Optional group:
OPZIONALI - (show)
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12
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20401656 -
BIOGEOGRAPHY
(objectives)
The student must be able to interpret the distributional processes of living organisms at global and local scale, according to both ecollgical and historical (palaeogeographic-palaeoecological) view. Processes must be explained by dispersal/vicariance hypotheses, according to the most recent techniques.
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BOLOGNA MARCO ALBERTO
( syllabus)
(a) Introductive elements.
What is Biogeography: This Science which considers synthetically information from Geography, Palaeogeography, Geology, Ecology, Palaeoecology, Phylogenetic Systematics, Faunistic, Floristic, Population Genetics, Evolutionary Biology. Summary of principles of Evolutionary Biology (micro and macro-evolution), Systematics (Phenetist, Evolutionary and Cladistic schools), ecosystem and population Ecology. Speciation models, radiation. Natural and anthropic causes of extinction. Biogeography and Conservation of Nature.
Story of Biogeography: The founders of the Science: Buffon, de Candolle, von Humboldt, Lyell, Hooker, Sclater, Darwin, Wallace, Haeckel, Merriam, Simpson, Darlington, Holdaus, Gridelli, De Lattin, Furon, La Greca, Croizat, Wilson e MacArthur, Rozen e Platnick, Morrone, Avise, Hewitt.
Biogeographic schools of the XX century: Historical Biogeography, bridges, filters, dispersal and dispersion; Croizat and Panbiogeography; Cladistic Biogeography; Ecological Biogeography; Statistic Biogeography; Molecular Biogeography and Phylogeography. The Italian School of Biogeography: Gridelli, La Greca, Baccetti, Ruffo, Vigna Taglianti, Poldini; the Italian Society of Biogeography.
(b) Historical Biogeography
Land and marine Biogeography: History of life on the Earth: Tectonic of terrestrial plates and the Continental drift Theory; macro-plates and micro-plates; evolution and displacement of terrestrial masses and seas; evolution of terrestrial ecosystems. Climatic and biogeographic effects of plates tectonic. Effects of Pliocene-Pleistocene glaciations; Pleistocene glacial refugia; megafauna extinction; expansion and contraction of biomes. Effects of glaciations on lands and seas in temperate and tropical regions.
The terrestrial biogeographic regions: Floristic realms and Zoogeographic Regions. Causes of floras and faunas differentiation of Biogeographic regions. Regions and sub-regions. Marine Biogeographic Regions. Palaearctic Region (boundaries; sub-regions; distinctive elements). Nearctic Region (boundaries; sub-regions; distinctive elements). Oriental (Indo-Malayan) Region (boundaries; sub-regions; distinctive elements). Afrotropical Region (boundaries; sub-regions; distinctive elements). Neotropical Region (boundaries; sub-regions; distinctive elements). Australian-Oceanic (Australasian) Region (boundaries; sub-regions; distinctive elements)). Antarctic (boundaries; sub-regions; distinctive elements). Transitional Biogeographic Regions: Saharo-Sindian; Chinese; Indo-Australian (Wallacea); Meso-American. Regionalization of floras and faunas.
Biomes and Biogeographic Regions: Effects of climate and climatic cycles. Characteristics and geological origin in the Biogeographic regions. Effects of water circulation and of the sea depth on the marine regions. Biomes, and their distribution on the lands; dynamics of biomes. Marine biomes. Differences between biomes and biogeographic regions. Biomes and ecosystems. Anthropic transformation of biomes.
Biogeography of the Mediterranean area and the Europe: Tethys and Paratethys and Mediterranean origin. Shift, migration and positioning of microplates. Biogeography of Cenozoic: Messianian salinity crisis; Pliocene-Pleistocene effects of glaciations and refugia.
Range: specific and over-specific ranges; continuous, fragmented, disjunct ranges; historical and ecological causes of ranges; shape of ranges; terrestrial and marine ranges. Primary and Secondary ranges. Physical, ecological and palaeogeographic factors affecting limits of ranges: present barriers and limiting factors. Relicts. Endemism: ranges and conservation.
Generalized distributional models (chorotypes): examples in the Palaearctic and Afrotropical Regions. Examples of distribution of land plants and animals.
Dispersalist Biogeography (Simpson, Mayr). Dispersal and dispersion. Dispersion as biogeographic (range extension), evolutionary (genetic flow and speciation) and ecological process (niche realization). Overall similarity principles. Species-specific process and generalized models. Active and passive dispersal in plants and animals. Types of dispersal: jump dispersal, stepping stones dispersal. Dispersal and range enlargement. Barriers to dispersal (geographic and ecological). Colonization. Effects on biota due to immigrations.
Vicariance Biogeography. Vicariance (allopatric model; collapse of barrier model). Effects on biota. Cladistic Systematics and Vicariance Biogeography. Croizat’, Morrone’, Nelson’ and Platnick’ Vicariance models.
Distribution and abundance of populations. Variation of distribution and time. Range dynamic and conservation. Fossil and present ranges. Local and complete extinction.
Geographic variation in species (morphological and genetic characteristics). Continuous and discrete variation. Evolutionary and biogeographic importance of variation. Geographic variation and conservation. Geography of divergence and regionalization.
(c) Ecological Biogeography
Ecological Biogeography: present causes of species distribution; realized niche; colonization and competition. Distribution and dynamics of communities, ecosystems and biomes.
Island Biogeography: Wilson and Mac Arthur theory; experimental confirmation and problematic examples; Island Biogeography and Conservation Biology. Examples on geographic and ecological islands and on mountain peaks.
(d) New methods of biogeographic analysis
Molecular Biogeography. Phylogeography (mtDNA, nDNA, molecular and statistical methods). Examples on glacial refugia and postglacial spread.
Statistical Biogeography. Analysis of molecular data in Biogeography; dating; direction of dispersal; time of vicariance.
Cartographic representation of the biogeographic diversity: traditional cartography, areograms, georeferenced databases, GIS and remote-sensing systems. Mapping the ranges.
( reference books)
Lomolino M.V., Riddle B.R. & Whittaker R.J., Biogeography. Biological Diversity across Space and Time. Sinauer, Sunderland, USA.
Also useful: Zunino M. & Zullini A., Biogeografia. La dimensione spaziale dell’evoluzione. Ambrosiana, Milano.
The teacher supplies students with specialist literature and additional material.
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6
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BIO/05
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40
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10
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20410278 -
MICROBIOLOGIA AMBIENTALE
(objectives)
1. acquire knowledge of the fundamental role of microorganisms in ecosystems and of the factors affecting their distribution and interactions with other organisms:
- metabolic and functional biodiversity, structure and dynamics of microbial communities
- bacteria and archea taxonomic groups
2. knowledge of traditional, molecular and cultivation-independent methods for identification/typing and analysis of microbial populations
3. evaluation of the multiple potential applications of environmental microorganisms also as bioindicators
4. acquisition of critical skills by reading scientific articles.
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VISAGGIO DANIELA
( syllabus)
1. Evolution and systematics of microorganisms: origin of bacteria; molecular phylogeny; 16S rRNA gene and evolution; fundamentals of systematics of microorganisms
2. Metabolic diversity in microorganisms: chemolithotrophy; fermentations; anaerobia; phototrophy
3. Functional diversity of microorganisms: phototrophic and chemotrophic bacteria
4. Study methods in microbial ecology: a) cultivation methods; b) methods independent of cultivation: microscopy, genetic analysis; metagenomics
5. Microbial ecosystems: a) principles of ecology; b) Microbial interactions (Quorum sensing; Biofilm);
c) Terrestrial environment (the soil); d) Aquatic environments (sea); c) Extreme environments (abysses; hydrothermal springs)
6. Microbial role in nutrient cycles: carbon, nitrogen, sulfur; others
7. Symbiosis between microorganisms and between microorganisms and different organisms such as a) plants, b) mammals, c) man; d) insects; e) aquatic invertebrates
8. Microorganisms in anthropized environments: bioremediation of contaminated sites; water treatment; biocorrosion; recovery of minerals from mines
( reference books)
Brock. Biologia dei microrganismi
Microbiologia generale, ambientale e industriale • 14/Ed. • Con MyLab
Michael T. Madigan - John M. Martinko - David A. Stahl - Kelly S. Bender - Daniel H. Buckley
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6
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BIO/19
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40
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10
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20410259 -
ENTOMOLOGIA
(objectives)
The main formative targets are:
1) the acquisition of a basic knowledge on morphology, anatomy, physiology and evolution of the main insect groups.
2) the acquisition of both theoretical and practical knowledge on systematics and classification of the hexapoda.
3) the construction of a solid cultural background for an advanced discussion on causes and effects of the amazing evolutionary success and diversity of insects and on their importance in basic and applied studies.
4) the acquisition of the tools for the insect taxonomic identification, expecially for those orders and families present in the italian fauna.
5) to stimulate the curiosity and the ability of critically observe the nature.
6) the self-evaluation by the student of the competence whitin the animal biology, and in particular in the entomology.
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6
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BIO/05
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40
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ITA |
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20410295 -
ETNOBOTANICA ED ETNOZOOLOGIA
(objectives)
The relationship between humans and the environment: ethnobotany to ethnoecology.
Methods used in ethnobiology. Uses of wild plants (medicinal, food, handicrafts, cosmetics).
Ethnobotany and its possible applications (e.g., education, urban home-gardens, tourism, food sector, herbalism, pharmacognosy).
Ethnobiology in various geographical and cultural contexts and relationships with anthropology.
The contribution of ethnozoology to zoology and biogeography. Folk taxonomy and its relationship with the scientific taxonomy.
Traditional and Local Ecological Knowledge.
Overview of subsistence strategies of indigenous communities (hunter-gatherers, farmers, pastoralists).
The role of ethnobiology in environmental conservation and restoration.
Concepts of adaptation, resilience, vulnerability and tipping points in Social-Ecological Systems.
An analysis of the tragedy of the commons in social-ecological systems (e.g., unregulated fishing and hunting, threatened species).
Traditional management systems of Common resource systems.
Ethnobiology and Ecosystem Services
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SAVO VALENTINA
( syllabus)
The relationship between humans and the environment: ethnobotany to ethnoecology. Methods used in ethnobiology. Uses of wild plants (medicinal, food, handicrafts, cosmetics). Ethnobotany and its possible applications (e.g., education, urban home-gardens, tourism, food sector, herbalism, pharmacognosy). Ethnobiology in various geographical and cultural contexts and relationships with anthropology. The contribution of ethnozoology to zoology and biogeography. Folk taxonomy and its relationship with the scientific taxonomy. Traditional and Local Ecological Knowledge. Overview of subsistence strategies of indigenous communities (hunter-gatherers, farmers, pastoralists). The role of ethnobiology in environmental conservation and restoration. Concepts of adaptation, resilience, vulnerability and tipping points in Social-Ecological Systems. An analysis of the tragedy of the commons in social-ecological systems (e.g., unregulated fishing and hunting, threatened species). Traditional management systems of Common resource systems. Ethnobiology and Ecosystem Services.
( reference books)
Caneva G., Pieroni A., Guarrera P.M. (eds) 2013. Etnobotanica: Conservazione di un patrimonio culturale immateriale come risorsa per uno sviluppo sostenibile nel bacino del Mediterraneo. Edipuglia Bari.
Office Hours: every day of the week by appointment by email: valentina.savo@uniroma3.it
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BIO/03
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40
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Attività formative affini ed integrative
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| 1
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BIO/05
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10
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Attività formative affini ed integrative
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ITA |
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20401676 -
FRESH WATER ECOLOGY
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I modulo
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3
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BIO/07
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20
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II modulo
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3
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BIO/07
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20
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20410597 -
Methods and techniques of education and naturalistic and environmental dissemination
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20410597-1 -
Primo modulo
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3
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BIO/07
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20
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5
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20410597-2 -
Secondo modulo
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3
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BIO/07
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20
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5
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20402025 -
Bioindication and Environmental Monitoring
(objectives)
Knowing the importance of the bioindication and the use of plants and animals as bioindicators for monitoring environmental quality status (water, air, soil).
Have a thorough knowledge of the instrumental methods, acquisition methodology, data analysis in the field of bioindication and ecosystem monitoring.
Acquire the knowledge for using the modern systems of bioindication, biomonitoring and bioremediation.
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CESCHIN SIMONA
( syllabus)
The Bioindication: basic concepts. Main ecological characteristics of a biological indicator. Two ways for bioindicating: react and bioaccumulate. The homeostasis of the bioindicators. Time and ecological relationship of the bioindicator responses to environmental changes. The meaning of disturbance, stress and stressor. Analysis of the main environmental stressors (chemico-physical pollution, biological pollution by alien species, anthropogenic impact) and of the relative biological responses. Bioindication in different levels of biological organization (Biomarkers and Bioindicators). Assessment of the plant and animal community status and evaluation and monitoring of the environmental quality and ecosystem integrity. Bioindication and environmental monitoring in aquatic, terrestrial and aerial environment. Examples of application of the standardized and experimental bioindication and biomonitoring techniques (from Ecotoxicological essays to phyotoremediation of contaminated matrices). Bioindication and environmental monitoring. Evaluation and monitoring of the environmental quality by Ecological and Biotic Indices. Bioindication and Environmental monitoring in Italy. International and national Agencies, Authorities, Institutions for environmental monitoring.
( reference books)
Pdfs of the lessons performed during the course.
Studying in the book: Bioindicatori ambientali, 1998, edited by F. Sartori, Graphic Arts Juri Iodice, Sannazzaro (PV).
The teacher receives Mon, Wed, Fri from 9.00 to 10.00 by appointment via email: simona.ceschin@uniroma3.it
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6
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BIO/02
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40
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5
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20402508 -
NATURAL PRODUCTS AND ENVIRONMENTAL CHEMISTRY
(objectives)
The course aims at giving:
1) a general knowledge of the biosynthetic pathways of secondary metabolism;
2) information about the main natural products derived from microorganism, plants and animals and their role in natural environment;
3) knowledge on the structure/biological activity relationship of the main secondary metabolites used in pharmaceutical and healthcare industry.
4) attainment of the basic educational background necessary to understand the chemical equilibria that regulate the origins, the transport, the transformations and the effects of the environmental chemical species, either of natural or human origin.
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TOFANI DANIELA
( syllabus)
Introductory notes on the chemistry of natural substances. Characteristics of secondary metabolites. Allelopatic substances. The biosintetic ways of secondary metabolism.
Metabolism of acetate. Prostaglandins. Aromatic polychetides. Anthraquinones. Cannabinoids. Aflatoxins. Tetracycline.
The metabolism of shikimato. Biogenesis of shikimato. Cinnamic acids. Lignins. Fenilpropani. Benzoic acids. Coumarins. Flavonoids. Tannins. Isoflavones. Terpenoid chinons.
The metabolism of the mevalonate. Biogenesis of mevalonic acid. The various types of terpens and derived compounds. Iridoids. Gibberellins. Structural characteristics of animal steroids. Phytosterols.
Alcaloids: definition, original amino acids and nomenclature. Biosynthesis and activities of the main types of alcaloids: cocaine, nicotine, curari, morphine, loganin, lysergic acid, coniine.
Notes on carbohydrates. Cianogenic glucosides. Streptomycin.
Secondary metabolites of peptidic origin. Interferons. Opious peptides. Peptidic toxins: ricina and botulino. Penicillins.
Basic principles of environmental chemistry. Interactions between the various spheres in which the terrestrial environment is divided.
The atmosphere: notes on training and depositing of the ozone (buco dell'ozono); effect of cfc and halon. Notes on oxidizing and polluting species and their monitoring. The particulate: ipa and phthalates. The serra effect: main gas-greenhouse and their gwp. The kyoto protocol.
The hydrosphere. Chemical-physical properties of water and water bodies. TIC, TOC, TC. Biodegradable organic pollutants (COD, BOD5), of difficult oxidation and toxic (LD50 and LOD50).
Bioaccumulation and biomagnification. Metabolism of some pesticides.
( reference books)
P.M. Dewick : Medicinal Natural Products, Wiley
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6
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CHIM/06
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44
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5
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20410301 -
ECOLOGIA E GESTIONE DEGLI ECOSISTEMI COSTIERI
(objectives)
Major goals of this course are: the training in the ecology of coastal ecosystems and the achievement of solid skills in this sector, the understanding of its relationship with other ecological disciplines (animal ecology, plant ecology) and the strengthening of the knowledge acquired previously (botany, zoology, ecology).
This course aims to analyze the wide biodiversity of coastal ecosystems, at national and European level and the major threats. Furthermore, the acquisition of a broad skills in the methodologies and techniques related to the collection, both in the laboratory and in the field, of biological and environmental data.
Finally, the course aims to develop the comprehensive training necessary for the analysis and management of coastal ecosystems addressed to their protection, conservation and enhancement, both in natural contexts or heavily modified by man.
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BIO/03
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16
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Attività formative affini ed integrative
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| 2
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BIO/05
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16
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Attività formative affini ed integrative
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ITA |
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20410208 -
Biologia marina
(objectives)
The course is one of the optional training activities of the Master’s Degree in “Biodiversity and management of Ecosystems” and allows students to acquire a basic knowledge of Marine Biology and of the marine environment conservation, with a specific attention given to the Mediterranean Sea.
Educational objectives of the course are:
1) to acquire basic skills of Oceanography, related to the physico-chemical factors and the movement of the sea;
2) to acquire basic skills related to the biology and adaptations of marine organisms, as well as the most important Mediterranean species and habitats of conservation interest and Mediterranean biogeography;
3) to improve knowledge about monitoring and data collection techniques in the marine environment;
4) to acquire the concepts and skills related to the critical issues existing in the Mediterranean Sea, and the tools availablefor its management and protection.
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SCALICI MASSIMILIANO
( syllabus)
1) INTRODUCTORY LIMNOLOGY: PHYSICAL-CHEMICAL PROPERTIES OF WATER (TEMPERATURE-DENSITY, TRANSPARENCY, SALT COMPOSITION, SALINITY, CONDUCTIVITY, HARDNESS); WATER BODY THERMAL BALANCE; AQUATIC MOVEMENTS (CURRENTS, TIDE, SEICHE); DISSOLVED OXYGEN AND REGULATING FACTORS; CARBON DIOXIDE, BICARBONATE, CARBONATE, BUFFER SYSTEM, MINERAL ACIDITY AND ALKALINITY; NUTRIENT CYCLES; ORGANIC MATTER, TOTAL SOLIDS, SUSPENDED MATERIAL, SEDIMENTS, BOD AND COD.
2) AQUATIC LIFE: PLANCTON, NECTON E BENTHOS; CLASSIFICATION, METABOLISM AND LIFE CYCLES, COLLECTION METHODS AND TOOLS, ABUNDANCE AND BIOMASS ASSESSMENT; WATER COLUMN AND SEDIMENT ECOLOGY: PRIMARY PRODUCTION, SCRAPERS, SHREDDERS, AND SCAVENGERS: ENERGETIC FLOW IN FOOD PYRAMIDS AND WEBS; EXAMPLES OF SEA AND COASTAL AREAS
( reference books)
Cognetti G., Sarà M., Magazzù G. - Biologia Marina. Edizioni Calderini, Roma, 1999. 596 pagine.
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6
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BIO/07
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40
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20410492 -
Tecniche di campionamento zoologico
(objectives)
The course aims at providing the theoretical and practical basis for data collection aimed at carrying out zoological research.
- The student will learn the criteria for choosing the model and sampling techniques most suitable for:
(i) the selected animal group (invertebrate, vertebrate, aquatic, terrestrial, flier etc.),
(ii) the type of research to be carried out on it (ecological, taxonomic, phylogenetic , anatomical, etc.),
(iii) the biology and ecology of the study species and populations (e.g. behaviour, spatial structure, biological cycle),
(iv) the evaluation of the number of sample units,
(v) the context of the sampling effort,
(vi) the spatial and temporal pattern of sampling.
- Through simulations in the laboratory and in the field, the student will learn the techniques for sampling the main Metazoan taxonomic groups, based on direct and indirect samplings, qualitative and quantitative collections, capture-marking-recapture methods, radiotrekking, traps (with or without attractants , photo-traps, light traps, pheromones, etc.)
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6
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BIO/05
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32
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20410207 -
Biochimica della nutrizione
(objectives)
The Nutrition Biochemistry course is aimed at providing to the students the basic knowledge to understand the molecular mechanisms by which the human organism uses macro- and micro-nutrients to produce the energy needed to maintain the order which characterizes every living being.
In particular, the objectives of the course are the comprehension of the pathways through which the different groups of nutrients (carbohydrates, lipids, proteins, vitamins and minerals) and other substances of natural and non-natural origin (ethanol, stimulant beverages, xenobiotics) are assimilated and transformed in the human body, and how they influence its metabolic status.
Finally, one of the aims is also that of illustrating the production of reactive oxygen species linked to metabolism and the protective role exerted by antioxidant compounds of dietary origin.
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Derived from
20410207 Biochimica della nutrizione in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 POLTICELLI FABIO
( syllabus)
- General overview of the plastic and energetic function of nutrients
- Uptake and usage of
- Vitamins
- Carbohydrates
- Lipids
- Amino acids and proteins
- Metabolism of the main alcoholic and psychoactive drinks of nutritional value
- Signal transduction and regulation of metabolic pathways
- Metabolic regulation of the nutrition-fasting cycle
- Reactive oxygen species
- Endogenous and exogenous antioxidants
- Xenobiotics
( reference books)
- Leuzzi, Bellocco, Barreca “Biochimica della Nutrizione” Ed. Zanichelli
- Arienti "Le basi molecolari della nutrizione"
- Cozzani, Dainese "Biochimica degli alimenti e della nutrizione" Ed. Piccin.
- General Biochemistry textbooks adopted for the Biochemistry Course of the bachelor degree in Biological Sciences.
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6
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BIO/10
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48
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20401653 -
BIOCHEMISTRY AND MOLECULAR CLINICAL BIOLOGY
(objectives)
Main goals of the course are:
i) to provide an overview of the activities of a clinical laboratory looking at the organizational context and current business;
ii) to illustrate the various stages which are at the basis of main analytical methods, either molecular or biochemical, used in biomedical laboratories for modern diagnostic purposes;
iii) to provide the key of interpretation for the obtained results from a pathophysiological point of view. to promote a critical approach towards laboratory diagnosis.
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6
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BIO/12
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48
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20410600 -
Methods for studying the functioning of proteins and enzymes
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20410486 -
Laboratorio di neurobiologia cellulare
(objectives)
The aims of this course are:
1) to gain knowledge of the specialized cellular architecture of glia and neurons;
2) to deepen the knowledge of cellular and molecular mechanisms involved in cell communication between glia and neurons.
Special emphasis will be given to nitric oxide-regulated pathways. in this course students can use state of the art equipment and learn current techniques employed in cell biology research labs.
Moreover students are allowed to critically discuss the scientific literature in the field of neurobiology.
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Derived from
20410486 Laboratorio di neurobiologia cellulare in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 PERSICHINI TIZIANA
( syllabus)
Cultural knowledge: The aims of this course are: to gain knowledge of the specialized cellular architecture of glia and neurons; to deepen the knowledge of cellular and molecular mechanisms involved in cell communication between glia and neurons. Special emphasis will be given to nitric oxide-regulated pathways. In this course students can use state of the art equipment and learn current techniques employed in cell biology research labs. Moreover students are allowed to critically discuss the scientific literature in the field of glial cell biology.
Methodological skills: to know how to design an experiment using glial cell cultures, to acquire and analyze the data obtained from the laboratory activity.
Topics:
The course will deepen the following topics: morphology and ultrastructure of glial cells; Properties and functions of astrocytes; homeostasis of pH, K and volume; The neuro-glial-vascular unit, mechanism of cerebral blood flow regulation; gliotransmitters release and the tripartite synapse; The role of nitric oxide as neurotransmitter and neurotoxic factor; Microglia: activation, motility and immune surveillance; Reactive astrocytosis, neurodegenerative and infectious diseases. Cellular response to oxidative stress. The laboratory activity will be mainly devoted to the study of nitric oxide as cellular messenger in glial cell cultures. Experimental procedures include but are not limited to the following: Preparation of whole, cytoplasmic and nuclear extracts, Western Blot; Analysis of gene expression and transcription factor activation (RNA extraction, RT-PCR, EMSA, TransAM-ELISA); Modulation of gene expression (Oligo-Decoy); Cell Transfection; Analysis of nitric oxide (NO) pathway and determination of NO in living cells and in cell extracts.
( reference books)
BRUCE R. RANSOM, HELMUT KETTENMANN. “NEUROGLIA”
– THIRD EDITION – 2012 OXFORD UNIVERSITY PRESS
Slides in PDF format of all the lectures will be provided by the teacher.
The teacher receives the students at least once a week by appointment via e-mail: tiziana.persichini@uniroma3.it
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6
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BIO/06
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32
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20
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20402204 -
BIO-ORGANIC CHEMISTRY
(objectives)
The course will address the chemical transformations shared by organic chemistry and biological systems. Indeed, although the functional group elaborations are formally the same, the followed reaction pathways result to be quite different with respect to the experimental conditions of both organic syntheses and biological processes.
In such a context, the enzymatic action modes in living systems will be compared with the key role performed by temperature, pressure, ph, catalysts and solvents.
Keeping this in mind, a few of the most well-known chemical reaction mechanisms will be studied, underlining, step by step, the main similarities and distinctions with the analogous biological transformations.
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Derived from
20402204 CHIMICA BIOORGANICA in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 N0 GASPERI TECLA
( syllabus)
Cultural skills (Knowledge of): The course aims to provide students with the chemical basis of the structure, the properties, and the reactivity of biological molecules, as well as the main notions for understanding the logic that regulates bio-organic chemistry processes.
Methodological skills (How to carry out): at the end of the course, the student will be able to analyze and discuss the catalytic mechanism of the most important classes of enzymes, as well as to understand the importance of the organic chemistry applied to the study of biological systems, to biocatalysis, and to the development of biologically active molecules.
Introduction to Bio-organic Chemistry (A short overview of the most common functional groups involved in biological processes, highlighting their main features).
Organic chemistry mechanisms to explain key steps in pivotal biological pathways:
• Electrophilic Addition Reactions:
regioselective epoxidation of alkenes; the action of squalene epoxidase in squalene/lanosterol transformation.
• Nucleophilic Substitution Reactions
bimolecular Nucleophilic Substitution Reaction (SN2): the S-adenosylmethionine (SAM) role in the methyltransferase-catalyzed reactions;
carbocation chemistry in the nucleophilic substitution reaction (SN1): the IPP isomerase.
• Elimination reactions:
β-elimination reaction and the enolase role in the synthesis of the phosphoenolpyruvate (PEP).
• Nucleophilic Carbonyl Addition Reactions
imine and enamine formation; how Schiff bases act in the PLP-dependent enzymatic catalysis;
acetals and sucrose synthase;
Michael additions and the histidine ammonia-lyase function.
• Isomerization and epimerization:
keto-enol tautomerism and ribose-5-phosphate isomerase catalysis;
Inversion and retention of the stereochemical configuration: the glucosidase mechanism.
• Carbonyl condensation reactions:
aldol condensation promoted by aldolases (classes I and II)
Claisen condensation and the acetyl synthase function in the fatty acids synthesis.
• Acyl Nucleophilic Substitutions:
the hydrolysis of esters and the mechanism of Human Pancreatic Lipase;
esterification reactions and the synthesis of triacylglycerols by means of acyl-CoA synthetase and acyltransferase;
amide bond formation; asparagine synthetase vs glutamine synthetase;
the hydrolysis of amides and the chymotrypsin action mode.
• Oxidations and reductions
metal hydride and the reduction of the ketone carbonyl group in acetoacetyl ACP due to the β-keto thioester reductase;
Baeyer-Villinger oxidation and the hydroxyacetophenone monooxygenase;
ozonolysis reactions and dioxygenase enzyme activity.
• Carboxylation reactions:
Grignard reactions in CO2 atmosphere; mechanisms of both the pyruvate carboxylase and Ribulose-1,5-bisphosphate carboxylase oxygenase (RuBiscO);
the decarboxylation reaction in both malonic and acetoacetic synthesis; the key role of thiamine pyrophosphate (TPP) in the 1-deoxy-D-xylulose 5-phosphate synthase catalysis.
• Noteworthy examples: pyruvate dehydrogenase complex, the kynurenine catalysis and the tryptophan metabolism; anomalous features in histidine metabolism.
( reference books)
Libri di testo:
John McMurry, Tadhg Begley in “Chimica Bio-Organica”, Zanichelli Ed. spa
T.W. Graham Solomons; Craig B. Fryhle in “Organic Chemistry”, 10th Edition, Wiley.
John McMurry in “Chimica Organica”, Piccin-Nuova Libreria
Bruno Botta in “Chimica Organica” Edi-ermes
Lecture notes and bibliographical references will be provided
The teacher receives Tuesday from 17.00 to 19.00 by appointment via e-mail: tecla.gasperi@uniroma3.it
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6
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CHIM/06
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48
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20410599 -
Molecular genetics
(objectives)
The course aim to provide a wider and deeper outlook of genetics topics not addressed in the course of genetics.
Special attention will be paied to the role of human genome (and epigenome) in the regulation of complex biological processes and in the individual response to endogenous and exogenous factors.
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Derived from
20410599 Genetica molecolare in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 BERARDINELLI FRANCESCO
( syllabus)
- GENOME (ORGANIZATION, STRUCTURAL GENOMICS, COMPARATIVE GENOMICS AND FUNCTUNIAL GENOMICS). EPIGENOME (METHYLATION, HISTONE CODE, CHROMATIN 3D ARCHITECTURE, NON-CODING RNA). EXAMPLES OF EPIGENETIC REGULATION: CELL DIFFERENTIATION AND GENETIC MECHANISMS OF SEX DETERMINATION (HOW DOES SEX IS GENETICALLY DETERMINED, INACTIVATION OF X CHROMOSOME, SEX-DEPENDENT PHONOTYPIC EFFECTS).
- CELL CYCLE REGULATION, SENESCENCE AND APOPTOSIS. GENETIC OF AGING (GENETIC THEORIES OF AGING, GERONTOGENES AND GENES INVOLVED IN LONGEVITY, AGING IN ANIMAL MODELS, MOLECULAR AND CELLULAR AGING). CANCER GENETICS (ONCOGENES, ONCO-SUPPRESSOR GENES, CHROMOSOMAL REARRANGEMENTS INVOLVED IN CANCER, THE CANCER STEM CELLS THEORY). INDIVIDUAL GENETIC RESPONSE AND PHARMACOGENETICS.
( reference books)
- HUMAN MOLECULAR GENETICS, Tom Strachan, Andrew Read, Zanichelli
- Scientific articles and teaching material provided by the teacher
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6
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BIO/18
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40
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10
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20401777 -
PUBLIC HEALTH
(objectives)
General objectives
at the end of the course, the student will be able to design epidemiological studies to address public health problems and to identify activities to prevent chronic and infectious diseases.
Specific objectives:
-to know the major mortality and morbidity indicators
-to identify the epidemiological study more appropriate to describe the burden of major diseases in the population and to assess the relation between diseases and possible -risk factors associated to them
-to interpret epidemiological data
-to discuss the importance of the health education and of the health promotion
-to list and discuss problems related to water supply, sanitation and waste management
-to argue about necessary controls/monitoring to protect the environment and the community
-to design health promotion programmes.
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6
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MED/42
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48
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20401821 -
IMMUNOLOGY
(objectives)
Cellular and molecular mechanisms involved in the immune response with a particular interest for those implicated in the response against pathogens.
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6
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MED/04
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48
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20410270 -
LABORATORIO DI BIOTECNOLOGIE DEI MICRORGANISMI
(objectives)
The main educational goals of the course are:
1) acquisition of knowledge on advanced methodologies in microbial biotechnology;
2) acquisition of appropriate methodologies and communication skills for the isolation, observation, description and engineering of industrial microorganisms;
3) acquisition of applied knowledge for drafting and executing experimental protocols;
4) acquisition of knowledge and skills for retrieving relevant scientific literature from on-line databases and for critically reviewing it.
The expected learning outcomes are the increase of the student theoretical knowledge in the field of microbial biotechnology, of its practical skills for the design and execution of laboratory experiments, and of its critical ability to search and evaluate scientific literature data.
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Derived from
20410270 LABORATORIO DI BIOTECNOLOGIE DEI MICRORGANISMI in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 RAMPIONI GIORDANO
( syllabus)
The course aims at providing to the student:
- adequate knowledge and understanding on advanced methodologies in microbial biotechnology, appropriate methodologies and communication skills for the isolation, observation, description and engineering of industrial microorganisms;
- adequate applied knowledge for drafting and executing experimental protocols, and for retrieving and critically reviewing relevant scientific literature from on-line databases (making judgements).
Programme
During the laboratory practices and the corresponding theoretic lessons, the following topics will be covered:
- isolation of microorganisms of industrial relevance from the environment, preparation of growth media and cultivation techniques;
- transposon–based mutagenesis (generation and screening of mutant libraries);
- genetic transfer processes (conjugation and transformation);
- use of whole-cell bacterial biosensors for gauging specific molecules produced by other microorganisms.
The following topics will be covered in additional theoretic lessons:
- development of innovative therapeutic strategies based on biotechnological processes;
- development of biosensors and reporter systems for the identification of new drugs;
- application of synthetic biology to microbial biotechnology;
- properties of the regulatory networks and their application to biotechnological processes.
( reference books)
Selected topics will be available on suggested Microbiology and Microbial Biotechnology books, as indicated in the following reference list. Specific research papers and experimental protocols will be provided during theoretic lessons on advanced research topics and laboratory practices.
Innovative teaching will be promoted by cloud-sharing of power-point presentations illustrating the main topics of the course. Moreover, students will be encouraged to make use of web-based resources and databases to autonomously increase their knowledge on specific advanced topics.
Students will be received at the best of their convenience if an appointment has been fixed at the end of the lessons or by email.
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6
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CHIM/11
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28
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25
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20410212 -
Genetica umana applicata
(objectives)
1. To consolidate knowledge in Human Genetics acquired during previous basic courses, with particular reference to biological mechanisms involved in genetic diseases
2. To carry on theorical notions on a practical point of view by the knoledge of diagnostic laboratory methods and strategies.
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6
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BIO/18
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48
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20410213 -
Nutrienti di origine vegetale
(objectives)
The course "Nutrients of plant origin" is part of the Plant Physiology training activities of the Master of Science in Biology for Molecular, Cellular and Patho-physiological Research. This course provides basic knowledge relating to the qualitative and quantitative composition and nutritional properties of plant-based foods and their derived processed counterparts. In particular, the course provides 1) an overview of the plants used for human nutrition and their use for the preparation of food products, with an outline of the influence of processing processes on the nutritional properties; 2) an in-depth picture of the main nutrients, aromas and other substances useful for human nutrition present in food of plant origin; 3) a summary of the anti-nutritional factors, allergens and toxic compounds present in some foods of plant origin.
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Derived from
20410213 Nutrienti di origine vegetale in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 CONA ALESSANDRA
( syllabus)
Climate change and food security. Plant varieties and phenotypic plasticity. Effect of environmental conditions on primary and secondary metabolism: food quality and production of aromas, flavors and toxins. Origin of agriculture and plant domestication. Characteristics of the main crops: Poaceae, Fabaceae, Rosaceae, Solanaceae, Brassicaceae. Domestication of Triticum turgidum var. dicoccum, Triticum turgidum var. durum e Triticum. Aestivum. Plant genetic improvement and “the green revolution”. Plant biotechnology for the development of crop plants resistant to environmental stress and/or herbicides and with high nutritional value. Primary and secondary metabolism. Secondary metabolism: terpenes, phenols, alkaloids, cyanogenic glycosides, glucosinolates, non-protein amino acids. Nutritional properties of secondary metabolites: metabolites with toxic effects and metabolites with positive effects on human health. Aromatic plants, spice plants and nervine plants (tea, coffee, cocoa). Natural dyes in food. Bioactive metabolites as food supplements. Primary metabolism: nutritional values of the different plant organs and nutrients bioavailability. Nutrients from plants: carbohydrates (sucrose and starch from different sources), soluble and insoluble dietary fibers, lipids and oils (olive oil and seed oil), proteins, minerals, vitamins and antioxidants. Effects of storage conditions and pre- and post-harvest diseases on nutritional quality of plant foods. Allergy and intolerances caused by plant substances present in crop species.
( reference books)
1) Piante alimentari. Biologia, composizione chimica, utilizzazione. Rinallo C.; Piccin.
2) Biologia delle Piante. Vol 2: Interazioni con l’ambiente e Domesticazione. Smith A. M. et al.; Zanichelli.
3) La chimica e gli alimenti. Nutrienti e aspetti nutraceutici. Luisa Mannina, Maria Daglia, Alberto Ritieni; CEA.
4) Alimentazione, Nutrizione e Salute. Lucantonio Debellis, Alessandro Poli; Edises.
5) Articoli scientifici e lezioni in power point fornite dal docente
The professor receives every day by appointment via e-mail: alessandra.cona@uniroma3.it
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6
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BIO/04
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40
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10
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20410214 -
Nutrigenomica
(objectives)
The course will deal with diet-genome interactions and the application of nutritional strategies in health maintenance.
Students should become familiar with the concept that external molecules present in our foods can affect human metabolism and gene expression in different cells and tissues. The course will address the utilization of the concept of “system biology” to nutrition.
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6
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BIO/11
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48
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20402377 -
GENERAL PATHOLOGY
(objectives)
The aims of the course are:
• know the aetiology and the molecular mechanisms of the human diseases;
• know how to interpret the pathophysiological mechanisms of the human diseases.
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6
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MED/04
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48
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20410491 -
Fisiologia della risposta cellulare allo stress
(objectives)
The primary objective of the course is to enlarge and update student’s knowledge about the physiology and regulation of cellular functions mainly regarding the molecular mechanisms activated by cells in response to stressing conditions to maintain intracellular homeostasis.
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Derived from
20410491 Fisiologia della risposta cellulare allo stress in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 FIOCCHETTI MARCO
( syllabus)
Introduction to the molecular mechanisms of cellular functions regulation: membrane and nuclear receptors, mechanisms of intracellular signal transduction and amplification through protein’s post-translational modifications (e.g. phosphorylation).
Definition of cellular stress and physiological tolerance range. Description of intracellular mechanisms, at DNA, RNA and protein levels, through which cells sense and respond to a broad variety of stressing conditions, focusing the attention mainly on physiological response and cell adaptation to extracellular stressing stimuli, including heat, osmotic, hypoxic, oxidative and nutrient stresses.
Evaluation of intracellular organelles- specific stress response, including mitochondria- and ER-stress response.
Description of down-stream molecular mechanisms activated by cells in response to stress and devote to re-establish the intracellular homeostasis and to adapt themselves to the changed conditions. Brief description of the abnormal stress response and adaptation in pathological cell degeneration (e.g. cancer).
Definition and update of the state-of-art about the laboratory research approaches applied to the study of the physiological stress response and adaptation and the molecular mechanisms behind these functions.
( reference books)
All the study/research materials and PDF files of lessons are available at the Course's Moodle Web site:
https://scienze.el.uniroma3.it/course/view.php?id=20
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6
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BIO/09
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48
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20402518 -
TOXICOLOGY
(objectives)
The course aims to provide students with fundamental knowledge on the basic principles of toxicology. In particular, the toxicodynamic and toxicokinetic mechanisms that are behind the toxic effects produced by different natural and synthesized xenobiotics, and the process of evaluation of toxicological risks will be analyzed. This knowledge will allow students to acquire specific professional skills useful in experimental and analytical research laboratories and to carry out professional activities in the pharmaco-toxicological field to protect the safety of the environment, food, cosmetic products and drugs, of both synthetic and natural origin.
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6
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BIO/14
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48
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20410321 -
VIROLOGIA ANIMALE GENERALE ED APPLICATA
(objectives)
Deepening the knowledge about animal viruses (origins, classification, replicative strategies, virulence, immunoevasion mechanisms) and their applications (antiviral vaccines, viral vectors for gene expression, oncolytic viruses).
-
Derived from
20410321 VIROLOGIA ANIMALE GENERALE ED APPLICATA in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 AFFABRIS ELISABETTA
( syllabus)
The course describes and compares the replication cycles of different animal viruses that infect vertebrate hosts to gain insight into: origin of viruses, structure, evolution, virus-cell interactions, host defense mechanisms and strategies of viral immunoevasion, methods of detection, identification and titration, antiviral drugs and profilaxis of viral infections. In particular, it will be described viruses of the following viral families: Parvoviridae, Poliomaviridae, Papillomaviridae, Adenoviridae, Herpesviridae, Poxviridae, Picornaviridae, Flaviviridae, Coronaviridae, Ortomixoviridae, Rabdoviridae, Retroviridae, Hepadnaviridae. In addition, introduction to applied virology will be provided (i.e., vaccine development, viral vectors and oncolytic viruses). Students will be able to apply the acquired knowledge to understand in-depth texts and experimental data related to the discipline.
( reference books)
All the detailed list of topics covered during the lessons, the PDF files of power point presentations used during the course and supplementary material for exam preparation are available in the Moodle platform of the course.
Adopted text book:
- N. J. Dimmock, A. J. Easton, K. N. Leppard - Introduction to Modern Virology - Seventh edition 2016 -Wiley Blackwell - ISBN 978-1-119-97810-7
- Leonard Norkin – Virology: Molecular Biology and Pathogenesis - ASM (American Society for Microbiology) Press (this text book is more detailed)
Students are received at the end of the lessons or by appointment via email (elisabetta.affabris@uniroma3.it).
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6
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BIO/19
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40
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10
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20410496 -
Laboratorio di neuroscienze
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20410495 -
Microbiomica
(objectives)
The goal of the Microbiomics course is to provide information about the structure, dynamics, evolution, and methods to investigate complex microbial communities as a whole. The rapid progress of omic sciences (genomics, transcriptomics, proteomics and metabolomics) combined with high-throughput genome sequencing, global gene expression analysis tools, and powerful analytical method of metabolites has made feasible the analysis of complex and diverse microbial communities and their products as a whole.
The course is intended to provide state-of-art information on the impact of the microbiota in agriculture, food production, as well as animal and human health
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6
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BIO/19
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48
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20410527 -
Neurobiologia molecolare dello sviluppo
(objectives)
The Course aims to provide the student with advanced knowledge and skills in molecular biology of neurodevelopment, with particular reference to the central nervous system of vertebrates.
The aim of the first module is to provide the student with general knowledge about the cellular processes that lead, in the course of early and late embryogenesis, to the formation of the central nervous system from the neural tube. Advanced concepts on morphogenetic processes ensuring the achievement of the general cytoarchitecture of telecephalon, diencephalon, mesencephalon, metencephalon, myelencephalon and spinal cord will be provided. In particular, the student will acquire knowledge and skills on neuronal migration processes (under normal and pathological conditions) that lead to the layering of the cerebral cortex, spinal cord, and cerebellum. Advanced knowledge and expertise will also be provided on the cellular processes underlying adult neurogenesis and neurodegeneration, focusing on the role of apoptosis and autophagy. The student, through an interactive teaching will acquire skills in the study of pathological conditions, such as the most common neurodegenerative disorders (Alzheimer's disease, Parkinson's disease, Huntington's chorea).
The aim of the second module is to provide the student with general knowledge regarding the gene expression underlying the differentiation and morphogenesis of the nervous tissue. These molecular mechanisms will be addressed in different study models. It will be highlighted how neurogenesis and plasticity have profound functional implications in the nervous system throughout the life of the individual. The student, by means an interactive teaching, will acquire skills on new biomolecular technologies to study the development and functionality of the nervous system under physiological and pathological conditions.
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Derived from
20410527 Neurobiologia molecolare dello sviluppo in Biologia per la ricerca molecolare, cellulare e fisiopatologica LM-6 MORENO SANDRA, CERVELLI MANUELA, Colasuonno Fiorella
( syllabus)
Overview of the development of multicellular organisms. Ectodermal derivation of neural tissue in invertebrates and vertebrates. Primary neurulation: cellular and molecular mechanisms of neural plate formation, neural folds, neural groove and neural tube. Secondary neurulation. Neural tube closure defects in mammals: genetic and environmental causes. Morphogenesis and differentiation of the brain and spinal cord. Role of cell death in central nervous system morphogenesis: apoptotic mechanisms. Layering of cerebral and cerebellar cortical structures. Congenital diseases related to neuronal migration defects: the case of peroxisomal disorders. Neural stem cells: neuronal and glial differentiation. Neurogenesis in the adult brain: the subventricular and subgranular areas of the mammalian dentate gyrus. Pathways regulating activity of the neurogenic niche. Neurogenesis and neurodegeneration in the senescent brain. Neurodegenerative diseases related to aging: common features and anatomical and genetic-molecular specificities. Protein aggregates, role of apoptosis and autophagy and therapies against neurodegeneration, based on stem cell transplants and endogenous regeneration.
( reference books)
Gilbert: "Developmental Biology", 9th Edition, Sinauer Associates
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BIO/06
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20
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5
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Attività formative affini ed integrative
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| 3
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BIO/11
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20
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5
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Attività formative affini ed integrative
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20410594 -
L’Agenda 2030 delle Nazioni Unite per lo sviluppo sostenibile - Le implicazioni per le Scienze della Vita e della Terra
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Modulo di Base
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3
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20
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Elective activities
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L’Agenda 2030 delle Nazioni Unite per lo sviluppo sostenibile - Le implicazioni per le Scienze della Vita e della Terra
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3
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GEO/03
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28
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Università Roma Tre