Teaching code

4S008408

Credits

9

Coordinator

Sandra Torriani

Language

Italian

Scientific Disciplinary Sector (SSD)

BIO/19 - MICROBIOLOGY

Moodle Seminars 0

The teaching is organized as follows:

Learning objectives

Module: THEORETICAL LECTURES The course is designed to introduce students to the basic knowledge of the microbial world as well as to illustrate the main methodological tools for research in microbiology, with a detailed comparison of the properties among the different type of microorganisms, both prokaryotes and eukaryotes, including bacteria, archaea, yeasts, filamentous fungi, and - in a distinct section, since non-cellular organisms – the viruses. During the first series of lectures, general themes will be addressed such as morphological and functional diversity, genetic, biochemical and metabolic features, evolutionary aspects and ecology of microorganisms, including how they interact with specific environmental factors. In the second series of lectures, microorganisms will be discussed as reference systems for fundamental studies dealing with molecular biology as well as biochemistry and metabolic regulatory mechanisms. Also elements will be provided about the methods for microbe cultivation and on strategies for the control of microbial growth and the conditioning of the metabolism. The third part of lectures will cover the detailed study of particularly important microbial groups to be defined with the Students. Module: LABORATORY PRACTICES This laboratory module is designed to guide students in the acquisition of techniques and in the development of manipulative skills all necessary for the identification and the study of both structural and functional characteristics of the microorganisms of interest, as well as for a proper handling of microbial cultures within research activities. The main objective of the module is to provide students with the basic tools, represented by traditional analytical procedures in microbiology, but also with the knowledge of advanced techniques, based on molecular methods of investigation, useful for basic research but even the definition of the correct approach to issues related to the many themes of applied microbiology.

Prerequisites and basic notions

All the basic courses of the 1st year.
Pre-requisites: General and cellular biology
Knowledge of biochemistry
Basic bioinformatics skills

Program

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1. MICROBIAL EVOLUTION AND DIVERSITY: Origin and Evolution of the Microbial Life; Bacteria; Archaea; Eukaryotic Cell and Eukaryotic Microorganisms; Microbial Taxonomy and Systematics.
2. PRINCIPLES OF MICROBIOLOGY: Cell Structure and Function in Bacteria, Archaea and Fungi (Yeast and Moulds);
3. MICROBIAL GROWTH: Microbial Nutrition, Culture and Growth Aspects; Antimicrobial Agents and Microbial Growth Control.
4. METABOLIC DIVERSITY: Phototrophy and autotrophy , Aerobic (EMP pathway, Enther-Doudoroff pathway, Hexose Monophosphate Shunt + electron transport chain and proton motive force generation) and Anaerobic Respiration Fermentations (homolactic and heterolactic, mixed-acid, butane-diol, propionic, butanol/acetone fermentations), Chemolithotrophy; Other biosyntheses (ammonia assimilation, nitrogen fixation).
5. VIRAL DIVERSITY: Overview of Different Viral Groups; Bacteriophages.
6. HINTS on BACTERIAL GENETICS: Mutations; Genetic Recombination: Transformation, Conjugation, Transduction, and MOLECULAR BIOLOGY AND GENE EXPRESSION Molecular Biology of Bacteria: Cloning Vectors and Expression Vectors; Regulation of Gene Expression.
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7. MICROBIAL INTERACTIONS. Type of relationships between microorganisms (commensalism, parasitism, mutualism). The microbial consortia. Symbiotic associations: interactions between species. The mycorrhizae.
8. MICROBIAL BIODIVERSITY AND INVESTIGATION METHODS: The cultivable and non-cultivable microbial biodiversity. Identification, classification, and nomenclature of cultivable biodiversity. The nomenclature: rules and tools (Code of the nomenclature and LPSN - List of Prokaryotic Names with Standing in Nomenclature). The concept of species, the definition of strain and type strain. The classical systematic approaches (phenetic, numerical, polyphasic), the phylogenetic approach. The investigation techniques, from the hybridization of total DNA to the sequencing and comparison of genomes and levels of taxonomic resolution. Non-cultivable biodiversity: culture-independent study techniques (PCR-DGGE, metabarcoding, metagenomics) and their nomenclature (Candidatus).
9. GROUPS OF MICROORGANISMS: The taxonomic levels and the main groups of microorganisms Proteobacteria, Firmicutes, Actinobacteria, Deinococcus-Thermus.
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UL: laboratorio
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The aim of the laboratory is to demonstrate to the student some techniques of microbiological analysis of a natural source, through the use of analytical methods based on morphological, physiological and biochemical tests to evaluate the types of microorganisms present which in the source itself and to classify them by a taxonomical approach. In the first teaching credit, it will be displayed some techniques of plate count using general-purpose media to count and isolate bacteria and fungi, microbial growth patterns in tube and plate, motility assay and culture maintaining methods. In the second teaching credit, it will be displayed some methods used to carry out a preliminary identification of bacteria and fungi. Optical microscopy for morphological analysis of cells, sugar patterns assimilation and fermentation, cell staining methods and enzymatic assays.
Molecular methods: (a) Total DNA extraction from liquid culture: i) DNA detection by means of agarose gel electrophoresis, ii) DNA quantification on BioPhotometer through analysis of 260/280 and 260/320 ratios – (b) PCR amplification of the 16S rRNA gene sequence – (c) BOX-PCR analysis and observation of BOX profiles by agarose gel electrophoresis – (d) Analysis of 16S rRNA gene sequences of sonme unknown isolates by comparison with genetic sequence data banks: i) NCBI; ii) Ez-Taxon.- e) construction of phylogenetic trees by using 16S rRNA sequences of strains belonging to Bacillus sp. and Pseudomonas sp.
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UL: laboratorio
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The aim of the laboratory is to demonstrate to the student some techniques of microbiological analysis of a natural source, through the use of analytical methods based on morphological, physiological and biochemical tests to evaluate the types of microorganisms present which in the source itself and to classify them by a taxonomical approach. In the first teaching credit, it will be displayed some techniques of plate count using general-purpose media to count and isolate bacteria and fungi, microbial growth patterns in tube and plate, motility assay and culture maintaining methods. In the second teaching credit, it will be displayed some methods used to carry out a preliminary identification of bacteria and fungi. Optical microscopy for morphological analysis of cells, sugar patterns assimilation and fermentation, cell staining methods and enzymatic assays.
Molecular methods: (a) Total DNA extraction from liquid culture: i) DNA detection by means of agarose gel electrophoresis, ii) DNA quantification on BioPhotometer through analysis of 260/280 and 260/320 ratios – (b) PCR amplification of the 16S rRNA gene sequence – (c) BOX-PCR analysis and observation of BOX profiles by agarose gel electrophoresis – (d) Analysis of 16S rRNA gene sequences of sonme unknown isolates by comparison with genetic sequence data banks: i) NCBI; ii) Ez-Taxon.- e) construction of phylogenetic trees by using 16S rRNA sequences of strains belonging to Bacillus sp. and Pseudomonas sp.

Bibliography

Didactic methods

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Frontal lessons. In case of limitations due to COVID, supporting video material (recordings) will be provided.
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UL: laboratorio
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The laboratory will consist of group exercises, as well as lectures aimed at preparing practical activities and analyzing and discussing the results obtained.
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UL: laboratorio
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The laboratory will consist of group exercises, as well as lectures aimed at preparing practical activities and analyzing and discussing the results obtained.

Learning assessment procedures

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UL: teoria
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There are no ongoing tests. The exam will consist of an oral assessment of the degree of learning achieved on the course program. The exam consists of three or four questions posed to each candidate. The exam has a total duration of approximately 30 minutes.
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At the end of the practice lessons the student must be draw up a report on the results obtained in laboratory and related comments. The manuscript must be given to laboratory teachers within 15 days from the end of the practical experiences. Based on the report evaluation, a score of maximum 2 points will be attributed and it will be added to the final exam score.
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UL: laboratorio
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At the end of the practice lessons the student must be draw up a report on the results obtained in laboratory and related comments. The manuscript must be given to laboratory teachers within 15 days from the end of the practical experiences. Based on the report evaluation, a score of maximum 2 points will be attributed and it will be added to the final exam score.

Evaluation criteria

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UL: teoria
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Evaluation criteria are the degree of learning achieved on the course program, the clarity of presentation, the property of the specific technical-scientific language.
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UL: laboratorio
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Evaluation criteria include: knowledge of information, properties of language, clarity of presentation / writing.
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UL: laboratorio
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Evaluation criteria include: knowledge of information, properties of language, clarity of presentation / writing.

Criteria for the composition of the final grade

The final evaluation is expressed out of thirty. The report on the laboratory exercises will be associated with a maximum score of 2 points which contribute to the composition of the final grade and any honors.

Exam language

------------------------ UL: teoria ------------------------ La prova viene svolta in italiano (possibile in inglese per studenti Erasmus) ------------------------ UL: laboratorio ------------------------ la prova sarà svolta in lingua italiana (possibile inglese per studenti Erasmus) ------------------------ UL: laboratorio ------------------------ la prova sarà svolta in lingua italiana (possibile inglese per studenti Erasmus)