Biotechnological and Chemical Sciences in Diagnostics

BASIC AND APPLIED MOLECULAR BIOLOGY

BASIC AND APPLIED MOLECULAR BIOLOGY

Academic year 2023/2024

Sommario del corso

• Course objectives
• Results of learning outcomes
• Program
• Course delivery
• Learning assessment methods
• Support activities
• Teaching tools
• Course card

Course objectives

This course is articulated in two parts. The first part is aimed at providing a synthetic view of the basic molecular biology knowledge normally acquired in the undergraduate course of biology and biotechnology, tailored to provide all the bases to follow the more applied second part. The objectives of this module consist in providing solid information about the biochemical structure of DNA and RNA, DNA dynamic organization within the chromatin, the replication and recombination mechanisms, DNA repair, and transcriptional and epigenetic regulation of gene expression, including the role of non-coding RNAs in regulating gene expression.
The second part of the course will focus on the experimental technologies originating from the molecular biology knoweldge, thus providing the tools to translate the molecular knowledge in both pre-clinical and clinical diagnostic technologies.

Results of learning outcomes

At the end of the course, the student should have a deep knowledge of: 

• biochemical structure of DNA and RNA. 
• DNA dynamic organization within the chromatin
• replication and recombination mechanisms
• DNA repair mechanisms
• DNA recombination
• transcriptional and epigenetic regulation of gene expression,
  role of non-coding RNA in regulating gene expression.
• Advanced molecular technologies to manipulate DNA structure and gene expression.
• Advanced molecular technologies exploiting nucleic acids and protein biochemical and biological properties for pre-clinical and clinical diagnostic technologies.
  
  In addition the students will acquire skills in the analysis of current scientific literature, and learn how to use these skills for the development of new cell-based diagnostic tools in specific contexts.

Program

1. A) START MODULE

DNA

• Intro centrality of DNA: Avery experiments and central dogma of Molecular Biology
• DNA structure
• RNA structure
• Chromatin structure, its remodeling and DNA methylation.
  • Nucleosomes
  • Histones, reversible post-translational modifications
  • Histone code, i.e. the biochemical implications of Histone modifications
  • DNA methylation and its biochemical implications
  •  

Chromosomes:

• Telomeres, centromeres
• Chromosomes duplication:
  • Chromatin replication
  • DNA replication

Genome Expression

• Transcription
  • Transcription regulation (cooperativity, repression, ..)
  • epigenetics, nucleosome positioning and remodelling, readers, 
  • gene expression factory: elongation, maturation, splicing, transport, non-sense mediated decay
  • DNA topology, Insulator
• mRNA functions
  • mRNA structure
  • Ribosomal RNA e tRNA
  • lincRNA – 
  • small structural RNAs (snoRNA, miRNA)
• mRNA translation and its regulation

Homologous Ricombination
DNA repair

• DNA decay and chemical modifications
• DNA repair mechanisms
• Biochemical and biological consequense of defective DNA repair

1. B) Curricular module

• Macromolecule interactions: relevance of molecular shape and its biological technological implications
  • Protein-protein: antigen-antibodies (western blot, ELISA, immune-precipaitations)
  • Humanized antibodies, phage display, single chain antibodies
  • Carbohydrates-proteins and carbohydrates-carbohydrates interactions
  • Tag-based interaction technologies (biological-based tags, biotin-based tags,…)
  • Strategies to detect macromolecules interactions in intact cells (FRET, FRAP, proximity ligation assays)
• FACS-based technologies
• Technologies for gene expression quantification
  • Hybridization technologies (direct and inverted hybridization)
  • Synthesis/amplification based-technologies (PCR, RT-PCR)
• DNA sequencing technologies from Sanger, NGS, nanopore and their applications
• Diagnostic applications
• Stategies to identify/validate/measurea biomarkers
  • NGS and more
  • Molecular diagnosis by omics/molecular diagnostics and precision medicine: methods, applications
  • Metagenomics and metatranscriptomics
• Synthetic biology and Synthetic biology-based diagnostics 
  • Synthetic biomarkers, also genetically encoded
  • Toehold RNA switches
  • CRISPR Cas-based
  • Optogenetics (although it is not diagnostic yet)

Course delivery

The course will be articulated in two modules:

A) a START module consisting of pre-recorded lectures followed by in presence lectures to discuss the subjects presented. Power point slides will be made available to the students. 

B) in presence lectures addressing the second curricular part of the program. The didactic material will mainly consist of scientific papers which will be analysed in class. The students will receive the relevant bibliography. The active participation at the discussion is strongly encouraged.

Learning assessment methods

Learning assessment related to the Start module will be assayed by a multiple choice test at the end of the Module itself. 

Learning of the curricular module will be assayed through an oral exam on the subjects discussed during the course. 

Support activities

Further scientific papers will be suggested to deepen some topics. 

• Teaching material
• Exams and finals
• Class schedule
• Go to Moodle
• Register for the course
• Enrolled students
• Invia email agli studenti registrati
• Export table