Optional group:
CARATTERIZZANTI - (show)
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12
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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 Molecolare, Cellulare e della Salute 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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Core compulsory activities
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ITA |
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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 Molecolare, Cellulare e della Salute LM-6 PERSICHINI TIZIANA, D'Ezio Veronica
( 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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Core compulsory activities
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ITA |
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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 Molecolare, Cellulare e della Salute 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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Core compulsory activities
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ITA |
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20410212 -
Genetica umana applicata
(objectives)
The main aims of the course are:
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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Core compulsory activities
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ITA |
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20410278 -
MICROBIOLOGIA AMBIENTALE
(objectives)
The main aims of the course are:
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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Derived from
20410278 MICROBIOLOGIA AMBIENTALE in Biodiversità e Tutela dell'Ambiente LM-6 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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Core compulsory activities
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ITA |
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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 Molecolare, Cellulare e della Salute 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 the main agricultural species. 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. Gluten.
( 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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Core compulsory activities
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ITA |
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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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Core compulsory activities
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ITA |
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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 Molecolare, Cellulare e della Salute 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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Core compulsory activities
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ITA |
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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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Derived from
20410495 Microbiomica in Biologia Molecolare, Cellulare e della Salute LM-6 CHEBBI ALIF
( syllabus)
This course is designed to equip students with key concepts for analyzing their microbiome-related multi-omics data and how to handle large datasets. It contains plenary lectures, case studies, practical lessons, and a final seminar, as follows:
Plenary lectures:
1 Introduction to the history of DNA studies and sequencing of genomes.
2 Introduction to the genomics for prokaryotes and its techniques (sequencing, annotation, gene family content, duplications, and deletions).
3 Comparing the recent next-generation sequencing (NGS) platforms; Analytical databases, tools, and pipelines (annotations); Phylogeny based on 16S, 25-28S, ITS.
4 Inferring the mechanisms of evolution from large genomic data sets: Horizontal gene transfer and mobilome; alignment; synteny detection; Multiple whole gene alignments.
5 Pan-genome and core-genome/ dispensable genome concepts.
6 Metagenomics approaches; Transcriptomics and gene chips; Proteome and interactome and Metabolomics.
7 Biotechnology and synthetic biology by omics: 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; Flow cytometry; Microfluidic techniques; High-throughput systems; Gas chromatography techniques.
8 Introduction to microbial ecology and new microbiome-related approaches.
Case studies:
Case study: Sequencing data preparation and analyses.
Cases study: Analysing microbiomes: alpha and beta diversity and main tools.
Case study: Analysing shotgun samples (Read-based and assembly-based approaches).
Case study: Studying procaryote gene virulences and antibiotic resistance genes (ARGs) and manipulating large datasets.
Case study: Cave microbiomes and omics under oligotrophic conditions.
Case study: Study of the biodegradation of hydrocarbons using NGS tools and bioremediation approaches.
Case study: Microbiota and food.
Practical classes:
- Practical classes: Introduction to Bash and Unix shell and command language.
- Practical classes: Manipulating microbial datasets with R and tidy verse:
- Practical classes: 16S metabarcoding studies and multiple profiling approaches (Alpha diversity, beta diversity, and others);
- Practical classes: Analyzing shotgun sequencing samples and different pipelines.
At the end-of-course, each student is asked to present a project during a seminar course (20 min/student). The projects will be selected during the lessons.
For any questions related to microbiomics courses, please contact us via:
Dr. Alif Chebbi, alif.chebbi@uniroma3.it (Researcher Bio19, Roma Tre university)
Dr. Irene Artuso, Irene.artuso@uniroma3.it (Postdoc and bioinformatician, Roma Tre university)
( reference books)
Books and basic tools:
"Brock biology of microorganisms" di Michael T. Madigan (Autore), Kelly S. Bender (Autore), Daniel H. Buckley (Autore), W. Matthew Sattley (Autore), David A. Stahl (Autore): capitoli 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 (Italian or English)
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
Introducing the Shell (only basic command lines).
Introduction to RStudio (only basic concepts).
R packages for data science (https://www.tidyverse.org/)
QIIME 2.
DADA2.
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6
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BIO/19
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48
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-
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-
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Core compulsory activities
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ITA |
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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).
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Derived from
20410321 VIROLOGIA ANIMALE GENERALE ED APPLICATA in Biologia Molecolare, Cellulare e della Salute 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, strategies of replication, 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:
- Leonard Norkin – Virology: Molecular Biology and Pathogenesis - ASM (American Society for Microbiology) Press (this text book is more detailed to study the different virus life cycles)
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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Core compulsory activities
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ITA |
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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 Molecolare, Cellulare e della Salute LM-6 MORENO SANDRA, ROSSI MARIANNA NICOLETTA, PRICE RACHEL
( 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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Core compulsory activities
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BIO/11
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20
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5
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Core compulsory activities
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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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Derived from
20401653 BIOCHIMICA E BIOLOGIA MOLECOLARE CLINICA in Biologia Molecolare, Cellulare e della Salute LM-6 N0 VENARUBEA MATTIA
( syllabus)
The laboratory medicine role in the clinical context. Elements of biomedical laboratory organization. The sectors of the biomedical laboratory. The roles and duties of the laboratory staff. Role of statistics in laboratory medicine. Evaluation of analytical performance: precision, trueness, limit of blank, limit of detection and sensitivity. Biological variability. Performance of a diagnostic test. Elements of metrology. Measurements and physical quantities in the laboratory. the pre-analytical phase. patient-related variability. Sample-related variability. Principles of immunochemistry. The immunochemical dosage. Immunochemical methods: turbidimetry and neplelometry. Enzymatic determinations. Muscle enzymes. Liver enzymes. Pancreatic enzymes. Bone enzymes. Clinical biochemistry of jaundice. Bilirubin metabolism. Classification of jaundice. Gilbert's syndrome and Crigler-Najjar syndrome. Neonatal jaundice. Protein diagnostics.
Dyslipidemias. Lipoproteins: chylomicrons, VLDL and IDL, LDL, HDL, Apolipoproteins. Metabolism of lipids and lipoproteins. Cardiovascular risk associated with dyslipidemia. Diagnosis of dyslipidemias. Treatment and therapy. Hematological diagnosis. Anemia: definition, causes and diagnosis. Hemoglobin, hematocrit, cell counts, erythrocyte indices, reticulocytes. Leukocyte formula. Laboratory test for platelet changes. Immunohematology. Erythrocyte blood group antigens. Antibodies. Antigen-antiboby reaction. Determination of group AB0, type D and Rh phenotype. Search for anti-erythrocyte antibodies. Direct and indirect Coombs test. Application of molecular biology to erythrocyte immunohematology. Hemostasis. Stages of haemostasis. Fibrinolysis. Congenital disorders of coagulation factors. PT, PTT, Fbg. Thrombin time. Anticoagulant therapy. Laboratory diagnostics of kidney diseases. Nitrogen. Urea. Creatinine. Estimation of glomerular filtrate. Low molecular weight plasma proteins. Proteinurias. Albuminuria. Physical, chemical and morphological urine examination. Electrolyte analysis. Water balance. Sodium and potassium balance. Blood gas analysis. Cardiac biomarkers. Study of the endocrine system. Pituitary gland. Thyroid. Testicle. Ovary. The laboratory role in the diagnosis of diabetes mellitus. Screening and diagnosis. Srveillance. Fasting blood sugar. Post-prandial blood sugar. Oral glucose load curve. Chetonic bodies. Albuminuria. Glycated hemoglobin. Insulin and C petide. Tumor markers. Biological liquids. Cephalorachidian fluid examination. Clinical Molecular Biology. Type of test and biological sample. Susceptibility Diagnosis. Early diagnosis: newborn screening. Disease diagnosis: cystic fibrosis, x-linked diseases. Prenatal diagnosis of hereditary and non-hereditary genetic diseases. Chronic myeloid leukemia. Inflammation biomarkers. C-reactive protein. VES. Pro calcitonin. Sepsis biomarkers. Mass spectrometry in clinical biochemistry and laboratory medicine. Drugs of abuse. Neonatal screening. Proteomics
( reference books)
M. Ciaccio, G. Lippi - Biochimica clinica e medicina di laboratorio - Edises Universitaria, Ed. II/2018
H. Loffler, J. Rastetter - Atlante di ematologia clinica - Antonio Delfino Editore, Ed. V.
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6
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BIO/12
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48
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-
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-
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Core compulsory activities
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ITA |
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20410493 -
Psychobiology
(objectives)
The course will address the main topics of interest in psychobiology, with the aim of promoting a basic knowledge of the subject, of the main experimental paradigms and methods used in psychobiology.
The aim of the course is therefore to provide knowledge of the biological and neuropsychological fundamentals and correlates of behavior and psychological functions in humans and animals, as well as the main methods and techniques used in psychobiological research.
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Derived from
20410493 Psicobiologia in Biologia Molecolare, Cellulare e della Salute LM-6 TREZZA VIVIANA
( syllabus)
Introduction to psychobiology: field of investigation and history
Introduction to the biological basis of behavior
Genes per environment interaction in typical and atypical brain development
Cognitive, affective and social development in childhood and adolescence
Learning and conditioning: neural substrates, pathological aspects, experimental paradigms
Memory: types of memory, neural substrates, pathological aspects, experimental paradigms
Emotion and motivation: neural substrates, pathological aspects, experimental paradigms
Psychotropic substances and the neurobiology of reward processes
Social behavior: neural substrates, pathological aspects, experimental paradigms
( reference books)
Principles of neural science, Eric R. Kandel, MD; James H. Schwartz, MD, PhD; Thomas M. Jessell, PhD; Steven A. Siegelbaum, PhD; and A. J. Hudspeth
- The slides of the lessons will be made available to students
To get an appointment with the Professor, email to: viviana.trezza@uniroma3.it
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6
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BIO/14
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48
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Core compulsory activities
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ITA |
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Optional group:
AFFINI E INTEGR - (show)
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12
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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
-
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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BIO/10
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20410212 -
Genetica umana applicata
(objectives)
The main aims of the course are:
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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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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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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BIO/18
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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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VENARUBEA MATTIA
( syllabus)
The laboratory medicine role in the clinical context. Elements of biomedical laboratory organization. The sectors of the biomedical laboratory. The roles and duties of the laboratory staff. Role of statistics in laboratory medicine. Evaluation of analytical performance: precision, trueness, limit of blank, limit of detection and sensitivity. Biological variability. Performance of a diagnostic test. Elements of metrology. Measurements and physical quantities in the laboratory. the pre-analytical phase. patient-related variability. Sample-related variability. Principles of immunochemistry. The immunochemical dosage. Immunochemical methods: turbidimetry and neplelometry. Enzymatic determinations. Muscle enzymes. Liver enzymes. Pancreatic enzymes. Bone enzymes. Clinical biochemistry of jaundice. Bilirubin metabolism. Classification of jaundice. Gilbert's syndrome and Crigler-Najjar syndrome. Neonatal jaundice. Protein diagnostics.
Dyslipidemias. Lipoproteins: chylomicrons, VLDL and IDL, LDL, HDL, Apolipoproteins. Metabolism of lipids and lipoproteins. Cardiovascular risk associated with dyslipidemia. Diagnosis of dyslipidemias. Treatment and therapy. Hematological diagnosis. Anemia: definition, causes and diagnosis. Hemoglobin, hematocrit, cell counts, erythrocyte indices, reticulocytes. Leukocyte formula. Laboratory test for platelet changes. Immunohematology. Erythrocyte blood group antigens. Antibodies. Antigen-antiboby reaction. Determination of group AB0, type D and Rh phenotype. Search for anti-erythrocyte antibodies. Direct and indirect Coombs test. Application of molecular biology to erythrocyte immunohematology. Hemostasis. Stages of haemostasis. Fibrinolysis. Congenital disorders of coagulation factors. PT, PTT, Fbg. Thrombin time. Anticoagulant therapy. Laboratory diagnostics of kidney diseases. Nitrogen. Urea. Creatinine. Estimation of glomerular filtrate. Low molecular weight plasma proteins. Proteinurias. Albuminuria. Physical, chemical and morphological urine examination. Electrolyte analysis. Water balance. Sodium and potassium balance. Blood gas analysis. Cardiac biomarkers. Study of the endocrine system. Pituitary gland. Thyroid. Testicle. Ovary. The laboratory role in the diagnosis of diabetes mellitus. Screening and diagnosis. Srveillance. Fasting blood sugar. Post-prandial blood sugar. Oral glucose load curve. Chetonic bodies. Albuminuria. Glycated hemoglobin. Insulin and C petide. Tumor markers. Biological liquids. Cephalorachidian fluid examination. Clinical Molecular Biology. Type of test and biological sample. Susceptibility Diagnosis. Early diagnosis: newborn screening. Disease diagnosis: cystic fibrosis, x-linked diseases. Prenatal diagnosis of hereditary and non-hereditary genetic diseases. Chronic myeloid leukemia. Inflammation biomarkers. C-reactive protein. VES. Pro calcitonin. Sepsis biomarkers. Mass spectrometry in clinical biochemistry and laboratory medicine. Drugs of abuse. Neonatal screening. Proteomics
( reference books)
M. Ciaccio, G. Lippi - Biochimica clinica e medicina di laboratorio - Edises Universitaria, Ed. II/2018
H. Loffler, J. Rastetter - Atlante di ematologia clinica - Antonio Delfino Editore, Ed. V.
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6
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BIO/12
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20410278 -
MICROBIOLOGIA AMBIENTALE
(objectives)
The main aims of the course are:
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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Derived from
20410278 MICROBIOLOGIA AMBIENTALE in Biodiversità e Tutela dell'Ambiente LM-6 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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BIO/19
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10
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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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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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BIO/06
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20
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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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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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20410493 -
Psicobiologia
(objectives)
The course will address the main topics of interest in psychobiology, with the aim of promoting a basic knowledge of the subject, of the main experimental paradigms and methods used in psychobiology.
The aim of the course is therefore to provide knowledge of the biological and neuropsychological fundamentals and correlates of behavior and psychological functions in humans and animals, as well as the main methods and techniques used in psychobiological research.
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TREZZA VIVIANA
( syllabus)
Introduction to psychobiology: field of investigation and history
Introduction to the biological basis of behavior
Genes per environment interaction in typical and atypical brain development
Cognitive, affective and social development in childhood and adolescence
Learning and conditioning: neural substrates, pathological aspects, experimental paradigms
Memory: types of memory, neural substrates, pathological aspects, experimental paradigms
Emotion and motivation: neural substrates, pathological aspects, experimental paradigms
Psychotropic substances and the neurobiology of reward processes
Social behavior: neural substrates, pathological aspects, experimental paradigms
( reference books)
Principles of neural science, Eric R. Kandel, MD; James H. Schwartz, MD, PhD; Thomas M. Jessell, PhD; Steven A. Siegelbaum, PhD; and A. J. Hudspeth
- The slides of the lessons will be made available to students
To get an appointment with the Professor, email to: viviana.trezza@uniroma3.it
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BIO/14
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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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CHEBBI ALIF
( syllabus)
This course is designed to equip students with key concepts for analyzing their microbiome-related multi-omics data and how to handle large datasets. It contains plenary lectures, case studies, practical lessons, and a final seminar, as follows:
Plenary lectures:
1 Introduction to the history of DNA studies and sequencing of genomes.
2 Introduction to the genomics for prokaryotes and its techniques (sequencing, annotation, gene family content, duplications, and deletions).
3 Comparing the recent next-generation sequencing (NGS) platforms; Analytical databases, tools, and pipelines (annotations); Phylogeny based on 16S, 25-28S, ITS.
4 Inferring the mechanisms of evolution from large genomic data sets: Horizontal gene transfer and mobilome; alignment; synteny detection; Multiple whole gene alignments.
5 Pan-genome and core-genome/ dispensable genome concepts.
6 Metagenomics approaches; Transcriptomics and gene chips; Proteome and interactome and Metabolomics.
7 Biotechnology and synthetic biology by omics: 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; Flow cytometry; Microfluidic techniques; High-throughput systems; Gas chromatography techniques.
8 Introduction to microbial ecology and new microbiome-related approaches.
Case studies:
Case study: Sequencing data preparation and analyses.
Cases study: Analysing microbiomes: alpha and beta diversity and main tools.
Case study: Analysing shotgun samples (Read-based and assembly-based approaches).
Case study: Studying procaryote gene virulences and antibiotic resistance genes (ARGs) and manipulating large datasets.
Case study: Cave microbiomes and omics under oligotrophic conditions.
Case study: Study of the biodegradation of hydrocarbons using NGS tools and bioremediation approaches.
Case study: Microbiota and food.
Practical classes:
- Practical classes: Introduction to Bash and Unix shell and command language.
- Practical classes: Manipulating microbial datasets with R and tidy verse:
- Practical classes: 16S metabarcoding studies and multiple profiling approaches (Alpha diversity, beta diversity, and others);
- Practical classes: Analyzing shotgun sequencing samples and different pipelines.
At the end-of-course, each student is asked to present a project during a seminar course (20 min/student). The projects will be selected during the lessons.
For any questions related to microbiomics courses, please contact us via:
Dr. Alif Chebbi, alif.chebbi@uniroma3.it (Researcher Bio19, Roma Tre university)
Dr. Irene Artuso, Irene.artuso@uniroma3.it (Postdoc and bioinformatician, Roma Tre university)
( reference books)
Books and basic tools:
"Brock biology of microorganisms" di Michael T. Madigan (Autore), Kelly S. Bender (Autore), Daniel H. Buckley (Autore), W. Matthew Sattley (Autore), David A. Stahl (Autore): capitoli 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 (Italian or English)
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
Introducing the Shell (only basic command lines).
Introduction to RStudio (only basic concepts).
R packages for data science (https://www.tidyverse.org/)
QIIME 2.
DADA2.
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BIO/19
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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:
• 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 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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PETTINICCHIO VALENTINA
( syllabus)
Introduction and general aspects: definition and public health tasks. Primary, secondary and tertiary prevention.
General epidemiology: epidemiological methodology; sources and methods of collecting epidemiological data. Main measures used in Epidemiology (frequency, prevalence, incidence, rates).
Epidemiological studies: descriptive, analytical, experimental methodology.
Epidemiology and prevention of infectious diseases. Features and ways of spreading of infectious diseases. Epidemiology: etiological agents. Temporal and spatial distribution of infectious diseases (sporadic, endemic, epidemic, pandemic disease). Direct prophylaxis: notification, assessment, isolation, disinfection and disinfestation. Specific prophylaxis: vaccine, serum and chemoprophylaxis.
Epidemiology and prevention of non-communicable diseases. Epidemiology: etiology, risk factors, distribution and frequency of non-communicable diseases of social interest in Italy.
Prevention: primary (strengthening of organic defenses, modification of behavior, intervention on the environment), secondary (mass and selective screening), tertiary (rehabilitation and social reintegration).
The main chronic non-communicable diseases: cardiovascular diseases, tumors.
Environmental hygiene and food safety. Atmospheric air: chemical-physical characteristics, urban air pollution (sources, contaminants, effects), prevention. Water for human use: physical, chemical and microbiological characteristics; correction of water intended for human consumption. Urban waste water: study of the characteristics and methods of purification and disposal. Municipal solid waste: classification, characteristics, collection and disposal methods. Food: food-borne infections and food poisoning.
Hospital hygiene and nosocomial infections. The challenge of antibiotic resistance.
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MED/42
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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).
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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, strategies of replication, 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:
- Leonard Norkin – Virology: Molecular Biology and Pathogenesis - ASM (American Society for Microbiology) Press (this text book is more detailed to study the different virus life cycles)
Students are received at the end of the lessons or by appointment via email (elisabetta.affabris@uniroma3.it).
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BIO/19
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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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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 the main agricultural species. 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. Gluten.
( 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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BIO/04
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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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BIO/11
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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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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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20410723 -
Bioorganic Chemistry with Laboratory
(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 and contrasted 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. Some of these reactions will be carried out experimentally in the didactic laboratory, while their course will be monitored by means of different chromatographic techniques. Finally, the different obtained products will be purified and fully characterised employing various spectroscopic techniques.
Prerequisites: Good knowledge concerning the basic principles of Organic Chemistry and Biochemistry
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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 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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TOFANI DANIELA
( 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 about 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 phosphoenol pyruvate (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 the 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 in histidine metabolism.
( reference books)
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
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6
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CHIM/06
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24
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30
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Related or supplementary learning activities
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ITA |
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20410725 -
Photobiology
(objectives)
The Course provides the fundamentals of light and living organism interactions, focusing on the use of light for diagnosis and therapy. Photoproduction of energy (photosynthesis and its applications in green energy production), photophysical phenomena, light propagation in human tissues and use of light in the treatment of tumours and other pathologies are described in details. Biomedical applications related to photodiagnosis, photosensitivity, phototherapy, photodynamic therapy and photosensitizing drugs are examined. In addition, part of the course covers topics related to Optogenetics, a novel technique that uses light to control neurons, which have been genetically modified to express light-sensitive ion channels. Optogenetics uses a combination of optical and genetic techniques to control the activities of individual neurons in living tissues.
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Derived from
20810218 PHOTOBIOLOGY in Biomedical Engineering LM-21 LUCIDI MASSIMILIANO
( syllabus)
Aim: The Course provides the fundamentals of light and living organism interactions, focusing on the use of light for diagnosis and therapy. Photoproduction of energy (photosynthesis and its applications in green energy production), photophysical phenomena, light propagation in human tissues and use of light in the treatment of tumours and other pathologies are described in details. Biomedical applications related to photodiagnosis, photosensitivity, phototherapy, photodynamic therapy and photosensitizing drugs are examined. In addition, part of the course covers topics related to Optogenetics, a novel technique that uses light to control neurons, which have been genetically modified to express light-sensitive ion channels. Optogenetics uses a combination of optical and genetic techniques to control the activities of individual neurons in living tissues.
Topics
Fundamentals of light propagation in biological tissues
Interactions between light and molecules; electronic states of a molecule and the transitions between them: difference between bioluminescence, phosphorescence, fluorescence and other non-radiative phenomena; interactions between light, cell and tissues; effects of light propagation in biological tissues; fundamentals of the most employed light sources used in biomedical diagnostic devices.
Basics of biology
Cellular structure and types; chemical building blocks; cellular processes (central dogma of Biology): replication, transcription, translation, biosynthesis and energy production; protein classification and function; organization of cells in tissues; morphological and physiological description of the main tissue in human body.
Basic principles of genetic engineering and DNA manipulation
Polymerase chain reaction (PCR); restriction enzymes; cloning process. Genetic manipulation of microorganisms and superior organisms.
Biosensors
Principles; biorecognition; optical transduction; molecular basis of biosensors generation; bioluminescence, colorimetric, fluorescence and FRET-based sensors. Applications of biosensors in human oncology, bioremediation, food safety and drug production. Main devices and imaging techniques employed for biosensor detection.
Super-resolution imaging: techniques and biological applications
Physical principles and biomedical applications of different optical-super-resolution techniques (i.e., two and multi-photon microscopy, STORM, PALM, STED, expansion microscopy, rescan confocal microscopy, LLS, SIM). Physical principles and biomedical applications of different non-optical super-resolution techniques: electron microscopy (TEM, SEM, STEM); AFM.
Microarray Technology
Definitions and applications of Omic Sciences; typology of microarrays (DNA, protein, cell and tissue microarrays).
Photosynthesis
Plastids in plants; light and dark reactions; Calvin cycle and carbon fixation; ecological aspects on photosynthesis; natural and artificial photosynthesis for green energy generation.
Spectral tuning in Biology
Major pigments in biological systems; chemistry behind pigment photoefficiency (resonance theory, chemical environment and modifications in light absorption properties); chromatic acclimation and chromatic adaptation; molecular aspects of chromatic acclimation.
Visual tuning in humans
Human eye anatomy; human eye aberration: wave and chromatic aberrations, intraocular scattering; OCT; retina tissue organization; cytology of rod and cone cells; rhodopsin and retinal: structure and functions; retinal photocycle: molecular isomerization at the basis of vision; phototransduction cascade in vertebrate photoreceptors.
Optogenetics
General description of optogenetic molecular tools; opsins in animals; mechanisms of genetic construct delivery into mammalians; optrodes: applications and limitations.
Photophysiology and Phototoxicity
Vitamin D: photosynthesis and metabolism in human body; evolutionary aspects of vitamin D-mediated regulation of calcium homeostasis; human skin organization and differentiation of skin cell types; melanin production and functions; effects of ultraviolet radiation; effects of photodamaging on cells; mechanisms of DNA repair after photodamaging: homologous recombination, mismatch repair, Nucleotide Excision Repair, photolyase and UVR-mediated repair; photosensitivity diseases; light-dependent circadian cycle.
Fundamentals of the photothermal therapeutic effects of light sources
Interaction of light and physical sensing; phototherapy; photodynamic therapy; photosensitizing drugs.
Guided tour in the RomaTre Department of Sciences on the facilities and equipment studied in the course (luminometer, fluorimeter, flow-cytometer, devices for genetic manipulation).
Guided tour in the RomaTre Department of Sciences on confocal microscopes.
Guided tour in the LIME laboratories on the TEM, SEM and AFM microscopes.
( reference books)
Prasad PN. Introduction to Biophotonics 2nd edition. Wiley-Interscience, Hoboken, NJ. 2003;
Björn LO. Photobiology: The Science of Life and Light, 2nd edition. Springer-Verlag, New York. 2008.
Alberts B, Bray D, Hopkin K, Johnson AD, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Essential Cell Biology. 3rd edition. Garland Science. 2010.
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6
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48
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Elective activities
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ITA |
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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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MORENO SANDRA
( 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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ROSSI MARIANNA NICOLETTA
( syllabus)
Genes and networks involved in neural induction with particular attention to the regulatory role of micro RNAs.
Molecular pathways of polarity and segmentation. Molecular organizers of neurodevelopment. Determination and differentiation of neuronal cells.
The anteroposterior axis and the Hox genes: characterization and role in the anteroposterior specification of the organism.
Growth and direction of axons.
Long non-coding RNA and circRNA in brain development.
Role of regulatory RNAs in translational control of synapse.
Molecular mechanisms of adult neurogenesis.
Role of Polyamines in the modulation of glutamate receptors. Interaction between glutamatergic system, serotonergic system and polyamine metabolism.
Animal models used in neuronal diseases.
NGS techniques for the study of neurodevelopment
( reference books)
Lo sviluppo del sistema nervoso. Authors: Dan H. Sanes; Thomas A. Reh; William A. Harris. Publishing house: Zanichelli
Lecture slides will be provided.
The professor receives every day from 10.00 to 11.00 by appointment via e-mail: mariannanicoletta.rossi@uniroma3.it
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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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ITA |
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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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ITA |
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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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ITA |
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Università Roma Tre