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The Barcelona Institute of Science and Technology

6 ARTICLES PUBLISHED IN JoVE

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.

Developmental Biology

Direct Force Measurements of Subcellular Mechanics in Confinement using Optical Tweezers

Frederic Català-Castro¹, Valeria Venturini^2,3, Santiago Ortiz-Vásquez¹, Verena Ruprecht^2,4, Michael Krieg¹

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.

Neuroscience

Hippocampal Neuronal Cultures to Detect and Study New Pathogenic Antibodies Involved in Autoimmune Encephalitis

Marina Cunquero¹, Esther Aguilar², Pablo Loza-Alvarez¹, 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.

Neuroscience

Calcium Imaging In Electrically Stimulated Flat-Mounted Retinas

Marina Cunquero¹, Maria Marsal¹, Gustavo Castro-Olvera¹, Steven T. Walston², F. Taygun Duvan², José Gabriel Macias-Montero³, Carles Puigdengoles³, Mokhtar Chmeissani³, Jose A. Garrido^2,4, Pablo Loza-Alvarez¹

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.

Developmental Biology

Early Unguided Human Brain Organoid Neurovascular Niche Modeling into the Permissive Chick Embryo Chorioallantoic Membrane

Luciano Fiore^1,2, Jan Arderiu³, 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 Bianchelli⁹, 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.

Biology

Capturing Cytoskeleton-Based Agitation of the Mouse Oocyte Nucleus Across Spatial Scales

Gaëlle Letort^1,2, Philippe Mailly¹, Adel Al Jord^1,3, Maria Almonacid¹

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.