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University College Dublin

8 ARTICLES PUBLISHED IN JoVE

Neuroscience

Measurement & Analysis of the Temporal Discrimination Threshold Applied to Cervical Dystonia

Rebecca B Beck^*1, Eavan M McGovern^*1,2,3, John S Butler⁴, Dorina Birsanu¹, Brendan Quinlivan¹, Ines Beiser^1,2,3, Shruti Narasimham¹, Sean O'Riordan^2,3, Michael Hutchinson^2,3, Richard B Reilly^1,5

¹School of Engineering, Trinity College Dublin, The University of Dublin, ²Department of Neurology, St. Vincent's University Hospital, ³School of Medicine and Medical Sciences, University College Dublin, ⁴School of Mathematical Sciences, Dublin Institute of Technology, ⁵School of Medicine Trinity College Dublin, The University of Dublin

Methods for the measurement and analysis of the temporal discrimination threshold are presented, and its application to the study of the pathogenesis of cervical dystonia are discussed.

Immunology and Infection

Dissecting Multi-protein Signaling Complexes by Bimolecular Complementation Affinity Purification (BiCAP)

Jordan F. Hastings¹, Jeremy Z.R. Han¹, Robert F. Shearer^1,2, Sean P. Kennedy^1,3, Mary Iconomou^1,4, Darren N. Saunders⁵, David R. Croucher^1,6,7

¹The Kinghorn Cancer Centre, Garvan Institute of Medical Research, ²Ubiquitin Signaling Group, Protein Signaling Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, ³RCSI Molecular Medicine, Royal College of Surgeons in Ireland, ⁴Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, ⁵School of Medical Sciences, University of New South Wales, ⁶St Vincent's Hospital Clinical School, University of New South Wales, ⁷School of Medicine and Medical Science, University College Dublin

This manuscript describes the protocol for Bimolecular Complementation Affinity Purification (BiCAP). This novel method facilitates the specific isolation and downstream proteomic characterization of any two interacting proteins, while excluding un-complexed individual proteins as well as complexes formed with competing binding partners.

Biology

Tissue Collection of Bats for -Omics Analyses and Primary Cell Culture

Laurel R. Yohe^*1,2, Paolo Devanna^*3, Kalina T.J. Davies⁴, Joshua H.T. Potter⁴, Stephen J. Rossiter⁴, Emma C. Teeling⁵, Sonja C. Vernes^*3,6, Liliana M. Dávalos^*2,7

¹Department of Geology & Geophysics, Yale University, ²Department of Ecology & Evolution, Stony Brook University, ³Neurogenetics of Vocal Communication, Max Planck Institute for Psycholinguistics, ⁴School of Biological and Chemical Sciences, Queen Mary University of London, ⁵School of Biology & Environmental Science, University College Dublin, ⁶Donders Institute for Brain, Cognition and Behavior, ⁷Consortium for Inter-Disciplinary Environmental Research, Stony Brook University

This is a protocol for the optimal tissue preparation for genomic, transcriptomic, and proteomic analyses of bats caught in the wild. It includes protocols for bat capture and dissection, tissue preservation, and cell culturing of bat tissue.

Biology

Laser Capture Microdissection on Surgical Tissues to Identify Aberrant Gene Expression in Impaired Wound Healing in Type 2 Diabetes

Rachael Williams^*1, Irene Castellano-Pelicena^*1,2, Aaiad H.A Al-Rikabi^1,3, Stephen K. Sikkink¹, Richard Baker¹, Kirsten Riches-Suman¹, M Julie Thornton¹

¹Centre for Skin Sciences, University of Bradford, ²The Charles Institute of Dermatology, School of Medicine, University College Dublin, ³University of Baghdad

This technique provides a guide to inflicting ex vivo wounds, performing laser capture microdissection and quantifying changes in gene expression related to poor wound healing processes in diabetes using clinically relevant human tissue.

Environment

Sampling, Identification and Characterization of Microplastics Release from Polypropylene Baby Feeding Bottle during Daily Use

Dunzhu Li^*1,2, Luming Yang^*1,2, Rachel Kavanagh¹, Liwen Xiao^2,3, Yunhong Shi^1,2, Daniel K. Kehoe¹, Emmet D. Sheerin^1,4, Yurii K. Gun’ko^4,5, John J. Boland^1,4, Jing Jing Wang¹

¹AMBER Research Centre and Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, ²Department of Civil, Structural and Environmental Engineering, Trinity College Dublin, ³TrinityHaus, Trinity College Dublin, ⁴School of Chemistry, Trinity College Dublin, ⁵BEACON, Bioeconomy SFI Research Centre, University College Dublin

This study detailed a reliable and cost-effective protocol for microplastics collection and detection from the daily use of plastic products.

Biology

A Robust Method for the Large-Scale Production of Spheroids for High-Content Screening and Analysis Applications

Alannah S. Chalkley¹, Margaritha M. Mysior¹, Jeremy C. Simpson¹

¹Cell Screening Laboratory, UCD School of Biology and Environmental Science, University College Dublin

This protocol details a method for the production of three different types of spheroids in a manner that makes them suitable for large-scale high-content screening and analysis. In addition, examples are presented showing how they can be analyzed at spheroid and individual cell levels.

Bioengineering

Rapid Antibody Glycoengineering in Chinese Hamster Ovary Cells

Masue Marbiah^*1,2, Pavlos Kotidis^*1,3, Roberto Donini^1,4, Itzcóatl A. Gómez⁵, Ioscani Jimenez del Val⁵, Stuart M. Haslam⁴, Karen M. Polizzi^1,2, Cleo Kontoravdi¹

¹Department of Chemical Engineering, Imperial College London, ²Imperial College Centre for Synthetic Biology, Imperial College London, ³BioPharm Process Research, GlaxoSmithKline Research and Development, ⁴Department of Life Science, Imperial College London, ⁵School of Chemical & Bioprocess Engineering, University College Dublin

The glycosylation pattern of an antibody determines its clinical performance, thus industrial and academic efforts to control glycosylation persist. Since typical glycoengineering campaigns are time- and labor-intensive, the generation of a rapid protocol to characterize the impact of glycosylation genes using transient silencing would prove useful.

Biology

Quantitative Determination of De Novo Fatty Acid Synthesis in Brown Adipose Tissue Using Deuterium Oxide

Rory Turner^*1, Rajib Mukherjee^*2, Martina Wallace¹, Joan Sanchez-Gurmaches^2,3,4

¹UCD Conway Institute and UCD Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, ²Division of Endocrinology, Cincinnati Children’s Hospital Medical Center, Cincinnati, ³Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, ⁴Department of Pediatrics, University of Cincinnati College of Medicine

Here, we present an inexpensive quantitative method utilizing deuterium oxide and gas chromatography mass spectrometry (GCMS) for the analysis of total fatty acid de novo lipogenesis in brown adipose tissue in vivo.