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SIB Swiss Institute of Bioinformatics

4 ARTICLES PUBLISHED IN JoVE

Medicine

Improved Protocol For Laser Microdissection Of Human Pancreatic Islets From Surgical Specimens

Dorothée Sturm^1,2, Lorella Marselli³, Florian Ehehalt^1,2, Daniela Richter¹, Marius Distler², Stephan Kersting^1,2, Robert Grützmann², Krister Bokvist⁴, Philippe Froguel⁵, Robin Liechti⁶, Anne Jörns⁷, Paolo Meda⁸, Gustavo Bruno Baretton⁹, Hans-Detlev Saeger², Anke M. Schulte¹⁰, Piero Marchetti³, Michele Solimena¹

¹Molecular Diabetology, Paul Langerhans Institute Dresden, ²Department of GI-, Thoracic- and Vascular Surgery, University Hospital Carl Gustav Carus, University of Technology Dresden, ³Department of Endocrinology and Metabolism, Metabolic Unit University of Pisa, ⁴Labs DC0522, Lilly Corporate Center, ⁵Genomics, Faculty of Medicine Imperial College London, ⁶Vital-IT, SIB Swiss Institute of Bioinformatics, ⁷Clinical Biochemistry, Hannover Medical School, ⁸Cell Physiology and Metabolism, Medical School, University of Geneva, ⁹Department of Pathology, University Hospital Carl Gustav Carus, University of Technology Dresden, ¹⁰R&D DIAB Division / Translational Medicine, Sanofi-Aventis

Laser microdissection is a technique that allows the recovery of selected cells from minute amounts of parenchyma. Here we describe a protocol for acquiring human pancreatic islets from surgical specimens to be used for transcriptomic studies. Our protocol improves the intrinsic autofluorescence of human beta cells, thus facilitating their collection.

Cancer Research

Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment

Cinzia Donato^*1, Barbara M. Szczerba^*1, Manuel C. Scheidmann^*1, Francesc Castro-Giner^1,2, Nicola Aceto¹

¹Cancer Metastasis Laboratory, Department of Biomedicine, University of Basel and University Hospital Basel, ²SIB Swiss Institute of Bioinformatics

Here, we present an integrated workflow to identify phenotypic and molecular features that characterize circulating tumor cells (CTCs). We combine live immunostaining and robotic micromanipulation of single and clustered CTCs with single cell-based techniques for downstream analysis and assessment of metastasis-seeding ability.

Biology

Exploring m⁶A and m⁵C Epitranscriptomes upon Viral Infection: an Example with HIV

Sara Cristinelli¹, Paolo Angelino², Angela Ciuffi¹

¹Institute of Microbiology, Lausanne University Hospital and University of Lausanne, ²Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics

The role of RNA modifications in viral infections is just starting to be explored and could highlight new viral-host interaction mechanisms. In this work, we provide a pipeline to investigate m⁶A and m⁵C RNA modifications in the context of viral infections.

Biology

Bioinformatics Resources for the Study of Glycan-Mediated Protein Interactions

Frédérique Lisacek^1,2,3

¹Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, ²Computer Science Department, University of Geneva, ³Section of Biology, University of Geneva

This protocol illustrates how to explore, compare, and interpret human protein glycomes with online resources.