Teaching code

4S008190

Credits

12

Coordinator

Antonella Furini

Language

Italian

Scientific Disciplinary Sector (SSD)

AGR/07 - AGRICULTURAL GENETICS

Moodle Seminars 0

The teaching is organized as follows:

Learning objectives

The course aims to provide basic knowledge of recombinant DNA technologies and methodologies applied to molecular genetic and genomic analysis. Frontal lessons will be introductory to traditional genetic methodologies and to the most advanced ones to analyze genes and their functions. Laboratory lessons will apply the background from frontal lessons by using the most common methodologies of molecular genetics used for prokaryotes and eukaryotes. At the end of the course the student will know the principal techniques related to the extraction, analysis and manipulation of nucleic acids; protein expression in heterologous systems; the techniques used for genetic transformation of animal and plant organisms; the methods for gene expression analysis and for studying protein-protein interactions. The acquired knowledge will enable the students to understand the methodological approaches used in scientific research in molecular genetics and to use molecular technologies for specific laboratory experiments.

Prerequisites and basic notions

The student must have taken the Molecular Biology exam.

Program

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MM: teoria
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1) Cloning: - Plasmid vectors, selection markers and reporter genes (e.g. GFP); - E. coli transformation - Selection of recombinants - Methods of cloning: (i) Vectors based on restriction enzymes; (ii) PCR amplification and cloning of DNA fragments through T/A cloning: pGEM vectors; (iii) Cloning mediated by DNA topoisomerase, TOPO Cloning; (iv) Cloning by recombination: Gateway and Golden Gate Assembly systems; 2) Genetic transformation of plants (leaf disks and protoplasts) and animals (Prof. Furini). 3) Bacteriophage λ, Cosmids, BAC, YAC, genomic libraries and cDNA libraries, transformation of yeast cells; 4) Genomic DNA extraction, plasmid DNA extraction, phage DNA extraction; 5) DNA and genome analysis by hybridization (Southern blotting) and amplification, molecular markers; 6) Sanger DNA sequencing, NGS sequencing and third generation sequencing; genome sequencing and genomics; 7) Random and site specific mutagenesis; 8) Genome editing, CRISPR/Cas9; 9) Forward and reverse genetics to study gene function, gene silencing (Prof. Bellin). 10) RNA extraction and gene expression analysis by Northern blotting, RT-PCR and Real Time RT-PCR; 11) Large-scale expression analysis, transcriptomic platforms based on microarray and RNA-Seq; 12) Reporter genes and their use for functional studies and gene expression analysis; 13) DNA-protein interaction in the regulation of gene expression: chromatin immunoprecipitation (ChIP), shift assay, luciferase assay (Prof. Zenoni) 14) Sub-cellular targeting for recombinant protein production in heterologous systems (comparison between prokaryotic and eukaryotic systems); 15) Description of the systems used to study the sub-cellular localization of a protein; 16) Factors that influence the stability of a protein and its evaluation; 17) Techniques used for the quantification of solubilized proteins (western blot, ELISA, enzymatic assays (Prof. ssa Avesani).
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MM: laboratorio
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Preparation of constructs for plant and yeast transformation. Students will clone the GFP gene in a TOPO-cloning vector and subsequently into a Gateway vector by recombination: The gene of interest will be amplified by PCR and cloned in a vector thanks to the activity of the DNA isomerase I. From this construct (entry clone), the gene of interest will be transferred by recombination in two different Gateway vectors (destination vectors), for the expression in plant and yeast. During the procedure, recombinant constructs will be amplified in E. coli and purified by miniprep procedure. Final constructs will be utilized for genetic transformation of plants (Prof. Furini) and yeast in following experience.
Site-specific mutagenesis: planning of the mutagenesis, primer design for mutagenesis, PCR amplification and phosphorylation, ligation and digestion with DpnI for mutagenized plasmid enrichment, transformation of competent cells, recovery and screening of mutant plasmids and validation by evaluation of activity of the expressed protein (Prof. ssa Bellin).
Genomic DNA analysis: genomic DNA extraction. Evaluation of DNA yield and quality based on spectrophotometric analysis and evaluation on agarose gel. Genomic DNA analysis for the presence of trans gene by PCR (Prof.ssa Furini).
Gene expression analysis in a transgenic organism by real-time RT-PCR: Extraction of RNA from the transgenic organism and from the wild type. Evaluation of the quality and quantity of the extracted RNA, treatment with DNAse, reverse transcription and real-time RT-PCR reaction. Evaluation of the different levels of expression of the transgene in the wild type and in the transgenic organism by calculating the deltadeltaCt. Cell isolation from tissue and visualization of protein encoded by reporter gene though optical microscopy.
Total Soluble Protein extraction from leaf tissue and from yeast and quantification. Evaluation of the yields of GFP production in plant systems and in yeast by ELISA and by fluorimetric analysis. (Prof. ssa Broccanello).

Didactic methods

Lectures will be delivered in-person only, without the use of video lectures and online teaching. Those who, due to Covid cannot attend in person (to be demonstrated by presenting the appropriate certificate), will be able to take advantage of the recorded video lectures. To take the examination students are required to attend at least 50% of laboratory lessons.

Learning assessment procedures

The final evaluation will be performed by a written exam, including open and multiple-choice questions concerning both the theory and practical activities. The positive evaluation of the exam concerning the parts given in the first term will be mandatory for assessing the exam of the second term.

Evaluation criteria

Completeness of the content;
competence in the use of the specialized lexicon;
grade of of thirty.

Criteria for the composition of the final grade

The final score will be calculated from the weighted averages of each part, including the evaluation of the laboratory reports.

Exam language

italiano