University of Turku View Institution's Website 7 articles published in JoVE Environment Quantification of the Potential Impact of Glyphosate-Based Products on Microbiomes Suni Anie Mathew1, Anne Muola1, Kari Saikkonen1, Irma Saloniemi2, Marjo Helander2, Pere Puigbò2,3,4 1Biodiversity Unit, University of Turku, 2Department of Biology, University of Turku, 3Nutrition and Health Unit, Eurecat Technology Centre of Catalonia, 4Department of Biochemistry and Biotechnology, Rovira i Virgili University Glyphosate-based products (GBP) are the most common broad-spectrum herbicides worldwide. In this article, we introduce general guidelines to quantify the effect of GBP on microbiomes, from field experiments to bioinformatics analyses. Developmental Biology Transillumination-Assisted Dissection of Specific Stages of the Mouse Seminiferous Epithelial Cycle for Downstream Immunostaining Analyses Juho-Antti Mäkelä1, Sheyla Cisneros-Montalvo1, Tiina Lehtiniemi1, Opeyemi Olotu1, Hue M. La3,4, Jorma Toppari1,2, Robin M. Hobbs3,4, Martti Parvinen1, Noora Kotaja1 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland, 2Department of Pediatrics, Turku University Hospital, Turku, Finland, 3Centre for Reproductive Health, Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia, 4Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia This protocol describes transillumination-assisted microdissection of segments of adult mouse seminiferous tubules representing specific stages of seminiferous epithelial cycle, and cell types therein, and subsequent immunostaining of squash preparations and intact tubule segments. Biochemistry Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation Mahlet Z. Tamirat1, Kari J. Kurppa2, Klaus Elenius2,3,4, Mark S. Johnson1 1Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 2Medicity Research Laboratories and Institute of Biomedicine, University of Turku, 3Turku Bioscience Centre, University of Turku and Åbo Akademi University, 4Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital The objective of this protocol is to use molecular dynamics simulations to examine the dynamic structural changes that occur due to activating mutations of the EGFR kinase protein. Developmental Biology Enrichment of Pachytene Spermatocytes and Spermatids from Mouse Testes Using Standard Laboratory Equipment Matteo Da Ros*1, Tiina Lehtiniemi*1, Opeyemi Olotu1, Oliver Meikar1, Noora Kotaja1 1Institute of Biomedicine, University of Turku Presented here is a protocol for enriching pachytene spermatocytes, round spermatids, and elongating spermatids from adult mouse testes using a discontinuous bovine serum albumin density gradient with standard laboratory equipment. Biochemistry Analysis of Thylakoid Membrane Protein Complexes by Blue Native Gel Electrophoresis Marjaana Rantala1, Virpi Paakkarinen1, Eva-Mari Aro1 1Molecular Plant Biology, Department of Biochemistry, University of Turku A protocol for the elucidation of plant thylakoid protein complex organization and composition with blue native polyacrylamide gel electrophoresis (BN-PAGE) and 2D-SDS-PAGE is described. The protocol is optimized for Arabidopsis thaliana, but can be used for other plant species with minor modifications. Developmental Biology Analysis of Epididymal Protein Synthesis and Secretion Wei Zhou1,2, Petra Sipilä3, Geoffry N. De Iuliis1,2, Matthew D. Dun2,4, Brett Nixon1,2 1Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, 2Hunter Medical Research Institute, 3Department of Physiology, Turku Center for Disease Modeling, Institute of Biomedicine, University of Turku, 4School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle Here, we report the immunofluorescence localization of dynamin to illustrate the protocols for the detection of proteins in paraffin-embedded mouse epididymal sections and those of an immortalized epididymal cell line (mECap18). We also describe the protocols for the isolation of secretory proteins from both epididymal fluid and conditioned cell media. Biology Changes in Mammary Gland Morphology and Breast Cancer Risk in Rats Sonia de Assis1, Anni Warri1,2, M. Idalia Cruz1, Leena Hilakivi-Clarke1 1Department of Oncology, Georgetown University, 2Institute of Biomedicine, University of Turku Medical Faculty Our protocol describes how to dissect the rat abdominal mammary gland and how to prepare mammary gland whole mounts. It also describes how to analyze mammary gland morphology using three end-points (number of terminal end buds, epithelial elongation and differentiation) and to use these results to predict mammary cancer risk in rats which were exposed to dietary modifications in utero or during prepuberty.