Learning objectives
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.
Prerequisites
It is appreciated a good knowledge of Genetics, Mathematics,and Chemistry.
It is also appreciated a good knowledge of the English language.
Course unit content
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).
Full programme
FIRST LESSON
Use of genes encoding 16S and 5S ribosomal RNA as markers of genetic affinities between eukaryotes, bacteria and archaea.
Multiple alignment of sequences and construction of phylogenetic trees.
The origin of mitochondria, deduced from analysis of databases of DNA sequences.
Nucleotide and amino acid sequence analysis in low molecular weight "heat shock" genes of animals and plants.
ID: Applied knowledge and understanding
ID: Ability to learn
SECOND LESSON
The analysis of the principal components in the reconstruction of the genetic relationships between "heat shock" genes of animals and plants.
The transfer RNA gene in eukaryotes: description of its transcriptional promoters.
Algorithm for the search of eukaryotic tRNA genes in databases with the "weight matrix" method.
ID: Applied knowledge and understanding
ID: Ability to learn
THIRD LESSON
Different use of the synonymous codons in the yeast Saccharomyces cerevisiae. Correlation between the copy number of tRNA genes and the translational efficiency.
ID: Knowledge and understanding
ID: Communication skills
FOURTH LESSON
Linear regression and multiple linear regression, bivariate and multivariate statistics respectively. Application of a multiple regression model on gene expression in the yeast Saccharomyces cerevisiae.
ID: Applied knowledge and understanding
ID: Ability to learn
FIFTH LESSON
Molecular clock and evolution of primates, based on the immunological distance between albumins.
Molecular clock and evolution of primates, based on sequences of mitochondrial DNA and of globin pseudogenes.
ID: Autonomy of judgment
ID: Communication skills
ID: Ability to learn
SIXTH LESSON
Origin of the Anatomically Modern Human from comparative analysis of repetitive DNA sequences. The analysis of ALU sequences is in agreement with the hypothesis of a monocentric origin of humans in Africa.
ID: Autonomy of judgment
ID: Communication skills
ID: Ability to learn
SEVENTH LESSON
Reconstruction of the ancient evolutionary history of Anatomically Modern Human (migrations out of Africa into the rest of the world) from sequence analysis of symbiotic viruses with a mechanism of transmission vertical-like: the case of the hepatitis G virus.
ID: Knowledge and understanding
ID: Communication skills
EIGHTH LESSON
Reconstruction of the ancient evolutionary history of Anatomically Modern Human (migrations out of Africa into the rest of the world) from sequence analysis of symbiotic viruses with a mechanism of transmission vertical-like: the case of the JC polyomavirus.
ID: Knowledge and understanding
ID: Communication skills
NINTH LESSON
Possible transmission of the European JC polyomavirus strain from European Archaic Human (Neanderthal) to our ancestors.
ID: Knowledge and understanding
ID: Communication skills
TENTH LESSON
Genome sequence properties of SARS-CoV-2, the causative agent of the COVID19 pandemic. Molecular opportunism.
ID: Knowledge and understanding
ID: Communication skills
ELEVENTH LESSON
The linear discriminant analysis (multivariate statistics). Identification of the carriers of sickle cell disease in the Po Delta.
ID: Applied knowledge and understanding
ID: Ability to learn
TWELFTH LESSON
Use of linear discriminant analysis in the prediction of the determinants of thermal stability: the case of the enzyme glutamate dehydrogenase in thermophilic bacteria
ID: Applied knowledge and understanding
ID: Ability to learn
Bibliography
Lesson slides
Teaching methods
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.
Other information
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.
