Carnegie Institution for Science View Institution's Website 9 articles published in JoVE Biology Fast Colony Forming Unit Counting in 96-Well Plate Format Applied to the Drosophila Microbiome Ren Dodge1, William B. Ludington1,2 1Department of Embryology, Carnegie Institution for Science, 2Department of Biology, Johns Hopkins University This method quantifies microbial abundance using a 96-well plate format to plate colony forming units (CFUs) and is applied to the Drosophila microbiome in whole fly homogenate samples. CFUs are counted with an automated image analysis software provided here. Genetics Isolation of Giant Lampbrush Chromosomes from Living Oocytes of Frogs and Salamanders Joseph G. Gall1, Zehra F. Nizami1 1Department of Embryology, Carnegie Institution for Science We present simple techniques for isolating giant transcriptionally active lampbrush chromosomes from living oocytes of frogs and salamanders. We describe how to observe these chromosomes "alive" by phase contrast or differential interference contrast, and how to fix them for fluorescent in situ hybridization or immunofluorescent staining. Biology High-fat Feeding Paradigm for Larval Zebrafish: Feeding, Live Imaging, and Quantification of Food Intake Jessica P. Otis1, Steven A. Farber1,2 1Department of Embryology, Carnegie Institution for Science, 2Department of Biology, Johns Hopkins University Zebrafish are emerging as a valuable model of dietary lipid processing and metabolic disease. Described are protocols of lipid-rich larval feeds, live imaging of dietary fluorescent lipid analogs, and quantification of food intake. These techniques can be applied to a variety of screening, imaging, and hypothesis driven inquiry techniques. Chemistry Metal-silicate Partitioning at High Pressure and Temperature: Experimental Methods and a Protocol to Suppress Highly Siderophile Element Inclusions Neil R. Bennett1,2, James M. Brenan1, Yingwei Fei2 1Department of Earth Science, University of Toronto, 2Geophysical Laboratory, Carnegie Institution of Washington We present a procedure to determine the metal-silicate partitioning of siderophile elements, emphasizing techniques that suppress the formation of metal inclusions in experiments for the noble metals. The results of these experiments are used to demonstrate the effect of core-formation on the highly siderophile element composition of the mantle. Biology A New Approach for the Comparative Analysis of Multiprotein Complexes Based on 15N Metabolic Labeling and Quantitative Mass Spectrometry Kerstin Trompelt1, Janina Steinbeck1, Mia Terashima1,2, Michael Hippler1 1Institute of Plant Biology and Biotechnology, University of Münster, 2Department of Plant Biology, Carnegie Institution for Science The described comparative, quantitative proteomic approach aims at obtaining insights into the composition of multiprotein complexes under different conditions and is demonstrated by comparing genetically different strains. For quantitative analysis equal volumes of different fractions from a sucrose density gradient are mixed and analyzed by mass spectrometry. Engineering Simulation of the Planetary Interior Differentiation Processes in the Laboratory Yingwei Fei1 1Geophysical Laboratory, Carnegie Institution of Washington The high-pressure and high-temperature experiments described here mimic planet interior differentiation processes. The processes are visualized and better understood by high-resolution 3D imaging and quantitative chemical analysis. Engineering Synthesis and Microdiffraction at Extreme Pressures and Temperatures Barbara Lavina1, Przemyslaw Dera2, Yue Meng3 1High Pressure Science and Engineering Center, Department of Physics and Astronomy, University of Nevada, Las Vegas, 2GeoSoilEnviroCARS, University of Chicago, 3High Pressure Collaborative Access Team, Carnegie Institution of Washington The laser heated diamond anvil cell combined with synchrotron micro-diffraction techniques allows researchers to explore the nature and properties of new phases of matter at extreme pressure and temperature (PT) conditions. Heterogeneous samples can be characterized in situ under high pressure by 2D mapping and combined powder, single-crystal and multigrain diffraction approaches. Engineering Bringing the Visible Universe into Focus with Robo-AO Christoph Baranec1,2, Reed Riddle1, Nicholas M. Law3, A.N. Ramaprakash4, Shriharsh P. Tendulkar2, Khanh Bui1, Mahesh P. Burse4, Pravin Chordia4, Hillol K. Das4, Jack T.C. Davis1, Richard G. Dekany1, Mansi M. Kasliwal5, Shrinivas R. Kulkarni1,2, Timothy D. Morton2, Eran O. Ofek6, Sujit Punnadi4 1Caltech Optical Observatories, California Institute of Technology, 2Department of Astronomy, California Institute of Technology, 3Dunlap Institute for Astronomy and Astrophysics, University of Toronto, 4Inter-University Centre for Astronomy & Astrophysics, 5Observatories of the Carnegie Institution for Science, 6Benoziyo Center for Astrophysics, Weizmann Institute of Science Light from astronomical objects must travel through the earth's turbulent atmosphere before it can be imaged by ground-based telescopes. To enable direct imaging at maximum theoretical angular resolution, advanced techniques such as those employed by the Robo-AO adaptive-optics system must be used. Bioengineering Time-lapse Fluorescence Imaging of Arabidopsis Root Growth with Rapid Manipulation of The Root Environment Using The RootChip Guido Grossmann1, Matthias Meier2,3,4, Heather N. Cartwright1, Davide Sosso1, Stephen R. Quake2,3, David W. Ehrhardt1, Wolf B. Frommer1 1Department of Plant Biology, Carnegie Institution for Science, 2Howard Hughes Medical Institute, 3Departments of Applied Physics and Bioengineering, Stanford University, 4Department of Microsystems Engineering (IMTEK) and Center for Biological Signaling Studies (BIOSS), University of Freiburg This article provides a protocol for cultivation of Arabidopsis seedlings in the RootChip, a microfluidic imaging platform that combines automated control of growth conditions with microscopic root monitoring and FRET-based measurement of intracellular metabolite levels.
