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The Barcelona Institute of Science and Technology

6 ARTICLES PUBLISHED IN JoVE

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Genetics

Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C)
Tian V. Tian 1,2,3, Enrique Vidal 1,2, Thomas Graf 1,2, Grégoire Stik 1,2
1Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 2Universitat Pompeu Fabra, 3Vall d'Hebron Institute of Oncology

We report the application of quantitative chromosome conformation capture followed by high-throughput sequencing in embryoid bodies generated from embryonic stem cells. This technique allows to identify and quantitate the contacts between putative enhancers and promoter regions of a given gene during embryonic stem cell differentiation.

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Developmental Biology

Direct Force Measurements of Subcellular Mechanics in Confinement using Optical Tweezers
Frederic Català-Castro 1, Valeria Venturini 2,3, Santiago Ortiz-Vásquez 1, Verena Ruprecht 2,4, Michael Krieg 1
1Neurophotonics and Mechanical Systems Biology, Institut de Ciències Fotòniques, ICFO, 2Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 3Institut de Ciències Fotòniques, ICFO, 4Universitat Pompeu Fabra (UPF)

Here, we present a protocol to investigate the intracellular mechanical properties of isolated embryonic zebrafish cells in three-dimensional confinement with direct force measurement by an optical trap.

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Neuroscience

Hippocampal Neuronal Cultures to Detect and Study New Pathogenic Antibodies Involved in Autoimmune Encephalitis
Marina Cunquero 1, Esther Aguilar 2, Pablo Loza-Alvarez 1, Jesús Planagumà 1,2
1ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 2Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona

Autoimmune encephalitis is a new category of antibody-mediated diseases of the central nervous system. Hippocampal neurons can be used to discover and characterize these antibodies. This article provides a protocol for primary cell culture and immunostaining to determine autoantibodies in the serum and cerebrospinal fluid of patients.

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Neuroscience

Calcium Imaging In Electrically Stimulated Flat-Mounted Retinas
Marina Cunquero 1, Maria Marsal 1, Gustavo Castro-Olvera 1, Steven T. Walston 2, F. Taygun Duvan 2, José Gabriel Macias-Montero 3, Carles Puigdengoles 3, Mokhtar Chmeissani 3, Jose A. Garrido 2,4, Pablo Loza-Alvarez 1
1Institut de Ciències Fotòniques (ICFO), The Barcelona Institute of Science and Technology, 2Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, 3Institut de Física d'Altes Energies (IFAE), The Barcelona Institute of Science and Technology, Campus UAB, 4Institució Catalana de Recerca i Estudis Avançats (ICREA)

Retinal prostheses have the ability to generate visual perceptions. To advance the development of new prostheses, ex vivo methods are needed to test devices before implantation. This article provides a comprehensive protocol for studying calcium activity in the retinal ganglion cell layer when subjected to electrical stimulation.

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Developmental Biology

Early Unguided Human Brain Organoid Neurovascular Niche Modeling into the Permissive Chick Embryo Chorioallantoic Membrane
Luciano Fiore 1,2, Jan Arderiu 3, Andrea Martí-Sarrias 3,4, Isabel Turpín 3,4, Ruth I. Pareja 3,5, Arcadi Navarro 5,6,7,8, Mariana Holubiec 2,9, Julieta Bianchelli 9, Tomas Falzone 2,9, Gonzalo Spelzini 1,2, Gabriel Scicolone 1,2, Sandra Acosta 3,4
1Instituto de Biología Celular y Neurociencias “Prof. E. De Robertis” (IBCN), CONICET - Universidad de Buenos Aires, 2Facultad de Medicina, Departamento de Biología Celular, Histología, Embriología y Genética, Universidad de Buenos Aires, 3Institute of Neurosciences, Pathology and Experimental Therapeutics Dept, University of Barcelona, 4Functional Neurogenomics Group, Neurodevelopmental Disorders, IDIBELL, L’Hospitalet de Llobregat, 5IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 6Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, 7Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 8BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, 9Instituto de Investigación en Biomedicina (IBioBA) – CONICET – Instituto Partner de la Sociedad Max Planck

Here, we present a protocol to engraft human brain organoids at multiple maturation stages into the chick chorioallantoic membrane (CAM). Brain organoids were grown following unguided standardized protocols.

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Biology

Capturing Cytoskeleton-Based Agitation of the Mouse Oocyte Nucleus Across Spatial Scales
Gaëlle Letort 1,2, Philippe Mailly 1, Adel Al Jord 1,3, Maria Almonacid 1
1Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, 2Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS, 3Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology

This protocol provides an experimental framework to document the physical impact of the cytoskeleton on nuclear shape and the internal membrane-less organelles in the mouse oocyte system. The framework can be adapted for use in other cell types and contexts.

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