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Francis Crick Institute

4 ARTICLES PUBLISHED IN JoVE

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Biology

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
Julian Konig 1, Kathi Zarnack 2, Gregor Rot 3, Tomaz Curk 3, Melis Kayikci 1, Blaz Zupan 3, Daniel J. Turner 4, Nicholas M. Luscombe 2, Jernej Ule 1
1Laboratory of Molecular Biology, Medical Research Council - MRC, 2European Bioinformatics Institute, EMBL Heidelberg, 3Computer and Information Science, University of Ljubljana, 4Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute

The spatial arrangement of RNA-binding proteins on a transcript is a key determinant of post-transcriptional regulation. Therefore, we developed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) that allows precise genome-wide mapping of the binding sites of an RNA-binding protein.

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Environment

Streamlined Sampling and Cultivation of the Pelagic Cosmopolitan Larvacean, Oikopleura dioica
Aki Masunaga 1, Andrew W. Liu 1, Yongkai Tan 1, Andrew Scott 1, Nicholas M. Luscombe 1,2,3
1Okinawa Institute of Science and Technology Graduate University, 2Francis Crick Institute, 3UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London

Oikopleura dioica is a tunicate model organism in various fields of biology. We describe sampling methods, species identification, culturing setup, and culturing protocols for the animals and algal feed. We highlight key factors that helped strengthen the culture system and discuss the possible problems and resolutions.

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Immunology and Infection

Assessing Respiratory Immune Responses to Haemophilus Influenzae
Lovisa Dousha 1,2, Roleen Sharma 1,2, Steven Lim 2,3, James Ngui 2,4, Ashley M. Buckle 5, Paul T. King 1,2
1Monash Lung and Sleep, Monash Medical Centre, 2Monash University Department of Medicine, Monash Medical Centre, 3Flow Cytometry Science Technology Platform, Francis Crick Institute, 4Clinical Immunology, Monash Medical Centre, 5Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University

Haemophilus influenzae induces inflammation in the respiratory tract. This article will focus on the use of flow cytometry and confocal microscopy to define immune responses by phagocytes and lymphocytes in response to this bacterium.

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Biochemistry

Hybrid Ensemble and Single-molecule Assay to Image the Motion of Fully Reconstituted CMG
Daniel Ramírez Montero 1, Humberto Sánchez 1, Edo van Veen 1, Theo van Laar 1, Belén Solano 1, John F. X. Diffley 2, Nynke H. Dekker 1,3
1Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2Chromosome Replication Laboratory, Francis Crick Institute, 3Department of Physics and Kavli Institute of Nanoscience Discovery, University of Oxford

We report a hybrid ensemble and single-molecule assay to directly image and quantify the motion of fluorescently labeled, fully reconstituted Cdc45/Mcm2-7/GINS (CMG) helicase on linear DNA molecules held in place in an optical trap.

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