University of Helsinki View Institution's Website 29 articles published in JoVE Neuroscience Quantified Assessment of Infant's Gross Motor Abilities Using a Multisensor Wearable Elisa Taylor1, Manu Airaksinen1, Anastasia Gallen1, Tuuli Immonen2, Elina Ilén3, Taru Palsa1,2, Leena M. Haataja1,2, Sampsa Vanhatalo1,4 1BABA Center, Pediatric Research Center, Department of Clinical Neurophysiology, New Children's Hospital and HUS Imaging, Helsinki, University Hospital, 2Department of Pediatric Neurology, Children's Hospital, Helsinki University Hospital and University of Helsinki, 3Department of Materials Science and Engineering, Universitat Politècnica de Catalunya, 4Department of Physiology, University of Helsinki This paper outlines the assessment of infants' gross motor performance with a multisensor wearable and its fully automated deep learning-based analysis pipeline. The method quantifies the posture and movement patterns of infants from lying supine until they master walking independently. Biology Zebrafish Corneal Wound Healing: From Abrasion to Wound Closure Imaging Analysis Kaisa Ikkala1, Sini Raatikainen1, Frederic Michon1,2 1Institute of Biotechnology, HiLIFE, University of Helsinki, 2Institute for Neurosciences of Montpellier, Univ Montpellier This protocol focuses on damaging the ocular surface of zebrafish through abrasion to assess the subsequent wound closure at the cellular level. This approach exploits an ocular burr to partly remove the corneal epithelium and uses scanning electron microscopy to track changes in cell morphology during wound closure. Neuroscience Measuring Properties of the Membrane Periodic Skeleton of the Axon Initial Segment using 3D-Structured Illumination Microscopy (3D-SIM) David Micinski1, Lauri Lahti2, Amr Abouelezz1,3,4 1Minerva Foundation Institute for Medical Research, 2Department of Computer Science, Aalto University School of Science, 3HiLIFE - Neuroscience Center, University of Helsinki, 4HiLIFE - Institute of Biotechnology, University of Helsinki The present protocol describes a method to visualize and measure actin rings and other components of the membrane periodic skeleton of the axon initial segment using cultured rat hippocampal neurons and 3D-structured illumination microscopy (3D-SIM). Biology High-Resolution Respirometry to Assess Bioenergetics in Cells and Tissues Using Chamber- and Plate-Based Respirometers Ryan Awadhpersad1, Christopher B. Jackson1 1Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki Assessing oxidative phosphorylation using high-resolution respirometers has become an integral part of the functional analysis of mitochondria and cellular energy metabolism. Here, we present protocols for the analysis of cellular energy metabolism using chamber and microplate-based high-resolution respirometers and discuss the key benefits of each device. Developmental Biology Use of Trowell-Type Organ Culture to Study Regulation of Dental Stem Cells Emma Juuri*1,2, Anamaria Balic*1 1Research Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, 2Department of Oral and Maxillofacial diseases, Faculty of Medicine, University of Helsinki The Trowell-type organ culture method has been used to unravel complex signaling networks that govern tooth development and, more recently, for studying regulation involved in stem cells of the continuously growing mouse incisor. Fluorescent-reporter animal models and live-imaging methods facilitate in-depth analyses of dental stem cells and their specific niche microenvironment. Immunology and Infection Contact-Free Co-Culture Model for the Study of Innate Immune Cell Activation During Respiratory Virus Infection Zhe Zhang Ryan Lew*1, Jing Liu*1, Hsiao Hui Ong1, Vivian Jiayi Tan2, Annika Luukkainen3, Yew Kwang Ong1,4, Mark Thong1,4, Kia Joo Puan5, Vincent Tak Kwong Chow2,6, Kai Sen Tan1,2,6, De Yun Wang1,6 1Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, 2Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 3Haartman Institute, Medicum, University of Helsinki, 4Department of Otolaryngology, Head and Neck Surgery, National University Hospital, National University Health System, 5Agency for Science, Technology and Research (A*STAR), Singapore Immunology Network (SIgN), 6NUHS Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore This protocol details an investigation of the early interactions between virally infected nasal epithelial cells and innate cell activation. Individual subsets of immune cells can be distinguished based on their activation in response to viral infections. They can then be further investigated to determine their effects on early antiviral responses. Chemistry Preparation of Silver-Palladium Alloyed Nanoparticles for Plasmonic Catalysis under Visible-Light Illumination Erandi Peiris1, Sébastien Hanauer1, Kjell Knapas1, Pedro H. C. Camargo1 1Department of Chemistry, University of Helsinki Presented here is a protocol for the synthesis of silver-palladium (Ag-Pd) alloy nanoparticles (NPs) supported on ZrO2 (Ag-Pd/ZrO2). This system allows for harvesting energy from visible light irradiation to accelerate and control molecular transformations. This is illustrated by nitrobenzene reduction under light irradiation catalyzed by Ag-Pd/ZrO2 NPs. Neuroscience Studying Pre-formed Fibril Induced α-Synuclein Accumulation in Primary Embryonic Mouse Midbrain Dopamine Neurons Safak Er1, Irena Hlushchuk1, Mikko Airavaara2, Piotr Chmielarz1,3, Andrii Domanskyi1 1Institute of Biotechnology, HiLIFE, University of Helsinki, 2Neuroscience Center, HiLIFE, University of Helsinki, 3Department of Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences Here, we present a detailed protocol to study neuronal α-synuclein accumulation in primary mouse dopamine neurons. Phosphorylated α-synuclein aggregates in neurons are induced with pre-formed α-synuclein fibrils. Automated imaging of immunofluorescently labeled cells and unbiased image analysis make this robust protocol suitable for medium-to-high throughput screening of drugs that inhibit α-synuclein accumulation. Genetics LINE-1 Methylation Analysis in Mesenchymal Stem Cells Treated with Osteosarcoma-Derived Extracellular Vesicles Snehadri Sinha*1,2, Bettina Mannerström*1,2, Riitta Seppänen-Kaijansinkko1,2, Sippy Kaur1,2 1Department of Oral and Maxillofacial Diseases, University of Helsinki, 2Helsinki University Hospital Described here is the use of a methylation-specific probe amplification method to analyze methylation levels of LINE-1 elements in mesenchymal stem cells treated with osteosarcoma-derived extracellular vesicles. Ultracentrifugation, a popular procedure for separating extracellular vesicles from fetal bovine serum, is also demonstrated. Biochemistry Screening for Thermotoga maritima Membrane-Bound Pyrophosphatase Inhibitors Keni Vidilaseris*1, Niklas G. Johansson*2, Ainoleena Turku2, Alexandros Kiriazis2, Gustav Boije af Gennäs2, Jari Yli-Kauhaluoma2, Henri Xhaard2, Adrian Goldman1,3 1Research Program in Molecular and Integrative Biosciences, University of Helsinki, 2Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, 3School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds Here we present a screening method for membrane-bound pyrophosphatase (from Thermotoga maritima) inhibitors based on the molybdenum blue reaction in a 96 well plate format. Cancer Research Detection of Retrotransposition Activity of Hot LINE-1s by Long-Distance Inverse PCR Barun Pradhan1,2, Liisa Kauppi1,2 1Systems Oncology Research Program, University of Helsinki, 2Department of Biochemistry and Developmental Biology, Medicum, University of Helsinki This article outlines a simple PCR-based assay to monitor the activity of an active LINE-1 retrotransposon and to map de novo retrotranspositions in a given genome. Using the MCF7 cell line, we demonstrate herein how this method can be applied to detect activity of a LINE-1 located at 22q12.1. Engineering Scattering And Absorption of Light in Planetary Regoliths Karri Muinonen1,2, Timo Väisänen1, Julia Martikainen1, Johannes Markkanen1,3, Antti Penttilä1, Maria Gritsevich1,4, Jouni Peltoniemi1,2, Jürgen Blum5, Joonas Herranen1, Gorden Videen6,7, Göran Maconi1, Petteri Helander1, Ari Salmi1, Ivan Kassamakov1, Edward Haeggström1 1Department of Physics, University of Helsinki, 2Finnish Geospatial Research Institute FGI, National Land Survey, 3Max Planck Institute for Solar System Research, 4Institute of Physics and Technology, Ural Federal University, 5Institut für Geophysik und Extraterrestrische Physik, Technische Universität Braunschweig, 6Space Science Institute, 7Army Research Laboratory Numerical and experimental methods are presented for multiple scattering of light in discrete random media of densely-packed particles. The methods are utilized to interpret the observations of asteroid (4) Vesta and comet 67P/Churyumov-Gerasimenko. Behavior Lexical Decision Task for Studying Written Word Recognition in Adults with and without Dementia or Mild Cognitive Impairment Alexandre Nikolaev1, Eve Higby2,3, JungMoon Hyun4, Sameer Ashaie5,6 1Helsinki Collegium for Advanced Studies, University of Helsinki, 2University of California, Riverside, 3California State University, East Bay, 4Hunter College, City University of New York, 5Feinberg School of Medicine, Northwestern University, 6Shirley Ryan AbilityLab This article describes how to implement a simple lexical decision experiment to assess written word recognition in neurologically healthy participants and in individuals with dementia and cognitive decline. We also provide a detailed description of reaction time analysis using principal components analysis (PCA) and mixed-effects modeling. Cancer Research Fully Human Tumor-based Matrix in Three-dimensional Spheroid Invasion Assay Erika Naakka1, Katja Tuomainen1, Henrik Wistrand*1, Miila Palkama*1, Ilida Suleymanova1, Ahmed Al-Samadi1, Tuula Salo1,2,3,4 1Department of Oral and Maxillofacial Diseases, Clinicum, Faculty of Medicine, University of Helsinki, 2Cancer and Translational Medicine Research Unit, University of Oulu, 3Medical Research Center, Oulu University Horspital, 4Helsinki University Hospital Tumor microenvironment is an essential part of cancer growth and invasion. To mimic carcinoma progression, a biologically relevant human matrix is needed. This protocol introduces an improvement for the in vitro three-dimensional spheroid invasion assay by applying a human leiomyoma-based matrix. The protocol also introduces a computer-based cell invasion analysis. Cancer Research Predicting In Vivo Payloads Delivery using a Blood-brain Tumor-barrier in a Dish Vadim Le Joncour1, Sinem Karaman1,2, Pirjo Maarit Laakkonen1,3 1Research Programs Unit, Translational Cancer Medicine Research Program, University of Helsinki, 2Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, 3Laboratory Animal Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki Drug targeting to central nervous system tumors is a major challenge. Here we describe a protocol to produce an in vitro mimic of the blood-brain tumor-barrier using murine and/or human cells and discuss their relevance for the predictability of central nervous system tumor targeting in vivo. Biology Analysis of Mitochondrial Respiratory Chain Complexes in Cultured Human Cells using Blue Native Polyacrylamide Gel Electrophoresis and Immunoblotting Svetlana Konovalova1 1Research Programs Unit, Molecular Neurology, University of Helsinki This protocol demonstrates the analysis of mitochondrial respiratory chain complexes by blue native polyacrylamide gel electrophoresis. Here the method applied to cultured human cells is described. Medicine An Ex Vivo Tissue Culture Model for Fibrovascular Complications in Proliferative Diabetic Retinopathy Erika Gucciardo1, Sirpa Loukovaara2, Ani Korhonen1, Kaisa Lehti1,3 1Research Programs Unit, Genome-Scale Biology, Biomedicum Helsinki, University of Helsinki, 2Unit of Vitreoretinal Surgery, Ophthalmology, University of Helsinki and Helsinki University Hospital, 3Department of Microbiology, Tumor, and Cell Biology (MTC), Karolinska Institutet Here, we present a protocol to study the pathophysiology of proliferative diabetic retinopathy by using patient-derived, surgically-excised, fibrovascular tissues for three-dimensional native tissue characterization and ex vivo culture. This ex vivo culture model is also amenable for testing or developing new treatments. Immunology and Infection Establishment and Analysis of Tumor Slice Explants As a Prerequisite for Diagnostic Testing Ashwini S. Nagaraj1, Jie Bao1, Annabrita Hemmes1, Mafalda Machado1, Katja Närhi1, Emmy W. Verschuren1 1Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki We provide a method for the generation, cultivation and systematic analysis of organotypic slices derived from murine lung tumors. We also describe how to optimize for slice thickness, and how to select drug concentrations to treat tumor slices. Medicine Corneal Epithelial Abrasion with Ocular Burr As a Model for Cornea Wound Healing Solja Kalha1, Alison Kuony1, Frederic Michon1,2 1Helsinki Institute of Life Science, Institute of Biotechnology, University of Helsinki, 2School of Medicine and Institute for Science and Technology in Medicine, Keele University This protocol describes a method to inflict an abrasion to the ocular surface of the mouse, and to follow the wound healing process thereafter. The protocol takes advantage of an ocular burr to partially remove the surface epithelium of the eye in anaesthetized mice. Developmental Biology A Neural Network-Based Identification of Developmentally Competent or Incompetent Mouse Fully-Grown Oocytes Federica Cavalera1, Mario Zanoni1, Valeria Merico1, Thi Thu Hien Bui1,2, Martina Belli1,3, Lorenzo Fassina4, Silvia Garagna1, Maurizio Zuccotti1 1Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, 2Institute of Biotechnology, University of Helsinki, 3Department of Reproductive Medicine, University of California San Diego, 4Dipartimento di Ingegneria Industriale e dell'Informazione, University of Pavia Here, we present a protocol for non-invasive assessment of oocyte developmental competence performed during their in vitro maturation from the germinal vesicle to the metaphase II stage. This method combines time-lapse imaging with particle image velocimetry (PIV) and neural network analyses. Immunology and Infection A Platform of Anti-biofilm Assays Suited to the Exploration of Natural Compound Libraries Malena E. Skogman1, Pia M. Vuorela1, Adyary Fallarero1 1Pharmaceutical Design and Discovery (PharmDD), Faculty of Pharmacy, University of Helsinki Biofilm infections show high tolerance towards chemotherapy. No single assay captures the complexity of biofilms. Instead, complementary assays are needed. We present a screening platform (developed for S. aureus) that combines assays for viability, biomass, and biofilm matrix. It allows anti-biofilm drug discovery, including the assessment of long-term chemotherapeutic effects. Medicine The Helsinki Rat Microsurgical Sidewall Aneurysm Model Serge Marbacher1, Johan Marjamaa1, Essam Abdelhameed1, Juha Hernesniemi1, Mika Niemelä1, Juhana Frösen1 1Neurosurgery Research Group, University of Helsinki, Helsinki, Finland Microsurgical sidewall aneurysms in rats are created by end-to-side anastomosis of an aortic graft to the abdominal aorta. We present step-by-step instructions and discuss anatomical and surgical details for successful experimental saccular aneurysm creation. Neuroscience In Vivo Two-Photon Microscopy of Single Nerve Endings in Skin Mikhail Yuryev1, Dmitry Molotkov1 1Neuroscience Center, University of Helsinki The protocol for dynamic longitudinal imaging and selective laser lesion of nerve endings in reporter transgenic mice is presented. Engineering Coherent anti-Stokes Raman Scattering (CARS) Microscopy Visualizes Pharmaceutical Tablets During Dissolution Andrew L. Fussell1, Peter Kleinebudde2, Jennifer Herek1, Clare J. Strachan3, Herman L. Offerhaus1 1Optical Sciences Group, MESA+ Institute, University of Twente, 2Institute of Pharmaceutics and Biopharmaceutics, Heinrich-Heine University, 3Division of Pharmaceutical Technology, Faculty of Pharmacy, University of Helsinki Coherent anti-Stokes Raman scattering (CARS) microscopy is combined with an intrinsic flow-through dissolution setup to allow in situ and real-time visualization of the surface of pharmaceutical tablets undergoing dissolution. Using this custom-built setup, it is possible to correlate CARS videos with drug dissolution profiles recorded using inline UV absorption spectroscopy. Behavior Flat-floored Air-lifted Platform: A New Method for Combining Behavior with Microscopy or Electrophysiology on Awake Freely Moving Rodents Mikhail Kislin1, Ekaterina Mugantseva1, Dmitry Molotkov1, Natalia Kulesskaya1, Stanislav Khirug1, Ilya Kirilkin2, Evgeny Pryazhnikov1,2, Julia Kolikova2, Dmytro Toptunov2, Mikhail Yuryev1, Rashid Giniatullin3, Vootele Voikar4, Claudio Rivera1, Heikki Rauvala1, Leonard Khiroug1 1Neuroscience Center, University of Helsinki, 2Neurotar LTD, 3A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, 4Laboratory Animal Center, University of Helsinki This method creates a tangible, familiar environment for the mouse to navigate and explore during microscopic imaging or single-cell electrophysiological recordings, which require firm fixation of the animal’s head. Biology One-step Purification of Twin-Strep-tagged Proteins and Their Complexes on Strep-Tactin Resin Cross-linked With Bis(sulfosuccinimidyl) Suberate (BS3) Konstantin I Ivanov1, Marta Bašić1, Markku Varjosalo2, Kristiina Mäkinen1 1Department of Food and Environmental Sciences, University of Helsinki, 2Institute of Biotechnology, University of Helsinki A method is described for efficient purification of twin-Strep-tagged fusion proteins and their specific complexes on modified streptavidin (Strep-Tactin) resin covalently cross-linked with Bis(sulfosuccinimidyl) suberate (BS3). The method has the advantages of fast speed, good target protein recovery and high purity, and is compatible with subsequent analysis by mass spectrometry. Medicine Acute Brain Trauma in Mice Followed By Longitudinal Two-photon Imaging Mikhail Paveliev1, Mikhail Kislin1, Dmitry Molotkov1, Mikhail Yuryev1, Heikki Rauvala1, Leonard Khiroug1 1Neuroscience Center, University of Helsinki Acute brain trauma is a severe injury that has no adequate treatment to date. Multiphoton microscopy allows studying longitudinally the process of acute brain trauma development and probing therapeutical strategies in rodents. Two models of acute brain trauma studied with in vivo two-photon imaging of brain are demonstrated in this protocol. Neuroscience Preterm EEG: A Multimodal Neurophysiological Protocol Susanna Stjerna1, Juha Voipio2, Marjo Metsäranta3, Kai Kaila2,4, Sampsa Vanhatalo1 1Department of Children's Clinical Neurophysiology, Helsinki University Hospital, University of Helsinki, 2Department of Biosciences, University of Helsinki, 3Department of Pediatrics, Helsinki University Hospital, University of Helsinki, 4Neuroscience Center, University of Helsinki This video explains the background theory of the neonatal EEG activity and the sensory responses, followed by a live demonstration of their recording in neonatal intensive care unit. Neuroscience Gene Delivery to Postnatal Rat Brain by Non-ventricular Plasmid Injection and Electroporation Dmitry A. Molotkov1, Alexey Y. Yukin1,2, Ramil A. Afzalov1,2, Leonard S. Khiroug1 1Neuroscience Center, University of Helsinki, 2Faculty of Biological and Enviromental Sciences, University of Helsinki This protocol describes a non-viral method of delivery of genetic constructs to a certain area of living rodent brain. The method consists of plasmid preparation, micropipette fabrication, neonatal rat pup surgery, microinjection of the construct, and in vivo electroporation.
