Learning objectives
The aim of the course is to make the student familiar with the most modern methods of analysis of microbial communities, to enable him to read, critically, scientific articles on this subject and to give him the tools to evaluate, through these analyses, the impacts that several environmental factors (pollution, climatic variations, anthropic activities of various kinds, etc.) may have on processes in which microorganisms play a key role.
Prerequisites
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Course unit content
The course provides a multidisciplinary approach to the study of biodiversity and analysis of microbial communities. At the end of the course students will have basic knowledge relevant to the study of microbial ecosystems. In particular will know: - the main cultural and molecular techniques for the identification of micro-organisms, phylogenetic analysis methods, the principles of omics technologies applied the description of microbial communities as well as methods for the study of their functional activity .
Full programme
Structure of a microbial community - biodiversity indices of microbial communities. Traditional methods of analysis based on pure culture cultivation: isolation and identification of microbial species by biochemical and serological methods.
Molecular methods applied to microorganisms isolated in pure culture: PCR, analysis by agarose gel electrophoresis, real-time PCR, cloning, sequencing, RAPD analysis, rep-PCR, ARDRA, RISA, ARISA.
Application of molecular techniques to the study of microbial communities, without cultivation of microorganisms: isolation of environmental DNA, genetic fingerprinting techniques ARDRA, SSCP, T-RFLP, DGGE, RISA, LH-PCR, RAPD. High throughput sequencing techniques and their application to the study of microbial communities. DNA / RNA Stable isotope probing. Fluorescent in situ hybridization (FISH CARD-FISH, Raman-FISH, NanoSIMS). Microarray
Bibliography
Bibliographic material will be provided by the teacher. It will refer to the most updated scientific literature
Teaching methods
Given the particular situation related to the SARS-Cov-2 pandemic, some lessons will be carried out by video recording in order to make the student learn the theory. Then, in direct video connection with the teacher, in silico analysis of DNA sequences, searches in databases etc will be done in order to make the student familiar with the tools normally used in such analyses. If possible, some of the most common molecular techniques described in the theoretical part (environmental DNA extraction, PCR, digestion with restriction enzymes, electrophoresis on agarose gel) will be illustrated in laboratory.
Assessment methods and criteria
The student will be asked to choose an article dealing with analysis of microbial communities in a given context (for example the effect of remediation practices and their impact on the microbial communities of a contaminated site, or the analysis of microbial successions in the production of fermented foods, or the analysis of the intestinal microbiota of animals subjected to different diets etc etc). The student will read the article, elaborate a PowerPoint presentation illustrating the work and discuss it with the teacher and the other students in (virtual) class. The active participation in the discussion of the other students is also part of the exam (and will be evaluated). Upon completion of the exam, the teacher will ask a question on one of the topics covered in class or in the laboratory. The exam will verify the level of competence reached by the student and the autonomy of judgment.
For students who have not participated in online activities (not attending), the exam will consist of an oral question on the topics developed in class by the teacher.
Other information
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2030 agenda goals for sustainable development
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