1Department of Neuroscience, IRCCS - Istituto di Ricerche Farmacologiche Mario Negri
A way to gain new insights into the complexity of the brain inflammatory response is presented. We describe immunofluorescence-based protocols followed by three-dimensional confocal analysis to investigate the pattern of co-expression of microglia/macrophage phenotype markers in a mouse model of focal ischemia.
Published September 4, 2013. Keywords: Neurobiology, Neuroscience, Molecular Biology, Cellular Biology, Medicine, Biomedical Engineering, Anatomy, Physiology, Central Nervous System Diseases, Neurodegenerative Diseases, biology (general), immunology, life sciences, animal models, Inflammation, stroke, alternative activation, brain injury, brain, imaging, confocal microscopy, three-dimensional imaging, clinical techniques, mouse, animal model
1Department of Physics and Astronomy, University of Maine
We demonstrate the use of fluorescence photo activation localization microscopy (FPALM) to simultaneously image multiple types of fluorescently labeled molecules within cells. The techniques described yield the localization of thousands to hundreds of thousands of individual fluorescent labeled proteins, with a precision of tens of nanometers within single cells.
Published December 9, 2013. Keywords: Basic Protocol, Microscopy, Super-resolution imaging, Multicolor, single molecule, FPALM, Localization microscopy, fluorescent proteins
1Department of Mechanical and Aerospace Engineering, The George Washington University, 2Department of Mechanical and Aeronautical Engineering, Clarkson University
Vocal fold polyps can disrupt vocal fold dynamics and thus can have devastating consequences on a patient's ability to communicate. Three-dimensional flow separation induced by a wall-mounted model polyp and its impact on the wall pressure loading are examined using particle image velocimetry, skin friction line visualization, and wall pressure measurements.
Published February 3, 2014. Keywords: Bioengineering, oil-flow visualization, vocal fold polyp, three-dimensional flow separation, aerodynamic pressure loadings
1The Rowland Institute, Harvard University, 2Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista
The three-dimensional locations of weakly-scattering objects can be uniquely identified using digital inline holographic microscopy (DIHM), which involves a minor modification to a standard microscope. Our software uses a simple imaging heuristic coupled with Rayleigh-Sommerfeld back-propagation to yield the three-dimensional position and geometry of a microscopic phase object.
Published February 8, 2014. Keywords: Basic Protocol, holography, digital inline holographic microscopy (DIHM), Microbiology, microscopy, 3D imaging, Streptococcus bacteria
1Department of Chemistry and Biochemistry, University of Notre Dame, 2Freimann Life Science Center, University of Notre Dame, 3Department of Biological Sciences, University of Notre Dame, 4Notre Dame Integrated Imaging Facility, University of Notre Dame, 5MakerBot Industries LLC, 6Departments of Biological Sciences, Aerospace and Mechanical Engineering, and Anthropology, University of Notre Dame, 7Harper Cancer Research Institute, University of Notre Dame
Using modern plastic extrusion and printing technologies, it is now possible to quickly and inexpensively produce physical models of X-ray CT data taken in a laboratory. The three -dimensional printing of tomographic data is a powerful visualization, research, and educational tool that may now be accessed by the preclinical imaging community.
Published March 22, 2013. Keywords: Medicine, Anatomy, Physiology, Molecular Biology, Biomedical Engineering, Bioengineering, Chemistry, Biochemistry, Materials Science, Engineering, Manufactured Materials, Technology, Animal Structures, Life Sciences (General), 3D printing, X-ray Computed Tomography, CT, CT scans, data extrusion, additive printing, in vivo imaging, clinical techniques, imaging
1Department of Neuroscience, Erasmus MC, 2TNO Human Factors
A method is described to measure three-dimensional vestibulo ocular reflexes (3D VOR) in humans using a six degrees of freedom (6DF) motion simulator. The gain and misalignment of the 3D angular VOR provide a direct measure of the quality of vestibular function. Representative data on healthy subjects are provided
Published May 23, 2013. Keywords: Neurobiology, Neuroscience, Medicine, Anatomy, Physiology, Biomedical Engineering, Ophthalmology, vestibulo ocular reflex, eye movements, torsion, balance disorders, rotation translation, equilibrium, eye rotation, motion, body rotation, vestibular organ, clinical techniques
1Basic Medical Sciences, University of Arizona College of Medicine - Phoenix
A rotating cell culture system that allows epithelial cells to grow under physiological conditions resulting in 3-D cellular aggregate formation is described. The aggregates generated display in vivo-like characteristics not observed in conventional culture models and serve as a more accurate organotypic model system for a multitude of scientific investigations.
Published April 3, 2012. Keywords: Cellular Biology, Rotating wall vessel bioreactor, female reproductive tract, human epithelial cells, three-dimensional in vitro cell culture, organotypic mucosal models, vaginal epithelial cells, microbicide, herpes simplex virus, toxicology, host-pathogen interactions, hormone receptors
1Biomedical Engineering Department, Georgia Institute of Technology
An adhesion frequency assay for measuring receptor-ligand interaction kinetics when both molecules are anchored on the surfaces of the interacting cells is described. This mechanically-based assay is exemplified using a micropipette-pressurized human red blood cell as adhesion sensor and integrin αLβ2 and intercellular adhesion molecule-1 as interacting receptors and ligands.
Published November 2, 2011. Keywords: Bioengineering, Two-dimensional binding, affinity and kinetics, micropipette manipulation, receptor-ligand interaction
1Molecular Biophysics and Biochemistry, Yale University
This article describes a standard method to get a three-dimensional (3D) reconstruction of biological macromolecules using negative staining electron microscopy (EM). In this protocol, we explain how to get the 3D structure of the Saccharomyces cerevisiae exosome complex at medium resolution using the random conical tilt reconstruction method (RCT).
Published March 28, 2011. Keywords: Structural Biology, Electron microscopy, single particle three-dimensional reconstruction, exosome complex, negative staining
1Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, 2Department of Pediatrics, University of Cincinnati College of Medicine
The material here describes a method developed to preserve the three-dimensional chromatin structure of testicular germ cells. This has been termed the three-dimensional (3D) slide method. This method improves sensitivity for detection of subnuclear structures and is applicable for immunofluorescence, DNA, and RNA fluorescence in situ hybridization (FISH).
Published January 10, 2014. Keywords: Basic Protocol, Chromatin, Germ cells, Sex chromosomes, Testis, Meiotic sex chromosome inactivation, Postmeiotic sex chromatin