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Okinawa Institute of Science and Technology Graduate University

5 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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Behavior

New Variations for Strategy Set-shifting in the Rat
Sho Aoki 1, Andrew W. Liu 1, Aya Zucca 1, Stefano Zucca 1, Jeffery R. Wickens 1
1Neurobiology Research Unit, Okinawa Institute of Science and Technology

Set-shifting, a form of behavioral flexibility, requires an attentional shift from one stimulus dimension to another. We extended an established rodent set-shifting task1 by requiring attention to different stimuli according to context. The task was combined with specific lesions to identify neuron subtypes underlying a successful shift.

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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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Neuroscience

In Vivo Wireless Optogenetic Control of Skilled Motor Behavior
Diana L. Rodriguez-Munoz 1, Omar Jaidar 2, Marcela Palomero-Rivero 1, Mario A. Arias-Garcia 3, Gordon W. Arbuthnott 4, Violeta G. Lopez-Huerta 1
1Institute of Cellular Physiology, National University of Mexico, 2Department of Neurosurgery, Stanford University, 3Facultad de Psicologia, National University of Mexico, 4Brain Mechanisms for Behaviour Unit, Okinawa Institute of Science and Technology Graduate University

The present protocol describes how to use wireless optogenetics combined with high-speed videography in a single pellet reach-to-grasp task to characterize the neural circuits involved in the performance of skilled motor behavior in freely moving mice.

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Neuroscience

Aversive Associative Learning and Memory Formation by Pairing Two Chemicals in Caenorhabditis elegans
Mihiro Shibutani 1, Suteera Vibulyaseck 1, Ichiro N. Maruyama 1
1Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University

We have previously developed protocols for Caenorhabditis elegans to form short- and long-term associative memories by massed and spaced training, respectively. Here, detailed protocols are described for the conditioning of C. elegans by pairing 1-propanol and hydrochloric acid as conditioned and unconditioned stimuli, respectively, to form aversive associative memory.

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