| Course code | ITUMOL01 |
| Course title | Molecular Tools to Study Microbial Ecology |
| Institution | Istanbul Technical University |
| Course address | Istanbul Technical University Faculty of Civil Engineering, Department of Environmental Engineering, 34469 Maslak/Istanbul, Turkey |
| City | Istanbul |
| Minimum year of study | 2nd year |
| Minimum level of English | Good |
| Minimum level of French | None |
| Key words | Molecular Microbial Ecology, Environmental Biotechnology, PCR, Real Time PCR, Fluorescence in situ hybridization, Denaturant Gradient Gel Electrophoresis, Cloning, Sequencing, Phylogenetic Analysis |
| Language | English |
| Professor responsible | Orhan Ince |
| Telephone | +90 212 2856570 |
| Fax | +90 212 2856587 |
| oince@ins.itu.edu.tr | |
| Participating professors | Bahar Ince, Candan Tamerler Behar, Ece Sen, Nilgun Ayman Oz, Mustafa Kolukirik, Ozge Eyice, Zeynep Cetecioglu |
| Number of places | Minimum: 10, Maximum: 20, Reserved for local students: 0 |
| Objectives | The main goal of the course is to: 1. Discuss importance of studying microbial ecology of natural and engineered ecosystems. 2. Discuss advantages of molecular tools over traditional cultivation based methods to study microbial ecology. 3. Present selected DNA and RNA targeted molecular methods used in microbial ecology 4. Apply DNA extraction, polymerase chain reaction (PCR), Real Time PCR, Fluorescence in situ hybridization (FISH), Denaturant Gradient Gel Electrophoresis (DGGE), Cloning-sequencing and phylogenetic analysis of genes retrieved from environmental samples. |
| Programme to be followed | Five 2-hour lectures:1. Introduction to microbial ecology of natural and engineered ecosystems, basics of DNA extraction, PCR and agarose gel electrophoresis2. Importance of studying microbial ecology, basics of Q-PCR and DGGE3. Advantages of molecular tools for evaluation, basics of cloning and sequencing 4. DNA/RNA targeted molecular methods used in microbial ecology-I, basics of FISH. 5. DNA/RNA targeted molecular methods used in microbial ecology-II, basics of bioinformatics Five 4-hour laboratory studies: 1. DNA extraction, PCR and agarose gel electrophoresis2. Q-PCR and DGGE3. Cloning and Sequencing4. FISHBioinformatics |
| Prerequisites | Basic knowledge of molecular biology and microbiology. |
| Course exam | An evaluation test at the end of the course. |
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