidine (TEMP) that reacts with singlet oxygen, forming a stable nitroxyl radical (TEMPO). TEMPO has earlier been quantified with electron paramagnetic resonance (EPR) spectroscopy. In this study, we designed an ultra-high-performance liquid chromatographic-tandem mass spectrometric (UHPLC-ESI-MS/MS) quantification method for TEMPO and showed that the method based on multiple reaction monitoring (MRM) can be used for the measurements of singlet oxygen from both nonbiological and biological samples. Results obtained with both UHPLC-ESI-MS/MS and EPR methods suggest that plant thylakoid membranes produce 3.7 × 10(-7) molecules of singlet oxygen per chlorophyll molecule in a second when illuminated with the photosynthetic photon flux density of 2000 μmol m(-2 ) s(-1). PMID:24849296

  11. Langley 8-foot high-temperature tunnel oxygen measurement system

    NASA Technical Reports Server (NTRS)

    Sprinkle, Danny R.; Chen, Tony D.; Chaturvedi, Sushil K.

    1991-01-01

    In order to ensure that there is a proper amount of oxygen necessary for sustaining test engine operation for hypersonic propulsion systems testing at the NASA Langley 8-foot high-temperature tunnel, a quickly responding real-time measurement system of test section oxygen concentration has been designed and tested at Langley. It is built around a zirconium oxide-based sensor which develops a voltage proportional to the oxygen partial pressure of the test gas. The voltage signal is used to control the amount of oxygen being injected into the combustor air. The physical operation of the oxygen sensor is described, as well as the sampling system used to extract the test gas from the tunnel test section. Results of laboratory tests conducted to verify sensor accuracy and response time performance are discussed, as well as the final configuration of the system to be installed in the tunnel.

  12. [Study of plasma temperature measurements for oxygen discharge].

    PubMed

    Li, Liu-Cheng; Wang, Zeng-Qiang; Li, Gu-Fu; Duo, Li-Ping

    2011-10-01

    A radio-frequency discharge setup was constructed by two shell-shaped copper electrodes and a 30 cm long pyrex glass tube (i. d. = 1.65 cm) to examine the gas temperature of oxygen plasma in electric discharge oxygen iodine laser. The discharge was supplied by a 500 watt, 13.56 MHz radio-frequency power. The gas pressure in the discharge cavity was 1 330 Pa. The temperature of oxygen discharge plasma was measured by using the P branch of O2 (b, v = 0) rotational emission spectrum. Two methods were used to deduce the oxygen gas temperature. They are Boltzman plotting method and computer simulating spectrum method, respectively. Gauss fitting method was used to distinguish spectrum peaks for lower resolution spectrum. The spectrum peak area was used to characterize the optical emission intensity. The gas temperature of oxygen discharge plasma was obtained by Boltzmann plotting method. Alternatively, the optical emission spectrum was simulated by computer modeling with spectrometer slit function which was obtained by He-Ne laser. Consequently, the gas temperature of oxygen plasma was obtained by comparing the computer simulating spectrum and the experimentally observed spectrum according to the least square fitting rule. The measurement results with the two methods agree well. It was concluded that the simple optical technique can be used conveniently in the temperature diagnostics of oxygen radio-frequency discharge plasma. PMID:22250527

  13. Fetal oxygenation measurement using wireless near infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Macnab, Andrew; Shadgan, Babak; Janssen, Patricia; Rurak, Dan

    2012-03-01

    Background: Fetal well-being is determined in large part by how well the placenta is able to supply oxygen and nutrients, but current technology is unable to directly measure how well a placenta functions. Near-infrared spectroscopy (NIRS) utilizes optical methods to measure tissue oxygenation. This pilot project evaluated the feasibility of NIRS for fetal monitoring through the maternal abdominal wall using a sheep model. Methods: A miniature wireless 2-wavelength NIRS device was placed on the abdominal skin over the placenta of a pregnant ewe whose fetus had been chronically catheterized to allow arterial sampling for measurement of arterial oxygen saturation. The NIRS device has 3-paired light emitting diodes and a single photodiode detector; allowing measurement of an index of tissue oxygen saturation (TSI%). Fetal limb TSI% values were compared before and during fetal breathing movements. Correlation was made during these events between arterial values and placental TSI% monitored continuously in real time. Results: Serial measurements were obtained in a single experiment. The correlation between transcutaneous NIRS derived TSI% and direct arterial oxygen saturation was very high (R2=0.86). Measures of fetal limb TSI% were declined after episodes of fetal breathing (P<0.005). Conclusions: This correlation suggests that NIRS is sensitive enough to detect changes in fetal tissue oxygenation noninvasively through the maternal abdominal wall in real-time in a sheep model. NIRS data confirmed that fetal breathing movements decrease arterial oxygen saturation in fetal lambs. If validated by further study this optical methodology could be applied as means of monitoring fetal wellbeing in humans.

  14. Noninvasive measurement of cerebral oxygen saturation and cerebral phronetal function

    NASA Astrophysics Data System (ADS)

    Li, Shengli; Zhang, Aiyu; Xu, Min; Jin, Taiyi

    1998-08-01

    Using the Near-Infrared Spectroscopy (NIRS), the noninvasive measurement of cerebral oxygen concentration can be achieved in vivo based on the Lambert-Beer Law. In this paper, we discuss the possibility of studying higher brain functions through combining cerebral oxygen saturation and cerebral function measurement. Event-related experiments are introduced to measure the cerebral phronetal function. Time domain curves show sight differences among these experiment results. However, with the aid of DFT, experiment data of all five human volunteers show the frequency near 20 Hz or 40 Hz is evoked depending on the difficulty of the mental tasks. The results demonstrate the feasibility of cerebral functions study by means of cerebral oxygen saturation measurement analyzed in the frequency domain.

  15. The measurement of hemoglobin oxygen saturation using multiwavelength photoacoustic microscopy

    NASA Astrophysics Data System (ADS)

    Deng, Zilin; Yang, Xiaoquan; Yu, Lejun; Gong, Hui

    2009-10-01

    Hemoglobin oxygen saturation (SO2) is one of the most critical functional parameters to the metabolism. In this paper, we mainly introduced some initial results of measuring blood oxygen using multi-wavelength photoacoustic microscopy (PAM). In phantom study, we demonstrate the photoacoustic signal amplitude increases linearly with the concentration of red or blue ink. Then the calculated concentration of red ink in double-ink mixtures with PAM has a 5% difference with the result measured with spectrophotometric analysis. In ex vivo experiment, the measured result exhibt 15% difference between the PAM and spectrophotometric analysis. Experiment results suggest that PAM could be used to determine the SO2 quantitatively.

  16. The measurement of hemoglobin oxygen saturation using multiwavelength photoacoustic microscopy

    NASA Astrophysics Data System (ADS)

    Deng, Zilin; Yang, Xiaoquan; Yu, Lejun; Gong, Hui

    2010-02-01

    Hemoglobin oxygen saturation (SO2) is one of the most critical functional parameters to the metabolism. In this paper, we mainly introduced some initial results of measuring blood oxygen using multi-wavelength photoacoustic microscopy (PAM). In phantom study, we demonstrate the photoacoustic signal amplitude increases linearly with the concentration of red or blue ink. Then the calculated concentration of red ink in double-ink mixtures with PAM has a 5% difference with the result measured with spectrophotometric analysis. In ex vivo experiment, the measured result exhibt 15% difference between the PAM and spectrophotometric analysis. Experiment results suggest that PAM could be used to determine the SO2 quantitatively.

  17. Gloxy: an oxygen-sensitive coal for accurate measurement of low oxygen tensions in biological systems.

    PubMed

    James, P E; Grinberg, O Y; Goda, F; Panz, T; O'Hara, J A; Swartz, H M

    1997-07-01

    This paper describes the characteristics of a new oxygen sensitive, paramagnetic material that has some significant advantages for measurements of tissue pO2 by in vivo EPR. This paramagnetic component of Welsh coal, termed "gloxy" was found to have valuable EPR features that allow accurate measurement of low oxygen tensions in vivo; these include large oxygen-dependent changes in linewidth, a high number of paramagnetic spin centers (resulting in high signal amplitude), and stability in tissue allowing repeated pO2 measurements to be made in vivo with high precision. Renal pO2 was measured deep in the medulla region of isolated perfused kidneys and found to be lower than that in the cortex (1.7 +/- 0.05 and 7.1 +/- 0.3 mm Hg, respectively). The quality of the EPR signal obtained from the renal outer medulla and also from tumors in mice was such that the pO2 measurements were obtained with a precision of +/-3% of the measured pO2 (Kidney: 1.7 +/- 0.05 mmHg; Tumor: 1.37 +/- 0.04 mmHg). In vitro tests on the viability of cells and in vivo studies using Gloxy demonstrate the stability and inertness of this oxygen-sensitive material. PMID:9211379

  18. Temperature measurements from oxygen isotope ratios of fish otoliths.

    PubMed

    Devereux, I

    1967-03-31

    Measurements have shown that the temperature of a fish's habitat can be deduced from the Oxygen isotope ratio of its otoliths (ear bones). Isotope ratios Obtained from fossil otoliths indicate a water temperature which agrees wiht that found by isotope measurements on associated benthonic foraminifera. PMID:6020293

  19. A Single-Cell Assay for Time Lapse Studies of Exosome Secretion and Cell Behaviors.

    PubMed

    Chiu, Yu-Jui; Cai, Wei; Shih, Yu-Ru V; Lian, Ian; Lo, Yu-Hwa

    2016-07-01

    To understand the inhomogeneity of cells in biological systems, there is a growing demand on the capability of characterizing the properties of individual single cells. Since single-cell studies require continuous monitoring of the cell behaviors, an effective single-cell assay that can support time lapsed studies in a high throughput manner is desired. Most currently available single-cell technologies cannot provide proper environments to sustain cell growth and, proliferation of single cells and convenient, noninvasive tests of single-cell behaviors from molecular markers. Here, a highly versatile single-cell assay is presented that can accommodate different cellular types, enable easy and efficient single-cell loading and culturing, and be suitable for the study of effects of in vitro environmental factors in combination with drug screening. One salient feature of the assay is the noninvasive collection and surveying of single-cell secretions at different time points, producing unprecedented insight of single-cell behaviors based on the biomarker signals from individual cells under given perturbations. Above all, the acquired information is quantitative, for example, measured by the number of exosomes each single-cell secretes for a given time period. Therefore, our single-cell assay provides a convenient, low-cost, and enabling tool for quantitative, time lapsed studies of single-cell properties. PMID:27254278

  20. Magnetic levitation of single cells.

    PubMed

    Durmus, Naside Gozde; Tekin, H Cumhur; Guven, Sinan; Sridhar, Kaushik; Arslan Yildiz, Ahu; Calibasi, Gizem; Ghiran, Ionita; Davis, Ronald W; Steinmetz, Lars M; Demirci, Utkan

    2015-07-14

    Several cellular events cause permanent or transient changes in inherent magnetic and density properties of cells. Characterizing these changes in cell populations is crucial to understand cellular heterogeneity in cancer, immune response, infectious diseases, drug resistance, and evolution. Although magnetic levitation has previously been used for macroscale objects, its use in life sciences has been hindered by the inability to levitate microscale objects and by the toxicity of metal salts previously applied for levitation. Here, we use magnetic levitation principles for biological characterization and monitoring of cells and cellular events. We demonstrate that each cell type (i.e., cancer, blood, bacteria, and yeast) has a characteristic levitation profile, which we distinguish at an unprecedented resolution of 1 × 10(-4) g ⋅ mL(-1). We have identified unique differences in levitation and density blueprints between breast, esophageal, colorectal, and nonsmall cell lung cancer cell lines, as well as heterogeneity within these seemingly homogenous cell populations. Furthermore, we demonstrate that changes in cellular density and levitation profiles can be monitored in real time at single-cell resolution, allowing quantification of heterogeneous temporal responses of each cell to environmental stressors. These data establish density as a powerful biomarker for investigating living systems and their responses. Thereby, our method enables rapid, density-based imaging and profiling of single cells with intriguing applications, such as label-free identification and monitoring of heterogeneous biological changes under various physiological conditions, including antibiotic or cancer treatment in personalized medicine. PMID:26124131

  1. Magnetic levitation of single cells

    PubMed Central

    Durmus, Naside Gozde; Tekin, H. Cumhur; Guven, Sinan; Sridhar, Kaushik; Arslan Yildiz, Ahu; Calibasi, Gizem; Davis, Ronald W.; Steinmetz, Lars M.; Demirci, Utkan

    2015-01-01

    Several cellular events cause permanent or transient changes in inherent magnetic and density properties of cells. Characterizing these changes in cell populations is crucial to understand cellular heterogeneity in cancer, immune response, infectious diseases, drug resistance, and evolution. Although magnetic levitation has previously been used for macroscale objects, its use in life sciences has been hindered by the inability to levitate microscale objects and by the toxicity of metal salts previously applied for levitation. Here, we use magnetic levitation principles for biological characterization and monitoring of cells and cellular events. We demonstrate that each cell type (i.e., cancer, blood, bacteria, and yeast) has a characteristic levitation profile, which we distinguish at an unprecedented resolution of 1 × 10−4 g⋅mL−1. We have identified unique differences in levitation and density blueprints between breast, esophageal, colorectal, and nonsmall cell lung cancer cell lines, as well as heterogeneity within these seemingly homogenous cell populations. Furthermore, we demonstrate that changes in cellular density and levitation profiles can be monitored in real time at single-cell resolution, allowing quantification of heterogeneous temporal responses of each cell to environmental stressors. These data establish density as a powerful biomarker for investigating living systems and their responses. Thereby, our method enables rapid, density-based imaging and profiling of single cells with intriguing applications, such as label-free identification and monitoring of heterogeneous biological changes under various physiological conditions, including antibiotic or cancer treatment in personalized medicine. PMID:26124131

  2. A comparison of measurements of the oxygen nightglow and atomic oxygen in the lower thermosphere

    NASA Technical Reports Server (NTRS)

    Siskind, David E.; Sharp, William E.

    1991-01-01

    The relationship between the oxygen nightglow and the atomic oxygen density in the lower thermosphere was investigated. This was done using data from two sounding rocket experiments conducted over White Sands Missile Range (32-deg N, 106-deg W). The first flight was launched on November 2, 1978 while the second was launched on December 7, 1981. Both flights contained resonance lamps to measure the atomic oxygen density. The peak density in both cases was near 1.9 x 10 to the 11th/cu cm. In addition, the 1978 flight contained a photometer to measure the 5577 A green line, while the 1981 flight contained photometers to measure the green line, the UV nightglow, and the 7620 A (0,0) atmospheric band. Empirical models of these airglow features were used to compare with the O density measurements. In the case of the atmospheric band, excellent agreement is seen concerning the shape of the atomic oxygen profile, while some discrepancies were seen with the Herzberg band and the green line. In all cases, the absolute value of our peak O density appeared to be about 2.5 times lower, for a given airglow intensity, than previous measurements.

  3. Cerebral Blood Oxygenation Measurement Based on Oxygen-dependent Quenching of Phosphorescence

    PubMed Central

    Sakadžić, Sava; Roussakis, Emmanuel; Yaseen, Mohammad A.; Mandeville, Emiri T.; Srinivasan, Vivek J.; Arai, Ken; Ruvinskaya, Svetlana; Wu, Weicheng; Devor, Anna; Lo, Eng H.; Vinogradov, Sergei A.; Boas, David A.

    2011-01-01

    Monitoring of the spatiotemporal characteristics of cerebral blood and tissue oxygenation is crucial for better understanding of the neuro-metabolic-vascular relationship. Development of new pO2 measurement modalities with simultaneous monitoring of pO2 in larger fields of view with higher spatial and/or temporal resolution will enable greater insight into the functioning of the normal brain and will also have significant impact on diagnosis and treatment of neurovascular diseases such as stroke, Alzheimer's disease, and head injury. Optical imaging modalities have shown a great potential to provide high spatiotemporal resolution and quantitative imaging of pO2 based on hemoglobin absorption in visible and near infrared range of optical spectrum. However, multispectral measurement of cerebral blood oxygenation relies on photon migration through the highly scattering brain tissue. Estimation and modeling of tissue optical parameters, which may undergo dynamic changes during the experiment, is typically required for accurate estimation of blood oxygenation. On the other hand, estimation of the partial pressure of oxygen (pO2) based on oxygen-dependent quenching of phosphorescence should not be significantly affected by the changes in the optical parameters of the tissue and provides an absolute measure of pO2. Experimental systems that utilize oxygen-sensitive dyes have been demonstrated in in vivo studies of the perfused tissue as well as for monitoring the oxygen content in tissue cultures, showing that phosphorescence quenching is a potent technology capable of accurate oxygen imaging in the physiological pO2 range. Here we demonstrate with two different imaging modalities how to perform measurement of pO2 in cortical vasculature based on phosphorescence lifetime imaging. In first demonstration we present wide field of view imaging of pO2 at the cortical surface of a rat. This imaging modality has relatively simple experimental setup based on a CCD camera and a

  4. Microscopic oxygen imaging based on fluorescein bleaching efficiency measurements.

    PubMed

    Beutler, Martin; Heisterkamp, Ines M; Piltz, Bastian; Stief, Peter; De Beer, Dirk

    2014-05-01

    Photobleaching of the fluorophore fluorescein in an aqueous solution is dependent on the oxygen concentration. Therefore, the time-dependent bleaching behavior can be used to measure of dissolved oxygen concentrations. The method can be combined with epi-fluorescence microscopy. The molecular states of the fluorophore can be expressed by a three-state energy model. This leads to a set of differential equations which describe the photobleaching behavior of fluorescein. The numerical solution of these equations shows that in a conventional wide-field fluorescence microscope, the fluorescence of fluorescein will fade out faster at low than at high oxygen concentration. Further simulation showed that a simple ratio function of different time-points during a fluorescence decay recorded during photobleaching could be used to describe oxygen concentrations in an aqueous solution. By careful choice of dye concentration and excitation light intensity the sensitivity in the oxygen concentration range of interest can be optimized. In the simulations, the estimation of oxygen concentration by the ratio function was very little affected by the pH value in the range of pH 6.5-8.5. Filming the fluorescence decay by a charge-coupled-device (ccd) camera mounted on a fluorescence microscope allowed a pixelwise estimation of the ratio function in a microscopic image. Use of a microsensor and oxygen-consuming bacteria in a sample chamber enabled the calibration of the system for quantification of absolute oxygen concentrations. The method was demonstrated on nitrifying biofilms growing on snail and mussel shells, showing clear effects of metabolic activity on oxygen concentrations. PMID:24610786

  5. Nanosecond fluorescence microscopy of single cells

    NASA Astrophysics Data System (ADS)

    Keating, Susan M.; Wensel, Theodore G.

    1990-05-01

    A microscope based time-correlated single photon counting instrument has been used to measure nanosecond fluorescence decays from single cells. The excitation source for the instrument is a frequency doubled train of picosecond pulses from the cavity dumped output of a synchronously pumped dye laser. The dye laser is pumped by a mode-locked argon ion laser. In the microscope, the sample is excited and the emission collected using epi-illumination optics before being transmitted through an adjustable diaphragm, which can be closed to 10 μm in diameter. A Hamamatsu R928 photomultiplier is used to collect the fluorescence which is then analyzed using a non-linear least squares procedure. The microscope has been used to measure the intensity decays of model probes to determine the instrument performance and sensitivity. In addition, intensity and anisotropy decays collected from fura-2 loaded into single adherent rat basophilic leukemia cells were measured to demonstrate that the nanosecond fluorescence microscope can be used to obtain information about the environment and mobility of fluorescent probes in single cells.

  6. Advances in High-Throughput Single-Cell Microtechnologies

    PubMed Central

    Weaver, Westbrook M.; Tseng, Peter; Kunze, Anja; Masaeli, Mahdohkht; Chung, Aram J.; Dudani, Jaideep S.; Kittur, Harsha; Kulkarni, Rajan P.; Di Carlo, Dino

    2013-01-01

    Micro-scale biological tools that have allowed probing of individual cells - from the genetic, to proteomic, to phenotypic level - have revealed important contributions of single cells to direct normal and diseased body processes. In analyzing single cells, sample heterogeneity between and within specific cell types drives the need for high-throughput and quantitative measurement of cellular parameters. In recent years, high-throughput single-cell analysis platforms have revealed rare genetic subpopulations in growing tumors, begun to uncover the mechanisms of antibiotic resistance in bacteria, and described the cell-to-cell variations in stem cell differentiation and immune cell response to activation by pathogens. This review surveys these recent technologies, presenting their strengths and contributions to the field, and identifies needs still unmet toward the development of high-throughput single-cell analysis tools to benefit life science research and clinical diagnostics. PMID:24484889

  7. Cerebral blood oxygenation measurement based on oxygen-dependent quenching of phosphorescence.

    PubMed

    Sakadžić, Sava; Roussakis, Emmanuel; Yaseen, Mohammad A; Mandeville, Emiri T; Srinivasan, Vivek J; Arai, Ken; Ruvinskaya, Svetlana; Wu, Weicheng; Devor, Anna; Lo, Eng H; Vinogradov, Sergei A; Boas, David A

    2011-01-01

    Monitoring of the spatiotemporal characteristics of cerebral blood and tissue oxygenation is crucial for better understanding of the neuro-metabolic-vascular relationship. Development of new pO2 measurement modalities with simultaneous monitoring of pO2 in larger fields of view with higher spatial and/or temporal resolution will enable greater insight into the functioning of the normal brain and will also have significant impact on diagnosis and treatment of neurovascular diseases such as stroke, Alzheimer's disease, and head injury. Optical imaging modalities have shown a great potential to provide high spatiotemporal resolution and quantitative imaging of pO2 based on hemoglobin absorption in visible and near infrared range of optical spectrum. However, multispectral measurement of cerebral blood oxygenation relies on photon migration through the highly scattering brain tissue. Estimation and modeling of tissue optical parameters, which may undergo dynamic changes during the experiment, is typically required for accurate estimation of blood oxygenation. On the other hand, estimation of the partial pressure of oxygen (pO2) based on oxygen-dependent quenching of phosphorescence should not be significantly affected by the changes in the optical parameters of the tissue and provides an absolute measure of pO2. Experimental systems that utilize oxygen-sensitive dyes have been demonstrated in in vivo studies of the perfused tissue as well as for monitoring the oxygen content in tissue cultures, showing that phosphorescence quenching is a potent technology capable of accurate oxygen imaging in the physiological pO2 range. Here we demonstrate with two different imaging modalities how to perform measurement of pO2 in cortical vasculature based on phosphorescence lifetime imaging. In first demonstration we present wide field of view imaging of pO2 at the cortical surface of a rat. This imaging modality has relatively simple experimental setup based on a CCD camera and a

  8. Optical manipulation for single-cell studies.

    PubMed

    Ramser, Kerstin; Hanstorp, Dag

    2010-04-01

    In the last decade optical manipulation has evolved from a field of interest for physicists to a versatile tool widely used within life sciences. This has been made possible in particular due to the development of a large variety of imaging techniques that allow detailed information to be gained from investigations of single cells. The use of multiple optical traps has high potential within single-cell analysis since parallel measurements provide good statistics. Multifunctional optical tweezers are, for instance, used to study cell heterogeneity in an ensemble, and force measurements are used to investigate the mechanical properties of individual cells. Investigations of molecular motors and forces on the single-molecule level have led to discoveries that would have been difficult to make with other techniques. Optical manipulation has prospects within the field of cell signalling and tissue engineering. When combined with microfluidic systems the chemical environment of cells can be precisely controlled. Hence the influence of pH, salt concentration, drugs and temperature can be investigated in real time. Fast advancing technical developments of automated and user-friendly optical manipulation tools and cross-disciplinary collaboration will contribute to the routinely use of optical manipulation techniques within the life sciences. PMID:19718682

  9. FIELD MEASUREMENT OF DISSOLVED OXYGEN: A COMPARISON OF METHODS

    EPA Science Inventory

    The ability to confidently measure the concentration of dissolved oxygen (D.O.) in ground water is a key aspect of remedial selection and assessment. Presented here is a comparison of the commonly practiced methods for determining D.O. concentrations in ground water, including c...

  10. Monitoring microvascular free flaps with tissue oxygen measurement and PET.

    PubMed

    Schrey, Aleksi R; Kinnunen, Ilpo A J; Grénman, Reidar A; Minn, Heikki R I; Aitasalo, Kalle M J

    2008-07-01

    Tissue oxygen measurement and positron emission tomography (PET) were evaluated as methods for predicting ischemia in microvascular free flaps of the head and neck. Ten patients with head and neck squamous cell cancer underwent resection of the tumour followed by microvascular reconstruction with a free flap. Tissue oxygenation of the flap (P(ti)O(2)) was continuously monitored for three postoperative (POP) days and the blood flow of the flap was assessed using oxygen-15 labelled water and PET. In three free flaps a perfusion problem was suspected due to a remarkable drop in P(ti)O(2)-values, due to two anastomosis problems and due to POP turgor. No flap losses occurred. During the blood flow measurements with PET [mean 8.5 mL 100 g(-1) min(-1 )(SD 2.5)], the mean P(ti)O(2) of the flaps [46.8 mmHg (SD 17.0)] appeared to correlate with each other in each patient (p<0.05, n=10). Tissue oxygenation measurement is a feasible monitoring system of free flaps. The perfusion-study with PET correlates with P(ti)O(2)-measurement. PMID:18231800

  11. OXYGEN CONSUMPTION MEASURED WITH MICROCOMPUTER-ASSISTED WARBURG MANOMETRY

    EPA Science Inventory

    The authors have developed and tested an automated system that measures in vitro oxygen consumption by Warburg manometry in as many as 16 units that are under the simultaneous control of a microcomputer which requires attention at the beginning of the study only. The all-glass Su...

  12. Single Cell Chromatography, LDRD Feasibility Study

    SciTech Connect

    Knize, M G; Bailey, C G

    2007-02-22

    A limitation in the mass spectrometry of biological materials is the reduced ion formation caused by sample complexity. We proposed to develop an enabling technology, single cell planar chromatography, which will greatly increase the amount of chemical information that can be obtained from single biological cells when using imaging mass spectrometry or other surface analysis methods. The sample preparation methods were developed for the time-of-flight secondary mass spectrometer (ToF-SIMS) at LLNL. This instrument has a measured zeptomole (10{sup -21} mole, 600 atoms) limit-of-detection for a molecule with a mass to charge ratio of 225[1]. Our goal was to use planar chromatographic separation to approach similar low limits of detection even with the chemically complex contents of a single cell. The process was proposed to reduce ion suppression and at the same time expose more of the cell contents to the ion beam. The method of work was to deposit biological cells on a silicon chip with suitable chromatographic and electrical properties, dissolve the cell with a droplet of solvent, allow the solvent to evaporate, and then allow the movement of cell contents laterally by immersing an edge of the chip in to a chromatographic solvent, that then moves through the chromatographic matrix allowing the components to interact with, and be separated by, the chromatographic substrate. This process is a miniaturized version of thin layer chromatography with detection by surface mass spectrometry.

  13. ASRDI oxygen technology survey. Volume 4: Low temperature measurement

    NASA Technical Reports Server (NTRS)

    Sparks, L. L.

    1974-01-01

    Information is presented on temperature measurement between the triple point and critical point of liquid oxygen. The criterion selected is that all transducers which may reasonably be employed in the liquid oxygen (LO2) temperature range are considered. The temperature range for each transducer is the appropriate full range for the particular thermometer. The discussion of each thermometer or type of thermometer includes the following information: (1) useful temperature range, (2) general and particular methods of construction and the advantages of each type, (3) specifications (accuracy, reproducibility, response time, etc.), (4) associated instrumentation, (5) calibrations and procedures, and (6) analytical representations.

  14. Oxygen concentration measurement in liquid lead-bismuth eutectic

    SciTech Connect

    Darling, T. W.; Li, N.

    2001-01-01

    Liquid lead-bismuth (Pb-Bi) eutectic (LBE) may see extensive use as a coolant fluid, and perhaps also as a spallation target, in next generation nuclear energy systems. While it is not as reactive as alkali metal liquids, it does present a long term corrosion problem with some materials, notably stainless steels. Mitigation of the corrosion problem may be achieved by producing and maintaining a protective oxide on exposed surfaces, through control of the concentration of dissolved oxygen in the LBE. We have developed an oxygen sensor based on available zirconia-based solid electrolytes used in the automotive industry, which represents a relatively inexpensive source of reproducible and reliable components. We will present the design considerations and characteristics of our sensor unit, and describe its use in the LBE test loop at Los Alamos for measurement and control of dissolved oxygen concentration.

  15. Measuring oxygen uptake in fishes with bimodal respiration.

    PubMed

    Lefevre, S; Bayley, M; McKenzie, D J

    2016-01-01

    Respirometry is a robust method for measurement of oxygen uptake as a proxy for metabolic rate in fishes, and how species with bimodal respiration might meet their demands from water v. air has interested researchers for over a century. The challenges of measuring oxygen uptake from both water and air, preferably simultaneously, have been addressed in a variety of ways, which are briefly reviewed. These methods are not well-suited for the long-term measurements necessary to be certain of obtaining undisturbed patterns of respiratory partitioning, for example, to estimate traits such as standard metabolic rate. Such measurements require automated intermittent-closed respirometry that, for bimodal fishes, has only recently been developed. This paper describes two approaches in enough detail to be replicated by the interested researcher. These methods are for static respirometry. Measuring oxygen uptake by bimodal fishes during exercise poses specific challenges, which are described to aid the reader in designing experiments. The respiratory physiology and behaviour of air-breathing fishes is very complex and can easily be influenced by experimental conditions, and some general considerations are listed to facilitate the design of experiments. Air breathing is believed to have evolved in response to aquatic hypoxia and, probably, associated hypercapnia. The review ends by considering what realistic hypercapnia is, how hypercapnic tropical waters can become and how this might influence bimodal animals' gas exchange. PMID:26358224

  16. Single-Cell Genomics for Virology.

    PubMed

    Ciuffi, Angela; Rato, Sylvie; Telenti, Amalio

    2016-01-01

    Single-cell sequencing technologies, i.e., single cell analysis followed by deep sequencing investigate cellular heterogeneity in many biological settings. It was only in the past year that single-cell sequencing analyses has been applied in the field of virology, providing new ways to explore viral diversity and cell response to viral infection, which are summarized in the present review. PMID:27153082

  17. Single-Cell Genomics for Virology

    PubMed Central

    Ciuffi, Angela; Rato, Sylvie; Telenti, Amalio

    2016-01-01

    Single-cell sequencing technologies, i.e., single cell analysis followed by deep sequencing investigate cellular heterogeneity in many biological settings. It was only in the past year that single-cell sequencing analyses has been applied in the field of virology, providing new ways to explore viral diversity and cell response to viral infection, which are summarized in the present review. PMID:27153082

  18. Redefining Signaling Pathways with an Expanding Single-Cell Toolbox.

    PubMed

    Gaudet, Suzanne; Miller-Jensen, Kathryn

    2016-06-01

    Genetically identical cells respond heterogeneously to uniform environmental stimuli. Consequently, investigating the signaling networks that control these cell responses using 'average' bulk cell measurements can obscure underlying mechanisms and misses information emerging from cell-to-cell variability. Here we review recent technological advances including live-cell fluorescence imaging-based approaches and microfluidic devices that enable measurements of signaling networks, dynamics, and responses in single cells. We discuss how these single-cell tools have uncovered novel mechanistic insights for canonical signaling pathways that control cell proliferation (ERK), DNA-damage responses (p53), and innate immune and stress responses (NF-κB). Future improvements in throughput and multiplexing, analytical pipelines, and in vivo applicability will all significantly expand the biological information gained from single-cell measurements of signaling pathways. PMID:26968612

  19. A microfluidic approach to parallelized transcriptional profiling of single cells

    PubMed Central

    Sun, Hao; Olsen, Timothy; Zhu, Jing; Tao, Jianguo; Ponnaiya, Brian; Amundson, Sally A.; Brenner, David J.; Lin, Qiao

    2016-01-01

    The ability to correlate single-cell genetic information with cellular phenotypes is of great importance to biology and medicine, as it holds the potential to gain insight into disease pathways that is unavailable from ensemble measurements. We present a microfluidic approach to parallelized, rapid, quantitative analysis of messenger RNA from single cells via RT-qPCR. The approach leverages an array of single-cell RT-qPCR analysis units formed by a set of parallel microchannels concurrently controlled by elastomeric pneumatic valves, thereby enabling parallelized handling and processing of single cells in a drastically simplified operation procedure using a relatively small number of microvalves. All steps for single-cell RT-qPCR, including cell isolation and immobilization, cell lysis, mRNA purification, reverse transcription and qPCR, are integrated on a single chip, eliminating the need for off-chip manual cell and reagent transfer and qPCR amplification as commonly used in existing approaches. Additionally, the approach incorporates optically transparent microfluidic components to allow monitoring of single-cell trapping without the need for molecular labeling that can potentially alter the targeted gene expression and utilizes a polycarbonate film as a barrier against evaporation to minimize the loss of reagents at elevated temperatures during the analysis. We demonstrate the utility of the approach by the transcriptional profiling for the induction of the cyclin-dependent kinase inhibitor 1a and the glyceraldehyde 3-phosphate dehydrogenase in single cells from the MCF-7 breast cancer cell line. Furthermore, the methyl methanesulfonate is employed to allow measurement of the expression of the genes in individual cells responding to a genotoxic stress. PMID:27194954

  20. Microfluidic single-cell whole-transcriptome sequencing.

    PubMed

    Streets, Aaron M; Zhang, Xiannian; Cao, Chen; Pang, Yuhong; Wu, Xinglong; Xiong, Liang; Yang, Lu; Fu, Yusi; Zhao, Liang; Tang, Fuchou; Huang, Yanyi

    2014-05-13

    Single-cell whole-transcriptome analysis is a powerful tool for quantifying gene expression heterogeneity in populations of cells. Many techniques have, thus, been recently developed to perform transcriptome sequencing (RNA-Seq) on individual cells. To probe subtle biological variation between samples with limiting amounts of RNA, more precise and sensitive methods are still required. We adapted a previously developed strategy for single-cell RNA-Seq that has shown promise for superior sensitivity and implemented the chemistry in a microfluidic platform for single-cell whole-transcriptome analysis. In this approach, single cells are captured and lysed in a microfluidic device, where mRNAs with poly(A) tails are reverse-transcribed into cDNA. Double-stranded cDNA is then collected and sequenced using a next generation sequencing platform. We prepared 94 libraries consisting of single mouse embryonic cells and technical replicates of extracted RNA and thoroughly characterized the performance of this technology. Microfluidic implementation increased mRNA detection sensitivity as well as improved measurement precision compared with tube-based protocols. With 0.2 M reads per cell, we were able to reconstruct a majority of the bulk transcriptome with 10 single cells. We also quantified variation between and within different types of mouse embryonic cells and found that enhanced measurement precision, detection sensitivity, and experimental throughput aided the distinction between biological variability and technical noise. With this work, we validated the advantages of an early approach to single-cell RNA-Seq and showed that the benefits of combining microfluidic technology with high-throughput sequencing will be valuable for large-scale efforts in single-cell transcriptome analysis. PMID:24782542

  1. Highly sensitive thermometer using a vacuum-packed Si resonator in a microfluidic chip for the thermal measurement of single cells.

    PubMed

    Inomata, Naoki; Toda, Masaya; Ono, Takahito

    2016-09-21

    A highly sensitive thermometer system for a living cell is proposed, fabricated, and evaluated. The system possesses a resonant thermal sensor surrounded by vacuum in a microfluidic chip. The measurement principle relies on resonant frequency tracking of the resonator in temperature variations due to the heat from a sample cell; the heat is conducted from the sample cell in the microfluidic channel via a heat guide connecting the resonator to a sample stage. This configuration can reduce heat loss from the resonator to the surroundings and damping in water. Two types of resonators are prepared, i.e., a cantilevered resonator and a double-supported resonator. The resonator sizes as a sensor are 30 × 50 × 1.5 μm in the cantilevered resonator, 30 × 75 × 0.40 μm in the double-supported one, respectively. The temperature and thermal resolutions of 79 μK and 1.90 nW, respectively, are achieved using the double-supported resonator. Two types of heat emissions from single brown fat cells are detected; one is continuous heat generation in the presence of chemical stimulation by a norepinephrine solution, and the other is pulsed without any stimulation. PMID:27526966

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

    PubMed

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

    2015-12-16

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

  3. Electrodeformation for single cell mechanical characterization

    NASA Astrophysics Data System (ADS)

    Chen, Jian; Abdelgawad, Mohamed; Yu, Liming; Shakiba, Nika; Chien, Wei-Yin; Lu, Zhe; Geddie, William R.; Jewett, Michael A. S.; Sun, Yu

    2011-05-01

    This paper presents the use of electrodeformation as a method for single cell mechanical characterization in which mechanical properties of SiHa and ME180 cells (two cervical cancer cell lines) were quantified. Cells were directly placed between two microelectrodes with a rectangular ac electric field applied, and cell deformation was recorded under certain experimental conditions. Numerical simulations were performed to model cell electrodeformation based on the Maxwell stress tensor formulation. In these simulations, effects of cell electrical property variations on their electrodeformed behavior were investigated. By comparing the measured morphological changes with those obtained from numerical simulations, we were able to quantify Young's modulus of SiHa cells (601 ± 183 Pa) and ME180 cells (1463 ± 649 Pa). These values were consistent with Young's modulus values (SiHa: 400 ± 290 Pa and ME180: 1070 ± 580 Pa) obtained from conventional micropipette aspiration.

  4. Single cell protein as an occupational hazard.

    PubMed Central

    Ekenvall, L; Dölling, B; Göthe, C J; Ebbinghaus, L; von Stedingk, L V; Wasserman, J

    1983-01-01

    Single cell protein (SCP) intended for animal feed purposes was produced in a pilot plant. The SCP consisted of Methylomonas methanolica, a pseudomonas species which is an obligate methanol user. The SCP was cultured in fermenters and later dewatered and dried in a spray-drier. Seven of eight research workers had febrile reactions 6-12 hours after exposure to SCP dust. All workers had high titres of IgG and IgM antibodies against the pseudomonas species as measured with indirect ELISA and passive haemagglutination techniques. The mechanism behind the febrile reaction is judged to be a non-immunological reaction caused by endotoxins. By increasing the particle size of the SCP through using different drying procedures, a product which generated less dust was obtained. PMID:6830720

  5. Intrinsic oxygen fugacity measurements of some Allende Type B inclusions

    NASA Technical Reports Server (NTRS)

    Kozul, Jean M.; Hewins, Roger H.; Ulmer, Gene C.

    1988-01-01

    The intrinsic oxygen fugacities (IOFs) of two type B Ca-rich and Al-rich inclusions (CAI) from the Allende meteorite were measured using the solid-electrolyte double-cell IOF technique of Ulmer et al. (1976). The measurements were compared to calculated and experimentally extrapolated fO2 of type B phases. It was found that the IOFs of the type B are 6-8 orders of magnitude more oxidized (H2/H2O = 1-10) than the canonical solar nebular gas (H2/H2O = 100-2000). It is suggested that some local fO2 enhancing mechanism, such as dust or gas concentrations, or the release of oxygen-rich vapors during CAI volatilization in the type B inclusions was in operation at temperatures higher than 700 C.

  6. Overview of single-cell elastic light scattering techniques.

    PubMed

    Kinnunen, Matti; Karmenyan, Artashes

    2015-05-01

    We present and discuss several modern optical methods based on elastic light scattering (ELS), along with their technical features and applications in biomedicine and life sciences. In particular, we review some ELS experiments at the single-cell level and explore new directions of applications. Due to recent developments in experimental systems (as shown in the literature), ELS lends itself to useful applications in the life sciences. Of the developed methods, we cover elastic scattering spectroscopy, optical tweezer-assisted measurement, goniometers, Fourier transform light scattering (FTLS), and microscopic methods. FTLS significantly extends the potential analysis of single cells by allowing monitoring of dynamical changes at the single-cell level. The main aim of our review is to demonstrate developments in the experimental investigation of ELS in single cells including issues related to theoretical “representations” and modeling of biological systems (cells, cellular systems, tissues, and so on). Goniometric measurements of ELS from optically trapped single cells are shown and the importance of the experimental verification of theoretical models of ELS in the context of biomedical applications is discussed. PMID:25760756

  7. Integrated Electrowetting Nanoinjector for Single Cell Transfection

    PubMed Central

    Shekaramiz, Elaheh; Varadarajalu, Ganeshkumar; Day, Philip J.; Wickramasinghe, H. Kumar

    2016-01-01

    Single cell transfection techniques are essential to understand the heterogeneity between cells. We have developed an integrated electrowetting nanoinjector (INENI) to transfect single cells. The high transfection efficiency, controlled dosage delivery and ease of INENI fabrication promote the widespread application of the INENI in cell transfection assays. PMID:27374766

  8. Device for measuring oxygen activity in liquid sodium

    DOEpatents

    Roy, P.; Young, R.S.

    1973-12-01

    A composite ceramic electrolyte in a configuration (such as a closed end tube or a plate) suitable to separate liquid sodium from a reference electrode with a high impedance voltmeter connected to measure EMF between the sodium and the reference electrode as a measure of oxygen activity in the sodium is described. The composite electrolyte consists of zirconiacalcia with a bonded layer of thoria-yttria. The device is used with a gaseous reference electrode on the zirconia-calcia side and liquid sodium on the thoria-yttria side of the electrolyte. (Official Gazette)

  9. Leaf water oxygen isotope measurement by direct equilibration.

    PubMed

    Song, Xin; Barbour, Margaret M

    2016-08-01

    The oxygen isotope composition of leaf water imparts a signal to a range of molecules in the atmosphere and biosphere, but has been notoriously difficult to measure in studies requiring a large number of samples as a consequence of the labour-intensive extraction step. We tested a method of direct equilibration of water in fresh leaf samples with CO2 , and subsequent oxygen isotope analysis on an optical spectrometer. The oxygen isotope composition of leaf water measured by the direct equilibration technique was strongly linearly related to that of cryogenically extracted leaf water in paired samples for a wide range of species with differing anatomy, with an R(2) of 0.95. The somewhat more enriched values produced by the direct equilibration method may reflect lack of full equilibration with unenriched water in the vascular bundles, but the strong relationship across a wide range of species suggests that this difference can be adequately corrected for using a simple linear relationship. PMID:27147584

  10. Single cell correlation fractal dimension of chromatin

    PubMed Central

    Récamier, Vincent; Izeddin, Ignacio; Bosanac, Lana; Dahan, Maxime; Proux, Florence; Darzacq, Xavier

    2014-01-01

    Chromatin is a major nuclear component, and it is an active matter of debate to understand its different levels of spatial organization, as well as its implication in gene regulation. Measurements of nuclear chromatin compaction were recently used to understand how DNA is folded inside the nucleus and to detect cellular dysfunctions such as cancer. Super-resolution imaging opens new possibilities to measure chromatin organization in situ. Here, we performed a direct measure of chromatin compaction at the single cell level. We used histone H2B, one of the 4 core histone proteins forming the nucleosome, as a chromatin density marker. Using photoactivation localization microscopy (PALM) and adaptive optics, we measured the three-dimensional distribution of H2B with nanometric resolution. We computed the distribution of distances between every two points of the chromatin structure, namely the Ripley K(r) distribution. We found that the K(r) distribution of H2B followed a power law, leading to a precise measurement of the correlation fractal dimension of chromatin of 2.7. Moreover, using photoactivable GFP fused to H2B, we observed dynamic evolution of chromatin sub-regions compaction. As a result, the correlation fractal dimension of chromatin reported here can be interpreted as a dynamically maintained non-equilibrium state. PMID:24637833

  11. Oxygen measurements in brain stem slices exposed to normobaric hyperoxia and hyperbaric oxygen.

    PubMed

    Mulkey, D K; Henderson, R A; Olson, J E; Putnam, R W; Dean, J B

    2001-05-01

    We previously reported (J Appl Physiol 89: 807-822, 2000) that < or =10 min of hyperbaric oxygen (HBO(2); < or = 2,468 Torr) stimulates solitary complex neurons. To better define the hyperoxic stimulus, we measured PO(2) in the solitary complex of 300-microm-thick rat medullary slices, using polarographic carbon fiber microelectrodes, during perfusion with media having PO(2) values ranging from 156 to 2,468 Torr. Under control conditions, slices equilibrated with 95% O(2) at barometric pressure of 1 atmospheres absolute had minimum PO(2) values at their centers (291 +/- 20 Torr) that were approximately 10-fold greater than PO(2) values measured in the intact central nervous system (10-34 Torr). During HBO(2), PO(2) increased at the center of the slice from 616 +/- 16 to 1,517 +/- 15 Torr. Tissue oxygen consumption tended to decrease at medium PO(2) or = 1,675 Torr to levels not different from values measured at PO(2) found in all media in metabolically poisoned slices (2-deoxy-D-glucose and antimycin A). We conclude that control medium used in most brain slice studies is hyperoxic at normobaric pressure. During HBO(2), slice PO(2) increases to levels that appear to reduce metabolism. PMID:11299283

  12. Single-cell genome sequencing: current state of the science.

    PubMed

    Gawad, Charles; Koh, Winston; Quake, Stephen R

    2016-03-01

    The field of single-cell genomics is advancing rapidly and is generating many new insights into complex biological systems, ranging from the diversity of microbial ecosystems to the genomics of human cancer. In this Review, we provide an overview of the current state of the field of single-cell genome sequencing. First, we focus on the technical challenges of making measurements that start from a single molecule of DNA, and then explore how some of these recent methodological advancements have enabled the discovery of unexpected new biology. Areas highlighted include the application of single-cell genomics to interrogate microbial dark matter and to evaluate the pathogenic roles of genetic mosaicism in multicellular organisms, with a focus on cancer. We then attempt to predict advances we expect to see in the next few years. PMID:26806412

  13. A single cell penetration system by ultrasonic driving

    NASA Astrophysics Data System (ADS)

    Zhou, Zhaoying; Xiao, Mingfei; Yang, Xing; Wu, Ting

    2008-12-01

    The researches of single cell's control and operation are the hotspots in whole world. Among the various technologies, the transmission of ectogenic genetic materials between cell membrane is very significant. Imitating the Chinese traditional acupuncture therapy, a new ultrasonic resonance driving method, is imported to drive a cell's penetration probe. A set of the single cell penetration system was established to perform this function. This system includes four subsystems: driving part, micromanipulation part, observation and measurement part, and actuation part. Some fish egg experiments indicate that this system is workable and effective.

  14. Comparison of two sediment oxygen demand measurement techniques

    SciTech Connect

    Truax, D.D.; Sindala, A.; Sartain, H.

    1995-09-01

    Measuring the sediment oxygen demand rate in deep water can be difficult. Yet this parameter can be a significant component in ecological models of deep water systems. The results of a study to characterize the oxygen demand in the benthos of more than 210 km (130 mi) of the Tennessee-Tombigbee Waterway are presented here. Sampling was performed with a modified Shelby tube apparatus, which allowed the collection of samples at depths of more than 7 m (25 ft) without the use of divers. Results of in-situ analyses performed by the U.S. Environmental Protection Agency (EPA) are correlated with data from a sampling and laboratory methodology developed for this project. The laboratory setup used a sealed, cylindrical chamber through which water was continuously recirculated. The results of both procedures were statistically equivalent throughout the majority of the waterway. Only in areas where the channel bottom consisted of extremely porous media did the sampling and laboratory methodology yield questionable results. The results obtained indicate that sediment oxygen demand of the section of the waterway studied ranged between 0.5 g O{sub 2}/m{sup 2}-day and 1.5 g O{sub 2}/m{sup 2}-day.

  15. Automated Single Cell Data Decontamination Pipeline

    SciTech Connect

    Tennessen, Kristin; Pati, Amrita

    2014-03-21

    Recent technological advancements in single-cell genomics have encouraged the classification and functional assessment of microorganisms from a wide span of the biospheres phylogeny.1,2 Environmental processes of interest to the DOE, such as bioremediation and carbon cycling, can be elucidated through the genomic lens of these unculturable microbes. However, contamination can occur at various stages of the single-cell sequencing process. Contaminated data can lead to wasted time and effort on meaningless analyses, inaccurate or erroneous conclusions, and pollution of public databases. A fully automated decontamination tool is necessary to prevent these instances and increase the throughput of the single-cell sequencing process

  16. Near-infrared measurements of brain oxygenation in stroke.

    PubMed

    Moreau, François; Yang, Runze; Nambiar, Vivek; Demchuk, Andrew M; Dunn, Jeff F

    2016-07-01

    We investigated the feasibility of using frequency-domain near-infrared spectroscopy (fdNIRS) to study brain oxygenation in the first few hours of stroke onset. The OxiplexTS(®) fdNIRS system was used in this study. Using a standard probing protocol based on surface landmarks, we measured brain tHb and [Formula: see text] in healthy volunteers, cadavers, and acute stroke patients within 9 h of stroke onset and 3 days later. We obtained measurements from 11 controls, 5 cadavers, and 5 acute stroke patients. [Formula: see text] values were significantly lower in cadavers compared to the controls and stroke patients. Each stroke patient had at least one area with reduced [Formula: see text] on the stroke side compared to the contralateral side. The evolution of tHb and [Formula: see text] at 3 days differed depending on whether a large infarct occurred. This study shows the proof of principle that quantified measurements of brain oxygenation using NIRS could be used in the hectic environment of acute stroke management. It also highlights the current technical limitations and future challenges in the development of this unique bedside monitoring tool for stroke. PMID:26958577

  17. Sound speed measurements in liquid oxygen-liquid nitrogen mixtures

    NASA Technical Reports Server (NTRS)

    Zuckerwar, A. J.; Mazel, D. S.

    1985-01-01

    The sound speed in liquid oxygen (LOX), liquid nitrogen (LN2), and five LOX-LN2 mixtures was measured by an ultrasonic pulse-echo technique at temperatures in the vicinity of -195.8C, the boiling point of N2 at a pressure of I atm. Under these conditions, the measurements yield the following relationship between sound speed in meters per second and LN2 content M in mole percent: c = 1009.05-1.8275M+0.0026507 M squared. The second speeds of 1009.05 m/sec plus or minus 0.25 percent for pure LOX and 852.8 m/sec plus or minus 0.32 percent for pure LN2 are compared with those reported by past investigators. Measurement of sound speed should prove an effective means for monitoring the contamination of LOX by Ln2.

  18. Single-cell analysis of dihydroartemisinin-induced apoptosis through reactive oxygen species-mediated caspase-8 activation and mitochondrial pathway in ASTC-a-1 cells using fluorescence imaging techniques

    NASA Astrophysics Data System (ADS)

    Lu, Ying-Ying; Chen, Tong-Sheng; Wang, Xiao-Ping; Li, Li

    2010-07-01

    Dihydroartemisinin (DHA), a front-line antimalarial herbal compound, has been shown to possess promising anticancer activity with low toxicity. We have previously reported that DHA induced caspase-3-dependent apoptosis in human lung adenocarcinoma cells. However, the cellular target and molecular mechanism of DHA-induced apoptosis is still poorly defined. We use confocal fluorescence microscopy imaging, fluorescence resonance energy transfer, and fluorescence recovery after photobleaching techniques to explore the roles of DHA-elicited reactive oxygen species (ROS) in the DHA-induced Bcl-2 family proteins activation, mitochondrial dysfunction, caspase cascade, and cell death. Cell Counting Kit-8 assay and flow cytometry analysis showed that DHA induced ROS-mediated apoptosis. Confocal imaging analysis in a single living cell and Western blot assay showed that DHA triggered ROS-dependent Bax translocation, mitochondrial membrane depolarization, alteration of mitochondrial morphology, cytochrome c release, caspase-9, caspase-8, and caspase-3 activation, indicating the coexistence of ROS-mediated mitochondrial and death receptor pathway. Collectively, our findings demonstrate for the first time that DHA induces cell apoptosis by triggering ROS-mediated caspase-8/Bid activation and the mitochondrial pathway, which provides some novel insights into the application of DHA as a potential anticancer drug and a new therapeutic strategy by targeting ROS signaling in lung adenocarcinoma therapy in the future.

  19. Efficient Synergistic Single-Cell Genome Assembly

    PubMed Central

    Movahedi, Narjes S.; Embree, Mallory; Nagarajan, Harish; Zengler, Karsten; Chitsaz, Hamidreza

    2016-01-01

    As the vast majority of all microbes are unculturable, single-cell sequencing has become a significant method to gain insight into microbial physiology. Single-cell sequencing methods, currently powered by multiple displacement genome amplification (MDA), have passed important milestones such as finishing and closing the genome of a prokaryote. However, the quality and reliability of genome assemblies from single cells are still unsatisfactory due to uneven coverage depth and the absence of scattered chunks of the genome in the final collection of reads caused by MDA bias. In this work, our new algorithm Hybrid De novo Assembler (HyDA) demonstrates the power of coassembly of multiple single-cell genomic data sets through significant improvement of the assembly quality in terms of predicted functional elements and length statistics. Coassemblies contain significantly more base pairs and protein coding genes, cover more subsystems, and consist of longer contigs compared to individual assemblies by the same algorithm as well as state-of-the-art single-cell assemblers SPAdes and IDBA-UD. Hybrid De novo Assembler (HyDA) is also able to avoid chimeric assemblies by detecting and separating shared and exclusive pieces of sequence for input data sets. By replacing one deep single-cell sequencing experiment with a few single-cell sequencing experiments of lower depth, the coassembly method can hedge against the risk of failure and loss of the sample, without significantly increasing sequencing cost. Application of the single-cell coassembler HyDA to the study of three uncultured members of an alkane-degrading methanogenic community validated the usefulness of the coassembly concept. HyDA is open source and publicly available at http://chitsazlab.org/software.html, and the raw reads are available at http://chitsazlab.org/research.html. PMID:27243002

  20. Efficient Synergistic Single-Cell Genome Assembly.

    PubMed

    Movahedi, Narjes S; Embree, Mallory; Nagarajan, Harish; Zengler, Karsten; Chitsaz, Hamidreza

    2016-01-01

    As the vast majority of all microbes are unculturable, single-cell sequencing has become a significant method to gain insight into microbial physiology. Single-cell sequencing methods, currently powered by multiple displacement genome amplification (MDA), have passed important milestones such as finishing and closing the genome of a prokaryote. However, the quality and reliability of genome assemblies from single cells are still unsatisfactory due to uneven coverage depth and the absence of scattered chunks of the genome in the final collection of reads caused by MDA bias. In this work, our new algorithm Hybrid De novo Assembler (HyDA) demonstrates the power of coassembly of multiple single-cell genomic data sets through significant improvement of the assembly quality in terms of predicted functional elements and length statistics. Coassemblies contain significantly more base pairs and protein coding genes, cover more subsystems, and consist of longer contigs compared to individual assemblies by the same algorithm as well as state-of-the-art single-cell assemblers SPAdes and IDBA-UD. Hybrid De novo Assembler (HyDA) is also able to avoid chimeric assemblies by detecting and separating shared and exclusive pieces of sequence for input data sets. By replacing one deep single-cell sequencing experiment with a few single-cell sequencing experiments of lower depth, the coassembly method can hedge against the risk of failure and loss of the sample, without significantly increasing sequencing cost. Application of the single-cell coassembler HyDA to the study of three uncultured members of an alkane-degrading methanogenic community validated the usefulness of the coassembly concept. HyDA is open source and publicly available at http://chitsazlab.org/software.html, and the raw reads are available at http://chitsazlab.org/research.html. PMID:27243002

  1. Oxygen solubilities of media used in electrochemical respiration measurements.

    PubMed

    Rasmussen, Hans N; Rasmussen, Ulla F

    2003-08-01

    Solubility data are presented as equations from which the oxygen concentration of arbitrary media may be calculated with an accuracy of about 1%. These equations, covering the range 5-40 degrees C, are based on measurements with a modification of the physical method of St. Helen and Fatt (I. Fatt, Polarographic Oxygen Sensors, CRC Press, Cleveland (1976)). Solutions of the following compounds were measured: EDTA (ethylenediaminetetraacetic acid), EGTA (ethyleneglycol-bis(2-aminoethylether)tetraacetic acid), glucose, Hepes (N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid), lactobionic acid (galactosylgluconic acid), magnesium chloride, mannitol, Mes (2-(N-morpholino)ethanesulfonic acid), potassium chloride, potassium phosphate, sodium chloride, sucrose, taurine, and Tris (tris(hydroxymethyl)aminomethane). The present data are compared with solubility data obtained with the method involving oxidation of calibrated amounts of reduced nicotinamide adenine dinucleotide (e.g., R.W. Estabrook, Methods Enzymol. 10 (1967) 41-47) and with the kinetic method of Reynafarje et al. (Anal. Biochem. 145 (1985) 406-418). It is concluded that the former method produces reliable results provided that some simple precautions are taken. The kinetic method, however, appears to have produced calibration errors up to about 5%. PMID:12842113

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

    PubMed

    Kippner, Linda E; Kim, Jinhee; Gibson, Greg; Kemp, Melissa L

    2014-01-01

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

  3. Photosensitized generation of singlet oxygen in porous silicon studied by simultaneous measurements of luminescence of nanocrystals and oxygen molecules

    SciTech Connect

    Gongalsky, M. B.; Kharin, A. Yu.; Zagorodskikh, S. A.; Osminkina, L. A.; Timoshenko, V. Yu.

    2011-07-01

    Photosensitization of singlet oxygen generation in porous silicon (PSi) was investigated by simultaneous measurements of the photoluminescence (PL) of silicon nanocrystals (nc-Si) and the infrared emission of the {sup 1}{Delta}-state of oxygen molecules at 1270 nm (0.98 eV) at room temperature. Photodegradation of the nc-Si PL properties was found to correlate with the efficiency of singlet oxygen generation. The quantum efficiency of singlet oxygen generation in PSi was estimated to be about 1%, while the lifetime of singlet oxygen was about fifteen ms. The kinetics of nc-Si PL intensity under cw excitation undergoes a power law dependence with the exponent dependent on the photon energy of luminescence. The experimental results are explained with a model of photodegradation controlled by the diffusion of singlet oxygen molecules in a disordered structure of porous silicon.

  4. Phenotype classification of single cells using SRS microscopy, RNA sequencing, and microfluidics (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Streets, Aaron M.; Cao, Chen; Zhang, Xiannian; Huang, Yanyi

    2016-03-01

    Phenotype classification of single cells reveals biological variation that is masked in ensemble measurement. This heterogeneity is found in gene and protein expression as well as in cell morphology. Many techniques are available to probe phenotypic heterogeneity at the single cell level, for example quantitative imaging and single-cell RNA sequencing, but it is difficult to perform multiple assays on the same single cell. In order to directly track correlation between morphology and gene expression at the single cell level, we developed a microfluidic platform for quantitative coherent Raman imaging and immediate RNA sequencing (RNA-Seq) of single cells. With this device we actively sort and trap cells for analysis with stimulated Raman scattering microscopy (SRS). The cells are then processed in parallel pipelines for lysis, and preparation of cDNA for high-throughput transcriptome sequencing. SRS microscopy offers three-dimensional imaging with chemical specificity for quantitative analysis of protein and lipid distribution in single cells. Meanwhile, the microfluidic platform facilitates single-cell manipulation, minimizes contamination, and furthermore, provides improved RNA-Seq detection sensitivity and measurement precision, which is necessary for differentiating biological variability from technical noise. By combining coherent Raman microscopy with RNA sequencing, we can better understand the relationship between cellular morphology and gene expression at the single-cell level.

  5. Accurate measurement of oxygen consumption in children undergoing cardiac catheterization.

    PubMed

    Li, Jia

    2013-01-01

    Oxygen consumption (VO(2) ) is an important part of hemodynamics using the direct Fick principle in children undergoing cardiac catheterization. Accurate measurement of VO(2) is vital. Obviously, any error in the measurement of VO(2) will translate directly into an equivalent percentage under- or overestimation of blood flows and vascular resistances. It remains common practice to estimate VO(2) values from published predictive equations. Among these, the LaFarge equation is the most commonly used equation and gives the closest estimation with the least bias and limits of agreement. However, considerable errors are introduced by the LaFarge equation, particularly in children younger than 3 years of age. Respiratory mass spectrometry remains the "state-of-the-art" method, allowing highly sensitive, rapid and simultaneous measurement of multiple gas fractions. The AMIS 2000 quadrupole respiratory mass spectrometer system has been adapted to measure VO(2) in children under mechanical ventilation with pediatric ventilators during cardiac catheterization. The small sampling rate, fast response time and long tubes make the equipment a unique and powerful tool for bedside continuous measurement of VO(2) in cardiac catheterization for both clinical and research purposes. PMID:22488802

  6. Using oxygen species to measure marine production in Drake Passage

    NASA Astrophysics Data System (ADS)

    Castro Morales, Karel; Cassar, Nicolas; Bender, Michael; Kaiser, Jan

    2010-05-01

    Marine biological production is key to understanding the global carbon cycle, particularly the role of the Southern Ocean as a sink of CO2. Measurements of oxygen in the surface ocean allow quantifying marine biological productivity, since CO2 and O2 are linked via photosynthesis and respiration. Measurements of O2/Ar ratios and dissolved O2 isotopologues, together with wind-speed gas exchange parameterizations, give estimates of biological oxygen air-sea fluxes (Fbio) and gross photosynthetic production (G) in the mixed layer (zmix). In the absence of vertical mixing, Fbio can be used as a proxy for net community production (N). O2/Ar ratios and O2 concentrations were measured continuously in the uncontaminated seawater supply on board the RRS James Clark Ross along two sections across Drake Passage (DP). The DP1 section (southbound, 27 February-3 March 2007) represented mid-summer; DP2 represented early autumn (northbound, 12-15 April, 2007). The time difference between the two transects was 40 days. Weighted average gas exchange rates were calculated using the WOCE-NODC ocean mixed layer depth climatology and ECMWF wind speeds over 60 days prior to sample collection. The WOCE-NODC climatology shows a deepening of the zmix by on average 46 m within 40 days. The sea surface temperature decreased about 2.4 °C from DP1 to DP2. This reflects the seasonal transition from late summer to early autumn. In agreement with previous observations, we observed a strong north-south gradient of biological oxygen production in the DP. Our results also show high temporal variability over the course of 40 days. During late summer, the physical supersaturation contributes to about 3.6% of the total O2 supersaturation (?O2) for the Subantarctic and Polar Frontal Zones (SAZ and PFZ, respectively). In the other hand, the biological O2 supersaturation (?O2/Ar) showed mainly positive and homogeneous values (~1%) along the Antarctic Zone and Southern Antarctic Circumpolar Current Zone

  7. Continuous Dissolved Oxygen Measurements and Modelling Metabolism in Peatland Streams

    PubMed Central

    Dick, Jonathan J.; Soulsby, Chris; Birkel, Christian; Malcolm, Iain; Tetzlaff, Doerthe

    2016-01-01

    Stream water dissolved oxygen was monitored in a 3.2km2 moorland headwater catchment in the Scottish Highlands. The stream consists of three 1st order headwaters and a 2nd order main stem. The stream network is fringed by peat soils with no riparian trees, though dwarf shrubs provide shading in the lower catchment. Dissolved oxygen (DO) is regulated by the balance between atmospheric re-aeration and the metabolic processes of photosynthesis and respiration. DO was continuously measured for >1 year and the data used to calibrate a mass balance model, to estimate primary production, respiration and re-aeration for a 1st order site and in the 2nd order main stem. Results showed that the stream was always heterotrophic at both sites. Sites were most heterotrophic in the summer reflecting higher levels of stream metabolism. The 1st order stream appeared more heterotrophic which was consistent with the evident greater biomass of macrophytes in the 2nd order stream, with resulting higher primary productivity. Comparison between respiration, primary production, re-aeration and potential physical controls revealed only weak relationships. However, the most basic model parameters (e.g. the parameter linking light and photosynthesis) controlling ecosystem processes resulted in significant differences between the sites which seem related to the stream channel geometry. PMID:27556278

  8. Continuous Dissolved Oxygen Measurements and Modelling Metabolism in Peatland Streams.

    PubMed

    Dick, Jonathan J; Soulsby, Chris; Birkel, Christian; Malcolm, Iain; Tetzlaff, Doerthe

    2016-01-01

    Stream water dissolved oxygen was monitored in a 3.2km2 moorland headwater catchment in the Scottish Highlands. The stream consists of three 1st order headwaters and a 2nd order main stem. The stream network is fringed by peat soils with no riparian trees, though dwarf shrubs provide shading in the lower catchment. Dissolved oxygen (DO) is regulated by the balance between atmospheric re-aeration and the metabolic processes of photosynthesis and respiration. DO was continuously measured for >1 year and the data used to calibrate a mass balance model, to estimate primary production, respiration and re-aeration for a 1st order site and in the 2nd order main stem. Results showed that the stream was always heterotrophic at both sites. Sites were most heterotrophic in the summer reflecting higher levels of stream metabolism. The 1st order stream appeared more heterotrophic which was consistent with the evident greater biomass of macrophytes in the 2nd order stream, with resulting higher primary productivity. Comparison between respiration, primary production, re-aeration and potential physical controls revealed only weak relationships. However, the most basic model parameters (e.g. the parameter linking light and photosynthesis) controlling ecosystem processes resulted in significant differences between the sites which seem related to the stream channel geometry. PMID:27556278

  9. Research highlights: microfluidic-enabled single-cell epigenetics.

    PubMed

    Dhar, Manjima; Khojah, Reem; Tay, Andy; Di Carlo, Dino

    2015-11-01

    Individual cells are the fundamental unit of life with diverse functions from metabolism to motility. In multicellular organisms, a single genome can give rise to tremendous variability across tissues at the single-cell level due to epigenetic differences in the genes that are expressed. Signals from the local environment or a history of signals can drive these variations, and tissues have many cell types that play separate roles. This epigenetic heterogeneity is of biological importance in normal functions such as tissue morphogenesis and can contribute to development or resistance of cancer, or other disease states. Therefore, an improved understanding of variations at the single cell level are fundamental to understanding biology and developing new approaches to combating disease. Traditional approaches to characterize epigenetic modifications of chromatin or the transcriptome of cells have often focused on blended responses of many cells in a tissue; however, such bulk measures lose spatial and temporal differences that occur from cell to cell, and cannot uncover novel or rare populations of cells. Here we highlight a flurry of recent activity to identify the mRNA profiles from thousands of single-cells as well as chromatin accessibility and histone marks on single to few hundreds of cells. Microfluidics and microfabrication have played a central role in the range of new techniques, and will likely continue to impact their further development towards routine single-cell epigenetic analysis. PMID:26405849

  10. Computational analysis of signaling patterns in single cells

    PubMed Central

    Davis, Denise M.; Purvis, Jeremy E.

    2014-01-01

    Signaling proteins are flexible in both form and function. They can bind to multiple molecular partners and integrate diverse types of cellular information. When imaged by time-lapse microscopy, many signaling proteins show complex patterns of activity or localization that vary from cell to cell. This heterogeneity is so prevalent that it has spurred the development of new computational strategies to analyze single-cell signaling patterns. A collective observation from these analyses is that cells appear less heterogeneous when their responses are normalized to, or synchronized with, other single-cell measurements. In many cases, these transformed signaling patterns show distinct dynamical trends that correspond with predictable phenotypic outcomes. When signaling mechanisms are unclear, computational models can suggest putative molecular interactions that are experimentally testable. Thus, computational analysis of single-cell signaling has not only provided new ways to quantify the responses of individual cells, but has helped resolve longstanding questions surrounding many well-studied human signaling proteins including NF-κB, p53, ERK1/2, and CDK2. A number of specific challenges lie ahead for single-cell analysis such as quantifying the contribution of non-cell autonomous signaling as well as the characterization of protein signaling dynamics in vivo. PMID:25263011

  11. Estimating peak oxygen uptake based on postexercise measurements in swimming.

    PubMed

    Chaverri, Diego; Iglesias, Xavier; Schuller, Thorsten; Hoffmann, Uwe; Rodríguez, Ferran A

    2016-06-01

    To assess the validity of postexercise measurements in estimating peak oxygen uptake (V̇O2peak) in swimming, we compared oxygen uptake (V̇O2) measurements during supramaximal exercise with various commonly adopted methods, including a recently developed heart rate - V̇O2 modelling procedure. Thirty-one elite swimmers performed a 200-m maximal swim where V̇O2 was measured breath-by-breath using a portable gas analyzer connected to a respiratory snorkel, 1 min before, during, and 3 min postexercise. V̇O2peak(-20-0) was the average of the last 20 s of effort. The following postexercise measures were compared: (i) first 20-s average (V̇O2peak(0-20)); (ii) linear backward extrapolation (BE) of the first 20 s (BE(20)), 30 s, and 3 × 20-, 4 × 20-, and 3 or 4 × 20-s averages; (iii) semilogarithmic BE at 20 s (LOG(20)) and at the other same time intervals as in linear BE; and (iv) predicted V̇O2peak using mathematical modelling (pV̇O2(0-20)]. Repeated-measures ANOVA and post-hoc Bonferroni tests compared V̇O2peak (criterion) and each estimated value. Pearson's coefficient of determination (r(2)) was used to assess correlation. Exercise V̇O2peak(-20-0) (mean ± SD 3531 ± 738 mL·min(-1)) was not different (p > 0.30) from pV̇O2(0-20) (3571 ± 735 mL·min(-1)), BE(20) (3617 ± 708 mL·min(-1)), or LOG(20) (3627 ± 746 mL·min(-1)). pV̇O2(0-20) was very strongly correlated with exercise V̇O2peak (r(2) = 0.962; p < 0.001), and showed a low standard error of the estimate (146 mL·min(-1), 4.1%) and the lowest mean difference (40 mL·min(-1); 1.1%). We confirm that the new modelling procedure based on postexercise V̇O2 and heart rate measurements is a valid and accurate procedure for estimating V̇O2peak in swimmers and avoids the estimation bias produced by other methods. PMID:27226382

  12. Ambient air measurements of monoterpenes, oxygenated terpenes, and sesquiterpenes

    NASA Astrophysics Data System (ADS)

    Bouvier-Brown, N. C.; Goldstein, A. H.

    2007-12-01

    Chemical ozone loss within the forest canopy and the presence of biogenic VOC (BVOC) oxidation products in and above the canopy indirectly suggest the presence of very reactive BVOCs at Blodgett Forest. As a part of the 2007 BEARPEX campaign at this coniferous forest in the Sierra Nevada Mountains of California (1300 m elevation, 38.90° N, 120.63° W,), we quantified ambient concentrations of terpenes using a modified in-situ gas chromatograph with a mass spectrometer and a flame ionization detector (GC-MS-FID). The range of terpenes observed in ambient air matched enclosure based measurements of branch level emissions. To our knowledge, these observations represent the first quantification of the oxygenated monoterpene methyl chavicol and various sesquiterpenes in ambient air. Details of the instrument modifications, diurnal profiles of the terpenes, and comparison to branch level emissions will be presented.

  13. Measurement and chemical kinetic model predictions of detonation cell size in methanol-oxygen mixtures

    NASA Astrophysics Data System (ADS)

    Eaton, R.; Zhang, B.; Bergthorson, J. M.; Ng, H. D.

    2012-03-01

    In this study, detonation cell sizes of methanol-oxygen mixtures are experimentally measured at different initial pressures and compositions. Good agreement is found between the experiment data and predictions based on the chemical length scales obtained from a detailed chemical kinetic model. To assess the detonation sensitivity in methanol-oxygen mixtures, the results are compared with those of hydrogen-oxygen and methane-oxygen mixtures. Based on the cell size comparison, it is shown that methanol-oxygen is more detonation sensitive than methane-oxygen but less sensitive than hydrogen-oxygen.

  14. A modified procedure for measuring oxygen-18 content of nitrate

    NASA Astrophysics Data System (ADS)

    Ahmed, M. A.; Aly, A. I. M.; Abdel Monem, N.; Hanafy, M.; Gomaa, H. E.

    2012-11-01

    SummaryMass spectrometric analysis of O-isotopic composition of nitrate has many potential applications in studies of environmental processes. Through this work, rapid, reliable, precise, broadly applicable, catalyst-free, low-priced and less labor intensive procedure for measuring δ18O of nitrate using Isotope Ratio Mass Spectrometer has been developed and implemented. The conditions necessary to effect complete nitrate recovery and complete removal of other oxygen containing anions and dissolved organic carbon (DOC) without scarifying the isotopic signature of nitrate were investigated. The developed procedure consists of two main parts: (1) wet chemistry train for extraction and purification of nitrate from the liquid matrix; (2) off-line pyrolysis of extracted nitrate salt with activated graphite at 550 °C for 30 min. The conditions necessary to effect complete nitrate recovery and complete removal of other oxygen containing compounds were investigated. Dramatic reduction in processing times needed for analysis of δ18O of nitrate at natural abundance level was achieved. Preservation experiments revealed that chloroform (99.8%) is an effective preservative. Isotopic contents of some selected nitrate salts were measured using the modified procedure and some other well established methods at two laboratories in Egypt and Germany. Performance assessment of the whole developed analytical train was made using internationally distributed nitrate isotopes reference materials and real world sample of initial zero-nitrate content. The uncertainty budget was evaluated using the graphical nested hierarchal approach. The obtained results proved the suitability for handling samples of complicated matrices. Reduction of consumables cost by about 80% was achieved.

  15. Technologies for Single-Cell Isolation

    PubMed Central

    Gross, Andre; Schoendube, Jonas; Zimmermann, Stefan; Steeb, Maximilian; Zengerle, Roland; Koltay, Peter

    2015-01-01

    The handling of single cells is of great importance in applications such as cell line development or single-cell analysis, e.g., for cancer research or for emerging diagnostic methods. This review provides an overview of technologies that are currently used or in development to isolate single cells for subsequent single-cell analysis. Data from a dedicated online market survey conducted to identify the most relevant technologies, presented here for the first time, shows that FACS (fluorescence activated cell sorting) respectively Flow cytometry (33% usage), laser microdissection (17%), manual cell picking (17%), random seeding/dilution (15%), and microfluidics/lab-on-a-chip devices (12%) are currently the most frequently used technologies. These most prominent technologies are described in detail and key performance factors are discussed. The survey data indicates a further increasing interest in single-cell isolation tools for the coming years. Additionally, a worldwide patent search was performed to screen for emerging technologies that might become relevant in the future. In total 179 patents were found, out of which 25 were evaluated by screening the title and abstract to be relevant to the field. PMID:26213926

  16. Technologies for Single-Cell Isolation.

    PubMed

    Gross, Andre; Schoendube, Jonas; Zimmermann, Stefan; Steeb, Maximilian; Zengerle, Roland; Koltay, Peter

    2015-01-01

    The handling of single cells is of great importance in applications such as cell line development or single-cell analysis, e.g., for cancer research or for emerging diagnostic methods. This review provides an overview of technologies that are currently used or in development to isolate single cells for subsequent single-cell analysis. Data from a dedicated online market survey conducted to identify the most relevant technologies, presented here for the first time, shows that FACS (fluorescence activated cell sorting) respectively Flow cytometry (33% usage), laser microdissection (17%), manual cell picking (17%), random seeding/dilution (15%), and microfluidics/lab-on-a-chip devices (12%) are currently the most frequently used technologies. These most prominent technologies are described in detail and key performance factors are discussed. The survey data indicates a further increasing interest in single-cell isolation tools for the coming years. Additionally, a worldwide patent search was performed to screen for emerging technologies that might become relevant in the future. In total 179 patents were found, out of which 25 were evaluated by screening the title and abstract to be relevant to the field. PMID:26213926

  17. Single-cell transcriptomics for microbial eukaryotes.

    PubMed

    Kolisko, Martin; Boscaro, Vittorio; Burki, Fabien; Lynn, Denis H; Keeling, Patrick J

    2014-11-17

    One of the greatest hindrances to a comprehensive understanding of microbial genomics, cell biology, ecology, and evolution is that most microbial life is not in culture. Solutions to this problem have mainly focused on whole-community surveys like metagenomics, but these analyses inevitably loose information and present particular challenges for eukaryotes, which are relatively rare and possess large, gene-sparse genomes. Single-cell analyses present an alternative solution that allows for specific species to be targeted, while retaining information on cellular identity, morphology, and partitioning of activities within microbial communities. Single-cell transcriptomics, pioneered in medical research, offers particular potential advantages for uncultivated eukaryotes, but the efficiency and biases have not been tested. Here we describe a simple and reproducible method for single-cell transcriptomics using manually isolated cells from five model ciliate species; we examine impacts of amplification bias and contamination, and compare the efficacy of gene discovery to traditional culture-based transcriptomics. Gene discovery using single-cell transcriptomes was found to be comparable to mass-culture methods, suggesting single-cell transcriptomics is an efficient entry point into genomic data from the vast majority of eukaryotic biodiversity. PMID:25458215

  18. Ultrasensitive detection of proteins and sugars at single-cell level

    PubMed Central

    Watabe, Satoshi; Morikawa, Mika; Kaneda, Mugiho; Nakaishi, Kazunari; Nakatsuma, Akira; Ninomiya, Masaki; Yoshimura, Teruki; Miura, Toshiaki; Ito, Etsuro

    2016-01-01

    ABSTRACT Each cell produces its own responses even if it appears identical to other cells. To analyze these individual cell characteristics, we need to measure trace amounts of molecules in a single cell. Nucleic acids in a single cell can be easily amplified by polymerase chain reaction, but single-cell measurement of proteins and sugars will require de novo techniques. In the present study, we outline the techniques we have developed toward this end. For proteins, our ultrasensitive enzyme-linked immunosorbent assay (ELISA) coupled with thionicotinamide-adenine dinucleotide cycling can detect proteins at subattomoles per assay. For sugars, fluorescence correlation spectroscopy coupled with glucose oxidase-catalyzed reaction allows us to measure glucose at tens of nM. Our methods thus offer versatile techniques for single-cell-level analyses, and they are hoped to strongly promote single-cell biology as well as to develop noninvasive tests in clinical medicine. PMID:27064305

  19. Airborne chemistry single cell level

    NASA Astrophysics Data System (ADS)

    Nilsson, Staffan; Viberg, Peter; Spegel, Peter; Santesson, Sabina; Cedergren, Eila; Degerman, Eva; Johansson, Tomas; Nilsson, Johan

    2002-11-01

    A miniaturized analysis system for the studying of living cells and biochemical reactions in microdrops was developed. Cell studies were performed using single adipocytes in 250-nL drops. Continuous flow-through droplet dispensers, developed in-house, were used for additions to the levitated droplet. Addition of b-adrenergic agonists stimulates the lipolysis in the adipocytes, leading to free fatty acid release and a consequent pH decrease of the surrounding buffer, a change that can be easily followed using a pH-dependent fluorophore continuously monitored by fluorescence imaging detection. An analytical method using capillary electrophoresis and nanospray mass spectrometry for measurement of the cAMP level in activated single adipocytes are now being developed for future use in combination with the levitation technique. The levitation approach was also employed for the screening of nucleation conditions for macromolecules. Here, the acoustic levitator offers a simplified way to determine the main features of the phase diagram (i.e., precipitation diagram). Using the droplet dispensers, different types and amounts of precipitation agents are injected into the levitated drop, allowing a systematic search for nucleation conditions that is not possible using standard crystallization methods. Once the precipitation diagram has been obtained, optimization using standard methods is employed to grow the crystals.

  20. Biochemical oxygen demand measurement by mediator method in flow system.

    PubMed

    Liu, Ling; Bai, Lu; Yu, Dengbin; Zhai, Junfeng; Dong, Shaojun

    2015-06-01

    Using mediator as electron acceptor for biochemical oxygen demand (BOD) measurement was developed in the last decade (BODMed). However, until now, no BOD(Med) in a flow system has been reported. This work for the first time describes a flow system of BOD(Med) method (BOD(Med)-FS) by using potassium ferricyanide as mediator and carbon fiber felt as substrate material for microbial immobilization. The system can determine the BOD value within 30 min and possesses a wider analytical linear range for measuring glucose-glutamic acid (GGA) standard solution from 2 up to 200 mg L(-1) without the need of dilution. The analytical performance of the BOD(Med)-FS is comparable or better than that of the previously reported BOD(Med) method, especially its superior long-term stability up to 2 months under continuous operation. Moreover, the BOD(Med)-FS has same determination accuracy with the conventional BOD5 method by measuring real samples from a local wastewater treatment plant (WWTP). PMID:25863368

  1. Measuring and interpreting respiratory critical oxygen pressures in roots

    PubMed Central

    Armstrong, William; Webb, Trevor; Darwent, Marcus; Beckett, Peter M.

    2009-01-01

    Background and Aims Respiratory critical oxygen pressures (COPR) determined from O2-depletion rates in media bathing intact or excised roots are unreliable indicators of respiratory O2-dependency in O2-free media and wetlands. A mathematical model was used to help illustrate this, and more relevant polarographic methods for determining COPR in roots of intact plants are discussed. Methods Cortical [O2] near the root apex was monitored indirectly (pea seedlings) from radial oxygen losses (ROL) using sleeving Pt electrodes, or directly (maize) using microelectrodes; [O2] in the root was controlled by manipulating [O2] around the shoots. Mathematical modelling of radial diffusive and respiratory properties of roots used Michaelis–Menten enzyme kinetics. Key Results Respiration declined only when the O2 partial pressure (OPP) in the cortex of root tips fell below 0·5–4·5 kPa, values consistent with depressed respiration near the centre of the stele as confirmed by microelectrode measurements and mathematical modelling. Modelling predictions suggested that the OPP of a significant core at the centre of roots could be below the usual detection limits of O2-microelectrodes but still support some aerobic respiration. Conclusions In O2-free media, as in wetlands, the COPR for roots is likely to be quite low, dependent upon the respiratory demands, dimensions and diffusion characteristics of the stele/stelar meristem and the enzyme kinetics of cytochrome oxidase. Roots of non-wetland plants may not differ greatly in their COPRs from those of wetland species. There is a possibility that trace amounts of O2 may still be present in stelar ‘anaerobic’ cores where fermentation is induced at low cortical OPPs. PMID:18819952

  2. Oxygen tension measurement using an automatic blood gas analyser1

    PubMed Central

    Becket, J; Chakrabarti, M K; Gillies, I D S; Orchard, C; Hall, G M; Bourdillon, P J

    1981-01-01

    Two different methods of assessing the reliability of the oxygen electrode of one model of an automatic blood gas analyser (BGA) have been studied. In the first, a single automatic BGA was assessed by using outdated bank blood which was pumped around a small extracorporeal circuit into which known gas mixtures were passed. Oxygen tension was varied between 2 and 16 kPa. In the second, fresh heparinized blood was tonometered with calibrated gases and submitted to the automatic BGA used in the first part of the study and also to three other identical machines. Each of the machines was between 3 and 4 years old. Eighteen different units of blood were used in the first part of the study. The correlation coefficient between the automatic BGA and the Po2 in the extracorporeal circuit varied between 0.29 and 0.99. 31% of the total of 209 measurements made by the automatic BGA were more than 1.2 kPa from the reference value, 25% of them being between 1.2 and 4.0 kPa from the reference value. In the second part of the study, the correlation coefficient between this automatic BGA and the tonometered blood was 0.96. The correlation coefficients for the 3 other identical BGAs were 0.84, 0.97 and 0.88, indicating that the BGA used in the first part of the study was no worse than any of the others. It is suggested that although clinicians are likely to ignore readings of an automatic BGA that are more than 4.0 kPa from the true value and are likely to repeat the investigation, readings between 1.2 and 4.0 kPa from the true value may adversely affect patient management. PMID:7288796

  3. Oxygen tension measurement using an automatic blood gas analyser.

    PubMed

    Becket, J; Orchard, C; Chakrabarti, M K; Hall, G M; Gillies, I D; Bourdillon, P J

    1981-08-01

    Two different methods of assessing the reliability of the oxygen electrode of one model of an automatic blood gas analyser (BGA) have been studied. In the first, a single automatic BGA was assessed by using outdated bank blood which was pumped around a small extracorporeal circuit into which known gas mixtures were passed. Oxygen tension was varied between 2 and 16 kPa. In the second, fresh heparinized blood was tonometered with calibrated gases and submitted to the automatic BGA used in the first part of the study and also to three other identical machines. Each of the machines was between 3 and 4 years old.Eighteen different units of blood were used in the first part of the study. The correlation coefficient between the automatic BGA and the Po(2) in the extracorporeal circuit varied between 0.29 and 0.99. 31% of the total of 209 measurements made by the automatic BGA were more than 1.2 kPa from the reference value, 25% of them being between 1.2 and 4.0 kPa from the reference value. In the second part of the study, the correlation coefficient between this automatic BGA and the tonometered blood was 0.96. The correlation coefficients for the 3 other identical BGAs were 0.84, 0.97 and 0.88, indicating that the BGA used in the first part of the study was no worse than any of the others.It is suggested that although clinicians are likely to ignore readings of an automatic BGA that are more than 4.0 kPa from the true value and are likely to repeat the investigation, readings between 1.2 and 4.0 kPa from the true value may adversely affect patient management. PMID:7288796

  4. Thermomicrocapillaries as temperature biosensors in single cells

    NASA Astrophysics Data System (ADS)

    Herth, Simone; Giesguth, Miriam; Wedel, Waldemar; Reiss, Günther; Dietz, Karl-Josef

    2013-03-01

    Temperature is an important physical parameter in biology and its deviation from optimum can cause damage in biosystems. Thermocouples based on the Seebeck effect can be structured on glass microcapillaries to obtain thermomicrocapillaries (TMCs) usable in a micromanipulation setup. The suitability of the setup was proven by monitoring the temperature increase upon illumination of leaves and single cells following insertion of the TMC. The increase was 1.5 K in green tissue and 0.75 K in white leaf sections due to lower absorption. In single cells of trichomes, the increase was 0.5 K due to heat dissipation to the surrounding air.

  5. Method for physiologic phenotype characterization at the single-cell level in non-interacting and interacting cells

    NASA Astrophysics Data System (ADS)

    Kelbauskas, Laimonas; Ashili, Shashanka P.; Houkal, Jeff; Smith, Dean; Mohammadreza, Aida; Lee, Kristen B.; Forrester, Jessica; Kumar, Ashok; Anis, Yasser H.; Paulson, Thomas G.; Youngbull, Cody A.; Tian, Yanqing; Holl, Mark R.; Johnson, Roger H.; Meldrum, Deirdre R.

    2012-03-01

    Intercellular heterogeneity is a key factor in a variety of core cellular processes including proliferation, stimulus response, carcinogenesis, and drug resistance. However, cell-to-cell variability studies at the single-cell level have been hampered by the lack of enabling experimental techniques. We present a measurement platform that features the capability to quantify oxygen consumption rates of individual, non-interacting and interacting cells under normoxic and hypoxic conditions. It is based on real-time concentration measurements of metabolites of interest by means of extracellular optical sensors in cell-isolating microwells of subnanoliter volume. We present the results of a series of measurements of oxygen consumption rates (OCRs) of individual non-interacting and interacting human epithelial cells. We measured the effects of cell-to-cell interactions by using the system's capability to isolate two and three cells in a single well. The major advantages of the approach are: 1. ratiometric, intensity-based characterization of the metabolic phenotype at the single-cell level, 2. minimal invasiveness due to the distant positioning of sensors, and 3. ability to study the effects of cell-cell interactions on cellular respiration rates.

  6. TOPAZ-2 single-cell TFE electric insulation properties study

    SciTech Connect

    Vasilchenko, A.V.; Izhvanov, O.L.

    1996-03-01

    TOPAZ-II single cell thermoinic fuel element (TFE) electric insulation parameters under testing with electric heating were measured. TFE electric design schematic, experimental procedure and measurements results are described. Collector resistance was measured in helium at 420{endash}890 K. Metal ceramic ceals insulation properties were measured in vacuum P=10{sup {minus}4} Pa and in cesium vapor P=10{sup {minus}1}{minus}260 Pa, at 420{endash}730 K. Results of separate TFE are compared with the data; that were measured during nuclear power system (NPS) Ya-21U test. Based upon this data NPS power losses were estimated. {copyright} {ital 1996 American Institute of Physics.}

  7. Laser tweezers Raman spectroscopy of single cells

    NASA Astrophysics Data System (ADS)

    Chen, De

    Raman scattering is an inelastic collision between the vibrating molecules inside the sample and the incident photons. During this process, energy exchange takes place between the photon and the scattering molecule. By measuring the energy change of the photon, the molecular vibration mode can be probed. The vibrational spectrum contains valuable information about the disposition of atomic nuclei and chemical bonds within a molecule, the chemical compositions and the interactions between the molecule and its surroundings. In this dissertation, laser tweezers Raman spectroscopy (LTRS) technique is applied for the analysis of biological cells and human cells at single cell level. In LTRS, an individual cell is trapped in aqueous medium with laser tweezers, and Raman scattering spectra from the trapped cell are recorded in real-time. The Raman spectra of these cells can be used to reveal the dynamical processes of cell growth, cell response to environment changes, and can be used as the finger print for the identification of a bacterial cell species. Several biophysical experiments were carried out using LTRS: (1) the dynamic germination process of individual spores of Bacillus thuringiensis was detected via Ca-DPA, a spore-specific biomarker molecule; (2) inactivation and killing of Bacillus subtilis spores by microwave irradiation and wet heat were studied at single cell level; (3) the heat shock activation process of single B. subtilis spores were analyzed, in which the reversible transition from glass-like state at low temperature to liquid-like state at high temperature in spore was revealed at the molecular level; (4) the kinetic processes of bacterial cell lysis of E. coli by lysozyme and by temperature induction of lambda phage were detected real-time; (5) the fixation and rehydration of human platelets were quantitatively evaluated and characterized with Raman spectroscopy method, which provided a rapid way to quantify the quality of freeze-dried therapeutic

  8. NADH-dependent biosensor in Saccharomyces cerevisiae: principle and validation at the single cell level

    PubMed Central

    2014-01-01

    A reporter system was constructed to measure perturbations in the NADH/NAD+ co-factor balance in yeast, by using the green fluorescent protein gene under the control of the GPD2 promoter that is induced under conditions of excess of NADH. High fluorescence levels were obtained in a glycerol 3-phosphate dehydrogenase double deletion strain (gpd1Δgpd2Δ), which is deficient in the ability to regenerate NAD+ via glycerol formation. The responsiveness of the reporter system to externally induced perturbations in NADH oxidation was also evaluated in the gpd1Δgpd2Δ strain background by addition of acetoin, as well as by introduction of a set of heterologous xylose reductases (XRs) having different selectivities for NADH. Addition of acetoin during cell proliferation under oxygen-limited conditions resulted in a more than 2-fold decrease in mean fluorescence intensity as compared to the control experiment. Strains carrying XRs with different selectivities for NADH could be distinguished at the single cell level, so that the XR with the highest selectivity for NADH displayed the lowest fluorescence. In conclusion, the designed system successfully allowed for monitoring perturbations in the cellular redox metabolism caused by environmental changes, or by heterologous gene expression. The reporter system displayed high resolution in distinguishing cytosolic NADH oxidation capacity and hence has potential to be used for high-throughput screening based on the fluorescence of single cells. PMID:25401080

  9. Microwave-induced thermogenetic activation of single cells

    SciTech Connect

    Safronov, N. A.; Fedotov, I. V.; Ermakova, Yu. G.; Matlashov, M. E.; Belousov, V. V.; Sidorov-Biryukov, D. A.; Fedotov, A. B.; Zheltikov, A. M.

    2015-04-20

    Exposure to a microwave field is shown to enable thermogenetic activation of individual cells in a culture of cell expressing thermosensitive ion channels. Integration of a microwave transmission line with an optical fiber and a diamond quantum thermometer has been shown to allow thermogenetic single-cell activation to be combined with accurate local online temperature measurements based on an optical detection of electron spin resonance in nitrogen–vacancy centers in diamond.

  10. Single cell multiplexed assay for proteolytic activity using droplet microfluidics.

    PubMed

    Ng, Ee Xien; Miller, Miles A; Jing, Tengyang; Chen, Chia-Hung

    2016-07-15

    Cellular enzymes interact in a post-translationally regulated fashion to govern individual cell behaviors, yet current platform technologies are limited in their ability to measure multiple enzyme activities simultaneously in single cells. Here, we developed multi-color Förster resonance energy transfer (FRET)-based enzymatic substrates and use them in a microfluidics platform to simultaneously measure multiple specific protease activities from water-in-oil droplets that contain single cells. By integrating the microfluidic platform with a computational analytical method, Proteolytic Activity Matrix Analysis (PrAMA), we are able to infer six different protease activity signals from individual cells in a high throughput manner (~100 cells/experimental run). We characterized protease activity profiles at single cell resolution for several cancer cell lines including breast cancer cell line MDA-MB-231, lung cancer cell line PC-9, and leukemia cell line K-562 using both live-cell and in-situ cell lysis assay formats, with special focus on metalloproteinases important in metastasis. The ability to measure multiple proteases secreted from or expressed in individual cells allows us to characterize cell heterogeneity and has potential applications including systems biology, pharmacology, cancer diagnosis and stem cell biology. PMID:26995287

  11. Defining cell types and states with single-cell genomics

    PubMed Central

    Trapnell, Cole

    2015-01-01

    A revolution in cellular measurement technology is under way: For the first time, we have the ability to monitor global gene regulation in thousands of individual cells in a single experiment. Such experiments will allow us to discover new cell types and states and trace their developmental origins. They overcome fundamental limitations inherent in measurements of bulk cell population that have frustrated efforts to resolve cellular states. Single-cell genomics and proteomics enable not only precise characterization of cell state, but also provide a stunningly high-resolution view of transitions between states. These measurements may finally make explicit the metaphor that C.H. Waddington posed nearly 60 years ago to explain cellular plasticity: Cells are residents of a vast “landscape” of possible states, over which they travel during development and in disease. Single-cell technology helps not only locate cells on this landscape, but illuminates the molecular mechanisms that shape the landscape itself. However, single-cell genomics is a field in its infancy, with many experimental and computational advances needed to fully realize its full potential. PMID:26430159

  12. Quantitating intracellular oxygen tension in vivo by phosphorescence lifetime measurement

    PubMed Central

    Hirakawa, Yosuke; Yoshihara, Toshitada; Kamiya, Mako; Mimura, Imari; Fujikura, Daichi; Masuda, Tsuyoshi; Kikuchi, Ryohei; Takahashi, Ippei; Urano, Yasuteru; Tobita, Seiji; Nangaku, Masaomi

    2015-01-01

    Hypoxia appears to have an important role in pathological conditions in many organs such as kidney; however, a method to quantify intracellular oxygen tension in vivo has not been well established. In this study, we established an optical method to quantify oxygen tension in mice kidneys using a cationic lipophilic phosphorescence probe, BTPDM1, which has an intracellular oxygen concentration-sensitive phosphorescence lifetime. Since this probe is distributed inside the tubular cells of the mice kidney, we succeeded in detecting acute renal hypoxic conditions and chronic kidney disease. This technique enabled us to estimate intracellular partial pressures of oxygen in vivo by extrapolating the calibration curve generated from cultured tubular cells. Since intracellular oxygen tension is directly related to cellular hypoxic reactions, such as the activation of hypoxia-inducible factors, our method will shed new light on hypoxia research in vivo. PMID:26644023

  13. ASRDI oxygen technology survey. Volume 5: Density and liquid level measurement instrumentation for the cryogenic fluids oxygen, hydrogen, and nitrogen

    NASA Technical Reports Server (NTRS)

    Roder, H. M.

    1974-01-01

    Information is presented on instrumentation for density measurement, liquid level measurement, quantity gauging, and phase measurement. Coverage of existing information directly concerned with oxygen was given primary emphasis. A description of the physical principle of measurement for each instrumentation type is included. The basic materials of construction are listed if available from the source document for each instrument discussed. Cleaning requirements, procedures, and verification techniques are included.

  14. Design and optimization of a widely tunable semiconductor laser for blood oxygenation and blood flow measurements

    NASA Astrophysics Data System (ADS)

    Feng, Yafei; Deng, Haoyu; Song, Guangyi; He, Jian-Jun

    2014-11-01

    A method for measuring blood oxygenation and blood flow rate using a single widely tunable semiconductor laser is proposed and investigated. It is shown that a 700-nm-band tunable laser gives the highest sensitivity for blood oxygen measurement. The corresponding tunable laser is designed using the V-coupled cavity structure. The wavelength tuning range can reach 8 nm, which is sufficient for the blood oxygenation measurement in the 700-nm-band by using the Beer- Lambert law. In contrast to conventional blood oxygenation measurement method based on two LEDs, the laser can be used at the same time to measure the blood flow rate based on the Doppler principle.

  15. Studying bacterial quorum-sensing at the single cell level

    NASA Astrophysics Data System (ADS)

    Delfino Perez, Pablo; Pelakh, Leslie; Young, Jonathan; Johnson, Elaine; Hagen, Stephen

    2010-03-01

    Like many bacterial species, Vibrio fischeri can detect its own population density through a quorum sensing (QS) mechanism. The bacterium releases a signal molecule (AI, autoinducer), which accumulates at high population density and triggers a genetic switch. In V.fischeri this leads to bioluminescence. Little is known about how stochastic gene expression affects QS at the level of single cells. We are imaging the luminescence of individual V.fischeri cells in a flow chamber and directly measuring the intercell variability in AI activation of the QS circuit. Our single-cell luminescence experiments allow us to track cells over time and characterize variations in their response to AI levels. We find heterogeneous response to the external signal: at a given AI concentration some cells may be strongly luminescent while others are virtually dark. The analysis of noise in the individual cell response can eventually lead to a better understanding of how cells use QS to gather information about their environment.

  16. Single-cell nanotoxicity assays of superparamagnetic iron oxide nanoparticles.

    PubMed

    Eustaquio, Trisha; Leary, James F

    2012-01-01

    Properly evaluating the nanotoxicity of nanoparticles involves much more than bulk-cell assays of cell death by necrosis. Cells exposed to nanoparticles may undergo repairable oxidative stress and DNA damage or be induced into apoptosis. Exposure to nanoparticles may cause the cells to alter their proliferation or differentiation or their cell-cell signaling with neighboring cells in a tissue. Nanoparticles are usually more toxic to some cell subpopulations than others, and toxicity often varies with cell cycle. All of these facts dictate that any nanotoxicity assay must be at the single-cell level and must try whenever feasible and reasonable to include many of these other factors. Focusing on one type of quantitative measure of nanotoxicity, we describe flow and scanning image cytometry approaches to measuring nanotoxicity at the single-cell level by using a commonly used assay for distinguishing between necrotic and apoptotic causes of cell death by one type of nanoparticle. Flow cytometry is fast and quantitative, provided that the cells can be prepared into a single-cell suspension for analysis. But when cells cannot be put into suspension without altering nanotoxicity results, or if morphology, attachment, and stain location are important, a scanning image cytometry approach must be used. Both methods are described with application to a particular type of nanoparticle, a superparamagnetic iron oxide nanoparticle (SPION), as an example of how these assays may be applied to the more general problem of determining the effects of nanomaterial exposure to living cells. PMID:22975957

  17. CONTINUOUS, AUTOMATED AND SIMULTANEOUS MEASUREMENT OF OXYGEN UPTAKE AND CARBON DIOXIDE EVOLUTION IN BIOLOGICAL SYSTEMS

    EPA Science Inventory

    Commercial respirometers are capable of continuously and automatically measuring oxygen uptake in bioreactors. A method for continuously and automatically measuring carbon dioxide evolution can be retrofitted to commercial respirometers. Continuous and automatic measurements of...

  18. A simplified headspace biochemical oxygen demand test protocol based on oxygen measurements using a fiber optic probe.

    PubMed

    Min, Booki; Kohler, David; Logan, Bruce E

    2004-01-01

    Batch respirometric tests have many advantages over the conventional biochemical oxygen demand (BOD) method for analysis of wastewaters, including the use of nondiluted samples, a more rapid exertion of oxygen demand, and reduced sample preparation time. The headspace biochemical oxygen demand (HBOD) test can be used to obtain oxygen demands in 2 or 3 days that can predict 5-day biochemical oxygen demand (BOD5) results. The main disadvantage of the HBOD and other respirometric tests has been the lack of a simple and direct method to measure oxygen concentrations in the gas phase. The recent commercial production of a new type of fiber optic oxygen probe, however, provides a method to eliminate this disadvantage. This fiber optic probe, referred to here as the HBOD probe, was tested to see if it could be used in HBOD tests. Gas-phase oxygen measurements made with the HBOD probe took only a few seconds and were not significantly different from those made using a gas chromatograph (t test: n = 15, R2 = 0.9995, p < 0.001). In field tests using the HBOD probe procedure, the probe greatly reduced sample analysis time compared with previous HBOD and BOD protocols and produced more precise results than the BOD test for wastewater samples from two treatment plants (University Area Joint Authority [UAJA] Wastewater Treatment Plant in University Park, Pennsylvania, and The Pennsylvania State University [PSU] Wastewater Treatment Plant in University Park). Headspace biochemical oxygen demand measurements on UAJA primary clarifier effluent were 59.9 +/- 2.4% after 2 days (HBOD2) and 73.0 +/- 3.1% after 3 days (HBOD) of BOD, values, indicating that BOD5 values could be predicted by multiplying HBOD2 values by 1.67 +/- 0.07 or HBOD3 by 1.37 +/- 0.06. Similarly, tests using PSU wastewater samples could be used to provide BOD5 estimates by multiplying the HBOD2 by 1.24 +/- 0.04 or by multiplying the HBOD3 by 0.97 +/- 0.03. These results indicate that the HBOD fiber optic probe can

  19. Characterization of a single cell of Chlorella in a microfluidic channel using amperometric electrode arrays.

    PubMed

    Song, Young Seok; Bai, Seoung Jai

    2014-11-01

    Electrochemical characteristics of O2 and/or mediators secreted by a single cell of Chlorella fusea were analyzed by using amperometric measurements on microelectrodes embedded in a microfluidic device. A single cell was trapped in a microfluidic channel, which simplifies the mass transfer phenomenon, i.e., one-dimensional distribution of solutes in the channel. Such amperometric measurements allowed us to obtain more refined data in a localized space and to understand photosynthetic behavior of algae at the single cell level. In addition, the concentration of a photosynthetic mediator, p-benzoquinone, was numerically calculated by using the finite element method. PMID:24966046

  20. Measurement and Control of Oxygen Partial Pressure in an Electrostatic Levitator

    NASA Technical Reports Server (NTRS)

    SanSoucie, Michael P.; Rogers, Jan R.

    2014-01-01

    Recently the NASA Marshall Space Flight Center electrostatic levitation (ESL) laboratory has been upgraded to include an oxygen control system. This system allows the oxygen partial pressure within the vacuum chamber to be measured and controlled, at elevated temperatures, theoretically in the range from 10(exp -36) to 10(exp 0) bar. The role of active surface agents in liquid metals is fairly well known; however, published surface tension data typically has large scatter, which has been hypothesized to be caused by the presence of oxygen. The surface tension of metals is affected by even a small amount of adsorption of oxygen. It has even been shown that oxygen partial pressures may need to be as low as 10(exp -24) bar to avoid oxidation. While electrostatic levitation is done under high vacuum, oxide films or dissolved oxygen may have significant effects on materials properties, such as surface tension and viscosity. Therefore, the ability to measure and control the oxygen partial pressure within the chamber is highly desirable. The oxygen control system installed at MSFC contains a potentiometric sensor, which measures the oxygen partial pressure, and an oxygen ion pump. In the pump, a pulse-width modulated electric current is applied to yttrium-stabilized zirconia, resulting in oxygen transfer into or out of the system. Also part of the system is a control unit, which consists of temperature controllers for the sensor and pump, PID-based current loop for the ion pump, and a control algorithm. This system can be used to study the effects of oxygen on the thermophysical properties of metals, ceramics, glasses, and alloys. It can also be used to provide more accurate measurements by processing the samples at very low oxygen partial pressures. The oxygen control system will be explained in more detail and an overview of its use and limitations in an electrostatic levitator will be described. Some preliminary measurements have been made, and the results to date will

  1. Quantification of Circadian Rhythms in Single Cells

    PubMed Central

    Westermark, Pål O.; Welsh, David K.; Okamura, Hitoshi; Herzel, Hanspeter

    2009-01-01

    Bioluminescence techniques allow accurate monitoring of the circadian clock in single cells. We have analyzed bioluminescence data of Per gene expression in mouse SCN neurons and fibroblasts. From these data, we extracted parameters such as damping rate and noise intensity using two simple mathematical models, one describing a damped oscillator driven by noise, and one describing a self-sustained noisy oscillator. Both models describe the data well and enabled us to quantitatively characterize both wild-type cells and several mutants. It has been suggested that the circadian clock is self-sustained at the single cell level, but we conclude that present data are not sufficient to determine whether the circadian clock of single SCN neurons and fibroblasts is a damped or a self-sustained oscillator. We show how to settle this question, however, by testing the models' predictions of different phases and amplitudes in response to a periodic entrainment signal (zeitgeber). PMID:19956762

  2. Digital microfluidic immunocytochemistry in single cells.

    PubMed

    Ng, Alphonsus H C; Dean Chamberlain, M; Situ, Haozhong; Lee, Victor; Wheeler, Aaron R

    2015-01-01

    We report a new technique called Digital microfluidic Immunocytochemistry in Single Cells (DISC). DISC automates protocols for cell culture, stimulation and immunocytochemistry, enabling the interrogation of protein phosphorylation on pulsing with stimulus for as little as 3 s. DISC was used to probe the phosphorylation states of platelet-derived growth factor receptor (PDGFR) and the downstream signalling protein, Akt, to evaluate concentration- and time-dependent effects of stimulation. The high time resolution of the technique allowed for surprising new observations-for example, a 10 s pulse stimulus of a low concentration of PDGF is sufficient to cause >30% of adherent fibroblasts to commit to Akt activation. With the ability to quantitatively probe signalling events with high time resolution at the single-cell level, we propose that DISC may be an important new technique for a wide range of applications, especially for screening signalling responses of a heterogeneous cell population. PMID:26104298

  3. Tree inference for single-cell data.

    PubMed

    Jahn, Katharina; Kuipers, Jack; Beerenwinkel, Niko

    2016-01-01

    Understanding the mutational heterogeneity within tumors is a keystone for the development of efficient cancer therapies. Here, we present SCITE, a stochastic search algorithm to identify the evolutionary history of a tumor from noisy and incomplete mutation profiles of single cells. SCITE comprises a flexible Markov chain Monte Carlo sampling scheme that allows the user to compute the maximum-likelihood mutation history, to sample from the posterior probability distribution, and to estimate the error rates of the underlying sequencing experiments. Evaluation on real cancer data and on simulation studies shows the scalability of SCITE to present-day single-cell sequencing data and improved reconstruction accuracy compared to existing approaches. PMID:27149953

  4. Measuring Spatial and Temporal Heterogeneity of Dissolved Oxygen in Streambed Sediments Using Pressure Sensitive Paint (PSP)

    NASA Astrophysics Data System (ADS)

    Huynh, K. T.; Salus, A.; Xie, M.; Roche, K. R.; Packman, A. I.

    2014-12-01

    Pressure sensitive paints (PSP) have been largely used in aerodynamic applications to measure pressure distributions on complex bodies such as aircraft. One common family of PSPs employ fluorescent pigments that are quenched in the presence of oxygen, yielding an inverse relationship between fluorescence intensity and oxygen concentration that is used to measure pressure in aerodynamic applications through the partial pressure of oxygen. These PSPs offer unexplored potential for visualizing dissolved oxygen (DO) concentration distributions on surfaces underwater. PSP was used to measure dissolved oxygen concentrations in streambed sediments in a laboratory flume. Two PSP-coated 2.5 cm diameter spheres were emplaced in a bed of similar material, and imaged under varying DO concentrations. Calibration curves relating fluorescence intensity to dissolved oxygen concentration were developed on a pixel-by-pixel basis, enabling spatial patterns of oxygen to be resolved in the sediment bed. This method of measuring dissolved oxygen concentration is advantageous because of its fast response time and ability to measure heterogeneous oxygen distributions in sediments. Future work will explore the combined effects of stream flow and biofilm growth on oxygen distributions in streambed sediments.

  5. Single-cell analysis of circadian dynamics in tissue explants

    PubMed Central

    Lande-Diner, Laura; Stewart-Ornstein, Jacob; Weitz, Charles J.; Lahav, Galit

    2015-01-01

    Tracking molecular dynamics in single cells in vivo is instrumental to understanding how cells act and interact in tissues. Current tissue imaging approaches focus on short-term observation and typically nonendogenous or implanted samples. Here we develop an experimental and computational setup that allows for single-cell tracking of a transcriptional reporter over a period of >1 wk in the context of an intact tissue. We focus on the peripheral circadian clock as a model system and measure the circadian signaling of hundreds of cells from two tissues. The circadian clock is an autonomous oscillator whose behavior is well described in isolated cells, but in situ analysis of circadian signaling in single cells of peripheral tissues is as-yet uncharacterized. Our approach allowed us to investigate the oscillatory properties of individual clocks, determine how these properties are maintained among different cells, and assess how they compare to the population rhythm. These experiments, using a wide-field microscope, a previously generated reporter mouse, and custom software to track cells over days, suggest how many signaling pathways might be quantitatively characterized in explant models. PMID:26269583

  6. Single-cell printing based on impedance detection

    PubMed Central

    Schoendube, J.; Wright, D.; Zengerle, R.; Koltay, P.

    2015-01-01

    Label-free isolation of single cells is essential for the growing field of single-cell analysis. Here, we present a device which prints single living cells encapsulated in free-flying picoliter droplets. It combines inkjet printing and impedance flow cytometry. Droplet volume can be controlled in the range of 500 pl–800 pl by piezo actuator displacement. Two sets of parallel facing electrodes in a 50 μm × 55 μm channel are applied to measure the presence and velocity of a single cell in real-time. Polystyrene beads with <5% variation in diameter generated signal variations of 12%–17% coefficients of variation. Single bead efficiency (i.e., printing events with single beads vs. total number of printing events) was 73% ± 11% at a throughput of approximately 9 events/min. Viability of printed HeLa cells and human primary fibroblasts was demonstrated by culturing cells for at least eight days. PMID:25759750

  7. A stochastic transcriptional switch model for single cell imaging data

    PubMed Central

    Hey, Kirsty L.; Momiji, Hiroshi; Featherstone, Karen; Davis, Julian R.E.; White, Michael R.H.; Rand, David A.; Finkenstädt, Bärbel

    2015-01-01

    Gene expression is made up of inherently stochastic processes within single cells and can be modeled through stochastic reaction networks (SRNs). In particular, SRNs capture the features of intrinsic variability arising from intracellular biochemical processes. We extend current models for gene expression to allow the transcriptional process within an SRN to follow a random step or switch function which may be estimated using reversible jump Markov chain Monte Carlo (MCMC). This stochastic switch model provides a generic framework to capture many different dynamic features observed in single cell gene expression. Inference for such SRNs is challenging due to the intractability of the transition densities. We derive a model-specific birth–death approximation and study its use for inference in comparison with the linear noise approximation where both approximations are considered within the unifying framework of state-space models. The methodology is applied to synthetic as well as experimental single cell imaging data measuring expression of the human prolactin gene in pituitary cells. PMID:25819987

  8. A stochastic transcriptional switch model for single cell imaging data.

    PubMed

    Hey, Kirsty L; Momiji, Hiroshi; Featherstone, Karen; Davis, Julian R E; White, Michael R H; Rand, David A; Finkenstädt, Bärbel

    2015-10-01

    Gene expression is made up of inherently stochastic processes within single cells and can be modeled through stochastic reaction networks (SRNs). In particular, SRNs capture the features of intrinsic variability arising from intracellular biochemical processes. We extend current models for gene expression to allow the transcriptional process within an SRN to follow a random step or switch function which may be estimated using reversible jump Markov chain Monte Carlo (MCMC). This stochastic switch model provides a generic framework to capture many different dynamic features observed in single cell gene expression. Inference for such SRNs is challenging due to the intractability of the transition densities. We derive a model-specific birth-death approximation and study its use for inference in comparison with the linear noise approximation where both approximations are considered within the unifying framework of state-space models. The methodology is applied to synthetic as well as experimental single cell imaging data measuring expression of the human prolactin gene in pituitary cells. PMID:25819987

  9. Mie scatter corrections in single cell infrared microspectroscopy.

    PubMed

    Konevskikh, Tatiana; Lukacs, Rozalia; Blümel, Reinhold; Ponossov, Arkadi; Kohler, Achim

    2016-06-23

    Strong Mie scattering signatures hamper the chemical interpretation and multivariate analysis of the infrared microscopy spectra of single cells and tissues. During recent years, several numerical Mie scatter correction algorithms for the infrared spectroscopy of single cells have been published. In the paper at hand, we critically reviewed existing algorithms for the correction of Mie scattering and suggest improvements. We developed an iterative algorithm based on Extended Multiplicative Scatter Correction (EMSC), for the retrieval of pure absorbance spectra from highly distorted infrared spectra of single cells. The new algorithm uses the van de Hulst approximation formula for the extinction efficiency employing a complex refractive index. The iterative algorithm involves the establishment of an EMSC meta-model. While existing iterative algorithms for the correction of resonant Mie scattering employ three independent parameters for establishing a meta-model, we could decrease the number of parameters from three to two independent parameters, which reduced the calculation time for the Mie scattering curves for the iterative EMSC meta-model by a factor of 10. Moreover, by employing the Hilbert transform for evaluating the Kramers-Kronig relations based on a FFT algorithm in Matlab, we further improved the speed of the algorithm by a factor of 100. For testing the algorithm we simulate distorted apparent absorbance spectra by utilizing the exact theory for the scattering of infrared light at absorbing spheres, taking into account the high numerical aperture of infrared microscopes employed for the analysis of single cells and tissues. In addition, the algorithm was applied to measured absorbance spectra of single lung cancer cells. PMID:27034998

  10. Single cell microfluidics for systems oncology

    NASA Astrophysics Data System (ADS)

    Fan, Rong

    2012-02-01

    The singular term ``cancer'' is never one kind of disease, but deceivingly encompasses a large number of heterogeneous disease states, which makes it impossible to completely treat cancer using a generic approach. Rather systems approaches are urgently required to assess cancer heterogeneity, stratify patients and enable the most effective, individualized treatment. The heterogeneity of tumors at the single cell level is reflected by the hierarchical complexity of the tumor microenvironment. To identify all the cellular components, including both tumor and infiltrating immune cells, and to delineate the associated cell-to-cell signaling network that dictates tumor initiation, progression and metastasis, we developed a single cell microfluidics chip that can analyze a panel of proteins that are potentially associated inter-cellular signaling network in tumor microenvironment from hundreds of single cells in parallel. This platform integrates two advanced technologies -- microfluidic single cell handling and ultra-high density protein array. This device was first tested for highly multiplexed profiling of secreted proteins including tumor-immune signaling molecules from monocytic leukemia cells. We observed profound cellular heterogeneity with all functional phenotypes quantitatively identified. Correlation analysis further indicated the existence of an intercellular cytokine network in which TNFα-induced secondary signaling cascades further increased functional cellular diversity. It was also exploited to evaluate polyfunctionality of tumor antigen-specific T cells from melanoma patients being treated with adoptive T cell transfer immunotherapy. This platform could be further extended to analyze both solid tumor cells (e.g. human lung carcinoma cells) and infiltrating immune cells (e.g. macrophages) so as to enable systems analysis of the complex tumor microenvironment from small amounts of clinical specimens, e.g. skinny needle biopsies. Thus, it could potentially

  11. Computing tumor trees from single cells.

    PubMed

    Davis, Alexander; Navin, Nicholas E

    2016-01-01

    Computational methods have been developed to reconstruct evolutionary lineages from tumors using single-cell genomic data. The resulting tumor trees have important applications in cancer research and clinical oncology.Please see related Research articles: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0929-9 and http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0936-x . PMID:27230879

  12. Measurement of oxygen consumption during muscle flaccidity exercise by near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Fukuda, K.; Fukawa, Y.

    2013-03-01

    Quantitative measurement oxygen consumption in the muscles is important to evaluate the effect of the exercise. Near-infrared spectroscopy (NIRS) is a noninvasive method for measuring muscle oxygenation. However, measurement results are affected by blood volume change due to changes in the blood pressure. In order to evaluate changes in blood volume and to improve measurement accuracy, we proposed a calculation method of three-wavelength measurement with considering the scattering factor and the measurement with monitoring blood flow for measuring the temporal change of the oxygen concentration more precisely. We applied three-wavelength light source (680nm, 808nm and 830nm) for the continued wave measurement. Two detectors (targeted detector and the reference detector) were placed near the target muscle and apart from it. We measured the blood flow by controlling the intravascular pressure and the oxygen consumption with the handgrip exercise in the forearm. The measured results show that the scattering factor contains the artifact at the surface and the blood flow in the artery and the vein in the same phase. The artifact and the blood flow in the same phase are reduced from the oxygenated and the deoxygenated hemoglobin densities. Thus our proposed method is effective for reducing the influence of the artifact and the blood flow in the same phase from the oxygen consumption measurement. Further, it is shown that the oxygen consumption is measured more accurately by subtracting the blood flow measured by the reference detector.

  13. Single cell elemental analysis using nuclear microscopy

    NASA Astrophysics Data System (ADS)

    Ren, M. Q.; Thong, P. S. P.; Kara, U.; Watt, F.

    1999-04-01

    The use of Particle Induced X-ray Emission (PIXE), Rutherford Backscattering Spectrometry (RBS) and Scanning Transmission Ion Microscopy (STIM) to provide quantitative elemental analysis of single cells is an area which has high potential, particularly when the trace elements such as Ca, Fe, Zn and Cu can be monitored. We describe the methodology of sample preparation for two cell types, the procedures of cell imaging using STIM, and the quantitative elemental analysis of single cells using RBS and PIXE. Recent work on single cells at the Nuclear Microscopy Research Centre,National University of Singapore has centred around two research areas: (a) Apoptosis (programmed cell death), which has been recently implicated in a wide range of pathological conditions such as cancer, Parkinson's disease etc, and (b) Malaria (infection of red blood cells by the malaria parasite). Firstly we present results on the elemental analysis of human Chang liver cells (ATTCC CCL 13) where vanadium ions were used to trigger apoptosis, and demonstrate that nuclear microscopy has the capability of monitoring vanadium loading within individual cells. Secondly we present the results of elemental changes taking place in individual mouse red blood cells which have been infected with the malaria parasite and treated with the anti-malaria drug Qinghaosu (QHS).

  14. Dynamic oxygenation measurements using a phosphorescent coating within a mammary window chamber mouse model

    PubMed Central

    Schafer, Rachel; Gmitro, Arthur F.

    2015-01-01

    Phosphorescent lifetime imaging was employed to measure the spatial and temporal distribution of oxygen partial pressure in tissue under the coverslip of a mammary window chamber breast cancer mouse model. A thin platinum-porphyrin coating, whose phosphorescent lifetime varies monotonically with oxygen partial pressure, was applied to the coverslip surface. Dynamic temporal responses to induced modulations in oxygenation levels were measured using this approach. PMID:25780753

  15. Measurement in a marine environment using low cost sensors of temperature and dissolved oxygen

    USGS Publications Warehouse

    Godshall, F.A.; Cory, R.L.; Phinney, D.E.

    1974-01-01

    Continuous records of physical parameters of the marine environment are difficult as well as expensive to obtain. This paper describes preliminary results of an investigative program with the purpose of developing low cost time integrating measurement and averaging devices for water temperature and dissolved oxygen. Measurements were made in an estuarine area of the Chesapeake Bay over two week periods. With chemical thermometers average water temperature for the two week period was found to be equal to average water temperature measured with thermocouples plus or minus 1.0 C. The slow diffusion of oxygen through the semipermiable sides of plastic bottles permitted the use of water filled bottles to obtain averaged oxygen measurements. Oxygen measurements for two week averaging times using 500 ml polyethylene bottles were found to vary from conventionally measured and averaged dissolved oxygen by about 1.8 mg/l. ?? 1974 Estuarine Research Federation.

  16. Techniques for Measuring Low Earth Orbital Atomic Oxygen Erosion of Polymers

    NASA Technical Reports Server (NTRS)

    deGroh, Kim K.; Banks, Bruce A.; Demko, Rikako

    2002-01-01

    Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene) are commonly used spacecraft materials due to their desirable properties such as flexibility, low density, and in the case of FEP, a low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low Earth orbit (LEO) environment are exposed to energetic atomic oxygen. Atomic oxygen reaction with polymers causes erosion, which is a threat to spacecraft durability. It is therefore important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. The most common technique for determining E is through mass loss measurements. For limited duration exposure experiments, such as shuttle experiments, where the atomic oxygen fluence is often so low that mass loss measurements can not produce acceptable uncertainties, recession measurements based on atomic force microscopy analyses can be used. Equally necessary to knowing the mass loss or recession depth for determining the erosion yield of polymers is the knowledge of the atomic oxygen fluence that the polymers were exposed to in space. This paper discusses the procedures and relevant issues for mass loss and recession depth measurements for passive atomic oxygen erosion yield characterization of polymers, along with techniques for active atomic oxygen fluence and erosion characterization. One active atomic oxygen erosion technique discussed is a new technique based on optical measurements. Details including the use of both semi-transparent and opaque polymers for active erosion measurement are reviewed.

  17. In situ fiber-optic oxygen consumption measurements from a working mouse heart.

    PubMed

    Zhao, Y; Richman, A; Storey, C; Radford, N B; Pantano, P

    1999-09-01

    Luminescence-based imaging-fiber oxygen sensors (IFOSs) were utilized for the in situ measurement of oxygen consumption from intact perfused mouse hearts. IFOSs were fabricated using a technically expedient, photoinitiated polymerization reaction whereby an oxygen-sensitive polymer matrix was immobilized in a precise location on an imaging fiber's distal face. The oxygen-sensing layer used in this work comprised a transition metal complex, Ru(Ph2phen)3(2+), entrapped in a gaspermeable photopolymerizable siloxane membrane (PS802). The transduction mechanism was based upon the oxygen collisional quenching of the ruthenium complex luminescence; detection was performed utilizing an epi-fluorescence microscope/charge coupled device imaging system. IFOS measurements from working mouse hearts were validated through concurrent, blind, ex situ blood gas analyzer (BGA) measurements. The BGA and IFOS methodologies were utilized successfully to measure oxygen concentrations in aortic and pulmonary artery perfusates from the working mouse heart before and after isoproterenol administration. Coupled with coronary-flow measurements, these data were used to calculate myocardial oxygen consumption. Regression analysis of measurements of myocardial oxygen consumption showed that there was a strong correlation between the values generated by the BGA sampling and those obtained via in situ IFOS methods. To our knowledge, this research represents the first report of in situ fiber-optic sensor monitoring of oxygen content from the intact, beating mouse heart. PMID:10489534

  18. A system using solid ceramic oxygen electrolyte cells to measure oxygen fugacities in gas-mixing systems

    NASA Technical Reports Server (NTRS)

    Williams, R. J.; Mullins, O.

    1976-01-01

    Details are given for the construction and operation of a 101.3 kN/sq m (1 atmosphere) redox control system. A solid ceramic oxygen electrolyte cell is used to monitor the oxygen fugacity in the furnace. The system consists of a vertical quench, gas mixing furnace with heads designed for mounting the electrolyte cell and with facilities for inserting and removing the samples. The system also contains the high input impedance electronics necessary for measurements, a simplified version of a gas mixing apparatus, and devices for experiments under controlled rates of change relative to temperature and redox state. The calibration and maintenance of the system are discussed.

  19. JSC systems using solid ceramic oxygen electrolyte cells to measure oxygen fugacites in gas-mixing systems

    NASA Technical Reports Server (NTRS)

    Williams, R. J.; Mullins, O.

    1981-01-01

    Details are given for the construction and operation of a 101.3 KN/sq meter (1 atmosphere) redox control system. A solid ceramic oxygen electrolyte cell is used to monitor the oxygen fugacity in the furnace. The system consists of a vertical quench gas mixing furnace with heads designed for mounting the electrolyte cell and with facilities for inserting and removing the samples, a simplified version of a gas mixing apparatus, and devices for experiments under controlled rates of change of temperature. A thermogravimetric analysis system employing these techniques of redox control and measurement is also described. The calibration and maintenance of the system are discussed.

  20. GRAPHITE ELECTRODE FOR THE MEASUREMENT OF REDOX POTENTIAL AND OXYGEN DIFFUSION RATE IN SOIL

    EPA Science Inventory

    The objective of the project was to evaluate control measurements that might be made at land treatment sites to determine the effectiveness of operation in the management of hazardous wastes. Initial studies were on measurement of oxygen concentration and oxygen diffusion rate (O...

  1. A Simple Experiment To Measure the Content of Oxygen in the Air Using Heated Steel Wool

    ERIC Educational Resources Information Center

    Vera, Francisco; Rivera, Rodrigo; Nunez, Cesar

    2011-01-01

    The typical experiment to measure the oxygen content in the atmosphere uses the rusting of steel wool inside a closed volume of air. Two key aspects of this experiment that make possible a successful measurement of the content of oxygen in the air are the use of a closed atmosphere and the use of a chemical reaction that involves the oxidation of…

  2. Line Profile Measurements of Atomic Oxygen at 1300 A with a VUV Raman Shifter

    NASA Technical Reports Server (NTRS)

    Sharma, Surendra P.; Exberger, Richard J.; Meyer, Scott A.; Gilmore, John O.

    1994-01-01

    We are currently developing an atomic oxygen diagnostic to study the degree of oxygen dissociation in ground-based facilities. The absorption of the (sub 3)P - (sup 3)S(sup 0) resonance triplet in the vacuum ultraviolet is a direct measure of the ground state number density of atomic oxygen. Although the integrated line strength is well known for these transitions, the line profile is not. We report the results of a series of experiments in which the line profile is measured in shock-heated oxygen. An ArF excimer laser and a hydrogen Raman shifter generate tunable VUV radiation at the resonance wavelength. The test gas is dissociated oxygen, generated in the Electric Arc Shock Tube (EAST) Facility at NASA-Ames Research Center. By measuring the absorption of known concentrations of atomic oxygen, we are able to study the absorption line profile. The results will serve as a calibration to apply this diagnostic in other flowfields.

  3. Clonal genotype and population structure inference from single-cell tumor sequencing.

    PubMed

    Roth, Andrew; McPherson, Andrew; Laks, Emma; Biele, Justina; Yap, Damian; Wan, Adrian; Smith, Maia A; Nielsen, Cydney B; McAlpine, Jessica N; Aparicio, Samuel; Bouchard-Côté, Alexandre; Shah, Sohrab P

    2016-07-01

    Single-cell DNA sequencing has great potential to reveal the clonal genotypes and population structure of human cancers. However, single-cell data suffer from missing values and biased allelic counts as well as false genotype measurements owing to the sequencing of multiple cells. We describe the Single Cell Genotyper (https://bitbucket.org/aroth85/scg), an open-source software based on a statistical model coupled with a mean-field variational inference method, which can be used to address these problems and robustly infer clonal genotypes. PMID:27183439

  4. Fast serial analysis of active cholesterol at the plasma membrane in single cells.

    PubMed

    Tian, Chunxiu; Zhou, Junyu; Wu, Zeng-Qiang; Fang, Danjun; Jiang, Dechen

    2014-01-01

    Previously, our group has utilized the luminol electrochemiluminescence to analyze the active cholesterol at the plasma membrane in single cells by the exposure of one cell to a photomultiplier tube (PMT) through a pinhole. In this paper, fast analysis of active cholesterol at the plasma membrane in single cells was achieved by a multimicroelectrode array without the pinhole. Single cells were directly located on the microelectrodes using cell-sized microwell traps. A cycle of voltage was applied on the microelectrodes sequentially to induce a peak of luminescence from each microelectrode for the serial measurement of active membrane cholesterol. A minimal time of 1.60 s was determined for the analysis of one cell. The simulation and the experimental data exhibited a semisteady-state distribution of hydrogen peroxide on the microelectrode after the reaction of cholesterol oxidase with the membrane cholesterol, which supported the relative accuracy of the serial analysis. An eight-microelectrode array was demonstrated to analyze eight single cells in 22 s serially, including the channel switching time. The results from 64 single cells either activated by low ion strength buffer or the inhibition of intracellular acyl-coA/cholesterol acyltransferase (ACAT) revealed that most of the cells analyzed had the similar active membrane cholesterol, while few cells had more active cholesterol resulting in the cellular heterogeneity. The fast single-cell analysis platform developed will be potentially useful for the analysis of more molecules in single cells using proper oxidases. PMID:24328095

  5. Investigating evolutionary perspective of carcinogenesis with single-cell transcriptome analysis

    PubMed Central

    Zhang, Xi; Zhang, Cheng; Li, Zhongjun; Zhong, Jiangjian; Weiner, Leslie P.; Zhong, Jiang F.

    2013-01-01

    We developed phase-switch microfluidic devices for molecular profiling of a large number of single cells. Whole genome microarrays and RNA-sequencing are commonly used to determine the expression levels of genes in cell lysates (a physical mix of millions of cells) for inferring gene functions. However, cellular heterogeneity becomes an inherent noise in the measurement of gene expression. The unique molecular characteristics of individual cells, as well as the temporal and quantitative information of gene expression in cells, are lost when averaged among all cells in cell lysates. Our single-cell technology overcomes this limitation and enables us to obtain a large number of single-cell transcriptomes from a population of cells. A collection of single-cell molecular profiles allows us to study carcinogenesis from an evolutionary perspective by treating cancer as a diverse population of cells with abnormal molecular characteristics. Because a cancer cell population contains cells at various stages of development toward drug resistance, clustering similar single-cell molecular profiles could reveal how drug-resistant sub-clones evolve during cancer treatment. Here, we discuss how single-cell transcriptome analysis technology could enable the study of carcinogenesis from an evolutionary perspective and the development of drug-resistance in leukemia. The single-cell transcriptome analysis reported here could have a direct and significant impact on current cancer treatments and future personalized cancer therapies. PMID:23706768

  6. A convenient, optimized pipeline for isolation, fluorescence microscopy and molecular analysis of live single cells

    PubMed Central

    2014-01-01

    Background Heterogeneity within cell populations is relevant to the onset and progression of disease, as well as development and maintenance of homeostasis. Analysis and understanding of the roles of heterogeneity in biological systems require methods and technologies that are capable of single cell resolution. Single cell gene expression analysis by RT-qPCR is an established technique for identifying transcriptomic heterogeneity in cellular populations, but it generally requires specialized equipment or tedious manipulations for cell isolation. Results We describe the optimization of a simple, inexpensive and rapid pipeline which includes isolation and culture of live single cells as well as fluorescence microscopy and gene expression analysis of the same single cells by RT-qPCR. We characterize the efficiency of single cell isolation and demonstrate our method by identifying single GFP-expressing cells from a mixed population of GFP-positive and negative cells by correlating fluorescence microscopy and RT-qPCR. Conclusions Single cell gene expression analysis by RT-qPCR is a convenient means for investigating cellular heterogeneity, but is most useful when correlating observations with additional measurements. We demonstrate a convenient and simple pipeline for multiplexing single cell RT-qPCR with fluorescence microscopy which is adaptable to other molecular analyses. PMID:24834016

  7. Get to Understand More from Single-Cells: Current Studies of Microfluidic-Based Techniques for Single-Cell Analysis

    PubMed Central

    Lo, Shih-Jie; Yao, Da-Jeng

    2015-01-01

    This review describes the microfluidic techniques developed for the analysis of a single cell. The characteristics of microfluidic (e.g., little sample amount required, high-throughput performance) make this tool suitable to answer and to solve biological questions of interest about a single cell. This review aims to introduce microfluidic related techniques for the isolation, trapping and manipulation of a single cell. The major approaches for detection in single-cell analysis are introduced; the applications of single-cell analysis are then summarized. The review concludes with discussions of the future directions and opportunities of microfluidic systems applied in analysis of a single cell. PMID:26213918

  8. Vacuum Ultraviolet Absorption Measurements of Atomic Oxygen in a Shock Tube

    NASA Technical Reports Server (NTRS)

    Meyer, Scott Andrew

    1995-01-01

    The absorption of vacuum ultraviolet light by atomic oxygen has been measured in the Electric Arc-driven Shock Tube (EAST) Facility at NASA-Ames Research Center. This investigation demonstrates the instrumentation required to determine atomic oxygen concentrations from absorption measurements in impulse facilities. A shock wave dissociates molecular oxygen, producing a high temperature sample of atomic oxygen in the shock tube. A probe beam is generated with a Raman-shifted ArF excimer laser. By suitable tuning of the laser, absorption is measured over a range of wavelengths in the region of the atomic line at 130.49 nm. The line shape function is determined from measurements at atomic oxygen densities of 3x10(exp 17) and 9x10(exp 17) cm(exp -3). The broadening coefficient for resonance interactions is deduced from this data, and this value is in accord with available theoretical models.

  9. Vacuum Ultraviolet Absorption Measurements of Atomic Oxygen in a Shock Tube

    NASA Technical Reports Server (NTRS)

    Meyer, Scott Andrew

    1995-01-01

    The absorption of vacuum ultraviolet light by atomic oxygen has been measured in the Electric Arc-driven Shock Tube (EAST) Facility at NASA-Ames Research Center. This investigation demonstrates the instrumentation required to determine atomic oxygen concentrations from absorption measurements in impulse facilities. A shock wave dissociates molecular oxygen, producing a high temperature sample of atomic oxygen in the shock tube. A probe beam is generated with a Raman-shifted ArF excimer laser. By suitable tuning of the laser, absorption is measured over a range of wavelengths in the region of the atomic line at 130.49 nm. The line shape function is determined from measurements at atomic oxygen densities of 3 x 10(exp 17) and 9 x 10(exp 17) cm(exp -3). The broadening coefficient for resonance interactions is deduced from this data, and this value is in accord with available theoretical models.

  10. Vacuum Ultraviolet Absorption Measurements of Atomic Oxygen in a Shock Tube.

    NASA Astrophysics Data System (ADS)

    Meyer, Scott Andrew

    The absorption of vacuum ultraviolet light by atomic oxygen has been measured in the Electric Arc-driven Shock Tube (EAST) Facility at NASA-Ames Research Center. This investigation demonstrates the instrumentation required to determine atomic oxygen concentrations from absorption measurements in impulse facilities. A shock wave dissociates molecular oxygen, producing a high temperature sample of atomic oxygen in the shock tube. A probe beam is generated with a Raman-shifted ArF excimer laser. By suitable tuning of the laser, absorption is measured over a range of wavelengths in the region of the atomic line at 130.49 nm. The line shape function is determined from measurements at atomic oxygen densities of 3 times 10 ^{17} and 9 times 10^{17} cm ^{-3}. The broadening coefficient for resonance interactions is deduced from this data, and this value is in accord with available theoretical models.

  11. Vacuum Ultraviolet Absorption Measurements of Atomic Oxygen in a Shock Tube

    NASA Technical Reports Server (NTRS)

    Meyer, Scott Andrew

    1995-01-01

    The absorption of vacuum ultraviolet light by atomic oxygen has been measured in the Electric Arc-driven Shock Tube (EAST) Facility at NASA-Ames Research Center. This investigation demonstrates the instrumentation required to determine atomic oxygen concentrations from absorption measurements in impulse facilities. A shock wave dissociates molecular oxygen, producing a high temperature sample of atomic oxygen in the shock tube. A probe beam is generated with a Raman-shifted ArF excimer laser. By suitable tuning of the laser, absorption is measured over a range of wavelengths in the region of the atomic line at 130.49 nm. The line shape function is determined from measurements at atomic oxygen densities of 3 x 10(exp 17) and 9 x 10(exp 17)/cu cm. The broadening coefficient for resonance interactions is deduced from this data, and this value is in accord with available theoretical models.

  12. Single Cell Adhesion Assay Using Computer Controlled Micropipette

    PubMed Central

    Salánki, Rita; Hős, Csaba; Orgovan, Norbert; Péter, Beatrix; Sándor, Noémi; Bajtay, Zsuzsa; Erdei, Anna; Horvath, Robert; Szabó, Bálint

    2014-01-01

    Cell adhesion is a fundamental phenomenon vital for all multicellular organisms. Recognition of and adhesion to specific macromolecules is a crucial task of leukocytes to initiate the immune response. To gain statistically reliable information of cell adhesion, large numbers of cells should be measured. However, direct measurement of the adhesion force of single cells is still challenging and today’s techniques typically have an extremely low throughput (5–10 cells per day). Here, we introduce a computer controlled micropipette mounted onto a normal inverted microscope for probing single cell interactions with specific macromolecules. We calculated the estimated hydrodynamic lifting force acting on target cells by the numerical simulation of the flow at the micropipette tip. The adhesion force of surface attached cells could be accurately probed by repeating the pick-up process with increasing vacuum applied in the pipette positioned above the cell under investigation. Using the introduced methodology hundreds of cells adhered to specific macromolecules were measured one by one in a relatively short period of time (∼30 min). We blocked nonspecific cell adhesion by the protein non-adhesive PLL-g-PEG polymer. We found that human primary monocytes are less adherent to fibrinogen than their in vitro differentiated descendants: macrophages and dendritic cells, the latter producing the highest average adhesion force. Validation of the here introduced method was achieved by the hydrostatic step-pressure micropipette manipulation technique. Additionally the result was reinforced in standard microfluidic shear stress channels. Nevertheless, automated micropipette gave higher sensitivity and less side-effect than the shear stress channel. Using our technique, the probed single cells can be easily picked up and further investigated by other techniques; a definite advantage of the computer controlled micropipette. Our experiments revealed the existence of a sub

  13. Single cell analysis demonstrates how nutrient deprivation creates apoptotic and quiescent cell populations in tumor cylindroids

    PubMed Central

    Kim, Byoung-jin; Forbes, Neil S.

    2016-01-01

    Understanding how quiescent and apoptotic populations form in tumors is necessary because these cell types can considerably diminish therapeutic efficacy. Most cancer therapeutics are ineffective against quiescent cells because they target rapidly proliferating cells. Distinguishing apoptosis is important because apoptotic cells are committed to death and do not require treatment. Regrowth of quiescent cell can lead to tumor reoccurrence and metastasis, which are the leading causes of cancer mortality. We hypothesized that cylindroid cultures and acridine orange staining could be used to determine how nutrient diffusion creates apoptotic and quiescent regions in tumors. To test this hypothesis we developed a microscopy technique to measure cellular DNA and RNA content in single cells using thin cylindroids and acridine orange staining. Cell classification was compared to flow cytometry of cells grown in defined monolayer cultures. The presence of apoptosis was confirmed by morphological nuclear analysis. The effect of diffusion was determined by varying incubation time, cylindroid size, and exposing cylindroids to nutrient-deficient media. Four overlapping regions were identified as a function of cylindroid radius: an outer viable/quiescent region; a second quiescent/apoptotic region; a third late-stage apoptotic region; and an inner dead region. In monolayer cultures the absence of glutamine and growth factors induced apoptosis and hypoxia induced quiescence. Treating with nutrient-deficient media suggested that cells became quiescent near the periphery because of glucose and oxygen limitations, and became apoptotic and died further from the edge because of glutamine and growth factor limitations. These results show that cellular microenvironments can be identified in cylindroids using simple acridine orange staining and that single cell florescence can be measured in three-dimensional culture. The developed techniques will be useful for developing cancer

  14. Nanofountain Probe Electroporation of Single Cells

    PubMed Central

    Kang, Wonmo; Yavari, Fazel; Minary-Jolandan, Majid; Giraldo-Vela, Juan P.; Safi, Asmahan; McNaughton, Rebecca L.; Parpoil, Victor; Espinosa, Horacio D.

    2013-01-01

    The ability to precisely deliver molecules into single cells is of great interest to biotechnology researchers for advancing applications in therapeutics, diagnostics, and drug delivery toward the promise of personalized medicine. The use of bulk electroporation techniques for cell transfection has increased significantly in the last decade, but the technique is nonspecific and requires high voltage, resulting in variable efficiency and low cell viability. We have developed a new tool for electroporation using nanofountain probe (NFP) technology, which can deliver molecules into cells in a manner that is highly efficient and gentler to cells than bulk electroporation or microinjection. Here we demonstrate NFP electroporation (NFP-E) of single HeLa cells within a population by transfecting them with fluorescently labeled dextran and imaging the cells to evaluate the transfection efficiency and cell viability. Our theoretical analysis of the mechanism of NFP-E reveals that application of the voltage creates a localized electric field between the NFP cantilever tip and the region of the cell membrane in contact with the tip. Therefore, NFP-E can deliver molecules to a target cell with minimal effect of the electric potential on the cell. Our experiments on HeLa cells confirm that NFP-E offers single cell selectivity, high transfection efficiency (>95%), qualitative dosage control, and very high viability (92%) of transfected cells. PMID:23650871

  15. Single Molecule and Single Cell Epigenomics

    PubMed Central

    Hyun, Byung-Ryool; McElwee, John L.; Soloway, Paul D.

    2014-01-01

    Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells. PMID:25204781

  16. Atomic oxygen-metal surface studies as applied to mass spectrometer measurements of upper planetary atmospheres

    NASA Technical Reports Server (NTRS)

    Sjolander, G. W.

    1976-01-01

    The problem of atomic oxygen loss in mass spectrometer ion sources can be reduced to an understanding of the possible surface interactions between oxygen atoms and the metal surface of the ion source. Results are presented for an experimental study in which an atomic oxygen beam apparatus and a mass spectrometer were used to measure the oxygen atom reflection, recombination, general surface reaction, and occlusion probabilities on six different engineering surfaces as a function of atomic oxygen exposure. The materials studied are gold, Nichrome V, aluminum, titanium, silver, and platinum. The variation in measured reflection probability seems to occur with metals that form oxides, Nichrome V being stable in terms of reflection stability. Recombination is observed an all surfaces except aluminum and platinum. Variation in the complete set of measurements in a single experiment is the result of varying surface conditions.

  17. Single-cell MALDI Tandem Mass Spectrometry: Unambiguous Assignment of Small Biomolecules from Single Chlamydomonas reinhardtii Cells.

    PubMed

    Krismer, Jasmin; Steinhoff, Robert F; Zenobi, Renato

    2016-01-01

    The analysis of compounds from single cells is a major challenge in analytical life science. Labeling strategies, for instance fluorescence detection, are well established for measuring proteins with single cell sensitivity, but they mostly fail to detect small molecules. More recently mass spectrometry has entered the realm of single cell sensitivity and enables the label-free and highly parallelized detection of small biomolecules from single cells. The assignment of signals detected in single cells, however, generally has to rely on measurements in whole cell culture extracts. Isobaric structures, contaminations, higher noise levels and the high variability in the abundance of peaks between single cells complicate the assignment of peaks in single-cell spectra. Tandem mass spectrometry would be very useful for compound identification via mass spectrometry directly in single-cell analyses. Here we present the first single cell tandem mass spectra collected using matrix-assisted laser-desorption/ionization. The spectra obtained allow the assignment of most compounds detected in the spectra. We also show that the fragmentation is not restricted to the most abundant peaks in the spectra, but over a dynamic range of more than one order of magnitude. PMID:27131106

  18. An Inexpensive Electrode and Cell for Measurement of Oxygen Uptake in Chemical and Biochemical Systems.

    ERIC Educational Resources Information Center

    Brunet, Juan E.; And Others

    1983-01-01

    The continuous measurement of oxygen consumption in an enzymatic reaction is a frequent experimental fact and extremely important in the enzymatic activity of oxygenase. An electrochemical system, based on a polarographic method, has been developed to monitor the oxygen uptake. The system developed and electrode used are described. (JN)

  19. System for measuring oxygen consumption rates of mammalian cells in static culture under hypoxic conditions.

    PubMed

    Kagawa, Yuki; Miyahara, Hirotaka; Ota, Yuri; Tsuneda, Satoshi

    2016-01-01

    Estimating the oxygen consumption rates (OCRs) of mammalian cells in hypoxic environments is essential for designing and developing a three-dimensional (3-D) cell culture system. However, OCR measurements under hypoxic conditions are infrequently reported in the literature. Here, we developed a system for measuring OCRs at low oxygen levels. The system injects nitrogen gas into the environment and measures the oxygen concentration by an optical oxygen microsensor that consumes no oxygen. The developed system was applied to HepG2 cells in static culture. Specifically, we measured the spatial profiles of the local dissolved oxygen concentration in the medium, then estimated the OCRs of the cells. The OCRs, and also the pericellular oxygen concentrations, decreased nonlinearly as the oxygen partial pressure in the environment decreased from 19% to 1%. The OCRs also depended on the culture period and the matrix used for coating the dish surface. Using this system, we can precisely estimate the OCRs of various cell types under environments that mimic 3-D culture conditions, contributing crucial data for an efficient 3-D culture system design. PMID:26558344

  20. Airborne Lidar Measurements of Atmospheric Pressure Made Using the Oxygen A-Band

    NASA Technical Reports Server (NTRS)

    Riris, Haris; Rodriquez, Michael; Allan, Graham R.; Hasselbrack, William E.; Stephen, Mark A.; Abshire, James B.

    2011-01-01

    We report on airborne measurements of atmospheric pressure using a fiber-laser based lidar operating in the oxygen A-band near 765 nm and the integrated path differential absorption measurement technique. Our lidar uses fiber optic technology and non-linear optics to generate tunable laser radiation at 765 nm, which overlaps an absorption line pair in the Oxygen A-band. We use a pulsed time resolved technique, which rapidly steps the laser wavelength across the absorption line pair, a 20 cm telescope and photon counting detector to measure Oxygen concentrations.

  1. Making an honest measurement scale out of the oxygen isotope delta-values.

    PubMed

    Gat, Joel R; DeBievre, Paul

    2002-01-01

    The differential measurement of the abundance of oxygen isotopes based on reference materials, such as VSMOW for the case of water, was used because the precision of the absolute mass-spectrometric determination of the abundance fell short of the differences to be measured. Since then these measurements have been much improved, so that a calibration scheme of the oxygen isotope abundance in water, carbonates, silica, phosphates, sulfates, nitrates and organic materials is suggested, based on an accredited primary standard of oxygen in air and using standard fluorination and O(2) to CO(2) conversion techniques. PMID:12442297

  2. Detecting Bacterial Surface Organelles on Single Cells Using Optical Tweezers.

    PubMed

    Zakrisson, Johan; Singh, Bhupender; Svenmarker, Pontus; Wiklund, Krister; Zhang, Hanqing; Hakobyan, Shoghik; Ramstedt, Madeleine; Andersson, Magnus

    2016-05-10

    Bacterial cells display a diverse array of surface organelles that are important for a range of processes such as intercellular communication, motility and adhesion leading to biofilm formation, infections, and bacterial spread. More specifically, attachment to host cells by Gram-negative bacteria are mediated by adhesion pili, which are nanometers wide and micrometers long fibrous organelles. Since these pili are significantly thinner than the wavelength of visible light, they cannot be detected using standard light microscopy techniques. At present, there is no fast and simple method available to investigate if a single cell expresses pili while keeping the cell alive for further studies. In this study, we present a method to determine the presence of pili on a single bacterium. The protocol involves imaging the bacterium to measure its size, followed by predicting the fluid drag based on its size using an analytical model, and thereafter oscillating the sample while a single bacterium is trapped by an optical tweezer to measure its effective fluid drag. Comparison between the predicted and the measured fluid drag thereby indicate the presence of pili. Herein, we verify the method using polymer coated silica microspheres and Escherichia coli bacteria expressing adhesion pili. Our protocol can in real time and within seconds assist single cell studies by distinguishing between piliated and nonpiliated bacteria. PMID:27088225

  3. Membrane Transport of Singlet Oxygen Monitored by Dipole Potential Measurements

    PubMed Central

    Sokolov, Valerij S.; Pohl, Peter

    2009-01-01

    Abstract The efficiency of photodynamic reactions depends on 1), the penetration depth of the photosensitizer into the membrane and 2), the sidedness of the target. Molecules which are susceptible to singlet oxygen (1O2) experience less damage when separated from the photosensitizer by the membrane. Since 1O2 lifetime in the membrane environment is orders of magnitude longer than the time required for nonexcited oxygen (O2) to cross the membrane, this observation suggests that differences between the permeabilities or membrane partition of 1O2 and O2 exist. We investigated this hypothesis by releasing 1O2 at one side of a planar membrane while monitoring the kinetics of target damage at the opposite side of the same membrane. Damage to the target, represented by dipole-modifying molecules (phloretin or phlorizin), was indicated by changes in the interleaflet dipole potential difference Δϕb. A simple analytical model allowed estimation of the 1O2 interleaflet concentration difference from the rate at which Δϕb changed. It confirmed that the lower limit of 1O2 permeability is ∼2 cm/s; i.e., it roughly matches O2 permeability as predicted by Overton's rule. Consequently, the membrane cannot act as a barrier to 1O2 diffusion. Differences in the reaction rates at the cytoplasmic and extracellular membrane leaflets may be attributed only to 1O2 quenchers inside the membrane. PMID:18931253

  4. The Oxygen Ratio: A Fuel-Independent Measure of Mixture Stoichiometry

    SciTech Connect

    Mueller, C J; Musculus, M P; Pickett, L M; Pitz, W J; Westbrook, C K

    2003-12-19

    The pollutant-formation characteristics and other properties of a combustion reaction typically depend strongly on the proximity of the mixture to its stoichiometric condition, i.e., the ''mixture stoichiometry.'' A quantitative, widely applicable measure of this mixture property is therefore a critical independent variable in the study of combustion systems. Such a parameter enables the clear separation of mixture stoichiometry effects from other effects (e.g., fuel molecular structure, product temperature, diluent concentration, pressure). The parameter most often used to quantify mixture stoichiometry is the equivalence ratio. Unfortunately, the equivalence ratio fails to properly account for oxygen in oxygenates, i.e., compounds that have oxygen chemically bound within the fuel molecule. This manuscript introduces the oxygen ratio, a parameter that properly characterizes mixture stoichiometry for a broader class of reactants than does the equivalence ratio, including oxygenates. A detailed definition of the oxygen ratio is provided and used to show its relationship to the equivalence ratio. The definition is also used to quantify errors involved when the equivalence ratio is used as a measure of mixture stoichiometry with oxygenates. Proper usage of the oxygen ratio is discussed and the oxygen ratio is used to interpret results in a practical example.

  5. New instrumentation for optical measuring of oxygen in gas or dissolved in liquids

    NASA Astrophysics Data System (ADS)

    Trettnak, W.; Gruber, W.; Reininger, F.; O'Leary, P.; Klimant, I.

    The optical oxygen sensor is a novel device for the determination of oxygen in gases or dissolved in liquids. It is based on the measurement principle of fluorescence quenching, which is completely different from that of polarographic oxygen sensors (today the most widespread devices for oxygen detection). The new instrument offers features and advantages, which render it not only a realistic alternative, but, for specific applications, make it superior to existing electrochemical methods. The system is based on low-cost semiconductor devices (light-emitting diodes, photodiodes, low-cost analogue and digital components) and new LED-compatible oxygen-sensitive membranes. The flow cell of the instrument may be thermostatted and the sensor can be calibrated by a simple two-point calibration procedure. The optical oxygen sensor is particularly suitable for measuring dissolved oxygen in respirometry, since no oxygen is consumed by the device and the signal is independent of sample flowrate or stirring speed. Typical fields of application are monitoring of oxygen in ground and drinking water, in process controll in bioreactors and in breath gas and blood gas analysis.

  6. Direct measurement of local dissolved oxygen concentration spatial profiles in a cell culture environment.

    PubMed

    Kagawa, Yuki; Matsuura, Katsuhisa; Shimizu, Tatsuya; Tsuneda, Satoshi

    2015-06-01

    Controlling local dissolved oxygen concentration (DO) in media is critical for cell or tissue cultures. Various biomaterials and culture methods have been developed to modulate DO. Direct measurement of local DO in cultures has not been validated as a method to test DO modulation. In the present study we developed a DO measurement system equipped with a Clark-type oxygen microelectrode manipulated with 1 μm precision in three-dimensional space to explore potential applications for tissue engineering. By determining the microelectrode tip position precisely against the bottom plane of culture dishes with rat or human cardiac cells in static monolayer culture, we successfully obtained spatial distributions of DO in the medium. Theoretical quantitative predictions fit the obtained data well. Based on analyses of the variance between samples, we found the data reflected "local" oxygen consumption in the vicinity of the microelectrode and the detection of temporal changes in oxygen consumption rates of cultured cells was limited by the diffusion rate of oxygen in the medium. This oxygen measuring system monitors local oxygen consumption and production with high spatial resolution, and can potentially be used with recently developed oxygen modulating biomaterials to design microenvironments and non-invasively monitor local DO dynamics during culture. PMID:25565074

  7. Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.

    PubMed

    Leung, Kaston; Klaus, Anders; Lin, Bill K; Laks, Emma; Biele, Justina; Lai, Daniel; Bashashati, Ali; Huang, Yi-Fei; Aniba, Radhouane; Moksa, Michelle; Steif, Adi; Mes-Masson, Anne-Marie; Hirst, Martin; Shah, Sohrab P; Aparicio, Samuel; Hansen, Carl L

    2016-07-26

    The genomes of large numbers of single cells must be sequenced to further understanding of the biological significance of genomic heterogeneity in complex systems. Whole genome amplification (WGA) of single cells is generally the first step in such studies, but is prone to nonuniformity that can compromise genomic measurement accuracy. Despite recent advances, robust performance in high-throughput single-cell WGA remains elusive. Here, we introduce droplet multiple displacement amplification (MDA), a method that uses commercially available liquid dispensing to perform high-throughput single-cell MDA in nanoliter volumes. The performance of droplet MDA is characterized using a large dataset of 129 normal diploid cells, and is shown to exceed previously reported single-cell WGA methods in amplification uniformity, genome coverage, and/or robustness. We achieve up to 80% coverage of a single-cell genome at 5× sequencing depth, and demonstrate excellent single-nucleotide variant (SNV) detection using targeted sequencing of droplet MDA product to achieve a median allelic dropout of 15%, and using whole genome sequencing to achieve false and true positive rates of 9.66 × 10(-6) and 68.8%, respectively, in a G1-phase cell. We further show that droplet MDA allows for the detection of copy number variants (CNVs) as small as 30 kb in single cells of an ovarian cancer cell line and as small as 9 Mb in two high-grade serous ovarian cancer samples using only 0.02× depth. Droplet MDA provides an accessible and scalable method for performing robust and accurate CNV and SNV measurements on large numbers of single cells. PMID:27412862

  8. Oxygenator Safety Evaluation: A Focus on Connection Grip Strength and Arterial Temperature Measurement Accuracy

    PubMed Central

    Newland, Richard F.; Baker, Robert A.; Sanderson, Andrew J.; Tuble, Sigrid C.; Tully, Phil J.

    2012-01-01

    Abstract: This report describes the assessment of three specific safety-related specifications in the consideration of an alternate oxygenator; first the grip strength relationship between various oxygenator connectors and SMARxT® tubing, second, the grip strength of various biopassive tubings and an isolated SMARxT® connector, and finally, the accuracy of the arterial outlet temperature measurement. Grip strength experiments for the connections between the SMARxT® tubing and the venous reservoir outlet and the oxygenator venous inlet and oxygenator arterial outlet of the Medtronic Affinity®, Sorin Synthesis®, Sorin Primox®, and Terumo Capiox® RX25 oxygenators were performed. In addition we compared the grip strength of polyvinyl chloride, Physio®, Trillium®, Carmeda®, X-Coating®, and SMARxT® tubing. The accuracy of the integrated arterial outlet temperature probes was determined by comparing the temperatures measured by the integrated probe with a precision reference thermometer. Connector grip strength comparisons for the evaluation oxygenators with SMARxT® tubing showed significant variation between oxygenators and connections (p = .02). Evaluation of the arterial outlet showed significant variation between evaluation oxygenators, while at the venous reservoir outlet and oxygenator inlet, there were no significant differences. Grip strength comparison data for the various tubing types demonstrated a main effect for tubing type F(5, 18) = 8.01, p = .002, ηp2 = .77. Temperature accuracy measurements demonstrated that all oxygenators overread the arterial outlet temperature at 15°C, whilst at temperatures ≥25°C, all oxygenators underread the arterial outlet temperature. The integrity of SMARxT® tubing connection is influenced by the connector type, and may decline over time, highlighting the importance to not consider interchanging components of the bypass circuit as inconsequential. PMID:22893983

  9. Digital Microfluidics for Manipulation and Analysis of a Single Cell

    PubMed Central

    He, Jie-Long; Chen, An-Te; Lee, Jyong-Huei; Fan, Shih-Kang

    2015-01-01

    The basic structural and functional unit of a living organism is a single cell. To understand the variability and to improve the biomedical requirement of a single cell, its analysis has become a key technique in biological and biomedical research. With a physical boundary of microchannels and microstructures, single cells are efficiently captured and analyzed, whereas electric forces sort and position single cells. Various microfluidic techniques have been exploited to manipulate single cells through hydrodynamic and electric forces. Digital microfluidics (DMF), the manipulation of individual droplets holding minute reagents and cells of interest by electric forces, has received more attention recently. Because of ease of fabrication, compactness and prospective automation, DMF has become a powerful approach for biological application. We review recent developments of various microfluidic chips for analysis of a single cell and for efficient genetic screening. In addition, perspectives to develop analysis of single cells based on DMF and emerging functionality with high throughput are discussed. PMID:26389890

  10. Digital Microfluidics for Manipulation and Analysis of a Single Cell.

    PubMed

    He, Jie-Long; Chen, An-Te; Lee, Jyong-Huei; Fan, Shih-Kang

    2015-01-01

    The basic structural and functional unit of a living organism is a single cell. To understand the variability and to improve the biomedical requirement of a single cell, its analysis has become a key technique in biological and biomedical research. With a physical boundary of microchannels and microstructures, single cells are efficiently captured and analyzed, whereas electric forces sort and position single cells. Various microfluidic techniques have been exploited to manipulate single cells through hydrodynamic and electric forces. Digital microfluidics (DMF), the manipulation of individual droplets holding minute reagents and cells of interest by electric forces, has received more attention recently. Because of ease of fabrication, compactness and prospective automation, DMF has become a powerful approach for biological application. We review recent developments of various microfluidic chips for analysis of a single cell and for efficient genetic screening. In addition, perspectives to develop analysis of single cells based on DMF and emerging functionality with high throughput are discussed. PMID:26389890

  11. Single-cell transcriptome sequencing: recent advances and remaining challenges

    PubMed Central

    Liu, Serena; Trapnell, Cole

    2016-01-01

    Single-cell RNA-sequencing methods are now robust and economically practical and are becoming a powerful tool for high-throughput, high-resolution transcriptomic analysis of cell states and dynamics. Single-cell approaches circumvent the averaging artifacts associated with traditional bulk population data, yielding new insights into the cellular diversity underlying superficially homogeneous populations. Thus far, single-cell RNA-sequencing has already shown great effectiveness in unraveling complex cell populations, reconstructing developmental trajectories, and modeling transcriptional dynamics. Ongoing technical improvements to single-cell RNA-sequencing throughput and sensitivity, the development of more sophisticated analytical frameworks for single-cell data, and an increasing array of complementary single-cell assays all promise to expand the usefulness and potential applications of single-cell transcriptomic profiling. PMID:26949524

  12. High-Content Quantification of Single-Cell Immune Dynamics

    PubMed Central

    Junkin, Michael; Kaestli, Alicia J.; Cheng, Zhang; Jordi, Christian; Albayrak, Cem; Hoffmann, Alexander; Tay, Savaş

    2016-01-01

    Summary Cells receive time-varying signals from the environment and generate functional responses by secreting their own signaling molecules. Characterizing dynamic input-output relationships in single cells is crucial for understanding and modeling cellular systems. We developed an automated microfluidic system that delivers precisely defined dynamical inputs to individual living cells and simultaneously measures key immune parameters dynamically. Our system combines nanoliter immunoassays, microfluidic input generation, and time-lapse microscopy, enabling study of previously untestable aspects of immunity by measuring time-dependent cytokine secretion and transcription factor activity from single cells stimulated with dynamic inflammatory inputs. Employing this system to analyze macrophage signal processing under pathogen inputs, we found that the dynamics of TNF secretion are highly heterogeneous and surprisingly uncorrelated with the dynamics of NF-κB, the transcription factor controlling TNF production. Computational modeling of the LPS/TLR4 pathway shows that post-transcriptional regulation by TRIF is a key determinant of noisy and uncorrelated TNF secretion dynamics in single macrophages. PMID:27050527

  13. JGI Genomic Single-cell Assembly Workflow

    SciTech Connect

    Trong, S.

    2011-09-16

    JIGSAW is a software package disigned to quality control and assemble genomic DNA sequences from single-cell bacterial and archaeal genomes. Amplification of singel-cell genomes using multiple displacement amplification technology presents challenges that magnify the amount of contaminants in the sample and produce non uniform depth of sequence coverage. these factors pose problems whan assembling the genomic data using currently availible short read assembles. The software addresses these problems by removing contaminants and normalizing the sequence read coverage prior to assemble. A hybrid assembly approach using two different open source genome assembly tools is then applied to piece together the DNA fragments. Additional reporting of QC metrics for the input sample and the genome assembly is provided for further analysis.

  14. The niche in single-cell technologies.

    PubMed

    Donati, Giacomo

    2016-03-01

    The niche is the microenvironment in which each cell exists and is able to keep its own peculiar characteristics. The importance of the niche has been intensively studied especially in the context of stem cells, as it is responsible for both the maintenance of stemness and activation of differentiation. In the past few years, a variety of single-cell technologies have shed light on the extraordinary variability that characterizes different stem cell populations both in vitro and in vivo, but in most cases positional information is lost. Recent developments of new technologies aim to integrate both the transcriptomic profiling of cells and their spatial location. In this review I will discuss the state of the art of these technologies and the integration with others approaches that will be important in the study of stem cell populations. PMID:26620629

  15. Single-cell protein from waste cellulose

    NASA Technical Reports Server (NTRS)

    Dunlap, C. E.; Callihan, C. D.

    1973-01-01

    The recycle, reuse, or reclamation of single cell protein from liquid and solid agricultural waste fibers by a fermentation process is reported. It is shown that cellulose comprises the bulk of the fibers at 50% to 55% of the dry weight of the refuse and that its biodegradability is of prime importance in the choice of a substrate. The application of sodium hydroxide followed by heat and pressure serves to de-polymerize and disrupt lignin structure while swelling the cellulose to increase water uptake and pore volume. Some of the lignin, hemi-celluloses, ash, and cellulose of the material is hydrolized and solubilized. Introduction of microorganisms to the substrate fibers mixed with nutrients produces continuous fermentation of cellulose for further protein extraction and purification.

  16. Nanosensing at the single cell level✩

    PubMed Central

    Vo-Dinh, Tuan

    2013-01-01

    This article presents an overview of the development, operation, and applications of optical nanobiosensors for use in in vivo detection of biotargets in individual living cells. The nanobiosensors are equipped with immobilized bioreceptor probes (e.g., antibodies, enzyme substrate) selective to specific molecular targets. Laser excitation is transmitted into the fiber producing an evanescent field at the tip of the fiber in order to excite target molecules bound to the bioreceptors immobilized at the fiber tips. A photometric system detects the optical signal (e.g., fluorescence) originated from the analyte molecules or from the analyte–bioreceptor reaction. Examples of detection of biospecies and molecular signaling pathways of apoptosis in a living cell are discussed to illustrate the potential of the nanobiosensor technology for single cell analysis. PMID:24839348

  17. JGI Genomic Single-cell Assembly Workflow

    Energy Science and Technology Software Center (ESTSC)

    2011-09-16

    JIGSAW is a software package disigned to quality control and assemble genomic DNA sequences from single-cell bacterial and archaeal genomes. Amplification of singel-cell genomes using multiple displacement amplification technology presents challenges that magnify the amount of contaminants in the sample and produce non uniform depth of sequence coverage. these factors pose problems whan assembling the genomic data using currently availible short read assembles. The software addresses these problems by removing contaminants and normalizing the sequencemore » read coverage prior to assemble. A hybrid assembly approach using two different open source genome assembly tools is then applied to piece together the DNA fragments. Additional reporting of QC metrics for the input sample and the genome assembly is provided for further analysis.« less

  18. Image-guided optical measurement of blood oxygen saturation within capillary vessels (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Akons, Kfir; Zeidan, Adel; Yeheskely-Hayon, Daniella; Minai, Limor; Yelin, Dvir

    2016-03-01

    Values of blood oxygenation levels are useful for assessing heart and lung conditions, and are frequently monitored during routine patient care. Independent measurement of the oxygen saturation in capillary blood, which is significantly different from that of arterial blood, is important for diagnosing tissue hypoxia and for increasing the accuracy of existing techniques that measure arterial oxygen saturation. Here, we developed a simple, non-invasive technique for measuring the reflected spectra from individual capillary vessels within a human lip, allowing local measurement of the blood oxygen saturation. The optical setup includes a spatially incoherent broadband light that was focused onto a specific vessel below the lip surface. Backscattered light was imaged by a camera for identifying a target vessel and pointing the illumination beam to its cross section. Scattered light from the vessel was then collected by a single-mode fiber and analyzed by a fast spectrometer. Spectra acquired from small capillary vessels within a volunteer lip showed the characteristic oxyhemoglobin absorption bands in real time and with a high signal-to-noise ratio. Measuring capillary oxygen saturation using this technique would potentially be more accurate compared to existing pulse oximetry techniques due to its insensitivity to the patient's skin color, pulse rate, motion, and medical condition. It could be used as a standalone endoscopic technique for measuring tissue hypoxia or in conjunction with conventional pulse oximetry for a more accurate measurement of oxygen transport in the body.

  19. Single-Cell Analysis of Growth and Cell Division of the Anaerobe Desulfovibrio vulgaris Hildenborough.

    PubMed

    Fievet, Anouchka; Ducret, Adrien; Mignot, Tâm; Valette, Odile; Robert, Lydia; Pardoux, Romain; Dolla, Alain R; Aubert, Corinne

    2015-01-01

    Recent years have seen significant progress in understanding basic bacterial cell cycle properties such as cell growth and cell division. While characterization and regulation of bacterial cell cycle is quite well-documented in the case of fast growing aerobic model organisms, no data has been so far reported for anaerobic bacteria. This lack of information in anaerobic microorganisms can mainly be explained by the absence of molecular and cellular tools such as single cell microscopy and fluorescent probes usable for anaerobes and essential to study cellular events and/or subcellular localization of the actors involved in cell cycle. In this study, single-cell microscopy has been adapted to study for the first time, in real time, the cell cycle of a bacterial anaerobe, Desulfovibrio vulgaris Hildenborough (DvH). This single-cell analysis provides mechanistic insights into the cell division cycle of DvH, which seems to be governed by the recently discussed so-called incremental model that generates remarkably homogeneous cell sizes. Furthermore, cell division was reversibly blocked during oxygen exposure. This may constitute a strategy for anaerobic cells to cope with transient exposure to oxygen that they may encounter in their natural environment, thereby contributing to their aerotolerance. This study lays the foundation for the first molecular, single-cell assay that will address factors that cannot otherwise be resolved in bulk assays and that will allow visualization of a wide range of molecular mechanisms within living anaerobic cells. PMID:26696987

  20. Single-Cell Analysis of Growth and Cell Division of the Anaerobe Desulfovibrio vulgaris Hildenborough

    PubMed Central

    Fievet, Anouchka; Ducret, Adrien; Mignot, Tâm; Valette, Odile; Robert, Lydia; Pardoux, Romain; Dolla, Alain R.; Aubert, Corinne

    2015-01-01

    Recent years have seen significant progress in understanding basic bacterial cell cycle properties such as cell growth and cell division. While characterization and regulation of bacterial cell cycle is quite well-documented in the case of fast growing aerobic model organisms, no data has been so far reported for anaerobic bacteria. This lack of information in anaerobic microorganisms can mainly be explained by the absence of molecular and cellular tools such as single cell microscopy and fluorescent probes usable for anaerobes and essential to study cellular events and/or subcellular localization of the actors involved in cell cycle. In this study, single-cell microscopy has been adapted to study for the first time, in real time, the cell cycle of a bacterial anaerobe, Desulfovibrio vulgaris Hildenborough (DvH). This single-cell analysis provides mechanistic insights into the cell division cycle of DvH, which seems to be governed by the recently discussed so-called incremental model that generates remarkably homogeneous cell sizes. Furthermore, cell division was reversibly blocked during oxygen exposure. This may constitute a strategy for anaerobic cells to cope with transient exposure to oxygen that they may encounter in their natural environment, thereby contributing to their aerotolerance. This study lays the foundation for the first molecular, single-cell assay that will address factors that cannot otherwise be resolved in bulk assays and that will allow visualization of a wide range of molecular mechanisms within living anaerobic cells. PMID:26696987

  1. Impact of red blood cell transfusion on global and regional measures of oxygenation.

    PubMed

    Roberson, Russell S; Bennett-Guerrero, Elliott

    2012-01-01

    Anemia is common in critically ill patients. Although the goal of transfusion of red blood cells is to increase oxygen-carrying capacity, there are contradictory results about whether red blood cell transfusion to treat moderate anemia (e.g., hemoglobin 7-10 g/dL) improves tissue oxygenation or changes outcomes. Whereas increasing levels of anemia eventually lead to a level of critical oxygen delivery, increased cardiac output and oxygen extraction are homeostatic mechanisms the body uses to prevent a state of dysoxia in the setting of diminished oxygen delivery due to anemia. In order for cardiac output to increase in the face of anemia, normovolemia must be maintained. Transfusion of red blood cells increases blood viscosity, which may actually decrease cardiac output (barring a state of hypovolemia prior to transfusion). Studies have generally shown that transfusion of red blood cells fails to increase oxygen uptake unless oxygen uptake/oxygen delivery dependency exists (e.g., severe anemia or strenuous exercise). Recently, near-infrared spectroscopy, which approximates the hemoglobin saturation of venous blood, has been used to investigate whether transfusion of red blood cells increases tissue oxygenation in regional tissue beds (e.g., brain, peripheral skeletal muscle). These studies have generally shown increases in near-infrared spectroscopy derived measurements of tissue oxygenation following transfusion. Studies evaluating the effect of transfusion on the microcirculation have shown that transfusion increases the functional capillary density. This article will review fundamental aspects of oxygen delivery and extraction, and the effects of red blood cell transfusion on tissue oxygenation as well as the microcirculation. PMID:22238040

  2. Detecting Antigen-Specific T Cell Responses: From Bulk Populations to Single Cells

    PubMed Central

    Phetsouphanh, Chansavath; Zaunders, John James; Kelleher, Anthony Dominic

    2015-01-01

    A new generation of sensitive T cell-based assays facilitates the direct quantitation and characterization of antigen-specific T cell responses. Single-cell analyses have focused on measuring the quality and breadth of a response. Accumulating data from these studies demonstrate that there is considerable, previously-unrecognized, heterogeneity. Standard assays, such as the ICS, are often insufficient for characterization of rare subsets of cells. Enhanced flow cytometry with imaging capabilities enables the determination of cell morphology, as well as the spatial localization of the protein molecules within a single cell. Advances in both microfluidics and digital PCR have improved the efficiency of single-cell sorting and allowed multiplexed gene detection at the single-cell level. Delving further into the transcriptome of single-cells using RNA-seq is likely to reveal the fine-specificity of cellular events such as alternative splicing (i.e., splice variants) and allele-specific expression, and will also define the roles of new genes. Finally, detailed analysis of clonally related antigen-specific T cells using single-cell TCR RNA-seq will provide information on pathways of differentiation of memory T cells. With these state of the art technologies the transcriptomics and genomics of Ag-specific T cells can be more definitively elucidated. PMID:26274954

  3. Oxygen consumption measurements during continual centrifugation of mice.

    NASA Technical Reports Server (NTRS)

    Fethke, W.; Cook, K. M.; Porter, S. M.; Wunder, C. C.

    1973-01-01

    A simple method is described for measurement of metabolism of conscious, unrestrained animals, during chronic centrifugation or other conditions of isolation (23.75 hr/day) from the investigators in an essentially normal atmospheric environment for as long as seven days. This involves telemetry of pressure changes in a metabolic chamber. At 7 G's, increased O2 intake lasting two to seven days and a decreased excursion of the day-night difference were measured for male white mice with less effect or even an opposite effect at lower fields. Base-line measurements of metabolic rate per mouse are less affected by animal size than expected from the surface area law.

  4. Predicting stochastic gene expression dynamics in single cells.

    PubMed

    Mettetal, Jerome T; Muzzey, Dale; Pedraza, Juan M; Ozbudak, Ertugrul M; van Oudenaarden, Alexander

    2006-05-01

    Fluctuations in protein numbers (noise) due to inherent stochastic effects in single cells can have large effects on the dynamic behavior of gene regulatory networks. Although deterministic models can predict the average network behavior, they fail to incorporate the stochasticity characteristic of gene expression, thereby limiting their relevance when single cell behaviors deviate from the population average. Recently, stochastic models have been used to predict distributions of steady-state protein levels within a population but not to predict the dynamic, presteady-state distributions. In the present work, we experimentally examine a system whose dynamics are heavily influenced by stochastic effects. We measure population distributions of protein numbers as a function of time in the Escherichia coli lactose uptake network (lac operon). We then introduce a dynamic stochastic model and show that prediction of dynamic distributions requires only a few noise parameters in addition to the rates that characterize a deterministic model. Whereas the deterministic model cannot fully capture the observed behavior, our stochastic model correctly predicts the experimental dynamics without any fit parameters. Our results provide a proof of principle for the possibility of faithfully predicting dynamic population distributions from deterministic models supplemented by a stochastic component that captures the major noise sources. PMID:16648266

  5. Block-Cell-Printing for live single-cell printing

    PubMed Central

    Zhang, Kai; Chou, Chao-Kai; Xia, Xiaofeng; Hung, Mien-Chie; Qin, Lidong

    2014-01-01

    A unique live-cell printing technique, termed “Block-Cell-Printing” (BloC-Printing), allows for convenient, precise, multiplexed, and high-throughput printing of functional single-cell arrays. Adapted from woodblock printing techniques, the approach employs microfluidic arrays of hook-shaped traps to hold cells at designated positions and directly transfer the anchored cells onto various substrates. BloC-Printing has a minimum turnaround time of 0.5 h, a maximum resolution of 5 µm, close to 100% cell viability, the ability to handle multiple cell types, and efficiently construct protrusion-connected single-cell arrays. The approach enables the large-scale formation of heterotypic cell pairs with controlled morphology and allows for material transport through gap junction intercellular communication. When six types of breast cancer cells are allowed to extend membrane protrusions in the BloC-Printing device for 3 h, multiple biophysical characteristics of cells—including the protrusion percentage, extension rate, and cell length—are easily quantified and found to correlate well with their migration levels. In light of this discovery, BloC-Printing may serve as a rapid and high-throughput cell protrusion characterization tool to measure the invasion and migration capability of cancer cells. Furthermore, primary neurons are also compatible with BloC-Printing. PMID:24516129

  6. Limitations of fitting angular scattering from single cells (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Fan, Xing; Cannaday, Ashley E.; Berger, Andrew J.

    2016-04-01

    The literature contains several reports of Mie-like fits to angular-domain elastic scattering measurements from multiple cells or isolated mitochondria. In these studies, the sampling volume typically contains hundreds or thousands of mitochondria, allowing for the size distribution of mitochondria to be modeled as a smooth function, (e.g. Gaussian or log-normal) with a small number of free parameters. In the case of a single-cell volume containing significantly fewer mitochondria, the true size distribution will no longer be as smooth. Increasing the number of free parameters can lead to unstable fits, however, as the forward-directed angular scattering pattern from such a population illuminated with 785 nm light is a monotonically decaying radial function with few distinct features. Using simulations, we have investigated the limitations of modeling single-cell mitochondrial scattering using smooth population distributions of Mie scatterers. In different instances, the fidelity of the estimated size information can be limited by the number of organelles, the angular detection range, or the non-ideality of the data (both speckle and shot noise). We will describe the conditions under which each of these effects dominates. We will also discuss whether mean and standard deviation are the best sizes to report from such Mie modeling, or if there are other size parameters that have greater fidelity to the true, non-smooth size distributions.

  7. Single-cell force spectroscopy of pili-mediated adhesion

    NASA Astrophysics Data System (ADS)

    Sullan, Ruby May A.; Beaussart, Audrey; Tripathi, Prachi; Derclaye, Sylvie; El-Kirat-Chatel, Sofiane; Li, James K.; Schneider, Yves-Jacques; Vanderleyden, Jos; Lebeer, Sarah; Dufrêne, Yves F.

    2013-12-01

    Although bacterial pili are known to mediate cell adhesion to a variety of substrates, the molecular interactions behind this process are poorly understood. We report the direct measurement of the forces guiding pili-mediated adhesion, focusing on the medically important probiotic bacterium Lactobacillus rhamnosus GG (LGG). Using non-invasive single-cell force spectroscopy (SCFS), we quantify the adhesion forces between individual bacteria and biotic (mucin, intestinal cells) or abiotic (hydrophobic monolayers) surfaces. On hydrophobic surfaces, bacterial pili strengthen adhesion through remarkable nanospring properties, which - presumably - enable the bacteria to resist high shear forces under physiological conditions. On mucin, nanosprings are more frequent and adhesion forces larger, reflecting the influence of specific pili-mucin bonds. Interestingly, these mechanical responses are no longer observed on human intestinal Caco-2 cells. Rather, force curves exhibit constant force plateaus with extended ruptures reflecting the extraction of membrane nanotethers. These single-cell analyses provide novel insights into the molecular mechanisms by which piliated bacteria colonize surfaces (nanosprings, nanotethers), and offer exciting avenues in nanomedicine for understanding and controlling the adhesion of microbial cells (probiotics, pathogens).

  8. Cell tracing dyes significantly change single cell mechanics

    PubMed Central

    Lulevich, Valentin; Shih, Yi-Ping; Lo, Su Hao; Liu, Gang-yu

    2009-01-01

    Cell tracing dyes are very frequently utilized in cellular biology research because they provide highly sensitive fluorescent tags that do not compromise cellular functions such as growth and proliferation. In many investigations concerning cellular adhesion and mechanics, fluorescent dyes have been employed with the assumption of little impact on the results. Using the single-cell compression technique developed by our team, the single-cell mechanics of MDA-MB-468 and MLC-SV40 cells were investigated as a function of dye uptake. Cell tracing dyes increase living cell stiffness 3-6 times and cell-to-probe adhesion up to 7 times. These results suggest a more significant effect than toxins, such as Thrombin. A simple analytical model was derived to enable the extraction of the Young’s moduli of the cell membrane and cytoskeleton from the force-deformation profiles measured for individual cells. The increase in Young’s modulus of the membrane is 3-7 times, which is more significant than that of the cytoskeleton (1.1-3.4 times). We propose that changes in cell mechanics upon the addition of fluorescent tracing dye are primarily due to incorporation of amphiphilic dye molecules into the cellular plasma membrane, which increases the lateral interaction among phospholipid chains and thus enhances their rigidity and adhesion. PMID:19366241

  9. In vivo lipidomics using single-cell Raman spectroscopy

    PubMed Central

    Wu, Huawen; Volponi, Joanne V.; Oliver, Ann E.; Parikh, Atul N.; Simmons, Blake A.; Singh, Seema

    2011-01-01

    We describe a method for direct, quantitative, in vivo lipid profiling of oil-producing microalgae using single-cell laser-trapping Raman spectroscopy. This approach is demonstrated in the quantitative determination of the degree of unsaturation and transition temperatures of constituent lipids within microalgae. These properties are important markers for determining engine compatibility and performance metrics of algal biodiesel. We show that these factors can be directly measured from a single living microalgal cell held in place with an optical trap while simultaneously collecting Raman data. Cellular response to different growth conditions is monitored in real time. Our approach circumvents the need for lipid extraction and analysis that is both slow and invasive. Furthermore, this technique yields real-time chemical information in a label-free manner, thus eliminating the limitations of impermeability, toxicity, and specificity of the fluorescent probes common in currently used protocols. Although the single-cell Raman spectroscopy demonstrated here is focused on the study of the microalgal lipids with biofuel applications, the analytical capability and quantitation algorithms demonstrated are applicable to many different organisms and should prove useful for a diverse range of applications in lipidomics. PMID:21310969

  10. Skeletal Muscle Oxygenation Measured by EPR Oximetry Using a Highly Sensitive Polymer-Encapsulated Paramagnetic Sensor.

    PubMed

    Hou, H; Khan, N; Nagane, M; Gohain, S; Chen, E Y; Jarvis, L A; Schaner, P E; Williams, B B; Flood, A B; Swartz, H M; Kuppusamy, P

    2016-01-01

    We have incorporated LiNc-BuO, an oxygen-sensing paramagnetic material, in polydimethylsiloxane (PDMS), which is an oxygen-permeable, biocompatible, and stable polymer. We fabricated implantable and retrievable oxygen-sensing chips (40 % LiNc-BuO in PDMS) using a 20-G Teflon tubing to mold the chips into variable shapes and sizes for in vivo studies in rats. In vitro EPR measurements were used to test the chip's oxygen response. Oxygen induced linear and reproducible line broadening with increasing partial pressure (pO2). The oxygen response was similar to that of bare (unencapsulated) crystals and did not change significantly on sterilization by autoclaving. The chips were implanted in rat femoris muscle and EPR oximetry was performed repeatedly (weekly) for 12 weeks post-implantation. The measurements showed good reliability and reproducibility over the period of testing. These results demonstrated that the new formulation of OxyChip with 40 % LiNc-BuO will enable the applicability of EPR oximetry for long-term measurement of oxygen concentration in tissues and has the potential for clinical applications. PMID:27526163

  11. Microvascular oxygen tension and flow measurements in rodent cerebral cortex during baseline conditions and functional activation

    PubMed Central

    Yaseen, Mohammad A; Srinivasan, Vivek J; Sakadžić, Sava; Radhakrishnan, Harsha; Gorczynska, Iwona; Wu, Weicheng; Fujimoto, James G; Boas, David A

    2011-01-01

    Measuring cerebral oxygen delivery and metabolism microscopically is important for interpreting macroscopic functional magnetic resonance imaging (fMRI) data and identifying pathological changes associated with stroke, Alzheimer's disease, and brain injury. Here, we present simultaneous, microscopic measurements of cerebral blood flow (CBF) and oxygen partial pressure (pO2) in cortical microvessels of anesthetized rats under baseline conditions and during somatosensory stimulation. Using a custom-built imaging system, we measured CBF with Fourier-domain optical coherence tomography (OCT), and vascular pO2 with confocal phosphorescence lifetime microscopy. Cerebral blood flow and pO2 measurements displayed heterogeneity over distances irresolvable with fMRI and positron emission tomography. Baseline measurements indicate O2 extraction from pial arterioles and homogeneity of ascending venule pO2 despite large variation in microvessel flows. Oxygen extraction is linearly related to flow in ascending venules, suggesting that flow in ascending venules closely matches oxygen demand of the drained territory. Oxygen partial pressure and relative CBF transients during somatosensory stimulation further indicate arteriolar O2 extraction and suggest that arterioles contribute to the fMRI blood oxygen level dependent response. Understanding O2 supply on a microscopic level will yield better insight into brain function and the underlying mechanisms of various neuropathologies. PMID:21179069

  12. Measurement of atmospheric oxygen concentration by near-infrared absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Hoffnagle, J.

    2013-12-01

    Variations in the concentration of molecular oxygen in the atmosphere have been shown to provide important constraints on the global carbon dioxide budget (1). Numerous technologies have been explored to measure oxygen concentration, including detection of paramagnetism, gas chromatography, fuel cells, mass spectroscopy, interferometry, and absorption spectroscopy from the UV to IR. Geophysical applications impose severe demands on the precision of an oxygen concentration sensor. Oxygen variations are conventionally expressed using the delta notation applied to the O2/N2 ratio; a change of approximately 5 per meg in delta corresponds to a 1 ppm change in the atmospheric mole fraction of oxygen. Because of the large resevoir of oxygen in the atmosphere, variations of oxygen concentration are small and measurement precision on the order of several per meg is needed to extract geophysically useful information. We describe an instrument that determines the oxygen content of an atmospheric sample by using wavelength-scanned cavity ring-down spectroscopy (WS-CRDS) to measure an absorption line in the 1.2 micron band of the oxygen molecule. The CRDS method provides very high precision measurements of the optical absorption coefficient, better than 0.1 ppb/cm in 1 s measurement time, and large dynamic range. The sample temperature and pressure are stabilized to better than 5 mK and 2 Pa, respectively. The precision of the oxygen concentration measurement was characterized by the Allan variance of repeated measurements of a tank of dry air. For a 5 minute averaging period, the Allan variance of the concentration was 1 ppm. Moreover, the Allan variance continued to decline for longer time scales, reaching 0.4 ppm (corresponding to 2 per meg in delta of O2/N2) after one hour. This work demonstrates the possibility of spectroscopic measurement of molecular oxygen concentration with high precision on the time scale of minutes and good long term stability. 1. R. F. Keeling and S

  13. Oxygen measurements in thin ribbon silicon. [edge-defined film-fed grown

    NASA Technical Reports Server (NTRS)

    Hyland, S. L.; Ast, D. G.; Baghdadi, A.

    1987-01-01

    The oxygen content of thin silicon ribbons grown by the dendritic web technique was measured using a modification of the ASTM method based on Fourier transform infrared spectroscopy. Web silicon was found to have a high oxygen content, ranging from 13 to 19 ppma, calculated from the absorption peak associated with interstitial oxygen and using the new ASTM conversion coefficient. The oxygen concentration changed by about 10 percent along the growth direction of the ribbon. In some samples, a shoulder was detected on the absorption peak. A similar shoulder in Czochralski grown material has been variously interpreted in the literature as due to a complex of silicon, oxygen, and vacancies, or to a phase of SiO2 developed along dislocations in the material. In the case of web silicon, it is not clear which is the correct interpretation.

  14. New Active Optical Technique Developed for Measuring Low-Earth-Orbit Atomic Oxygen Erosion of Polymers

    NASA Technical Reports Server (NTRS)

    Banks, Bruce A.; deGroh, Kim K.; Demko, Rikako

    2003-01-01

    Polymers such as polyimide Kapton (DuPont) and Teflon FEP (DuPont, fluorinated ethylene propylene) are commonly used spacecraft materials because of desirable properties such as flexibility, low density, and in the case of FEP, a low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low-Earth-orbit (LEO) environment are exposed to energetic atomic oxygen. Atomic oxygen reaction with polymers causes erosion, which is a threat to spacecraft performance and durability. It is, therefore, important to understand the atomic oxygen erosion yield E (the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. The most common technique for determining E is a passive technique based on mass-loss measurements of samples exposed to LEO atomic oxygen during a space flight experiment. There are certain disadvantages to this technique. First, because it is passive, data are not obtained until after the flight is completed. Also, obtaining the preflight and postflight mass measurements is complicated by the fact that many polymers absorb water and, therefore, the mass change due to water absorption can affect the E data. This is particularly true for experiments that receive low atomic oxygen exposures or for samples that have a very low E. An active atomic oxygen erosion technique based on optical measurements has been developed that has certain advantages over the mass-loss technique. This in situ technique can simultaneously provide the erosion yield data on orbit and the atomic oxygen exposure fluence, which is needed for erosion yield determination. In the optical technique, either sunlight or artificial light can be used to measure the erosion of semitransparent or opaque polymers as a result of atomic oxygen attack. The technique is simple and adaptable to a rather wide range of polymers, providing that they have a sufficiently high optical absorption coefficient. If one covers a photodiode with a

  15. Preparation of gravimetric standards for measurements of atmospheric oxygen and reevaluation of atmospheric oxygen concentration

    NASA Astrophysics Data System (ADS)

    Tohjima, Yasunori; Machida, Toshinobu; Watai, Tomonori; Akama, Isao; Amari, Taketo; Moriwaki, Yasushi

    2005-06-01

    Fourteen standard mixtures composed of ambient levels of CO2, Ar, O2, and N2 have been prepared in 10-L high-pressure aluminum cylinders by a gravimetric technique for atmospheric O2 measurements. A highly precise balance with a precision of 2.5 mg is used to determine the masses of individual components in the cylinders. To balance the buoyant forces on both sides of the balance beam during weighing the gravimetric standard cylinder, a same sized cylinder is placed on a pan on the opposite side of the beam. In addition, the cylinders of the gravimetric standards and a tare cylinder are alternately weighed to compensate for the drift of the zero-point of the balance. To determine the mole fractions accurately, the mass of each component is corrected for the buoyancy changes caused by the expansion of the cylinder, and the molecular masses of the source O2 and N2 gases are corrected for their isotopic compositions. The differences in the O2 mole fractions of the 14 gravimetric standards range about 100 ppm (μmol mol-1). The gravimetric mole fractions are compared with the analyzed values of CO2, Ar, O2 + Ar, and (O2 + Ar)/N2. The reproducibility of the gravimetric technique is determined from the standard deviations of the differences between the gravimetric and analyzed values, and is quantified as 15.5 per meg for the O2/N2 ratio and 2.9 ppm for the O2 mole fraction. The gravimetric scale is applied to the measurements from air samples collected at Hateruma Island, Japan. The average Ar mole fraction for the air samples collected from June 2003 through June 2004 is 9333 ± 2 ppm. On the basis of this Ar mole fraction, the annual average mole fractions of O2 and N2 in 2000 are evaluated to be 209392 ± 3 ppm and 780876 ± 2 ppm, respectively.

  16. [Measurement of multi-wavelength pulse oxygen saturation based on dynamic spectroscopy].

    PubMed

    Wang, Xiao-Fei; Zhao, Wen-Jun

    2014-05-01

    The present paper puts forward multi-wavelength pulse oxygen saturation measurement based on dynamic spectroscopy to do the non-invasive determination of oxygen saturation. Compared to conventional ways, the new method makes full use of more wavelengths light and improves the measurement accuracy. During the experiment, the in-vivo measurements were carried out on 60 patients and their spectroscopic data were collected by the high sensitivity type fiber optic spectrometer. Singletrial estimation method was used to extract the dynamic spectroscopy at the wavelengths of 606. 44 approximately 987. 55 nm. Oxygen saturation obtained from arterial blood gas analysis is regarded as the true value. Synergy interval partial least square (siPLS) was used to establish the calibration model of subjects' oxygen saturation values against dynamic spectroscopy data. The relative error of prediction is +/-0. 017 6, but the relative error of the subjects in the same set measured by the patient monitor which was two-wavelength measure system is +/-0. 116 4. Measurement results show that the use of the high sensitivity type fiber optic spectrometer to collect multi-wavelength spectroscopic data and dynamic spectroscopy method to process data can do better in improving the accuracy of the oxygen saturation measurement. PMID:25095431

  17. Development of 200-channel mapping system for tissue oxygenation measured by near-infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Niwayama, Masatsugu; Kohata, Daisuke; Shao, Jun; Kudo, Nobuki; Hamaoka, Takatumi; Katsumura, Toshihito; Yamamoto, Katsuyuki

    2000-07-01

    Near-infrared spectroscopy (NIRS) is a very useful technique for noninvasive measurement of tissue oxygenation. Among various methods of NIRS, continuous wave near-infrared spectroscopy (CW- NIRS) is especially suitable for real-time measurement and for practical use. CW-NIRS has recently been applied in vivo reflectance imaging of muscle oxygenation and brain activity. However, conventional mapping systems do not have a sufficient mapping area at present. Moreover, they do not enable quantitative measurement of tissue oxygenation because conventional NIRS is based on the inappropriate assumption that tissue is homogeneous. In this study, we developed a 200-channel mapping system that enables measurement of changes in oxygenation and blood volume and that covers a wider area (30 cm x 20 cm) than do conventional systems. The spatial resolution (source- detector separation) of this system is 15 mm. As for the effcts of tissue inhomogeneity on muscle oxygenation measurement, subcutaneous adipose tissue greatly reduces measurement sensitivity. Therefore, we also used a correction method for influence of the subcutaneous fat layer so that we could obtain quantitative changes in concentrations of oxy- and deoxy- hemoglobin. We conducted exercise tests and measured the changed in hemoglobin concentration in the thigh using the new system. The working muscles in the exercises could be imaged, and the heterogeneity of the muscles was shown. These results demonstrated the new 200-channel mapping system enables observation of the distribution of muscle metabolism and localization of muscle function.

  18. Emergent Collective Chemotaxis without Single-Cell Gradient Sensing

    NASA Astrophysics Data System (ADS)

    Camley, Brian A.; Zimmermann, Juliane; Levine, Herbert; Rappel, Wouter-Jan

    2016-03-01

    Many eukaryotic cells chemotax, sensing and following chemical gradients. However, experiments show that even under conditions when single cells cannot chemotax, small clusters may still follow a gradient. This behavior is observed in neural crest cells, in lymphocytes, and during border cell migration in Drosophila, but its origin remains puzzling. Here, we propose a new mechanism underlying this "collective guidance," and study a model based on this mechanism both analytically and computationally. Our approach posits that contact inhibition of locomotion, where cells polarize away from cell-cell contact, is regulated by the chemoattractant. Individual cells must measure the mean attractant value, but need not measure its gradient, to give rise to directional motility for a cell cluster. We present analytic formulas for how the cluster velocity and chemotactic index depend on the number and organization of cells in the cluster. The presence of strong orientation effects provides a simple test for our theory of collective guidance.

  19. Preliminary results of oxygen isotope ratio measurement with a particle-gamma coincidence method

    NASA Astrophysics Data System (ADS)

    Borysiuk, Maciek; Kristiansson, Per; Ros, Linus; Abdel, Nassem S.; Elfman, Mikael; Nilsson, Charlotta; Pallon, Jan

    2015-04-01

    The possibility to study variations in the oxygen isotopic ratio with photon tagged nuclear reaction analysis (pNRA) is evaluated in the current work. The experiment described in the article was performed at Lund Ion Beam Analysis Facility (LIBAF) with a 2 MeV deuteron beam. Isotopic fractionation of light elements such as carbon, oxygen and nitrogen is the basis of many analytical tools in hydrology, geology, paleobiology and paleogeology. IBA methods provide one possible tool for measurement of isotopic content. During this experimental run we focused on measurement of the oxygen isotopic ratio. The measurement of stable isotopes of oxygen has a number of applications; the particular one driving the current investigation belongs to the field of astrogeology and specifically evaluation of fossil extraterrestrial material. There are three stable isotopes of oxygen: 16O, 17O and 18O. We procured samples highly enriched with all three isotopes. Isotopes 16O and 18O were easily detected in the enriched samples, but no significant signal from 17O was detected in the same samples. The measured yield was too low to detect 18O in a sample with natural abundances of oxygen isotopes, at least in the current experimental setup, but the spectral line from the reaction with 16O was clearly visible.

  20. Phosphorescent nanoparticles for quantitative measurements of oxygen profiles in vitro and in vivo

    PubMed Central

    Choi, Nak Won; Verbridge, Scott S.; Williams, Rebecca M.; Chen, Jin; Kim, Ju-Young; Schmehl, Russel; Farnum, Cornelia E.; Zipfel, Warren R.; Fischbach, Claudia; Stroock, Abraham D.

    2012-01-01

    We present the development and characterization of nanoparticles loaded with a custom phosphor; we exploit these nanoparticles to perform quantitative measurements of the concentration of oxygen within three-dimensional (3-D) tissue cultures in vitro and blood vessels in vivo. We synthesized a customized ruthenium (Ru)-phosphor and incorporated it into polymeric nanoparticles via self-assembly. We demonstrate that the encapsulated phosphor is non-toxic with and without illumination. We evaluated two distinct modes of employing the phosphorescent nanoparticles for the measurement of concentrations of oxygen: 1) in vitro, in a 3-D microfluidic tumor model via ratiometric measurements of intensity with an oxygen-insensitive fluorophore as a reference, and 2) in vivo, in mouse vasculature using measurements of phosphorescence lifetime. With both methods, we demonstrated micrometer-scale resolution and absolute calibration to the dissolved oxygen concentration. Based on the ease and customizability of the synthesis of the nanoparticles and the flexibility of their application, these oxygen-sensing polymeric nanoparticles will find a natural home in a range of biological applications, benefiting studies of physiological as well as pathological processes in which oxygen availability and concentration play a critical role. PMID:22240511

  1. The potential of single-cell profiling in plants.

    PubMed

    Efroni, Idan; Birnbaum, Kenneth D

    2016-01-01

    Single-cell transcriptomics has been employed in a growing number of animal studies, but the technique has yet to be widely used in plants. Nonetheless, early studies indicate that single-cell RNA-seq protocols developed for animal cells produce informative datasets in plants. We argue that single-cell transcriptomics has the potential to provide a new perspective on plant problems, such as the nature of the stem cells or initials, the plasticity of plant cells, and the extent of localized cellular responses to environmental inputs. Single-cell experimental outputs require different analytical approaches compared with pooled cell profiles and new tools tailored to single-cell assays are being developed. Here, we highlight promising new single-cell profiling approaches, their limitations as applied to plants, and their potential to address fundamental questions in plant biology. PMID:27048384

  2. Fluorescence lifetime imaging to quantify sub-cellular oxygen measurements in live macrophage during bacterial invasion

    NASA Astrophysics Data System (ADS)

    Dragavon, Joe; Amiri, Megdouda; Marteyn, Benoit; Sansonetti, Philipe; Shorte, Spencer

    2011-03-01

    Fluorophore concentration, the surrounding microenvironment, and photobleaching greatly influence the fluorescence intensity of a fluorophore, increasing the difficulty to directly observe micro-environmental factors such as pH and oxygen. However, the fluorescence lifetime of a fluorophore is essentially independent of both the fluorophore concentration and photobleaching, providing a viable alternative to intensity measurements. The development of fluorescence lifetime imaging (FLI) allows for the direct measurement of the microenvironment surrounding a fluorophore. Pt-porphyrin is a fluorophore whose optical properties include a very stable triplet excited state. This energy level overlaps strongly with the ground triplet state of oxygen, making the phosphorescent lifetime directly proportional to the surrounding oxygen concentration. Initial experiments using this fluorophore involved the use of individual microwells coated with the porphyrin. Cells were allowed to enter the micro-wells before being sealed to create a diffusionally isolated volume. The decrease in the extracellular oxygen concentration was observed using FLI. However, this isolation technique provides only the consumption rate but cannot indicate the subcellular oxygen distribution. To improve upon this, live macrophages are loaded with the porphyrin and the fluorescence lifetime determined using a Lambert Instruments Lifa-X FLI system. Initial results indicate that an increase in subcellular oxygen is observed upon initial exposure to invasive bacteria. A substantial decrease in oxygen is observed after about 1 hour of exposure. The cells remain in this deoxygenated state until the bacteria are removed or cell death occurs.

  3. Analysis and methodology for measuring oxygen concentration in liquid sodium with a plugging meter

    SciTech Connect

    Nollet, B. K.; Hvasta, M.; Anderson, M.

    2012-07-01

    Oxygen concentration in liquid sodium is a critical measurement in assessing the potential for corrosion damage in sodium-cooled fast reactors (SFRs). There has been little recent work on sodium reactors and oxygen detection. Thus, the technical expertise dealing with oxygen measurements within sodium is no longer readily available in the U.S. Two methods of oxygen detection that have been investigated are the plugging meter and the galvanic cell. One of the overall goals of the Univ. of Wisconsin's sodium research program is to develop an affordable, reliable galvanic cell oxygen sensor. Accordingly, attention must first be dedicated to a well-known standard known as a plugging meter. Therefore, a sodium loop has been constructed on campus in effort to develop the plugging meter technique and gain experience working with liquid metal. The loop contains both a galvanic cell test section and a plugging meter test section. Consistent plugging results have been achieved below 20 [wppm], and a detailed process for achieving effective plugging has been developed. This paper will focus both on an accurate methodology to obtain oxygen concentrations from a plugging meter, and on how to easily control the oxygen concentration of sodium in a test loop. Details of the design, materials, manufacturing, and operation will be presented. Data interpretation will also be discussed, since a modern discussion of plugging data interpretation does not currently exist. (authors)

  4. Novel needle-electrochemical microsensor for in-vitro and in-vivo measurements of oxygen

    NASA Astrophysics Data System (ADS)

    Xu, Weiya; Ma, Wentao; Li, Kaiyang; Hu, Jiming; Li, Hongyi; Cao, Lianxin; Song, Yu; Zhao, Lan

    2001-09-01

    Electrochemical microsensors have been applied in the field of biomedicine for many years. The aim of this work was to develop a novel oxygen sensor to monitor the partial pressure of oxygen in tissues and acupuncture points. The functions of microsensor were evaluated through in vitro experiments. In vivo in tissues and acupuncture points. The data from oxygen microsensor were compared with the data from blood gas analyzer. The measurements depend on the physiological changes of experimental animal. The further development of this new sensor is to be a tool for meridian research.

  5. Live single-cell laser tag

    PubMed Central

    Binan, Loïc; Mazzaferri, Javier; Choquet, Karine; Lorenzo, Louis-Etienne; Wang, Yu Chang; Affar, El Bachir; De Koninck, Yves; Ragoussis, Jiannis; Kleinman, Claudia L.; Costantino, Santiago

    2016-01-01

    The ability to conduct image-based, non-invasive cell tagging, independent of genetic engineering, is key to cell biology applications. Here we introduce cell labelling via photobleaching (CLaP), a method that enables instant, specific tagging of individual cells based on a wide array of criteria such as shape, behaviour or positional information. CLaP uses laser illumination to crosslink biotin onto the plasma membrane, coupled with streptavidin conjugates to label individual cells for genomic, cell-tracking, flow cytometry or ultra-microscopy applications. We show that the incorporated mark is stable, non-toxic, retained for several days, and transferred by cell division but not to adjacent cells in culture. To demonstrate the potential of CLaP for genomic applications, we combine CLaP with microfluidics-based single-cell capture followed by transcriptome-wide next-generation sequencing. Finally, we show that CLaP can also be exploited for inducing transient cell adhesion to substrates for microengineering cultures with spatially patterned cell types. PMID:27198043

  6. Value-added food: single cell protein.

    PubMed

    Anupama; Ravindra, P

    2000-10-01

    The alarming rate of population growth has increased the demand for food production in third-world countries leading to a yawning gap in demand and supply. This has led to an increase in the number of hungry and chronically malnourished people. This situation has created a demand for the formulation of innovative and alternative proteinaceous food sources. Single cell protein (SCP) production is a major step in this direction. SCP is the protein extracted from cultivated microbial biomass. It can be used for protein supplementation of a staple diet by replacing costly conventional sources like soymeal and fishmeal to alleviate the problem of protein scarcity. Moreover, bioconversion of agricultural and industrial wastes to protein-rich food and fodder stocks has an additional benefit of making the final product cheaper. This would also offset the negative cost value of wastes used as substrate to yield SCP. Further, it would make food production less dependent upon land and relieve the pressure on agriculture. This article reviews diversified aspects of SCP as an alternative protein-supplementing source. Various potential strains and substrates that could be utilized for SCP production are described. Nutritive value and removal of nucleic acids and toxins from SCP as a protein-supplementing source are discussed. New processes need to be exploited to improve yield. In that direction the solid state fermentation (SSF) method and its advantages for SCP production are highlighted. PMID:14538097

  7. Live single-cell laser tag.

    PubMed

    Binan, Loïc; Mazzaferri, Javier; Choquet, Karine; Lorenzo, Louis-Etienne; Wang, Yu Chang; Affar, El Bachir; De Koninck, Yves; Ragoussis, Jiannis; Kleinman, Claudia L; Costantino, Santiago

    2016-01-01

    The ability to conduct image-based, non-invasive cell tagging, independent of genetic engineering, is key to cell biology applications. Here we introduce cell labelling via photobleaching (CLaP), a method that enables instant, specific tagging of individual cells based on a wide array of criteria such as shape, behaviour or positional information. CLaP uses laser illumination to crosslink biotin onto the plasma membrane, coupled with streptavidin conjugates to label individual cells for genomic, cell-tracking, flow cytometry or ultra-microscopy applications. We show that the incorporated mark is stable, non-toxic, retained for several days, and transferred by cell division but not to adjacent cells in culture. To demonstrate the potential of CLaP for genomic applications, we combine CLaP with microfluidics-based single-cell capture followed by transcriptome-wide next-generation sequencing. Finally, we show that CLaP can also be exploited for inducing transient cell adhesion to substrates for microengineering cultures with spatially patterned cell types. PMID:27198043

  8. Silicon dioxide thin film mediated single cell nucleic acid isolation.

    PubMed

    Bogdanov, Evgeny; Dominova, Irina; Shusharina, Natalia; Botman, Stepan; Kasymov, Vitaliy; Patrushev, Maksim

    2013-01-01

    A limited amount of DNA extracted from single cells, and the development of single cell diagnostics make it necessary to create a new highly effective method for the single cells nucleic acids isolation. In this paper, we propose the DNA isolation method from biomaterials with limited DNA quantity in sample, and from samples with degradable DNA based on the use of solid-phase adsorbent silicon dioxide nanofilm deposited on the inner surface of PCR tube. PMID:23874571

  9. Silicon Dioxide Thin Film Mediated Single Cell Nucleic Acid Isolation

    PubMed Central

    Bogdanov, Evgeny; Dominova, Irina; Shusharina, Natalia; Botman, Stepan; Kasymov, Vitaliy; Patrushev, Maksim

    2013-01-01

    A limited amount of DNA extracted from single cells, and the development of single cell diagnostics make it necessary to create a new highly effective method for the single cells nucleic acids isolation. In this paper, we propose the DNA isolation method from biomaterials with limited DNA quantity in sample, and from samples with degradable DNA based on the use of solid-phase adsorbent silicon dioxide nanofilm deposited on the inner surface of PCR tube. PMID:23874571

  10. Nitrogen assimilation by single cells in hot springs

    NASA Astrophysics Data System (ADS)

    Poret-peterson, A. T.; Romaniello, S. J.; Bose, M.; Williams, P.; Elser, J. J.; Shock, E.; Anbar, A. D.; Hartnett, H. E.

    2012-12-01

    Microorganisms drive biogeochemical cycles and require nutrients, such as ammonium and nitrate, to function. As a result, following nutrient flows provides opportunities to study how microbial activity influences ecosystem-level processes. Most past measurements of microbial nutrient uptake rely on bulk measurements, which are informative but provide little information about heterogeneity among community members involved in elemental transformations, nor about possible effects of physiological state or taxonomic identity. Since microbial communities tend to be phylogenetically and physiologically diverse, it is reasonable to expect that community members will respond differently to nutrient addition. Here, we examine nitrogen assimilation (via addition of 15N-labeled ammonium or nitrate) in Yellowstone hot spring microbial communities. Using the NanoSIMS, we imaged cells at a very high spatial resolution (nanometer scale) necessary to determine 15N enrichments in single micron-sized cells. We compare the N isotopic enrichments observed in single cells to that determined in bulk sediments by standard isotope ratio mass spectrometry. NanoSIMS imaging of 56 individual cells from sediments of an acidic hot spring (pH 4.7, T=67oC) incubated with 15N-ammonium shows that about two-thirds of the cells (38) exhibited 15N-enrichment. Most cells had 15N enrichments from 0.39 to 0.91 atom %, while some cells were much more significantly enriched. Bulk analyses of sediments show that ammonium assimilation and nitrate assimilation readily occurred at this spring. These findings show that microbes in this hot spring may differentially take up ammonium, which may arise from a number of factors including differences in cellular N requirements, growth rates, and the ability to transport ammonium. This work represents some of the first single-cell isotopic measurements from an extreme environment. Efforts are underway to image sediment samples from other hot springs and to pair Nano

  11. Microfluidic Probe for Single-Cell Lysis and Analysis in Adherent Tissue Culture

    PubMed Central

    Lauffenburger, Douglas A.; Han, Jongyoon

    2014-01-01

    Single-cell analysis provides information critical to understanding key disease processes that are characterized by significant cellular heterogeneity. Few current methods allow single-cell measurement without removing cells from the context of interest, which not only destroys contextual information but also may perturb the process under study. Here we present a microfluidic probe that lyses single adherent cells from standard tissue culture and captures the contents to perform single-cell biochemical assays. We use this probe to measure kinase and housekeeping protein activities, separately or simultaneously, from single human hepatocellular carcinoma cells in adherent culture. This tool has the valuable ability to perform measurements that clarify connections between extracellular context, signals and responses, especially in cases where only a few cells exhibit a characteristic of interest. PMID:24594667

  12. Continuous cultivation of fission yeast: analysis of single-cell protein synthesis kinetics

    SciTech Connect

    Agar, D.W.; Bailey, J.E.

    1981-01-01

    A fundamental problem in microbial reactor analysis is identification of the relation between environment and individual cell metabolic activity. Population balance equations provide a link between experimental measurements of composition frequency functions in microbial populations on the one hand and macromolecule synthesis kinetics and cell division control parameters for single cells on the other. Flow microfluorometry measurements of frequency functions for single-cell protein content in Schizosaccharomyces pombe in balanced exponential growth were analyzed by 2 different methods. One approach utilizes the integrated form of the population balance equation known as the Collins-Richmond equation, and the other method involves optimization of parameters in assumed kinetic and cell division functional forms to fit measured frequency functions with corresponding model solutions. Both data interpretation techniques indicate that rates of protein synthesis increase most in low-protein-content cells as the population specific growth rate increases, leading to parabolic single-cell protein synthesis kinetics at large specific growth rates. Utilization of frequency function data for an asynchronous population is in this case a far more sensitive method for determination of single-cell kinetics than is monitoring the metabolic dynamics of a single cell or, equivalently, synchronous culture analyses.

  13. DESIGN AND PERFORMANCE OBJECTIVES OF THE SINGLE CELL TEST SYSTEM FOR SO2 DEPOLARIZED ELECTROLYZER DEVELOPMENT

    SciTech Connect

    Steimke, J

    2007-01-15

    The single cell test system development for the SRNL sulfur dioxide-depolarized electrolyzer has been completed. Operating experience and improved operating procedures were developed during test operations in FY06 and the first quarter of FY07. Eight different cell configurations, using various MEA designs, have been tested. The single cell test electrolyzer has been modified to overcome difficulties experienced during testing, including modifications to the inlet connection to eliminate minute acid leaks that caused short circuits. The test facility was modified by adding a water bath for cell heating, thus permitting operation over a wider range of flowrates and cell temperatures. Modifications were also identified to permit continuous water flushing of the cathode to remove sulfur, thus extending operating time between required shutdowns. This is also expected to permit a means of independently measuring the rate of sulfur formation, and the corresponding SO{sub 2} flux through the membrane. This report contains a discussion of the design issues being addressed by the single cell test program, a test matrix being conducted to address these issues, and a summary of the performance objectives for the single cell test system. The current primary objective of single cell test system is to characterize and qualify electrolyzer configurations for the following 100-hour longevity tests. Although the single cell test system development is considered complete, SRNL will continue to utilize the test facility and the single cell electrolyzer to measure the operability and performance of various cell design configurations, including new MEA's produced by the component development tasks.

  14. Chemical Cytometry: Fluorescence-Based Single-Cell Analysis

    NASA Astrophysics Data System (ADS)

    Cohen, Daniella; Dickerson, Jane A.; Whitmore, Colin D.; Turner, Emily H.; Palcic, Monica M.; Hindsgaul, Ole; Dovichi, Norman J.

    2008-07-01

    Cytometry deals with the analysis of the composition of single cells. Flow and image cytometry employ antibody-based stains to characterize a handful of components in single cells. Chemical cytometry, in contrast, employs a suite of powerful analytical tools to characterize a large number of components. Tools have been developed to characterize nucleic acids, proteins, and metabolites in single cells. Whereas nucleic acid analysis employs powerful polymerase chain reaction-based amplification techniques, protein and metabolite analysis tends to employ capillary electrophoresis separation and ultrasensitive laser-induced fluorescence detection. It is now possible to detect yoctomole amounts of many analytes in single cells.

  15. Single cell analysis: the new frontier in 'Omics'

    SciTech Connect

    Wang, Daojing; Bodovitz, Steven

    2010-01-14

    Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of 'Omics' technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity.

  16. LUMOS - A Sensitive and Reliable Optode System for Measuring Dissolved Oxygen in the Nanomolar Range

    PubMed Central

    Lehner, Philipp; Larndorfer, Christoph; Garcia-Robledo, Emilio; Larsen, Morten; Borisov, Sergey M.; Revsbech, Niels-Peter; Glud, Ronnie N.; Canfield, Donald E.; Klimant, Ingo

    2015-01-01

    Most commercially available optical oxygen sensors target the measuring range of 300 to 2 μmol L-1. However these are not suitable for investigating the nanomolar range which is relevant for many important environmental situations. We therefore developed a miniaturized phase fluorimeter based measurement system called the LUMOS (Luminescence Measuring Oxygen Sensor). It consists of a readout device and specialized “sensing chemistry” that relies on commercially available components. The sensor material is based on palladium(II)-5,10,15,20-tetrakis-(2,3,4,5,6-pentafluorphenyl)-porphyrin embedded in a Hyflon AD 60 polymer matrix and has a KSV of 6.25 x 10-3 ppmv-1. The applicable measurement range is from 1000 nM down to a detection limit of 0.5 nM. A second sensor material based on the platinum(II) analogue of the porphyrin is spectrally compatible with the readout device and has a measurement range of 20 μM down to 10 nM. The LUMOS device is a dedicated system optimized for a high signal to noise ratio, but in principle any phase flourimeter can be adapted to act as a readout device for the highly sensitive and robust sensing chemistry. Vise versa, the LUMOS fluorimeter can be used for read out of less sensitive optical oxygen sensors based on the same or similar indicator dyes, for example for monitoring oxygen at physiological conditions. The presented sensor system exhibits lower noise, higher resolution and higher sensitivity than the electrochemical STOX sensor previously used to measure nanomolar oxygen concentrations. Oxygen contamination in common sample containers has been investigated and microbial or enzymatic oxygen consumption at nanomolar concentrations is presented. PMID:26029920

  17. ACE EPAM and Van Allen Probes RBSPICE measurements of interplanetary oxygen injection to the inner magnetosphere

    NASA Astrophysics Data System (ADS)

    Patterson, J. D.; Manweiler, J. W.; Gerrard, A. J.; Lanzerotti, L. J.

    2015-12-01

    On March 17, 2015, a significant oxygen-rich interplanetary event was measure by the Advanced Composition Explorer (ACE) Electron Proton Alpha Monitor (EPAM) instrument. At the same time the Van Allen Probes Radiation Belt Storm Probes Ion Composition Experiment (RBSPICE) instrument recorded significant enhancements of oxygen in the inner magnetosphere. We present a detailed analysis of this event utilizing a new method of exploiting the EPAM Pulse Height Analyzer (PHA) data to precisely resolve helium and oxygen spectra within the 0.5 to 5 MeV/nuc range. We also present the flux, partial particle pressures, and pitch angle distributions of the ion measurements from RBSPICE. During this event, both EPAM and RBSPICE measured O:He ratios greater than 10:1. The pitch angle distributions from RBSPICE-B show a strong beam of oxygen at an L ~ 5.8 early on March 17th during orbit. The timing between the observations of the oxygen peak at ACE and the beam observed at RBSPICE-B is consistent with the travel-time required for energetic particle transport from L1 to Earth and access to the magnetosphere. We assert that the oxygen seen by RBSPICE during the initial phase of this event is the result of direct injection from the interplanetary medium of energetic ions. This poster contains the observations and detailed calculations to support this assertion.

  18. Oxygen Isotope Measurements of a Rare Murchison Type A CAI and Its Rim

    NASA Technical Reports Server (NTRS)

    Matzel, J. E. P.; Simon, J. I.; Hutcheon, I. D.; Jacobsen, B.; Simon, S. B.; Grossman, L.

    2013-01-01

    Ca-, Al-rich inclusions (CAIs) from CV chondrites commonly show oxygen isotope heterogeneity among different mineral phases within individual inclusions reflecting the complex history of CAIs in both the solar nebula and/or parent bodies. The degree of isotopic exchange is typically mineral-specific, yielding O-16-rich spinel, hibonite and pyroxene and O-16-depleted melilite and anorthite. Recent work demonstrated large and systematic variations in oxygen isotope composition within the margin and Wark-Lovering rim of an Allende Type A CAI. These variations suggest that some CV CAIs formed from several oxygen reservoirs and may reflect transport between distinct regions of the solar nebula or varying gas composition near the proto-Sun. Oxygen isotope compositions of CAIs from other, less-altered chondrites show less intra-CAI variability and 16O-rich compositions. The record of intra-CAI oxygen isotope variability in CM chondrites, which commonly show evidence for low-temperature aqueous alteration, is less clear, in part because the most common CAIs found in CM chondrites are mineralogically simple (hibonite +/- spinel or spinel +/- pyroxene) and are composed of minerals less susceptible to O-isotopic exchange. No measurements of the oxygen isotope compositions of rims on CAIs in CM chondrites have been reported. Here, we present oxygen isotope data from a rare, Type A CAI from the Murchison meteorite, MUM-1. The data were collected from melilite, hibonite, perovskite and spinel in a traverse into the interior of the CAI and from pyroxene, melilite, anorthite, and spinel in the Wark-Lovering rim. Our objectives were to (1) document any evidence for intra-CAI oxygen isotope variability; (2) determine the isotopic composition of the rim minerals and compare their composition(s) to the CAI interior; and (3) compare the MUM-1 data to oxygen isotope zoning profiles measured from CAIs in other chondrites.

  19. Position-specific measurement of oxygen isotope ratios in cellulose: Isotopic exchange during heterotrophic cellulose synthesis

    NASA Astrophysics Data System (ADS)

    Waterhouse, John S.; Cheng, Shuying; Juchelka, Dieter; Loader, Neil J.; McCarroll, Danny; Switsur, V. Roy; Gautam, Lata

    2013-07-01

    We describe the first reported method for the measurement of oxygen isotope ratios at each position in the glucose units of the cellulose molecule. The overall process comprises a series of synthetic organic sequences, by which α-cellulose is hydrolysed to glucose, and oxygen atoms at specific positions in the glucose molecule are removed in samples of benzoic acid for measurement of δ18O. Values of δ18O at specific positions in cellulose are calculated from these δ18O values and the overall δ18O value of the cellulose. We apply the method to determine the degree to which oxygen atoms at each position undergo isotopic exchange with water during heterotrophic cellulose synthesis, such as occurs in the cambium of trees. To do this we extract α-cellulose from wheat seedlings germinated in the dark in aqueous media of differing oxygen isotope ratios. Results indicate that oxygen atoms at positions 5 and 6 (O-5 and O-6 respectively) undergo around 80% exchange with medium water, O-3 undergoes around 50% exchange, and O-2 and O-4 do not undergo isotopic exchange. The results have important implications for extracting palaeoclimatic records from oxygen isotope time series obtained from tree ring cellulose. As O-5 and O-6 undergo significant exchange with medium water during heterotrophic cellulose synthesis, oxygen isotopes at these positions in tree ring cellulose should carry a predominantly trunk (source) water signal. On the other hand, O-2 and O-4 should retain the isotopic signature of leaf water in tree ring cellulose. Our method therefore potentially enables the separate reconstruction of past temperature and humidity data from oxygen isotope ratios of tree ring cellulose - something that has hitherto not been possible. The measured degrees of isotopic exchange are to some extent unexpected and cannot be fully explained using current biochemical mechanisms, suggesting that knowledge of these processes is incomplete.

  20. Brief inhalation method to measure cerebral oxygen extraction fraction with PET: Accuracy determination under pathologic conditions

    SciTech Connect

    Altman, D.I.; Lich, L.L.; Powers, W.J. )

    1991-09-01

    The initial validation of the brief inhalation method to measure cerebral oxygen extraction fraction (OEF) with positron emission tomography (PET) was performed in non-human primates with predominantly normal cerebral oxygen metabolism (CMRO2). Sensitivity analysis by computer simulation, however, indicated that this method may be subject to increasing error as CMRO2 decreases. Accuracy of the method under pathologic conditions of reduced CMRO2 has not been determined. Since reduced CMRO2 values are observed frequently in newborn infants and in regions of ischemia and infarction in adults, we determined the accuracy of the brief inhalation method in non-human primates by comparing OEF measured with PET to OEF measured by arteriovenous oxygen difference (A-VO2) under pathologic conditions of reduced CMRO2 (0.27-2.68 ml 100g-1 min-1). A regression equation of OEF (PET) = 1.07 {times} OEF (A-VO2) + 0.017 (r = 0.99, n = 12) was obtained. The absolute error in oxygen extraction measured with PET was small (mean 0.03 {plus minus} 0.04, range -0.03 to 0.12) and was independent of cerebral blood flow, cerebral blood volume, CMRO2, or OEF. The percent error was higher (19 {plus minus} 37), particularly when OEF is below 0.15. These data indicate that the brief inhalation method can be used for measurement of cerebral oxygen extraction and cerebral oxygen metabolism under pathologic conditions of reduced cerebral oxygen metabolism, with these limitations borne in mind.

  1. Comparison of atomic oxygen measurements by incoherent scatter and satellite-borne mass spectrometer techniques

    NASA Technical Reports Server (NTRS)

    Hedin, A. E.; Alcayde, D.

    1974-01-01

    Atomic oxygen densities determined by the incoherent scatter technique are compared to densities deduced from satellite-borne mass spectrometer measurements and are found to agree within experimental error. The diurnal variations inferred from the incoherent scatter measurements do show, however, some departure from diurnal variations found by modeling the mass spectrometer results. Some implications of these departures are briefly discussed.

  2. Easily fabricated magnetic traps for single-cell applications

    NASA Astrophysics Data System (ADS)

    Koschwanez, John H.; Carlson, Robert H.; Meldrum, Deirdre R.

    2007-04-01

    We describe a simple and inexpensive method of fabricating single cell magnetic traps within a polydimethylsiloxane (PDMS) device. These traps were developed as part of an automated system that captures individual yeast cells in a microfluidic device and analyzes each cell as it buds. To make the traps, PdCl2 catalyst is rubbed with vinyl foam onto plasma-patterned PDMS, and then Co-Ni-B alloy is electrolessly deposited onto the catalyst at a moderate temperature. We demonstrate individual yeast cell capture and estimate the capture force (1.9-4.4 pN) by measuring the flow speed required to remove the cell from its trap in a microfluidic channel.

  3. Single cell mechanics of keratinocyte cells.

    PubMed

    Lulevich, Valentin; Yang, Hsin-ya; Isseroff, R Rivkah; Liu, Gang-yu

    2010-11-01

    Keratinocytes represent the major cell type of the uppermost layer of human skin, the epidermis. Using AFM-based single cell compression, the ability of individual keratinocytes to resist external pressure and global rupturing forces is investigated and compared with various cell types. Keratinocytes are found to be 6-70 times stiffer than other cell types, such as white blood, breast epithelial, fibroblast, or neuronal cells, and in contrast to other cell types they retain high mechanic strength even after the cell's death. The absence of membrane rupturing peaks in the force-deformation profiles of keratinocytes and their high stiffness during a second load cycle suggests that their unique mechanical resistance is dictated by the cytoskeleton. A simple analytical model enables the quantification of Young's modulus of keratinocyte cytoskeleton, as high as 120-340 Pa. Selective disruption of the two major cytoskeletal networks, actin filaments and microtubules, does not significantly affect keratinocyte mechanics. F-actin is found to impact cell deformation under pressure. During keratinocyte compression, the plasma membrane stretches to form peripheral blebs. Instead of blebbing, cells with depolymerized F-actin respond to pressure by detaching the plasma membrane from the cytoskeleton underneath. On the other hand, the compression force of keratinocytes expressing a mutated keratin (cell line, KEB-7) is 1.6-2.2 times less than that for the control cell line that has normal keratin networks. Therefore, we infer that the keratin intermediate filament network is responsible for the extremely high keratinocyte stiffness and resilience. This could manifest into the rugged protective nature of the human epidermis. PMID:20728993

  4. Single cell genomics of subsurface microorganisms

    NASA Astrophysics Data System (ADS)

    Stepanauskas, R.; Onstott, T. C.; Lau, C.; Kieft, T. L.; Woyke, T.; Rinke, C.; Sczyrba, A.; van Heerden, E.

    2012-12-01

    Recent studies have revealed unexpected abundance and diversity of microorganisms in terrestrial and marine subsurface, providing new perspectives over their biogeochemical significance, evolution, and the limits of life. The now commonly used research tools, such as metagenomics and PCR-based gene surveys enabled cultivation-unbiased analysis of genes encoded by natural microbial communities. However, these methods seldom provide direct evidence for how the discovered genes are organized inside genomes and from which organisms do they come from. Here we evaluated the feasibility of an alternative, single cell genomics approach, in the analysis of subsurface microbial community composition, metabolic potential and microevolution at the Sanford Underground Research Facility (SURF), South Dakota, and the Witwaterstrand Basin, South Africa. We successfully recovered genomic DNA from individual microbial cells from multiple locations, including ultra-deep (down to 3,500 m) and low-biomass (down to 10^3 cells mL^-1) fracture water. The obtained single amplified genomes (SAGs) from SURF contained multiple representatives of the candidate divisions OP3, OP11, OD1 and uncharacterized archaea. By sequencing eight of these SAGs, we obtained the first genome content information for these phylum-level lineages that do not contain a single cultured representative. The Witwaterstrand samples were collected from deep fractures, biogeochemical dating of which suggests isolation from tens of thousands to tens of millions of years. Thus, these fractures may be viewed as "underground Galapagos", a natural, long-term experiment of microbial evolution within well-defined temporal and spatial boundaries. We are analyzing multiple SAGs from these environments, which will provide detailed information about adaptations to life in deep subsurface, mutation rates, selective pressures and gene flux within and across microbial populations.

  5. A new measuring device for non-invasive determination of oxygen partial pressure and oxygen conductance of the skin and other tissues.

    PubMed

    Niehoff, K; Barnikol, W K

    1999-01-01

    About fifty percent of the oxygen consumption of the skin is supplied by diffusion through the surface. This portion of the skin oxygen supply becomes of high importance in case of arterial occlusion. The oxygen permeation coefficient (P) of the upper layers and the oxygen pressure field within the skin determine the diffusive oxygen uptake from the outside. To our knowledge, the permeation coefficient (P) until now was only estimated by indirect methods of little practicability (Baumberger et al., 1951; Eberhard et al., 1978). An oxygen partial pressure of the skin is conventionally measured by modified CLARK type electrodes. A disadvantage of this so-called transcutaneous electrode is its oxygen consumption and the fixed coupling of the consumption with the oxygen pressure to be determined. Therefore the measurement always induces a systematic error (the so-called stirring effect) which depends, among other factors, on the oxygen availability of the skin under the electrode. The new device combines a consumption-free oxygen partial pressure detector on the basis of luminescence quenching by oxygen with an independently working specific oxygen consumer realized by an active galvanic chain (silver-lead element). The chain permits setting any oxygen mass flow (mO2) in a certain range by varying the electrode current choosing different resistors within the electrical circuit. According to the diffusion law, the surface oxygen pressure (ePO2) being measured is a linear function of the oxygen flow (mO2) directed to the cathode: ePO2 identical to -(1/P).(mO2/A) + icPO2; A: area under the cathode. The intracutaneous oxygen partial pressure (icPO2) is a virtual quantity defined by the equation given. Only by using an active electrode different oxygen mass flows can be set and so the oxygen conductance of the upper skin layers can be assessed. First experiments on human skin in the gluteal region of an adult delivered an estimated value of the permeation coefficient (P): 2

  6. Oxygen plasma flow properties deduced from laser-induced fluorescence and probe measurements.

    PubMed

    Löhle, Stefan; Eichhorn, Christoph; Steinbeck, Andreas; Lein, Sebastian; Herdrich, Georg; Röser, Hans-Peter; Auweter-Kurtz, Monika

    2008-04-10

    Estimation of the local dissociation degree and the local mass-specific enthalpy of a pure oxygen plasma flow determined mainly from laser-induced fluorescence measurements are reported. Measurements have been conducted for several generator parameters in an inductively heated plasma wind tunnel. Additional probe measurements of total pressure together with the deduced translational temperature are used to estimate the local mass-specific enthalpy. For a reference condition, full dissociation has been measured. The measured translational temperature of atomic oxygen for this condition is T = 3500 K. Subsequently, the local mass-specific enthalpy has been derived using these local density and temperature measurements. For the reference condition the estimated value of h = 27 MJ/kg is in good agreement with the probe measurements and results from diode laser absorption spectroscopy. PMID:18404183

  7. The Choroidal Eye Oximeter - An instrument for measuring oxygen saturation of choroidal blood in vivo

    NASA Technical Reports Server (NTRS)

    Laing, R. A.; Danisch, L. A.; Young, L. R.

    1975-01-01

    The Choroidal Eye Oximeter is an electro-optical instrument that noninvasively measures the oxygen saturation of choroidal blood in the back of the human eye by a spectrophotometric method. Since choroidal blood is characteristic of blood which is supplied to the brain, the Choroidal Eye Oximeter can be used to monitor the amount of oxygen which is supplied to the brain under varying external conditions. The instrument consists of two basic systems: the optical system and the electronic system. The optical system produces a suitable bi-chromatic beam of light, reflects this beam from the fundus of the subject's eye, and onto a low-noise photodetector. The electronic system amplifies the weak composite signal from the photodetector, computes the average oxygen saturation from the area of the fundus that was sampled, and displays the value of the computed oxygen saturation on a panel meter.

  8. Flexible Sheet-Type Sensor for Noninvasive Measurement of Cellular Oxygen Metabolism on a Culture Dish.

    PubMed

    Kojima, Mari; Takehara, Hiroaki; Akagi, Takanori; Shiono, Hirofumi; Ichiki, Takanori

    2015-01-01

    A novel flexible sensor was developed for the noninvasive oxygen metabolism measurement of cultivated cells and tissues. This device is composed of a transparent double-layered polymer sheet of ethylene-vinyl alcohol (EVOH) and poly(dimethylsiloxane) (PDMS) having an array of microhole structures of 90 μm diameter and 50 μm depth on its surface. All the microhole structures were equipped with a 1-μm-thick optical chemical sensing layer of platinum porphyrin-fluoropolymer on their bottom. The three-dimensional microstructures of the sensor were fabricated by a newly developed simple and low-cost production method named self-aligned hot embossing. The device was designed to be attached slightly above the cells cultivated on a dish to form a temporarily closed microspace over the target cells during measurement. Since the change in oxygen concentration is relatively fast in the microcompartmentalized culture medium, a rapid evaluation of the oxygen consumption rate is possible by measuring the phosphorescence lifetime of the platinum porphyrin-fluoropolymer. The combined use of the device and an automated optical measurement system enabled the high-throughput sensing of cellular oxygen consumption (100 points/min). We monitored the oxygen metabolism of the human breast cancer cell line MCF7 on a Petri dish and evaluated the oxygen consumption rate to be 0.72 ± 0.12 fmol/min/cell. Furthermore, to demonstrate the utility of the developed sensing system, we demonstrated the mapping of the oxygen consumption rate of rat brain slices and succeeded in visualizing a clear difference among the layer structures of the hippocampus, i.e., the cornu ammonis (CA1 and CA3) and dentate gyrus (DG). PMID:26624889

  9. Flexible Sheet-Type Sensor for Noninvasive Measurement of Cellular Oxygen Metabolism on a Culture Dish

    PubMed Central

    Akagi, Takanori; Shiono, Hirofumi; Ichiki, Takanori

    2015-01-01

    A novel flexible sensor was developed for the noninvasive oxygen metabolism measurement of cultivated cells and tissues. This device is composed of a transparent double-layered polymer sheet of ethylene-vinyl alcohol (EVOH) and poly(dimethylsiloxane) (PDMS) having an array of microhole structures of 90 μm diameter and 50 μm depth on its surface. All the microhole structures were equipped with a 1-μm-thick optical chemical sensing layer of platinum porphyrin-fluoropolymer on their bottom. The three-dimensional microstructures of the sensor were fabricated by a newly developed simple and low-cost production method named self-aligned hot embossing. The device was designed to be attached slightly above the cells cultivated on a dish to form a temporarily closed microspace over the target cells during measurement. Since the change in oxygen concentration is relatively fast in the microcompartmentalized culture medium, a rapid evaluation of the oxygen consumption rate is possible by measuring the phosphorescence lifetime of the platinum porphyrin-fluoropolymer. The combined use of the device and an automated optical measurement system enabled the high-throughput sensing of cellular oxygen consumption (100 points/min). We monitored the oxygen metabolism of the human breast cancer cell line MCF7 on a Petri dish and evaluated the oxygen consumption rate to be 0.72 ± 0.12 fmol/min/cell. Furthermore, to demonstrate the utility of the developed sensing system, we demonstrated the mapping of the oxygen consumption rate of rat brain slices and succeeded in visualizing a clear difference among the layer structures of the hippocampus, i.e., the cornu ammonis (CA1 and CA3) and dentate gyrus (DG). PMID:26624889

  10. Flame temperature measurements by radar resonance-enhanced multiphoton ionization of molecular oxygen.

    PubMed

    Wu, Yue; Sawyer, Jordan; Zhang, Zhili; Adams, Steven F

    2012-10-01

    Here we report nonintrusive local rotational temperature measurements of molecular oxygen, based on coherent microwave scattering (radar) from resonance-enhanced multiphoton ionization (REMPI) in room air and hydrogen/air flames. Analyses of the rotational line strengths of the two-photon molecular oxygen C(3)Π(v=2)←X(3)Σ(v'=0) transition have been used to determine the hyperfine rotational state distribution of the ground X(3)Σ(v'=0) state. Rotationally resolved 2+1 REMPI spectra of the molecular oxygen C(3)Π(v=2)←X(3)Σ(v'=0) transition at different temperatures were obtained experimentally by radar REMPI. Rotational temperatures have been determined from the resulting Boltzmann plots. The measurements in general had an accuracy of ~±60 K in the hydrogen/air flames at various equivalence ratios. Discussions about the decreased accuracy for the temperature measurement at elevated temperatures have been presented. PMID:23033104

  11. Measuring and modeling oxygen diffusion in niobium-vanadium and niobium-palladium alloys

    NASA Astrophysics Data System (ADS)

    Hennessey, Theresa P.

    Niobium alloys are under consideration for high-temperature aerospace applications, but they have poor oxidation resistance and need high-temperature coatings for protection in severe environments. Our approach to creating an oxidation-resistant Nb alloy is to identify substitutional solute elements that lower the diffusivity of oxygen in Nb. In theory, this will induce a transition from internal to external oxidation and promote the formation of a desirable, protective oxide scale. The objective of this particular project is to compare the oxygen diffusivity in Nb alloys that contain either trap or repulsive sites. In Nb, oxygen atoms diffuse via an interstitial mechanism, and they can interact with substitutional solute atoms in different ways. The interstitial sites adjacent to a substitutional atom constitute a "zone of influence". If the sites in this zone have a lower energy than the normal sites, they are called "trap" sites. If these sites have a higher energy, they are called "repulsive" sites. Oxygen diffusion is inhibited in both cases: trap sites hold the oxygen and keep it from diffusing further, while repulsive sites block the path of the oxygen. Two new mathematical models for interstitial diffusion in these systems were derived from probability and statistical thermodynamic theory. The models were verified using a new random-walk computer simulation of oxygen diffusion through Nb alloys. These models were also tested experimentally by measuring oxygen diffusivity in Nb-V and Nb-Pd alloys. These results showed that V atoms create trap sites for oxygen atoms, confirming previous work. However, there was not enough data to prove definitively that Pd atoms create repulsive sites, as expected by theory.

  12. Simultaneous Noninvasive Determination of Regional Myocardial Perfusion and Oxygen Content in Rabbits: Toward Direct Measurement of Myocardial Oxygen Consumption at MR Imaging1

    PubMed Central

    Reeder, Scott B.; Holmes, A. Alexander; McVeigh, Elliot R.; Forder, John R.

    2007-01-01

    PURPOSE To determine whether myocardial arterial perfusion and oxygen concentration can be quantified simultaneously from the same images by using spin labeling and the blood oxygenation level-dependent (BOLD) effect with fast spin-echo (SE) imaging. MATERIALS AND METHODS A T2-weighted fast SE pulse sequence was written to image isolated, arrested, blood-perfused rabbit hearts (n = 6) at 4.7 T. Perfusion images with intensity in units of milliliters per minute per gram that covered the entire left ventricle with 0.39 × 0.39 × 3.00-mm resolution were obtained in less than 15 minutes with a 32-fold reduction in imaging time from that of a previous study. Estimates of oxygen concentration were made from the same images acquired for calculation of perfusion images. RESULTS Estimates of regional myocardial oxygen content could be made from the perfusion images; this demonstrated the feasibility of three-dimensional calculation of regional oxygen consumption, which requires concomitant measurement of both oxygen content and flow. Fast SE imaging was shown to bas sensitive to hemoglobin desaturation as standard SE imaging. Perfusion abnormalities and oxygen deficits were easily identified and verified qualitatively with gadopentetate dimeglumine on both perfusion and BOLD images obtained after coronary arterial ligation. CONCLUSION T2-weighted fast SE imaging combined with perfusion-sensitive spin labeling can be used to measure myocardial arterial perfusion and oxygen concentration. This provides the groundwork for calculation of regional myocardial oxygen consumption. PMID:10478241

  13. Quantitative Tissue Oxygen Measurement in Multiple Organs Using 19F MRI in a Rat Model

    PubMed Central

    Liu, Siyuan; Shah, Sameer J.; Wilmes, Lisa J.; Feiner, John; Kodibagkar, Vikram D.; Wendland, Michael F.; Mason, Ralph P.; Hylton, Nola; Hopf, Harriet W.; Rollins, Mark D.

    2011-01-01

    Measurement of individual organ tissue oxygen levels can provide information to help evaluate and optimize medical interventions in many areas including wound healing, resuscitation strategies, and cancer therapeutics. Echo planar 19F MRI has previously focused on tumor oxygen measurement at low oxygen levels (pO2) < 30 mmHg. It uses the linear relationship between spin-lattice relaxation rate (R1) of hexafluorobenzene (HFB) and pO2. The feasibility of this technique for a wider range of pO2 values and individual organ tissue pO2 measurement was investigated in a rat model. Spin-lattice relaxation times (T1=1/R1) of HFB were measured using 19F saturation recovery echo planar imaging (EPI). Initial in vitro studies validated the linear relationship between R1 and pO2 from 0 mmHg to 760 mmHg oxygen partial pressure at 25°C, 37°C, and 41°C at 7 Tesla for HFB. In vivo experiments measured rat tissue oxygen (ptO2) levels of brain, kidney, liver, gut, muscle and skin during inhalation of both 30% and 100% oxygen. All organ ptO2 values significantly increased with hyperoxia (p<0.001). This study demonstrates that 19F MRI of HFB offers a feasible tool to measure regional ptO2 in vivo, and that hyperoxia significantly increases ptO2 of multiple organs in a rat model. PMID:21688315

  14. UV Decontamination of MDA Reagents for Single Cell Genomics

    SciTech Connect

    Lee, Janey; Tighe, Damon; Sczyrba, Alexander; Malmatrom, Rex; Clingenpeel, Scott; Malfatti, Stephanie; Rinke, Christian; Wang, Zhong; Stepanauskas, Ramunas; Cheng, Jan-Fang; Woyke, Tanja

    2011-03-18

    Single cell genomics, the amplification and sequencing of genomes from single cells, can provide a glimpse into the genetic make-up and thus life style of the vast majority of uncultured microbial cells, making it an immensely powerful and increasingly popular tool. This is accomplished by use of multiple displacement amplification (MDA), which can generate billions of copies of a single bacterial genome producing microgram-range DNA required for shotgun sequencing. Here, we address a key challenge inherent to this approach and propose a solution for the improved recovery of single cell genomes. While DNA-free reagents for the amplification of a single cell genome are a prerequisite for successful single cell sequencing and analysis, DNA contamination has been detected in various reagents, which poses a considerable challenge. Our study demonstrates the effect of UV irradiation in efficient elimination of exogenous contaminant DNA found in MDA reagents, while maintaining Phi29 activity. Consequently, we also find that increased UV exposure to Phi29 does not adversely affect genome coverage of MDA amplified single cells. While additional challenges in single cell genomics remain to be resolved, the proposed methodology is relatively quick and simple and we believe that its application will be of high value for future single cell sequencing projects.

  15. Microfluidic techniques for high throughput single cell analysis.

    PubMed

    Reece, Amy; Xia, Bingzhao; Jiang, Zhongliang; Noren, Benjamin; McBride, Ralph; Oakey, John

    2016-08-01

    The microfabrication of microfluidic control systems and the development of increasingly sensitive molecular amplification tools have enabled the miniaturization of single cells analytical platforms. Only recently has the throughput of these platforms increased to a level at which populations can be screened at the single cell level. Techniques based upon both active and passive manipulation are now capable of discriminating between single cell phenotypes for sorting, diagnostic or prognostic applications in a variety of clinical scenarios. The introduction of multiphase microfluidics enables the segmentation of single cells into biochemically discrete picoliter environments. The combination of these techniques are enabling a class of single cell analytical platforms within great potential for data driven biomedicine, genomics and transcriptomics. PMID:27032065

  16. Combined photoacoustic microscopy and optical coherence tomography can measure metabolic rate of oxygen

    PubMed Central

    Liu, Tan; Wei, Qing; Wang, Jing; Jiao, Shuliang; Zhang, Hao F.

    2011-01-01

    We proposed to measure the metabolic rate of oxygen (MRO2) in small animals in vivo using a multimodal imaging system that combines laser-scanning optical-resolution photoacoustic microscopy (LSOR-PAM) and spectral-domain optical coherence tomography (SD-OCT). We first tested the capability of the multimodal system to measure flow rate in a phantom made of two capillary tubes of different diameters. We then demonstrated the capability of measuring MRO2 by imaging two parallel vessels selected from the ear of a Swiss Webster mouse. The hemoglobin oxygen saturation (sO2) and the vessel diameter were measured by the LSOR-PAM and the blood flow velocity was measured by the SD-OCT, from which blood flow rate and MRO2 were further calculated. The measured blood flow rates in the two vessels agreed with each other. PMID:21559147

  17. Use of an Oxygen-Insensitive Microscale Biosensor for Methane To Measure Methane Concentration Profiles in a Rice Paddy

    PubMed Central

    Damgaard, Lars R.; Revsbech, Niels Peter; Reichardt, Wolfgang

    1998-01-01

    An oxygen-insensitive microscale biosensor for methane was constructed by furnishing a previously described biosensor with an oxygen guard. The guard consisted of a glass capillary containing heterotrophic bacteria, which consumed oxygen diffusing through the tip membrane, thus preventing it from diffusing into the methane-sensing unit. Oxygen microprofiles were measured through the oxygen guard capillary, demonstrating the principle and limitations of the method. When the tip of the guard capillary was exposed to 100% oxygen at 21°C, heterotrophic oxygen consumption prevented oxygen from diffusing further than 170 μm into the capillary, whereas atmospheric levels of oxygen were consumed within 50 μm. The capacity of the oxygen guard for scavenging oxygen decreased with decreasing temperature, and atmospheric levels of oxygen caused oxygen penetration to 200 μm at 5°C. The sensors could be manufactured with tip diameters as small as 25 μm, and response times were about 1 min at room temperature. Pore water profiles of methane concentrations in a rice paddy soil were measured, and a strong correlation between the depths of oxygen penetration and methane appearance was observed as a function of the light regimen; this finding confirmed the role of microbenthic photosynthesis in limiting methane emissions from surfaces of waterlogged sediments and soils. PMID:16349527

  18. New Approach to Investigate the Cytotoxicity of Nanomaterials Using Single Cell Mechanics

    PubMed Central

    2015-01-01

    Current in vitro methods to assess nanomaterial cytotoxicity involve various assays to monitor specific cellular dysfunction, such as metabolic imbalance or inflammation. Although high throughput, fast, and animal-free, these in vitro methods suffer from unreliability and lack of relevance to in vivo situations. New approaches, especially with the potential to reliably relate to in vivo studies directly, are in critical need. This work introduces a new approach, single cell mechanics, derived from atomic force microscopy-based single cell compression. The single cell based approach is intrinsically advantageous in terms of being able to directly correlate to in vivo investigations. Its reliability and potential to measure cytotoxicity is evaluated using known systems: zinc oxide (ZnO) and silicon dioxide (SiO2) nanoparticles (NP) on human aortic endothelial cells (HAECs). This investigation clearly indicates the reliability of single cell compression. For example, ZnO NPs cause significant changes in force vs relative deformation profiles, whereas SiO2 NPs do not. New insights into NPs–cell interactions pertaining to cytotoxicity are also revealed from this single cell mechanics approach, in addition to a qualitative cytotoxicity conclusion. The advantages and disadvantages of this approach are also compared with conventional cytotoxicity assays. PMID:24417356

  19. Relating Single Cell Heterogeneity To Genotype During Cancer Progression

    NASA Astrophysics Data System (ADS)

    Rajaram, Satwik

    2013-03-01

    Progression of normal cells towards cancer is driven by a series of genetic changes. Traditional population-averaged measurements have found that cell signalling activities are increasingly altered during this progression. Despite the fact that cancer cells are known to be highly heterogeneous, the response of individual pathways to specific genetic changes remains poorly characterized at a single cell level. Do signalling alterations in a pathway reflect a shift of the whole population, or changes to specific subpopulations? Are alterations to pathways independent, or are cells with alterations in one pathway more likely to be abnormal in another due to crosstalk? We are building a computational framework that analyzes immunofluorescence microscopy images of cells to identify alterations in individual pathways at a single-cell level. A primary novelty of our approach is a ``change of basis'' that allows us to understand signalling in cancer cells in terms of the much better understood patterns of signalling in normal cells. This allows us to model heterogeneous populations of cancer cells as a mixture of distinct subpopulations, each with a specific combination of signalling pathways altered beyond the normal baseline. We used this framework to analyze human bronchial epithelial cell lines containing a series of genetic modifications commonly seen in lung cancer. We confirmed expected trends (such as a population-wide epithelial mesenchymal transition following the last of our series of modifications) and are presently studying the relation between the mutational profiles of cancer cells and pathway crosstalk. Our framework will help establish a more natural basis for future investigations into the phenotype-genotype relationship in heterogeneous populations.

  20. Mixture models for single-cell assays with applications to vaccine studies.

    PubMed

    Finak, Greg; McDavid, Andrew; Chattopadhyay, Pratip; Dominguez, Maria; De Rosa, Steve; Roederer, Mario; Gottardo, Raphael

    2014-01-01

    Blood and tissue are composed of many functionally distinct cell subsets. In immunological studies, these can be measured accurately only using single-cell assays. The characterization of these small cell subsets is crucial to decipher system-level biological changes. For this reason, an increasing number of studies rely on assays that provide single-cell measurements of multiple genes and proteins from bulk cell samples. A common problem in the analysis of such data is to identify biomarkers (or combinations of biomarkers) that are differentially expressed between two biological conditions (e.g. before/after stimulation), where expression is defined as the proportion of cells expressing that biomarker (or biomarker combination) in the cell subset(s) of interest. Here, we present a Bayesian hierarchical framework based on a beta-binomial mixture model for testing for differential biomarker expression using single-cell assays. Our model allows the inference to be subject specific, as is typically required when assessing vaccine responses, while borrowing strength across subjects through common prior distributions. We propose two approaches for parameter estimation: an empirical-Bayes approach using an Expectation-Maximization algorithm and a fully Bayesian one based on a Markov chain Monte Carlo algorithm. We compare our method against classical approaches for single-cell assays including Fisher's exact test, a likelihood ratio test, and basic log-fold changes. Using several experimental assays measuring proteins or genes at single-cell level and simulations, we show that our method has higher sensitivity and specificity than alternative methods. Additional simulations show that our framework is also robust to model misspecification. Finally, we demonstrate how our approach can be extended to testing multivariate differential expression across multiple biomarker combinations using a Dirichlet-multinomial model and illustrate this approach using single-cell gene

  1. Measurement of atomic oxygen and related airglows in the lower thermosphere

    NASA Technical Reports Server (NTRS)

    Thomas, R. J.; Young, R. A.

    1981-01-01

    Instruments on board a sounding rocket were used to make simultaneous observations of atomic oxygen density and airglow emissions between 80 and 120 km. Atomic oxygen was measured with a resonance lamp and was found to have a peak density of 6 x 10 to the 11th at 94 km. Similar structure is seen in the oxygen density profile on both uplegs and downlegs. The following airglow emissions were measured by using vertical-viewing photometers: Herzberg I bands near 300 nm; O(1S) green line at 557.7 nm; background at 566 nm; O2(1 Delta g) bands at 1.27 microns; and OH (X 2 pi) Meinel bands near 1.7 microns.

  2. Measurement of atomic oxygen in the middle atmosphere using solid electrolyte sensors and catalytic probes

    NASA Astrophysics Data System (ADS)

    Eberhart, M.; Löhle, S.; Steinbeck, A.; Binder, T.; Fasoulas, S.

    2015-09-01

    The middle- and upper-atmospheric energy budget is largely dominated by reactions involving atomic oxygen (O). Modeling of these processes requires detailed knowledge about the distribution of this oxygen species. Understanding the mutual contributions of atomic oxygen and wave motions to the atmospheric heating is the main goal of the rocket project WADIS (WAve propagation and DISsipation in the middle atmosphere). It includes, amongst others, our instruments for the measurement of atomic oxygen that have both been developed with the aim of resolving density variations on small vertical scales along the trajectory. In this paper the instrument based on catalytic effects (PHLUX: Pyrometric Heat Flux Experiment) is introduced briefly. The experiment employing solid electrolyte sensors (FIPEX: Flux φ(Phi) Probe Experiment) is presented in detail. These sensors were laboratory calibrated using a microwave plasma as a source of atomic oxygen in combination with mass spectrometer reference measurements. The spectrometer was in turn calibrated for O with a method based on methane. In order to get insight into the horizontal variability, the rocket payload had instrument decks at both ends. Each housed several sensor heads measuring during both the up- and downleg of the trajectory. The WADIS project comprises two rocket flights during different geophysical conditions. Results from WADIS-1 are presented, which was successfully launched in June 2013 from the Andøya Space Center, Norway. FIPEX data were sampled at 100 Hz and yield atomic oxygen density profiles with a vertical resolution better than 9 m. This allows density variations to be studied on very small spatial scales. Numerical simulations of the flow field around the rocket were done at several points of the trajectory to assess the influence of aerodynamic effects on the measurement results. Density profiles peak at 3 × 1010 cm-3 at altitudes of 93.6 and 96 km for the up- and downleg, respectively.

  3. Measurement of atomic oxygen in the middle atmosphere using solid electrolyte sensors and catalytic probes

    NASA Astrophysics Data System (ADS)

    Eberhart, M.; Löhle, S.; Steinbeck, A.; Binder, T.; Fasoulas, S.

    2015-03-01

    The atmospheric energy budget is largely dominated by reactions involving atomic oxygen (O). Modeling of these processes requires detailed knowledge about the distribution of this oxygen species. Understanding the mutual contributions of atomic oxygen and wave motions to the atmospheric heating is the main goal of the rocket campaign WADIS. It includes, amongst others, two of our instruments for the measurement of atomic oxygen that have both been developed with the aim of resolving density variations on small vertical scales along the trajectory. In this paper the instrument based on catalytic effects (PHLUX) is introduced briefly. The experiment employing solid electrolyte sensors (FIPEX) is presented in detail. These sensors were laboratory calibrated using a microwave plasma as a source for atomic oxygen in combination with mass spectrometer reference measurements. The spectrometer was in turn calibrated for O with a method based on methane. In order to get insight into the horizontal variability the rocket payload had instrument decks at both ends. Each housed several sensor heads measuring during both the up- and downleg of the trajectory. The WADIS campaign comprises two rocket flights during different geophysical conditions. Results from WADIS-1 are presented which was successfully launched in June 2013 from Andøya Rocket Range, Norway. FIPEX data was sampled with 100 Hz and yield atomic oxygen density profiles with a vertical resolution better than 10 m. Numerical simulations of the flow field around the rocket were done at several points of the trajectory to assess the influence of aerodynamic effects on the measurement results. Density profiles peak at 3 × 1010 cm-3 at altitudes of 93.6 and 96 km for up- and downleg respectively.

  4. Electrochemical Technology for Oxygen Removal and Measurement in the CELSS Test Facility, Engineering Development Unit

    NASA Technical Reports Server (NTRS)

    Drews, Michael E.; Covington, Al (Technical Monitor)

    1994-01-01

    , the amount of oxygen that is removed from the EDU is directly proportional to the cell input current via Faraday's constant, potentially allowing for a mol/electron measurement of photosynthetic rate. The currently operative oxygen removal system has maintained reduced oxygen set points within the EDU, and preparation is underway to verify of the accuracy of electrochemical measurement of oxygen production and hence, photosynthesis. This paper examines the working principles of the electrochemical cell, outlines the overall design of the oxygen removal system and its integration with other EDU subsystems, and summarizes test results obtained over crop growth cycles in the CTF-EDU.

  5. An irradiation system for photodynamic therapy with a fiber-optic sensor for measuring tissue oxygen

    NASA Astrophysics Data System (ADS)

    Quintanar, L.; Fabila, D.; Stolik, S.; de la Rosa, J. M.

    2013-11-01

    Photodynamic Therapy is a well known treatment based on the interaction of light of specific wavelength with a photosensitizing drug. In the presence of oxygen molecules, the illumination of the photosensitizer can activate the production of reactive oxygen species, which leads to the death of target cells within the treated tissue. In order to obtain the best therapy response, the tissue oxygen concentration should be measured to adjust the therapy parameters before and during the treatment. In this work, an irradiation system for 5-Aminolevulinic Acid Photodynamic Therapy is presented. It allows the application of visible light radiation of 630 nm using as a light source a high-brightness light emitting diode with an optical-power automatic control considering a light depth-distribution model. A module to measure the tissue oxygen saturation has been implemented into the system. It is based on two light emitting diodes of 660 nm and 940 nm as light sources, a photodiode as a detector and a new handheld fiber optic reflectance pulse oximetry sensor for estimating the blood oxygen saturation within the tissue. The pulse oximetry sensor was modeled through multilayered Monte Carlo simulations to study the behavior of the sensor with changes in skin thickness and melanin content.

  6. Instrument for stable high temperature Seebeck coefficient and resistivity measurements under controlled oxygen partial pressure

    SciTech Connect

    Ihlefeld, Jon F.; Brown-Shaklee, Harlan James; Sharma, Peter Anand

    2015-04-28

    The transport properties of ceramic materials strongly depend on oxygen activity, which is tuned by changing the partial oxygen pressure (pO2) prior to and during measurement. Within, we describe an instrument for highly stable measurements of Seebeck coefficient and electrical resistivity at temperatures up to 1300 K with controlled oxygen partial pressure. An all platinum construction is used to avoid potential materials instabilities that can cause measurement drift. Two independent heaters are employed to establish a small temperature gradient for Seebeck measurements, while keeping the average temperature constant and avoiding errors associated with pO2-induced drifts in thermocouple readings. Oxygen equilibrium is monitored using both an O2 sensor and the transient behavior of the resistance as a proxy. A pO2 range of 10-25–100 atm can be established with appropriate gas mixtures. Seebeck measurements were calibrated against a high purity platinum wire, Pt/Pt–Rh thermocouple wire, and a Bi2Te3 Seebeck coefficient Standard Reference Material. To demonstrate the utility of this instrument for oxide materials we present measurements as a function of pO2 on a 1 % Nb-doped SrTiO3 single crystal, and show systematic changes in properties consistent with oxygen vacancy defect chemistry. Thus, an approximately 11% increase in power factor over a pO2 range of 10-19–10-8 atm at 973 K for the donor-doped single crystals is observed.

  7. Instrument for stable high temperature Seebeck coefficient and resistivity measurements under controlled oxygen partial pressure

    DOE PAGESBeta

    Ihlefeld, Jon F.; Brown-Shaklee, Harlan James; Sharma, Peter Anand

    2015-04-28

    The transport properties of ceramic materials strongly depend on oxygen activity, which is tuned by changing the partial oxygen pressure (pO2) prior to and during measurement. Within, we describe an instrument for highly stable measurements of Seebeck coefficient and electrical resistivity at temperatures up to 1300 K with controlled oxygen partial pressure. An all platinum construction is used to avoid potential materials instabilities that can cause measurement drift. Two independent heaters are employed to establish a small temperature gradient for Seebeck measurements, while keeping the average temperature constant and avoiding errors associated with pO2-induced drifts in thermocouple readings. Oxygen equilibriummore » is monitored using both an O2 sensor and the transient behavior of the resistance as a proxy. A pO2 range of 10-25–100 atm can be established with appropriate gas mixtures. Seebeck measurements were calibrated against a high purity platinum wire, Pt/Pt–Rh thermocouple wire, and a Bi2Te3 Seebeck coefficient Standard Reference Material. To demonstrate the utility of this instrument for oxide materials we present measurements as a function of pO2 on a 1 % Nb-doped SrTiO3 single crystal, and show systematic changes in properties consistent with oxygen vacancy defect chemistry. Thus, an approximately 11% increase in power factor over a pO2 range of 10-19–10-8 atm at 973 K for the donor-doped single crystals is observed.« less

  8. Embedded silver PDMS electrodes for single cell electrical impedance spectroscopy

    NASA Astrophysics Data System (ADS)

    Wei, Yuan; Xu, Zhensong; Cachia, Mark A.; Nguyen, John; Zheng, Yi; Wang, Chen; Sun, Yu

    2016-09-01

    This paper presents a microfluidic device with wide channels and embedded AgPDMS electrodes for measuring the electrical properties of single cells. The work demonstrates the feasibility of using a large channel design and embedded electrodes for impedance spectroscopy to circumvent issues such as channel clogging and limited device re-usability. AgPDMS electrodes were formed on channel sidewalls for impedance detection and cell electrical properties measurement. Equivalent circuit models were used to interpret multi-frequency impedance data to quantify each cell’s cytoplasm conductivity and specific membrane capacitance. T24 cells were tested to validate the microfluidic system and modeling results. Comparisons were then made by measuring two leukemia cell lines (AML-2 and HL-60) which were found to have different cytoplasm conductivity values (0.29  ±  0.15 S m‑1 versus 0.47  ±  0.20 S m‑1) and specific membrane capacitance values (41  ±  25 mF m‑2 versus 55  ±  26 mF m‑2) when the cells were flown through the wide channel and measured by the AgPDMS electrodes.

  9. FIELD MEASUREMENT OF DISSOLVED OXYGEN: A COMPARISON OF METHODS: JOURNAL ARTICLE

    EPA Science Inventory

    NRMRL-ADA- 00160 Wilkin*, R.T., McNeil*, M.S., Adair*, C.J., and Wilson*, J.T. Field Measurement of Dissolved Oxygen: A Comparison of Methods. Ground Water Monitoring and Remediation (Fall):124-132 (2001). EPA/600/J-01/403. The abili...

  10. Atmospheric Airborne Pressure Measurements using the Oxygen A Band for the ASCENDS Mission

    NASA Astrophysics Data System (ADS)

    Riris, H.; Rodriguez, M.

    2014-12-01

    We report on an airborne demonstration of atmospheric oxygen optical depth measurements with an Integrated Path Differential Absorption (IPDA) lidar using a fiber-based laser system and a photon counting detector. Accurate knowledge of atmospheric temperature and pressure is required for NASA's Active Sensing of CO2 Emissions over Nights, Days and Seasons (ASCENDS) space mission, and climate modeling studies. The lidar uses a doubled Erbium Doped Fiber amplifier and single photon counting detector to measure oxygen absorption at 765 nm. Our approach uses a sequence of laser pulses at increasing wavelengths that sample a pair of absorption lines in the Oxygen A-band at 764.7 nm. The O2 lines were selected after careful spectroscopic analysis to minimize the O2 line temperature dependence and the availability of the transmitter and receiver technology to maximize transmitter power, doubling efficiency, and detector sensitivity. We compare our 2013 and 2014 Oxygen IPDA lidar measurements and evaluate the impact of receiver dynamic range, transmitter stability and signal to noise ratio on the differential optical depth measurements.

  11. RELATIONSHIPS BETWEEN NEAR-BOTTOM DISSOLVED OXYGEN AND SEDIMENT PROFILE CAMERA MEASUREMENTS

    EPA Science Inventory

    The United States Environmental Protection Agency (U.S. EPA) and other environmental authorities regulate concentrations of dissolved oxygen (DO) as a measure of nutrient-related eutrophication in estuarine and coastal waters. However, in situ DO concentrations are extremely var...

  12. A Fiber Optic Catalytic Sensor for Neutral Atom Measurements in Oxygen Plasma

    PubMed Central

    Zaplotnik, Rok; Vesel, Alenka; Mozetic, Miran

    2012-01-01

    The presented sensor for neutral oxygen atom measurement in oxygen plasma is a catalytic probe which uses fiber optics and infrared detection system to measure the gray body radiation of the catalyst. The density of neutral atoms can be determined from the temperature curve of the probe, because the catalyst is heated predominantly by the dissipation of energy caused by the heterogeneous surface recombination of neutral atoms. The advantages of this sensor are that it is simple, reliable, easy to use, noninvasive, quantitative and can be used in plasma discharge regions. By using different catalyst materials the sensor can also be applied for detection of neutral atoms in other plasmas. Sensor design, operation, example measurements and new measurement procedure for systematic characterization are presented. PMID:22666005

  13. Measurement of cell respiration and oxygenation in standard multichannel biochips using phosphorescent O2-sensitive probes.

    PubMed

    Kondrashina, Alina V; Papkovsky, Dmitri B; Dmitriev, Ruslan I

    2013-09-01

    Measurement of cell oxygenation and oxygen consumption is useful for studies of cell bioenergetics, metabolism, mitochondrial function, drug toxicity and common pathophysiological conditions. Here we present a new platform for such applications which uses commercial multichannel biochips (μ-slides, Ibidi) and phosphorescent O2 sensitive probes. This platform was evaluated with both extracellular and intracellular O2 probes, several different cell types and treatments including mitochondrial uncoupling and inhibition, depletion of extracellular Ca(2+) and inhibition of V-ATPase and histone deacetylases. The results show that compared to the standard microwell plates currently used, the μ-slide platform provides facile O2 measurements with both suspension and adherent cells, higher sensitivity and reproducibility, and faster measurement time. It also allows re-perfusion and multiple treatments of cells and multi-parametric analyses in conjunction with other probes. Optical measurements are conducted on standard fluorescence readers and microscopes. PMID:23803790

  14. Magnetic susceptibility measurement of solid oxygen at pressures up to 3.3 GPa

    SciTech Connect

    Mito, M. Yamaguchi, S.; Tsuruda, H.; Deguchi, H.; Ishizuka, M.

    2014-01-07

    The magnetic susceptibility of solid oxygen had long been observed only in the restricted pressure region below 0.8 GPa. We succeeded in extending the pressure region up to 3.3 GPa by clamping condensed oxygen in the sample chamber of a miniature diamond anvil cell and measuring the dc magnetic susceptibility using a superconducting quantum interference device magnetometer. In this experiment, the well-known α–β and β–γ transitions are observed in the phase diagram, suggesting consistency with the previous results of X-ray and Raman studies. In addition, a new magnetic anomaly is observed in the β phase.

  15. Single-cell Transcriptome Study as Big Data

    PubMed Central

    Yu, Pingjian; Lin, Wei

    2016-01-01

    The rapid growth of single-cell RNA-seq studies (scRNA-seq) demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing (NGS)-based studies, we propose a workflow that accounts for the unique characteristics of scRNA-seq data and primary objectives of single-cell studies. PMID:26876720

  16. Single-cell label-free photoacoustic flowoxigraphy in vivo

    PubMed Central

    Wang, Lidai; Maslov, Konstantin; Wang, Lihong V.

    2013-01-01

    Label-free functional imaging of single red blood cells (RBCs) in vivo holds the key to uncovering the fundamental mechanism of oxygen metabolism in cells. To this end, we developed single-RBC photoacoustic flowoxigraphy (FOG), which can image oxygen delivery from single flowing RBCs in vivo with millisecond-scale temporal resolution and micrometer-scale spatial resolution. Using intrinsic optical absorption contrast from oxyhemoglobin (HbO2) and deoxyhemoglobin (HbR), FOG allows label-free imaging. Multiple single-RBC functional parameters, including total hemoglobin concentration (CHb), oxygen saturation (sO2), sO2 gradient (), flow speed (vf), and oxygen release rate (rO2), have been quantified simultaneously in real time. Working in reflection instead of transmission mode, the system allows minimally invasive imaging at more anatomical sites. We showed the capability to measure relationships among sO2, , vf, and rO2 in a living mouse brain. We also demonstrated that single-RBC oxygen delivery was modulated by changing either the inhalation gas or blood glucose. Furthermore, we showed that the coupling between neural activity and oxygen delivery could be imaged at the single-RBC level in the brain. The single-RBC functional imaging capability of FOG enables numerous biomedical studies and clinical applications. PMID:23536296

  17. Noninvasive Measurement of Microvascular and Interstitial Oxygen Profiles in a Human Tumor in SCID Mice

    NASA Astrophysics Data System (ADS)

    Torres Filho, Ivo P.; Leunig, Michael; Yuan, Fan; Intaglietta, Marcos; Jain, Rakesh K.

    1994-03-01

    Simultaneous measurements of intravascular and interstitial oxygen partial pressure (Po_2) in any tissue have not previously been reported, despite the importance of oxygen in health and in disease. This is due to the limitations of current techniques, both invasive and noninvasive. We have optically measured microscopic profiles of Po_2 with high spatial resolution in subcutaneous tissue and transplanted tumors in mice by combining an oxygen-dependent phosphorescence quenching method and a transparent tissue preparation. The strengths of our approach include the ability to follow Po_2 in the same location for several weeks and to relate these measurements to local blood flow and vascular architecture. Our results show that (i) Po_2 values in blood vessels in well-vascularized regions of a human colon adenocarcinoma xenograft are comparable to those in surrounding arterioles and venules, (ii) carbogen (95% O_2/5% CO_2) breathing increases microvascular Po_2 in tumors, and (iii) in unanesthetized and anesthetized mice Po_2 drops to hypoxic values at <200 μm from isolated vessels but drops by <5 mmHg (1 mmHg = 133 Pa) in highly vascularized tumor regions. Our method should permit noninvasive evaluations of oxygen-modifying agents and offer further mechanistic information about tumor pathophysiology in tissue preparations where the surface of the tissue can be observed.

  18. Tissue oxygenation during exercise measured with NIRS: reproducibility and influence of wavelengths.

    PubMed

    Gerz, Erwin; Geraskin, Dmitri; Franke, Julia; Platen, Petra; Steimers, André; Kohl-Bareis, Matthias

    2013-01-01

    Near-infrared spectroscopy (NIRS) is widely used for the measurement of skeletal muscle oxygenation during exercise as it reflects muscle metabolism, and most studies report a large variability between subjects. Here we assess the data quality of tissue oxygen saturation (SO2) and oxygenated (oxyHb) and deoxygenated (deoxyHb) haemoglobin concentrations recorded during an incremental cycling protocol in nine healthy volunteers. The protocol was repeated three times on the same day and a fourth session on a different day to estimate the reproducibility of the method with a broadband, spatially resolved spectroscopy (SRS) system. We found that the inter-subject variation in SO2 (standard deviation ≈ 6 %) was considerably larger than the reproducibility (≈ 1.5 %) both for the same-day and different-day tests. The reproducibility of changes in SO2 was better than 1 %. PMID:23852492

  19. Flagellates as model system for gravity detection of single cells

    NASA Astrophysics Data System (ADS)

    Lebert, Michael; Richter, Peter; Daiker, Viktor; Schuster, Martin; Tebart, Jenny; Strauch, Sebastian M.; Donat-Peter, H.

    Euglena gracilis is a unicellular, photosynthetic organism which uses light and gravity as en-vironmental hints to reach and stay in horizons of the water column which are optimal for growth and reproduction. The orientation in respect to light (so called positive and nega-tive phototaxis, i.e. movement toward or away of a light source) was well known and fairly good understood. In contrast, knowledge about the movement away from the centre of gravity (negative gravitaxis) was rather scarce. Over a century it was unclear whether orientation in respect to the gravity vector is based on a physical or a physiological mechanism. Recent results clearly favour the latter. Knock-down mutants (RNAi) were characterized which define certain key components of the gravitactic signal transduction chain. These key components include a TRP-like channel, a gravitaxis-specific calmodulin and a protein kinase A. The molecular characterization of these components is currently performed and will be presented. Euglena is not only a model system for the close understanding of gravity detection in single cells, but can also be used as photosynthetic component, i.e. oxygen source and carbon dioxide as well as nitrogenic components sink in Closed Environmental Systems (CES). Due CES are systems of choice in times of scarce flight opportunities. They allow a massive sample sharing and combine possibilities to do microgravity research for biologists but also for engineers, physicists and material scientists. Recent attempts include Aquacells and Omegahab. In the near future miniaturized systems (Chinese ShenZhou) as well as advanced CES will be flown or tested, respectively. Current attempts and plans will be presented.

  20. Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data.

    PubMed

    Ezer, Daphne; Moignard, Victoria; Göttgens, Berthold; Adryan, Boris

    2016-08-01

    Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete pipeline for the analysis of single cell qPCR data that uses the mathematics behind bursty expression to develop more accurate and robust algorithms for analyzing the origin of heterogeneity in experimental samples, specifically an algorithm for clustering cells by their bursting behavior (Simulated Annealing for Bursty Expression Clustering, SABEC) and a statistical tool for comparing the kinetic parameters of bursty expression across populations of cells (Estimation of Parameter changes in Kinetics, EPiK). We applied these methods to hematopoiesis, including a new single cell dataset in which transcription factors (TFs) involved in the earliest branchpoint of blood differentiation were individually up- and down-regulated. We could identify two unique sub-populations within a seemingly homogenous group of hematopoietic stem cells. In addition, we could predict regulatory mechanisms controlling the expression levels of eighteen key hematopoietic transcription factors throughout differentiation. Detailed information about gene regulatory mechanisms can therefore be obtained simply from high throughput single cell gene expression data, which should be widely applicable given the rapid expansion of single cell genomics. PMID:27551778

  1. Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data

    PubMed Central

    Moignard, Victoria; Göttgens, Berthold; Adryan, Boris

    2016-01-01

    Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete pipeline for the analysis of single cell qPCR data that uses the mathematics behind bursty expression to develop more accurate and robust algorithms for analyzing the origin of heterogeneity in experimental samples, specifically an algorithm for clustering cells by their bursting behavior (Simulated Annealing for Bursty Expression Clustering, SABEC) and a statistical tool for comparing the kinetic parameters of bursty expression across populations of cells (Estimation of Parameter changes in Kinetics, EPiK). We applied these methods to hematopoiesis, including a new single cell dataset in which transcription factors (TFs) involved in the earliest branchpoint of blood differentiation were individually up- and down-regulated. We could identify two unique sub-populations within a seemingly homogenous group of hematopoietic stem cells. In addition, we could predict regulatory mechanisms controlling the expression levels of eighteen key hematopoietic transcription factors throughout differentiation. Detailed information about gene regulatory mechanisms can therefore be obtained simply from high throughput single cell gene expression data, which should be widely applicable given the rapid expansion of single cell genomics. PMID:27551778

  2. A high precision apparatus for intracellular thermal response at single-cell level

    NASA Astrophysics Data System (ADS)

    Tian, Wenjuan; Wang, Cangling; Wang, Jianqing; Chen, Qiuhua; Sun, Jianfei; Li, Can; Wang, Xing; Gu, Ning

    2015-09-01

    In this work, a nanoprobe that is highly thermo-sensitive to tiny temperature changes was prepared based on a thermocouple metal junction. A series of electro-element apparatuses were integrated to accomplish single-cell temperature measurement. The temperature measurement probe (TMP) was constructed by tungsten (W), polyurethane (PU), and platinum (Pt). The tip size of TMP was characterized at less than 500 nm, and the tip angle was between 10 and 20° with the resistance in the range of 500 to 1500 Ω. The single-cell temperature measurement probes were calibrated and calculated with a Seebeck coefficient ranging from 6 to 8 μV °C-1 at a precision of 0.1 °C. Monitoring the temperature at a single-cell level by inserting the TMP in marine lung epithelia (MLE)-12 cells displayed that the stimulation of lipopolysaccharide (LPS) and cobalt chloride induced different single-cell temperature fluctuation. This investigation could help reveal complex cellular functions and develop novel diagnoses.

  3. A high precision apparatus for intracellular thermal response at single-cell level.

    PubMed

    Tian, Wenjuan; Wang, Cangling; Wang, Jianqing; Chen, Qiuhua; Sun, Jianfei; Li, Can; Wang, Xing; Gu, Ning

    2015-09-01

    In this work, a nanoprobe that is highly thermo-sensitive to tiny temperature changes was prepared based on a thermocouple metal junction. A series of electro-element apparatuses were integrated to accomplish single-cell temperature measurement. The temperature measurement probe (TMP) was constructed by tungsten (W), polyurethane (PU), and platinum (Pt). The tip size of TMP was characterized at less than 500 nm, and the tip angle was between 10 and 20° with the resistance in the range of 500 to 1500 Ω. The single-cell temperature measurement probes were calibrated and calculated with a Seebeck coefficient ranging from 6 to 8 μV °C(-1) at a precision of 0.1 °C. Monitoring the temperature at a single-cell level by inserting the TMP in marine lung epithelia (MLE)-12 cells displayed that the stimulation of lipopolysaccharide (LPS) and cobalt chloride induced different single-cell temperature fluctuation. This investigation could help reveal complex cellular functions and develop novel diagnoses. PMID:26267315

  4. Distinguishing phosphate from fertilizers and wastewater treatment plant effluents in Western Canada using oxygen isotope measurements

    NASA Astrophysics Data System (ADS)

    Fau, Veronique; Nightingale, Michael; Tamburini, Frederica; Mayer, Bernhard

    2014-05-01

    The successful application of oxygen isotope ratios as a tracer for phosphate in aquatic ecosystems requires that different sources of phosphate are isotopically distinct. The objective of this study was to determine whether the oxygen isotope ratios of phosphate from fertilizers and effluents from wastewater treatment plants in Western Canada are isotopically distinct. Therefore, we carried out oxygen isotope analyses on phosphate in effluent from five different wastewater treatment plants (WWTP) in the Bow River watershed of Alberta, Canada. Samples were collected directly from the final effluent (post-UV) in Banff and Canmore upstream of Calgary, and from effluents of Calgary's WWTPs at Bonnybrook, Fish Creek and Pine Creek. We also carried out oxygen isotope analyses on a variety of phosphate-containing fertilizers that are widely used in Western Canada. Historically, most of the phosphate contained in manufactured fertilizers sold in Alberta came from two distinct deposits: 1) a weathered Pliocene igneous carbonatite located in eastern Canada, and 2) the Permian Phosphoria Formation in the western USA. Phosphate (PO43-) contained in the water or the fertilizer was concentrated and quantitatively converted to pure silver phosphate (Ag3PO4). The silver phosphate was then reduced with carbon in an oxygen free environment using a TC/EA pyrolysis reactor linked to a mass spectrometer where 18O/16O ratios of CO were measured in continuous flow mode. Preparation of samples for δ18OPO4 analyses was conducted using the Magnesium Induced Coprecipitation (MAGIC) method. Expected oxygen isotope ratios for phosphate in equilibrium with water (δ18Oeq) were calculated using the Longinelli and Nuti equation: T (° C) = 111.4 - 4.3 (δ18Oeq - δ18Owater). Measured δ18O values of phosphate for fertilizer samples varied from 8 to 25 oÈ®n average, fertilizer samples of sedimentary origin had higher δ18O values (15.8) than those of igneous origin (11.5). Phosphate isotopic

  5. Monte Carlo method for calculating oxygen abundances and their uncertainties from strong-line flux measurements

    NASA Astrophysics Data System (ADS)

    Bianco, F. B.; Modjaz, M.; Oh, S. M.; Fierroz, D.; Liu, Y. Q.; Kewley, L.; Graur, O.

    2016-07-01

    We present the open-source Python code pyMCZ that determines oxygen abundance and its distribution from strong emission lines in the standard metallicity calibrators, based on the original IDL code of Kewley and Dopita (2002) with updates from Kewley and Ellison (2008), and expanded to include more recently developed calibrators. The standard strong-line diagnostics have been used to estimate the oxygen abundance in the interstellar medium through various emission line ratios (referred to as indicators) in many areas of astrophysics, including galaxy evolution and supernova host galaxy studies. We introduce a Python implementation of these methods that, through Monte Carlo sampling, better characterizes the statistical oxygen abundance confidence region including the effect due to the propagation of observational uncertainties. These uncertainties are likely to dominate the error budget in the case of distant galaxies, hosts of cosmic explosions. Given line flux measurements and their uncertainties, our code produces synthetic distributions for the oxygen abundance in up to 15 metallicity calibrators simultaneously, as well as for E(B- V) , and estimates their median values and their 68% confidence regions. We provide the option of outputting the full Monte Carlo distributions, and their Kernel Density estimates. We test our code on emission line measurements from a sample of nearby supernova host galaxies (z < 0.15) and compare our metallicity results with those from previous methods. We show that our metallicity estimates are consistent with previous methods but yield smaller statistical uncertainties. It should be noted that systematic uncertainties are not taken into account. We also offer visualization tools to assess the spread of the oxygen abundance in the different calibrators, as well as the shape of the estimated oxygen abundance distribution in each calibrator, and develop robust metrics for determining the appropriate Monte Carlo sample size. The code

  6. Airborne Lidar Measurements of Atmospheric Pressure Made Using the Oxygen A-Band

    NASA Technical Reports Server (NTRS)

    Riris, Haris; Rodriquez, Michael D.; Allan, Graham R.; Hasselbrack, William E.; Mao, Jianping; Stephen, Mark A.; Abshire, James B.

    2012-01-01

    Accurate measurements of greenhouse gas mixing ratios on a global scale are currently needed to gain a better understanding of climate change and its possible impact on our planet. In order to remotely measure greenhouse gas concentrations in the atmosphere with regard to dry air, the air number density in the atmosphere is also needed in deriving the greenhouse gas concentrations. Since oxygen is stable and uniformly mixed in the atmosphere at 20.95%, the measurement of an oxygen absorption in the atmosphere can be used to infer the dry air density and used to calculate the dry air mixing ratio of a greenhouse gas, such as carbon dioxide or methane. OUT technique of measuring Oxygen uses integrated path differential absorption (IPDA) with an Erbium Doped Fiber Amplifier (EDF A) laser system and single photon counting module (SPCM). It measures the absorbance of several on- and off-line wavelengths tuned to an O2 absorption line in the A-band at 764.7 nm. The choice of wavelengths allows us to maximize the pressure sensitivity using the trough between two absorptions in the Oxygen A-band. Our retrieval algorithm uses ancillary meteorological and aircraft altitude information to fit the experimentally obtained lidar O2 line shapes to a model atmosphere and derives the pressure from the profiles of the two lines. We have demonstrated O2 measurements from the ground and from an airborne platform. In this paper we will report on our airborne measurements during our 2011 campaign for the ASCENDS program.

  7. Surface Measurements of Oxygen, Carbon Dioxide and Water Vapor Fluxes Using AN Automated Chamber System

    NASA Astrophysics Data System (ADS)

    Fentabil, M. M.; Fazackerley, S.; Nichol, C. F.

    2011-12-01

    The various soil respiration measurements that are available depend on measuring the emitted CO2 flux as organic carbon is respired aerobically. Comparative studies among the four well known methods (the open-flow infra-red gas analyzer method; the closed chamber method; the dynamic closed chamber method; and the alkali absorption method) under field conditions and laboratory experiments show differences. The discrepancies observed in these methods under field conditions could be evaluated by incorporating O2 flux measurement in addition to CO2 flux measurement. However, this is hampered by the absence of suitable equipment for measuring oxygen influx at the soil surface. A system to measure O2 fluxes at the soil surface using chamber methods has been developed. A gas handling subsystem and O2 analyser has been incorporated into an existing non-steady state automated chamber system originally designed for CO2 and H2O flux monitoring. The system consists of four 60 L soil chambers connected to temperature-controlled datalogger housing. During a measurement cycle, the chamber lid closes and the system measures changes of CO2/H2O and depletion of O2in the chamber headspace. Samples for CO2 /H2O circulate in a closed path between the chamber and an IR gas analyser. An air sample for O2 analysis is sub-sampled from this circulating air stream. Air samples for O2 are first dried using a two-stage Nafion drier. Mass flows and pressures are balanced at the pascal level prior to the gas passing into a ppm level fuel-cell oxygen analyser (Sable Systems Oxzilla). The chamber sample airstream is measured against a reference gas identically handled in a parallel air stream. A makeup gas of dry N2 is injected back to the chamber to return equimolar amounts of gas to replace the wet air removed, and hence prevent pressure fluctuation in the headspace of the chamber. The implementation of automated control of gas drying and sampling, pressure balancing, flow regulation and self

  8. Measurement of oxygen saturation in venous blood by dynamic near IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Nitzan, Meir; Babchenko, Anatoly; Khanokh, Boris; Taitelbaum, Haim

    2000-04-01

    A method for the measurement of oxygen saturation in the venous blood, SvO2, based on optical measurements of light absorption in the infrared region is presented. The method consists of applying relatively low external pressure of 25 mm Hg on the forearm, thereby increasing the venous blood volume in the tissue, and comparing the light absorption before and after the external pressure application. SvO2 has been determined from light absorption measurements in two wavelengths, before and after the pressure application, using a formula derived for two adjacent wavelengths. The method has been applied to the hands and fingers of 17 healthy male subjects, using wavelengths of 767 and 811 nm. SaO2, the oxygen saturation for arterial blood, was also obtained from photoplethysmographic measurements in these two wavelengths (pulse oximetry) using the same formula. The mean (+/- SD) value of SaO2 was 94.5%(+/- 3.0). The mean value of SvO2 was 86.2%(+/- 4.1) for the finger and 80.0%(+/- 8.2) for the hand. These SvO2 values are reasonable for the finger and the hand where arterio-venous anastomoses exist. The method enables the measurement of SvO2 in the limbs, a parameter which is related to tissue blood flow and oxygen consumption.

  9. Correlation of oxygenation and perfusion sensitive MRI with invasive micro probe measurements in healthy mice brain.

    PubMed

    Sedlacik, Jan; Reitz, Matthias; Bolar, Divya S; Adalsteinsson, Elfar; Schmidt, Nils O; Fiehler, Jens

    2015-03-01

    The non-invasive assessment of (patho-)physiological parameters such as, perfusion and oxygenation, is of great importance for the characterization of pathologies e.g., tumors, which may be helpful to better predict treatment response and potential outcome. To better understand the influence of physiological parameters on the investigated oxygenation and perfusion sensitive MRI methods, MRI measurements were correlated with subsequent invasive micro probe measurements during free breathing conditions of air, air+10% CO2 and 100% O2 in healthy mice brain. MRI parameters were the irreversible (R2), reversible (R2') and effective (R2*) transverse relaxation rates, venous blood oxygenation level assessed by quantitative blood oxygenation level dependent (qBOLD) method and cerebral blood flow (CBF) assessed by arterial spin labeling (ASL) using a 7 T small animal MRI scanner. One to two days after MRI, tissue perfusion and pO2 were measured by Laser-Doppler flowmetry and fluorescence quenching micro probes, respectively. The tissue pO2 values were converted to blood oxygen saturation by using the Hill equation. The animals were anesthetized by intra peritoneal injection of ketamine-xylazine-acepromazine (10-2-0.3 mg/ml · kg). Results for normal/hypercapnia/hyperoxia conditions were: R2[s(∧)-1] = 20.7/20.4/20.1, R2*[s(∧)-1] = 31.6/29.6/25.9, R2'[s-(∧)1] = 10.9/9.2/5.7, qBOLD venous blood oxygenation level = 0.43/0.51/0.56, CBF[ml · min(∧)-1 · 100 g(∧)-1] = 70.6/105.5/81.8, Laser-Doppler flowmetry[a.u.] = 89.2/120.2/90.6 and pO2[mmHg] = 6.3/32.3/46.7. All parameters were statistically significantly different with P < 0.001 between all breathing conditions. All MRI and the corresponding micro probe measurements were also statistically significantly (P ≤ 0.03) correlated with each other. However, converting the tissue pO2 to blood oxygen saturation = 0.02/0.34/0.63, showed only very limited agreement with the qBOLD venous blood oxygenation level. We found

  10. Monovar: single-nucleotide variant detection in single cells.

    PubMed

    Zafar, Hamim; Wang, Yong; Nakhleh, Luay; Navin, Nicholas; Chen, Ken

    2016-06-01

    Current variant callers are not suitable for single-cell DNA sequencing, as they do not account for allelic dropout, false-positive errors and coverage nonuniformity. We developed Monovar (https://bitbucket.org/hamimzafar/monovar), a statistical method for detecting and genotyping single-nucleotide variants in single-cell data. Monovar exhibited superior performance over standard algorithms on benchmarks and in identifying driver mutations and delineating clonal substructure in three different human tumor data sets. PMID:27088313

  11. Alveolar partial pressures of carbon dioxide and oxygen measured by a helium washout technique.

    PubMed Central

    Jordanoglou, J; Tatsis, G; Danos, J; Gougoulakis, S; Orfanidou, D; Gaga, M

    1990-01-01

    A non-invasive technique was developed for measuring alveolar carbon dioxide and oxygen tension during tidal breathing. This was achieved by solving the Bohr equations for mean alveolar carbon dioxide and oxygen tensions (PACO2, PAO2) from known values of the dead-space:tidal volume ratio measured by helium washout, and from the mixed expired partial pressure of carbon dioxide and oxygen. The derived values of wPACO2 and wPAO2 were compared with PaCO2 obtained from arterial gas analysis and PAO2 calculated from the ideal air equation. Four normal subjects and 58 patients were studied. Calculated and measured PCO2 values agreed closely with a difference in mean values (wPACO2 - PaCO2) of 0.01 kPa; the SD of the differences was 0.7 kPa. The difference in mean values between wPAO2 and PAO2 was 0.02 kPa; the SD of the differences was 0.93 kPa. The method is simple and not time consuming, and requires no special cooperation from the patients. It can be applied in the laboratory or at the bedside to any subject breathing tidally. Physiological deadspace:tidal volume ratio, PAO2 and PACO2, static lung volumes, respiratory exchange ratio, carbon dioxide production, oxygen uptake, tidal volume, and total ventilation can be measured with acceptable accuracy and reproducibility in one test. An arterial blood sample is needed initially to provide an independent measure of PaCO2 and for measurement of the alveolar-arterial PO2 difference. Subsequently, PaCO2 can be estimated from wPACO2 sufficiently well for clinical purposes and PaO2 or SaO2 can be monitored by non-invasive methods. Images PMID:2118690

  12. Atomic oxygen dosimetry measurements made on STS-46 by CONCAP 2

    NASA Technical Reports Server (NTRS)

    Gregory, J. C.; Miller, G. P.; Pettigrew, P. J.; Raikar, G. N.; Cross, Jon B.; Lan, E.; Renschler, C. L.; Sutherland, W. T.

    1995-01-01

    With increasing flight duration and the possibility of a permanent facility in space, long-term monitoring of material degradation due to atomic oxygen is increasing in importance. Reliance on models to determine the fluence of atomic oxygen is not only necessarily complex but also imprecise due to the strong dependence of oxygen concentration on day/night, latitude and solar activity. Mass-spectroscopy, the traditional method for determining the gas phase species densities at low pressure, is not only expensive but is limited in the area that it can monitor. Our group has developed a simple and inexpensive dosimeter to measure the atomic oxygen fluence via the change in resistance as the sensor element is gradually oxidized. The sensors consisted of thin-film circuit elements deposited on a suitable substrate. Four-point resistance measurements were used to monitor the change in resistance. Results obtained using silver and carbon dosimeters flown on STS-46 (CONCAP 2-01) will be discussed.

  13. Near-infrared spectroscopy measurement of blood oxygenation content and its application in sports practice

    NASA Astrophysics Data System (ADS)

    Xu, Guodong; Gong, Hui; Ge, Xinfa; Luo, Qingming

    2003-12-01

    To research the change characteristics of blood oxygenation content in skeletal muscle, the change regularity between blood oxygenation content and exercise intensity as well as HbO2 and blood lactate acid while taking incremental exercises, we took an in vivo, real-time and continuous measurement on the blood oxygenation content of eight sportsmen when they did incremental exercises of five degrees on a power bicycle using a portable tissue oximeter which is based on the principle of near-infrared spectroscopy(NIRS), simultaneously, we detected the blood lactate acid of subjects after each degree of incremental physical load instantly using a blood lactate analysis equipment. The results showed that the content of HbO2 descended regularly while that of Hb ascended; blood volume decreased; and the density of lactate increased as the intensity of exercises was heightened. The statistics analyses showed that the relationship between HbO2 and blood lactate is rather close (correlation coefficient r=-0.918). With this discovery, a theoretical basis in measuring the relative change of blood oxygenation content non-invasively was evidenced, and a novel technology for assessing the physical situation of sportsman, grasping sports density and evaluating the training effect could be imported.

  14. Inside Single Cells: Quantitative Analysis with Advanced Optics and Nanomaterials

    PubMed Central

    Cui, Yi; Irudayaraj, Joseph

    2014-01-01

    Single cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single cell activity. In order to obtain quantitative information (e.g. molecular quantity, kinetics and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single cell studies both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live cell analysis. Although a considerable proportion of single cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single cell analysis. PMID:25430077

  15. Biased Allelic Expression in Human Primary Fibroblast Single Cells

    PubMed Central

    Borel, Christelle; Ferreira, Pedro G.; Santoni, Federico; Delaneau, Olivier; Fort, Alexandre; Popadin, Konstantin Y.; Garieri, Marco; Falconnet, Emilie; Ribaux, Pascale; Guipponi, Michel; Padioleau, Ismael; Carninci, Piero; Dermitzakis, Emmanouil T.; Antonarakis, Stylianos E.

    2015-01-01

    The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability. PMID:25557783

  16. Microfluidic single-cell analysis of intracellular compounds

    PubMed Central

    Chao, Tzu-Chiao; Ros, Alexandra

    2008-01-01

    Biological analyses traditionally probe cell ensembles in the range of 103–106 cells, thereby completely averaging over relevant individual cell responses, such as differences in cell proliferation, responses to external stimuli or disease onset. In past years, this fact has been realized and increasing interest has evolved for single-cell analytical methods, which could give exciting new insights into genomics, proteomics, transcriptomics and systems biology. Microfluidic or lab-on-a-chip devices are the method of choice for single-cell analytical tools as they allow the integration of a variety of necessary process steps involved in single-cell analysis, such as selection, navigation, positioning or lysis of single cells as well as separation and detection of cellular analytes. Along with this advantageous integration, microfluidic devices confine single cells in compartments near their intrinsic volume, thus minimizing dilution effects and increasing detection sensitivity. This review overviews the developments and achievements of microfluidic single-cell analysis of intracellular compounds in the past few years, from proof-of-principle devices to applications demonstrating a high biological relevance. PMID:18682362

  17. Inside single cells: quantitative analysis with advanced optics and nanomaterials.

    PubMed

    Cui, Yi; Irudayaraj, Joseph

    2015-01-01

    Single-cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites, and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single-cell activity. To obtain quantitative information (e.g., molecular quantity, kinetics, and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single-cell studies, both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live-cell analysis. Although a considerable proportion of single-cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single-cell analysis. PMID:25430077

  18. Single cells from human primary colorectal tumors exhibit polyfunctional heterogeneity in secretions of ELR+ CXC chemokines

    PubMed Central

    Adalsteinsson, Viktor; Tahirova, Narmin; Tallapragada, Naren; Yao, Xiaosai; Campion, Liam; Angelini, Alessandro; Douce, Thomas B.; Huang, Cindy; Bowman, Brittany; Williamson, Christina; Kwon, Douglas S.; Wittrup, K. Dane; Love, J. Christopher

    2014-01-01

    Cancer is an inflammatory disease of tissue that is largely influenced by the interactions between multiple cell types, secreted factors, and signal transduction pathways. While single-cell sequencing continues to refine our understanding of the clonotypic heterogeneity within tumors, the complex interplay between genetic variations and non-genetic factors ultimately affects therapeutic outcome. Much has been learned through bulk studies of secreted factors in the tumor microenvironment, but the secretory behavior of single cells has been largely uncharacterized. Here we directly profiled the secretions of ELR+ CXC chemokines from thousands of single colorectal tumor and stromal cells, using an array of subnanoliter wells and a technique called microengraving to characterize both the rates of secretion of several factors at once and the numbers of cells secreting each chemokine. The ELR+ CXC chemokines are highly redundant, pro-angiogenic cytokines that signal via either or both of the CXCR1 and CXCR2 receptors, exerting profound impacts on tumor growth and progression. We find that human primary colorectal tumor and stromal cells exhibit polyfunctional heterogeneity in the combinations and magnitudes of secretions for these chemokines. In cell lines, we observe similar variance: phenotypes observed in bulk can be largely absent among the majority of single cells, and discordances exist between secretory states measured and gene expression for these chemokines among single cells. Together, these measures suggest secretory states among tumor cells are complex and can evolve dynamically. Most importantly, this study reveals new insight into the intratumoral phenotypic heterogeneity of human primary tumors. PMID:23995780

  19. Quantitative photoacoustic blood oxygenation measurement of whole porcine blood samples using a multi-wavelength semiconductor laser system

    NASA Astrophysics Data System (ADS)

    Friedrich, Claus-Stefan; Mienkina, Martin P.; Brenner, Carsten; Gerhardt, Nils C.; Jörger, Manfred; Strauß, Andreas; Beckmann, Martin F.; Schmitz, Georg; Hofmann, Martin R.

    2011-07-01

    We present a photoacoustic measurement system based on semiconductor lasers for blood oxygenation measurements. It permits to use four different optical wavelengths (650nm, 808nm, 850nm, 905nm) to generate photoacoustic signals. As the optical extinction coefficient of oxygenated hemoglobin and deoxygenated hemoglobin is different at specific wavelengths, a blood oxygenation measurement by a multi-wavelength photoacoustic laser system is feasible. Especially at 650nm, the clear difference between the extinction coefficients of the two hemoglobin derivates permits to determine the blood oxygenation in combination with other near infrared wavelengths. A linear model based on tabulated values of extinction coefficients for fully oxygenated and fully deoxygenated hemoglobin is presented. We used heparin stabilized whole porcine blood samples to model the optical behavior of human blood, as the optical absorption behavior of porcine hemoglobin does not differ significantly from human hemoglobin. To determine the real oxygen saturation values of the blood samples, we measured the partial oxygen pressure with an IRMA Trupoint Blood Analysis System. The oxygen saturation values were calculated from a dissociation curve for porcine blood. The results of the photoacoustic measurement are in qualitatively good agreement with the predicted linear model. Further, we analyze the abilities and the limitations of quantitative oxygenation measurements.

  20. Benchmark oxygen-oxygen pair-distribution function of ambient water from x-ray diffraction measurements with a wide Q-range

    SciTech Connect

    Skinner, Lawrie B.; Huang, Congcong; Schlesinger, Daniel; Pettersson, Lars G. M.; Nilsson, Anders; Benmore, Chris J.

    2013-02-21

    Four recent x-ray diffraction measurements of ambient liquid water are reviewed here. Each of these measurements represents a significant development of the x-ray diffraction technique applied to the study of liquid water. Sources of uncertainty from statistical noise, Q-range, Compton scattering, and self-scattering are discussed. The oxygen-hydrogen contribution to the measured x-ray scattering pattern was subtracted using literature data to yield an experimental determination, with error bars, of the oxygen-oxygen pair-distribution function, g{sub OO}(r), which essentially describes the distribution of molecular centers. The extended Q-range and low statistical noise of these measurements has significantly reduced truncation effects and related errors in the g{sub OO}(r) functions obtained. From these measurements and error analysis, the position and height of the nearest neighbor maximum in g{sub OO}(r) were found to be 2.80(1) A and 2.57(5) respectively. Numerical data for the coherent differential x-ray scattering cross-section I{sub X}(Q), the oxygen-oxygen structure factor S{sub OO}(Q), and the derived g{sub OO}(r) are provided as benchmarks for calibrating force-fields for water.

  1. Measurements and Analysis of Oxygen Bubble Distributions in LiCl-KCl Molten Salt

    SciTech Connect

    Ryan W. Bezzant; Supathorn Phongikaroon; Michael F. Simpson

    2013-03-01

    Transparent system experimental studies have been performed to provide measurement and analysis of oxygen bubble distributions and mass transfer coefficients at different sparging rates ranging from 0.05 to 0.20 L/min in LiCl-KCl molten salt at 500 degrees C using a high-speed digital camera and an oxygen sensor. The results reveal that bubble sizes and rise velocities increased with an increase in oxygen sparging rate. The bubbles observed were ellipsoidal in shape, and an equivalent diameter based on the ellipsoid volume was calculated. The average equivalent bubble diameters at 500 degrees C and these oxygen sparging rates range from 2.63 to 4.07 mm. Results show that the bubble equivalent diameters at each respective sparging rate are normally distributed. A Fanning friction factor correlation was produced to predict a bubble’s rise velocity based on its equivalent diameter. The oxygen mass transfer coefficients for four sparging rates were calculated using the oxygenation model. These calculated values were within the order of magnitude of 10-2 cm/sec and followed a decreasing trend corresponding to an increasing bubble size and sparging rate. The diffusivities were calculated based on two different types of mechanisms, one based on physics of the bubbles and the other on systematic properties. The results reveal that diffusivity values calculated from bubble physics are 1.65 to 8.40 x 10-5 cm2/sec, which are within the range suggested by literature for gases in liquids of a similar viscosity.

  2. Non-destructive measurement of carbonic anhydrase activity and the oxygen isotope composition of soil water

    NASA Astrophysics Data System (ADS)

    Jones, Sam; Sauze, Joana; Ogée, Jérôme; Wohl, Steven; Bosc, Alexandre; Wingate, Lisa

    2016-04-01

    oxygen isotope composition of ambient CO2. This non-destructive approach was tested through laboratory incubations of air-dried soils that were re-wetted with water of known isotopic composition. Performance was assessed by comparing estimates of the soil water oxygen isotope composition derived from open chamber flux measurements with those measured in the irrigation water and soil water extracted following incubations. The influence of soil pH and bovine carbonic anhydrase additions on these estimates was also investigated. Coherent values were found between the soil water composition estimates obtained from the dual steady state approach and those measured for irrigation waters. Estimates of carbonic anhydrase activity made using this approach also reflected well artificial increases to the concentration of carbonic anhydrase and indicated that this activity was sensitive to soil pH.

  3. Reduced-Gravity Measurements of the Effect of Oxygen on Properties of Zirconium

    NASA Technical Reports Server (NTRS)

    Zhao, J.; Lee, J.; Wunderlich, R.; Fecht, H.-J.; Schneider, S.; SanSoucie, M.; Rogers, J.; Hyers, R.

    2016-01-01

    The influence of oxygen on the thermophysical properties of zirconium is being investigated using MSL-EML (Material Science Laboratory - Electromagnetic Levitator) on ISS (International Space Station) in collaboration with NASA, ESA (European Space Agency), and DLR (German Aerospace Center). Zirconium samples with different oxygen concentrations will be put into multiple melt cycles, during which the density, viscosity, surface tension, heat capacity, and electric conductivity will be measured at various undercooled temperatures. The facility check-up of MSL-EML and the first set of melting experiments have been successfully performed in 2015. The first zirconium sample will be tested near the end of 2015. As part of ground support activities, the thermophysical properties of zirconium and ZrO were measured using a ground-based electrostatic levitator located at the NASA Marshall Space Flight Center. The influence of oxygen on the measured surface tension was evaluated. The results of this research will serve as reference data for those measured in ISS.

  4. Single Nanowire Probe for Single Cell Endoscopy and Sensing

    NASA Astrophysics Data System (ADS)

    Yan, Ruoxue

    The ability to manipulate light in subwavelength photonic and plasmonic structures has shown great potentials in revolutionizing how information is generated, transformed and processed. Chemically synthesized nanowires, in particular, offers a unique toolbox not only for highly compact and integrated photonic modules and devices, including coherent and incoherent light sources, waveguides, photodetectors and photovoltaics, but also for new types of nanoscopic bio-probes for spot cargo delivery and in-situ single cell endoscopy and sensing. Such nanowire probes would enable us to carry out intracellular imaging and probing with high spatial resolution, monitor in-vivo biological processes within single living cells and greatly improve our fundamental understanding of cell functions, intracellular physiological processes, and cellular signal pathways. My work is aimed at developing a material and instrumental platform for such single nanowire probe. Successful optical integration of Ag nanowire plasmonic waveguides, which offers deep subwavelength mode confinement, and conventional photonic waveguides was demonstrated on a single nanowire level. The highest plasmonic-photonic coupling efficiency coupling was found at small coupling angles and low input frequencies. The frequency dependent propagation loss was observed in Ag nanowire and was confirmed by quantitative measurement and in agreement with theoretical expectations. Rational integration of dielectric and Ag nanowire waveguide components into hybrid optical-plasmonic routing devices has been demonstrated. This capability is essential for incorporating sub-100nm Ag nanowire waveguides into optical fiber based nanoprobes for single cell endoscopy. The nanoprobe system based on single nanowire waveguides was demonstrated by optically coupling semiconductor or metal nanowire with an optical fiber with tapered tip. This nanoprobe design requires minimal instrumentation which makes it cost efficient and readily

  5. Atmospheric Airborne Pressure Measurements Using the Oxygen A Band for the ASCENDS Mission

    NASA Astrophysics Data System (ADS)

    Rodriguez, M.; Riris, H.; Abshire, J. B.; Allan, G. R.; Stephen, M.; Hasselbrack, W.; Mao, J.

    2012-12-01

    We report on airborne atmospheric pressure measurements using fiber-based laser technology and the oxygen A-band at 765 nm. Remote atmospheric temperature and pressure measurements are needed for NASA's Active Sensing of CO2 Emissions Over Nights, Days, and Seasons (ASCENDS) mission. ASCENDS will measure atmospheric CO2 dry mixing ratios on a global scale. Remote atmospheric pressure measurements are necessary to normalize ASCENDS CO2 measurements. Our work, funded by the ESTO IIP program, uses erbium doped fiber optic amplifiers and non-linear optics technology to tune laser radiation over the Oxygen A-band between 764.5 nm and 765 nm. Surface reflections are fiber-coupled from a receiver telescope to photon counting detectors. Our pulsed, time gated approach resolves ground reflections from cloud returns. This system successfully recorded O2 absorption spectra during two airborne campaigns aboard a NASA DC-8. Airborne data has been analyzed and fitted to HITRAN reference spectra based upon aircraft meteorological data. Our algorithm linearly scales the HITRAN reference until measurement errors are minimized. Atmospheric pressure changes are estimated by comparing the differential optical depth of the optimum scaled HITRAN spectra to the differential optical depth of the nominal HITRAN spectra. On flights over gradually sloping terrain, these results compare favorably with ground-based observations and predictions from computer models. Measurement uncertainty is commensurate with photon counting noise. We plan to reduce measurement uncertainty in future campaigns by improving transmitter pulse energy and increasing wavelength sweep frequency.

  6. Singlet-oxygen generation at gas-liquid interfaces: A significant artifact in the measurement of singlet-oxygen yields from ozone-biomolecule reactions

    SciTech Connect

    Kanofsky, J.R.; Sima, P.D. )

    1993-09-01

    Several ozone-biomolecule reactions have previously been shown to generate singlet oxygen in high yields. For some of these ozone-biomolecule reactions, we now show that the apparent singlet-oxygen yields determined from measurements of 1270 nm chemiluminescence were artifactually elevated by production of gas-phase singlet oxygen. The gas-phase singlet oxygen results from the reaction of gas-phase ozone with biomolecules near the surface of the solution. Through the use of a flow system that excludes air from the reaction chamber, accurate singlet-oxygen yields can be obtained. The revised singlet-oxygen yields (mol 1O2 per mol O3) for the reactions of ozone with cysteine, reduced glutathione, NADH, NADPH, human albumin, methionine, uric acid and oxidized glutathione are 0.23 +/- 0.02, 0.26 +/- 0.2, 0.48 +/- 0.04, 0.41 +/- 0.01, 0.53 +/- 0.06, 1.11 +/- 0.04, 0.73 +/- 0.05 and 0.75 +/- 0.01, respectively. These revised singlet-oxygen yields are still substantial.

  7. Optical triple sensor for measuring pH, oxygen, and carbon dioxide in bioreactors

    NASA Astrophysics Data System (ADS)

    Weigl, Bernhard H.; Holobar, Andrej; Trettnak, Wolfgang; Klimant, Ingo; Kraus, H.; O'Leary, Paul; Wolfbeis, Otto S.

    1993-04-01

    A triple sensor unit consisting of opto-chemical sensors for measurement of pH, oxygen, and carbon dioxide is presented. The pH sensor and the CO2 sensor are based on the color change of a pH-sensitive dye immobilized on a polymeric support. The resulting changes in absorption are monitored through optical fibers at one or two analytical wavelengths. The oxygen sensor is based on the quenching of the fluorescence of a metalorganic dye. The operation principle and the performance of all three sensors are described thoroughly with respect to their application in bioreactors. All three sensors are fully LED compatible. The chemical and mechanical stability, especially against common sterilization methods, are described in some detail. A calibration and measurement software comprising fit routines for the sensors and a mathematical treatment of the results are presented as well.

  8. Instrumentation for optical measurement of dissolved oxygen based on solid state technology

    NASA Astrophysics Data System (ADS)

    Gruber, Wolfgang R.; Klimant, Ingo; Wolfbeis, Otto S.

    1993-05-01

    A number of measurement schemes for the determination of dissolved or gaseous oxygen have been reported, most of them based on fluorescence quenching methods. They have the disadvantage of requiring large and heavy instrumentation and, therefore, are not suitable for micro-integrated technologies. As a result, the applicability is greatly limited. We introduce a system based on semiconductor devices (LEDs, photodiodes, low cost analogue and digital components) which is well suited for hybrid solutions, and represents a realistic alternative to existing micro integrated electrochemical probes. New LED-compatible sensor membranes were developed and characterized. The influence of straylight on the overall transfer function of the sensor system was investigated and possibilities for reduction or even elimination of this influence are presented. The overall performance of the instrument in terms of sensitivity, detection limits, long-term stability, and reproducibility is presented. The system was applied to the measurement of dissolved oxygen in drinking water and sea water.

  9. Direct Measurements of Oxygen Gradients in Spheroid Culture System Using Electron Parametric Resonance Oximetry.

    PubMed

    Langan, Laura M; Dodd, Nicholas J F; Owen, Stewart F; Purcell, Wendy M; Jackson, Simon K; Jha, Awadhesh N

    2016-01-01

    Advanced in vitro culture from tissues of different origin includes three-dimensional (3D) organoid micro structures that may mimic conditions in vivo. One example of simple 3D culture is spheroids; ball shaped structures typically used as liver and tumour models. Oxygen is critically important in physiological processes, but is difficult to quantify in 3D culture: and the question arises, how small does a spheroid have to be to have minimal micro-environment formation? This question is of particular importance in the growing field of 3D based models for toxicological assessment. Here, we describe a simple non-invasive approach modified for the quantitative measurement and subsequent evaluation of oxygen gradients in spheroids developed from a non-malignant fish cell line (i.e. RTG-2 cells) using Electron Paramagnetic Resonance (EPR) oximetry. Sonication of the paramagnetic probe Lithium phthalocyanine (LiPc) allows for incorporation of probe particulates into spheroid during its formation. Spectra signal strength after incorporation of probe into spheroid indicated that a volume of 20 μl of probe (stock solution: 0.10 mg/mL) is sufficient to provide a strong spectra across a range of spheroid sizes. The addition of non-toxic probes (that do not produce or consume oxygen) report on oxygen diffusion throughout the spheroid as a function of size. We provide evidence supporting the use of this model over a range of initial cell seeding densities and spheroid sizes with the production of oxygen distribution as a function of these parameters. In our spheroid model, lower cell seeding densities (∼2,500 cells/spheroid) and absolute size (118±32 μm) allow control of factors such as pre-existing stresses (e.g. ∼ 2% normoxic/hypoxic interface) for more accurate measurement of treatment response. The applied methodology provides an elegant, widely applicable approach to directly characterize spheroid (and other organoid) cultures in biomedical and toxicological

  10. Direct Measurements of Oxygen Gradients in Spheroid Culture System Using Electron Parametric Resonance Oximetry

    PubMed Central

    Langan, Laura M.; Dodd, Nicholas J. F.; Owen, Stewart F.; Purcell, Wendy M.; Jackson, Simon K.; Jha, Awadhesh N.

    2016-01-01

    Advanced in vitro culture from tissues of different origin includes three-dimensional (3D) organoid micro structures that may mimic conditions in vivo. One example of simple 3D culture is spheroids; ball shaped structures typically used as liver and tumour models. Oxygen is critically important in physiological processes, but is difficult to quantify in 3D culture: and the question arises, how small does a spheroid have to be to have minimal micro-environment formation? This question is of particular importance in the growing field of 3D based models for toxicological assessment. Here, we describe a simple non-invasive approach modified for the quantitative measurement and subsequent evaluation of oxygen gradients in spheroids developed from a non-malignant fish cell line (i.e. RTG-2 cells) using Electron Paramagnetic Resonance (EPR) oximetry. Sonication of the paramagnetic probe Lithium phthalocyanine (LiPc) allows for incorporation of probe particulates into spheroid during its formation. Spectra signal strength after incorporation of probe into spheroid indicated that a volume of 20 μl of probe (stock solution: 0.10 mg/mL) is sufficient to provide a strong spectra across a range of spheroid sizes. The addition of non-toxic probes (that do not produce or consume oxygen) report on oxygen diffusion throughout the spheroid as a function of size. We provide evidence supporting the use of this model over a range of initial cell seeding densities and spheroid sizes with the production of oxygen distribution as a function of these parameters. In our spheroid model, lower cell seeding densities (∼2,500 cells/spheroid) and absolute size (118±32 μm) allow control of factors such as pre-existing stresses (e.g. ∼ 2% normoxic/hypoxic interface) for more accurate measurement of treatment response. The applied methodology provides an elegant, widely applicable approach to directly characterize spheroid (and other organoid) cultures in biomedical and toxicological

  11. Single-cell PCR of genomic DNA enabled by automated single-cell printing for cell isolation.

    PubMed

    Stumpf, F; Schoendube, J; Gross, A; Rath, C; Niekrawietz, S; Koltay, P; Roth, G

    2015-07-15

    Single-cell analysis has developed into a key topic in cell biology with future applications in personalized medicine, tumor identification as well as tumor discovery (Editorial, 2013). Here we employ inkjet-like printing to isolate individual living single human B cells (Raji cell line) and load them directly into standard PCR tubes. Single cells are optically detected in the nozzle of the microfluidic piezoelectric dispenser chip to ensure printing of droplets with single cells only. The printing process has been characterized by using microbeads (10µm diameter) resulting in a single bead delivery in 27 out of 28 cases and relative positional precision of ±350µm at a printing distance of 6mm between nozzle and tube lid. Process-integrated optical imaging enabled to identify the printing failure as void droplet and to exclude it from downstream processing. PCR of truly single-cell DNA was performed without pre-amplification directly from single Raji cells with 33% success rate (N=197) and Cq values of 36.3±2.5. Additionally single cell whole genome amplification (WGA) was employed to pre-amplify the single-cell DNA by a factor of >1000. This facilitated subsequent PCR for the same gene yielding a success rate of 64% (N=33) which will allow more sophisticated downstream analysis like sequencing, electrophoresis or multiplexing. PMID:25771302

  12. Investigation of oesophageal photoplethysmographic signals and blood oxygen saturation measurements in cardiothoracic surgery patients.

    PubMed

    Kyriacou, P A; Powell, S; Langford, R M; Jones, D P

    2002-08-01

    Pulse oximeter probes attached to the finger may fail to estimate blood oxygen saturation (SpO2) in patients with compromised peripheral perfusion (e.g. hypothermic cardiopulmonary bypass surgery). The measurement of SpO2 from a central organ such as the oesophagus is suggested as an alternative to overcome this problem. A reflectance oesophageal pulse oximeter probe and a processing system implemented in LabVIEW were developed. The system was evaluated in clinical measurements on 50 cardiothoracic surgery patients. Oesophageal photoplethysmographic (PPG) signals with large amplitudes and high signal-to-noise ratios were measured from various depths within the oesophagus from all the cardiothoracic patients. The oesophageal PPG amplitudes from these patients were in good agreement with previous oesophageal PPG amplitude measurements from healthy anaesthetized patients. The oesophageal pulse oximeter SpO2 results agreed well with the estimated arterial oxygen saturation (SaO2) values inferred from the oxygen tension obtained by blood gas analysis. The mean (+/- SD) of the differences between the oesophageal pulse oximeter SpO2 readings and those from blood gas analysis was 0.02 +/- 0.88%. Also, the oesophageal pulse oximeter was found to be reliable and accurate in five cases of poor peripheral perfusion when a commercial finger pulse oximeter probe failed to estimate oxygen saturation values for at least 10 min. These results suggest that the arterial blood circulation to the oesophagus is less subject to vasoconstriction and decreased PPG amplitudes than are the peripheral sites used for pulse oximetry such as the finger. It is concluded that oesophageal SPO2 monitoring may be of clinical value. PMID:12214761

  13. Local Measurement of Flap Oxygen Saturation: An Application of Visible Light Spectroscopy.

    PubMed

    Nasseri, Nassim; Kleiser, Stefan; Reidt, Sascha; Wolf, Martin

    2016-01-01

    The aim was to develop and test a new device (OxyVLS) to measure tissue oxygen saturation by visible light spectroscopy independently of the optical pathlength and scattering. Its local applicability provides the possibility of real time application in flap reconstruction surgery. We tested OxyVLS in a liquid phantom with optical properties similar to human tissue. Our results were in good agreement with a conventional near infrared spectroscopy device. PMID:26782237

  14. Validation of a New NIRS Method for Measuring Muscle Oxygenation During Rhythmic Handgrip Exercise

    NASA Technical Reports Server (NTRS)

    Hagan, R. Donald; Soller, Babs R.; Soyemi, Olusola; Landry, Michelle; Shear, Michael; Wu, Jacqueline

    2006-01-01

    Near infrared spectroscopy (NIRS) is commonly used to measure muscle oxygenation during exercise and recovery. Current NIRS algorithms do not account for variation in water content and optical pathlength during exercise. The current effort attempts to validate a newly developed NIRS algorithm during rhythmic handgrip exercise and recovery. Six female subjects, aver age 28 +/- 6 yrs, participated in the study. A venous catheter was placed in the retrograde direction in the antecubital space. A NIRS sensor with 30 mm source-detector separation was placed on the flexor digitorum profundus. Subjects performed two 5-min bouts of rhythmic handgrip exercise (2 s contraction/1 s relaxation) at 15% and 30% of maximal voluntary contraction. Venous blood was sampled before each bout, during the last minute of exercise, and after 5 minutes of recovery. Venous oxygen saturation (SvO2) was measured with a I-stat CG-4+ cartridge. Spectra were collected between 700-900 nm. A modified Beer's Law formula was used to calculate the absolute concentration of oxyhemoglobin (HbO2), deoxyhemoglobin (Hb) and water, as well as effective pathlength for each spectrum. Muscle oxygen saturation (SmO2) was calculated from the HbO2 and Hb results. The correlation between SvO2 and SmO2 was determined. Optical pathlength and water varied significantly during each exercise bout, with pathlength increasing approximately 20% and water increasing about 2%. R2 between blood and muscle SO2 was found to be 0.74, the figure shows the relationship over SvO2 values between 22% and 82%. The NIRS measurement was, on average, 6% lower than the blood measurement. It was concluded that pathlength changes during exercise because muscle contraction causes variation in optical scattering. Water concentration also changes, but only slightly. A new NIRS algorithm which accounts for exercise-induced variation in water and pathlength provided an accurate assessment of muscle oxygen saturation before, during and after

  15. Localized, macromolecular transport for thin, adherent, single cells via an automated, single cell electroporation biomanipulator.

    PubMed

    Sakaki, Kelly; Esmaeilsabzali, Hadi; Massah, Shabnam; Prefontaine, Gratien G; Dechev, Nikolai; Burke, Robert D; Park, Edward J

    2013-11-01

    Single cell electroporation (SCE), via microcapillary, is an effective method for molecular, transmembrane transport used to gain insight on cell processes with minimal preparation. Although possessing great potential, SCE is difficult to execute and the technology spans broad fields within cell biology and engineering. The technical complexities, the focus and expertise demanded during manual operation, and the lack of an automated SCE platform limit the widespread use of this technique, thus the potential of SCE has not been realized. In this study, an automated biomanipulator for SCE is presented. Our system is capable of delivering molecules into the cytoplasm of extremely thin cellular features of adherent cells. The intent of the system is to abstract the technical challenges and exploit the accuracy and repeatability of automated instrumentation, leaving only the focus of the experimental design to the operator. Each sequence of SCE including cell and SCE site localization, tip-membrane contact detection, and SCE has been automated. Positions of low-contrast cells are localized and "SCE sites" for microcapillary tip placement are determined using machine vision. In addition, new milestones within automated cell manipulation have been achieved. The system described herein has the capability of automated SCE of "thin" cell features less than 10 μm in thickness. Finally, SCE events are anticipated using visual feedback, while monitoring fluorescing dye entering the cytoplasm of a cell. The execution is demonstrated by inserting a combination of a fluorescing dye and a reporter gene into NIH/3T3 fibroblast cells. PMID:23771309

  16. Single Cell Traction Microscopy within 3D Collagen Matrices

    NASA Astrophysics Data System (ADS)

    Wu, Mingming

    2014-03-01

    Mechanical interaction between the cell and its extracellular matrix (ECM) regulates cellular behaviors, including proliferation, differentiation, adhesion and migration. Cells require the three dimensional (3D) architectural support of the ECM to perform physiologically realistic functions. However, our current understanding of cell-ECM and cell-cell mechanical interactions is largely derived from 2D traction force microscopy, in which cells are cultured on a flat substrate. It is now clear that what we learn about cellular behavior on a 2D substrate does not always apply to cells embedded within a 3D biomatrix. 3D traction microscopy is emerging for mapping traction fields of single cells embedded in 3D gel, but current methods cannot account for the fibrous and nonlinear properties of collagen gel. In this talk, I will present a forward computation algorithm that we have developed for 3D cell traction measurements within collagen gels. The application of this technology to understanding cancer migration and invasion will be discussed. This work is supported by the National Center for Research Resources (5R21RR025801-03, NIH) and the National Institute of General Medical Sciences (8 R21 GM103388-03,NIH), and the Cornell Center on the Microenvironment & Metastasis.

  17. Single-cell dynamics reveals sustained growth during diauxic shifts.

    PubMed

    Boulineau, Sarah; Tostevin, Filipe; Kiviet, Daniel J; ten Wolde, Pieter Rein; Nghe, Philippe; Tans, Sander J

    2013-01-01

    Stochasticity in gene regulation has been characterized extensively, but how it affects cellular growth and fitness is less clear. We study the growth of E. coli cells as they shift from glucose to lactose metabolism, which is characterized by an obligatory growth arrest in bulk experiments that is termed the lag phase. Here, we follow the growth dynamics of individual cells at minute-resolution using a single-cell assay in a microfluidic device during this shift, while also monitoring lac expression. Mirroring the bulk results, the majority of cells displays a growth arrest upon glucose exhaustion, and resume when triggered by stochastic lac expression events. However, a significant fraction of cells maintains a high rate of elongation and displays no detectable growth lag during the shift. This ability to suppress the growth lag should provide important selective advantages when nutrients are scarce. Trajectories of individual cells display a highly non-linear relation between lac expression and growth, with only a fraction of fully induced levels being sufficient for achieving near maximal growth. A stochastic molecular model together with measured dependencies between nutrient concentration, lac expression level, and growth accurately reproduces the observed switching distributions. The results show that a growth arrest is not obligatory in the classic diauxic shift, and underscore that regulatory stochasticity ought to be considered in terms of its impact on growth and survival. PMID:23637881

  18. Mass spectrometry imaging and profiling of single cells

    PubMed Central

    Lanni, Eric J.; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

    2012-01-01

    Mass spectrometry imaging and profiling of individual cells and subcellular structures provide unique analytical capabilities for biological and biomedical research, including determination of the biochemical heterogeneity of cellular populations and intracellular localization of pharmaceuticals. Two mass spectrometry technologies—secondary ion mass spectrometry (SIMS) and matrix assisted laser desorption ionization mass spectrometry (MALDI MS)—are most often used in micro-bioanalytical investigations. Recent advances in ion probe technologies have increased the dynamic range and sensitivity of analyte detection by SIMS, allowing two- and three-dimensional localization of analytes in a variety of cells. SIMS operating in the mass spectrometry imaging (MSI) mode can routinely reach spatial resolutions at the submicron level; therefore, it is frequently used in studies of the chemical composition of subcellular structures. MALDI MS offers a large mass range and high sensitivity of analyte detection. It has been successfully applied in a variety of single-cell and organelle profiling studies. Innovative instrumentation such as scanning microprobe MALDI and mass microscope spectrometers enable new subcellular MSI measurements. Other approaches for MS-based chemical imaging and profiling include those based on near-field laser ablation and inductively-coupled plasma MS analysis, which offer complementary capabilities for subcellular chemical imaging and profiling. PMID:22498881

  19. Mechanics of Single Cells: Rheology, Time Dependence, and Fluctuations

    PubMed Central

    Massiera, Gladys; Van Citters, Kathleen M.; Biancaniello, Paul L.; Crocker, John C.

    2007-01-01

    The results of mechanical measurements on single cultured epithelial cells using both magnetic twisting cytometry (MTC) and laser tracking microrheology (LTM) are described. Our unique approach uses laser deflection for high-performance tracking of cell-adhered magnetic beads either in response to an oscillatory magnetic torque (MTC) or due to random Brownian or ATP-dependent forces (LTM). This approach is well suited for accurately determining the rheology of single cells, the study of temporal and cell-to-cell variations in the MTC signal amplitude, and assessing the statistical character of the tracers' random motion in detail. The temporal variation of the MTC rocking amplitude is surprisingly large and manifests as a frequency-independent multiplicative factor having a 1/f spectrum in living cells, which disappears upon ATP depletion. In the epithelial cells we study, random bead position fluctuations are Gaussian to the limits of detection both in the Brownian and ATP-dependent cases, unlike earlier studies on other cell types. PMID:17693461

  20. Reconstructing dynamic molecular states from single-cell time series.

    PubMed

    Huang, Lirong; Pauleve, Loic; Zechner, Christoph; Unger, Michael; Hansen, Anders S; Koeppl, Heinz

    2016-09-01

    The notion of state for a system is prevalent in the quantitative sciences and refers to the minimal system summary sufficient to describe the time evolution of the system in a self-consistent manner. This is a prerequisite for a principled understanding of the inner workings of a system. Owing to the complexity of intracellular processes, experimental techniques that can retrieve a sufficient summary are beyond our reach. For the case of stochastic biomolecular reaction networks, we show how to convert the partial state information accessible by experimental techniques into a full system state using mathematical analysis together with a computational model. This is intimately related to the notion of conditional Markov processes and we introduce the posterior master equation and derive novel approximations to the corresponding infinite-dimensional posterior moment dynamics. We exemplify this state reconstruction approach using both in silico data and single-cell data from two gene expression systems in Saccharomyces cerevisiae, where we reconstruct the dynamic promoter and mRNA states from noisy protein abundance measurements. PMID:27605167

  1. Probing single-cell mechanics with picosecond ultrasonics.

    PubMed

    Dehoux, Thomas; Abi Ghanem, Maroun; Zouani, Omar F; Ducousso, Mathieu; Chigarev, Nikolay; Rossignol, Clément; Tsapis, Nicolas; Durrieu, Marie-Christine; Audoin, Bertrand

    2015-02-01

    The mechanical properties of cells play a key role in several fundamental biological processes, such as migration, proliferation, differentiation and tissue morphogenesis. The complexity of the inner cell composition and the intricate meshwork formed by transmembrane cell-substrate interactions demands a non-invasive technique to probe cell mechanics and cell adhesion at a subcell scale. In this paper we review the use of laser-generated GHz acoustic waves--a technique called picosecond ultrasonics (PU)--to probe the mechanical properties of single cells. We first describe applications to vegetal cells and biomimetic systems. We show how these systems can be used as simple models to understand more complex animal cells. We then present an opto-acoustic bio-transducer designed for in vivo measurements in physiological conditions. We illustrate the use of this transducer through the simultaneous probing of the density and compressibility of Allium cepa cells. Finally, we demonstrate that this technique can quantify animal-cell adhesion on metallic surfaces by analyzing the acoustic pulses reflected off the cell-metal interface. This innovative approach allows investigating quantitatively cell mechanics without fluorescent labels or mechanical contact to the cell. PMID:25172112

  2. Single cell electric impedance topography: mapping membrane capacitance.

    PubMed

    Dharia, Sameera; Ayliffe, Harold E; Rabbitt, Richard D

    2009-12-01

    Single-cell electric impedance topography (sceTopo), a technique introduced here, maps the spatial distribution of capacitance (i.e. displacement current) associated with the membranes of isolated, living cells. Cells were positioned in the center of a circular recording chamber surrounded by eight electrodes. Electrodes were evenly distributed on the periphery of the recording chamber. Electric impedance measured between adjacent electrode pairs (10 kHz-5 MHz) was used to construct topographical maps of the spatial distribution of membrane capacitance. Xenopus Oocytes were used as a model cell to develop sceTopo because these cells consist of two visually distinguishable hemispheres, each with distinct membrane composition and structure. Results showed significant differences in the imaginary component of the impedance between the two oocyte hemispheres. In addition, the same circumferential array was used to map the size of the extracellular electrical shunt path around the cell, providing a means to estimate the location and shape of the cell in the recording chamber. PMID:19904403

  3. Thermal expansion measurement of (U,Pu)O2-x in oxygen partial pressure-controlled atmosphere

    NASA Astrophysics Data System (ADS)

    Kato, Masato; Ikusawa, Yoshihisa; Sunaoshi, Takeo; Nelson, Andrew T.; McClellan, Kenneth J.

    2016-02-01

    Thermal expansion of U0.7Pu0.3O2-x (x = 0, 0.01, 0.02, 0.03) and U0.52Pu0.48O2.00 was investigated by a unique dilatometry which measured in an oxygen partial pressure-controlled atmosphere. The oxygen partial pressure was controlled to hold a constant oxygen-to-metal ratio in the (U,Pu)O2-x during the measurement. Thermal expansion slightly increased with the decrease in oxygen-to-metal ratio. We proposed a relationship to describe thermal expansion as a function of temperature, O/M and Pu content.

  4. Bioinformatics approaches to single-cell analysis in developmental biology.

    PubMed

    Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

    2016-03-01

    Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. PMID:26358759

  5. Raman-activated cell sorting based on dielectrophoretic single-cell trap and release.

    PubMed

    Zhang, Peiran; Ren, Lihui; Zhang, Xu; Shan, Yufei; Wang, Yun; Ji, Yuetong; Yin, Huabing; Huang, Wei E; Xu, Jian; Ma, Bo

    2015-02-17

    Raman-activated cell sorting (RACS) is a promising single-cell technology that holds several significant advantages, as RACS is label-free, information-rich, and potentially in situ. To date, the ability of the technique to identify single cells in a high-speed flow has been limited by inherent weakness of the spontaneous Raman signal. Here we present an alternative pause-and-sort RACS microfluidic system that combines positive dielectrophoresis (pDEP) for single-cell trap and release with a solenoid-valve-suction-based switch for cell separation. This has allowed the integration of trapping, Raman identification, and automatic separation of individual cells in a high-speed flow. By exerting a periodical pDEP field, single cells were trapped, ordered, and positioned individually to the detection point for Raman measurement. As a proof-of-concept demonstration, a mixture of two cell strains containing carotenoid-producing yeast (9%) and non-carotenoid-producing Saccharomyces cerevisiae (91%) was sorted, which enriched the former to 73% on average and showed a fast Raman-activated cell sorting at the subsecond level. PMID:25607599

  6. SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

    PubMed Central

    Guo, Minzhe; Wang, Hui; Potter, S. Steven; Whitsett, Jeffrey A.; Xu, Yan

    2015-01-01

    A major challenge in developmental biology is to understand the genetic and cellular processes/programs driving organ formation and differentiation of the diverse cell types that comprise the embryo. While recent studies using single cell transcriptome analysis illustrate the power to measure and understand cellular heterogeneity in complex biological systems, processing large amounts of RNA-seq data from heterogeneous cell populations creates the need for readily accessible tools for the analysis of single-cell RNA-seq (scRNA-seq) profiles. The present study presents a generally applicable analytic pipeline (SINCERA: a computational pipeline for SINgle CEll RNA-seq profiling Analysis) for processing scRNA-seq data from a whole organ or sorted cells. The pipeline supports the analysis for: 1) the distinction and identification of major cell types; 2) the identification of cell type specific gene signatures; and 3) the determination of driving forces of given cell types. We applied this pipeline to the RNA-seq analysis of single cells isolated from embryonic mouse lung at E16.5. Through the pipeline analysis, we distinguished major cell types of fetal mouse lung, including epithelial, endothelial, smooth muscle, pericyte, and fibroblast-like cell types, and identified cell type specific gene signatures, bioprocesses, and key regulators. SINCERA is implemented in R, licensed under the GNU General Public License v3, and freely available from CCHMC PBGE website, https://research.cchmc.org/pbge/sincera.html. PMID:26600239

  7. RECENT ADVANCES IN HIGH TEMPERATURE ELECTROLYSIS AT IDAHO NATIONAL LABORATORY: SINGLE CELL TESTS

    SciTech Connect

    X. Zhang; J. E. O'Brien; R. C. O'Brien

    2012-07-01

    An experimental investigation on the performance and durability of single solid oxide electrolysis cells (SOECs) is under way at the Idaho National Laboratory. In order to understand and mitigate the degradation issues in high temperature electrolysis, single SOECs with different configurations from several manufacturers have been evaluated for initial performance and long-term durability. A new test apparatus has been developed for single cell and small stack tests from different vendors. Single cells from Ceramatec Inc. show improved durability compared to our previous stack tests. Single cells from Materials and Systems Research Inc. (MSRI) demonstrate low degradation both in fuel cell and electrolysis modes. Single cells from Saint Gobain Advanced Materials (St. Gobain) show stable performance in fuel cell mode, but rapid degradation in the electrolysis mode. Electrolyte-electrode delamination is found to have significant impact on degradation in some cases. Enhanced bonding between electrolyte and electrode and modification of the microstructure help to mitigate degradation. Polarization scans and AC impedance measurements are performed during the tests to characterize the cell performance and degradation.

  8. Reproducibility of cerebral tissue oxygen saturation measurements by near-infrared spectroscopy in newborn infants

    NASA Astrophysics Data System (ADS)

    Jenny, Carmen; Biallas, Martin; Trajkovic, Ivo; Fauchère, Jean-Claude; Bucher, Hans Ulrich; Wolf, Martin

    2011-09-01

    Early detection of cerebral hypoxemia is an important aim in neonatology. A relevant parameter to assess brain oxygenation may be the cerebral tissue oxygen saturation (StO2) measured by near-infrared spectroscopy (NIRS). So far the reproducibility of StO2 measurements was too low for clinical application, probably due to inhomogeneities. The aim of this study was to test a novel sensor geometry which reduces the influence of inhomogeneities. Thirty clinically stable newborn infants, with a gestational age of median 33.9 (range 26.9 to 41.9) weeks, birth weight of 2220 (820 to 4230) g, postnatal age of 5 (1 to 71) days were studied. At least four StO2 measurements of 1 min duration were carried out using NIRS on the lateral head. The sensor was repositioned between measurements. Reproducibility was calculated by a linear mixed effects model. The mean StO2 was 79.99 +/- 4.47% with a reproducibility of 2.76% and a between-infant variability of 4.20%. Thus, the error of measurement only accounts for 30.1% of the variability. The novel sensor geometry leads to considerably more precise measurements compared to previous studies with, e.g., ~5% reproducibility for the NIRO 300. The novel StO2 values hence have a higher clinical relevance.

  9. Direct measurement of oxygen consumption rates from attached and unattached cells in a reversibly sealed, diffusionally isolated sample chamber

    PubMed Central

    Strovas, Timothy J.; McQuaide, Sarah C.; Anderson, Judy B.; Nandakumar, Vivek; Kalyuzhnaya, Marina G.; Burgess, Lloyd W.; Holl, Mark R.; Meldrum, Deirdre R.; Lidstrom, Mary E.

    2011-01-01

    Oxygen consumption is a fundamental component of metabolic networks, mitochondrial function, and global carbon cycling. To date there is no method available that allows for replicate measurements on attached and unattached biological samples without compensation for extraneous oxygen leaking into the system. Here we present the Respiratory Detection System, which is compatible with virtually any biological sample. The RDS can be used to measure oxygen uptake in microliter-scale volumes with a reversibly sealed sample chamber, which contains a porphyrin-based oxygen sensor. With the RDS, one can maintain a diffusional seal for up to three hours, allowing for the direct measurement of respiratory function of samples with fast or slow metabolic rates. The ability to easily measure oxygen uptake in small volumes with small populations or dilute samples has implications in cell biology, environmental biology, and clinical diagnostics. PMID:21546993

  10. Atmospheric Airborne Pressure Measurements Using the Oxygen A Band for the ASCENDS Mission

    NASA Technical Reports Server (NTRS)

    Riris, Haris; Rodriguez, Mike; Stephen, Mark; Hasselbrack, William; Allan, Graham; Mao, Jianping; Kawa, Stephen R.; Weaver, Clark J.

    2010-01-01

    We report on airborne atmospheric pressure measurements using new fiber-based laser technology and the oxygen A-band at 765 nm. Remote measurements of atmospheric temperature and pressure are required for a number of NASA Earth science missions and specifically for the Active Sensing of CO2 Emissions Over Nights, Days, and Seasons (ASCENDS) mission. Accurate measurements of tropospheric CO2 on a global scale are very important in order to better understand its sources and sinks and to improve predictions on any future climate change. The ultimate goal of a CO2 remote sensing mission, such as ASCENDS, is to derive the CO2 concentration in the atmosphere in terms of mole fraction in unit of parts-per-million (ppmv) with regard to dry air. Therefore, both CO2 and the dry air number of molecules in the atmosphere are needed in deriving this quantity. O2 is a stable molecule and uniformly mixed in the atmosphere. Measuring the O2 absorption in the atmosphere can thus be used to infer the dry air number of molecules and then used to calculate CO2 concentration. With the knowledge of atmospheric water vapor, we can then estimate the total surface pressure needed for CO2 retrievals. Our work, funded by the ESTO IIP program, uses fiber optic technology and non-linear optics to generate 765 nm laser radiation coincident with the Oxygen A-band. Our pulsed, time gated technique uses several on- and off-line wavelengths tuned to the O2 absorption line. The choice of wavelengths allows us to measure the pressure by using two adjacent O2 absorptions in the Oxygen A-band. Our retrieval algorithm fits the O2 lineshapes and derives the pressure. Our measurements compare favorably with a local weather monitor mounted outside our laboratory and a local weather station.

  11. Atmospheric Airborne Pressure Measurements Using the Oxygen A Band for the ASCENDS Mission

    NASA Technical Reports Server (NTRS)

    Riris, Haris; Rodriguez, Mike; Stephen, Mark; Hasselbrack, William; Allan, Graham; Mao, Jiamping,; Kawa, Stephan R.; Weaver, Clark J.

    2011-01-01

    We report on airborne atmospheric pressure measurements using new fiber-based laser technology and the oxygen A-band at 765 nm. Remote measurements of atmospheric temperature and pressure are required for a number of NASA Earth science missions and specifically for the Active Sensing of CO2 Emissions Over Nights, Days, and Seasons (ASCENDS) mission. Accurate measurements of tropospheric CO2 on a global scale are very important in order to better understand its sources and sinks and to improve predictions on any future climate change. The ultimate goal of a CO2 remote sensing mission, such as ASCENDS, is to derive the CO2 concentration in the atmosphere in terms of mole fraction in unit of parts-per-million (ppmv) with regard to dry air. Therefore, both CO2 and the dry air number of molecules in the atmosphere are needed in deriving this quantity. O2 is a stable molecule and uniformly mixed in the atmosphere. Measuring the O2 absorption in the atmosphere can thus be used to infer the dry air number of molecules and then used to calculate CO2 concentration. With the knowledge of atmospheric water vapor, we can then estimate the total surface pressure needed for CO2 retrievals. Our work, funded by the ESTO IIP program, uses fiber optic technology and non-linear optics to generate 765 nm laser radiation coincident with the Oxygen A-band. Our pulsed, time gated technique uses several on- and off-line wavelengths tuned to the O2 absorption line. The choice of wavelengths allows us to measure the pressure by using two adjacent O2 absorptions in the Oxygen A-band. Our retrieval algorithm fits the O2 lineshapes and derives the pressure. Our measurements compare favorably with a local weather monitor mounted outside our laboratory and a local weather station.

  12. The measurement of sequential changes in cerebral blood flow and oxygen metabolism by positron computed tomography with continuous inhalation of oxygen-15 labeled gases

    SciTech Connect

    Tanada, S.; Yonekura, Y.; Senda, M.; Nishimura, K.; Tamaki, N.; Saji, H.; Fujita, T.; Kobayashi, A.; Taki, W.; Ishikawa, M.

    1984-01-01

    The use of continuous inhalation of oxygen-15 labeled gases is a widely accepted method to measure regional cerebral blood flow (CBF) and oxygen metabolism (CMRO/sub 2/) with positron computed tomography (PCT). The purpose of this study is to evaluate the feasibility to measure sequential changes in CBF and CMRO/sub 2/ by PCT. The functional images of CBF, oxygen extraction fraction (OEF), and CMRO/sub 2/ were obtained using continuous inhalation of oxygen-15 labeled carbon dioxide and oxygen. The effects of spinal drainage in CBF and CMRO/sub 2/ were studied in patients with hydrocephalus following subarachnoid hemorrhage due to the rupture of intracranial aneurysm. Following the measurement in control state, 20 ml of cerebrospinal fluid (CSF) were withdrawn gradually through lumbar puncture, and sequential PCT scans were performed. CBF and CMRO/sub 2/ were markedly depressed in the case with hydrocephalus. The drainage of CSF significantly improved OEF and CMRO/sub 2/, whereas CBF remained depressed. In patients with chronic cerebrovascular disease, the changes in CBF were studied with inhalation of 5% carbon dioxide (CO/sub 2/). CO/sub 2/ loading demonstrated the increase in CBF, while poor regional increase was observed in ''moyamoya'' disease, which permitted the assessment of vascular response to the elevation of plasma CO/sub 2/. The authors preliminary work indicated the potential usefulness of sequential PCT to study the changes in CBF and CMRO/sub 2/ with various interventions.

  13. Carbon nanoelectrodes for single-cell probing

    NASA Astrophysics Data System (ADS)

    Anderson, Sean E.; Bau, Haim H.

    2015-05-01

    Carbon nanoelectrodes with tip diameters ranging from tens to hundreds of nanometers are fabricated by pyrolitic deposition of carbon films along the entire inner surfaces of pulled-glass pipettes. The pulled end of each glass pipette is then etched to expose a desired length (typically, a few micrometers) of carbon pipe. The carbon film provides an electrically conductive path from the nanoscopic carbon tip to the distal, macroscopic end of the pipette, bridging between the nanoscale tip and the macroscale handle, without a need for assembly. We used our nanoelectrodes to penetrate into individual cells and cell nuclei and measured the variations in the electrode impedance upon cell and nucleus penetration as well as the electrode impedance as a function of cell penetration depth. Theoretical predictions based on a simple circuit model were in good agreement with experimental data.

  14. Carbon Nanoelectrodes for Single-Cell Probing

    PubMed Central

    Anderson, Sean E.; Bau, Haim H.

    2015-01-01

    Carbon nanoelectrodes with tip diameters ranging from tens to hundreds of nm are fabricated by pyrolitic deposition of carbon films along the entire inner surfaces of pulled-glass pipettes. The pulled end of each glass pipette is then etched to expose a desired length (typically, a few µm) of carbon pipe. The carbon film provides an electrically conductive path from the nanoscopic carbon tip to the distal, macroscopic end of the pipette, bridging between the nanoscale tip and the macroscale handle, without a need for assembly. We used our nanoelectrodes to penetrate into individual cells and cell nuclei and measured the variations in the electrode impedance upon cell and nucleus penetration as well as the electrode impedance as a function of cell penetration depth. Theoretical predictions based on a simple circuit model were in good agreement with experimental data. PMID:25876625

  15. Isolation and Characterization of Single Cells from Zebrafish Embryos.

    PubMed

    Samsa, Leigh Ann; Fleming, Nicole; Magness, Scott; Qian, Li; Liu, Jiandong

    2016-01-01

    The zebrafish (Danio rerio) is a powerful model organism to study vertebrate development. Though many aspects of zebrafish embryonic development have been described at the morphological level, little is known about the molecular basis of cellular changes that occur as the organism develops. With recent advancements in microfluidics and multiplexing technologies, it is now possible to characterize gene expression in single cells. This allows for investigation of heterogeneity between individual cells of specific cell populations to identify and classify cell subtypes, characterize intermediate states that occur during cell differentiation, and explore differential cellular responses to stimuli. This study describes a protocol to isolate viable, single cells from zebrafish embryos for high throughput multiplexing assays. This method may be rapidly applied to any zebrafish embryonic cell type with fluorescent markers. An extension of this method may also be used in combination with high throughput sequencing technologies to fully characterize the transcriptome of single cells. As proof of principle, the relative abundance of cardiac differentiation markers was assessed in isolated, single cells derived from nkx2.5 positive cardiac progenitors. By evaluation of gene expression at the single cell level and at a single time point, the data support a model in which cardiac progenitors coexist with differentiating progeny. The method and work flow described here is broadly applicable to the zebrafish research community, requiring only a labeled transgenic fish line and access to microfluidics technologies. PMID:27022828

  16. Automated single cell isolation from suspension with computer vision.

    PubMed

    Ungai-Salánki, Rita; Gerecsei, Tamás; Fürjes, Péter; Orgovan, Norbert; Sándor, Noémi; Holczer, Eszter; Horvath, Robert; Szabó, Bálint

    2016-01-01

    Current robots can manipulate only surface-attached cells seriously limiting the fields of their application for single cell handling. We developed a computer vision-based robot applying a motorized microscope and micropipette to recognize and gently isolate intact individual cells for subsequent analysis, e.g., DNA/RNA sequencing in 1-2 nanoliters from a thin (~100 μm) layer of cell suspension. It can retrieve rare cells, needs minimal sample preparation, and can be applied for virtually any tissue cell type. Combination of 1 μm positioning precision, adaptive cell targeting and below 1 nl liquid handling precision resulted in an unprecedented accuracy and efficiency in robotic single cell isolation. Single cells were injected either into the wells of a miniature plate with a sorting speed of 3 cells/min or into standard PCR tubes with 2 cells/min. We could isolate labeled cells also from dense cultures containing ~1,000 times more unlabeled cells by the successive application of the sorting process. We compared the efficiency of our method to that of single cell entrapment in microwells and subsequent sorting with the automated micropipette: the recovery rate of single cells was greatly improved. PMID:26856740

  17. Single-cell printer: automated, on demand, and label free.

    PubMed

    Gross, Andre; Schöndube, Jonas; Niekrawitz, Sonja; Streule, Wolfgang; Riegger, Lutz; Zengerle, Roland; Koltay, Peter

    2013-12-01

    Within the past years, single-cell analysis has developed into a key topic in cell biology to study cellular functions that are not accessible by investigation of larger cell populations. Engineering approaches aiming to access single cells to extract information about their physiology, phenotype, and genotype at the single-cell level are going manifold ways, meanwhile allowing separation, sorting, culturing, and analysis of individual cells. Based on our earlier research toward inkjet-like printing of single cells, this article presents further characterization results obtained with a fully automated prototype instrument for printing of single living cells in a noncontact inkjet-like manner. The presented technology is based on a transparent microfluidic drop-on-demand dispenser chip coupled with a camera-assisted automatic detection system. Cells inside the chip are detected and classified with this detection system before they are expelled from the nozzle confined in microdroplets, thus enabling a "one cell per droplet" printing mode. To demonstrate the prototype instrument's suitability for biological and biomedical applications, basic experiments such as printing of single-bead and cell arrays as well as deposition and culture of single cells in microwell plates are presented. Printing efficiencies greater than 80% and viability rates about 90% were achieved. PMID:24222537

  18. Metabolism of Peptide Reporters in Cell Lysates and Single Cells

    PubMed Central

    Proctor, Angela; Wang, Qunzhao; Lawrence, David S.; Allbritton, Nancy L.

    2013-01-01

    The stability of an Abl kinase substrate peptide in a cytosolic lysate and in single cells was characterized. In the cytosolic lysate, the starting peptide was metabolized at an average initial rate of 1.7 ± 0.3 zmol pg−;1 s−;1 with a t1/2 of 1.3 min. Five different fragments formed over time; however, a dominant cleavage site was identified. Multiple rational design cycles were utilized to develop a lead peptide with a phenylalanine and alanine replaced by an (N-methyl)phenylalanine and isoleucine, respectively, to attain cytosolic peptidase resistance while maintaining Abl substrate efficacy. This lead peptide possessed a 15-fold greater lifetime in the cytosolic lysate while attaining a 7-fold improvement in kcat as an Abl kinase substrate compared to the starting peptide. However, when loaded into single cells, the starting peptide and lead peptide possessed nearly identical degradation rates and an altered pattern of fragmentation relative to that in cell lysates. Preferential accumulation of a fragment with cleavage at an Ala-Ala bond in single cells suggested that dissimilar peptidases act on the peptides in the lysate versus single cells. A design strategy for peptide stabilization, analogous to that demonstrated for the lysate, should be effective for stabilization in single cells. PMID:22314840

  19. Automated single cell isolation from suspension with computer vision

    PubMed Central

    Ungai-Salánki, Rita; Gerecsei, Tamás; Fürjes, Péter; Orgovan, Norbert; Sándor, Noémi; Holczer, Eszter; Horvath, Robert; Szabó, Bálint

    2016-01-01

    Current robots can manipulate only surface-attached cells seriously limiting the fields of their application for single cell handling. We developed a computer vision-based robot applying a motorized microscope and micropipette to recognize and gently isolate intact individual cells for subsequent analysis, e.g., DNA/RNA sequencing in 1–2 nanoliters from a thin (~100 μm) layer of cell suspension. It can retrieve rare cells, needs minimal sample preparation, and can be applied for virtually any tissue cell type. Combination of 1 μm positioning precision, adaptive cell targeting and below 1 nl liquid handling precision resulted in an unprecedented accuracy and efficiency in robotic single cell isolation. Single cells were injected either into the wells of a miniature plate with a sorting speed of 3 cells/min or into standard PCR tubes with 2 cells/min. We could isolate labeled cells also from dense cultures containing ~1,000 times more unlabeled cells by the successive application of the sorting process. We compared the efficiency of our method to that of single cell entrapment in microwells and subsequent sorting with the automated micropipette: the recovery rate of single cells was greatly improved. PMID:26856740

  20. Measurement of time-resolved oxygen concentration changes in photosynthetic systems by nitroxide-based EPR oximetry.

    PubMed

    Strzalka, K; Walczak, T; Sarna, T; Swartz, H M

    1990-09-01

    The application of recent developments of EPR oximetry to photosynthetic systems is described and used to study rapid processes in isolated thylakoid membranes from spinach and in intact photoautotrophic soybean cells. Using the peak heights of 15N perdeuterated Tempone and two microwave power levels oxygen evolution and consumption were measured. The method measured time-resolved oxygen concentration changes in the micromolar range. Oxygen evolution was linearly proportionate to the chlorophyl concentration of thylakoid membrane over the range studied (0-2 mg/ml). Oxygen evolution associated with single turnover light pulses was consistent with the four state model. The time (t1/2) to reach equilibrium of oxygen concentrations after a single turnover pulse was 0.4-0.5 ms, indicating that the evolution of oxygen coupled to the S4-S0 transition may be shorter than reported previously. The time for equilibrium of oxygen after single turnover pulses in soybean cells was relatively long (400 ms), which suggests that there are significant barriers to the free diffusion of oxygen in this system. The method also was used to study oxygen consumption by the electron transport chain of photosystem I and photosystem II. We conclude that EPR oximetry can provide quantitative and time-resolved data on oxygen concentrations with a sensitivity that is useful for studies of such systems. PMID:2168161

  1. A simplified CARS measurement system for rapid determination of temperature and oxygen concentration

    NASA Technical Reports Server (NTRS)

    Fujii, Shoichi

    1987-01-01

    A new spectroscopic concept for the rapid determination of temperature and oxygen concentration by CARS (Coherent Anti-Stokes Raman Spectroscopy) was described. The ratio of two spectral regions in the broadband Q-branch spectrum was detected by photomultipliers in a monochromator, which ratio depends on temperature and species concentration. The comparison of the measured data with theory was made using a flat flame burner and an electric furnace, with reasonable results. Various optical techniques for alignment were introduced including a highly efficient, stable dye oscillator. The combination of the spectroscopic concept and the optical techniques will make the CARS measurement system rapid in data processing and simple in optical parts.

  2. Measurement of Oxygen A Band Line Parameters by Using Modulation Spectroscopy with Higher Harmonic Detection

    NASA Technical Reports Server (NTRS)

    Dharamsi, Amin

    1999-01-01

    Wavelength modulation spectroscopy is used to demonstrate that extremely weak absorption lines can be measured even when these lines suffer from interference from the wings of adjacent stronger lines. It is shown that the use of detection at several harmonics allows such interference to be examined clearly and conveniently. The results of experimental measurements on a weak magnetic dipole driven, spin-forbidden line in the oxygen A band, which experiences interference from the wings of a pair of adjacent lines towards the blue and red regions of line center, are presented. A comparison of the experimental results to theory is given.

  3. Single Cell Mass Cytometry for Analysis of Immune System Functional States

    PubMed Central

    Bjornson, Zach B.; Nolan, Garry P.; Fantl, Wendy J.

    2013-01-01

    Single cell mass cytometry facilitates high-dimensional, quantitative analysis of the effects of bioactive molecules on cell populations at single-cell resolution. Datasets are generated with antibody panels (upwards of 40) in which each antibody is conjugated to a polymer chelated with a stable metal isotope, usually in the Lanthanide series of the periodic table. Isotope labelled antibodies recognize surface markers to delineate cell types and intracellular signaling molecules to provide a measure of the network state—and thereby demarcating multiple cell state functions such as apoptosis, DNA damage and cell cycle. By measuring all these parameters simultaneously, the signaling state of an individual cell can be measured at its network state. This review will cover the basics of mass cytometry as well as outline steps already taken to allow it to stand aside traditional fluorescence based cytometry in the immunologist’s analytical arsenal in their study of immune states during infection. PMID:23999316

  4. A comprehensive strategy for the analysis of acoustic compressibility and optical deformability on single cells

    NASA Astrophysics Data System (ADS)

    Yang, Tie; Bragheri, Francesca; Nava, Giovanni; Chiodi, Ilaria; Mondello, Chiara; Osellame, Roberto; Berg-Sørensen, Kirstine; Cristiani, Ilaria; Minzioni, Paolo

    2016-04-01

    We realized an integrated microfluidic chip that allows measuring both optical deformability and acoustic compressibility on single cells, by optical stretching and acoustophoresis experiments respectively. Additionally, we propose a measurement protocol that allows evaluating the experimental apparatus parameters before performing the cell-characterization experiments, including a non-destructive method to characterize the optical force distribution inside the microchannel. The chip was used to study important cell-mechanics parameters in two human breast cancer cell lines, MCF7 and MDA-MB231. Results indicate that MDA-MB231 has both higher acoustic compressibility and higher optical deformability than MCF7, but statistical analysis shows that optical deformability and acoustic compressibility are not correlated parameters. This result suggests the possibility to use them to analyze the response of different cellular structures. We also demonstrate that it is possible to perform both measurements on a single cell, and that the order of the two experiments does not affect the retrieved values.

  5. Regional Changes in Cerebral Oxygenation During Repeated Passive Movement Measured by Functional Near-infrared Spectroscopy

    PubMed Central

    Sugawara, Kazuhiro; Onishi, Hideaki; Tsubaki, Atsuhiro; Takai, Haruna; Tokunaga, Yuta; Tamaki, Hiroyuki

    2015-01-01

    The aim of this study is to investigate the influence of passive movement repetition frequency at 1.5-Hz and 1-Hz on changes in cerebral oxygenation and assess the temporal properties of these changes using functional near-infrared spectroscopy (fNIRS). No significant differences in systemic hemodynamics were observed between resting and passive movement phases for either 1.5-Hz or 1-Hz trial. Changes in cortical oxygenation as measured by fNIRS in bilateral supplementary motor cortex (SMC), left primary motor cortex (M1), left primary somatosensory cortex (S1), and left posterior association area (PAA) during passive movement of the right index finger revealed greater cortical activity at only 1.5-Hz movement frequency. However, there were no significant differences in the time for peak oxyhemoglobin (oxyHb) among regions (bilateral SMC, 206.4 ± 14.4 s; left M1, 199.1 ± 14.8 s; left S1, 207.3 ± 9.4 s; left PAA, 219.1 ± 10.2 s). Therefore, our results that passive movement above a specific frequency may be required to elicit a changed in cerebral oxygenation, and the times of peak ΔoxyHb did not differ significantly among measured regions. PMID:26635590

  6. Global atomic oxygen density derived from OGO-6 1304 A airglow measurements

    NASA Technical Reports Server (NTRS)

    Strickland, D. J.; Thomas, G. E.

    1976-01-01

    Results are presented for analysis of data on the atomic oxygen 1304-A triplet in the earth's dayglow between 400 and 1100 km which were obtained with the OGO-6 UV photometer during a 40-day period that included both quiet and disturbed conditions. Variations in the atomic oxygen column density are analyzed by obtaining best-fit models in which the 1304-A emission is produced by solar resonance scattering and photoelectron excitation. It is shown that the column density can be determined uniquely from the measured 1304-A intensity, provided the excitation processes can be described quantitatively. The values of the excitation parameters are determined directly from the data, and the deduced variations in column density over the daytime atmosphere are found to agree well with the Jacchia (1971) models. The latitudinal dependence of the column-density variations during a geomagnetic storm are discussed, the results are compared with recent measurements of the solar 1304-A fluxes as well as with calculations of the photoelectron excitation, and a method is suggested for determining the absolute atomic oxygen densities.

  7. Two-photon absorption laser induced fluorescence measurement of atomic oxygen density in an atmospheric pressure air plasma jet

    NASA Astrophysics Data System (ADS)

    Conway, J.; Gogna, G. S.; Gaman, C.; Turner, M. M.; Daniels, S.

    2016-08-01

    Atomic oxygen number density [O] is measured in an air atmospheric pressure plasma jet (APPJ) using two-photon absorption laser induced fluorescence (TALIF). Gas flow is fixed at 8 slpm, the RF power coupled into the plasma jet varied between 5 W and 20 W, and the resulting changes in atomic oxygen density measured. Photolysis of molecular oxygen is employed to allow in situ calibration of the TALIF system. During calibration, O2 photo-dissociation and two-photon excitation of the resulting oxygen atoms are achieved within the same laser pulse. The atomic oxygen density produced by photolysis is time varying and spatially non-uniform which needs to be corrected for to calibrate the TALIF system for measurement of atomic oxygen density in plasma. Knowledge of the laser pulse intensity I 0(t), wavelength, and focal spot size allows correction factors to be determined using a rate equation model. Atomic oxygen is used for calibration and measurement, so the laser intensity can be increased outside the TALIF quadratic laser power dependence region without affecting the calibration reliability as the laser power dependence will still be the same for both. The atomic O density results obtained are not directly benchmarked against other known density measurement techniques. The results show that the plasma jet atomic oxygen content increases as the RF power coupled into the plasma increases.

  8. Twilight rocket measurements of high-latitude atomic oxygen density during the DYANA campaign

    NASA Astrophysics Data System (ADS)

    Ulwick, J. C.; Ratkowski, A. J.; Makhlouf, U.

    1994-12-01

    During the DYANA (DYnamics Adapted Network for the Atmosphere) campaign, a rocket containing a resonance fluorescence experiment for measurement of atomic oxygen concentrations was launced at twilight-dawn from ESRANGE, Kiruna, Sweden in March 1990. The measured atomic oxygen concetration rose very sharply near 80 km to about 10(exp 11) atoms/cu cm, achieved a peak value of 3 x 10(exp 11) atoms/cu cm between 90 to 105 km, and decreased with increasing rocket altitude to about 155 km where the instrument's noise level was reached. In addition, ground-based, near-infrared radiometric and spectral measurements of the mesospheric and lower thermospheric hydroxyl (OH) airglow emissions were also obtained during the night up to the time of rocket launch. We have used least-squares spectral fitting procedures to obtain the OH Meinel (3-1) band intensities and accurate (+/-2.5K) rotational temperatures from individual scans. The band intensities show considerable structure throughout the night, dropping sharply by about a factor of 3 during sunrise when the rocket was launched. The rotational temperatures were consistently around 225 K throughout the night and during the rocket flight. During the MAP/WINE campaign in February 1984, similar measurements using identical rocket-borne and ground-based techniques were made at night from ESRANGE. In this paper, the DYANA and MAP/WINE measurements are inter-compared and discussed and further compared with model calculations.

  9. Oxygenated hydrocarbons in ambient air: Methods and measurements using solid-phase microextraction

    SciTech Connect

    Zhou, J.; McLaren, R.

    1999-07-01

    A method is described for the measurement of oxygenated and aromatic hydrocarbons in ambient air that combines the use of solid-phase microextraction with GC-MS. The method has proven to be sensitive enough to measure a range of species above the detection limit at urban and rural locations. Advantages and disadvantages of the method are discussed following the discussion of calibration and measurement methods. Measured mixing ratios are reported for oxygenated and aromatic hydrocarbons in the urban city of Toronto and at a rural forested site in Borden, Ontario. Correlations between different species are used to identify possible sources. At the Borden site, measurements at two levels on a tower through the forest canopy are used to discuss possible sources of species at that site. A unifying theme for both sites is the observation of similar and high median levels of methanol, acetone and acetaldehyde. The comparison of data from the urban and forested sites in this study do not provide evidence for a significant biogenic source of methanol as seen in the southern USA, although it is not discounted.

  10. Measurements of elastohydrodynamic film thickness, wear and tempering behavior of high pressure oxygen turbopump bearings

    NASA Technical Reports Server (NTRS)

    Dufrane, K. F.; Merriman, T. L.; Kannel, J. W.; Stockwell, R. D.; Hauser, D.; Vanecho, J. A.

    1984-01-01

    The reusable design of the Space Shuttle requires a target life of 7.5 hours for the turbopumps of the Space Shuttle main engine (SSME). This large increase from the few hundred seconds required in single-use rockets has caused various problems with the bearings of the turbopumps. The berings of the high pressure oxygen turbopump (HPOTP) were of particular concern because of wear, spalling, and cage failures at service time well below the required 7.5 hours. Lubrication and wear data were developed for the bearings. Since the HPOTP bearings operate in liquid oxygen, conventional liquid lubricants cannot be applied. Therefore, solid lubricant coatings and lubricant transfer from the polytetrafluorethylene (FTFE) cage were the primary lubrication approaches for the bearings. Measurements were made using liquid nitrogen in a rolling disk machine to determine whether usable elastohydrodynamic films could be generated to assist in the bearing lubrication.

  11. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast

    PubMed Central

    Versari, Cristian; Cinquemani, Eugenio; Ferrari-Trecate, Giancarlo; Hersen, Pascal; Batt, Gregory

    2016-01-01

    Significant cell-to-cell heterogeneity is ubiquitously observed in isogenic cell populations. Consequently, parameters of models of intracellular processes, usually fitted to population-averaged data, should rather be fitted to individual cells to obtain a population of models of similar but non-identical individuals. Here, we propose a quantitative modeling framework that attributes specific parameter values to single cells for a standard model of gene expression. We combine high quality single-cell measurements of the response of yeast cells to repeated hyperosmotic shocks and state-of-the-art statistical inference approaches for mixed-effects models to infer multidimensional parameter distributions describing the population, and then derive specific parameters for individual cells. The analysis of single-cell parameters shows that single-cell identity (e.g. gene expression dynamics, cell size, growth rate, mother-daughter relationships) is, at least partially, captured by the parameter values of gene expression models (e.g. rates of transcription, translation and degradation). Our approach shows how to use the rich information contained into longitudinal single-cell data to infer parameters that can faithfully represent single-cell identity. PMID:26859137

  12. Single-cell vs. bulk activity properties of coastal bacterioplankton over an annual cycle in a temperate ecosystem.

    PubMed

    Morán, Xosé Anxelu G; Calvo-Díaz, Alejandra

    2009-01-01

    The connections between single-cell activity properties of heterotrophic planktonic bacteria and whole community metabolism are still poorly understood. Here, we show flow cytometry single-cell analysis of membrane-intact (live), high nucleic acid (HNA) content and actively respiring (CTC+) bacteria with samples collected monthly during 2006 in northern Spain coastal waters. Bulk activity was assessed by measuring 3H-Leucine incorporation and specific growth rates. Consistently, different single-cell relative abundances were found, with 60-100% for live, 30-84% for HNA and 0.2-12% for CTC+ cells. Leucine incorporation rates (2-153 pmol L(-1) h(-1)), specific growth rates (0.01-0.29 day(-1)) and the total and relative abundances of the three single-cell groups showed marked seasonal patterns. Distinct depth distributions during summer stratification and different relations with temperature, chlorophyll and bacterial biovolume suggest the existence of different controlling factors on each single-cell property. Pooled leucine incorporation rates were similarly correlated with the abundance of all physiological groups, while specific growth rates were only substantially explained by the percentage of CTC+ cells. However, the ability to reduce CTC proved notably better than the other two single-cell properties at predicting bacterial bulk rates within seasons, suggesting a tight linkage between bacterial individual respiration and biomass production at the community level. PMID:19120458

  13. Reliability of near infrared spectroscopy (NIRS) for measuring forearm oxygenation during incremental handgrip exercise.

    PubMed

    Celie, Bert; Boone, Jan; Van Coster, Rudy; Bourgois, Jan

    2012-06-01

    The purpose of this study was to test the reliability of a new handgrip exercise protocol measuring forearm oxygenation in 20 healthy subjects on two occasions. The retest took place 48 h later and at the same time of the day. The incremental exercise consisted of 2 min steps of cyclic handgrip contraction (1/2 Hz) separated by 1 min of recovery. The exercise started at 20% MVC, was increased with 10% MVC each step and was performed until exhaustion (69.5 and 73% MVC). Near infrared spectroscopy (NIRS) was used to measure deoxygenation (deoxy[Hb + Mb]) and oxygen saturation (SmO(2)) in the forearm muscles. Prior to the exercise protocol an arterial occlusion of the forearm was performed until deoxy(Hb + Mb) did no longer increase. Maximal increase in deoxy[Hb + Mb] during 10 s of each exercise bout was expressed relative to the occlusion amplitude. ICC was used to examine the test-retest reliability. Significant ICC's were reported at 50% (r = 0.466, p = 0.017) and 60% MVC (r = 0.553, p = 0.005). The group mean of the maximum increase in oxygen extraction was 45.6 ± 16.7% and at the retest 44.9 ± 17.0% with an ICC of r = 0.867 (p < 0.001) which could be classified (Landis and Koch 1979) as almost perfect. The absolute SmO(2) values showed reliable ICC's for every submaximal intensity except at 60% MVC. An ICC of r = 0.774 (p < 0.001) was found at maximal intensity. The results of the present study show that deoxy[Hb + Mb] and SmO(2) responses during this protocol are highly reliable and indicate that this protocol could be used to get insight into deoxygenation and oxygen saturation in a population with low exercise tolerance. PMID:21952981

  14. Tools for Single-Cell Kinetic Analysis of Virus-Host Interactions.

    PubMed

    Warrick, Jay W; Timm, Andrea; Swick, Adam; Yin, John

    2016-01-01

    Measures of cellular gene expression or behavior, when performed on individual cells, inevitably reveal a diversity of behaviors and outcomes that can correlate with normal or diseased states. For virus infections, the potential diversity of outcomes are pushed to an extreme, where measures of infection reflect features of the specific infecting virus particle, the individual host cell, as well as interactions between viral and cellular components. Single-cell measures, while revealing, still often rely on specialized fluid handling capabilities, employ end-point measures, and remain labor-intensive to perform. To address these limitations, we consider a new microwell-based device that uses simple pipette-based fluid handling to isolate individual cells. Our design allows different experimental conditions to be implemented in a single device, permitting easier and more standardized protocols. Further, we utilize a recently reported dual-color fluorescent reporter system that provides dynamic readouts of viral and cellular gene expression during single-cell infections by vesicular stomatitis virus. In addition, we develop and show how free, open-source software can enable streamlined data management and batch image analysis. Here we validate the integration of the device and software using the reporter system to demonstrate unique single-cell dynamic measures of cellular responses to viral infection. PMID:26752057

  15. Tools for Single-Cell Kinetic Analysis of Virus-Host Interactions

    PubMed Central

    Swick, Adam; Yin, John

    2016-01-01

    Measures of cellular gene expression or behavior, when performed on individual cells, inevitably reveal a diversity of behaviors and outcomes that can correlate with normal or diseased states. For virus infections, the potential diversity of outcomes are pushed to an extreme, where measures of infection reflect features of the specific infecting virus particle, the individual host cell, as well as interactions between viral and cellular components. Single-cell measures, while revealing, still often rely on specialized fluid handling capabilities, employ end-point measures, and remain labor-intensive to perform. To address these limitations, we consider a new microwell-based device that uses simple pipette-based fluid handling to isolate individual cells. Our design allows different experimental conditions to be implemented in a single device, permitting easier and more standardized protocols. Further, we utilize a recently reported dual-color fluorescent reporter system that provides dynamic readouts of viral and cellular gene expression during single-cell infections by vesicular stomatitis virus. In addition, we develop and show how free, open-source software can enable streamlined data management and batch image analysis. Here we validate the integration of the device and software using the reporter system to demonstrate unique single-cell dynamic measures of cellular responses to viral infection. PMID:26752057

  16. Single-cell bioelectrical impedance platform for monitoring cellular response to drug treatment.

    PubMed

    Asphahani, Fareid; Wang, Kui; Thein, Myo; Veiseh, Omid; Yung, Sandy; Xu, Jian; Zhang, Miqin

    2011-02-01

    The response of cells to a chemical or biological agent in terms of their impedance changes in real-time is a useful mechanism that can be utilized for a wide variety of biomedical and environmental applications. The use of a single-cell-based analytical platform could be an effective approach to acquiring more sensitive cell impedance measurements, particularly in applications where only diminutive changes in impedance are expected. Here, we report the development of an on-chip cell impedance biosensor with two types of electrodes that host individual cells and cell populations, respectively, to study its efficacy in detecting cellular response. Human glioblastoma (U87MG) cells were patterned on single- and multi-cell electrodes through ligand-mediated natural cell adhesion. We comparatively investigated how these cancer cells on both types of electrodes respond to an ion channel inhibitor, chlorotoxin (CTX), in terms of their shape alternations and impedance changes to exploit the fine detectability of the single-cell-based system. The detecting electrodes hosting single cells exhibited a significant reduction in the real impedance signal, while electrodes hosting confluent monolayer of cells showed little to no impedance change. When single-cell electrodes were treated with CTX of different doses, a dose-dependent impedance change was observed. This enables us to identify the effective dose needed for this particular treatment. Our study demonstrated that this single-cell impedance system may potentially serve as a useful analytical tool for biomedical applications such as environmental toxin detection and drug evaluation. PMID:21301069

  17. Defining heterogeneity within bacterial populations via single cell approaches.

    PubMed

    Davis, Kimberly M; Isberg, Ralph R

    2016-08-01

    Bacterial populations are heterogeneous, which in many cases can provide a selective advantage during changes in environmental conditions. In some instances, heterogeneity exists at the genetic level, in which significant allelic variation occurs within a population seeded by a single cell. In other cases, heterogeneity exists due to phenotypic differences within a clonal, genetically identical population. A variety of mechanisms can drive this latter strategy. Stochastic fluctuations can drive differential gene expression, but heterogeneity in gene expression can also be driven by environmental changes sensed by individual cells residing in distinct locales. Utilizing multiple single cell approaches, workers have started to uncover the extent of heterogeneity within bacterial populations. This review will first describe several examples of phenotypic and genetic heterogeneity, and then discuss many single cell approaches that have recently been applied to define heterogeneity within bacterial populations. PMID:27273675

  18. Disentangling neural cell diversity using single-cell transcriptomics.

    PubMed

    Poulin, Jean-Francois; Tasic, Bosiljka; Hjerling-Leffler, Jens; Trimarchi, Jeffrey M; Awatramani, Rajeshwar

    2016-08-26

    Cellular specialization is particularly prominent in mammalian nervous systems, which are composed of millions to billions of neurons that appear in thousands of different 'flavors' and contribute to a variety of functions. Even in a single brain region, individual neurons differ greatly in their morphology, connectivity and electrophysiological properties. Systematic classification of all mammalian neurons is a key goal towards deconstructing the nervous system into its basic components. With the recent advances in single-cell gene expression profiling technologies, it is now possible to undertake the enormous task of disentangling neuronal heterogeneity. High-throughput single-cell RNA sequencing and multiplexed quantitative RT-PCR have become more accessible, and these technologies enable systematic categorization of individual neurons into groups with similar molecular properties. Here we provide a conceptual and practical guide to classification of neural cell types using single-cell gene expression profiling technologies. PMID:27571192

  19. Spatial reconstruction of single-cell gene expression

    PubMed Central

    Satija, Rahul; Farrell, Jeffrey A.; Gennert, David; Schier, Alexander F.; Regev, Aviv

    2015-01-01

    Spatial localization is a key determinant of cellular fate and behavior, but spatial RNA assays traditionally rely on staining for a limited number of RNA species. In contrast, single-cell RNA-seq allows for deep profiling of cellular gene expression, but established methods separate cells from their native spatial context. Here we present Seurat, a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns. We applied Seurat to spatially map 851 single cells from dissociated zebrafish (Danio rerio) embryos, inferring a transcriptome-wide map of spatial patterning. We confirmed Seurat’s accuracy using several experimental approaches, and used it to identify a set of archetypal expression patterns and spatial markers. Additionally, Seurat correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups. Seurat will be applicable to mapping cellular localization within complex patterned tissues in diverse systems. PMID:25867923

  20. Review of methods to probe single cell metabolism and bioenergetics

    PubMed Central

    Vasdekis, Andreas E.; Stephanopoulos, Gregory

    2015-01-01

    Single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. Herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. Firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. We also highlight specific advances in microbiology for its implications in metabolic engineering. Methods for probing single cell physiology and metabolism are subsequently reviewed. The primary focus therein is on dynamic and high-content profiling strategies based on label-free and fluorescence microspectroscopy and microscopy. Non-dynamic approaches, such as mass spectrometry and nuclear magnetic resonance, are also briefly discussed. PMID:25448400

  1. Single cell electroporation using proton beam fabricated biochips

    NASA Astrophysics Data System (ADS)

    Homhuan, S.; Zhang, B.; Sheu, F.-S.; Bettiol, A. A.; Watt, F.

    2010-05-01

    We report the design and fabrication of a novel single cell electroporation biochip fabricated by the Proton Beam Writing technique (PBW), a new technique capable of direct-writing high-aspect-ratio nano and microstructures. The biochip features nickel micro-electrodes with straight-side walls between which individual cells are positioned. By applying electrical impulses across the electrodes, SYTOX® Green nucleic acid stain is incorporated into mouse neuroblastoma (N2a) cells. When the stain binds with DNA inside the cell nucleus, green fluorescence is observed upon excitation from a halogen lamp. Three parameters; electric field strength, pulse duration, and the number of pulses have been considered and optimized for the single cell electroporation. The results show that our biochip gives successfully electroporated cells . This single cell electroporation system represents a promising method for investigating the introduction of a wide variety of fluorophores, nanoparticles, quantum dots, DNAs and proteins into cells.

  2. Tunable Single-Cell Extraction for Molecular Analyses.

    PubMed

    Guillaume-Gentil, Orane; Grindberg, Rashel V; Kooger, Romain; Dorwling-Carter, Livie; Martinez, Vincent; Ossola, Dario; Pilhofer, Martin; Zambelli, Tomaso; Vorholt, Julia A

    2016-07-14

    Because of cellular heterogeneity, the analysis of endogenous molecules from single cells is of significant interest and has major implications. While micromanipulation or cell sorting followed by cell lysis is already used for subsequent molecular examinations, approaches to directly extract the content of living cells remain a challenging but promising alternative to achieving non-destructive sampling and cell-context preservation. Here, we demonstrate the quantitative extraction from single cells with spatiotemporal control using fluidic force microscopy. We further present a comprehensive analysis of the soluble molecules withdrawn from the cytoplasm or the nucleus, including the detection of enzyme activities and transcript abundances. This approach has uncovered the ability of cells to withstand extraction of up to several picoliters and opens opportunities to study cellular dynamics and cell-cell communication under physiological conditions at the single-cell level. PMID:27419874

  3. Single-cell RNA-seq: advances and future challenges

    PubMed Central

    Saliba, Antoine-Emmanuel; Westermann, Alexander J.; Gorski, Stanislaw A.; Vogel, Jörg

    2014-01-01

    Phenotypically identical cells can dramatically vary with respect to behavior during their lifespan and this variation is reflected in their molecular composition such as the transcriptomic landscape. Single-cell transcriptomics using next-generation transcript sequencing (RNA-seq) is now emerging as a powerful tool to profile cell-to-cell variability on a genomic scale. Its application has already greatly impacted our conceptual understanding of diverse biological processes with broad implications for both basic and clinical research. Different single-cell RNA-seq protocols have been introduced and are reviewed here—each one with its own strengths and current limitations. We further provide an overview of the biological questions single-cell RNA-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field. PMID:25053837

  4. Automated single cell sorting and deposition in submicroliter drops

    NASA Astrophysics Data System (ADS)

    Salánki, Rita; Gerecsei, Tamás; Orgovan, Norbert; Sándor, Noémi; Péter, Beatrix; Bajtay, Zsuzsa; Erdei, Anna; Horvath, Robert; Szabó, Bálint

    2014-08-01

    Automated manipulation and sorting of single cells are challenging, when intact cells are needed for further investigations, e.g., RNA or DNA sequencing. We applied a computer controlled micropipette on a microscope admitting 80 PCR (Polymerase Chain Reaction) tubes to be filled with single cells in a cycle. Due to the Laplace pressure, fluid starts to flow out from the micropipette only above a critical pressure preventing the precise control of drop volume in the submicroliter range. We found an anomalous pressure additive to the Laplace pressure that we attribute to the evaporation of the drop. We have overcome the problem of the critical dropping pressure with sequentially operated fast fluidic valves timed with a millisecond precision. Minimum drop volume was 0.4-0.7 μl with a sorting speed of 15-20 s per cell. After picking NE-4C neuroectodermal mouse stem cells and human primary monocytes from a standard plastic Petri dish we could gently deposit single cells inside tiny drops. 94 ± 3% and 54 ± 7% of the deposited drops contained single cells for NE-4C and monocytes, respectively. 7.5 ± 4% of the drops contained multiple cells in case of monocytes. Remaining drops were empty. Number of cells deposited in a drop could be documented by imaging the Petri dish before and after sorting. We tuned the adhesion force of cells to make the manipulation successful without the application of microstructures for trapping cells on the surface. We propose that our straightforward and flexible setup opens an avenue for single cell isolation, critically needed for the rapidly growing field of single cell biology.

  5. Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors.

    PubMed

    Mitra, A K; Mukherjee, U K; Harding, T; Jang, J S; Stessman, H; Li, Y; Abyzov, A; Jen, J; Kumar, S; Rajkumar, V; Van Ness, B

    2016-05-01

    Multiple myeloma (MM) is characterized by significant genetic diversity at subclonal levels that have a defining role in the heterogeneity of tumor progression, clinical aggressiveness and drug sensitivity. Although genome profiling studies have demonstrated heterogeneity in subclonal architecture that may ultimately lead to relapse, a gene expression-based prediction program that can identify, distinguish and quantify drug response in sub-populations within a bulk population of myeloma cells is lacking. In this study, we performed targeted transcriptome analysis on 528 pre-treatment single cells from 11 myeloma cell lines and 418 single cells from 8 drug-naïve MM patients, followed by intensive bioinformatics and statistical analysis for prediction of proteasome inhibitor sensitivity in individual cells. Using our previously reported drug response gene expression profile signature at the single-cell level, we developed an R Statistical analysis package available at https://github.com/bvnlabSCATTome, SCATTome (single-cell analysis of targeted transcriptome), that restructures the data obtained from Fluidigm single-cell quantitative real-time-PCR analysis run, filters missing data, performs scaling of filtered data, builds classification models and predicts drug response of individual cells based on targeted transcriptome using an assortment of machine learning methods. Application of SCATT should contribute to clinically relevant analysis of intratumor heterogeneity, and better inform drug choices based on subclonal cellular responses. PMID:26710886

  6. Formation of highly oxygenated organic aerosol in the atmosphere: Insights from the Finokalia Aerosol Measurement Experiments

    NASA Astrophysics Data System (ADS)

    Hildebrandt, Lea; Kostenidou, Evangelia; Mihalopoulos, Nikos; Worsnop, Douglas R.; Donahue, Neil M.; Pandis, Spyros N.

    2010-12-01

    Aged organic aerosol (OA) was measured at a remote coastal site on the island of Crete, Greece during the Finokalia Aerosol Measurement Experiments (FAME-08 and FAME-09), which were part of the EUCAARI intensive campaigns. Quadrupole aerosol mass spectrometers (Q-AMSs) were employed to measure the size-resolved chemical composition of non-refractory submicron aerosol (NR-PM1), and to estimate the extent of oxidation of the OA. The experiments provide unique insights into ambient oxidation of aerosol by measuring at the same site but under different photochemical conditions. NR-PM1 concentrations were about a factor of three lower during FAME-09 (winter) than during FAME-08 (summer). The OA sampled was significantly less oxidized and more variable in composition during the winter than during the early summer. Lower OH concentrations in the winter were the main difference between the two campaigns, suggesting that atmospheric formation of highly oxygenated OA is associated with homogeneous photochemical aging.

  7. Accurate, in vivo NIR measurement of skeletal muscle oxygenation through fat

    NASA Astrophysics Data System (ADS)

    Jin, Chunguang; Zou, Fengmei; Ellerby, Gwenn E. C.; Scott, Peter; Peshlov, Boyan; Soller, Babs R.

    2010-02-01

    Noninvasive near infrared (NIR) spectroscopic measurement of muscle oxygenation requires the penetration of light through overlying skin and fat layers. We have previously demonstrated a dual-light source design and orthogonalization algorithm that corrects for inference from skin absorption and fat scattering. To achieve accurate muscle oxygen saturation (SmO2) measurement, one must select the appropriate source-detector distance (SD) to completely penetrate the fat layer. Methods: Six healthy subjects were supine for 15min to normalize tissue oxygenation across the body. NIR spectra were collected from the calf, shoulder, lower and upper thigh muscles with long SD distances of 30mm, 35mm, 40mm and 45mm. Spectral preprocessing with the short SD (3mm) spectrum preceded SmO2 calculation with a Taylor series expansion method. Three-way ANOVA was used to compare SmO2 values over varying fat thickness, subjects and SD distances. Results: Overlying fat layers varied in thickness from 4.9mm to 19.6mm across all subjects. SmO2 measured at the four locations were comparable for each subject (p=0.133), regardless of fat thickness and SD distance. SmO2 (mean+/-std dev) measured at calf, shoulder, low and high thigh were 62+/-3%, 59+/-8%, 61+/-2%, 61+/-4% respectively for SD distance of 30mm. In these subjects no significant influence of SD was observed (p=0.948). Conclusions: The results indicate that for our sensor design a 30mm SD is sufficient to penetrate through a 19mm fat layer and that orthogonalization with short SD effectively removed spectral interference from fat to result in a reproducible determination of SmO2.

  8. Somatosensory evoked changes in cerebral oxygen consumption measured non-invasively in premature neonates

    PubMed Central

    Roche-Labarbe, Nadege; Fenoglio, Angela; Radakrishnan, Harsha; Kocienski-Filip, Marcia; Carp, Stefan A.; Dubb, Jay; Boas, David A.; Grant, P. Ellen; Franceschini, Maria Angela

    2013-01-01

    The hemodynamic functional response is used as a reliable marker of neuronal activity in countless studies of brain function and cognition. In newborns and infants, however, conflicting results have appeared in the literature concerning the typical response, and there is little information on brain metabolism and functional activation. Measurement of all hemodynamic components and oxygen metabolism is critical for understanding neurovascular coupling in the developing brain. To this end, we combined multiple near infrared spectroscopy techniques to measure oxy- and deoxy-hemoglobin concentrations, cerebral blood volume (CBV), and relative cerebral blood flow (CBF) in the somatosensory cortex of 6 preterm neonates during passive tactile stimulation of the hand. By combining these measures we estimated relative changes in the cerebral metabolic rate of oxygen consumption (rCMRO2). CBF starts increasing immediately after stimulus onset, and returns to baseline before blood volume. This is consistent with the model of pre-capillary arteriole active dilation driving the CBF response, with a subsequent CBV increase influenced by capillaries and veins dilating passively to accommodate the extra blood. rCMRO2 estimated using the steady-state formulation shows a biphasic pattern: an increase immediately after stimulus onset, followed by a post-stimulus undershoot due to blood flow returning faster to baseline than oxygenation. However, assuming a longer mean transit time from the arterial to the venous compartment, due to the immature vascular system of premature infants, reduces the post-stimulus undershoot and increases the flow/consumption ratio to values closer to adult values reported in the literature. We are the first to report changes in local rCBF and rCMRO2 during functional activation in preterm infants. The ability to measure these variables in addition to hemoglobin concentration changes is critical for understanding neurovascular coupling in the developing

  9. Single-Cell Isolation and Gene Analysis: Pitfalls and Possibilities

    PubMed Central

    Hodne, Kjetil; Weltzien, Finn-Arne

    2015-01-01

    During the last two decades single-cell analysis (SCA) has revealed extensive phenotypic differences within homogenous cell populations. These phenotypic differences are reflected in the stochastic nature of gene regulation, which is often masked by qualitatively and quantitatively averaging in whole tissue analyses. The ability to isolate transcripts and investigate how genes are regulated at the single cell level requires highly sensitive and refined methods. This paper reviews different strategies currently used for SCA, including harvesting, reverse transcription, and amplification of the RNA, followed by methods for transcript quantification. The review provides the historical background to SCA, discusses limitations, and current and future possibilities in this exciting field of research. PMID:26569222

  10. A microfluidic device enabling high-efficiency single cell trapping.

    PubMed

    Jin, D; Deng, B; Li, J X; Cai, W; Tu, L; Chen, J; Wu, Q; Wang, W H

    2015-01-01

    Single cell trapping increasingly serves as a key manipulation technique in single cell analysis for many cutting-edge cell studies. Due to their inherent advantages, microfluidic devices have been widely used to enable single cell immobilization. To further improve the single cell trapping efficiency, this paper reports on a passive hydrodynamic microfluidic device based on the "least flow resistance path" principle with geometry optimized in line with corresponding cell types. Different from serpentine structure, the core trapping structure of the micro-device consists of a series of concatenated T and inverse T junction pairs which function as bypassing channels and trapping constrictions. This new device enhances the single cell trapping efficiency from three aspects: (1) there is no need to deploy very long or complicated channels to adjust flow resistance, thus saving space for each trapping unit; (2) the trapping works in a "deterministic" manner, thus saving a great deal of cell samples; and (3) the compact configuration allows shorter flowing path of cells in multiple channels, thus increasing the speed and throughput of cell trapping. The mathematical model of the design was proposed and optimization of associated key geometric parameters was conducted based on computational fluid dynamics (CFD) simulation. As a proof demonstration, two types of PDMS microfluidic devices were fabricated to trap HeLa and HEK-293T cells with relatively significant differences in cell sizes. Experimental results showed 100% cell trapping and 90% single cell trapping over 4 × 100 trap sites for these two cell types, respectively. The space saving is estimated to be 2-fold and the cell trapping speed enhancement to be 3-fold compared to previously reported devices. This device can be used for trapping various types of cells and expanded to trap cells in the order of tens of thousands on 1-cm(2) scale area, as a promising tool to pattern large-scale single cells on specific

  11. Functionalized nanopipettes: toward label-free, single cell biosensors

    PubMed Central

    Actis, Paolo; Mak, Andy C.

    2010-01-01

    Nanopipette technology has been proven to be a label-free biosensor capable of identifying DNA and proteins. The nanopipette can include specific recognition elements for analyte discrimination based on size, shape, and charge density. The fully electrical read-out and the ease and low-cost fabrication are unique features that give this technology an enormous potential. Unlike other biosensing platforms, nanopipettes can be precisely manipulated with submicron accuracy and used to study single cell dynamics. This review is focused on creative applications of nanopipette technology for biosensing. We highlight the potential of this technology with a particular attention to integration of this biosensor with single cell manipulation platforms. PMID:20730113

  12. Molecular circuits for associative learning in single-celled organisms

    PubMed Central

    Fernando, Chrisantha T.; Liekens, Anthony M.L.; Bingle, Lewis E.H.; Beck, Christian; Lenser, Thorsten; Stekel, Dov J.; Rowe, Jonathan E.

    2008-01-01

    We demonstrate how a single-celled organism could undertake associative learning. Although to date only one previous study has found experimental evidence for such learning, there is no reason in principle why it should not occur. We propose a gene regulatory network that is capable of associative learning between any pre-specified set of chemical signals, in a Hebbian manner, within a single cell. A mathematical model is developed, and simulations show a clear learned response. A preliminary design for implementing this model using plasmids within Escherichia coli is presented, along with an alternative approach, based on double-phosphorylated protein kinases. PMID:18835803

  13. Single cell pattern formation and transient cytoskeletal arrays

    PubMed Central

    Bement, William M.; von Dassow, George

    2015-01-01

    A major goal of developmental biology is to explain the emergence of pattern in cell layers, tissues and organs. Developmental biologists now accept that reaction diffusion-based mechanisms are broadly employed in developing organisms to direct pattern formation. Here we briefly consider these mechanisms and then apply some of the concepts derived from them to several processes that occur in single cells: wound repair, yeast budding, and cytokinesis. Two conclusions emerge from this analysis: first, there is considerable overlap at the level of general mechanisms between developmental and single cell pattern formation; second, dynamic structures based on the actin cytoskeleton may be far more ordered than is generally recognized. PMID:24529246

  14. Single-cell growth analysis in a mixed cell culture

    NASA Astrophysics Data System (ADS)

    Ando, Jun; Bato, Mary Grace P.; Daria, Vincent Ricardo

    2008-06-01

    We perform single cell analysis of cell growth in a mixed cell culture. Two species of yeast cells: Saccharomyces cerevisiae and Candida albicans, are optically trapped using focused continuous-wave near infrared laser. Cell growth for both cells is inhibited only when the two species of cells are in contact with each other. This indicates cell-cell interaction mediated cell growth inhibition mechanism. Single cell level analysis of cell growth studied here contributes to the further understanding of yeast growth arrest in a mixed yeast culture.

  15. [Research on accurate measurement of oxygen content in coal using laser-induced breakdown spectroscopy in air environment].

    PubMed

    Yin, Wang-bao; Zhang, Lei; Wang, Le; Dong, Lei; Ma, Wei-guang; Jia, Suo-tang

    2012-01-01

    A technique about accurate measurement of oxygen content in coal in air environment using laser-induced breakdown spectroscopy (LIBS) is introduced in the present paper. Coal samples were excited by the laser, and plasma spectra were obtained. Combining internal standard method, temperature correction method and multi-line methods, the oxygen content of coal samples was precisely measured. The measurement precision is not less than 1.37% for oxygen content in coal analysis, so is satisfied for the requirement of coal-fired power plants in coal analysis. This method can be used in surveying, environmental protection, medicine, materials, archaeological and food safety, biochemical and metallurgy application. PMID:22497159

  16. An integrated image analysis platform to quantify signal transduction in single cells.

    PubMed

    Pelet, Serge; Dechant, Reinhard; Lee, Sung Sik; van Drogen, Frank; Peter, Matthias

    2012-10-01

    Microscopy can provide invaluable information about biological processes at the single cell level. It remains a challenge, however, to extract quantitative information from these types of datasets. We have developed an image analysis platform named YeastQuant to simplify data extraction by offering an integrated method to turn time-lapse movies into single cell measurements. This platform is based on a database with a graphical user interface where the users can describe their experiments. The database is connected to the engineering software Matlab, which allows extracting the desired information by automatically segmenting and quantifying the microscopy images. We implemented three different segmentation methods that recognize individual cells under different conditions, and integrated image analysis protocols that allow measuring and analyzing distinct cellular readouts. To illustrate the power and versatility of YeastQuant, we investigated dynamic signal transduction processes in yeast. First, we quantified the expression of fluorescent reporters induced by osmotic stress to study noise in gene expression. Second, we analyzed the dynamic relocation of endogenous proteins from the cytoplasm to the cell nucleus, which provides a fast measure of pathway activity. These examples demonstrate that YeastQuant provides a versatile and expandable database and an experimental framework that improves image analysis and quantification of diverse microscopy-based readouts. Such dynamic single cell measurements are highly needed to establish mathematical models of signal transduction pathways. PMID:22976484

  17. Determination of Sediment Oxygen Demand in the Ziya River Watershed, China: Based on Laboratory Core Incubation and Microelectrode Measurements.

    PubMed

    Rong, Nan; Shan, Baoqing; Wang, Chao

    2016-02-01

    A study coupling sedimentcore incubation and microelectrode measurement was performed to explore the sediment oxygen demand (SOD) at 16 stations in the Ziya River Watershed, a severely polluted and anoxic river system in the north of China. Total oxygen flux values in the range 0.19-1.41 g/(m²·d) with an average of 0.62 g/(m²·d) were obtained by core incubations, and diffusive oxygen flux values in the range 0.15-1.38 g/(m²·d) with an average of 0.51 g/(m²·d) were determined by microelectrodes. Total oxygen flux obviously correlated with diffusive oxygen flux (R² = 0.842). The microelectrode method produced smaller results than the incubation method in 15 of 16 sites, and the diffusive oxygen flux was smaller than the total oxygen flux. Although the two sets of SOD values had significant difference accepted by the two methods via the Wilcoxon signed-rank test (p < 0.05), the microelectrode method was shown to produce results that were similar to those from the core incubation method. The microelectrode method, therefore, could be used as an alternative method for traditional core incubation method, or as a method to verify SOD rates measured by other methods. We consider that high potential sediment oxygen demand would occur in the Ziya River Watershed when the dissolved oxygen (DO) recovered in the overlying water. PMID:26907307

  18. Bayesian Hierarchical Models for Protein Networks in Single-Cell Mass Cytometry

    PubMed Central

    Mitra, Riten; Müller, Peter; Qiu, Peng; Ji, Yuan

    2014-01-01

    We propose a class of hierarchical models to investigate the protein functional network of cellular markers. We consider a novel data set from single-cell proteomics. The data are generated from single-cell mass cytometry experiments, in which protein expression is measured within an individual cell for multiple markers. Tens of thousands of cells are measured serving as biological replicates. Applying the Bayesian models, we report protein functional networks under different experimental conditions and the differences between the networks, ie, differential networks. We also present the differential network in a novel fashion that allows direct observation of the links between the experimental agent and its putative targeted proteins based on posterior inference. Our method serves as a powerful tool for studying molecular interactions at cellular level. PMID:25574129

  19. A monolithic glass chip for active single-cell sorting based on mechanical phenotyping.

    PubMed

    Faigle, Christoph; Lautenschläger, Franziska; Whyte, Graeme; Homewood, Philip; Martín-Badosa, Estela; Guck, Jochen

    2015-03-01

    The mechanical properties of biological cells have long been considered as inherent markers of biological function and disease. However, the screening and active sorting of heterogeneous populations based on serial single-cell mechanical measurements has not been demonstrated. Here we present a novel monolithic glass chip for combined fluorescence detection and mechanical phenotyping using an optical stretcher. A new design and manufacturing process, involving the bonding of two asymmetrically etched glass plates, combines exact optical fiber alignment, low laser damage threshold and high imaging quality with the possibility of several microfluidic inlet and outlet channels. We show the utility of such a custom-built optical stretcher glass chip by measuring and sorting single cells in a heterogeneous population based on their different mechanical properties and verify sorting accuracy by simultaneous fluorescence detection. This offers new possibilities of exact characterization and sorting of small populations based on rheological properties for biological and biomedical applications. PMID:25537986

  20. BAYESIAN HIERARCHICAL MODELING FOR SIGNALING PATHWAY INFERENCE FROM SINGLE CELL INTERVENTIONAL DATA1

    PubMed Central

    Luo, Ruiyan; Zhao, Hongyu

    2011-01-01

    Recent technological advances have made it possible to simultaneously measure multiple protein activities at the single cell level. With such data collected under different stimulatory or inhibitory conditions, it is possible to infer the causal relationships among proteins from single cell interventional data. In this article we propose a Bayesian hierarchical modeling framework to infer the signaling pathway based on the posterior distributions of parameters in the model. Under this framework, we consider network sparsity and model the existence of an association between two proteins both at the overall level across all experiments and at each individual experimental level. This allows us to infer the pairs of proteins that are associated with each other and their causal relationships. We also explicitly consider both intrinsic noise and measurement error. Markov chain Monte Carlo is implemented for statistical inference. We demonstrate that this hierarchical modeling can effectively pool information from different interventional experiments through simulation studies and real data analysis. PMID:22162986

  1. From Molecules to Cells to Organisms: Understanding Health and Disease with Multidimensional Single-Cell Methods

    NASA Astrophysics Data System (ADS)

    Candia, Julián

    2013-03-01

    The multidimensional nature of many single-cell measurements (e.g. multiple markers measured simultaneously using Fluorescence-Activated Cell Sorting (FACS) technologies) offers unprecedented opportunities to unravel emergent phenomena that are governed by the cooperative action of multiple elements across different scales, from molecules and proteins to cells and organisms. We will discuss an integrated analysis framework to investigate multicolor FACS data from different perspectives: Singular Value Decomposition to achieve an effective dimensional reduction in the data representation, machine learning techniques to separate different patient classes and improve diagnosis, as well as a novel cell-similarity network analysis method to identify cell subpopulations in an unbiased manner. Besides FACS data, this framework is versatile: in this vein, we will demonstrate an application to the multidimensional single-cell shape analysis of healthy and prematurely aged cells.

  2. Optofluidic single-cell absorption flow analyzer for point-of-care diagnosis of malaria.

    PubMed

    Banoth, Earu; Kasula, Vamshi Krishna; Jagannadh, Veerendra Kalyan; Gorthi, Sai Siva

    2016-06-01

    In this work, an optofluidic flow analyzer, which can be used to perform malaria diagnosis at the point-of-care is demonstrated. The presented technique is based on quantitative optical absorption measurements carried out on a single cell level for a given population of Human Red Blood Cells (RBCs). By measuring the optical absorption of each RBC, the decrease in the Hemoglobin (Hb) concentration in the cytoplasm of the cell due to the invasion of malarial parasite is detected. Cells are assessed on a single cell basis, as they pass through a microfluidic channel. The proposed technique has been implemented with inexpensive off-the-shelf components like laser diode, photo-detector and a micro-controller. The ability of the optofluidic flow analyzer to asses about 308,049 cells within 3 minutes has been demonstrated. The presented technique is capable of detecting very low parasitemia levels with high sensitivity. PMID:26192714

  3. Measurement of the oxygen partial pressure and thermodynamic modeling of the U-Nd-O system

    NASA Astrophysics Data System (ADS)

    Lee, Seung Min; Knight, Travis W.; McMurray, Jacob W.; Besmann, Theodore M.

    2016-05-01

    Fission products greatly impact the properties of fuel necessitating a thorough understanding of the thermochemical properties of oxide fuels with fission products. However, thermochemical data for the U-Nd-O system is insufficient even though neodymium is a major fission product. As neodymium will likely be present as a solute in UO2, this research focuses on the study of (U1-yNdy)O2±x. Experimental measurements and analyses of the oxygen partial pressure (pO2)-temperature-oxygen to metal ratio (O/M ratio) relationships were performed using a thermogravimetric analyzer (TGA) and an oxygen analyzer. Thermodynamic computational modeling was performed using the CALPHAD (CALculation of PHAse Diagrams) method with the FactSage software. The Gibbs energy of the (U1-yNdy)O2±x solid solution was described by the compound energy formalism (CEF), which is based on earlier thermodynamic modeling data of the binary U-O system from Guéneau et al.. The thermodynamic and phase diagram data of the U-Nd-O system produced in this work show good agreement with the experimental data.

  4. Measurement of changes in blood oxygenation using Multispectral Optoacoustic Tomography (MSOT) allows assessment of tumor development

    NASA Astrophysics Data System (ADS)

    Tomaszewski, Michal R.; Quiros-Gonzalez, Isabel; Joseph, James; Bohndiek, Sarah E.

    2016-03-01

    The ability to evaluate tumor oxygenation in the clinic could indicate prognosis and enable treatment monitoring, since oxygen deficient cancer cells are more resistant to chemotherapy and radiotherapy. MultiSpectral Optoacoustic Tomography (MSOT) is a hybrid technique combining the high contrast of optical imaging with the spatial resolution and penetration depth similar to ultrasound. We aim to demonstrate that MSOT can be used to monitor the development of tumor vasculature. To establish the relationship between MSOT derived imaging biomarkers and biological changes during tumor development, we performed MSOT on nude mice (n=10) bearing subcutaneous xenograft U87 glioblastoma tumors using a small animal optoacoustic tomography system. The mice were maintained under inhalation anesthesia during imaging and respired oxygen content was modified between 21% and 100%. The measurements from early (week 4) and late (week 7) stages of tumor development were compared. To further explore the functionality of the blood vessels, we examined the evolution of changes in the abundance of oxy- and deoxyhemoglobin in the tumors in response to a gas challenge. We found that the kinetics of the change in oxygen saturation (SO2) were significantly different between small tumors and the healthy blood vessels in nearby normal tissue (p=0.0054). Furthermore, we showed that there was a significant difference in the kinetics of the gas challenge between small and large tumors (p=0.0015). We also found that the tumor SO2 was significantly correlated (p=0.0057) with the tumor necrotic fraction as assessed by H&E staining in histology. In the future, this approach may be of use in the clinic as a method for tumor staging and assessment of treatment response.

  5. Modeling the dynamics of metabolism in montane streams using continuous dissolved oxygen measurements

    NASA Astrophysics Data System (ADS)

    Birkel, Christian; Soulsby, Chris; Malcolm, Iain; Tetzlaff, Doerthe

    2013-09-01

    We inferred in-stream ecosystem processes in terms of photosynthetic productivity (P), system respiration (R), and reaeration capacity (RC) from a five parameter numerical oxygen mass balance model driven by radiation, stream and air temperature, and stream depth. This was calibrated to high-resolution (15 min), long-term (2.5 years) dissolved oxygen (DO) time series for moorland and forest reaches of a third-order montane stream in Scotland. The model was multicriteria calibrated to continuous 24 h periods within the time series to identify behavioral simulations representative of ecosystem functioning. Results were evaluated using a seasonal regional sensitivity analysis and a colinearity index for parameter sensitivity. This showed that >95 % of the behavioral models for the moorland and forest sites were identifiable and able to infer in-stream processes from the DO time series for around 40% and 32% of the time period, respectively. Monthly P/R ratios <1 indicate a heterotrophic system with both sites exhibiting similar temporal patterns; with a maximum in February and a second peak during summer months. However, the estimated net ecosystem productivity suggests that the moorland reach without riparian tree cover is likely to be a much larger source of carbon to the atmosphere (122 mmol C m-2 d-1) compared to the forested reach (64 mmol C m-2 d-1). We conclude that such process-based oxygen mass balance models may be transferable tools for investigating other systems; specifically, well-oxygenated upland channels with high hydraulic roughness and lacking reaeration measurements.

  6. Genetic programs constructed from layered logic gates in single cells

    PubMed Central

    Moon, Tae Seok; Lou, Chunbo; Tamsir, Alvin; Stanton, Brynne C.; Voigt, Christopher A.

    2014-01-01

    Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics1. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits2–6, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits1,7. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator–chaperone pairs are identified from type III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells. PMID:23041931

  7. A pilot study of a new spectrophotometry device to measure tissue oxygen saturation.

    PubMed

    Abel, Gemma; Allen, John; Drinnan, Michael

    2014-09-01

    Tissue oxygen saturation (SO2) measurements have the potential for far wider use than at present but are limited by device availability and portability for many potential applications. A device based on a small, low-cost general-purpose spectrophotometer (the Harrison device) might facilitate wider use. The aim of this study was to compare the Harrison device with a commercial instrument, the LEA O2C.Measurements were carried out on the forearm and finger of 20 healthy volunteers, using a blood pressure cuff on the upper arm to induce different levels of oxygenation. Repeatability of both devices was assessed, and the Bland-Altman method was used to assess agreement between them.The devices showed agreement in overall tracking of changes in SO2. Test-retest agreement for the Harrison device was worse than for O2C, with SD repeatability of 10.6% (forearm) or 18.6% (finger). There was no overall bias between devices, but mean (SD) difference of 1.2 (11.8%) (forearm) or 4.4 (11.5%) (finger) were outside of a clinically acceptable range.Disagreements were attributed to the stability of the Harrison probe and the natural SO2 variations across the skin surface increasing the random error. Therefore, though not equivalent to the LEA O2C, a probe redesign and averaged measurements may help establish the Harrison device as a low cost alternative. PMID:25119876

  8. Continuous measurements of greenhouse gases and atmospheric oxygen at the Namib Desert Atmospheric Observatory

    NASA Astrophysics Data System (ADS)

    Morgan, E. J.; Lavrič, J. V.; Seifert, T.; Chicoine, T.; Day, A.; Gomez, J.; Logan, R.; Sack, J.; Shuuya, T.; Uushona, E. G.; Vincent, K.; Schultz, U.; Brunke, E.-G.; Labuschagne, C.; Thompson, R. L.; Schmidt, S.; Manning, A. C.; Heimann, M.

    2015-06-01

    A new coastal background site has been established for observations of greenhouse gases (GHGs) in the central Namib Desert at Gobabeb, Namibia. The location of the site was chosen to provide observations for a data-poor region in the global sampling network for GHGs. Semi-automated continuous measurements of carbon dioxide, methane, nitrous oxide, carbon monoxide, atmospheric oxygen, and basic meteorology are made at a height of 21 m a.g.l., 50 km from the coast at the northern border of the Namib Sand Sea. Atmospheric oxygen is measured with a differential fuel cell analyzer (DFCA). Carbon dioxide and methane are measured with an early-model cavity ring-down spectrometer (CRDS); nitrous oxide and carbon monoxide are measured with an off-axis integrated cavity output spectrometer (OA-ICOS). Instrument-specific water corrections are employed for both the CRDS and OA-ICOS instruments in lieu of drying. The performance and measurement uncertainties are discussed in detail. As the station is located in a remote desert environment, there are some particular challenges, namely fine dust, high diurnal temperature variability, and minimal infrastructure. The gas handling system and calibration scheme were tailored to best fit the conditions of the site. The CRDS and DFCA provide data of acceptable quality when base requirements for operation are met, specifically adequate temperature control in the laboratory and regular supply of electricity. In the case of the OA-ICOS instrument, performance is significantly improved through the implementation of a drift correction through frequent measurements of a reference cylinder.

  9. Continuous measurements of greenhouse gases and atmospheric oxygen at the Namib Desert Atmospheric Observatory

    NASA Astrophysics Data System (ADS)

    Morgan, E. J.; Lavrič, J. V.; Seifert, T.; Chicoine, T.; Day, A.; Gomez, J.; Logan, R.; Sack, J.; Shuuya, T.; Uushona, E. G.; Vincent, K.; Schultz, U.; Brunke, E.-G.; Labuschagne, C.; Thompson, R. L.; Schmidt, S.; Manning, A. C.; Heimann, M.

    2015-02-01

    A new coastal background site has been established for observations of greenhouse gases (GHGs) in the central Namib Desert at Gobabeb, Namibia. The location of the site was chosen to provide observations for a data-poor region in the global sampling network for GHGs. Semi-automated, continuous measurements of carbon dioxide, methane, nitrous oxide, carbon monoxide, atmospheric oxygen, and basic meteorology are made at a height of 21 m a.g.l., 50 km from the coast at the northern border of the Namib Sand Sea. Atmospheric oxygen is measured with a differential fuel cell analyzer (DFCA). Carbon dioxide and methane are measured with an early-model cavity ring-down spectrometer (CRDS); nitrous oxide and carbon monoxide are measured with an off-axis integrated cavity output spectrometer (OA-ICOS). Instrument-specific water corrections are employed for both the CRDS and OA-ICOS instruments in lieu of drying. The performance and measurement uncertainties are discussed in detail. As the station is located in a remote desert environment, there are some particular challenges, namely fine dust, high diurnal temperature variability, and minimal infrastructure. The gas handling system and calibration scheme were tailored to best fit the conditions of the site. The CRDS and DFCA provide data of acceptable quality when base requirements for operation are met, specifically adequate temperature control in the laboratory and regular supply of electricity. In the case of the OA-ICOS instrument, performance is significantly improved through the implementation of a drift correction through frequent measurements of a working tank.

  10. Genomic Analysis at the Single-Cell Level

    PubMed Central

    Kalisky, Tomer; Blainey, Paul; Quake, Stephen R.

    2013-01-01

    Studying complex biological systems such as a developing embryo, a tumor, or a microbial ecosystem often involves understanding the behavior and heterogeneity of the individual cells that constitute the system and their interactions. In this review, we discuss a variety of approaches to single-cell genomic analysis. PMID:21942365

  11. Single-cell chromatin accessibility reveals principles of regulatory variation.

    PubMed

    Buenrostro, Jason D; Wu, Beijing; Litzenburger, Ulrike M; Ruff, Dave; Gonzales, Michael L; Snyder, Michael P; Chang, Howard Y; Greenleaf, William J

    2015-07-23

    Cell-to-cell variation is a universal feature of life that affects a wide range of biological phenomena, from developmental plasticity to tumour heterogeneity. Although recent advances have improved our ability to document cellular phenotypic variation, the fundamental mechanisms that generate variability from identical DNA sequences remain elusive. Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq) integrated into a programmable microfluidics platform. Single-cell ATAC-seq (scATAC-seq) maps from hundreds of single cells in aggregate closely resemble accessibility profiles from tens of millions of cells and provide insights into cell-to-cell variation. Accessibility variance is systematically associated with specific trans-factors and cis-elements, and we discover combinations of trans-factors associated with either induction or suppression of cell-to-cell variability. We further identify sets of trans-factors associated with cell-type-specific accessibility variance across eight cell types. Targeted perturbations of cell cycle or transcription factor signalling evoke stimulus-specific changes in this observed variability. The pattern of accessibility variation in cis across the genome recapitulates chromosome compartments de novo, linking single-cell accessibility variation to three-dimensional genome organization. Single-cell analysis of DNA accessibility provides new insight into cellular variation of the 'regulome'. PMID:26083756

  12. Multi-Omics of Single Cells: Strategies and Applications.

    PubMed

    Bock, Christoph; Farlik, Matthias; Sheffield, Nathan C

    2016-08-01

    Most genome-wide assays provide averages across large numbers of cells, but recent technological advances promise to overcome this limitation. Pioneering single-cell assays are now available for genome, epigenome, transcriptome, proteome, and metabolome profiling. Here, we describe how these different dimensions can be combined into multi-omics assays that provide comprehensive profiles of the same cell. PMID:27212022

  13. Tumor Heterogeneity, Single-Cell Sequencing, and Drug Resistance.

    PubMed

    Schmidt, Felix; Efferth, Thomas

    2016-01-01

    Tumor heterogeneity has been compared with Darwinian evolution and survival of the fittest. The evolutionary ecosystem of tumors consisting of heterogeneous tumor cell populations represents a considerable challenge to tumor therapy, since all genetically and phenotypically different subpopulations have to be efficiently killed by therapy. Otherwise, even small surviving subpopulations may cause repopulation and refractory tumors. Single-cell sequencing allows for a better understanding of the genomic principles of tumor heterogeneity and represents the basis for more successful tumor treatments. The isolation and sequencing of single tumor cells still represents a considerable technical challenge and consists of three major steps: (1) single cell isolation (e.g., by laser-capture microdissection), fluorescence-activated cell sorting, micromanipulation, whole genome amplification (e.g., with the help of Phi29 DNA polymerase), and transcriptome-wide next generation sequencing technologies (e.g., 454 pyrosequencing, Illumina sequencing, and other systems). Data demonstrating the feasibility of single-cell sequencing for monitoring the emergence of drug-resistant cell clones in patient samples are discussed herein. It is envisioned that single-cell sequencing will be a valuable asset to assist the design of regimens for personalized tumor therapies based on tumor subpopulation-specific genetic alterations in individual patients. PMID:27322289

  14. Single cell metastatic phenotyping using pulsed nanomechanical indentations

    NASA Astrophysics Data System (ADS)

    Babahosseini, Hesam; Strobl, Jeannine S.; Agah, Masoud

    2015-09-01

    The existing approach to characterize cell biomechanical properties typically utilizes switch-like models of mechanotransduction in which cell responses are analyzed in response to a single nanomechanical indentation or a transient pulsed stress. Although this approach provides effective descriptors at population-level, at a single-cell-level, there are significant overlaps in the biomechanical descriptors of non-metastatic and metastatic cells which precludes the use of biomechanical markers for single cell metastatic phenotyping. This study presents a new promising marker for biosensing metastatic and non-metastatic cells at a single-cell-level using the effects of a dynamic microenvironment on the biomechanical properties of cells. Two non-metastatic and two metastatic epithelial breast cell lines are subjected to a pulsed stresses regimen exerted by atomic force microscopy. The force-time data obtained for the cells revealed that the non-metastatic cells increase their resistance against deformation and become more stiffened when subjected to a series of nanomechanical indentations. On the other hand, metastatic cells become slightly softened when their mechanical microenvironment is subjected to a similar dynamical changes. This distinct behavior of the non-metastatic and metastatic cells to the pulsed stresses paradigm provided a signature for single-cell-level metastatic phenotyping with a high confidence level of ∼95%.

  15. Single-cell genomics for dissection of complex malaria infections

    PubMed Central

    Nair, Shalini; Nkhoma, Standwell C.; Serre, David; Zimmerman, Peter A.; Gorena, Karla; Daniel, Benjamin J.; Nosten, François; Anderson, Timothy J.C.; Cheeseman, Ian H.

    2014-01-01

    Most malaria infections contain complex mixtures of distinct parasite lineages. These multiple-genotype infections (MGIs) impact virulence evolution, drug resistance, intra-host dynamics, and recombination, but are poorly understood. To address this we have developed a single-cell genomics approach to dissect MGIs. By combining cell sorting and whole-genome amplification (WGA), we are able to generate high-quality material from parasite-infected red blood cells (RBCs) for genotyping and next-generation sequencing. We optimized our approach through analysis of >260 single-cell assays. To quantify accuracy, we decomposed mixtures of known parasite genotypes and obtained highly accurate (>99%) single-cell genotypes. We applied this validated approach directly to infections of two major malaria species, Plasmodium falciparum, for which long term culture is possible, and Plasmodium vivax, for which no long-term culture is feasible. We demonstrate that our single-cell genomics approach can be used to generate parasite genome sequences directly from patient blood in order to unravel the complexity of P. vivax and P. falciparum infections. These methods open the door for large-scale analysis of within-host variation of malaria infections, and reveal information on relatedness and drug resistance haplotypes that is inaccessible through conventional sequencing of infections. PMID:24812326

  16. Analysis of Intracellular Glucose at Single Cells Using Electrochemiluminescence Imaging.

    PubMed

    Xu, Jingjing; Huang, Peiyuan; Qin, Yu; Jiang, Dechen; Chen, Hong-Yuan

    2016-05-01

    Here, luminol electrochemiluminescence was first applied to analyze intracellular molecules, such as glucose, at single cells. The individual cells were retained in cell-sized microwells on a gold coated indium tin oxide (ITO) slide, which were treated with luminol, triton X-100, and glucose oxidase simultaneously. The broken cellular membrane in the presence of triton X-100 released intracellular glucose into the microwell and reacted with glucose oxidase to generate hydrogen peroxide, which induced luminol luminescence under positive potential. To achieve fast analysis, the luminescences from 64 individual cells on one ITO slide were imaged in 60 s using a charge-coupled device (CCD). More luminescence was observed at all the microwells after the introduction of triton X-100 and glucose oxidase suggested that intracellular glucose was detected at single cells. The starvation of cells to decrease intracellular glucose produced less luminescence, which confirmed that our luminescence intensity was correlated with the concentration of intracellular glucose. Large deviations in glucose concentration at observed single cells revealed high cellular heterogeneity in intracellular glucose for the first time. This developed electrochemiluminescence assay will be potentially applied for fast analysis of more intracellular molecules in single cells to elucidate cellular heterogeneity. PMID:27094779

  17. Separation of a single cell by red-laser manipulation

    NASA Astrophysics Data System (ADS)

    Shikano, Shuji; Horio, Koji; Ohtsuka, Yoshihiro; Eto, Yuzuro

    1999-10-01

    A single cell of yeast was separated from a bulk sample of yeast without causing damage to the cell. A focused red-laser light beam was used for trapping and transporting the cell. A specially designed microchannel separator played an essential role in the success of the separation.

  18. Modeling genome coverage in single-cell sequencing

    PubMed Central

    Daley, Timothy; Smith, Andrew D.

    2014-01-01

    Motivation: Single-cell DNA sequencing is necessary for examining genetic variation at the cellular level, which remains hidden in bulk sequencing experiments. But because they begin with such small amounts of starting material, the amount of information that is obtained from single-cell sequencing experiment is highly sensitive to the choice of protocol employed and variability in library preparation. In particular, the fraction of the genome represented in single-cell sequencing libraries exhibits extreme variability due to quantitative biases in amplification and loss of genetic material. Results: We propose a method to predict the genome coverage of a deep sequencing experiment using information from an initial shallow sequencing experiment mapped to a reference genome. The observed coverage statistics are used in a non-parametric empirical Bayes Poisson model to estimate the gain in coverage from deeper sequencing. This approach allows researchers to know statistical features of deep sequencing experiments without actually sequencing deeply, providing a basis for optimizing and comparing single-cell sequencing protocols or screening libraries. Availability and implementation: The method is available as part of the preseq software package. Source code is available at http://smithlabresearch.org/preseq. Contact: andrewds@usc.edu Supplementary information: Supplementary material is available at Bioinformatics online. PMID:25107873

  19. Enhanced single-cell printing by acoustophoretic cell focusing

    PubMed Central

    Leibacher, I.; Schoendube, J.; Dual, J.; Zengerle, R.; Koltay, P.

    2015-01-01

    Recent years have witnessed a strong trend towards analysis of single-cells. To access and handle single-cells, many new tools are needed and have partly been developed. Here, we present an improved version of a single-cell printer which is able to deliver individual single cells and beads encapsulated in free-flying picoliter droplets at a single-bead efficiency of 96% and with a throughput of more than 10 beads per minute. By integration of acoustophoretic focusing, the cells could be focused in x and y direction. This way, the cells were lined-up in front of a 40 μm nozzle, where they were analyzed individually by an optical system prior to printing. In agreement with acoustic simulations, the focusing of 10 μm beads and Raji cells has been achieved with an efficiency of 99% (beads) and 86% (Raji cells) to a 40 μm wide center region in the 1 mm wide microfluidic channel. This enabled improved optical analysis and reduced bead losses. The loss of beads that ended up in the waste (because printing them as single beads arrangements could not be ensured) was reduced from 52% ± 6% to 28% ± 1%. The piezoelectric transducer employed for cell focusing could be positioned on an outer part of the device, which proves the acoustophoretic focusing to be versatile and adaptable. PMID:25945135

  20. Tumor Heterogeneity, Single-Cell Sequencing, and Drug Resistance

    PubMed Central

    Schmidt, Felix; Efferth, Thomas

    2016-01-01

    Tumor heterogeneity has been compared with Darwinian evolution and survival of the fittest. The evolutionary ecosystem of tumors consisting of heterogeneous tumor cell populations represents a considerable challenge to tumor therapy, since all genetically and phenotypically different subpopulations have to be efficiently killed by therapy. Otherwise, even small surviving subpopulations may cause repopulation and refractory tumors. Single-cell sequencing allows for a better understanding of the genomic principles of tumor heterogeneity and represents the basis for more successful tumor treatments. The isolation and sequencing of single tumor cells still represents a considerable technical challenge and consists of three major steps: (1) single cell isolation (e.g., by laser-capture microdissection), fluorescence-activated cell sorting, micromanipulation, whole genome amplification (e.g., with the help of Phi29 DNA polymerase), and transcriptome-wide next generation sequencing technologies (e.g., 454 pyrosequencing, Illumina sequencing, and other systems). Data demonstrating the feasibility of single-cell sequencing for monitoring the emergence of drug-resistant cell clones in patient samples are discussed herein. It is envisioned that single-cell sequencing will be a valuable asset to assist the design of regimens for personalized tumor therapies based on tumor subpopulation-specific genetic alterations in individual patients. PMID:27322289

  1. Simultaneous in-situ measurements of neutral temperature and oxygen in the mesosphere during the WADIS sounding rocket project

    NASA Astrophysics Data System (ADS)

    Strelnikov, Boris; Lübken, Franz-Josef; Rapp, Markus; Grygalashvyly, Mykhaylo; Löhle, Stefan; Eberhart, Martin; Fasoulas, Stefanos; Hedin, Jonas; Gumbel, Jörg; Khaplanov, Mikhail; Stegman, Jacek; Friedrich, Martin

    2016-04-01

    The WADIS project (Wave propagation and dissipation in the middle atmosphere: energy budget and distribution of trace constituents) aimed at studying waves, their dissipation, and effects on trace constituents. The project comprised two sounding rocket campaigns conducted at the Andøya Space Center (69 °N, 16 °E). One sounding rocket was launched in summer 2013 and one in winter 2015. In-situ measurements delivered high resolution altitude-profiles of neutral temperature and density, as well as plasma and oxygen densities. Atomic oxygen was measured by two different techniques. Airglow photometers operated by MISU measured emissions from excited molecular oxygen at 1.27 um (daytime summer launch) and 762 nm (night-time winter launch), both of which can be used to infer altitude profiles of atomic oxygen. This is a well-proven technique and has been applied to sounding rocket and satellite measurements in the past. Solid electrolyte sensors (FIPEX) operated by IRS is a new technique for sounding rockets, which yielded atomic oxygen density profiles with a height resolution better than 10 m. The neutral air density and temperature was measured by the CONE instrument also with very heigh altitude resolution and precision. All these instruments were mounted on the same deck of the sounding rocket and, therefore delivered real common volume measurements. In this paper we present simultaneous in-situ temperature and oxygen density measurements and discuss how variability of these quantities may influence temperature derivations from OH airglow observations at mesopause heights.