Mammalia

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    Protocols in Current Issue
    An in vitro DNA Sensor-based Assay to Measure Receptor-specific Adhesion Forces of Eukaryotic Cells and Pathogens
    Authors:  Maurizio Wack, Tina Wiegand, Friedrich Frischknecht and E. Ada Cavalcanti-Adam, date: 09/05/2020, view: 716, Q&A: 0
    Motility of eukaryotic cells or pathogens within tissues is mediated by the turnover of specific interactions with other cells or with the extracellular matrix. Biophysical characterization of these ligand-receptor adhesions helps to unravel the ...
    The Peak Interval Procedure in Rodents: A Tool for Studying the Neurobiological Basis of Interval Timing and Its Alterations in Models of Human Disease
    Authors:  Fuat Balcı and David Freestone, date: 09/05/2020, view: 359, Q&A: 0
    Animals keep track of time intervals in the seconds to minutes range with, on average, high accuracy but substantial trial-to-trial variability. The ability to detect the statistical signatures of such timing behavior is an indispensable feature of ...
    Flow-cytometric Detection of Low-level Reactive Oxygen Species in Cell Lines and Primary Immune Cells
    Authors:  Kevin Bode, Corinna Link, Peter H. Krammer and Heiko Weyd, date: 09/05/2020, view: 905, Q&A: 0
    Depending on its concentration and cellular origin the production of reactive oxygen species (ROS) in the organism serves a variety of functions. While high concentrations during an oxidative burst are used to fight pathogens, low to moderate ...
    Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry
    Authors:  Hanae Sato, Robert H. Singer and John M. Greally, date: 09/05/2020, view: 611, Q&A: 0
    Dynamic histone changes occur as a central part of chromatin regulation. Deposition of histone variants and post-translational modifications of histones are strongly associated with properties of chromatin status. Characterizing the kinetics of ...
    Live-cell Imaging by Super-resolution Confocal Live Imaging Microscopy (SCLIM): Simultaneous Three-color and Four-dimensional Live Cell Imaging with High Space and Time Resolution
    Authors:  Kazuo Kurokawa and Akihiko Nakano, date: 09/05/2020, view: 674, Q&A: 0
    Many questions in cell biology can be solved by state-of-the-art technology of live cell imaging. One good example is the mechanism of membrane traffic, in which small membrane carriers are rapidly moving around in the cytoplasm to deliver cargo ...
    Optogenetic Tuning of Protein-protein Binding in Bilayers Using LOVTRAP
    Authors:  Doug Tischer and Orion D. Weiner, date: 09/05/2020, view: 662, Q&A: 0
    Modern microscopy methods are powerful tools for studying live cell signaling and biochemical reactions, enabling us to observe when and where these reactions take place from the level of a cell down to single molecules. With microscopy, each cell ...
    Identification of Socially-activated Neurons
    Authors:  Mary L. Phillips and Lucas Pozzo-Miller, date: 09/05/2020, view: 479, Q&A: 0
    Determining the neuronal circuitry responsible for specific behaviors is a major focus in the field of neurobiology. Activity-dependent immediate early genes (IEGs), transcribed and translated shortly after neurons discharge action potentials, have ...
    Multiplication and Growth Inhibition Activity Assays for the Zoonotic Malaria Parasite, Plasmodium knowlesi
    Authors:  Franziska Mohring, Thomas A. Rawlinson, Simon J. Draper and Robert W. Moon, date: 09/05/2020, view: 456, Q&A: 0
    Malaria remains a major cause of morbidity and mortality globally. Clinical symptoms of the disease arise from the growth and multiplication of Plasmodium parasites within the blood of the host. Thus in vitro assays to determine ...
    Measuring Breathing Patterns in Mice Using Whole-body Plethysmography
    Respiratory dysfunction is among the main cause of severe and fatal pathologies worldwide. The use of effective experimental models and methodologies for the study of the pulmonary pathophysiology is necessary to prevent, control and cure these ...
    BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
    Authors:  Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo, date: 09/05/2020, view: 754, Q&A: 0
    Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein ...
    Integration of Human Induced Pluripotent Stem Cell (hiPSC)-Derived Neurons into Rat Brain
    Authors:  Xiling Yin, Ted M. Dawson and Valina L. Dawson, date: 09/05/2020, view: 640, Q&A: 0
    Human neuron transplantation offers novel opportunities for modeling human neurologic diseases and potentially replacement therapies. However, the complex structure of the human cerebral cortex, which is organized in six layers with tightly ...
    An in vitro DNA Sensor-based Assay to Measure Receptor-specific Adhesion Forces of Eukaryotic Cells and Pathogens
    Authors:  Maurizio Wack, Tina Wiegand, Friedrich Frischknecht and E. Ada Cavalcanti-Adam, date: 09/05/2020, view: 716, Q&A: 0
    [Abstract] Motility of eukaryotic cells or pathogens within tissues is mediated by the turnover of specific interactions with other cells or with the extracellular matrix. Biophysical characterization of these ligand-receptor adhesions helps to unravel the molecular mechanisms driving migration. Traction force microscopy or optical tweezers are typically ...
    The Peak Interval Procedure in Rodents: A Tool for Studying the Neurobiological Basis of Interval Timing and Its Alterations in Models of Human Disease
    Authors:  Fuat Balcı and David Freestone, date: 09/05/2020, view: 359, Q&A: 0
    [Abstract] Animals keep track of time intervals in the seconds to minutes range with, on average, high accuracy but substantial trial-to-trial variability. The ability to detect the statistical signatures of such timing behavior is an indispensable feature of a good and theoretically-tractable testing procedure. A widely used interval timing procedure is the ...
    Flow-cytometric Detection of Low-level Reactive Oxygen Species in Cell Lines and Primary Immune Cells
    Authors:  Kevin Bode, Corinna Link, Peter H. Krammer and Heiko Weyd, date: 09/05/2020, view: 905, Q&A: 0
    [Abstract] Depending on its concentration and cellular origin the production of reactive oxygen species (ROS) in the organism serves a variety of functions. While high concentrations during an oxidative burst are used to fight pathogens, low to moderate amounts of ROS act as signaling molecules important for several physiological processes such as regulation ...
    Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry
    Authors:  Hanae Sato, Robert H. Singer and John M. Greally, date: 09/05/2020, view: 611, Q&A: 0
    [Abstract] Dynamic histone changes occur as a central part of chromatin regulation. Deposition of histone variants and post-translational modifications of histones are strongly associated with properties of chromatin status. Characterizing the kinetics of histone variants allows important insights into transcription regulation, chromatin maintenance and ...
    Live-cell Imaging by Super-resolution Confocal Live Imaging Microscopy (SCLIM): Simultaneous Three-color and Four-dimensional Live Cell Imaging with High Space and Time Resolution
    Authors:  Kazuo Kurokawa and Akihiko Nakano, date: 09/05/2020, view: 674, Q&A: 0
    [Abstract] Many questions in cell biology can be solved by state-of-the-art technology of live cell imaging. One good example is the mechanism of membrane traffic, in which small membrane carriers are rapidly moving around in the cytoplasm to deliver cargo proteins between organelles. For directly visualizing the events in membrane trafficking system, ...
    Optogenetic Tuning of Protein-protein Binding in Bilayers Using LOVTRAP
    Authors:  Doug Tischer and Orion D. Weiner, date: 09/05/2020, view: 662, Q&A: 0
    [Abstract] Modern microscopy methods are powerful tools for studying live cell signaling and biochemical reactions, enabling us to observe when and where these reactions take place from the level of a cell down to single molecules. With microscopy, each cell or molecule can be observed both before and after a given perturbation, facilitating better inference ...
    Identification of Socially-activated Neurons
    Authors:  Mary L. Phillips and Lucas Pozzo-Miller, date: 09/05/2020, view: 479, Q&A: 0
    [Abstract] Determining the neuronal circuitry responsible for specific behaviors is a major focus in the field of neurobiology. Activity-dependent immediate early genes (IEGs), transcribed and translated shortly after neurons discharge action potentials, have been used extensively to either identify or gain genetic access to neurons and brain regions ...
    Multiplication and Growth Inhibition Activity Assays for the Zoonotic Malaria Parasite, Plasmodium knowlesi
    Authors:  Franziska Mohring, Thomas A. Rawlinson, Simon J. Draper and Robert W. Moon, date: 09/05/2020, view: 456, Q&A: 0
    [Abstract] Malaria remains a major cause of morbidity and mortality globally. Clinical symptoms of the disease arise from the growth and multiplication of Plasmodium parasites within the blood of the host. Thus in vitro assays to determine how drug, antibody and genetic perturbations affect the growth rate of Plasmodium parasites ...
    Measuring Breathing Patterns in Mice Using Whole-body Plethysmography
    [Abstract] Respiratory dysfunction is among the main cause of severe and fatal pathologies worldwide. The use of effective experimental models and methodologies for the study of the pulmonary pathophysiology is necessary to prevent, control and cure these diseases. Plethysmography, a technique for the assessment of lung function, has been widely applied in ...
    BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
    Authors:  Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo, date: 09/05/2020, view: 754, Q&A: 0
    [Abstract] Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein conformational analysis and ligand binding calculations, using vetted methods and protocols can be a ...



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