Corso di laurea magistrale - Area di Scienze MM.FF.NN. - Accesso libero con verifica di requisiti e preparazione in ingresso - Classe LM-6 - (D.M. 270/2004)
Lingua: Italiano
Informazioni generali
o Classe: LM–6 (D.M. 270/04)
o Tipologia di corso: Magistrale
o Durata: 2 anni
o Tipo di accesso: Accesso libero con verifica di requisiti e preparazione in ingresso
o Area di afferenza: Scienze Matematiche, Fisiche e Naturali
o Dipartimento: Biologia
o Codice corso: P64
Descrizione e obiettivi formativi
Il corso si colloca nello spazio culturale e formativo della Biologia avanzata, per lo studio delle relazioni complesse che caratterizzano il mondo vivente. Intende formare specialisti in grado di cimentarsi con problemi di natura ambientale, dalla conservazione alla gestione sostenibile delle risorse rinnovabili, e specialisti in grado di applicare le loro conoscenze nell'ambito della biologia e dell'evoluzione umana in diversi settori che coprono aspetti di tipo forense e archeo-antropologico.
Il corso è articolato in modo da fornire:
- Una solida preparazione culturale nella biologia di base e in diversi settori della biologia applicata, con un'elevata preparazione scientifica e operativa nelle discipline biologiche di interesse; un'approfondita conoscenza della metodologia strumentale, degli strumenti analitici e delle tecniche di acquisizione e analisi dei dati.
- Conoscenze su temi avanzati della biologia animale e vegetale, dell'evoluzione biologica e dell'ecologia. Conoscenze sulle applicazioni ecologiche e sui principi dell'evoluzione biologica per l'interpretazione causale dei pattern della biodiversità alle scale del genoma, degli organismi, delle popolazioni, delle comunità e degli ecosistemi. Conoscenze sulla teoria degli ecosistemi e sui loro modelli e applicazioni ecologiche di supporto all'innovazione scientifica e tecnologica.
- Competenze particolari sulle caratteristiche biologiche della nostra specie umana da applicarsi in ambito biomedico, medico-legale, evoluzionistico, anche ai fini della conservazione del patrimonio demo-etno-antropologico. Competenze sulle metodiche per il recupero, l'estrazione e l'analisi del DNA a partire da materiale contemporaneo e archeologico con l'applicazione delle moderne tecniche di analisi molecolare.
- Capacità di affrontare i problemi con approccio sistemico e multidisciplinare, con particolare riferimento alla capacità di dialogo con le dimensioni economiche, sociali e giuridiche delle problematiche ecologiche. Capacità di utilizzare le conoscenze acquisite in sistemi di certificazione, nel supporto alle decisioni nella pubblica amministrazione, nei settori privati, in programmi di educazione ambientale.
Applicazioni ecologiche e dei principi dell'evoluzione biologica alla valorizzazione, conservazione e gestione della biodiversità.
Applicazioni ecologiche e dei principi della biologia evoluzionistica ad alcuni aspetti della medicina e della salute pubblica.
Sbocchi professionali
I laureati operano in strutture pubbliche o private, applicando le proprie conoscenze ai fini altamente professionali di promozione, progetto e sviluppo dell'innovazione scientifica e tecnologica, nei settori umano ed ecologico, anche nell'ambito dei sistemi di certificazione e controllo di qualità.
Tra le strutture vanno ricordate: università, enti di ricerca, soprintendenze, musei, aziende sanitarie locali, laboratori di analisi, laboratori di analisi di reperti biologici della Polizia di Stato e dell'Arma dei Carabinieri, enti pubblici e privati competenti in materia ambientale (Agenzie per l'Ambiente, Regioni, Province, Comuni, Parchi o Riserve naturali), studi professionali operanti in valutazione e controllo degli impatti ambientali, aziende agricole e della pesca, in cui la materia ambientale riguarda l'innovazione tecnologica e scientifica, le filiere produttive, i sistemi di certificazione e controllo anche nel contesto della cooperazione allo sviluppo in ONG ed organizzazioni governative.
Potranno avere accesso al Dottorato di Ricerca.
Potranno esercitare la libera professione previa iscrizione all'Albo Nazionale dei Biologi, dedicarsi all'insegnamento nelle scuole secondarie e/o occuparsi di divulgazione scientifica.
Condizione occupazionale (indicatori di efficacia e livello di soddisfazione dei laureandi):
http://statistiche.almalaurea.it/universita/statistiche/trasparenza?CODICIONE=0580207300700004
Valutazione della didattica - Studenti
Anno accademico precedente
Riferimenti web e contatti
Sito Web della Macroarea di Scienze: http://www.scienze.uniroma2.it
Sito Web del Corso: https://scienze.uniroma2.it/2022/11/01/biologia-ambientale-lm-6/
Coordinatore: Prof. Gabriele Gentile
Segreteria Didattica del Corso:
Anna Garofalo
e-mail: anna.garofalo@uniroma2.it
Tel. +39 06 7259.4806
Technological advances in DNA sequencing are greatly contributing to the expanding understanding of biodiversity at different hierarchical levels. The ability to obtain whole-genome sequences from non model organisms allows unprecedentedly detailed measures of genetic diversity and its spatial distribution in wild animals and plants. The ongoing development of analytical tools allows translating these measures into statistical inferences about the evolutionary histories of organisms, reconstructing the interaction of populations with their environment in terms of demography and natural selection. This kind of reconstructions is, in turn, essential for the definition of taxonomic and conservation units, for the identification of introgression into autochthonous population from allochthonous sources, for the evaluation of the adaptive potential of wild populations, for tracking of legal and illegal exploitation of biological resources and for developing predictive models addressing conservation strategies. This course presents the most important analytical tools for the reconstruction of demographic dynamics and identification of adaptive selection from genomic data, with examples of relevant applications for the conservation of natural populations and their adaptive potential.
The course introduces the student to one of the fundamental aspects of conservation biology: the long-term marking and tracking techniques of animal species, in particular those at risk of extinction. Students will be introduced to classic mark-recapture methods. They will then be exposed to more modern techniques that include the use of molecular tags and technologically advanced systems based on satellite tracking. In addition to illustrating different "data collection" methods, the course also introduces methods of organizing and managing data through the use of relational databases such as MySQL.
The course introduces students to the use of bioinformatic tools for the analysis of genetic and genomic data applied to the field of molecular biology. Students will learn how to use bionformatic tools (hardware and software) to independently carry out research analyses and develop models to test the validity of scientific hypotheses. In addition to illustrating different methods of analysis, the course also introduces methods of organizing and managing data through the use and consultation of molecular databases.
Course program Review of elementary probability theory Review of elementary theory of hypotheses testing Comparing two groups • Student’s t-test for independent samples • F-test of equality of variances • Student’s t-test in case of unequal variances • The central limit theorem. Application Statistics for small samples: non parametric methods • Order statistics and rank statistics • Rank based tests • Permutation tests Comparing more than two groups One way analysis of variance (ANOVA) • Variability within and among groups • Orthogonal contrasts • Introduction to multiplicity Molecular Analysis of Variance (MANOVA) Evaluating relative risk • Cohort study design • Case-control study design • χ2 test for independence • χ2 test for goodness of fit • Relative risk and odds ratio
Innate immunity: cells and molecules involved; MHC molecules and antigen presentation; Class I and Class II presentation, Cross-presentation; Activation of helper and cytotoxic T lymphocytes. Naive T lymphocytes, anergy, peripheral tolerance; T helper lymphocyte subpopulations (Th1, Th2, Th17, follicular T cells, regulatory T cells); Antibody immunity: structure and function of antibodies, isotypes and isotype switch; Mucosal immunity and oral tolerance; Virulence and pathogenicity of bacterial infections; Pathogenic bacteria and bioterrorism; Antibacterial immunity and mechanisms of evasion of host response by bacteria; Antiviral immunity (interferons, antibodies and cell-mediated immunity); Virus evasion mechanisms of the antiviral immune response; Protozoan and helminth infections and immune responses to parasitic infections; Mechanisms of evasion of the immune response by parasites; Hypersensitivity reactions; Poverty related Diseases: Tuberculosis; HIV, Malaria; Co-infections (Tuberculosis and HIV); Vaccines and vaccinations. Inactivated, attenuated and subunit vaccines; Adjuvants and delivery systems; Immunotherapy and antibiotics; The human microbiota.
Energy of ionizing- (IR) and non-ionizing radiation (NIR). Mode of interaction of radiation with matter; energy distribution, energy absorption and effects at the molecular, cellular and tissue levels. Differential radiosensitivity. Unit of measurement for IR. Direct clastogenic effects of IR. Dose-effect kinetics: lethality and survival curves. Threshold dose. Intensity and dose fractionation of IR. Oxygen effect. Human exposure to IR: somatic and germ-line risk. Bystander effect of IR.
The following topics will be covered during the course program: Structural and functional aspects of marine ecosystems, marine trophic food webs (pelagic and benthic) and secondary productivity. marine organisms life histories. Larval dispersal and settlement and recruitment processes. The distribution of organisms in space, concept of patchiness. Populations dynamics over time and space. Alien species, ecological role and interactions with native species. Pollution and degradation of marine ecosystems, climate change, marine acidification and Mediterranean tropicalization. Marine resource management and biodiversity conservation, overfishing marine protected areas and mariculture. Monitoring and study of coastal marine environments, lagoons, estuaries and main habitat types of the Mediterranean. Sampling methods, sediments analysis and classification. The role of sediments in the benthic habitat types and environmental contamination processes. Nutrients and primary productivity, measurement methods and conditioning factors, dystrophic processes in coastal and transitional waters.
Structure of biological membranes. Rafts and caveolae. Eptaelic receptors. Heterotrimeric G proteins. Cyclic nucleotides. Adenylate cyclase. Protein kinase A. Phosphodiesterase. Phosphatidylinositol and phosphorylated derivatives. Phospholipase C-beta. Role of IP3 and diacylglycerol as intracellular messengers. IP3 and ryanodine receptors. Intracellular homeostasis of Ca2 +. Protein kinase C and Ca2 + / calmodulin - dependent. Beta-arrestine and small G proteins. Eptaelic receptors in sensory physiology and in the control of cardiovascular function. Guanylate cyclase. Protein kinase G. The guanilate cyclase / cGMP-phosphodiesterase system in the control of smooth muscle and the mechanism of vision. Tyrosine kinase. Src. Receptors for growth factors. The Ras-Raf-MEK-MAP kinase pathway. PI-3 kinase and activation of PKB / Akt. Phospholipase C-beta. Structure and functions of neutrophin receptors. Insulin receptor and glucose uptake mechanism.
Introduction to nomenclature, species concepts and classification of phototrophs. Origin and evolution and of phototrophic prokaryotes and eukaryotes in the biosphere. Morphological, functional and phylogenetic diversity of photosynthetic organisms. Measuring biodiversity: approaches to the study of the diversity of Cyanobacteria, Algae and Embriophyta. Phototroph distribution patterns and relationships with the environment, with particular emphasis on aquatic systems (integrated into a global climate perspective). Acclimation and adaptation to abiotic and biotic environments. Some current concepts on biophysical, biomechanical, and physiological bases of the structure, form, growth, distribution, and abundance of aquatic phototrophs. Bioindicators, biomonitoring and bioremediation.
The course introduces to conservation biology, a synthesis discipline that uses approaches and methods from disciplines such as ecology, population biology, population genetics, molecular biology, applied to the conservation of species, intended as dynamic entities capable to respond to environmental changes. Criteria and principles for the adoption of the different conservation strategies are presented and discussed. Moreover, the practical aspects of the various approaches are examined through the study and analysis of real cases, with particular reference to aspects linked to the research lines carried out and coordinated by the teacher. Topics covered during the course include: evolutionary genetics of natural populations, loss of genetic variability in small populations, inbreeding and decreased fitness, fragmentation of populations. Definition and maintenance of evolutionary potential. Population size (N and Ne) and its estimators. Resolution of taxonomic uncertainties, genetic management of threatened species, adaptation to captivity, planning of head-start interventions and captive-breeding. The IUCN classification; criteria for conservation: species richness, rare species, endemisms; hotspot analysis, gap analysis.
rokaryotic cell. Taxonomy and phylogeny of Prokaryotes; the main functional groups in the different evolutionary phyla. Nutritional types of microorganisms. Chemotaxis. Influence of environmental factors on microbial growth. Biofilms. The metabolism: energy release and conservation. The mechanisms of growth and adaptation to the environment. Microbial communities and spatial organization: felts, rugs, biofilms. Role of microorganisms within biogeochemical cycles of: carbon, nitrogen, sulfur, iron, phosphorus. Microorganisms in the different environmental compartments: atmosphere, hydrosphere
Evolutionary devices of Higher Plants (pollen, seed, flower, fruit); co-evolutionary phenomena of plants; secondary metabolites (classification, biological and ecological function); phytocomplex; concept of medicinal plant, nutraceutic and phytopharmarmacology; dmicroRNA; influence of plant diet and drugs on human life; plant genetics; nuclear, plastid and mitochondrial DNA; plant ancient DNA; archaeobotany; forensic botany; analytical methods in plant genetics (DNA extraction, PCR, qPCR, DNA barcoding, microsatellites, RAPDs, etc.); genetics of plant populations (sampling, selection of markers, measurements); agrobiodiversity; germplasm conservation; domestication, distribution and diffusion of Higher Plants; archaeobotany.
Introduction to biological evolution, outline of the main evolutionary theories, fundamental principles of evolution. Principles of biological systematics and species concepts. Biodiversity. The population as an evolutionary unit. Polymorphisms and geographical variation in populations. Hardy-Weinberg equilibrium and evolutionary factors: mutation, gene drift and population size, gene flow, inbreeding and assortative mating, natural selection and sexual selection. Analysis of microevolutionary processes and adaptive landscape. Habitat fragmentation and population genetic structure, Use of Wright F statistics. Reproductive isolation mechanisms between species and modes of speciation. Interspecific hybridization and gene introgression. Classification, phylogenesis and phylogenetic reconstructions. Phylogeography. Coevolution. Further topics covered through reading and discussion of recent scientific papers published in the most prestigious journals in the field.
Introduction: definition of Ecology; levels of organization (individuals, populations, communities, ecosystems, biomes, biosphere); observation and experimentation; Ecology in practice: sample case studies; why mathematical models play a role in Ecology? Ecosystem: definition of ecosystem; ecosystem features; energy fluxes in ecosystems; production and decomposition; primary production and its controlling factors in aquatic and terrestrial ecosystems; secondary production; trophic structure of ecosystems; Pyramids of energy, biomass and numbers; trophic networks; stability. Environmental factors and biogeochemical cycles: environmental factors and relationships between organisms and their environment; biogeochemical cycles: nitrogen, carbon, phosphorus, sulfur; water cycle; interactions between man and biogeochemical cycles (eutrophication, greenhouse effect, acid rains, etc.) Population dynamics: definition of population; unitary and modular organisms; spatial distribution (random, regular, aggregate); age classes distribution; natality, immigration, mortality, emigration; mortality tables; survival curves; iteroparous and semelparous species; exponential and logistic growth; r and K strategies; effects of interspecific competition on two or more populations; interspecific competition model; effects of predation; Lotka-Volterra model and its extensions. Biological communities: definition of community; open and closed community concepts; community structure: analysis of gradients and successions; succession types; intermediate disturbance hypothesis; historical evolution of the ecological niche concept; Hutchinsonian ecological niche; habitat and ecological niche; ecological niche description: breadth (fundamental and realized niches, niche breadth indices, optimization theory, etc.) and overlap (indices of overlap); trophic and functional groups, guilds, etc. Interspecific interactions: neutralism, competition, amensalism, predation, commensalisms, mutualism, etc.; cryptic mimicry, aposematic coloration, Batesian and Müllerian mimicry; other consumer or predator defense mechanisms; evolution of the biodiversity concept. Biosphere and biomes: biosphere definition and features; biome definition and features; changes in climate at different spatial scales; changes in time; species distribution; divergent, convergent and parallel evolution; biomes: tropical rain forest, savanna, temperate prairies, desert, deciduous temperate forest, coniferous boreal forest and tundra; aquatic environments (streams and rivers , ponds and swamps, lakes, coastal lagoons, seas and oceans, coasts and estuaries).
Main fossils in the human evolutionary lineage. Models for the origin of our species. Neutral theory and molecular clock. Human-Apes divergence. Uniparental and autosomal markers in studies of Molecular Anthropology. The origin of Paleogenetics. Genomic libraries and Paleogenomics. NGS techniques fo the study of ancient DNA (shotgun and enrichment). Port-mortem damage of ancient DNA. Illumina NGS sequencing. Genomes of Neanderthal, Denisova and ancient human populations. Peopling of Europe. Peopling of the Americas. Ancient DNA and animal domestication (cat, horse). Ancient metagenomics, basic principles and tools. Reconstruction of ancient oral microbiomes. Analysis of ancient pathogens.
The course is divided into 3 sections, covering the following topics. 1 ) fundamentals of cytogenetics and karyotype analysis (2 CFU): Structural and functional organization of the chromosome. Centromeres and neocentromeres ; secondary constrictions; telomeres. Mitosis, meiosis, segregation mechanisms and check points. Mechanisms of variability - I: Meiotic recombination. Chromosome pairing, crossing over and recombination nodules in the production of normal and variant karyotypes. Mitotic recombination. Pseudo-dominance and position effect. Causes and effects of genomic instability in the onset of cancer. Methods for karyotype analysis. Conventional and replication banding of chromosomes. High resolution banding of the karyotype ( Multicolor FISH , SKY, CGH). 2 ) Mutagenesis and fundaments of radiogenetics (2 CFU): Mechanisms of variability - II: Mutations. Spontaneous and induced DNA damage, repair mechanisms of DNA primary damage. Physical, chemical and biological mutagens. Induction of stable and unstable structural chromosomal aberrations; numerical variations. Mitotic and meiotic consequences; genetic and epigenetic effects . Extra-replication of the genome: amplification mechanisms and consequences. Compatibility of different karyotypic rearrangements with animal and plant survival. 3 ) Environmental mutagenesis testing and methodological approaches (2 CFU): Measuring mutation frequency and mutation rate. Detection levels of DNA induced damage: 1 ) the primary lesion (early effect: genotoxicity), 2) mutation induction (permanent effect: mutagenicity) . Cytogenetic tests for genotoxicity (Comet assay) and mutagenesis (chromosomal aberrations , micronucleus test) . Mutagenic potential of contaminated environmental compartments ( air, water, soil); test systems (cells / tissues and organisms) in vitro and in vivo exposure; plant and animal bioindicators; in situ and ex situ exposure. Carcinogenic effects.
Essential nutrients. Vitamins. Microelements and macrominerals. Essential fatty acids and amino acids. Carbohydrate, protein and lipid metabolism. Biochemical mechanisms of foods digestion and nutrient uptake. Water. Dietary fibres. Ethanol metabolism. Functional foods and nutraceuticals. Energetics and dysfunctions of energetic homeostasis (obesity, metabolic syndrome, fasting). Tissue and organ metabolism. Human evolution diet and nutrition: correlated evolution of the brain development in Homo sapiens. Dietary changes during human evolution: implication in metabolic syndromes. Examples of genome-nutrients interactions (nutrigenomics).
Basic knowledge about the innovations in the fisheries sciences The scope of the research Stocks and Stock assessment Management and conservation The role of the aquaculture Genetics and biotechnology in aquaculture Labeling systems Case studies
Introduction to the study of ancient biomolecules such as DNA and proteins. Chemical and physical diagnostic methods to determine the state of preservation of the skeletal remains. Palaeodiet determination using both the stable isotopes analysis that metagenomics and metaproteomics analysis of dental calculus. Stable isotopes data analysis by Bayesian mixing model software. Ancient DNA study in order to reconstruct the migratory events that have affected ancient populations, deepening the NGS techniques. Moreover, ancient DNA study to reconstruct the phenotype of our ancestors investigating also the evolution of several genes.
The Primates: Distinctive features of the primate order compared to other mammals. Biogeography of Primates. Main adaptations of the Primates. The systematics of primates: Strepsirrini; Aplorrini: Platirrine and Catarrine. Evolution and phylogeny of primates: the karyotype of primates; the biomolecular bases of differentiation in primate species; inheritance of morphometric characters Ecology of the Primates: mating patterns and reproductive strategies; territoriality and depredation; the eating habits of primates, activity patterns; social behaviour; intelligence in primates, inter-individual communication and the origin of language. Palaeoprimatology. Observation of the Primates present at the Rome Biopark
Introduction to exo/esobiology. Requirements for life as we know it, the importance of carbon and water. Prebiotic chemistry , molecular evolution and cellular life. Fossil records and the origin of life. Extremophiles and life beyond Earth. The terrestrial analogs of Mars. Space as extreme environment. Astrobiological experiments in low Earth orbit, Expose e Biopan. Lithopanspermia.
Program: Theoretical lessons. Introduction and basic concepts, definition of funerary archaeology, forensic taphonomy, taphonomic research; the decomposition process; transformative processes; inhumation and cremation; classification of the different burials (primary, secondary, single, double, multiple); multiple burials and depositional chronology; corpse concealment; the minimum number of individuals; decomposition in a void and in filled space; orientation of the corpse; post-depositional movements; the archaeological excavation and the anthropological perspective; labile and persistent anatomical connections; compression of the skeleton; alterations of skeletal remains, biotic and abiotic factors; the anthropological documentation; the removal of the skeletal remains; body farms; examples and case-study. Practical lessons. Identification of different typologies of burials and decomposition modalities; Analysis of labile and persistent anatomical connections and potential compression of the skeleton; alterations of skeletal remains; multiple burials, estimation of the minimum number of individuals; writing anthropological documentation; case study simulation. Recommended sources Lecture notes Duday, H. 2009. The Archaeology of the Dead: Lectures in Archaeothanatology. Oxford : Oxbow Books Minozzi, S., Canci, A. 2015. Archeologia dei resti umani. Dallo scavo al laboratorio. Roma: Carocci Editore. Komang Ralebitso-Senior, T. 2018. Forensic Ecogenomics: the application of microbial ecology analyses in forensic contexts. London, UK; San Diego, CA: Academic Press
Concept of plant material conservation; germplasm; recalcitrant, intermediate and orthodox seeds; molecular germination mechanisms; plant DNA; propagation of plant material; genetic typing techniques; reactivation of germination and in vitro cell growth; red lists; endangered species; population genetics of plant species; biodiversity and monocultures; genetic variability; cultivars and varieties.
Concepts and definitions in Ecotoxicology. Exposure, bioaccumulation, effects at different levels of living matter organization. Dose-response relationships, hormesis. Toxicity tests. Standard ecotoxicological tests: tests on Daphnia, Artemia and Vibrio, models of bioremediation with microbes (Pseudomonas sp.); rationale of the tests, laboratory tests, data processing.
