First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Medicine
PHARMACEUTICAL BIOTECHNOLOGIES
Course unit
ADVANCED MOLECULAR BIOLOGY
MEP5070481, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2017/18

Information on the course unit
Degree course Second cycle degree in
PHARMACEUTICAL BIOTECHNOLOGIES
ME2193, Degree course structure A.Y. 2015/16, A.Y. 2017/18
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Number of ECTS credits allocated 6.0
Type of assessment Mark
Course unit English denomination ADVANCED MOLECULAR BIOLOGY
Department of reference Department of Pharmaceutical and Pharmacological Sciences
Mandatory attendance
Language of instruction English
Branch PADOVA

Lecturers
Teacher in charge DORIANNA SANDONA' BIO/11

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Core courses BIO/11 Molecular Biology 6.0

Mode of delivery (when and how)
Period First semester
Year 1st Year
Teaching method frontal

Organisation of didactics
Type of hours Credits Hours of
teaching
Hours of
Individual study
Shifts
Laboratory 1.0 15 10.0 No turn
Lecture 5.0 40 85.0 No turn

Calendar
Start of activities 02/10/2017
End of activities 19/01/2018

Syllabus
Prerequisites: Students must have a solid preparation in mathematics physics, chemistry and biology. Moreover it is requested a deep knowledge in the basic topics of molecular biology such as DNA replication and transcription, regulation of gene expression, translation. Students must have theoretical experience in the most common recombinant DNA techniques such as, cloning of DNA, recombinant protein production, determination of gene expression.
Students must have good knowledge of written and spoken English.
Target skills and knowledge: By the end of the course, students should have achieved the skill to design a methodological approach for: the identification and validation of specific markers, useful in diagnosis and prognosis of a pathology; the discovery and validation of new pharmacological targets; the design of biotechnological drugs such as recombinant proteins, recombinant antibodies, oligonucleotides, small interfering RNAs etc; the validation and development of new drugs.

The practical experience, concerning the silencing by RNA interference of a specific gene, will give to the students the knowledge and the competence to plan, carry out and evaluate the efficacy, in vitro, of a biotechnological approach that should become innovative therapy.
Examination methods: Evaluation will be subdivided in three parts:

1) Bibliographic search and oral presentation of the results. Each student will perform a bibliographic search regarding a particular aspect of a topic dealt with in classes. The results will be orally presented during a meeting with all students

2) Written report on the practical part of the course

3) Oral examination regarding the course topics
Assessment criteria: 1) Bibliographic search and oral presentation of the results. Evaluation is based on: capacity in finding scientific sources; relevance of the search with the chosen subject; scientific literature comprehension; identification of literature strength and weakness; organization and clarity of the talk (introduction, development, conclusions); participation in the general discussion with comments and questions.

2) Written report on the practical part of the course. The report, in addition to an in depth description and analysis of the results, should provide a critical evaluation of problems possibly raised during the practical course and of the potentiality of the application of such methodology

3) Oral examination regarding the course topics. Students must demonstrate to: know the course topics; focus and deal with a scientific problem; posses the skills to delineate a strategy to study a pathogenetic mechanism, identify disease markers or design a biotechnological drug.
Course unit contents: This is an advanced course of molecular biology that aims to broaden the knowledge in the field of pharmaceutical biotechnology. In particular the molecular mechanisms of several pathologies and the experiments planned to identify specific disease markers will be elucidated. The molecular mechanism of some drugs able “to cure” defective genes (for example by promoting exon skipping) will also be exposed.

Basic Molecular Biology, a brief review: Macromolecules and macromolecule interactions; Gene structure and gene transcription; Regulation of gene expression
Molecular tools for studying genes and gene activity, tecniche di mutagenesi, genome editing by CRISPR-Cas9 system, zinc finger nuclease,TAL effector nuclease
Epigenetic: DNA methylation and histone modification, gene expression and histone code, non coding RNAs
Post transcriptional gene regulation by microRNA: Expression, processing, mechanism of action of miRNA; miRNA and development; miRNA and cancer; miRNA and interfering RNA (RNAi); RNAi as tools to study gene function; RNAi and therapeutic perspectives
Molecular therapy of cancer: molecular basis of cancer (brief summary); cancer and epigenetic; oncogenes and oncosuppressors; miRNAs and cancer; innovative approaches to the molecular therapy of cancer; immunological therapy of cancer; recombinant antibodies, monoclonal antibodies, humanized antibodies, nanobodies; DNA vaccines
Protein stories: protein synthesis, protein targeting, protein folding (particularly in the Endoplasmic Reticulum); protein misfolding and unfolding (mutations and damages); protein degradation (ubiquitin-proteasome system, autophagy)
Disease therapies acting on either transcript maturation or translation: molecular basis of Duchenne muscular dystrophy and cystic fibrosis (brief summary), frame shift and non sense mutations; exon skipping, ODN therapy for correct reading frame rescue; efficiency of ODN delivery; non sense mutation degradation of the transcript; stop codon read through.

Finally, a practical course is planned in which GFP expression will be knock down by RNA interference. Students will utilize HEK293 cell line, both protein or shRNA expression vectors, transfection kit, methods to analyze the results (confocal microscopy and Western blotting). Students will seed and growth cells on coverslips and plastic wells, cells will be transfected, fixed for confocal analysis, lysed for Western blot assay (SDS-PAGE, blotting, incubation with specific antibodies.
Planned learning activities and teaching methods: The Advanced Molecular Biology course is organized in two parts:

40 hours of class teaching
The method of teaching is a mixture of direct instruction with formal lectures and inquiry-based learning approaches. Topics will be treated underlining in particular the methodological approach used to identify/describe a specific biologic phenomenon and/or molecular mechanism or to design and develop a specific biotech drug. Starting by the reading of specific papers, students will be foster to critically evaluate the content of the papers and to propose possible alternative strategies and solutions, taking advantage by their background and novel knowledge. Group analysis, brainstorming, as well as interactive question/answer time will be integral part of the class management. By these activities, students should acquire familiarity with the scientific methods, bibliographic source finding, data base inquiring and group working.

15 hours of practical activity
Small groups of 4-5 students will operate in a classical cell/biochemistry laboratory under the supervision of a tutor. Students will cultivate eukaryotic cells, that will be transfected with a vectors expressing a GFP-tagged protein. Knock down of the tagged-protein will be achieved by the transfection of a specific shRNA-coding vector. Transfection efficiency as well as knock down efficacy will be evaluated both qualitatively and quantitatively by gel electrophoresis and western blot, cytofluorimetry and immunofluorescence analyses. At the end of the practical course, students will be asked to prepare a written report of the activity reporting the results, a critical evaluation of the utilized procedure, underlining any possible encountered problem as well as the solution/s adopted for overcoming it. An estimation of the potentiality of the methodology utilized as novel therapeutic approach is also request. The practical course is intended to introduce students to some of the most common biotech methodologies, to promote the ability to work in group and to apply a rigorous scientific method.
Additional notes about suggested reading: research papers and reviews will be provided during the course
Textbooks (and optional supplementary readings)
  • Watson JD, Caudy AA, Myers RM, Witkowski JA, RECOMBINANT DNA Genes and genomes a short course.. --: --, --. in particolare capitoli 8 e 9 Cerca nel catalogo
  • Lewin B, GENES VIII. --: --, --. capitoli 29 e 30 Cerca nel catalogo
  • Allison LA, Fundamental Molecular Biology. --: --, --. capitoli 12-13 e 17 Cerca nel catalogo
  • Krebs JE, Goldstei ES, Kilpatrick ST, Lewins's GENES X. --: --, --. capitoli 29-30 Cerca nel catalogo