University of Pavia View Institution's Website 14 articles published in JoVE Biology Isolation and Screening from Soil Biodiversity for Fungi Involved in the Degradation of Recalcitrant Materials Marta Elisabetta Eleonora Temporiti1, Chiara Daccò1, Lidia Nicola1 1Laboratory of Mycology, Department of Earth and Environmental Sciences, University of Pavia Here, we present a protocol for screening soil biodiversity to look for fungal strains involved in the degradation of recalcitrant materials. First, fungal strains able to grow on humic acids or lignocellulose are isolated. Their activity is then tested both in enzymatic assays and on pollutants such as hydrocarbons and plastics. Neuroscience Abbiategrasso Brain Bank Protocol for Collecting, Processing and Characterizing Aging Brains Tino Emanuele Poloni*1,4, Valentina Medici*1, Arenn Faye Carlos1, Annalisa Davin2, Arcangelo Ceretti1, Michela Mangieri1, Paola Cassini1,4, Roberta Vaccaro3, Daniele Zaccaria3, Simona Abbondanza3, Matteo Bordoni5, Valentina Fantini2,6, Elena Fogato7, Cristina Cereda5, Mauro Ceroni8, Antonio Guaita1,2,3 1Department of Neurology and Neuropathology, Golgi-Cenci Foundation, 2Laboratory of Neurobiology and Neurogenetic, Golgi-Cenci Foundation, 3Department of Neuropsychology and Social Sciences, Golgi-Cenci Foundation, 4Department of Rehabilitation, ASP Golgi-Redaelli Geriatric Hospital, 5Genomic and Post-Genomic Center, IRCCS Mondino Foundation, 6Department of Brain and Behavioral Sciences, University of Pavia, 7Department of Pathology, ASP Golgi-Redaelli Geriatric Hospital, 8Department of Neurological Science, IRCCS Mondino Foundation, University of Pavia This protocol describes a method to track individual brain-aging trajectories through a brain donation program and proper characterization of brains. Brain donors are involved in a long-term longitudinal study including serial multi-dimensional assessments. The protocol contains a detailed description of brain processing and an accurate diagnostic methodology. Behavior Implementation of a Real-Time Psychosis Risk Detection and Alerting System Based on Electronic Health Records using CogStack Tao Wang1, Dominic Oliver2, Yamiko Msosa1, Craig Colling3, Giulia Spada2, Łukasz Roguski4, Amos Folarin1, Robert Stewart3,5, Angus Roberts1,3, Richard J. B. Dobson1,3,4,6, Paolo Fusar-Poli2,3,7,8 1 We demonstrate how to deploy a real-time psychosis risk calculation and alerting system based on CogStack, an information retrieval and extraction platform for electronic health records. Neuroscience Meta-analysis of Voxel-Based Neuroimaging Studies using Seed-based d Mapping with Permutation of Subject Images (SDM-PSI) Anton Albajes-Eizagirre1,2, Aleix Solanes1,2, Miquel Angel Fullana2,3, John P. A. Ioannidis4, Paolo Fusar-Poli5,6,7, Carla Torrent1,2,3,8, Brisa Solé1,2,3,8, Caterina Mar Bonnín1,2,3,8, Eduard Vieta1,2,3,8, David Mataix-Cols9, Joaquim Radua1,2,5,9 1 We detail how to conduct a meta-analysis of voxel-based neuroimaging studies using Seed-based d Mapping with Permutation of Subject Images (SDM-PSI). 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. Cancer Research Detection of a CDH1 Rare Transcript Variant in Fresh-frozen Gastric Cancer Tissues by Chip-based Digital PCR Chiara Molinari1, Raefa Abou Khouzam2, Samanta Salvi1, Tania Rossi1, Guglielmina Nadia Ranzani2, Daniele Calistri1 1Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 2Department of Biology and Biotechnology, University of Pavia The manuscript describes a chip-based digital PCR assay to detect a rare CDH1 transcript variant (CDH1a) in fresh-frozen normal and tumor tissues obtained from patients with gastric cancer. Immunology and Infection Building Up a High-throughput Screening Platform to Assess the Heterogeneity of HER2 Gene Amplification in Breast Cancers Giulia Ercoli1, Gianluca Lopez1,2, Camilla Ciapponi1,3, Chiara Corti1,2, Luca Despini4, Donatella Gambini5, Letterio Runza1, Concetta Blundo4, Amedeo Sciarra1, Nicola Fusco1,6 1 Heterogeneous distribution of HER2-positive cells can be observed in a subset of breast cancers and generates clinical dilemmas. Here, we introduce a reliable and cost-effective protocol to define, quantify, and compare HER2 intra-tumor genetic heterogeneity in a large series of heterogeneously processed breast cancers. Neuroscience A Novel Strategy Combining Array-CGH, Whole-exome Sequencing and In Utero Electroporation in Rodents to Identify Causative Genes for Brain Malformations Valerio Conti*1, Aurelie Carabalona*2,3,15, Emilie Pallesi-Pocachard2,3,4, Richard J. Leventer5,6,7, Fabienne Schaller2,3,8, Elena Parrini1, Agathe A. Deparis2,3, Françoise Watrin2,3, Emmanuelle Buhler2,3,8, Francesca Novara9, Stefano Lise10, Alistair T. Pagnamenta10, Usha Kini11, Jenny C. Taylor10, Orsetta Zuffardi9,12, Alfonso Represa2,3, David Antony Keays13, Renzo Guerrini1,14, Antonio Falace2,3, Carlos Cardoso2,3 1University of Florence, 2INSERM INMED, 3Aix-Marseille University, 4Plateforme Biologie Moléculaire et Cellulaire INMED, 5 Periventricular nodular heterotopia (PNH) is the most common form of malformation of cortical development (MCD) in adulthood but its genetic basis remains unknown in most sporadic cases. We have recently developed a strategy to identify novel candidate genes for MCDs and to directly confirm their causative role in vivo. Bioengineering An Experimental Protocol for Assessing the Performance of New Ultrasound Probes Based on CMUT Technology in Application to Brain Imaging Giulia Matrone1, Alessandro Ramalli2, Alessandro Stuart Savoia3, Fabio Quaglia4, Gloria Castellazzi5, Patrizia Morbini6, Marco Piastra1 1Department of Electrical, Computer and Biomedical Engineering, University of Pavia, 2Department of Information Engineering, University of Florence, 3Department of Engineering, Roma Tre University, 4FTMTR&D/SPA, STMicroelectronics, 5Brain Connectivity Center, BCC, Istituto Neurologico Nazionale Fondazione C. Mondino I.R.C.C.S., 6Department of Molecular Medicine - Unit of Pathology, University of Pavia, Foundation IRCCS Policlinico San Matteo The development of new ultrasound (US) probes based on Capacitive Micromachined Ultrasonic Transducer (CMUT) technology requires an early realistic assessment of imaging capabilities. We describe a repeatable experimental protocol for US image acquisition and comparison with magnetic resonance images, using an ex vivo bovine brain as an imaging target. Genetics Delivery of Nucleic Acids through Embryo Microinjection in the Worldwide Agricultural Pest Insect, Ceratitis capitata Paolo Gabrieli1, Francesca Scolari1 1Department of Biology and Biotechnology, University of Pavia The Mediterranean fruit fly (medfly) Ceratitis capitata (Diptera: Tephritidae) is a worldwide pest of agriculture. A deeper understanding of its biology is key to control medfly populations and thus reduce economic impact. Embryo microinjection is a fundamental tool allowing both germ-line transformation and reverse genetics studies in this species. Medicine Tissue Characterization after a New Disaggregation Method for Skin Micro-Grafts Generation Valeria Purpura1, Elena Bondioli1, Antonio Graziano2, Letizia Trovato2, Davide Melandri1, Martina Ghetti1, Andrea Marchesini3, Maria Gabriella Cusella De Angelis4,5, Laura Benedetti4,5, Gabriele Ceccarelli4,5, Michele Riccio3 1Burns Centre and Emilia Romagna Regional Skin Bank, 2Human Brain Wave srl, 3Plastic and Reconstructive Surgery, AOU “Ospedali Riuniti”, 4Department of Public Health, Experimental Medicine, Anatomy and Forensic, University of Pavia, 5C.H.T Centre for Health Technologies, University of Pavia The protocol describes a new method to disaggregate human tissues and to create autologous micro-grafts that, combined with collagen sponges, give rise to human bio-complexes ready to use in the treatment of skin lesions. Further, this system preserves cell viability of micro-grafts at different times after mechanical disaggregation. Developmental Biology Isolation and Characterization of Mouse Antral Oocytes Based on Nucleolar Chromatin Organization Manuela Monti1, Carlo Alberto Redi1,2 1Research Center for Regenerative Medicine, Fondazione IRCCS Policlinico San Matteo, 2Department of Biology and Biotechnology "L. Spallanzani", University of Pavia Here we present a protocol for the characterization of mouse antral oocytes based on nucleolar organization. Bioengineering Manufacturing Devices and Instruments for Easier Rat Liver Transplantation Graziano Oldani1,2, Stephanie Lacotte3, Lorenzo Orci1, Philippe Morel4, Gilles Mentha1, Christian Toso1 1Transplantation Division, Department of Surgery, University of Geneva Hospitals, 2Department of Surgery, University of Pavia, 3Department of Surgery, University of Geneva, 4Division of Abdominal Surgery, Department of Surgery, University of Geneva Hospitals We describe the design of the “quick-linker” device for easier orthotopic rat liver transplantation. Medicine Orthotopic Liver Transplantation in Rats Graziano Oldani1,2, Stephanie Lacotte3, Philippe Morel4, Gilles Mentha1, Christian Toso1 1Transplantation Division, Department of Surgery, University of Geneva Hospitals, 2Department of Surgery, University of Pavia, 3Department of Surgery, University of Geneva, 4Division of Abdominal Surgery, Department of Surgery, University of Geneva Hospitals We present an easy-to-establish revision of the classical two-cuff technique for orthotopic liver transplantation in rat.