Teaching: Courses and related reading and lecture material

Course Outline
This course is taught to second years and aims at giving a good breadth of evolution at different levels, including very general evolution concepts such as the Mechanisms of Speciation, Molecular Evolution and Phylogenetics and Population Genetics. The subject covers many angles and is enriched with examples from botany, zoology, morphological and molecular evolution. The course is distributed in about 20 lectures. Some of the theory covered by the course is:
1. Darwin, Theory of Evolution, Darwin and society
2. Genetic Variability, Allele Frequency
3. Hardy Weinberg Equilibrium, Selection, Mutation, Migration, Genetic Drift, Non random mating
4. Speciation
5. Mechanisms of divergence, Genetic drift, natural selection, sexual selection, reinforcement selection
6. Molecular evolution, Neutral theory of molecular evolution
7. Molecular phylogenetics
8. Phylogeny and sequence comparison
9. Evolution of development
10. Human Evolution.

Evolution of Protein Structures
This course focuses on the understanding of how natural selection constrains the evolution of protein structures. In particular, what makes the surface of protein structures more relaxed in terms of exploring different genotypic solution while the core being very selectively constrained is the question that motivates this course. To answer this question, the student is faced with the understanding of many fundamental concepts in structural biology as well as evolutionary biology. Some of the concepts include, but are not limited, to the following:
1. In vivo, in vitro, in silico, Proteins, Protein structure and conformation: Basic concepts, Proteins in diseases
2. Patterns and forms in protein structure, Helices and sheets, The hierarchical nature of protein architecture, Structure based classification of proteins protein folding: Intra-cellular pathogens and the survival of the flattest, Protein folding and disease: Amyloidoes, Parkinson, Huntington, Prion disease
3. Conformational changes in protein, Structural changes arising from changes in state of ligation, Hinge motions in proteins, Mechanisms of conformation changes (Haemoglobin, Serpins,muscle contraction), Higher level structural changes (GroELS)
4: Protein Structure Prediction and Determination, Methods of protein structure determination, Critical assessment of structure prediction, Homology modelling, Threading, Prediction of novel folds, Protein design
5. Evolution of Protein Structure and Function, Protein structure classification, Structural relationships among homologous proteins, Changes in proteins during evolution uncovers functionally/structurally important amino acid sites, Domain swapping, Classification of protein folding patterns, How do proteins evolve new functions?, Classification of protein functions
6. Molecular evolution, Evolution of Globins, Evolution of Serine proteinases, Evolution of visual pigments and related molecules)
7. Molecular Co-evolution and mutation epistatic effects on protein structure, Defining molecular co-evolution, Nonparametric methods to detect co-evolution, Parametric methods to detect coevolution, Intra-molecular co-evolution and prediction of amino acid sites three-dimensional proximity, Inter-protein co-evolution and the identification of protein protein interfaces
8. Some examples of the immune system, Antibody structure, Protein of the Major histocompatibility Complex, T-cell receptors, Cancer and protein structures