Massachusetts Institute of Technology

76 articles published in JoVE

• Medicine

  
  A Retrograde Implantation Approach for Peritoneal Dialysis Catheter Placement in Mice Saran Lotfollahzadeh¹, Mengwei Zhang¹, Marc Arthur Napoleon¹, Wenqing Yin¹, Josephine Orrick¹, Nagla Elzind¹, Austin Morrissey¹, Isaac E. Sellinger¹, Lauren D. Stern¹, Mostafa Belghasem², Jean M. Francis¹, Vipul C. Chitalia^{1,3,4 1}Renal Section, Department of Medicine, Boston University Aram V. Chobanian & Edward Avedisian School of Medicine, ²Department of Biomedical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, ³Veterans Affairs Boston Healthcare System, ⁴Institute of Medical Engineering and Sciences, Massachusetts Institute of Technology This article describes modifications of a procedure to implant a peritoneal dialysis catheter in a murine model to avoid major technical issues observed with the conventional techniques.

• Cancer Research

  
  Longitudinal Intravital Imaging Through Clear Silicone Windows Laura Maiorino*^1,2,3, Margaret Shevik*^1,4,5, José M. Adrover¹, Xiao Han^1,6, Elias Georgas^7,8, John Erby Wilkinson⁹, Harrison Seidner¹, Leonie Foerschner¹, David A. Tuveson¹, Yi-Xian Qin⁸, Mikala Egeblad^{1 1}Cold Spring Harbor Laboratory, ²Cold Spring Harbor Laboratory School of Biological Sciences, ³Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, ⁴Medical Scientist Training Program, School of Medicine, Stony Brook University, ⁵Graduate Program in Pharmacology, Stony Brook University, ⁶Graduate Program in Genetics, Stony Brook University, ⁷Graduate Program in Biomedical Engineering, Stony Brook University, ⁸Department of Biomedical Engineering, Stony Brook University, ⁹Department of Pathology, University of Michigan An approach is here presented for long-term intravital imaging using optically clear, silicone windows that can be glued directly to the tissue/organ of interest and the skin. These windows are cheaper and more versatile than others currently used in the field, and the surgical insertion causes limited inflammation and distress to the animals.

• Biochemistry

  
  Measuring Mitochondrial Electron Transfer Complexes in Previously Frozen Cardiac Tissue from the Offspring of Sow: A Model to Assess Exercise-Induced Mitochondrial Bioenergetics Changes Daniel Barrera¹, Sierra Upton², Megan Rauch³, Tara Notarianni⁴, Ki Suk Eum⁵, Megan Liberty⁶, Sarmila Venkoba Sah⁷, Robert Liu⁸, Sean Newcomer⁹, Linda E. May¹⁰, Emre Agbas¹¹, Jessica Sage¹², Edina Kosa⁷, Abdulbaki Agbas^{7,13 1}AdventHelath, ²University of Illinois Chicago School of Public Health, ³Lincoln Memorial University, ⁴Cincinnati Children’s Hospital Medical Center, ⁷Kansas City University, ⁸Roblex Rex Veterans Affairs Medical Center, ⁹California State University San Marcos, ¹⁰East Carolina University, ¹¹Massachusetts Institute of Technology, ¹²Boehringer Ingelheim Norway KS, ¹³Heartland Center for Mitochondrial Medicine Preparation of mitochondria-enriched samples from previously frozen archived solid tissues allowed the investigators to perform both functional and analytical assessments of mitochondria in various experimental modalities. This study demonstrates how to prepare mitochondria-enriched preparations from frozen heart tissue and perform analytical assessments of mitochondria.

• Engineering

  
  Lumped-Parameter and Finite Element Modeling of Heart Failure with Preserved Ejection Fraction Luca Rosalia*^1,2, Caglar Ozturk*¹, Ellen T. Roche^{1,2,3 1}Institute for Medical Engineering and Science, Massachusetts Institute of Technology, ²Health Science and Technology Program, Harvard/Massachusetts Institute of Technology, ³Department of Mechanical Engineering, Massachusetts Institute of Technology This work introduces two computational models of heart failure with preserved ejection fraction based on a lumped-parameter approach and finite element analysis. These models are used to evaluate the changes in the hemodynamics of the left ventricle and related vasculature induced by pressure overload and diminished ventricular compliance.

• Engineering

  
  Theoretical Calculation and Experimental Verification for Dislocation Reduction in Germanium Epitaxial Layers with Semicylindrical Voids on Silicon Motoki Yako¹, Yasuhiko Ishikawa², Eiji Abe¹, Kazumi Wada^{1,3 1}Department of Materials Engineering, The University of Tokyo, ²Department of Electrical and Electronic Information Engineering, Toyohashi University of Technology, ³Department of Materials Science and Engineering, Massachusetts Institute of Technology Theoretical calculation and experimental verification are proposed for a reduction of threading dislocation (TD) density in germanium epitaxial layers with semicylindrical voids on silicon. Calculations based on the interaction of TDs and surface via image force, TD measurements, and transmission electron microscope observations of TDs are presented.

• Chemistry

  
  Facile Synthesis of Colloidal Lead Halide Perovskite Nanoplatelets via Ligand-Assisted Reprecipitation Seung Kyun Ha¹, William A Tisdale^{1 1}Department of Chemical Engineering, Massachusetts Institute of Technology This work demonstrates facile room-temperature synthesis of colloidal quantum-confined lead halide perovskite nanoplatelets by ligand-assisted reprecipitation method. Synthesized nanoplatelets show spectrally narrow optical features and continuous spectral tunability throughout the visible range by varying the composition and thicknesses.

• Bioengineering

  
  High-resolution Imaging of Nuclear Dynamics in Live Cells under Uniaxial Tensile Strain Ekta Makhija¹, Anna Jagielska^1,2, Krystyn J. Van Vliet^{1,2,3 1}BioSystems and Micromechanics Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, CREATE, ²Department of Material Science and Engineering, Massachusetts Institute of Technology, ³Department of Biological Engineering, Massachusetts Institute of Technology Using a previously designed device to apply mechanical strain to adherent cells, this paper describes a redesigned substratum geometry and a customized apparatus for high-resolution single-cell imaging of strained cells with a 100x oil immersion objective.

• Cancer Research

  
  The Clinical Application of Tumor Treating Fields Therapy in Glioblastoma Mercedes M. Riley^1,2, Pyay San¹, Edwin Lok¹, Kenneth D. Swanson¹, Eric T. Wong^{1 1}Brain Tumor Center and Neuro-Oncology Unit, Department of Neurology, Harvard Medical School, Beth Israel Deaconess Medical Center, ²Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology Glioblastoma is the most common and aggressive primary brain malignancy in adults, with most tumors recurring after initial treatment. Tumor Treating Fields (TTFields) therapy is the newest treatment modality for glioblastoma. Here, we describe the proper application of TTFields-transducer arrays on patients and discuss theory and aspects of treatment.

• Engineering

  
  Design and Fabrication of an Optical Fiber Made of Water Mark L. Douvidzon¹, Shai Maayani², Leopoldo L. Martin³, Tal Carmon^{4 1}Department of Nanoscience and Nanotechnology, Russell Berrie Nanotechnology Institute (RBNI), Technion - Israel Institute of Technology, ²Department of Material Sciences and Engineering, MIT, ³Centro de Tecnologia Nanofotónica, Universitat Politècnica de València, ⁴Department of Mechanical Engineering, Technion - Israel Institute of Technology This protocol describes the design and manufacture of a water bridge and its activation as a water fiber. The experiment demonstrates that capillary resonances of the water fiber modulate its optical transmission.

• Genetics

  
  CRISPR Guide RNA Cloning for Mammalian Systems Sathiji Nageshwaran*^1,2, Alejandro Chavez*^1,2,3, Nan Cher Yeo^1,2, Xiaoge Guo^1,2, Alissa Lance-Byrne¹, Angela Tung¹, James J. Collins^1,4,5,6,7, George M. Church^{1,2 1}Wyss Institute for Biologically Inspired Engineering, Harvard University, ²Department of Genetics, Harvard Medical School, ³Department of Pathology, Massachusetts General Hospital, ⁴Institute for Medical Engineering & Science, Massachusetts Institute of Technology, ⁵Synthetic Biology Center, Massachusetts Institute of Technology, ⁶Department of Biological Engineering, Massachusetts Institute of Technology, ⁷Broad Institute Here, a simple, efficient, and cost-effective method of sgRNA cloning is outlined.

• Engineering

  
  Multiscale Structures Aggregated by Imprinted Nanofibers for Functional Surfaces Yeonho Jeong*¹, Seok Kim*², Nicholas Xuanlai Fang², Seunghang Shin¹, Hyunmin Choi¹, Seonjun Kim¹, Sin Kwon³, Young Tae Cho^{1 1}Department of Mechanical Engineering, Changwon National University, ²Department of Mechanical Engineering, Massachusetts Institute of Technology, ³Printed Electronics Research Team, Korea Institute of Machinery and Materials Presented is an easy method to fabricate nano-micro multiscale structures, for functional surfaces, by aggregating nanofibers fabricated using an anodic aluminum oxide filter.

• Biochemistry

  
  Analyzing Dynamic Protein Complexes Assembled On and Released From Biolayer Interferometry Biosensor Using Mass Spectrometry and Electron Microscopy Alexandra J. Machen¹, Pierce T. O'Neil¹, Bradley L. Pentelute², Maria T. Villar¹, Antonio Artigues¹, Mark T. Fisher^{1 1}Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, ²Department of Chemistry, Massachusetts Institute of Technology Here we present a protocol to monitor the assembly and disassembly of the anthrax toxin using biolayer interferometry (BLI). Following assembly/disassembly on the biosensor surface, the large protein complexes are released from the surface for visualization and identification of components of the complexes using electron microscopy and mass spectrometry, respectively.

• Biology

  
  Molecular Analysis of Endothelial-mesenchymal Transition Induced by Transforming Growth Factor-β Signaling Hiroshi I. Suzuki¹, Masafumi Horie^2,3, Hajime Mihira⁴, Akira Saito^{2 1}David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, ²Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, ³Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, ⁴Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo A protocol for in vitro induction of endothelial-mesenchymal transition (EndMT), which is useful for investigating cellular signaling pathways involved in EndMT, is described. In this experimental model, EndMT is induced by treatment with TGF-β in MS-1 endothelial cells.

• Immunology and Infection

  
  Label-free Neutrophil Enrichment from Patient-derived Airway Secretion Using Closed-loop Inertial Microfluidics Hyunryul Ryu¹, Kyungyong Choi^1,2, Yanyan Qu³, Taehong Kwon^1,2, Janet S. Lee^3,5, Jongyoon Han^{1,2,4 1}Research Laboratory of Electronics, Massachusetts Institute of Technology, ²Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, ³Department of Medicine, University of Pittsburgh, ⁴Department of Biological Engineering, Massachusetts Institute of Technology, ⁵Vascular Medicine Institute, University of Pittsburgh In this research, we demonstrate a label-free neutrophil separation method from clinical airway secretions using closed-loop operation of spiral inertial microfluidics. The proposed method would expand the clinical in vitro assays for various respiratory diseases.

• Engineering

  
  A Modular Microfluidic Technology for Systematic Studies of Colloidal Semiconductor Nanocrystals Robert W Epps¹, Kobi C Felton¹, Connor W Coley², Milad Abolhasani^{1 1}Chemical and Biomolecular Engineering, North Carolina State University, ²Chemical Engineering, Massachusetts Institute of Technology Detailed herein are the operation and assembly protocols of a modular microfluidic screening platform for the systematic characterization of colloidal semiconductor nanocrystal syntheses. Through fully adjustable system arrangements, highly efficient spectra collection may be carried out across 4 orders of magnitude reaction time scales within a mass transfer-controlled sampling space.

• Cancer Research

  
  Generation and Isolation of Cell Cycle-arrested Cells with Complex Karyotypes Ruoxi W. Wang*¹, Emily MacDuffie*¹, Stefano Santaguida^{1 1}Koch Institute for Integrative Cancer Research at MIT, Department of Biology, Massachusetts Institute of Technology Aneuploidy leads to genome instability, which eventually produces cell cycle-arrested cells with complex karyotypes. This paper provides a simple and convenient method to isolate aneuploid cells with complex karyotypes that cease to divide.

• Behavior

  
  Large Volume, Behaviorally-relevant Illumination for Optogenetics in Non-human Primates Leah C Acker^1,2,3, Erica N. Pino^1,4,5, Edward S. Boyden^1,6,7, Robert Desimone^{1,7 1}McGovern Institute, Massachusetts Institute of Technology, ²Harvard-MIT Division of Heath Sciences and Technology, ³Department of Anesthesiology, Duke University Medical Center, ⁴Department of Biology, Massachusetts Institute of Technology, ⁵Division of Pharmacoengineering and Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, ⁶Media Lab and Department of Biological Engineering, Massachusetts Institute of Technology, ⁷Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology A protocol to build a tissue penetrating illuminator for delivering light over large volumes with minimal diameter is presented.

• Biochemistry

  
  A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA Kan Xiong^1,2, Paul C. Blainey^{1,2 1}Broad Institute, Massachusetts Institute of Technology and Harvard Medical School, ²Dept. of Biological Engineering, Massachusetts Institute of Technology This protocol demonstrates a simple, robust and high throughput single molecule flow-stretching assay for studying one-dimensional (1D) diffusion of molecules along DNA.

• Genetics

  
  Detection of Copy Number Alterations Using Single Cell Sequencing Kristin A. Knouse^1,2,3, Jie Wu⁴, Austin Hendricks^{5 1}Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, ²Howard Hughes Medical Institute, ³Division of Health Sciences and Technology, Harvard Medical School, ⁴The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, ⁵BioMicro Center, Department of Biology, Massachusetts Institute of Technology Single cell sequencing is an increasingly popular and accessible tool for addressing genomic changes at high resolution. We provide a protocol that uses single cell sequencing to identify copy number alterations in single cells.

• Medicine

  
  A Multimodal Imaging- and Stimulation-based Method of Evaluating Connectivity-related Brain Excitability in Patients with Epilepsy Mouhsin M. Shafi^1,2,3, Susan Whitfield-Gabrieli⁴, Catherine J. Chu^1,5, Alvaro Pascual-Leone^1,2,3, Bernard S. Chang^{1,2 1}Department of Neurology, Harvard Medical School, ²Department of Neurology, Beth Israel Deaconess Medical Center, ³Berenson-Allen Center for Noninvasive Brain Stimulation, Beth Israel Deaconess Medical Center, ⁴Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, ⁵Department of Neurology, Massachusetts General Hospital Resting-state functional-connectivity MRI has identified abnormalities in patients with a wide range of neuropsychiatric disorders, including epilepsy due to malformations of cortical development. Transcranial Magnetic Stimulation in combination with EEG can demonstrate that patients with epilepsy have cortical hyperexcitability in regions with abnormal connectivity.

• Developmental Biology

  
  Isolation of Perivascular Multipotent Precursor Cell Populations from Human Cardiac Tissue James E. Baily¹, William C.W. Chen^2,3, Nusrat Khan⁴, Iain R. Murray⁴, Zaniah N. González Galofre⁴, Johnny Huard^5,6, Bruno Péault^{4,7 1}Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, ²Department of Bioengineering and Orthopaedic Surgery, University of Pittsburgh, ³Research Laboratory of Electronics and Department of Biological Engineering, Massachusetts Institute of Technology, ⁴MRC Centre for Regenerative Medicine, University of Edinburgh, ⁵Stem Cell Research Center, Department of Orthopaedic Surgery, University of Pittsburgh, ⁶Department of Orthopaedic Surgery, University of Texas Health Science Center at Houston, ⁷Department of Orthopaedic Surgery, UCLA Orthopaedic Hospital, David Geffen School of Medicine, University of California at Los Angeles Human cardiac tissue harbours multipotent perivascular precursor cell populations that may be suitable for myocardial regeneration. The technique described here allows for the simultaneous isolation and purification of two multipotent stromal cell populations associated with native blood vessels, i.e. CD146⁺CD34^- pericytes and CD34⁺CD146^- adventitial cells, from the human myocardium.

• Neuroscience

  
  Characterizing Multiscale Mechanical Properties of Brain Tissue Using Atomic Force Microscopy, Impact Indentation, and Rheometry Elizabeth Peruski Canovic¹, Bo Qing², Aleksandar S. Mijailovic³, Anna Jagielska², Matthew J. Whitfield², Elyza Kelly⁴, Daria Turner⁴, Mustafa Sahin⁴, Krystyn J. Van Vliet^{1,2 1}Department 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, ⁴ We present a set of techniques to characterize the viscoelastic mechanical properties of brain at the micro-, meso-, and macro-scales.

• Engineering

  
  Applying X-ray Imaging Crystal Spectroscopy for Use as a High Temperature Plasma Diagnostic Norman M. Cao¹, Andrés M. Mier Valdivia², John E. Rice^{3 1}Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, ²Department of Physics, Massachusetts Institute of Technology, ³Plasma Science and Fusion Center, Massachusetts Institute of Technology X-ray spectra provide a wealth of information on high temperature plasmas. This manuscript presents the operation of a high wavelength resolution spatially imaging X-ray spectrometer used to view hydrogen- and helium-like ions of medium atomic number elements in a tokamak plasma.

• Engineering

  
  Electrospray Deposition of Uniform Thickness Ge₂₃Sb₇S₇₀ and As₄₀S₆₀ Chalcogenide Glass Films Spencer Novak¹, Pao-Tai Lin^2,3, Cheng Li⁴, Nikolay Borodinov¹, Zhaohong Han⁵, Corentin Monmeyran⁵, Neil Patel⁵, Qingyang Du⁵, Marcin Malinowski⁴, Sasan Fathpour⁴, Chatdanai Lumdee⁴, Chi Xu⁴, Pieter G. Kik⁴, Weiwei Deng⁶, Juejun Hu⁷, Anuradha Agarwal⁷, Igor Luzinov¹, Kathleen Richardson^{4 1}Department of Materials Science and Engineering, Clemson University, ²Department of Materials Science and Engineering, Texas A&M University, ³Department of Electrical and Computer Engineering, Texas A&M University, ⁴College of Optics and Photonics, Center for Research and Education in Optics and Lasers (CREOL), University of Central Florida, ⁵Department of Materials Science and Engineering, Massachusetts Institute of Technology, ⁶Department of Mechanical Engineering, Virginia Polytechnic Institute, ⁷Microphotonics Center, Massachusetts Institute of Technology A method of uniform thickness solution-derived chalcogenide glass film deposition is demonstrated using computer numerical controlled motion of a single-nozzle electrospray.

• Engineering

  
  Creating Sub-50 Nm Nanofluidic Junctions in PDMS Microfluidic Chip via Self-Assembly Process of Colloidal Particles Xi Wei^1,2, Abeer Syed¹, Pan Mao³, Jongyoon Han⁴, Yong-Ak Song^{1,2 1}Division of Engineering, New York University Abu Dhabi (NYUAD), ²Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, ³Newomics, Inc., ⁴Department of Electrical Engineering and Computer Science, Department of Biological Engineering, MIT We propose a simple self-assembly technique of silica colloidal nanoparticles to create a nanofluidic junction between two microchannels in polydimethylsiloxane (PDMS). Using this technique, a nanoporous bead membrane with a pore size down to ~45 nm was built inside a microchannel and applied to electrokinetic preconcentration of DNA samples.

• Chemistry

  
  Reverse Microemulsion-mediated Synthesis of Monometallic and Bimetallic Early Transition Metal Carbide and Nitride Nanoparticles Sean T. Hunt¹, Yuriy Román-Leshkov^{1 1}Chemical Engineering, Massachusetts Institute of Technology A “removable ceramic coating method” is presented in visual format for the synthesis of non-sintered and metal-terminated monometallic and bimetallic early transition metal carbide and nitride nanoparticles with tunable sizes and crystal structures.

• Biology

  
  Simple Bulk Readout of Digital Nucleic Acid Quantification Assays Leanna S. Morinishi¹, Paul Blainey^{2 1}Broad Institute, ²Department of Biological Engineering, Massachusetts Institute of Technology We describe an endpoint digital assay for quantifying nucleic acids with a simplified (analog) readout. We measure bulk fluorescence of droplet-based digital assays using a standard qPCR machine rather than specialized instrumentation and confirm our results by microscopy.

• Biology

  
  Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis Alexandra Naba¹, Karl R. Clauser², Richard O. Hynes^{1 1}Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, ²Proteomics Platform, Broad Institute This protocol describes a procedure for enriching ECM proteins from tissues or tumors and deglycosylating and digesting the ECM-enriched preparations into peptides to analyze their protein composition by mass spectrometry.

• Engineering

  
  Making Record-efficiency SnS Solar Cells by Thermal Evaporation and Atomic Layer Deposition Rafael Jaramillo^2,4, Vera Steinmann^1,2, Chuanxi Yang³, Katy Hartman^2,4, Rupak Chakraborty^1,2, Jeremy R. Poindexter^2,4, Mariela Lizet Castillo², Roy Gordon⁵, Tonio Buonassisi^{1,2 1}Department of Mechanical Engineering, Massachusetts Institute of Technology, ²Laboratory for Manufacturing and Productivity, Massachusetts Institute of Technology, ³School of Engineering and Applied Sciences, Harvard University, ⁴Department of Materials Science and Engineering, Massachusetts Institute of Technology, ⁵Department of Chemistry & Chemical Biology, Harvard University Tin sulfide (SnS) is a candidate material for Earth-abundant, non-toxic solar cells. Here, we demonstrate the fabrication procedure of the SnS solar cells employing atomic layer deposition, which yields 4.36% certified power conversion efficiency, and thermal evaporation which yields 3.88%.

• Biology

  
  Sampling Blood from the Lateral Tail Vein of the Rat Graham Lee¹, Ki A. Goosens^{1,2 1}McGovern Institute for Brain Research, Massachusetts Institute of Technology, ²Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology Blood samples are useful for assessing biomarkers of physiological states or disease in vivo. Here we describe the methodology to sample blood from the lateral tail vein in the rat. This method provides rapid samples with minimal pain and invasiveness.

• Neuroscience

  
  In vivo Optogenetic Stimulation of the Rodent Central Nervous System Michelle M. Sidor¹, Thomas J. Davidson², Kay M. Tye³, Melissa R. Warden⁴, Karl Diesseroth^2,5, Colleen A. McClung^{1 1}Department 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.

• Bioengineering

  
  CometChip: A High-throughput 96-Well Platform for Measuring DNA Damage in Microarrayed Human Cells Jing Ge*¹, Somsak Prasongtanakij*², David K. Wood³, David M. Weingeist¹, Jessica Fessler¹, Panida Navasummrit², Mathuros Ruchirawat², Bevin P. Engelward^{1 1}Department of Biological Engineering, Massachusetts Institute of Technology, ²Environmental Toxicology, Chulabhorn Graduate Institute, ³Department of Biomedical Engineering, University of Minnesota We describe here a platform that allows comet assay detection of DNA damage with unprecedented throughput. The device patterns mammalian cells into a microarray and enables parallel processing of 96 samples. The approach facilitates analysis of base level DNA damage, exposure-induced DNA damage and DNA repair kinetics.

• Neuroscience

  
  Design and Fabrication of Ultralight Weight, Adjustable Multi-electrode Probes for Electrophysiological Recordings in Mice Philip M. Brunetti*¹, Ralf D. Wimmer*¹, Li Liang¹, Joshua H. Siegle², Jakob Voigts², Matthew Wilson², Michael M. Halassa^{1 1}The Neuroscience Institute, New York University Langone Medical Center, ²Department of Brain and Cognitive Science, Massachusetts Institute of Technology Understanding the neural substrates of behavior requires brain circuit ensemble recording. Because of its genetic tractability, the mouse offers a model for circuit dissection and disease mimicry. Here, a method of designing and fabricating miniaturized probes is described that is suitable for targeting deep brain structure in the mouse.

• Biology

  
  Facial Transplants in Xenopus laevis Embryos Laura A. Jacox*^1,3, Amanda J. Dickinson*⁴, Hazel Sive^{2,3 1}Biological 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.

• Neuroscience

  
  In vivo Postnatal Electroporation and Time-lapse Imaging of Neuroblast Migration in Mouse Acute Brain Slices Martina Sonego*¹, Ya Zhou*¹, Madeleine Julie Oudin², Patrick Doherty¹, Giovanna Lalli^{1 1}Wolfson Centre for Age-Related Diseases, King's College London, ²David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Neuroblast migration is a fundamental event in postnatal neurogenesis. We describe a protocol for efficient labeling of neuroblasts by in vivo postnatal electroporation and subsequent visualization of their migration using time-lapse imaging of acute brain slices. We include a description for the quantitative analysis of neuroblast dynamics by video tracking.

• Bioengineering

  
  Cell Squeezing as a Robust, Microfluidic Intracellular Delivery Platform Armon Sharei¹, Nahyun Cho¹, Shirley Mao¹, Emily Jackson¹, Roberta Poceviciute¹, Andrea Adamo¹, Janet Zoldan², Robert Langer^1,2, Klavs F Jensen^{1 1}Department of Chemical Engineering, Massachusetts Institute of Technology, ²David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology Rapid mechanical deformation of cells has emerged as a promising, vector-free method for intracellular delivery of macromolecules and nanomaterials. This protocol provides detailed steps on how to use the system for a broad range of applications.

• 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 Karnik⁶, Jeffrey M. Karp^{1,2,3,4,5 1} 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.

• Chemistry

  
  Particles without a Box: Brush-first Synthesis of Photodegradable PEG Star Polymers under Ambient Conditions Jenny Liu¹, Angela Xiaodi Gao¹, Jeremiah A. Johnson^{1 1}Department of Chemistry, Massachusetts Institute of Technology Poly(ethylene glycol) (PEG) brush-arm star polymers (BASPs) with narrow mass distributions and tunable nanoscopic sizes are synthesized in via ring opening metathesis polymerization (ROMP) of a PEG-norbornene macromonomer followed by transfer of portions of the resulting living brush initiator to vials containing varied amounts of a rigid, photo-cleavable bis-norbornene crosslinker.

• Biology

  
  Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology Zachary Z. Sun*¹, Clarmyra A. Hayes*², Jonghyeon Shin³, Filippo Caschera⁴, Richard M. Murray², Vincent Noireaux^{4 1}Department of Biology, California Institute of Technology, ²Department of Bioengineering, California Institute of Technology, ³Synthetic Biology Center, Department of Bioengineering, Massachusetts Institute of Technology, ⁴School of Physics and Astronomy, University of Minnesota This five-day protocol outlines all steps, equipment, and supplemental software necessary for creating and running an efficient endogenous Escherichia coli based TX-TL cell-free expression system from scratch. With reagents, the protocol takes 8 hours or less to setup a reaction, collect, and process data.

• Engineering

  
  Solid-state Graft Copolymer Electrolytes for Lithium Battery Applications Qichao Hu¹, Antonio Caputo², Donald R. Sadoway^{1 1}Materials Science and Engineering, Massachusetts Institute of Technology, ²Materials Processing Center, Massachusetts Institute of Technology Lithium ion batteries employ flammable and volatile organic electrolytes that are suitable for ambient temperature applications. A safer alternative to organic electrolytes are solid polymer batteries. Solid polymer batteries operate safely at high temperatures (>120 °C), thus making them applicable to high temperature applications such as deep oil drilling and hybrid electric vehicles. This paper will discuss (a) the polymer synthesis, (b) the polymer conduction mechanism, and (c) provide temperature cycling for both solid polymer and organic electrolytes.

• Engineering

  
  Scanning-probe Single-electron Capacitance Spectroscopy Kathleen A. Walsh¹, Megan E. Romanowich¹, Morewell Gasseller^1,2, Irma Kuljanishvili^1,3, Raymond Ashoori⁴, Stuart Tessmer^{1 1}Department of Physics and Astronomy, Michigan State University, ²Department of Chemistry & Biochemistry/Physics, Mercyhurst University, ³Department of Physics, Saint Louis University, ⁴Department of Physics, Massachusetts Institute of Technology Scanning-probe single-electron capacitance spectroscopy facilitates the study of single-electron motion in localized subsurface regions. A sensitive charge-detection circuit is incorporated into a cryogenic scanning probe microscope to investigate small systems of dopant atoms beneath the surface of semiconductor samples.

• Biology

  
  Acquiring Fluorescence Time-lapse Movies of Budding Yeast and Analyzing Single-cell Dynamics using GRAFTS Christopher J. Zopf¹, Narendra Maheshri^{1 1}Department of Chemical Engineering, Massachusetts Institute of Technology We present a simple protocol to obtain fluorescence microscopy movies of growing yeast cells, and a GUI-based software package to extract single-cell time series data. The analysis includes automated lineage and division time assignment integrated with visual inspection and manual curation of tracked data.

• Immunology and Infection

  
  Measuring Growth and Gene Expression Dynamics of Tumor-Targeted S. Typhimurium Bacteria Tal Danino*¹, Arthur Prindle*², Jeff Hasty^2,3,4, Sangeeta Bhatia^{1,5,6,7,8 1}Health Sciences and Technology, Massachusetts Institute of Technology, ²Department of Bioengineering, University of California, San Diego, ³Biocircuits Institute, University of California, San Diego, ⁴Molecular Biology Section, Division of Biological Science, University of California, San Diego, ⁵Broad Institute of Harvard and MIT, ⁶Department of Medicine, Brigham and Women's Hospital, ⁷Electrical Engineering and Computer Science and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, ⁸Howard Hughes Medical Institute The goal of these experiments is to generate quantitative time-course data on the growth and gene expression dynamics of attenuated S. typhimurium bacterial colonies growing inside tumors. This video covers tumor cell preparation and implantation, bacteria preparation and injection, whole-animal luminescence imaging, tumor excision, and bacterial colony counting.

• Biology

  
  Biochemical and High Throughput Microscopic Assessment of Fat Mass in Caenorhabditis Elegans Elizabeth C. Pino¹, Christopher M. Webster¹, Christopher E. Carr², Alexander A. Soukas^{1 1}Center for Human Genetic Research and Department of Medicine, Massachusetts General Hospital and Harvard Medical School, ²Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology We present robust biochemical and microscopic methods for studying Caenorhabditis elegans lipid stores. A rapid, simple, fixing-staining procedure for fluorescent lipid droplet imaging leverages the spectral properties of the lipophilic dye Nile red. We then present biochemical measurement of triglycerides and phospholipids using solid phase extraction and gas chromatography-mass spectrometry.

• Biology

  
  The Logic, Experimental Steps, and Potential of Heterologous Natural Product Biosynthesis Featuring the Complex Antibiotic Erythromycin A Produced Through E. coli Ming Jiang¹, Haoran Zhang², Blaine A. Pfeifer^{1 1}Chemical and Biological Engineering Department, State University of New York at Buffalo, ²Chemical Engineering Department, Massachusetts Institute of Technology The heterologous biosynthesis of erythromycin A through E. coli includes the following experimental steps: 1) genetic transfer; 2) heterologous reconstitution; and 3) product analysis. Each step will be explained in the context of the motivation, potential, and challenges in producing therapeutic natural products using E. coli as a surrogate host.

• Neuroscience

  
  Manual Drainage of the Zebrafish Embryonic Brain Ventricles Jessica T. Chang¹, Hazel Sive^{1 1}Department 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.

• Engineering

  
  Micro 3D Printing Using a Digital Projector and its Application in the Study of Soft Materials Mechanics Howon Lee¹, Nicholas X. Fang^{1 1}Department of Mechanical Engineering, Massachusetts Institute of Technology We demonstrate controlled pattern transformation of swelling gel tubes by elastic instability. A simple projection micro stereo-lithography setup is built using an off-the-shelf digital data projector to fabricate three-dimensional polymeric structures in a layer-by-layer fashion. Swelling hydrogel tubes under mechanical constraint display various circumferential buckling modes depending on dimension.

• Neuroscience

  
  An Assay for Permeability of the Zebrafish Embryonic Neuroepithelium Jessica T. Chang^1,2, Hazel Sive^{1,2 1}Department 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.

• Neuroscience

  
  Stereotaxic Surgery for Excitotoxic Lesion of Specific Brain Areas in the Adult Rat Elizabeth D. Kirby¹, Kelly Jensen², Ki A. Goosens³, Daniela Kaufer^{1,4 1}Helen Wills Neuroscience Institute, University of California Berkeley, ²Office of Laboratory Animal Care, University of California Berkeley, ³McGovern Institute for Brain Research & The Department of Brain and Cognitive Science, Massachusetts Institute of Technology, ⁴Integrative Biology Department, University of California Berkeley Targeted ablation of specific brain region(s) by infusion of an excitotoxin using stereotaxic coordinates is described. This technique could also be adapted for infusion of other chemicals into the rat brain.

• Bioengineering

  
  Polymer Microarrays for High Throughput Discovery of Biomaterials Andrew L. Hook¹, Chien-Yi Chang², Jing Yang¹, David J. Scurr¹, Robert Langer³, Daniel G. Anderson³, Steve Atkinson², Paul Williams², Martyn C. Davies¹, Morgan R. Alexander^{1 1}Laboratory of Biophysics and Surface Analysis, University of Nottingham, ²School of Molecular Medical Sciences, University of Nottingham, ³David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology A description of the formation of a polymer microarray using an on-chip photopolymerization technique. The high throughput surface characterization using atomic force microscopy, water contact angle measurements, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry and a cell attachment assay is also described.

• Immunology and Infection

  
  Determination of Molecular Structures of HIV Envelope Glycoproteins using Cryo-Electron Tomography and Automated Sub-tomogram Averaging Joel R. Meyerson^1,2, Tommi A. White¹, Donald Bliss³, Amy Moran³, Alberto Bartesaghi¹, Mario J. Borgnia¹, M. Jason V. de la Cruz¹, David Schauder¹, Lisa M. Hartnell¹, Rachna Nandwani^1,4, Moez Dawood⁵, Brianna Kim⁶, Jun Hong Kim⁷, John Sununu⁸, Lisa Yang⁹, Siddhant Bhatia¹⁰, Carolyn Subramaniam¹, Darrell E. Hurt¹¹, Laurent Gaudreault¹², Sriram Subramaniam^{1 1}Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, ²The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, ³National Library of Medicine, National Institutes of Health, ⁴Massachusetts Institute of Technology, ⁵William Fremd High School, ⁶University of Virginia, ⁷Duke University, ⁸Yale University, ⁹University of Notre Dame, ¹⁰Washington University in St. Louis, ¹¹Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, ¹²Thomas Jefferson High School for Science and Technology The protocol describes a high-throughput approach to determining structures of membrane proteins using cryo-electron tomography and 3D image processing. It covers the details of specimen preparation, data collection, data processing and interpretation, and concludes with the production of a representative target for the approach, the HIV-1 Envelope glycoprotein. These computational procedures are designed in a way that enables researchers and students to work remotely and contribute to data processing and structural analysis.

• Biology

  
  Quantification of Proteins Using Peptide Immunoaffinity Enrichment Coupled with Mass Spectrometry Lei Zhao*¹, Jeffrey R. Whiteaker*¹, Matthew E. Pope², Eric Kuhn³, Angela Jackson⁴, N. Leigh Anderson⁵, Terry W. Pearson², Steven A. Carr³, Amanda G. Paulovich^{1 1}Clinical Research Division, Fred Hutchinson Cancer Research Center - FHCRC, ²Department of Biochemistry and Microbiology, University of Victoria, ³Broad Institute of MIT and Harvard, ⁴Genome BC Proteomics Centre, University of Victoria, ⁵Plasma Proteome Institute Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) couples affinity enrichment of peptides with stable isotope dilution mass spectrometry (MRM-MS) to provide quantitative measurement of peptides as surrogates for their respective proteins. Here we describe the protocol using magnetic particles in a partially automated format.

• Bioengineering

  
  Studying Cell Rolling Trajectories on Asymmetric Receptor Patterns Chia-Hua Lee¹, Suman Bose², Krystyn J. Van Vliet¹, Jeffrey M. Karp³, Rohit Karnik^{2 1}Department 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.

• Immunology and Infection

  
  Transnuclear Mice with Pre-defined T Cell Receptor Specificities Against Toxoplasma gondii Obtained Via SCNT Oktay Kirak¹, Eva-Maria Frickel¹, Gijsbert M. Grotenbreg^1,2, Heikyung Suh¹, Rudolf Jaenisch^1,3, Hidde L. Ploegh^{1,3 1}Whitehead Institute for Biomedical Research, ²Departments of Microbiology and Biological Sciences, National University of Singapore, ³Department of Biology, Massachusetts Institute of Technology We demonstrate here that epigenetic reprogramming via Somatic Cell Nuclear Transfer (SCNT) can be used as a tool to generate mouse models with pre-defined T cell receptor (TCR) specificities. These transnuclear mice express the corresponding TCR from their endogenous locus under the control of the endogenous promoter.

• Biology

  
  Hi-C: A Method to Study the Three-dimensional Architecture of Genomes. Nynke L. van Berkum*¹, Erez Lieberman-Aiden*^2,3,4,5, Louise Williams*², Maxim Imakaev⁶, Andreas Gnirke², Leonid A. Mirny^3,6, Job Dekker¹, Eric S. Lander^{2,7,8 1}Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, ²Broad Institute of Harvard and Massachusetts Institute of Technology, ³Division of Health Sciences and Technology, Massachusetts Institute of Technology, ⁴Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University, ⁵Department of Applied Mathematics, Harvard University, ⁶Department of Physics, Massachusetts Institute of Technology, ⁷Department of Systems Biology, Harvard Medical School, ⁸Department of Biology, Massachusetts Institute of Technology The Hi-C method allows unbiased, genome-wide identification of chromatin interactions (1). Hi-C couples proximity ligation and massively parallel sequencing. The resulting data can be used to study genomic architecture at multiple scales: initial results identified features such as chromosome territories, segregation of open and closed chromatin, and chromatin structure at the megabase scale.

• Neuroscience

  
  Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits Stephanie Chan¹, Jacob Bernstein¹, Edward Boyden^{1 1}Biological Engineering, Brain and Cognitive Sciences, and McGovern Institute, Massachusetts Institute of Technology Controlling and analyzing neural circuits in vivo would be facilitated by a technology for delivery of viruses and other reagents to desired 3-dimensional sets of brain regions. We demonstrate customized fluidic injector array fabrication, and delivery of virally-encoded optical sensitizers, enabling optical manipulation of complex brain circuits.

• Biology

  
  Generation of Induced Pluripotent Stem Cells by Reprogramming Mouse Embryonic Fibroblasts with a Four Transcription Factor, Doxycycline Inducible Lentiviral Transduction System Brad Hamilton¹, Qiang Feng¹, Mike Ye¹, G Grant Welstead^{2 1}Stemgent, 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.

• Biology

  
  Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE) Heike Summer¹, René Grämer², Peter Dröge^{1 1}School of Biological Sciences, Nanyang Technological University, Singapore - NTU, ²Singapore-MIT Alliance for Reserach and Technology (SMART) Denaturing urea polyacrylamide gel electrophoresis is used to separate single-stranded DNA or RNA up to a limit of 500 nucleotides. Urea in combination with heat denatures samples and unstructured single strands migrate within the gel matrix according to their molecular weight.

• 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 1}Department 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.

• 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 1}Picower 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.

• Biology

  
  Vaccinia Virus Infection & Temporal Analysis of Virus Gene Expression: Part 3 Judy Yen¹, Ron Golan¹, Kathleen Rubins^{1 1}Whitehead 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.

• Biology

  
  Vaccinia Virus Infection & Temporal Analysis of Virus Gene Expression: Part 2 Judy Yen¹, Ron Golan¹, Kathleen Rubins^{1 1}Whitehead 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.

• Biology

  
  Vaccinia Virus Infection & Temporal Analysis of Virus Gene Expression: Part 1 Judy Yen¹, Ron Golan¹, Kathleen Rubins^{1 1}Whitehead 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.

• Biology

  
  Zebrafish Brain Ventricle Injection Jennifer H. Gutzman¹, Hazel Sive^{1,2 1}Whitehead 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.

• Biology

  
  Live Imaging of the Zebrafish Embryonic Brain by Confocal Microscopy Ellie Graeden^1,2, Hazel Sive^{1,2 1}Department 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.

• Biology

  
  Screening for Amyloid Aggregation by Semi-Denaturing Detergent-Agarose Gel Electrophoresis Randal Halfmann^1,2,3, Susan Lindquist^{1,2,3 1}Whitehead 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.

• Biology

  
  Interview: Protein Folding and Studies of Neurodegenerative Diseases Susan Lindquist^{1 1}Whitehead 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.

• Biology

  
  Generating iPS Cells from MEFS through Forced Expression of Sox-2, Oct-4, c-Myc, and Klf4 G. Grant Welstead¹, Tobias Brambrink¹, Rudolf Jaenisch^{1 1}Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology This video shows the procedure for generating induced pluripotent stem cells using inducible lentivirus that express Oct4, Sox2, c-Myc and Klf4.

• Biology

  
  Patterning of Embryonic Stem Cells Using the Bio Flip Chip Nikhil Mittal^1,2, Stephanie Flavin², Joel Voldman^{2 1}Dept 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.

• Biology

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

• Biology

  
  CD4+ T-Lymphocyte Capture Using a Disposable Microfluidic Chip for HIV Sang Jun Moon¹, Richard Lin², Utkan Demirci^{1 1}Bio-Acoustic-MEMS Laboratory in Medicine (BAMM), HST-Center for Bioengineering, Brigham and Women's Hospital, ²Massachusetts Institute of Technology

• Biology

  
  Silicon Microchips for Manipulating Cell-cell Interaction Elliot E Hui¹, Sangeeta N Bhatia^{1 1}Laboratory 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.

• Biology

  
  Large-Scale Screens of Metagenomic Libraries Vinh D. Pham¹, Tsultrim Palden¹, Edward F. DeLong^{1 1}Division of Biological Engineering, Department of Civil and Environmental Engineering, MIT - Massachusetts Institute of Technology

• Biology

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

• Biology

  
  Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers Justin R. Seymour¹, Marcos¹, Roman Stocker^{1 1}Environmental 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.

• Biology

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