Module 1.- The archaeological sites (2 credits)
Man & Nature in the ancient world: evolution of such relationship. Problems due to plant colonization in archaeological sites due to biodeterioration problems. Positive effects due to plants in the conservation and valorisation of cultural heritage and nature conservation. Cultural sites as refuge site for nature. Development and management of archaeological sites.
Module 2.- Historical gardens and parks (2 credits)
The origin of the gardens. Historical excursus in the Assyrian - Babylon’s, Egyptian, Roman, Medieval, Modern and Contemporary ages. The botanical management in historical gardens and parks. The botanical catalogues (PG/B) in the historical gardens and parks.
Module 3 Field practical activities (2 credits)
Excursions in significant sites: Colosseum and Horti Farnesiani on the Palatine. The archaeological sites of Appia Antica. Visit in historical gardens in Central Italy for some thematic deepening.

La Biologia vegetale per i beni culturali (vol.II), 2005 G. Caneva (a cura). Ed. Nardini, Firenze
and references on case-studies

Theory
- Intro to spatial ecology: from spatial patterns to ecological processes
- GIS: functions, geographical approach and modeling of reality
- Types of GIS software: open source and proprietary software
- Data models: vectorial (points, lines and polygons) and raster (pixel)
- Principles and methods in remote sensing: electromagnetic reflectance, remote sensed image resolution, active and passive sensors, remote sensing platforms

Practicals (software: GIS and R)
- Visualization of geographical objects(features) on a map
- Preparation of plant and animal maps
- Preparation and analysis of environmental maps (land use/land cover, habitat maps, photosynthetic activity, etc.) in time and in space
- Principles and methods of cartographic extraction of bio-environmental features
- Introduction to Species Distribution Modeling (SDM)

Materials, PDFs of lecture slides and scripts are made available during the course

Suggested textbooks:
- Geographic Information Systems in Ecology (Methods in Ecology), Carol A. Johnston, Blackwell Scientific Edition, Malden, MA, 1998, p. 239.
- An Introduction to R for Spatial Analysis and Mapping, Chris Brunsdon and Lex Comber, SAGE Publications Ltd; 2015, p. 360


Office hours are by appointment via email: marta.carboni@uniroma3.it

Plants are sessile organism. Main strategies of response to environmental stimuli. Re-modulation of developmental programs. Immobility and totipotency of plant cells. Role of plant cell wall in growth. Physiological and metabolic alteration. Cell-cell communication and long-distance communication: hormones, transcription factors, waves of reactive oxygen species and electrical signals. Perception of internal and external stimuli. Main classes of receptors and intracellular transduction pathways. Integration of different signals and signaling pathways. Secondary metabolism: biosynthesis and roles of secondary metabolites in plant/plant, plant/insects, plant/microorganism communication. Fundamentals of plant pathology: mechanism of infection and resistance. Host-pathogen interaction. Control of plant diseases by chemicals, biological fight, breeding and genetic engineering. Responses to abiotic stresses (drought, flooding, high salinity, high and low temperature, high light).

Practical laboratories
Analysis of the expression levels of amine oxidase-encoding genes in wounded and unwounded Arabidopsis seedlings: RNA extraction and quantification by RTqPCR (Reverse transcriptase quantitative polymerase chain reaction)
Observation under light microscopy of tissue-specific gene expression of copper amine oxidases (AtCuAO) after GUS-staining using 5-day-old PromAtCuAO-GUS-GFP Arabidopsis transgenic seedlings.

1) Interazioni Piante-Ambiente. Luigi Sanità di Toppi; Piccin Editore
2) Biologia delle Piante Vol. 2: Interazioni con l’ambiente e Domesticazione. Smith A. M. et al; Zanichelli Editore


The professor receives every day by appointment via e-mail: alessandra.cona@uniroma3.it

The study of animal communities and macroecology will be organized in different modules. (i) Co-occurrence: the co-occurrence module allows to test non-random models of co-occurrence of species in a presence-absence matrix; (ii) Macroecology: the study of the partitioning of physical space and ecological resources by species. Macro-ecological studies consist of the analysis of traits at the species level, such as body size, geographical area and average abundance, measured at large spatial scales; (iii) Niche overlap: the study of niche overlap has a long history in community ecology. Simple theories of of limiting similarity y and ecological character displacement predict that interspecific competition will lead to a reduction in the niche overlap of competing species. Testing this idea with empirical data leads to three questions: 1) which aspects of the niche should be measured? 2) How can the niche overlap between species pairs be quantified? 3) how much niche overlap would you expect in the absence of competition? (iv) Overlap of body size: this module allows to test for unusual patterns in the body sizes of coexisting species, and to compare those patterns to what might be expected in a random assemblage that was not structured by interspecific interactions; (v) Diversity of communities: the diversity of species is a central object of study both in the basic and applied ecology of communities. Two main issues will be addressed in the study of species diversity. The first is how can we quantify the diversity of an assemblage, and second, how we can compare statistically the diversity of two different assemblages; (vi) Functional groups or guilds: groups of species within a community that share common resources are considered guilds. This module will allow to incorporate the guild structure into community analyses.
- Through simulations in the laboratory and in the field, the student will learn the dynamics that determine the organization and structure of some selected animal communities.
- Interactive computer programs will be used for the analysis of null models in community ecology to test community models with experimental and non-experimental data. The Monte Carlo randomizations will be illustrated as an analytical method to compare real communities with "pseudo-communities" created using different algorithms. The wide applicability of null models in applied and basic animal ecology will be illustrated

NOTES AND POWER POINTS ARE PROVIDED BY THE TEACHER. THE FOLLOWING TEXTBOOKS HELP TO STUDY SOME ASPECTS OF THE PROGRAMME:
- BEGON, M., TOWNSEND, C.R., HARPER, J.L.— ECOLOGY: FROM INDIVIDUALS TO ECOSYSTEMS / 4TH ED. BLACKWELL PUBLISHING, OXFORD UK.
- BOITANI L. & FULLER T.K. (EDS.), 2000. RESEARCH TECHNIQUES IN ANIMAL ECOLOGY. CONTROVERSIES AND CONSEQUENCES. COLUMBIA UNIVERSITY PRESS, N.Y.;
- GOTELLI, N.J. AND A.M. ELLISON. 2004. A PRIMER OF ECOLOGICAL STATISTICS. SINAUER ASSOCIATES, INC., SUNDERLAND, MA.;
- GOTELLI, N.J. 2008. A PRIMER OF ECOLOGY. 4TH EDITION. SINAUER ASSOCIATES, INC., SUNDERLAND, MA.
- HENDERSON, P.A. 2003. PRACTICAL METHODS IN ECOLOGY. BLACKWELL SCIENCE LTD
- VERHOEF, H.F., MORIN, P.J. 2010. COMMUNITY ECOLOGY. PROCESSES, MODELS, AND APPLICATIONS. OXFORD UNIVERSITY PRESS, USA
- MITTELBACH, G.G., MCGILL, B.J. 2019. COMMUNITY ECOLOGY. OXFORD UNIVERSITY PRESS, USA.




Students are provided with a document that lists for each lesson topic which textbook and which chapters are most relevant for the study, and for each topic it lists recent scientific papers for further study. Students are also provided with PDFs of lessons and of scientific papers suggested.

Cultural skills (Knowledge of:) the course offers the conceptual bases for (A) the recognition of the main distinctive features of primates and their anatomical and behavioral adaptations in a comparative ecological and evolutionary perspectives and (B) an understanding of the main evolutionary trends of primates and the origin of human kind.
Methodological skills (Knowing how to perform:) acquiring the critical thinking through readings and discussions, recognition of the main management problems related to in-situ and ex-situ conservation.

SYLLABUS
Introduction to the order: evolution, phylogeny, taxonomy and systematics. Distinctive features of the primate order compared to other mammals. Anatomy of the primates' body: variability in body size; morphological characteristics and diversity in the skull (dental formulas, muscles of facial expressions), the brain and the senses; skeleton, limbs, nails and claws; digestive and reproductive system. Geographical distribution of primates and introduction to behavioral, social, ecological and life cycle characteristics. Distinctive features, adaptive radiation and phyletic relationships of the various primate taxa. Ecological adaptations and biogeography of primates: communities and patterns of primate diversity on a global scale. Adaptations of primates: functional relationships between morphological characteristics (e.g., size of the body, teeth, shape of the skeleton, sensory organs) and behavioral ecology (e.g., diet, use of the habitat, locomotion) in the study of the evolution of anatomical differences. Paleontological and biomolecular data for the study of evolution, phylogenesis and origin of primates. Adaptive theories on the origin of primates. Elements of paleo-primatology. Ancestral primates and fossils of prosimians. The first anthropoid monkeys and theories on the origin of the platyrrhine monkeys. Fossil platyrrhines. Fossil catarrhines. Fossil apes, early hominids and bipedal primates. The origin of humans: evolution and phylogenesis of the genus Homo. The relations between Homo sapiens and other recent forms of the genus Homo. Adaptive radiation of the primate order and main evolutionary trends. Main causes of the risk of primate species extinction. Problems related to primate in-situ and ex-situ conservation and the ethics of well-being in captive management.

RECOMMENDED TEXTBOOK:
Fleagle, J. G. (2013). Primate adaptation and evolution. Third Edition. Academic press.

TEXTBOOKS FOR FURTHER READINGS:
- Ankel-Simons, F. (2010). Primate anatomy: an introduction. Elsevier.
- Dixson, AF (2012). Primate Sexuality: Comparative Studies of the Prosimians, Monkeys, Apes

The professor receives every day from 9.00 to 10.00 by appointment via email: monica.carosi@uniroma3.it

HEME-PROTEINS. HEME METABOLISM AND RELATED DISEASES. HEME BIOSYNTHESIS AND RELATED DISEASES. IRON METABOLISM AND RELATED DISEASES. INORGANIC BIOFACTORS: OXYGEN, CARBON MONOXIDE, NITROGEN MONOXIDE, HYDROGEN SULFIDE. BIOCHEMICAL AND CELLULAR ROLES OF THE INORGANIC BIOFACTORS. ROLE IOF THE INORGANIC BIOFACTORS IN HUMANN DISEASES ONSET. THE THERAPEUTIC USE OF THE INORGANIC BIOFACTORS. REACTIVE OXYGEN AND NITROGEN SPECIES. MITOCHONDRIAL DISEASES. THE ENERGETIC MATTER OF CANCER CELLS. THE METABOLIC REQUIREMENTS OF CANCER CELLS: THE WARBURG EFFECT.

SCIENTIFIC PAPERS SUPPLIED BY THE TEACHER.
Support texts:
Siliprandi & Tettamanti "Biochimica Medica - strutturale, metabolica e funzionale" Ed. Piccin
- Chiurchiù & Maccarrone "I radicali liberi e la loro rilevanza in biomedicina: dai meccanismi molecolari alle prospettive terapeutiche" Ed Piccin

RECEPTION TIME: Monday 10 am

The course aims to provide the following skills and competencies:
Cultural competences (Knowledge of :) The Course aims to provide students with basic knowledge relating to thermodynamics and the kinetics of biological processes, particularly in relation to experimental activities in the laboratory.
Methodological skills (Know How to:) acquire and use experimental data relating to the study of interactions between proteins and ligands, enzyme kinetics and kinetic of binding
The programs is divided into:
1) Study of the interaction between receptors and ligands: methods at equilibrium and transient kinetics:
a) At equilibrium (thermodynamic parameters: Kd: dissociation constant at equilibrium, cooperativity, number of binding sites)
b) Rapid kinetics (kinetic parameters: k: velocity constants)
2) Study of enzymatic activity: steady state kinetics
a) In Steady State (when [ES] is almost constant during experimental observation)
b) In the presence of inhibitors
3) Time-resolved optical spectroscopy and complex kinetics
4) Absorption spectroscopy, fluorescence and circular dichroism

Recommended textbooks:
M. C. Bonaccorsi di Patti et al. Metodologie Biochimiche - Casa Editrice Ambrosiana
Ninfa/Ballou Metodologie di base per la Biochimica e la Biotecnologia - ed. Zanichelli
Reed et al. Metodologie di Base per le Scienze Biomolecolari- ed. Zanichelli
P. Silvestroni, Fondamenti di chimica - Casa Editrice Ambrosiana
D.M. Etter Introduction to MATLAB 7– Pearson Education, Inc.

Software to use
EXCEL (Office) or CALC (Open Office) * (for linear methods)
MATLAB (Mathworks) or OCTAVE (GNU Octave) * (for spectral analysis and non-linear methods)
GEPASI (P. Mendes et al.) * Or COPASI (Copasi dev. Group) * (for complex reactions)
(*) indicates free software
Lecture notes and calculation exercises will be provided

The professor receives every day from 8.00 to 9.00 or by appointment via e-mail: giovanni.antonini@uniroma3.it

1. BASIC TECHNOLOGIES OF GENE ANALYSIS; RESTRICTION ENZYMES; ELECTROPHORETIC ANALYSIS. 2. VECTORS; CLONING. 3. PCR; REAL TIME PCR; PCR APPLICATIONS. 4. GENETIC VARIABILITY APPLIED TO FORENSIC SCIENCE 5. GENE IDENTIFICATION; GENOMIC LIBRERIES AND cDNA LIBRERIES; YEAST TWO HYBRID SYSTEM 6. MUTAGENESIS. 7. RECOMBINANT PROTEIN PRODUCTION AND PURIFICATION. 8. FROM SANGER SEQUENCING TO NEXT-GENERATION SEQUENCING. 9. POST-GENOMICS ANALYSIS; TRANSCRIPTOMIC ANALYSIS; REPORTER GENES. 10. PROTEOMIC ANALYSIS. 11. PRODUCTION AND ANALYSIS OF TRANSGENIC PLANTS. 12. GENETIC MODIFICATION OF ANIMAL CELLS; TRANSGENIC ANIMALS CONSTRUCTION. 13. GENE TRAPPING; GENE TARGETING. 14. ANIMAL CLONING; GENE THERAPY. 15. THE CRISPR-CAS SYSTEM: EMERGING TECHNOLOGY AND APPLICATION AND APPLICATIONS.

Recommended textbooks:
1. ANALISI DEI GENI E GENOMI, REECE, EDISES.
2. DNA RICOMBINANTE, J.D.WATSON, A.A. CAUDY, R.M. MYERS E J.A. WITKOWSKI, ZANICHELLI.

Lecture slides will be provided.
The professor receives every day from 10.00 to 11.00 by appointment via e-mail: manuela.cervelli@uniroma3.it

LAWS OF THERMODYNAMICS: ENERGY, WORK AND HEAT. STATE FUNCTIONS: INTERNAL ENERGY, ENTHALPY, ENTROPY, FREE ENERGY. ELEMENTS OF SOLUTIONS THERMODYNAMICS: CHEMICAL POTENTIAL, IDEAL SOLUTIONS, REAL SOLUTIONS, ELECTROLITIC SOLUTIONS; EQUILIBRIUM CONSTANT. INTRODUCTION TO THE RADIATION MATTER INTERACTION (CLASSICAL MODEL). REM. SPECTROSCOPIES: VIBRATIONAL SPECTROSCOPY (FT-IR), ELECTRONIC SPECTROSCOPIES. UV-VIS ABSORPTION AND EMISSION. X-RAYS PHOTOEMISSION SPECTROSCOPY (XPS). INSTRUMENTATION. EXAMPLES OF APPLICATIONS TO THE INVESTIGATION OF THE ELECTRONIC AND CHEMICAL STRUCTURE OF BIOMOLECULES.

PETER ATKINS, JULIO DE PAULA: Physical Chemistry for the Life Sciences. ISBN: 9780199564286

INTRODUCTION: NATURE OF DRUGS, DRUG NOMENCLATURE, DRUG CLASSIFICATION. CLINICAL AND PRECLINICAL PHARMACOLOGY.
PRINCIPLES OF GENERAL PHARMACOLOGY- PHARMACOKINETICS: THE DYNAMICS OF DRUG ABSORPTION, DISTRIBUTION, BIOTRANSFORMATION AND ELIMINATION. MAIN PHARMACOKINETIC PARAMETERS. PHARMACODYNAMICS: MECHANISMS OF DRUG ACTION; DRUG RECEPTORS; DRUG-RECEPTOR INTERACTIONS; SIGNAL TRANSDUCTION MECHANISMS; AGONISTS AND ANTAGONISTS. NEUROTRANSMITTERS.
SYSTEMATIC PHARMACOLOGY- MECHANISM OF ACTION, THERAPEUTIC EFFECTS AND SIDE EFFECTS OF THE MAIN CLASSES OF DRUGS: AUTONOMIC DRUGS; DRUGS THAT ACT IN THE CENTRAL NERVOUS SYSTEM; CARDIOVASCULAR DRUGS; ANTI-INFLAMMATORY DRUGS; BRONCHODILATORS AND OTHER DRUGS USED IN ASTHMA; DRUGS USED IN GASTROINTESTINAL DISORDERS; CANCER CHEMOTHERAPY; ANTIMICROBIC DRUGS.

Clark, Finkel, Rey, Whalen. “Pharmacology", Lippincott's Illustrated Reviews, 5th Edition

Power-point files of the lessons will be provided
To get an appointment with the Professor, email to: viviana.trezza@uniroma3.it

INTRODUCTION TO ENDOCRINOLOGY (1 CFU)
HISTORY, CHEMICAL NATURE OF HORMONES, EVOLUTION OF CHEMICAL SIGNALS. ENDOCRINE GLANDS, HORMONE SYNTHESIS AND RELEASE (ENDOCRINE, AUTOCRINE, PARACRINE, AND INTRACRINE ACTIONS, HORMONAL RHYTMS) MECHANISMS OF HORMONE ACTIONS (SIGNALLING FROM MEMBRANE AND INTRACELLULAR RECEPTORS)
THE ENDOCRINE SYSTEM AND INTEGRATIVE PHYSIOLOGY (3 CFU)
REPRODUCTIVE ENDOCRINOLOGY (FETAL GROWTH, PREGNANCY, MATERNAL ADAPTATION TO PREGNANCY)
GROWTH (GROWTH FACTORS AND ONCOGENES IN FETAL GROWTH, POSTNATAL GROWTH, PUBERTY, HORMONESAND THE GENDER/SEX DIFFERENCES)
AGEING (THEORIES, HORMONE REPLACEMENT THERAPIES, GERIATRIC ENDOCRINOLOGY)
METABOLIC ENDOCRINOLOGY (REGULATION OF FOOD UPTAKE, REGULATION OF DIGESTIVE PROCESSES, OBESITY)

HORMONES AND ENVIRONMENTAL INJURIES (1 CFU)
STRESS ADAPTATION
ENVIRONMENTAL ENDOCRINE DISRUPTORS
DISORDERS OF THE ENDOCRINOLOGY SYSTEM (CELL GROWTH AND CANCER)
CRITICAL ANALYSIS OF SCIENTIFIC LITERATURE (1 CFU)

Review provided in the class room

THE COURSE (6 CFU) IS DIVIDED INTO TWO MAIN PARTS. THE FIRST ONE (5.5 CFU) IS AIMED AT DESCRIBING THE HISTORICAL AND NORMATIVE FRAMEWORK. THE SECOND ONE IS PLANNED TO FOCUS THE STUDY ON A VARIETY OF BOTH IN VITRO AND IN VIVO EXPERIMENTAL MODELS, WHOSE EMPLOYMENT IS USEFUL IN EITHER BIOLOGY APPLIED TO HUMAN HEALTH OR CELLULAR/MOLECULAR BIOLOGY. STARTING POINTS FOR DISCUSSIONS WILL BE PROVIDED, IN ORDER TO ENGAGE THE LEARNERS FOR THE WRITING OF A REPORT THAT WILL BE GOAL OF EXAMINATION. LABORATORY PRACTICES (0.5 CFU) WILL BE FIXED TOGETHER WITH THE STUDENTS WITH THE AIM OF ACQUIRING NEW TECHNIQUES ON SOME EXPERIMENTAL MODELS WIDELY USED IN BIOLOGICAL RESEARCH

TEXTBOOKS AND OTHER EDUCATIONAL MATERIAL FOR HOMEWORKS WILL BE SUGGESTED TO LEARNERS DURING THE COURSE.

GENERAL CONCEPTS AND LIFE CYCLES OF THE MAIN HUMAN PARASITES
TERMINOLOGY AND DEFINITIONS IN GENERAL PARASITOLOGY
CLASSIFICATION OF HUMAN PARASITES (PROTOZOA, PLATELMINTHS, NEMATODES AND ARTHROPODS)
MORPHOLOGICAL IDENTIFICATION OF PARASITES
BIOCHEMICAL AND MOLECULAR TECHNIQUES APPLIED TO PARASITE IDENTIFICATION AND SYSTEMATICS

TRANSMISSION PATTERNS THROUGH VECTORS: TRYPANOSOMATIDS, PLASMODIA, BABESIA,
FILARIAL WORMS, SCHISTOSOMES
TRANSMISSION PATTERNS THROUGH INGESTION: GIARDIA, AMOEBA, TOXOPLASMA, CRYPTOSPORIDIUM,
OPISTHORCHIS, TAPEWORMS, TRICHINELLA, TOXOCARA, PINWORMS
OTHER TRANSMISSION PATTERS: STRONGYLOIDES

IMMUNITY TO PARASITES AND PARASITE’S EVASION

PARASITIC DISEASES
TERMINOLOGY AND DEFINITIONS IN EPIDEMIOLOGY, PATHOGENESIS, CLINICAL FEATURES, DIAGNOSIS AND TREATMENT
MAJOR PARASITIC DISEASES ENDEMIC IN ITALY: LEISHMANIASIS, GIARDIASIS, TOXOPLASMOSIS,
CYSTICERCOSIS, ECHINOCOCCOSIS/HYDATIDOSIS, TRICHINELLOSIS, TOXOCARIASIS, DIROFILARIASIS, OXYURIASIS, PEDICULOSIS
MAJOR PARASITIC DISEASES IMPORTED INTO ITALY: AFRICAN TRYPANOSOMIASIS (SLEEPING SICKNESS),
AMERICAN TRYPANOSOMIASIS (CHAGAS DISEASE), AMEBIASIS, MALARIA, SCHISTOSOMIASIS

DE CARNERI – PARASSITOLOGIA MEDICA E DIAGNOSTICA PARASSITOLOGICA – CASA EDITRICE AMBROSIANA, 2013
GABRIELLA CANCRINI – PARASSITOLOGIA MEDICA ILLUSTRATA – LOMBARDO EDITORE, 2012

- Basics of Medical Genetics.
- The human genetic variability.
- Short Tandem Repeat (STR) Loci.
- Sample Collection, Storage, and Characterization.
- DNA Extraction Methods.
- DNA Quantification Methods.
- DNA Amplification
- Principles of Capillary Electrophoresis.
- The genetic identification profile.
- DNA Mixture Profiles.
- Lineage Markers.
- Principles of probability and statistical computing.
- The biostatistical interpretation.
- Forensic statistics applied to the kinship/paternity testing.
- Troubleshooting forensic DNA typing.

Genetica Medica Essenziale
Bruno Dalla Piccola – Giuseppe Novelli
CIC Edizioni Internazionali

Genetica medica pratica
Giuseppe Novelli - Emiliano Giardina
Aracne
Data di Pubblicazione: 2003

Advanced Topics in Forensic DNA Typing: Methodology
John M. Butler
National Institute of Standards and Technology
Gaithersburg, Maryland, USA
Academic Press is an imprint of Elsevier

Advanced Topics in Forensic DNA Typing: Interpretation
John M. Butler
National Institute of Standards and Technology
Gaithersburg, Maryland, USA
Academic Press is an imprint of Elsevier

(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.

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.

1. Evolution and systematic of microorganisms
Origin of bacteria; molecular phylogenesis; 16S rRNA gene and evolution; basis of microbial systematic
2. Metabolic diversity of microbes
Chemolitotrophy; fermentation; anaerobiosis; phototrophy
3. Functional diversity of microbes
Phototrophic and chemotrophic bacteria; bacteria in sulfur and nitrogen cycles
4. The principal phylogenesic groups of Bacteria
Proteobacteria, Firmicutes, Bacteroidetes, Ipertermofili
5. The principal phylogenetic groups of Archea
Phyla and evolution; Euryarchaeota;extremophiles
6. Methods in microbial ecology
Culture-based methods; functional analysis
Cultivation-independent techniques: microscope; genetic analysis; genome and metagenomic
7. Microbial ecosystems
Principles of ecology
Microbe environment: microbial interactions (Quorum sensing; Biofilm)
Terrestrial environment: soil
Aquatic environment: lakes, oceans
Extreme environments (deep sea; hydrothermal springs)
8. Microbial role in nutrient cycles
Carbon, nitrogen, sulfur, others
9. Symbiosis between microorganisms and between microorganisms and different organisms
Plants; rhizosphere; root nodules
Mammals; microbiome: bowel and rumen
10. Microorganisms in anthropized environments
Bioremediation of contaminated sites; water treatment; biocorrosion; mineral recovery from mines

Text book: Madigan et al., Brock Biology of microorganisms 14th edition

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.

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

The course is organised as follows:
- Concepts of communication
- Communication in different contexts
- How to make a presentation in different context
- How to write an article in different context
- How to prepare teaching material

Teaching material will be provided by the teachers

Bioindication: basic concepts. Main ecological characteristics of a Bioindicator. Two ways for bioindicating: react and bioaccumulate. The homeostasis of the Bioindicators. Time and ecological relationship of the bioindicators' responses to environmental variations (perturbations). What are a stress and a stressor.
Bioindication in different levels of biological organization. Integrity and funzionality of the Ecosystem. Status verification of the biocoenoses and evaluation of the environmental quality. Two different approaches: the theories of the Top-Down and of Buttom-Up.
Bioindication and environmental monitoring. Bioindication in aquatic, edaphic and atmospheric habitat. Examples of application of the bioindication techniques. Evaluation of the environmental quality by ecological and biotic indices. Standard and sperimental techniques for monitoring activities. The bioindication in Italy. Main European and Italian directives. International and national Agencies, Authorities, Institutions for environmental monitoring.

Pdfs of the lessons performed during the course and 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

-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.

P.M. DEWICK : "Medicinal Natural Products" Wiley Ed.
C. BAIRD, M. CANN “Environmantal Chemistry”,

THREE ARE THE MAIN ARGUMENTS OF THE COURSE: GENE TRANSFER TECHNIQUES; APPLICATIONS OF PLANT BIOTECHNOLOGY; ANALYSIS OF RISKS AND BENEFITS OF PLANT GENETIC MANIPULATION.
IN DETAIL, DURING THE COURSE THE FOLLOWING ARGUMENTS ARE DISCUSSED:
TECHNIQUES FOR GENE TRANSFER INTO THE NUCLEAR AND CHLOROPLASTIC GENOME; TECHNIQUES FOR IN VITRO CULTURE OF PLANT CELLS; USE OF SELECTABLE GENE MARKERS AND REPORTER GENES; STRATEGIES TO REMOVE SELECTABLE GENE MARKERS FROM TRANSGENIC PLANTS; INDUCIBLE EXPRESSION OF TRANSGENES IN PLANTS; TRANSIENT EXPRESSION OF GENES IN PLANTS; GENE SILENCING IN PLANTS; ‘GENE TARGETING’ IN PLANTS; GENOME EDITINGIN IN PLANTS; PLANTS WITH IMPROVED NUTRITIONAL VALUE; PRODUCTION OF ANTIBODIES AND VACCINES IN TRANSGENIC PLANTS; BIOTECHNOLOGICAL STRATEGIES TO OBTAIN PLANTS RESISTANT TO HERBICIDES, PATHOGENS AND ENVIRONMENTAL STRESSES; PLANTS WITH INCREASED PHOTOSYNTHETIC RATE; BIOSAFETY AND BIOETHICAL ISSUES RELATED TO PLANT BIOTECHNOLOGY; EMERGING TECHNOLOGIES AND PLANT BIOTECHNOLOGY.

-Recommended textbooks:

1. BIOCHEMISTRY AND MOLECULAR BIOLOGY OF PLANTS (2000) BUCHANAN B.B, GRUISSEM W., JONES R.L., AMERICAN SOCIETY OF PLANT PHYSIOLOGISTS, ROCKVILLE, MARYLAND.
2. BIOLOGIA CELLULARE E BIOTECNOLOGIE VEGETALI (2011) COZZOLINO S., DI SANSEBASTIANO G.P., FORNI C., GENRE A., LANFRANCO L., MICCHELI A., PASQUA G., TRAINOTTI L., VALLETTA A.
3. HANDBOOK OF PLANT BIOYECHNOLOGY (2004) CHRISTOU P., KLEE H., HOBOKEN, (N.J.), WILEY.
4. PLANT BIOTECHNOLOGY AND TRANSGENIC PLANTS (2002) OKSMAN-CALDENTEY K.-M., BARZ W.H., NEW YORK, DEKER.

-Scientific articles published in international journals (pdf files will be provided).

-Lecture notes will be provided.

Module A - Prof.ssa Alessandra di Masi
- Fat-soluble and water-soluble vitamins
- Macroelements
- Microelements
- Carbohydrates. Classification of carbohydrates. Carbohydrate biosynthesis. Digestion and absorption of carbohydrates. Fate and biological functions of carbohydrates. Regulation of carbohydrate metabolism.
- Lipids. Classification of lipids. Lipid digestion and absorption. Fate and biological functions of lipids. Regulation of carbohydrate metabolism.
- Proteins. Daily protein requirement. Nutritional properties of proteins. Protein digestion and amino acid fate. Biosynthesis of non-protein nitrogen compounds.

- Leuzzi, Bellocco, Barreca “Biochimica della Nutrizione” Ed. Zanichelli
- Cozzani, Dainese "Biochimica degli alimenti e della nutrizione" Ed. Piccin.
- Biochemistry texts used for the preparation of the Biochemistry exam of the three-year degree course in Biological Sciences.

RECEPTION TIME: Monday 10 am

• LABORATORY MEDICINE AND CLINICAL BIOCHEMISTRY
BIOCHEMICAL TESTS AND LABORATORY MANAGEMENT
PREANALYTICAL, ANALYTICAL AND BIOLOGICAL VARIABILITY
REFERENCE VALUES
• QUALITY CONTROL ASSURANCE
• ANALYTICAL METHODS
IMMUNOCHEMISTRY AND INTERFERENCES
• LABORATORY ANDCARDIOVASCULAR DISEASES
LIPOPROTEIN ALTERATIONS
LABORATORY AND DIABETES MELLITUS
MARKERS OF CARDIAC DISEASES
• LABORATORY AND RENAL FUNCTION
URINALYSIS
• LABORATORY AND LIVER
• LABORATORY AND NEUROLOGICAL DISEASES
CEREBROSPINAL FLUID
• LABORATORY AND ONCOLOGY
• LABORATORY AND MALE INFERTILITY
• INTRODUCING CLINICAL MOLECULAR BIOLOGY

Clinical Biochemistry: An Illustrated Colour Text- Allan Gaw MD, ICT, 2013

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.

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

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.

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

The course aims at providing to the student:
- adequate knowledge and understanding on advanced methodologies in bacterial genetics, appropriate methodologies and communication skills for the study of genotype-phenotype relationships in bacteria;
- adequate applied knowledge for the evaluation and drafting of experimental approaches, and for retrieving and critically reviewing relevant scientific literature from on-line databases (making judgements).

Programme
- structure, organization, functioning and evolution of the bacterial chromosome;
- methods for the sequencing and analysis of bacterial genomes;
- structure, organization, function and evolution of mobile genetic elements (plasmids and transposons);
- genetic and molecular bases of horizontal gene transfer;
- genetic and molecular bases of gene expression regulation and bistability in bacteria;
- genetic bases and experimental approaches for the study of antibiotic resistance and tolerance;
- methods for the identification and validation of essential genes;
- approaches for the identification and study of unculturable microorganisms

Selected topics will be available on suggested Bacterial Genetics 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 sharing power-point presentations illustrating the main topics of the course via email. Moreover, students will be encouraged to make use of web-based resources and databases to autonomously increase their knowledge on specific advanced topics.

Properties and Overview of Immune Responses: Cells and Tissues of the Immune System
Leukocyte Circulation and Migration into Tissues
Innate Immunity
Antigens and Antigen presentation
Immune Receptors and Signal Transduction
Lymphocyte T Development and Activation
Differentiation and Functions of CD4+ and CD8 +Effector T Cells
B Cell Activation and Antibody Production
Humoral Immunity
Immunologic Tolerance and Autoimmunity
Immunity to Microbes and Vaccines
Immunodeficiency and immunosenescence
Immunological techniques

SEMINAR:
PAMPS AND TLRS
DENDRITIC CELLS
MICRO-RNA
IMMUNOPHAGY
BIBLIOGRAPHIC RESARCH - PUBMED

- Abul K. Abbas, Andrew H. Lichtman, Shiv Pillai
IMMUNOLOGIA CELLULARE E MOLECOLARE
(8th Edition, Edizioni Edra)

- Peter Parham
IL SISTEMA IMMUNITARIO
(2nd Edition, Edizioni EdiSES)

Overview of developmental processes of pluricellular organisms. Germ cell layers. Ectodermal derivation of neural tissue in invertebrates e vertebrates. Specification of neuroectoderm and neurulation process in vertebrates. Primary neurulation: cellular e molecular mechanisms of neural plate, folds, furrow, and tube formation. Secondary neurulation. Neural tube defects in mammals: genetic and environmental causes of anencephaly and spina bifida. Morphogenesis and differentiation of the encephalon and spinal cord. Role of cell death in the morphogenesis of the central nervous system: apoptotic and autophagic pathways. Neural crest: specification and regionalization. Cell migration and differentiation of cephalic, cardiac, trunk, vagal e sacral neural crest. Multipotency e plasticity of neural crest cells. Layering of cortical structures in the cerebrum and cerebellum. Congenital diseseases associated with defects to neuronal migration: the case of peroxisomal disorders. Neural stem cells: neuronal and glial differentiation. Adult neurogenesis in mammals: the subventricular and subgranular zones. The concept of stem cell niche. Regulatory pathways of the neurogenic niche. Neurogenesis and neurodegeneration in the senescent brain. Age-related neurodegenerative diseases: common and specific features. Protein aggregates, role of apoptotic and autophagic pathways, and stem cell-based therapies against neurodegeneration.

Gilbert: "Developmental Biology", Tenth edition, Sinauer Associates, Inc., 2014
Sanes et al.: "Development of the nervous system", Elsevier Inc., 2012

Origin of agriculture and plant domestication. Characteristics of the main crops: Poaceae, Fabaceae, Rosaceae, Solanaceae, Brassicaceae. Nutritional values of the different plant organs and nutrients bioavailability. Primary and secondary metabolism. Nutrients from plants: proteins, lipids and oils, carbohydrates, fibers, minerals, vitamins and antioxidants. Nutritional values of secondary metabolism and bioactive compounds: terpenes, phenols, alkaloids, cyanogenic glucosides, glucosinolates, non-protein amino acids. Effects of the environmental conditions on primary and secondary metabolism: food quality and production of aromas, flavors and toxins. Plant bioactive compounds as dietary supplements. 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. Genetic improvement and biotechnology approaches to develop crop plants with high nutritive contents and resistant to environmental stress.

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. Lecture notes and scientific articles provided by the teacher

The professor receives every day by appointment via e-mail: alessandra.cona@uniroma3.it

Role of nutrients and bioactive dietary molecules in the regulation of gene expression; Application of "omics" methodologies in the study of system nutrition; effects of diet-genotype interaction on the individual response to dietary stimuli; Nutritional phenotype; elements of Bayesian statistics

Principles of Nutrigenetics and Nutrigenomics. Academic Press De Caterina, Martinez & Kohlmeier Eds
either (in italian)
Nutrigenomica ed epigenetica. Edra Ed. Galimberti et al Eds
A selection of scientific papers provided by the teacher

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.

The class will be provided with the study materials found by students and by the professor.

GENERAL PRINCIPLES. AIMS AND FIELDS OF TOXICOLOGY. CLASSIFICATION OF TOXIC AGENTS. MECHANISMS OF MOLECULAR AND CELL TOXICITY. RISK EVALUATION. TOXICOKINETICS: ABSORPTION, DISTRIBUTION, METABOLISM AND EXCRETION OF TOXIC AGENTS. ADVERSE DRUG REACTIONS, DRUG INTERACTIONS AND PRINCIPLES OF PHARMACOVIGILANCE. ANTIDOTES AND THEIR CLASSIFICATION. EXPERIMENTAL EVALUATION OF TOXIC EFFECTS IN IN VITRO AND IN VIVO MODELS AND DATA EXTRAPOLATION. SYSTEM AND ORGAN TOXICOLOGY. DEVELOPMENTAL AND FEEDING TOXICOLOGY. CLASSES OF TOXIC COMPOUNDS: METALS, PHYTODRUGS, NATURAL TOXINS. PSYCHOACTIVE AND DOPING DRUGS.

CASARETT & DOULL'S “ESSENTIALS OF TOXICOLOGY”, SECOND EDITION, MCGRAW HILL

Power-point files of the lessons will be provided. The files are also available on the MOODLE platform
To get an appointment with the Professor, email to: viviana.trezza@uniroma3.it

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, Rabdoviridae, Orthomixoviridae, Paramixoviridae, 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.

All the detailed list of topics covered during the lessons, the PDF files of power point presentations used during the course and further materials 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)
to complement the PDF files of the power point used by the teacher during the course.
Mandatory integrations of the PDF files regarding viral vectors (adenoviral, adeno-associated, retroviral and lentiviral vectors, poxvirus-based vectors) and oncolitic viruses (general introduction + oncolytic adenoviruses) can be found herebelow:
- Fields virology, Vth edition, 2007- D.M.Knipe and P.M.Howley editors-in-chief -Lippincot Williams & Wilkins publishers, cap.16 Viral vectors and their applications (on line access through Roma Tre Scientific Library)
- Stéphanie Durand and Andrea Cimarelli - The Inside Out of Lentiviral Vectors - Viruses 2011, 3, 132-159.
- Carina Elsner and Jens Bohne - The retroviral vector family: something for everyone. – Virus Genes 2017, 53:714-722
The teacher receives by appointment via email (elisabetta.affabris@uniroma3.it) or at the end of the lessons.

BASIC TOPICS: Introduction to the genomics of prokaryotes and its study techniques (sequencing, annotation, gene family content, duplications and deletions); Horizontal gene transfer and mobilome; metagenomics; Transcriptomics and gene chips; Proteome and interactome; metabolomics; Genomics of single cells; Systems biology and health; Genetic manipulations - Expression of heterologous genes in bacteria - Evolution of bacterial genomes; Molecular phylogeny; Microbial taxonomy methods and species concept; Classification of prokaryotes; Culture analysis of microbial communities; Enrichment cultures; Isolation of single cells; Laser forceps; Flow cytometry; Microfluidic techniques; High-throughput systems; Staining methods; Fluorescent in-situ hybridization (FISH); Gene amplification methods for the analysis of microbial communities; Microarray analysis of the genetic and functional diversity of microorganisms; Environmental genomics and study methods; Measurement of microbial activity in nature; Examples of symbiosis: lichens, intestinal polymicrobial systems (rumen); General information on the huiman microbiome; Gastrointestinal microbiota; Oral and airway microbiota; Microbiota of the urogenital tract and skin; Development and evolution of the human microbiota; Studies on humans and in animal models; Colonization, microbial sequences and stability of the intestinal microbiota; Diseases associated with intestinal dysbiosis; Diseases associated with dysbiosis of the oral cavity, skin and genital tract; Antibiotics, resistome and induced alterations of the microbiome; Probiotics and prebiotics; Microbiota and intestine-brain axis.
APPLICATIONS: Technologies for sequencing and NGS; Culturome and chemotaxonomy; Sequencing data preparation and analysis; Phylogeny based on 16S rRNA, 25-28S rRNA, ITS etc .; Tools to analyze the structure and dynamics of the microbiota: Whole Genome Sequencing (WGS) and metagenomics shotgun; Analytical databases, tools and pipelines (annotations); Resistome; Virulome; Virome.
IN-DEPTH: illustration of monothematic articles on the microbiota of humans, animals and plants, in relation to physio-pathological alterations. Groundbreaking articles and reviews will be selected from scientific journals year by year.

"Brock biology of microorganisms" (English) by Michael T. Madigan (Author), Kelly S. Bender (Author), Daniel H. Buckley (Author), W. Matthew Sattley (Author), David A. Stahl (Author): chapters 9.1-9.14; 12.1-12.5; 12.9; 12.11-12.13; 13.5-13.10; 19.1-19.12; 23.1; 23.12, 23.13; 24.1-24.11
Microbiota in health and disease: from pregnancy to childhood. Editors Pamela D. Browne, Eric Claassen and Michael D. Cabana Published: 2017 Pages: 344. eISBN: 978-90-8686-839-1 | ISBN: 978-90-8686-294-8 https://doi.org/10.3920/978-90-8686-839-1
The human microbiota: how microbial communities affect health and disease / edited by David N. Fredricks.
ISBN 978-0-470-47989-6

1. The concept of business system.
2. The transactional and competitive environment.
3. Theories on entrepreneurial purposes.
4. The stakeholder theory.
5. The management cycle: the organizational function.
6. The directional cycle: directional control.
7. The management cycle: the management of resources.
8. The directional cycle: directional control.
9. The overall strategies.
10. Market positioning and SWOT analysis.
11. Competitive strategies.
12. Marketing: the product policy.
13. Marketing: the price policy and the promotional policy.
14. Marketing: the distribution policy.
15. Production management.
16. Logistics and inventory management techniques.
17. Financial management.
18. The choice of funding sources and financial leverage.
19. Techniques for evaluating investment projects.
20. Planning of financial choices.
21. The balance sheet analysis by indices: outline.
22. The evaluation of the economic - structural potential.
23. The budgeting process.
24. Analysis of distribution costs.
25. Evaluation of company performance.

Sergio Sciarelli, business management, WKI

through a series of seminars and discussions on different aspects of biology profession, also with the participation of expert professional biologists,students would have a panoramic view of possible biology working activities in modern society
Lezione Introduttiva
Sicurezza nelle aziende
Sicurezza e qualità alimentare
Il Biologo nella industria farmaceutica 1 CRA
Il sistema HACCP
Il Biologo nella industria farmaceutica 2 Regulatory, Farmaco vigilanza,
Il ruolo del Biologo nell'azienda farmaceutica:
l'esperienza in Direzione Medica
Biologia Forense
Il Biologo nel Monitoraggio ambientale
informatore scientifico del farmaco
importanza della vaccinazione nell’età pediatrica
Citogenetica e Citogenomica
Biologo nel SSN
Il Biologo nel laboratorio di analisi
Il Biologo incontra il territorio
Principi base sulla brevettazione
Nutrigenomica
Il Biologo nella sicurezza nei luoghi di lavoro
Aspetti normativi della professione del Biologo
Il giornalismo scientifico
Il ruolo del biologo nell'azienda ospedaliera
Il Biologo nutrizionista
Il biologo nelle aziende alimentari
Il Biologo nelle aziende

Lecture notes and calculation exercises will be provided

The professor receives every day from 8.00 to 9.00 by appointment via e-mail: giovanni.antonini@uniroma3.it