High Throughput

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Falk Schreiber - One of the best experts on this subject based on the ideXlab platform.

  • htpheno an image analysis pipeline for High Throughput plant phenotyping
    BMC Bioinformatics, 2011
    Co-Authors: Anja Hartmann, Tobias Czauderna, Roberto Hoffmann, Nils Stein, Falk Schreiber
    Abstract:

    In the last few years High-Throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for High-Throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms. This paper presents an image analysis pipeline (HTPheno) for High-Throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening. HTPheno is applied to analyse two barley cultivars. HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in High-Throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.

Tom Misteli - One of the best experts on this subject based on the ideXlab platform.

  • hipla High Throughput imaging proximity ligation assay
    Methods, 2019
    Co-Authors: Leonid A Serebryannyy, Tom Misteli
    Abstract:

    Protein-protein interactions are essential for cellular structure and function. To delineate how the intricate assembly of protein interactions contribute to cellular processes in health and disease, new methodologies that are both Highly sensitive and can be applied at large scale are needed. Here, we develop HiPLA (High-Throughput imaging proximity ligation assay), a method that employs the well-established antibody-based proximity ligation assay in a High-Throughput imaging screening format as a novel means to systematically visualize protein interactomes. Using HiPLA with a library of antibodies targeting nuclear proteins, we probe the interaction of 60 proteins and associated post-translational modifications (PTMs) with the nuclear lamina in a model of the premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). We identify a subset of proteins that differentially interact with the nuclear lamina in HGPS. Using HiPLA in combination with quantitative indirect immunofluorescence, we find that the majority of differential interactions are accompanied by corresponding changes in expression of the interacting protein. Taken together, HiPLA offers a novel approach to probe cellular protein-protein interaction at a large scale and reveals mechanistic insights into the assembly of protein complexes.

  • hipla High Throughput imaging proximity ligation assay
    bioRxiv, 2018
    Co-Authors: Leonid A Serebryannyy, Tom Misteli
    Abstract:

    Protein-protein interactions are essential for cellular structure and function. To delineate how the intricate assembly of protein interactions contribute to cellular processes in health and disease, new methodologies that are both Highly sensitive and can be applied at large scale are needed. Here, we develop HiPLA (High-Throughput imaging proximity ligation assay), a method that employs the antibody-based proximity ligation assay in a High-Throughput imaging screening format to systematically probe protein interactomes. Using HiPLA, we probe the interaction of 60 proteins and associated PTMs with the nuclear lamina in a model of the premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). We identify a subset of proteins that differentially interact with the nuclear lamina in HGPS. In combination with quantitative indirect immunofluorescence, we find that the majority of differential interactions were accompanied by corresponding changes in expression of the interacting protein. Taken together, HiPLA offers a novel approach to probe cellular protein-protein interaction at a large scale and reveals mechanistic insights into the assembly of protein complexes.

George M Whitesides - One of the best experts on this subject based on the ideXlab platform.

  • High Throughput density measurement using magnetic levitation
    Journal of the American Chemical Society, 2018
    Co-Authors: Yunzhe Wang, Nicolas Deshler, Daniel J Preston, George M Whitesides
    Abstract:

    This work describes the development of an integrated analytical system that enables High-Throughput density measurements of diamagnetic particles (including cells) using magnetic levitation (MagLev), 96-well plates, and a flatbed scanner. MagLev is a simple and useful technique with which to carry out density-based analysis and separation of a broad range of diamagnetic materials with different physical forms (e.g., liquids, solids, gels, pastes, gums, etc.); one major limitation, however, is the capacity to perform High-Throughput density measurements. This work addresses this limitation by (i) re-engineering the shape of the magnetic fields so that the MagLev system is compatible with 96-well plates, and (ii) integrating a flatbed scanner (and simple optical components) to carry out imaging of the samples that levitate in the system. The resulting system is compatible with both biological samples (human erythrocytes) and nonbiological samples (simple liquids and solids, such as 3-chlorotoluene, choleste...

  • High-Throughput Density Measurement Using Magnetic Levitation
    2018
    Co-Authors: Yunzhe Wang, Nicolas Deshler, Daniel J Preston, George M Whitesides
    Abstract:

    This work describes the development of an integrated analytical system that enables High-Throughput density measurements of diamagnetic particles (including cells) using magnetic levitation (MagLev), 96-well plates, and a flatbed scanner. MagLev is a simple and useful technique with which to carry out density-based analysis and separation of a broad range of diamagnetic materials with different physical forms (e.g., liquids, solids, gels, pastes, gums, etc.); one major limitation, however, is the capacity to perform High-Throughput density measurements. This work addresses this limitation by (i) re-engineering the shape of the magnetic fields so that the MagLev system is compatible with 96-well plates, and (ii) integrating a flatbed scanner (and simple optical components) to carry out imaging of the samples that levitate in the system. The resulting system is compatible with both biological samples (human erythrocytes) and nonbiological samples (simple liquids and solids, such as 3-chlorotoluene, cholesterol crystals, glass beads, copper powder, and polymer beads). The High-Throughput capacity of this integrated MagLev system will enable new applications in chemistry (e.g., analysis and separation of materials) and biochemistry (e.g., cellular responses under environmental stresses) in a simple and label-free format on the basis of a universal property of all matter, i.e., density

Leonid A Serebryannyy - One of the best experts on this subject based on the ideXlab platform.

  • hipla High Throughput imaging proximity ligation assay
    Methods, 2019
    Co-Authors: Leonid A Serebryannyy, Tom Misteli
    Abstract:

    Protein-protein interactions are essential for cellular structure and function. To delineate how the intricate assembly of protein interactions contribute to cellular processes in health and disease, new methodologies that are both Highly sensitive and can be applied at large scale are needed. Here, we develop HiPLA (High-Throughput imaging proximity ligation assay), a method that employs the well-established antibody-based proximity ligation assay in a High-Throughput imaging screening format as a novel means to systematically visualize protein interactomes. Using HiPLA with a library of antibodies targeting nuclear proteins, we probe the interaction of 60 proteins and associated post-translational modifications (PTMs) with the nuclear lamina in a model of the premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). We identify a subset of proteins that differentially interact with the nuclear lamina in HGPS. Using HiPLA in combination with quantitative indirect immunofluorescence, we find that the majority of differential interactions are accompanied by corresponding changes in expression of the interacting protein. Taken together, HiPLA offers a novel approach to probe cellular protein-protein interaction at a large scale and reveals mechanistic insights into the assembly of protein complexes.

  • hipla High Throughput imaging proximity ligation assay
    bioRxiv, 2018
    Co-Authors: Leonid A Serebryannyy, Tom Misteli
    Abstract:

    Protein-protein interactions are essential for cellular structure and function. To delineate how the intricate assembly of protein interactions contribute to cellular processes in health and disease, new methodologies that are both Highly sensitive and can be applied at large scale are needed. Here, we develop HiPLA (High-Throughput imaging proximity ligation assay), a method that employs the antibody-based proximity ligation assay in a High-Throughput imaging screening format to systematically probe protein interactomes. Using HiPLA, we probe the interaction of 60 proteins and associated PTMs with the nuclear lamina in a model of the premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). We identify a subset of proteins that differentially interact with the nuclear lamina in HGPS. In combination with quantitative indirect immunofluorescence, we find that the majority of differential interactions were accompanied by corresponding changes in expression of the interacting protein. Taken together, HiPLA offers a novel approach to probe cellular protein-protein interaction at a large scale and reveals mechanistic insights into the assembly of protein complexes.

Ulrich Simon - One of the best experts on this subject based on the ideXlab platform.

  • advances in High Throughput screening of gas sensing materials
    Applied Surface Science, 2007
    Co-Authors: Maike Siemons, Tobias J Koplin, Ulrich Simon
    Abstract:

    The workflow of a High Throughput screening setup for the rapid identification of new and improved gas sensor materials is presented. The polyol method was applied to prepare nanoparticulate metal oxides as base materials. These materials have been modified by surface and volume doping. Using multielectrode substrates and High Throughput impedance spectroscopy (HT-IS) a wide range of materials could be screened on a short time scale. Selected examples reflect the state of the art for applying HT-IS in search of new selective gas sensing materials.

  • workflow for High Throughput screening of gas sensing materials
    Sensors, 2006
    Co-Authors: Tobias J Koplin, Maike Siemons, Cesar Ocenvalentin, Daniel Sanders, Ulrich Simon
    Abstract:

    The workflow of a High Throughput screening setup for the rapid identification of new and improved sensor materials is presented. The polyol method was applied to prepare nanoparticular metal oxides as base materials, which were functionalised by surface doping. Using multi-electrode substrates and High Throughput impedance spectroscopy (HT-IS) a wide range of materials could be screened in a short time. Applying HT-IS in search of new selective gas sensing materials a NO2-tolerant NO sensing material with reduced sensitivities towards other test gases was identified based on iridium doped zinc oxide. Analogous behaviour was observed for iridium doped indium oxide.