University of Bergen

9 ARTICLES PUBLISHED IN JoVE

Biochemistry

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Shashank Jariwala^*1, Lars Skjærven^*2, Xin-Qiu Yao¹, Barry J. Grant¹

¹Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, ²Department of Biomedicine, University of Bergen

A protocol for the online investigation of protein sequence-structure-dynamics relationships using Bio3D-web is presented.

Genetics

Multi-locus Variable-number Tandem-repeat Analysis of the Fish-pathogenic Bacterium Yersinia ruckeri by Multiplex PCR and Capillary Electrophoresis

Snorre Gulla¹, Saima Nasrin Mohammad¹, Duncan John Colquhoun^1,2

¹Fish Health Research Group, Norwegian Veterinary Institute, ²University of Bergen

The Multi-Locus Variable-number tandem-repeat Analysis (MLVA) assay presented here enables inexpensive, robust and portable high-resolution genotyping of the fish-pathogenic bacterium Yersinia ruckeri. Starting from pure cultures, the assay employs multiplex PCR and capillary electrophoresis to produce ten-loci MLVA profiles for downstream applications.

Genetics

Transcription Start Site Mapping Using Super-low Input Carrier-CAGE

Nevena Cvetesic^1,2, Elena Pahita^1,2, Boris Lenhard^1,2,3

¹Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, ²MRC London Institute of Medical Sciences, ³Sars International Centre for Marine Molecular Biology, University of Bergen

Cap Analysis of Gene Expression (CAGE) is a method for genome-wide quantitative mapping of mRNA 5’ends to capture RNA polymerase II transcription start sites at a single-nucleotide resolution. This work describes a low-input (SLIC-CAGE) protocol for generation of high-quality libraries using nanogram-amounts of total RNA.

Biology

Assessing Mineral Availability in Fish Feeds using Complementary Methods Demonstrated with the Example of Zinc in Atlantic Salmon

Marta S. Silva^1,2, Thea Stewart⁴, Heidi Amlund^1,3, Jens J. Sloth^1,3, Pedro Araujo¹, Erik-Jan Lock¹, Christer Hogstrand⁴, Robin Ørnsrud¹, Rune Waagbø^1,2, Antony Jesu Prabhu¹

¹Institute of Marine Research, ²Department of Biological Sciences, University of Bergen, ³National Food Institute, Technical University of Denmark, ⁴Metal metabolism group, Nutritional Sciences Division, King's College London

This article explains in detail a systematic approach to assess micro-mineral availability in Atlantic salmon. The methodology includes tools and models with increasing biological complexity: (1) chemical speciation analysis, (2) in vitro solubility, (3) uptake studies in cell lines, and (4) in vivo fish studies.

Cancer Research

A 3D Spheroid Model for Glioblastoma

Joris Guyon^1,2, Laetitia Andrique^1,2, Nadège Pujol^1,2, Gro Vatne Røsland^3,4, Gaelle Recher^1,5,6, Andreas Bikfalvi^1,2, Thomas Daubon^1,2,4

¹University Bordeaux, LAMC, ²INSERM U1029, University Bordeaux, ³Department of Biomedicine, University of Bergen, ⁴CNRS, IBGC UMR5095, ⁵LP2N, CNRS UMR 5298, IOA, ⁶Institut d'Optique Graduate School, IOA

Here, we describe an easy-to-use invasion assay for glioblastoma. This assay is suitable for glioblastoma stem-like cells. A Fiji macro for easy quantification of invasion, migration, and proliferation is also described.

Bioengineering

Real-Time Intravital Multiphoton Microscopy to Visualize Focused Ultrasound and Microbubble Treatments to Increase Blood-Brain Barrier Permeability

Charissa Poon^1,2, Melina Mühlenpfordt^*3, Marieke Olsman^*3, Spiros Kotopoulis^4,5, Catharina de Lange Davies³, Kullervo Hynynen^1,2,6

¹Physical Sciences Platform, Sunnybrook Research Institute, ²Institute of Biomedical Engineering, University of Toronto, ³Department of Physics, Norwegian University of Science and Technology, ⁴Department of Clinical Medicine, University of Bergen, ⁵Exact Therapeutics AS, ⁶Department of Medical Biophysics, University of Toronto

This protocol describes the surgical and technical procedures that enable real-time in vivo multiphoton fluorescence imaging of the rodent brain during focused ultrasound and microbubble treatments to increase blood-brain barrier permeability.

Neuroscience

Flow Cytometric Analysis of Multiple Mitochondrial Parameters in Human Induced Pluripotent Stem Cells and Their Neural and Glial Derivatives

Kristina Xiao Liang^*1,2, Anbin Chen^*1,2,3,4, Cecilie Katrin Kristiansen^1,2, Laurence A. Bindoff^1,2

¹Department of Clinical Medicine (K1), University of Bergen, ²Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Haukeland University Hospital, ³Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, ⁴Shandong Key Laboratory of Brain Function Remodeling

This study reports a novel approach to measure multiple mitochondrial functional parameters based on flow cytometry and double staining with two fluorescent reporters or antibodies to detect changes in mitochondrial volume, mitochondrial membrane potential, reactive oxygen species level, mitochondrial respiratory chain composition, and mitochondrial DNA.

Neuroscience

Application of Flow Cytometric Analysis for Measuring Multiple Mitochondrial Parameters in 3D Brain Organoids

Sharika Marjan^1,2, Tsering Yangzom^1,2, Cecilie Katrin Kristiansen^1,3, Anbin Chen⁴, Laurence A. Bindoff^1,5,6, Kristina Xiao Liang^1,3

¹Department of Clinical Medicine (K1), University of Bergen, ²Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, ³Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Haukeland University Hospital, ⁴Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, ⁵Department of Neurology, Haukeland University Hospital, ⁶National Advisory Unit for Congenital Metabolic Diseases, Oslo University Hospital

This protocol reports a unique method of using a streaming cytometer and multiple antibodies for simultaneous assessment of multiple mitochondrial functional parameters, including changes in mitochondrial volume, amounts of the mitochondrial respiratory chain (MRC) complex subunits, and mitochondrial DNA (mtDNA) replication.

Neuroscience

Religious Chanting and Self-Related Brain Regions: A Multi-Modal Neuroimaging Study

Hin Hung Sik¹, Stavros Skouras², Junling Gao¹, Hang Kin Leung¹, Siu Man Ng³, Kin Cheung Lee¹, Bonnie Wai Yan Wu¹

¹Buddhist Practices and Counselling Science Lab, Centre of Buddhist Studies, The University of Hong Kong, ²Department of Biological and Medical Psychology, Faculty of Psychology, University of Bergen, ³Department of Social Work and Social Administration, The University of Hong Kong, Hong Kong

Here, we present a protocol to investigate the neurophysiological correlates of various meditation forms, including religious chanting. This method uniquely integrates fMRI eigenvector results for region selection in electroencephalogram (EEG) source analysis using k-means clustering. The results provide an in-depth understanding of the neural processes involved in repetitive religious chanting.