Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols – the biological sequence – rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.
Spis treści
Molecules: Proteins and RNA.- Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example.- Gene3D and Understanding Proteome Evolution.- The Evolution of the Globins: We Thought We Understood It.- The Structurally Constrained Neutral Model of Protein Evolution.- Towards Unifying Protein Evolution Theory.- Molecules: Genomes.- A Twenty-First Century View of Evolution: Genome System Architecture, Repetitive DNA, and Natural Genetic Engineering.- Genomic Changes in Bacteria: From Free-Living to Endosymbiotic Life.- Phylogenetic Analysis.- Molecular Phylogenetics: Mathematical Framework and Unsolved Problems.- Phylogenetics and Computational Biology of Multigene Families.- Seqin R 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis.- Networks.- Evolutionary Genomics of Gene Expression.- From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation.- Populations.- Drift and Selection in Evolving Interacting Systems.- Adaptation in Simple and Complex Fitness Landscapes.- Genetic Variability in RNA Viruses: Consequences in Epidemiology and in the Development of New Stratgies for the Extinction of Infectivity.
O autorze
Ugo Bastolla is researcher in the laboratory of bioinformatics of the Centro de Astrobiologia in Madrid (Spain), on leave to the Centro de Biologia Molecular of the Spanish CSIC. Since his degree in physicswith Luca Peliti he has always been interested in biological topics, above all evolution. He got is Ph D in Rome with Giorgio Parisi workingon disordered dynamical systems inspired to biology and was postdoc in Julich (Germany) with Peter Grassberger, studying statistical mechanicalmodels of polymers, in Berlin (Germany) with E.W. Knapp studying simpleprotein models, in Golm (Germany) with Michael Laessig, studyingecological models, and finally in Madrid (Spain) in the bioinformaticsgroup of Alfonso Valencia. His main research interest consists in combiningsimple models of protein thermodynamics and evolution.
Markus Porto is professor of Theoretical Solid State Physics at the Institut fur Festkorperphysik at the Technische Universitat Darmstadt(Germany). He received his Ph D at the Universitat Giessen (Germany). Hisresearch interests cover many aspects of solid state and statisticalphysics, including transport and relaxation in disordered systems andbiophysics, as well as applying methods of statistical physics to modelmolecular evolution.
H. Eduardo Roman is Research Fellow at the Department of Physics of the University of Milan-Bicocca. He earned his Ph.D at the International Schoolfor Advanced Studies, Trieste (Italy), and has been Privat Dozent at the Universities of Hamburg and Giessen (Germany). His research interests covermany aspects of Statistical Physics, from fractals to stochastic phenomena, biophysics, proteins and evolution, and ab-initio electronic calculations inmolecules.
Michele Vendruscolo is a Royal Society University Research Fellow at the Department of Chemistry, University of Cambridge. He received his Ph D in Condensed Matter Physics in 1996 at the International School for Advanced Studies, Trieste (Italy). His research is mainly focussed on understandingthe biophysical principles regulating the behaviour and the evolution ofproteins.
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