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Lecturer(s)
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Nováková Eva, doc. RNDr. Ph.D.
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Course content
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Content of lectures: The course will cover the following topics: 1. Origin and evolution of life The students will be introduced to the basic concepts of the diversification of life, and the key facts that led to the evolution of various groups of bacteria, archaea, and unicellular eukaryotes. Microbial species concept will be discussed. 2. Microbial diversity in nature In this class the microorganisms, their diversity and biochemical and ecological characteristics, will be presented. Microbial interactions with other organisms will be introduced. 3. Symbiosis with bacteria Symbiosis will be reviewed, as a widespread and diverse ecological relationship involving microorganisms (and particularly bacteria). The microbiome and holobiont concepts will be introduced. 4. Introduction to microbial genomics The basic processes in genome evolution: selection vs. genetic drift will be discussed, along with mechanisms of DNA gains (HGT) and losses. Current sequencing, genomics and bioinformatics approaches will be overviewed for the following lesson. 5. Molecular tools in microbial ecology studies The molecular methodologies that have been and are currently used in microbial ecology will be described to provide an empirical basis for the further analyses the students will perform during the practical sessions. 6-7. High-throughput technologies: the 'omic' era This class will be split in both an introductory lecture about the so-called 'omic' technologies, and a practical session in which the students will start approaching the bioinformatics tools used for processing high-throughput data. 8-9. Community profiling: amplicon sequencing This class will consist mostly in a practical session on amplicon data analysis, supported by the explanation of the necessary theoretical concepts. Basic diversity indexes will be calculated and analyses of similarity will be performed. 10-11. Genomics: genome reconstruction, annotation and comparative genomics This class will consist mostly in a practical session on genomic data analysis, supported by the explanation of the necessary theoretical concepts. 12-13. Functional genomics: transcriptomics and proteomics This class will consist mostly in a practical session to show the students some of the bioinformatics tools used for transcriptomic and proteomic data analyses. 14. Potential applications in biotechnology and environmental preservation This class will be organized as a round table in which each student (individually or in small groups) will present a specific topic (i.e. from a research paper) and discuss it with the rest of the class. Content of practicals: (see above)
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Learning activities and teaching methods
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Monologic (reading, lecture, briefing), Dialogic (discussion, interview, brainstorming), Work with multi-media resources (texts, internet, IT technologies), Practical training, Case studies
- Class attendance
- 26 hours per semester
- Preparation for classes
- 50 hours per semester
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Learning outcomes
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1. To provide students with a theoretical background in microbial ecology and diversity. 2. To provide students with an introductory concept of symbiosis involving bacteria. 3. To provide students with a theoretical background in bacterial genomics. 4. To introduce students to the use of bioinformatics as a tool for microbial ecology studies.
The students will acquire the basic knowledge of theoretical background and current methodology used in microbial ecology and genomics.
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Prerequisites
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Students are not obliged to undertake any specific classes prior their enrolment in this class. Any prior knowledge of molecular biology and bacterial genomics is however advantageous for a full understanding of the class content.
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Assessment methods and criteria
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Oral examination, Student performance assessment
In order to pass this class, the students are obliged to actively participate in its theoretical and practical part. They have to prove their ability to use bioinformatic tools for microbiome analyses for which the hands on training have been provided. Finally, the students undertake an oral exam based on the content of both theoretical and practical part of this course. Students must successfully address at least 60% of discussed questions.
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Recommended literature
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" DeLong EF, Pace NR (2001). Environmental diversity of Bacteria and Archaea. Systematic Biology 50: 470-478. doi: 10.1080/10635150118513.
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" Moran NA (2006). Symbiosis. Current Biology 16: R866-R871. doi: 10.1016/j.cub.2006.09.019.
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" Navas-Molina JA, Peralta-Sánchez JM, González A, et al (2013) Chapter Nineteen - Advancing our understanding of the human microbiome using QIIME. In: DeLong EF (ed) Methods in Enzymology. Academic Press, pp 371-444.
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" Preheim SP, Perrotta AR, Friedman J, et al (2013) Chapter Eighteen - Computational methods for high-throughput comparative analyses of natural microbial communities. In: DeLong EF (ed) Methods in Enzymology. Academic Press, pp 353-370.
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" Sharpton TJ (2014). An introduction to the analysis of shotgun metagenomic data. Frontiers in Plant Science 5: 209. doi: 10.3389/fpls.2014.00209.
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" Xu J (2006). Microbial ecology in the age of genomics and metagenomics: Concepts, tools, and recent advances. Molecular Ecology 15: 1713-1731. doi: 10.1111/j.1365-294X.2006.02882.x.
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