The aim of the course is to provide notions of advanced biological technologies for the amplification and characterization of nucleic acids, and for the study of the genomes and transcriptomes, as well as notions concerning the investigation of chromatin, non-coding RNAs and for genome editing. Notions of bioinformatics for the genome analysis and the search of biological databases will be acquired. The course will also provide an overview of effective protocols for the use of cellular and animal modeling methods to turn lists of plausible genes into causative biomarkers.

1    Basics of bioinformatics
1.1    Primary and derivative database; gene ontology database; genome browsers; tools for DNA/protein sequence analysis (e.g. BLAST)
2    Nucleic acid amplification  
2.1    PCR-based and non-PCR-based techniques 
2.2    Techniques for Whole Genome Amplification and Whole Transcriptome Amplification  
3    Real-time PCR: principles and chemistries 
3.1    Absolute quantification of nucleic acids:  applications and data analysis 
3.2    Probe-based methods for genotyping 
3.3    Melting analysis and High Resolution Melt (HRM) analysis: : principles and examples of applications 
4    Digital PCR and droplet digital PCR
4.1    principles and applications in cfDNA analysis and prenatal diagnosis  
5    DNA Microarrays 
5.1    manufacturing principles 
5.2    planar microarrays and bead microarray 
5.3    applications in transcriptome analysis and in molecular diagnostics  (SNP arrays, CGH arrays, arrays for the detection and characterization of  microorganisms).
6    Next-generation sequencing (NGS)
6.1    Technologies based on pyrosequencing 
6.2    Technologies based on reversible terminators 
6.3    Technologies based on oligonucleotide ligation detection (SOLiD) 
6.4    Technologies based on hydrogen ion detection (ion torrent)
6.5    Third generation sequencing (PacBio sequencing)
7    NGS applications 
7.1    targeted resequencing, exome sequencing, deep-sequencing, transcriptomics, ChIP-sequencing, metagenomics and microbiome analysis, circulating cell free DNA analysis, single-cell analysis.
8    RNA interference
8.1    Techniques to study microRNAs 
8.2    miRNA-mediated gene silencing .    
9    Genome engineering through meganucleases-based methodsi
9.1    Zinc finger nucleases
9.2    TALEN nucleases
9.3     CRISPR/Cas9
9.4    CRISPR/Cas9 genome editing in cellular and animal models 
10    Cellular models of human disease 
10.1    Advantages and drawback of cellular models
10.2    Primary cell cultures and cell lines 
10.3    Cell culture techniques 
10.4    Stem cell (features, differentiation and use strategies)
10.5    Transient and stable gene transfer: the use of viral vectors 
10.6    Modulation of gene expression in animal cells (mutagenesis, gene knock-in and knock-out, antisense strategies)
11    Animal models
11.1    Invertebrates and vertebrates utilized in biomedical research 
11.2    Animal models of disease (Transgenic models knock-in, knock-out, conditional knock-out: Tet, Cre-lox systems)

Knowledge and ability of comprehension. The student must demonstrate the possession of a solid knowledge of basic molecular biology and knowledge of the fundamentals of molecular technologies covered during the course.

Ability to apply knowledge and comprehension The student must also show to be able to apply the acquired knowledge in a drug discovery research and/or clinical diagnostics or environmental context.

Autonomy of judgement The student will be able to critically evaluate the most appropriate biological technology to gain useful information in different therapeutics or diagnostics research contexts. 

Communication skills The student must be able to describe the biological technologies and experimental models listed in the course program using adequate scientific language and referring to concrete examples.

Learning skill. The student will be able to build his own learning path, using learning materials fournished by the teacher or autonomously acquired.

The teaching material prepared by the lecturer in addition to recommended textbooks (such as for instance slides, lecture notes, exercises, bibliography) and communications from the lecturer specific to the course can be found inside the Moodle platform › blended.uniurb.it

Laboratory practice covering qPCR and HRM analysis for detection of SNPs

Teaching

Lectures

Attendance

None

Course books

• Molecular diagnostics. Fundamentals, methods and clinical applications. Buckingham L. 3rd edition. 2019. Ed. F.A. DAVIS
• Tecniche e metodi per la biologia molecolare - Amaldi, Benedetti, Pesole, Plevani - 2020. CEA casa editrice ambrosiana (Zanichelli)
• Cellular and Animal Models in Human Genomics Research - Katherina Walz Juan I. Young - 2019 . Academic press (Elsevier)
• ppt files and scientific reviews published on international journals will be made available online (moodel platform)

Assessment

Oral examination. During the examination the student must demonstrate: that it has acquired full mastery of the concepts covered during the course; to be able to make logical connections between the techniques learned and their applications; to be able to illustrate the key concepts in a limited time and using appropriate scientific language.

Disability and Specific Learning Disorders (SLD)

Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.

To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.

Course books

• Molecular diagnostics. Fundamentals, methods and clinical applications. Buckingham L. 3rd edition. 2019. Ed. F.A. DAVIS
• Tecniche e metodi per la biologia molecolare - Amaldi, Benedetti, Pesole, Plevani - 2020. CEA casa editrice ambrosiana (Zanichelli)
• Cellular and Animal Models in Human Genomics Research - Katherina Walz Juan I. Young - 2019 . Academic press (Elsevier)
• ppt files and scientific reviews published on international journals will be made available online (moodel platform)

Assessment

Oral examination. During the examination the student must demonstrate: that it has acquired full mastery of the concepts covered during the course; to be able to make logical connections between the techniques learned and their applications; to be able to illustrate the key concepts in a limited time and using appropriate scientific language.

Disability and Specific Learning Disorders (SLD)

Students who have registered their disability certification or SLD certification with the Inclusion and Right to Study Office can request to use conceptual maps (for keywords) during exams.

To this end, it is necessary to send the maps, two weeks before the exam date, to the course instructor, who will verify their compliance with the university guidelines and may request modifications.