• Curriculum Vitae
  • Teaching
  • Appointments
  • Research

Present position
Full Professor of Molecular Biology, Dept. Chemical Life Sciences and Environmental Sustainability (SCVSA) University of Parma (UniPr). Coordinator of the PhD Course in Biotechnologies and Life Sciences. Deputy Director of the Regional Technopole Laboratory Biopharmanet-Tec. UniPr delegate and Member of the Executive Committee of the Interuniversity Consortium for Biotechnologies (CIB). Member of the National Scientific Qualification committee in Molecular Biology.

Teaching courses: “Basic Molecular Biology” (Bachelor Degree Course in ‘Biotechnologies’), “Eukaryotic Gene Expression Regulation” (Master Degree Course in ‘Genomic, Molecular and Industrial Biotechnologies’), Short Course of “Eukaryotic Molecular Biology” (Medical Specialties Schools in "Infectious Diseases" and “Oncology”).

Research interests
Functional genomics of microbial and animal cellular systems, eukaryotic gene expression, protein engineering applied to the development of novel recombinant peptide vaccines, epitope-tagged recombinant VHH antibodies ("nanobodies") and new antimicrobial compounds.

Professional experience
Research Associate (1984-86) and then Visiting Scientist (1990) in the laboratory of Karen Sprague, Institute of Molecular Biology, University of Oregon. Visiting scientist of the Japanese Society for the Promotion of Science (JSPS) at the University of Tokyo (Department of Biotechnology) in 2003, gave seminars and lectures in various Japanese Universities. Visiting scientist of the Federation of Korean Microbiological Societies (Seoul, South Korea) in 2007, hold a plenary lecture at the International FKMS Meeting and gave seminars on microbial genomics in various South-Korean Universities.

Author of over 120 scientific articles published in peer-reviewed international journals (https://scholar.google.it/scholar?hl=it&q=ottonello+simone&lr=&oq=ottone); main inventor or co-inventor in seven international patents dealing with novel recombinant peptide vaccines against Alzheimer's disease and human papillomavirus (HPV) and on in vivo re-engineered nanobodies.

H-index: 34 (Scopus); 40 (Google Scholar); over 4000 citations.

Principal investigator (or co-P. I.) in various national and international research projects dealing with eukaryotic gene expression, microbial genomics and protein engineering, including newly designed recombinant vaccines. Among them, several Regional (ER) an Industrial projects, the FIRB-MIUR project “Post-genome: Cellular Physiology and Engineering”, four PRIN-MIUR projects and an AIRC (2013) project dealing with the design, production and preclinical validation of a novel anti-HPV recombinant vaccine. Acts as referee for various scientific journals and national/international research foundations. Principal Investigator of the French-Italian Consortium TuberGENOMICS. Participating Investigator of the Consortium for Functional Glycomics (U.S.A.).

Research activity
Long-standing research experience in cellular biochemistry, molecular biology, functional genomics and protein engineering applied to various systems and biological problems. Research activity was initially focused on the development of molecular diagnostic tests for neurological disorders and on the transport and metabolism of vitamin A, with special emphasis on the structure and function of “retinol binding proteins”, including the set-up of the first in vitro systems capable of internalizing and esterifying retinol, and oxidizing it to retinoic acid, a transcriptional modulator. Subsequent research focused on the study of eukaryotic gene expression in various model organisms and the setting up of one of the first RNA polymerase III-dependent eukaryotic in vitro transcription systems specialized in the synthesis of tRNAs and 5S rRNA. Other studies, including a variety of functional (post)genomic approaches, have led to the identification of new genes and proteins involved in the response to various types of stress.
Among the most significant results, there are: i) the definition of the tRNA gene repertoire of the model eukaryote Saccharomyces cerevisiae; ii) the structure-function analysis of phytochelatin synthase and the discovery of a bifunctional enzyme capable of recognizing and repairing particular DNA strand-break lesions in plants; iii) the discovery of novel fungal proteins resembling the antiviral cyanobacterial lectin “cyanovirin”, followed by the determination of the 3D structure of five of them; iv) the discovery and extensive biochemical characterization, incuding 3D structure determination, of the first microbial phospholipase A2, an enzyme of significant biotechnological interest; v) the high-throughput exploitation of the yeast S. cerevisiae as a tool for gene function, stress response and bioactive small-molecule discovery; vi) the determination of the “methylome” of filamentous symbiotic fungus and the setting-up of an artificial DNA methylation system in the yeast S. cerevisiae (a DNA methylation incompetent organism); vii) the functional characterization of a new anti-Alzheimer drug compound (in collaboration with Chiesi Farmaceutici); viii) the design and experimental validation of a novel macromolecular platform, named TDMI (“Thioredoxin-Displayed Multipeptide Immunogens”) for the construction of thermostable recombinant antigens directed against HPV (in collaboration with the DKFZ/German Cancer Research Centre, Heidelberg and the IARC-WHO, Lyon); ix) the elucidation of the molecular bases (metabolic and gene expression-related) of T-lymphocyte exhaustion causally associated with chronic HBV and HCV infection (in collaboration with the Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology of the University Hospital of Parma.

For each of the above research lines, potential biotechnological applications have been taken into consideration. Among these: i) the setting up of an in vivo system relying on the use of tRNA genes as “helper” for high-level production of recombinant eukaryotic proteins encoded by mRNAs with a high “rare codon” content; ii) a high throughput system for the construction of recombinant immunogens via controlled multimerization (and more recently ‘gene synthesis’) of peptide epitopes into bacterial thioredoxin (TRX) and other scaffold proteins. Two immunogens of this kind, incorporating a human amyloid-β peptide fragment (Aβ 1-15) and a multipeptide derived from the minor HPV16 capsid protein L2, have recently been patented as prototype anti-Alzheimer and anti-HPV vaccines.

Recently developed technologies include: i) the use of TRX-based recombinant immunogens for the production of peptide-specific monoclonal and polyclonal antibodies; ii) a platform for the production/selection (via "ribosome or phage display") of target-specific VHH antibodies ("nanobodies") starting from a high-complexity synthetic library; iii) a high- throughput system for per the in vivo screening (in engineered Saccharomyces cerevisiae cells) of large collections of chemical compounds in order to identify inhibitors ("disruptors") of specific protein-protein interactions of therapeutic interest, especially antimicrobials.

Anno accademico di erogazione: 2020/2021

Anno accademico di erogazione: 2019/2020

Anno accademico di erogazione: 2018/2019

Anno accademico di erogazione: 2017/2018

Anno accademico di erogazione: 2016/2017

Anno accademico di erogazione: 2015/2016

Anno accademico di erogazione: 2014/2015


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