University of Chicago

45 articles published in JoVE

• Cancer Research

  
  Far-Red Fluorescent Senescence-Associated β-Galactosidase Probe for Identification and Enrichment of Senescent Tumor Cells by Flow Cytometry Amy Flor¹, Joanna Pagacz¹, DeShawn Thompson¹, Stephen Kron^{1 1}Department of Molecular Genetics and Cell Biology, University of Chicago A protocol for fluorescent, flow cytometric quantification of senescent cancer cells induced by chemotherapy drugs in cell culture or in murine tumor models is presented. Optional procedures include co-immunostaining, sample fixation to facilitate large batch or time point analysis, and the enrichment of viable senescent cells by flow cytometric sorting.

• Developmental Biology

  
  Eye Removal in Living Zebrafish Larvae to Examine Innervation-dependent Growth and Development of the Visual System Olivia L. Hagen¹, Yehyun Kim¹, Elaine Kushkowski^1,2, Hannah Rouse³, Kara L. Cerveny^{1 1}Department of Biology, Reed College, ²Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, ³Department of Cell and Developmental Biology, University College London The article explains how to surgically remove eyes from living zebrafish larvae as the first step toward investigating how retinal input influences optic tectum growth and development. In addition, the article provides information about larval anesthetization, fixation, and brain dissection, followed by immunohistochemistry and confocal imaging.

• Bioengineering

  
  An In vitro System to Gauge the Thrombolytic Efficacy of Histotripsy and a Lytic Drug Aarushi Bhargava¹, Samuel A. Hendley², Kenneth B. Bader^{1,2 1}Department of Radiology, University of Chicago, ²Graduate Program in Medical Physics, University of Chicago Histotripsy-aided lytic delivery or lysotripsy is under development for the treatment of deep vein thrombosis. An in vitro procedure is presented here to assess the efficacy of this combination therapy. Key protocols for the clot model, image guidance, and assessment of treatment efficacy are discussed.

• Engineering

  
  Building an Enhanced Flight Mill for the Study of Tethered Insect Flight Anastasia Bernat^{1 1}Department of Ecology and Evolution, University of Chicago This protocol uses three-dimensional (3D) printers and laser cutters found in makerspaces in order to create a more flexible flight mill design. By using this technology, researchers can reduce costs, enhance design flexibility, and generate reproducible work when constructing their flight mills for tethered insect flight studies.

• Bioengineering

  
  Silicon Nanowires and Optical Stimulation for Investigations of Intra- and Intercellular Electrical Coupling Menahem Y. Rotenberg*¹, Erik N. Schaumann*², Aleksander Prominski^1,2, Bozhi Tian^{1,2,3 1}The James Franck Institute, The University of Chicago, ²Department of Chemistry, The University of Chicago, ³The Institute for Biophysical Dynamics, The University of Chicago This protocol describes the use of silicon nanowires for intracellular optical bio-modulation of cell in a simple and easy to perform method. The technique is highly adaptable to diverse cell types and can be used for in vitro as well as in vivo applications.

• Chemistry

  
  An Externally-Heated Diamond Anvil Cell for Synthesis and Single-Crystal Elasticity Determination of Ice-VII at High Pressure-Temperature Conditions Xiaojing Lai^1,2, Feng Zhu², Jin S. Zhang³, Dongzhou Zhang^2,4, Sergey Tkachev⁴, Vitali B. Prakapenka⁴, Bin Chen^{2 1}Gemmological Institute, China University of Geosciences (Wuhan), ²Hawai'i Institute of Geophysics and Planetology, University of Hawai'i at Mānoa, ³Department of Earth and Planetary Sciences, University of New Mexico, ⁴Center for Advanced Radiation Sources, University of Chicago This work focuses on the standard protocol for preparing the externally-heated diamond anvil cell (EHDAC) for generating high-pressure and high-temperature (HPHT) conditions. The EHDAC is employed to investigate materials in Earth and planetary interiors under extreme conditions, which can be also used in solid state physics and chemistry studies.

• Chemistry

  
  Assembly and Characterization of Polyelectrolyte Complex Micelles Alexander E. Marras¹, Jeffrey R. Vieregg¹, Matthew V. Tirrell^{1 1}Pritzker School of Molecular Engineering, The University of Chicago We provide protocols and representative data for designing, assembling, and characterizing polyelectrolyte complex micelles, core-shell nanoparticles formed by polyelectrolytes and hydrophilic charged-uncharged block copolymers.

• Biology

  
  Quantification of Proliferative and Dead Cells in Enteroids Hua-Shan Li*¹, Shao-Fang Xu*¹, Jian-Ying Sheng*¹, Zhi-Hui Jiang¹, Jing Wang¹, Ning Ding¹, Tao Wang¹, Matthew A. Odenwald², Jerrold R. Turner^2,3, Wei-Qi He¹, Hong Xu¹, Juan-Min Zha^{1 1}Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Suda (CAM-SU) Genomic Resource Center, Medical College of Soochow University, Department of Oncology, The First Affiliated Hospital of Soochow University, ²Department of Pathology, University of Chicago, ³ The presented protocol uses flow cytometry to quantify the number of proliferating and dead cells in cultured mouse enteroids. This method is helpful to evaluate the effects of drug treatment on organoid proliferation and survival.

• Biochemistry

  
  Visualizing Surface T-Cell Receptor Dynamics Four-Dimensionally Using Lattice Light-Sheet Microscopy Jillian Rosenberg¹, Jun Huang^{1,2 1}Committee on Cancer Biology, The University of Chicago, ²Pritzker School of Molecular Engineering, The University of Chicago The goal of this protocol is to show how to use Lattice Light-Sheet Microscopy to four-dimensionally visualize surface receptor dynamics in live cells. Here T cell receptors on CD4⁺ primary T cells are shown.

• Engineering

  
  Procedure for the Transfer of Polymer Films Onto Porous Substrates with Minimized Defects Lorenzo Guio*¹, Claire Liu*¹, Dean Boures*¹, Patrick T. Getty*¹, Ruben Waldman^1,2, Xiaoying Liu¹, Seth B. Darling^{1,2,3,4 1}Institute for Molecular Engineering, University of Chicago, ²Chemical Sciences and Engineering Division, Argonne National Laboratory, ³Institute for Molecular Engineering, Argonne National Laboratory, ⁴Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center, Argonne National Laboratory We present a procedure for highly controlled and wrinkle-free transfer of block copolymer thin films onto porous support substrates using a 3D-printed drain chamber. The drain chamber design is of general relevance to all procedures involving transfer of macromolecular films onto porous substrates, which is normally done by hand in an irreproducible fashion.

• Biology

  
  4D Microscopy of Yeast Natalie Johnson¹, Benjamin S. Glick^{1 1}Department of Molecular Genetics and Cell Biology, University of Chicago This protocol describes the analysis of fluorescently labeled intracellular compartments in budding yeast using multi-color 4D (time-lapse 3D) confocal microscopy. The imaging parameters are chosen to capture adequate signals while limiting photodamage. Custom ImageJ plugins allow labeled structures to be tracked and quantitatively analyzed.

• Neuroscience

  
  Real-time Video Projection in an MRI for Characterization of Neural Correlates Associated with Mirror Therapy for Phantom Limb Pain Faddi G. Saleh Velez^1,2, Camila B. Pinto^1,3, Emma S. Bailin⁴, Marionna Münger¹, Andrew Ellison⁵, Beatriz T. Costa¹, David Crandell⁶, Nadia Bolognini^7,8, Lotfi B. Merabet⁴, Felipe Fregni^{1 1}Laboratory of Neuromodulation & Center for Clinical Research Learning, Department of Physical Medicine and Rehabilitation, Harvard Medical School, Spaulding Rehabilitation Hospital, ²University of Chicago Medical Center, Department of Neurology, University of Chicago, ³Department of Neuroscience and Behavior, Psychology Institute, University of Sao Paulo, ⁴The Laboratory for Visual Neuroplasticity, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, ⁵Center for Biomedical Imaging, Department of Anatomy and Neurobiology, Boston University School of Medicine, ⁶Spaulding Rehabilitation Hospital, Harvard Medical School, ⁷Department of Psychology & Milan Center for Neuroscience, University of Milano-Bicocca, ⁸Neuropsychological Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Auxologico Italiano We present a novel combined behavioral and neuroimaging protocol employing real-time video projection for the purpose of characterizing the neural correlates associated with mirror therapy within the magnetic resonance imaging scanner environment in leg amputee subjects with phantom limb pain.

• Bioengineering

  
  Conducting Multiple Imaging Modes with One Fluorescence Microscope Seongjin Park¹, Jiacheng Zhang², Matthew A. Reyer², Joanna Zareba^1,3, Andrew A. Troy⁴, Jingyi Fei^{1,2 1}Department of Biochemistry and Molecular Biology, University of Chicago, ²The Institute for Biophysical Dynamics, University of Chicago, ³Faculty of Chemistry, Wrocław University of Science and Technology, ⁴Nikon Instruments Inc. Here we present a practical guide of building an integrated microscopy system, which merges conventional epi-fluorescent imaging, single-molecule detection-based super-resolution imaging, and multi-color single-molecule detection, including single-molecule fluorescence resonance energy transfer imaging, into one set-up in a cost-efficient way.

• Immunology and Infection

  
  Generation of Escape Variants of Neutralizing Influenza Virus Monoclonal Antibodies Paul E. Leon^1,2, Teddy John Wohlbold^1,2, Wenqian He^1,2, Mark J. Bailey^1,2, Carole J. Henry³, Patrick C. Wilson³, Florian Krammer¹, Gene S. Tan^{1 1}Department of Microbiology, Icahn School of Medicine at Mount Sinai, ²Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, ³The Department of Medicine, Section of Rheumatology, The Knapp Center for Lupus and Immunology Research, The University of Chicago We describe a method by which we identify critical residues required for the binding of human or murine monoclonal antibodies that target the viral hemagglutinin of influenza A viruses. The protocol can be adapted to other virus surface glycoproteins and their corresponding neutralizing antibodies.

• Medicine

  
  Automated Radiochemical Synthesis of [¹⁸F]3F4AP: A Novel PET Tracer for Imaging Demyelinating Diseases Pedro Brugarolas¹, Mohammed Bhuiyan², Anna Kucharski², Richard Freifelder^{2 1}Department of Neurology, The University of Chicago, ²Department of Radiology, The University of Chicago We demonstrate the semi-automated radiochemical synthesis of [¹⁸F]3F4AP and quality control procedures.

• Immunology and Infection

  
  Isolation of the Side Population in Myc-induced T-cell Acute Lymphoblastic Leukemia in Zebrafish Margaret M. Pruitt^1,2, Wilfredo Marin¹, Michael R. Waarts¹, Jill L. O. de Jong^{1 1}Department of Pediatrics, Section of Hematology-Oncology, The University of Chicago, ²Department of Biology and Biotechnology, Worcester Polytechnic Institute Here, we describe a technique to isolate the side population cells from a zebrafish model of myc-induced T-cell acute lymphoblastic leukemia (T-ALL). This side population assay is highly sensitive and is described for zebrafish T-ALL, but it may be applicable to other malignant and non-malignant zebrafish cell types.

• Chemistry

  
  High Pressure Single Crystal Diffraction at PX^2 Dongzhou Zhang¹, Przemyslaw K. Dera¹, Peter J. Eng², Joanne E. Stubbs², Jin S. Zhang¹, Vitali B. Prakapenka², Mark L. Rivers^{2 1}Hawai’i Institute of Geophysics and Planetology, University of Hawai’i at Manoa, ²Center for Advanced Radiation Sources, University of Chicago In this report, we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell at the GSECARS 13-BM-C beamline at the Advanced Photon Source. ATREX and RSV programs are used to analyze the data.

• Cancer Research

  
  Advanced Animal Model of Colorectal Metastasis in Liver: Imaging Techniques and Properties of Metastatic Clones Go Oshima*^1,2, Melinda E. Stack*¹, Sean C. Wightman¹, Darren Bryan¹, Elizabeth Poli¹, Lai Xue¹, Kinga B. Skowron¹, Abhineet Uppal¹, Sean P. Pitroda², Xiaona Huang², Mitchell C. Posner¹, Samuel Hellman², Ralph R. Weichselbaum², Nikolai N. Khodarev^{2 1}Department of Surgery, The University of Chicago, ²Department of Radiation and Cellular Oncology and Ludwig Center for Metastasis Research, The University of Chicago The ability of metastatic clones to colonize distant sites depends on their proliferation capacity and/or their ability to survive in the host microenvironment without significant proliferation. Here, we present an animal model that allows quantitative visualization of both types of liver colonization by metastatic clones.

• Neuroscience

  
  Using Linear Agarose Channels to Study Drosophila Larval Crawling Behavior Xiao Sun¹, Ellie S. Heckscher^{1,2 1}Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, ²Department of Molecular Genetics and Cell Biology, University of Chicago The Drosophila larva is a powerful model system to study neural control of behavior. This publication describes the use of linear agarose channels to elicit sustained bouts of linear crawling and methods to quantify the dynamics of larval structures during repetitive crawling behavior.

• Biology

  
  Filtration Isolation of Nucleic Acids: A Simple and Rapid DNA Extraction Method Sally M. McFall¹, Mário F. Neto¹, Jennifer L. Reed¹, Robin L. Wagner^{2 1}Center for Innovation in Global Health Technologies (CIGHT), Department of Biomedical Engineering, Northwestern University, ²Pritzker School of Medicine, The University of Chicago We describe here a simple and rapid paper-based DNA extraction method of HIV proviral DNA from whole blood detected by quantitative PCR. This protocol can be extended for use in detecting other genetic markers or using alternative amplification methods.

• Neuroscience

  
  Quantification of Cerebral Vascular Architecture using Two-photon Microscopy in a Mouse Model of HIV-induced Neuroinflammation Christopher Nishimura¹, Oksana Polesskaya², Stephen Dewhurst¹, Jharon N. Silva^{1 1}Department of Microbiology and Immunology, University of Rochester Medical Center, ²Department of Human Genetics, University of Chicago This paper describes a method by which the vascular architecture in the brain can be quantified using in vivo and ex vivo two-photon microscopy.

• Medicine

  
  Modeling the Early Steps of Ovarian Cancer Dissemination in an Organotypic Culture of the Human Peritoneal Cavity Pamela N. Peters¹, Elizabeth M. Schryver¹, Ernst Lengyel¹, Hilary Kenny^{1 1}Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago Here, we present a protocol to construct a three-dimensional in vitro model of the lining of the peritoneal cavity, composed of primary human mesothelial cells and fibroblasts layered with extracellular matrix, as a tool to investigate ovarian cancer cell adhesion, invasion, and proliferation.

• Medicine

  
  In Vivo and Ex Vivo Approaches to Study Ovarian Cancer Metastatic Colonization of Milky Spot Structures in Peritoneal Adipose Venkatesh Krishnan¹, Robert Clark¹, Marina Chekmareva², Amy Johnson¹, Sophia George³, Patricia Shaw⁴, Victoria Seewaldt^4,5, Carrie Rinker-Schaeffer^{1 1}Section of Urology, Department of Surgery, The University of Chicago, ²Department of Pathology, Robert Wood Johnson Medical School, ³Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, ⁴Department of Laboratory Medicine and Pathobiology, Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University of Toronto, University Health Network, ⁵Departments of Medicine, Pharmacology, and Cancer Biology, Duke University Medical Center We outline a protocol that implements both in vivo and ex vivo approaches to study ovarian cancer colonization of peritoneal adipose tissues, particularly the omentum. Furthermore, we present a protocol to quantitate and analyze immune cell-structures in the omentum known as milky spots, which promote metastases of peritoneal adipose.

• Biology

  
  Surface Spreading and Immunostaining of Yeast Chromosomes Jennifer Grubb¹, M. Scott Brown^1,2, Douglas K. Bishop^{1,2 1}Department of Radiation and Cellular Oncology, University of Chicago, ²Department of Molecular Genetics and Cell Biology, University of Chicago A method for surface-spreading chromosomes from budding yeast is presented. This method is derived from a method previously described by Loidl and Klein. In addition, we demonstrate a procedure for immunostaining of spread chromosomes.

• Immunology and Infection

  
  Scalable High Throughput Selection From Phage-displayed Synthetic Antibody Libraries Shane Miersch^1,2, Zhijian Li^1,2, Rachel Hanna^1,2, Megan E. McLaughlin^1,2, Michael Hornsby^1,3, Tet Matsuguchi^1,3, Marcin Paduch^1,4, Annika Sääf^1,4, Jim Wells^1,3, Shohei Koide^1,4, Anthony Kossiakoff^1,4, Sachdev S. Sidhu^{1,2 1}The Recombinant Antibody Network, ²The Banting and Best Department of Medical Research, University of Toronto, ³Antibiome Center, University of California, San Francisco at Mission Bay, ⁴Department of Biochemistry and Molecular Biology, The University of Chicago A method is described with visual accompaniment for conducting scalable, high throughput selections from phage-displayed combinatorial synthetic antibody libraries against hundreds of antigens simultaneously. Using this parallel approach, we have isolated antibody fragments that exhibit high affinity and specificity for diverse antigens that are functional in standard immunoassays.

• Engineering

  
  Fast Imaging Technique to Study Drop Impact Dynamics of Non-Newtonian Fluids Qin Xu^1,2, Ivo Peters², Sam Wilken^1,2, Eric Brown³, Heinrich Jaeger^{1,2 1}Department of Physics, The University of Chicago, ²James Franck Institute, The University of Chicago, ³Department of Mechanical Engineering and Materials Science, Yale University Drop impact of non-Newtonian fluids is a complex process since different physical parameters influence the dynamics over a very short time (less than one tenth of a millisecond). A fast imaging technique is introduced in order to characterize the impact behaviors of different non-Newtonian fluids.

• Neuroscience

  
  Laser-scanning Photostimulation of Optogenetically Targeted Forebrain Circuits Charles C. Lee¹, Ying-Wan Lam², Kazuo Imaizumi¹, S. Murray Sherman^{2 1}Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, ²Department of Neurobiology, University of Chicago We describe a method for characterizing the functional topography and synaptic properties of forebrain circuits using an optogenetic approach to photostimulate neuronal populations in vitro.

• Chemistry

  
  Seeded Synthesis of CdSe/CdS Rod and Tetrapod Nanocrystals Karthish Manthiram*^1,4, Brandon J. Beberwyck*^2,4, Dmitri V. Talapin^5,6, A. Paul Alivisatos^{2,3,4 1}Department of Chemical Engineering, UC Berkeley, ²Department of Materials Science and Engineering, UC Berkeley, ³Department of Chemistry, UC Berkeley, ⁴Materials Sciences Division, Lawrence Berkeley National Laboratory, ⁵Department of Chemistry, University of Chicago, ⁶Center for Nanoscale Materials, Argonne National Laboratory A protocol for the seeded synthesis of rod-shaped and tetrapod-shaped multicomponent nanostructures consisting of CdS and CdSe is presented.

• Engineering

  
  Synthesis and Microdiffraction at Extreme Pressures and Temperatures Barbara Lavina¹, Przemyslaw Dera², Yue Meng^{3 1}High 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.

• Medicine

  
  Formation of Human Prostate Epithelium Using Tissue Recombination of Rodent Urogenital Sinus Mesenchyme and Human Stem Cells Yi Cai¹, Steven Kregel², Donald J. Vander Griend^{1,2 1}Department of Surgery, Section of Urology, University of Chicago, ²Committee on Cancer Biology, University of Chicago To unravel the earliest molecular mechanisms underlying prostate cancer initiation, novel and innovative human model systems and approaches are desperately needed. The potential of pre-prostatic urogenital sinus mesenchyme (UGSM) to induce pluripotent stem cell populations to form human prostate epithelium is a powerful experimental tool in prostate research.

• Medicine

  
  Murine Fetal Echocardiography Gene H. Kim^{1 1}Department of Medicine, Section of Cardiology, Institute for Cardiovascular Research, University of Chicago Fetal and perinatal death is a common feature when studying genetic alterations affecting cardiac development. High-frequency ultrasound imaging has improved 2-D resolution and can provide excellent information on early cardiac development and is an ideal method to detect the impact on cardiac structure and function prior to death.

• Engineering

  
  Concurrent Quantitative Conductivity and Mechanical Properties Measurements of Organic Photovoltaic Materials using AFM Maxim P. Nikiforov¹, Seth B. Darling^{1,2 1}Center for Nanoscale Materials, Argonne National Laboratory, ²Institute for Molecular Engineering, University of Chicago Organic photovoltaic (OPV) materials are inherently inhomogeneous at the nanometer scale. Nanoscale inhomogeneity of OPV materials affects performance of photovoltaic devices. In this paper, we describe a protocol for quantitative measurements of electrical and mechanical properties of OPV materials with sub-100 nm resolution.

• Biology

  
  Selective Capture of 5-hydroxymethylcytosine from Genomic DNA Yujing Li¹, Chun-Xiao Song², Chuan He², Peng Jin^{1 1}Department of Human Genetics, Emory University School of Medicine, ²Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago Described is a two-step labeling process using β-glucosyltransferase (β-GT) to transfer an azide-glucose to 5-hmC, followed by click chemistry to transfer a biotin linker for easy and density-independent enrichment. This efficient and specific labeling method enables enrichment of 5-hmC with extremely low background and high-throughput epigenomic mapping via next-generation sequencing.

• Neuroscience

  
  Modeling Neural Immune Signaling of Episodic and Chronic Migraine Using Spreading Depression In Vitro Aya D. Pusic*¹, Yelena Y. Grinberg*¹, Heidi M. Mitchell², Richard P. Kraig^{1 1}Department of Neurology and Committee on Neurobiology, The University of Chicago Medical Center, ²Department of Neurology, The University of Chicago Medical Center Migraine and its transformation to chronic migraine are immense healthcare burdens in need of improved treatment options. We seek to define how neural immune signaling modulates the susceptibility to migraine, modeled in vitro using spreading depression in hippocampal slice cultures, as a means to develop novel therapeutic targets.

• Biology

  
  Computer-assisted Large-scale Visualization and Quantification of Pancreatic Islet Mass, Size Distribution and Architecture Abraham Kim¹, German Kilimnik¹, Charles Guo¹, Joshua Sung¹, Junghyo Jo², Vipul Periwal², Piotr Witkowski³, Philip Dilorio⁴, Manami Hara^{1 1}Department of Medicine, University of Chicago, ²Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, ³Department of Surgery, University of Chicago, ⁴Diabetes Division, University of Massachusetts Novel computer-assisted methods of large-scale procurement and analysis of immunohistochemically stained pancreatic specimens are described: (1) Virtual Slice capture of the entire section; (2) Mass analysis of large-scale data; (3) Reconstruction of 2D Virtual Slices; (4) 3D islet mapping; and (5) Mathematical analysis.

• Medicine

  
  Generation of Comprehensive Thoracic Oncology Database - Tool for Translational Research Mosmi Surati¹, Matthew Robinson², Suvobroto Nandi², Leonardo Faoro², Carley Demchuk², Rajani Kanteti², Benjamin Ferguson¹, Tara Gangadhar², Thomas Hensing³, Rifat Hasina², Aliya Husain⁴, Mark Ferguson⁵, Theodore Karrison⁶, Ravi Salgia^{2 1}Pritzker School of Medicine, University of Chicago, ²Department of Medicine, University of Chicago, ³Department of Medicine, Northshore University Health Systems, ⁴Department of Pathology, University of Chicago, ⁵Department of Surgery, University of Chicago, ⁶Department of Biostatistics, University of Chicago A thoracic oncology database was developed to serve as a comprehensive repository for clinical and laboratory data for the purposes of translational research. The database will serve translational cancer researchers within the Thoracic Oncology Research Program. This database is adaptable to other cancer models, as well as other human diseases.

• Neuroscience

  
  Combining Computer Game-Based Behavioural Experiments With High-Density EEG and Infrared Gaze Tracking Keith J. Yoder^1,2, Matthew K. Belmonte^{1,3 1}Department of Human Development, Cornell University, ²Social Sciences Division, University of Chicago, ³National Brain Research Centre, Manesar, India Procedures for recording high-density EEG and gaze data during computer game-based cognitive tasks are described. Using a video game to present cognitive tasks enhances ecological validity without sacrificing experimental control.

• Bioengineering

  
  Preparation of Complaint Matrices for Quantifying Cellular Contraction Yvonne Aratyn-Schaus¹, Patrick W. Oakes¹, Jonathan Stricker², Stephen P. Winter³, Margaret L. Gardel^{1,2 1}Institute for Biophysical Dynamics, University of Chicago, ²Physics Department - James Franck Institute, University of Chicago, ³Interdisciplinary Scientist Training Program, University of Chicago In this video, we demonstrate the experimental techniques used to fabricate compliant, extracellular matrix (ECM) coated substrates suitable for cell culture, and which are amenable to traction force microscopy and observing effects of ECM stiffness on cell behavior.

• Neuroscience

  
  Strategies for Study of Neuroprotection from Cold-preconditioning Heidi M. Mitchell¹, David M. White¹, Richard P. Kraig^{1 1}Department of Neurology, The University of Chicago Medical Center We seek to define the neural immune signaling responsible for cold-preconditioning as means to identify novel targets for therapeutics development to protect brain before injury onset. We present strategies for such work that require biological systems, experimental manipulations plus technical capacities that are highly reproducible and sensitive.

• Biology

  
  Intraperitoneal Injection into Adult Zebrafish Mary D. Kinkel¹, Stefani C. Eames², Louis H. Philipson^2,3, Victoria E. Prince^{1 1}Department of Organismal Biology and Anatomy, The University of Chicago, ²Committee on Molecular Metabolism and Nutrition, The University of Chicago, ³Department of Medicine, The University of Chicago We demonstrate intraperitoneal injection into adult zebrafish. We use a 10 μl NanoFil microsyringe controlled by a Micro4 controller and UltraMicroPump III. This demonstration includes the use of cold water as an anesthetic.

• Biology

  
  Genome-wide Analysis of Aminoacylation (Charging) Levels of tRNA Using Microarrays John Zaborske¹, Tao Pan^{1 1}Department of Biochemistry and Molecular Biology, University of Chicago We describe a method for microarray analysis to determine relative aminoacylation levels of all tRNAs from S. cerivisiae.

• Biology

  
  In situ Quantification of Pancreatic Beta-cell Mass in Mice Abraham Kim¹, German Kilimnik¹, Manami Hara^{1 1}Department of Medicine, University of Chicago The following protocol outlines the process of pancreatic dissection for virtual slice imaging, and the subsequent quantification of all GFP-tagged beta-cells in the entire pancreas.

• Application Notes

  
  The NanoDrop 2000c Spectrophotometer - Microvolume Protein Concentration Determination (Spanish) - ADVERTISEMENT Theodore Karrison^{1 1}Department of Health Studies, University of Chicago

• Biology

  
  In Ovo Electroporations of HH Stage 10 Chicken Embryos Marissa C. Blank¹, Victor Chizhikov², Kathleen J. Millen^{2 1}Department of Molecular Genetics and Cell Biology, University of Chicago, ²Department of Human Genetics, University of Chicago Chick in ovo electroporation is a technique which allows genetic manipulation of the avian embryo. Common applications of this technique include functional analysis of genes and putative enhancer elements. This video demonstrates neural tube electroporation in HH 10 chick embryos. Injection technique and proper egg handling are discussed.

• Biology

  
  Understanding Cerebellar Pattern Formation Kathleen J. Millen^{1 1}Department of Neurology, University of Chicago