Biology

The course provides students with 6 CFU, including 48 hours of frontal lectures divided into two MODULES of 24 hours. MODULE I This part of the course aims to provide the student with a general knowledge of the content of the genomes of different organisms and how in various model systems the modern methodologies underlying functional genomics can be applied in basic and applied research. Structural Genomics Genome content and genome paradoxes: the C value. The genome sequence for gene mapping: association, physical, genetic and citogenetic maps the molecular markers (SNPs, SSR, FISH). Genes annotation and protein prediction. Mutation and bioinformatic analyses. Comparative and evolutionary genomics. Functional Genomics Model systems: pros and cons Drosophila melanogaster, Caenorhabditis elegans, Danio rerio e Mus musculus: Life cycle, development, anatomy and handling in the laboratory. Strategies for the generation of mutants and/or transgenic individuals in different model systems. Genetic and modifier screens. Targeted mutagenesis. Gene targeting e homologous recombination. Gene cloning. Mammalian and insect cell cultures in functional genomics. Genome-wide RNAi screens in model organisms. Genome editing: genome-wide CRISPR screen in a mouse model. A CRISPR/Cas9 vector system for tissue-specific gene disruption in zebrafish. A Drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Web tools for genomics resources search and analysis Flybase, Wormbase, The Zebrafish Model Organism Database (ZFIN). MODULE II This is an introduction to Genomics where the main methodologies underlying genomics, transcriptomics and proteomics and their practical use in basic and applied research are provided. Structural Genomics Evolution of the concept of gene: from Darwin's theories of heredity to the post-genomic era; the Human Genome Project. The Encode project. DNA (Sanger method, Maxam-Gilbert, BAC) and genome sequencing technologies. Automated sequencing. The Next-Generation Sequencing (NGS). The "Illumina" technology. Anatomy of genomes, genome size and number of genes. The non-coding DNA (ncDNA). RNA sequencing technologies. The transcriptome and high-throughput analysis of gene expression; WET lab and DRYLAB for a typical RNA-seq analysis (FASTQ, PHRED quality score, FASTQC). De-novo identification and differential expression analysis of mRNA and non-coding RNAs (ncRNA). Genetic and biochemical approaches to the study of the Interactome. The yeast two-hybrid system. Immunoprecipitation, Co-immunoprecipitation, Protein tagging and pull-down assays. Studying the interaction between PROTEIN (ChIP) and RNA (ChIRP) with the chromatin: the i) Chromatin Immunoprecipitation (ChIP) and the ii) Chromatin Isolation by RNA Purification (ChIRP). Functional Genomics "forward" and "reverse" genetics approaches. RNA interference (RNAi). Genomic editing: the CRISPR/CAS9 system. Functional analysis of mRNA and non-coding RNAs (ncRNA) in muscular and neuronal (mouse and human) differentiation systems. Web tools for genomics resources search and analysis Exercises in the computerized classroom. Elaboration and interpretation of genomic data. Biological databases (primary, secondary, specialized); the FLAT format; NCBI and resources: access via Taxonomy, Gene; Protein Map Viewer, Pubmed and Pubmed MeSH, Entrez; Genome browsers (UCSC), Ensembl, DDBJ, UniProt; Basics of gene ontology (GO). TARGETSCAN and miRTARBASE.

The course of Genomics is taught in the second semester of the 3rd year of the 3-year courses in Scienze Biologiche and it is included among the elective courses. Basic prerequisites for understanding the topics covered by the course are a basic knowledge of Genetics and Molecular Biology. The written comprehension of the English language is essential to take advantage of the scientific articles proposed by the teachers in addition to textbooks as didactic material.

For news on textbooks and teaching materials see: https://elearning2.uniroma1.it

Lectures are not mandatory.

The exam aims at verifying the level of knowledge and in-depth examination of the topics of the teaching program and the reasoning skills developed by the student. The evaluation is expressed in thirtieths (minimum grade 18/30, maximum mark 30/30 with summa cum laude). The evaluation consists of two oral interviews conducted on the same day by the two reference teachers on the topics covered in MODULES I and II. The overall exam allows verifying the achievement of the objectives in terms of knowledge and skills acquired, as well as communication skills. During the oral test property of language, clarity of exposition and critical capacity to solve genomic problems are also evaluated. Part of the exam consists of a practical computer test to evaluate the candidate's ability to apply the skills acquired in the consultation of biological databases. The time required for the tests is 40 minutes for oral interviews and 15 minutes for the practical computer test. The final grade will result from the average between the two oral tests and the practical computer test.

The course is structured in frontal theoretical lectures and computer exercises. In particular, there are 48 hours of total teaching (6 CFU), divided into two MODULES (MODULE I and MODULE II) of 24. Lectures are held 3 times per week and presented by the use of slides on Power-Point.