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MIT - Massachusetts Institute of Technology

29 ARTICLES PUBLISHED IN JoVE

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Biology

Large-Scale Screens of Metagenomic Libraries
Vinh D. Pham 1, Tsultrim Palden 1, Edward F. DeLong 1
1Division of Biological Engineering, Department of Civil and Environmental Engineering, MIT - Massachusetts Institute of Technology

Large-Scale Screens of Metagenomic Libraries

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Biology

Microbial Communities in Nature and Laboratory - Interview
Edward F. DeLong 1
1Division of Biological Engineering, Department of Civil and Environmental Engineering, MIT - Massachusetts Institute of Technology

Microbial Communities in Nature and Laboratory - Interview

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Biology

Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers
Justin R. Seymour 1, Marcos 1, Roman Stocker 1
1Environmental Microfluidics Group, MIT - Massachusetts Institute of Technology

The fabrication of microfluidic channels and their implementation in experiments for studying the chemotactic foraging behaviour of marine microbes within a patchy nutrient seascape and the swimming behaviour of bacteria within shear flow are described.

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Biology

Studies of Bacterial Chemotaxis Using Microfluidics - Interview
Roman Stocker 1
1Environmental Microfluidics Group, MIT - Massachusetts Institute of Technology

Studies of Bacterial Chemotaxis Using Microfluidics - Interview

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Biology

Silicon Microchips for Manipulating Cell-cell Interaction
Elliot E Hui 1, Sangeeta N Bhatia 1
1Laboratory for Multiscale Regenerative Technologies, MIT - Massachusetts Institute of Technology

This article describes an experimental approach for dynamic regulation of cell-cell interactions between adherent cells on a micrometer scale. Manipulation of intercellular communication between hepatocytes and stromal cell is demonstrated. The developed platform enables investigation of cell-cell interactions in a variety of biological processes, including development and pathogenesis.

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Biology

Micro-scale Engineering for Cell Biology
Joel Voldman 1
1Department of Electrical Engineering and Computer Science, MIT - Massachusetts Institute of Technology

Micro-scale Engineering for Cell Biology

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Biology

Patterning of Embryonic Stem Cells Using the Bio Flip Chip
Nikhil Mittal 1,2, Stephanie Flavin 2, Joel Voldman 2
1Dept of Physics, MIT - Massachusetts Institute of Technology, 2Department of Electrical Engineering and Computer Science, MIT - Massachusetts Institute of Technology

We demonstrate a simple method for placing cells at desired locations on a substrate. This method patterns cells by flipping a silicone chip containing microwells filled with cells onto the substrate. This method provides a new way to modulate diffusible and juxtacrine signaling between cells.

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Biology

Interview: Protein Folding and Studies of Neurodegenerative Diseases
Susan Lindquist 1
1Whitehead Institute for Biomedical Research, MIT - Massachusetts Institute of Technology

In this interview, Dr. Lindquist describes relationships between protein folding, prion diseases and neurodegenerative disorders. The problem of the protein folding is at the core of the modern biology. In addition to their traditional biochemical functions, proteins can mediate transfer of biological information and therefore can be considered a genetic material. This recently discovered function of proteins has important implications for studies of human disorders. Dr. Lindquist also describes current experimental approaches to investigate the mechanism of neurodegenerative diseases based on genetic studies in model organisms.

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Biology

Screening for Amyloid Aggregation by Semi-Denaturing Detergent-Agarose Gel Electrophoresis
Randal Halfmann 1,2,3, Susan Lindquist 1,2,3
1Whitehead Institute for Biomedical Research, 2Department of Biology, MIT - Massachusetts Institute of Technology, 3Howard Hughes Medical Institute

SDD-AGE is a useful technique for the detection and characterization of amyloid-like polymers in cells. Here we demonstrate an adaptation that makes this technique amenable to large-scale applications.

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Biology

Micro-drive Array for Chronic in vivo Recording: Drive Fabrication
Fabian Kloosterman 1,2, Thomas J. Davidson 1,2, Stephen N. Gomperts 1,2, Stuart P. Layton 1,2, Gregory Hale 1,2, David P. Nguyen 1,2, Matthew A. Wilson 1,2
1Picower Institute for Learning and Memory, MIT - Massachusetts Institute of Technology, 2Department of Brain and Cognitive Science, MIT - Massachusetts Institute of Technology

In this protocol we demonstrate how to fabricate a micro-drive array for chronic electrophysiological recordings in rats.

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Biology

Micro-drive Array for Chronic in vivo Recording: Tetrode Assembly
David P. Nguyen 1,2, Stuart P. Layton 1,2, Gregory Hale 1,2, Stephen N. Gomperts 1,2, Thomas J. Davidson 1,2, Fabian Kloosterman 1,2, Matthew A. Wilson 1,2
1Department of Brain and Cognitive Science, MIT - Massachusetts Institute of Technology, 2Picower Institute for Learning and Memory, MIT - Massachusetts Institute of Technology

In this protocol we demonstrate how to fabricate and condition tetrodes for use with a micro-drive array, which was designed for chronic electrophysiological recordings in rats. In addition, we illustrate the final stages of micro-drive array construction, which includes installing ground wires and a protective cone.

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Biology

Vaccinia Virus Infection & Temporal Analysis of Virus Gene Expression: Part 1
Judy Yen 1, Ron Golan 1, Kathleen Rubins 1
1Whitehead Institute for Biomedical Research, MIT - Massachusetts Institute of Technology

Protocol for Vaccinia infection of HeLa cells and analysis of host and viral gene expression. Part 1 of 3.

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Biology

Vaccinia Virus Infection & Temporal Analysis of Virus Gene Expression: Part 2
Judy Yen 1, Ron Golan 1, Kathleen Rubins 1
1Whitehead Institute for Biomedical Research, MIT - Massachusetts Institute of Technology

Protocol for Vaccinia infection of HeLa cells and analysis of host and viral gene expression. Part 2 of 3.

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Biology

Vaccinia Virus Infection & Temporal Analysis of Virus Gene Expression: Part 3
Judy Yen 1, Ron Golan 1, Kathleen Rubins 1
1Whitehead Institute for Biomedical Research, MIT - Massachusetts Institute of Technology

Protocol for Vaccinia infection of HeLa cells and analysis of host and viral gene expression. Part 3 describes the process of fluorescently labeling the amplified RNA from both host and viral samples by amino allyl coupling of dyes. Part 3 of 3.

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Biology

Live Imaging of the Zebrafish Embryonic Brain by Confocal Microscopy
Ellie Graeden 1,2, Hazel Sive 1,2
1Department of Biology, MIT - Massachusetts Institute of Technology, 2Whitehead Institute for Biomedical Research, MIT - Massachusetts Institute of Technology

In this video, we demonstrate a method by which to analyze the developing vertebrate brain in live zebrafish embryos at single cell resolution by confocal microscopy. This includes the method by which we inject the single-cell zebrafish embryo and subsequently mount and image the developing brain.

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Biology

Zebrafish Brain Ventricle Injection
Jennifer H. Gutzman 1, Hazel Sive 1,2
1Whitehead Institute for Biochemical Research, 2MIT - Massachusetts Institute of Technology

After neural tube formation, the neuroepithelium constricts and folds while the tube fills with embryonic cerebrospinal fluid (eCSF) to form the embryonic brain ventricles. We developed this ventricle injection technique to better visualize the fluid filled space in contrast to the neuroepithelial shape in a live embryo.

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Biology

Generation of Induced Pluripotent Stem Cells by Reprogramming Mouse Embryonic Fibroblasts with a Four Transcription Factor, Doxycycline Inducible Lentiviral Transduction System
Brad Hamilton 1, Qiang Feng 1, Mike Ye 1, G Grant Welstead 2
1Stemgent, 2Whitehead Institute for Biomedical Research, MIT - Massachusetts Institute of Technology

The Stemgent Dox Inducible Mouse TF Lentivirus Set can reprogram mouse embryonic fibroblasts (MEFs) to induced pluripotent stem (iPS) cells. Here we demonstrate the protocol for DOX-inducible expression of mouse reprogramming transcription factors Oct4, Sox2, Klf4 and c-Myc to generate iPS colonies that express common mES pluripotency markers.

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Bioengineering

Studying Cell Rolling Trajectories on Asymmetric Receptor Patterns
Chia-Hua Lee 1, Suman Bose 2, Krystyn J. Van Vliet 1, Jeffrey M. Karp 3, Rohit Karnik 2
1Department of Materials Science and Engineering, MIT - Massachusetts Institute of Technology, 2Department of Mechanical Engineering, MIT - Massachusetts Institute of Technology, 3HST Center for Biomedical Engineering and Harvard Stem Cell Institute, Brigham and Women's Hospital and Harvard Medical School

We describe a protocol to observe and analyze cell rolling trajectories on asymmetric receptor-patterned substrates. The resulting data are useful for engineering of receptor-patterned substrates for label-free cell separation and analysis.

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Neuroscience

An Assay for Permeability of the Zebrafish Embryonic Neuroepithelium
Jessica T. Chang 1,2, Hazel Sive 1,2
1Department of Biology, Massachusetts Institute of Technology, 2Whitehead Institute of Biomedical Research

We describe a live whole animal quantitative measurement for permeability of the embryonic zebrafish brain. The technique analyzes the ability to retain cerebrospinal fluid and molecules of different molecular weights within the neural tube lumen and quantifies their movement out of the ventricles. This method is useful for determining differences in epithelial permeability and maturation during development and disease.

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Neuroscience

Manual Drainage of the Zebrafish Embryonic Brain Ventricles
Jessica T. Chang 1, Hazel Sive 1
1Department of Biology, Whitehead Institute of Biomedical Research, Massachusetts Institute of Technology

We present a method to collect cerebrospinal fluid (CSF) and to create a system which lacks CSF within the embryonic zebrafish brain ventricular system. This allows for further examination of CSF composition and its requirement during embryonic brain development.

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Biology

Facial Transplants in Xenopus laevis Embryos
Laura A. Jacox *1,3, Amanda J. Dickinson *4, Hazel Sive 2,3
1Biological Sciences in Dental Medicine, Harvard University, 2Biology Department, Massachusetts Institute of Technology, 3Whitehead Institute, Massachusetts Institute of Technology, 4Biology Department, Virginia Commonwealth University

A technique for transplanting "Extreme Anterior Domain" facial tissue between Xenopus laevis embryos has been developed. Tissue can be moved from one gene expression background into another, allowing the study of local requirements for craniofacial development and for signaling interactions between facial regions.

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Bioengineering

Systematic Analysis of In Vitro Cell Rolling Using a Multi-well Plate Microfluidic System
Oren Levy 1,2,3,4,5, Priya Anandakumaran 1,2,3,4,5, Jessica Ngai 1,2,3,4,5, Rohit Karnik 6, Jeffrey M. Karp 1,2,3,4,5
1Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, 2Center for Regenerative Therapeutics, Brigham and Women's Hospital, 3Harvard Medical School, Harvard University, 4Harvard Stem Cell Institute, Harvard University, 5Harvard-MIT Division of Health Sciences and Technology, 6Department of Mechanical Engineering, Massachusetts Institute of Technology

This study used a multi-well plate microfluidic system, significantly increasing throughput of cell rolling studies under physiologically relevant shear flow. Given the importance of cell rolling in the multi-step cell homing cascade and the importance of cell homing following systemic delivery of exogenous populations of cells in patients, this system offers potential as a screening platform to improve cell-based therapy.

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Neuroscience

In vivo Optogenetic Stimulation of the Rodent Central Nervous System
Michelle M. Sidor 1, Thomas J. Davidson 2, Kay M. Tye 3, Melissa R. Warden 4, Karl Diesseroth 2,5, Colleen A. McClung 1
1Department of Psychiatry, University of Pittsburgh Medical Center, 2Department of Bioengineering, Stanford University, 3Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 4Department of Neurobiology and Behavior, Cornell University, 5Department of Psychiatry and Behavioral Sciences, Stanford University

Optogenetics has become a powerful tool for use in behavioral neuroscience experiments. This protocol offers a step-by-step guide to the design and set-up of laser systems, and provides a full protocol for carrying out multiple and simultaneous in vivo optogenetic stimulations compatible with most rodent behavioral testing paradigms.

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Neuroscience

Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry
Elizabeth Peruski Canovic 1, Bo Qing 2, Aleksandar S. Mijailovic 3, Anna Jagielska 2, Matthew J. Whitfield 2, Elyza Kelly 4, Daria Turner 4, Mustafa Sahin 4, Krystyn J. Van Vliet 1,2
1Department of Materials Science and Engineering, Massachusetts Institute of Technology, 2Department of Biological Engineering, Massachusetts Institute of Technology, 3Department of Mechanical Engineering, Massachusetts Institute of Technology, 4Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School

We present a set of techniques to characterize the viscoelastic mechanical properties of brain at the micro-, meso-, and macro-scales.

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Biology

Detecting and Characterizing Protein Self-Assembly In Vivo by Flow Cytometry
Shriram Venkatesan *1, Tejbir S. Kandola *1, Alejandro Rodríguez-Gama 1, Andrew Box 1, Randal Halfmann 1,2
1Stowers Institute for Medical Research, 2Department of Molecular and Integrative Physiology, The University of Kansas School of Medicine

This article describes a FRET-based flow cytometry protocol to quantify protein self-assembly in both S. cerevisiae and HEK293T cells.

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Bioengineering

Generating Controlled, Dynamic Chemical Landscapes to Study Microbial Behavior
Francesco Carrara 1, Douglas R. Brumley 2, Andrew M. Hein 3, Yutaka Yawata 4,5, M. Mehdi Salek 1, Kang Soo Lee 1, Elzbieta Sliwerska 1, Simon A. Levin 6, Roman Stocker 1
1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, 2School of Mathematics and Statistics, University of Melbourne, 3Institute of Marine Sciences, University of California, Santa Cruz, 4Faculty of Life and Environmental Sciences, University of Tsukuba, 5Microbiology Research Center for Sustainability, University of Tsukuba, 6Department of Ecology and Evolutionary Biology, Princeton University

A protocol for the generation of dynamic chemical landscapes by photolysis within microfluidic and millifluidic setups is presented. This methodology is suitable to study diverse biological processes, including the motile behavior, nutrient uptake, or adaptation to chemicals of microorganisms, both at the single cell and population level.

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Environment

In Situ Chemotaxis Assay to Examine Microbial Behavior in Aquatic Ecosystems
Estelle E. Clerc 1, Jean-Baptiste Raina 2, Bennett S. Lambert 3, Justin Seymour 2, Roman Stocker 1
1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, 2Climate Change Cluster, University of Technology Sydney, 3School of Oceanography, University of Washington

Presented here is the protocol for an in situ chemotaxis assay, a recently developed microfluidic device that enables studies of microbial behavior directly in the environment.

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Engineering

Patterning of Microorganisms and Microparticles through Sequential Capillarity-assisted Assembly
Roberto Pioli 1, Roman Stocker 1, Lucio Isa 2, Eleonora Secchi 1
1Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, 2Department of Materials, ETH Zurich

We present a technology that uses capillarity-assisted assembly in a microfluidic platform to pattern micro-sized objects suspended in a liquid, such as bacteria and colloids, into prescribed arrays on a polydimethylsiloxane substrate.

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Environment

A Microfluidic Platform to Study Bioclogging in Porous Media
Dorothee L. Kurz 1,2, Eleonora Secchi 1, Roman Stocker 1, Joaquin Jimenez-Martinez 1,2
1Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, 2Department Water Resources and Drinking Water, Swiss Federal Institute of Aquatic Science and Technology

The present protocol describes a microfluidic platform to study biofilm development in quasi-2D porous media by combining high-resolution microscopy imaging with simultaneous pressure difference measurements. The platform quantifies the influence of pore size and fluid flow rates in porous media on bioclogging.

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