Learning outcomes of the course unit
The first important educational objective of the course is to understand how the evolution of organisms can also be explained by molecular data.
The second major objective of the course is the ability to get into databases of DNA and protein sequences and to select the data required for a particular biological problem.
The third major objective of the course is the ability to analyze this data and interpret the results.
It is appreciated a good knowledge of Genetics, Mathematics,and Chemistry.
It is also appreciated a good knowledge of the English language.
Course contents summary
The purpose of the course is to provide an evolutionary view of biological processes at the molecular level. The availability of a huge amount of molecular data, generated in the last decades, allows us a large number of analyzes. They can be large-scale studies (for example the analysis of the genomes) or studies on niche topics (for example the origin of new genes in the virus through the "overprinting" mechanism). The course provides students with both the technical ability to enter into the databases, and the ability to extract biological information "ad hoc", and then analyze it in response to a variety of questions and hypotheses. The course consists, largely, of theory. It is needed to understand the most important topics of molecular evolution. It is still supplemented by computer exercises. Particular attention is dedicated to some particular case studies. They include both analysis of large amounts of data (eukaryotic genomes) and analysis of small amounts of data (a family of proteins, small viral genomes).
Molecular mechanisms at the basis of evolutionary processes
Homologous genes: orthologs and paralogs
Convergent and divergent evolution
Co-evolution of the gene families
Genetic distance between protein coding sequences
Construction of phylogenetic trees and statistical methods for evaluating their robustness
Use of phyloghenetic trees for reconstructing the genealogy of viral overlapping genes
Organization and evolution of genomes
Genomes of prokaryotic organisms (Escherichia coli, Methanococcus jannaschii, Mycoplasma genitalium)
Genomes of eukaryotic irganisms (Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana)
The genome of Homo sapiens
Single nucleotide polymorphisms (SNPs)
Comparative genomics of eukaryotic organisms
Prediction of protein coding genes: ORF analysis, intrinsic and estrinsic methods for identifying coding sequences
Databanks of nucleotide and protein sequences. Databanks of polymorphic sites and mutations.
Databank of mitochondrial DNA sequences
Databank of gene expression
Alignment of nucleiotide and protein sequences
Similarità between sequences and algorithms for their alignment
Natural selection and random genetic drift from analysis of synonymous and non-synonymous substitutions
Matrices of amino acid substitutions (PAM, BLOSUM)
Multiple alignement of amino acid sequences and profiles of structural priperties
Search for similarities in databanks
Search for functional motifs in nucleotide and protein sequences
Identification of transcriptional promoters with algorithms of “signal search”
Prediction of the junction sites between exons and introns
Different frequencies of synonymous codons in protein coding genes of eukaryotic and prokaryotic organisms
Genealogy of viral overlapping genes by “codon usage” approach
Search for “signal sequences” in proteins
Case studies of molecular evolution
Adaptation at molecular level: the comparative analysis between the amino acid sequences of the glutamate-deydrogenase enzyme from thermophilic and mesophilic bacteria identies a few regions important for thermostability
Reconstruction of prehistoric human migrations: sequence analysis of the genome of polyomavirus JC suggests a dual exit from Africa of our ancestors
A curious mode of evolution: the origin of the overlapping genes pol/S of hepatitis B virus can be explained by a mechanism of “modular evolution”
Bioinformatics and genome analyis: search for eukaryotic tRNA genes with a “signal search” algorithm
The choice of the synonymous codons for a given amino acid is not random: the preference for a few synonymous codons in Saccharomyces cerevisiae increases the efficiency of the translation process
Dan Graur & Wen-Hsiung Li - Fundamentals of molecular evolution - Sinauer Associates, Sunderland, MA
Lectures, in order to make clear to students the "why" and "how" of the main themes of molecular evolution. The course is also integrated by computer exercises.
Assessment methods and criteria
The assessment is based on an oral exam. The possibility that students propose their own subject of study is strongly encouraged. Particular attention is paid to the quality of the scientific language.
An important aspect of the course is the ability to pick up, in the lot of data of DNA and protein sequences, the more subtle details of some topics of molecular evolution.