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Course Description Course Name : Molecular Microbiology Course Code : KMB-507 Course Type : Optional Level of Course : Second Cycle Year of Study : 1 Course Semester : Fall and Spring (16 Weeks) ECTS : 4 Name of Lecturer(s) : Prof.Dr. FATİH KÖKSAL Learning Outcomes of the Course : Defines PCR and PCR-based methods. Explains the advanced electrophoresis methods . Identifies the number of SNPs by the method of sequencing. Applies PFGE method. Applies AFLP method. Applies Spoligotyping method. Applies MIRU-VNTR method. Mode of Delivery : Face-to-Face Prerequisites and Co-Prerequisites : None Recommended Optional Programme Components : None Aim(s) of Course : Teaching basic information about molecular methods used in the diagnosis and epidemiology of infectious diseases and their applications, advantages and disadvantages. Course Contents : In this lesson; the molecular methods used to evaluate epidemiology of Infections, their advantages and disadvantages and molecular typing methods used to identify the molecular structure of the bacterial cell such as AP-PCR, PCR-RFLP, multiplex-PCR and Real Time PCR, Electrophoresis techniques, AFLP, PFGE, MIRU-VNTR, Spoligotyping and Sequence analysis are taught through theoretical course, discussion and practice. Language of Instruction : Turkish Work Place : C.U Faculty of Medicine Department of Medical Microbiology meeting room and laboratories.   Course Outline /Schedule (Weekly) Planned Learning Activities Week Subject Student's Preliminary Work Learning Activities and Teaching Methods 1 The epidemiology of infection and moleculer methods Reading resources and lecture notes on the subject Verbal lecture, demonstration 2 Advantages and disadvantages of moleculer methods Reading resources and lecture notes on the subject Verbal lecture, demonstration 3 Bacterial Cell and moleculer structure. Reading resources and lecture notes on the subject Verbal lecture, demonstration 4 DNA structure and replication, SNP, deletions and insertion mutations of DNA Reading resources and lecture notes on the subject Verbal lecture, demonstration, discussion 5 RNA structural features Reading resources and lecture notes on the subject Verbal lecture, demonstration, discussion 6 Protein and bacterial cell proteins Reading resources and lecture notes on the subject Verbal lecture, demonstration, discussion 7 DNA replication in-vitro conditions: PCR and type Reading resources and lecture notes on the subject Verbal lecture, demonstration, discussion 8 Midterm Exam Midterm exam Written examination 9 Electrophoresis tecniques, SDS-PAGE, Western blotting and Southern blotting methods. Laboratory preparation Laboratory 10 AP-PCR, PCR-RFLP, Multipleks- PCR and Real Time PCR Laboratory preparation Laboratory 11 AFLP method Laboratory preparation Laboratory 12 PFGE method Laboratory preparation Laboratory 13 MIRU-VNTR method Laboratory preparation Laboratory 14 Spoligotyping method Laboratory preparation Laboratory 15 Sequencing method Laboratory preparation Laboratory 16/17 Final Exam Exam preparation Practical exam   Required Course Resources Resource Type Resource Name Recommended Course Material(s)  Molecular_Bacteriology Robert G. 2008  Lecture notes and slides Required Course Material(s)  Advances in Applied Microbiology A.I.Laskın ELSEVİER 2006  Quantitative PCR Protocols R.Udo. 2007   Assessment Methods and Assessment Criteria Semester/Year Assessments Number Contribution Percentage     Mid-term Exams (Written, Oral, etc.) 1 60     Homeworks/Projects/Others 1 40 Total 100 Rate of Semester/Year Assessments to Success 40   Final Assessments 100 Rate of Final Assessments to Success 60 Total 100   Contribution of the Course to Key Learning Outcomes # Key Learning Outcome Contribution* 1 Identifies morphological and physiological characteristics of microorganisms 5 2 Identificates genomic structures of microorganisms 5 3 Explains microorganisms virulance factors and infection mechanisms. 0 4 Defines the mechanisms of immune response and defense against microorganisms 0 5 Lists the antimicrobial agents. 0 6 Defines the mechanisms of resistance development against antimicrobial agents. 0 7 Lists the microscopy, culture, serological and molecular diagnostic principles used in the laboratory diagnosis of infectious microorganisms. 5 8 Lists microbiological tests for identification of microorganisms 5 9 Implements and applies the methods used in the period from receipt of the clinical specimens up to identification of the causative agent . 5 10 Prepares a suitable media, applicates the staining methods, biochemical tests and molecular diagnostic methods to identify microorganisms from clinical samples. 5 11 Applies the biochemical tests and basic microbiological staining methods which are necessary for microbiological identification . 5 12 Determines the microorganisms by using basic molecular diagnostic techniques. 5 13 Works individually or as a team member related to the field. 0 14 Carries out the missions given within the scope of research projects. 0 15 Develops a positive attitude and behaviour towards lifelong learning. 0 16 Evaluates own knowledge and new-learned knowledge in a critical view after graduating. 0 17 Communicates effectively. 0 18 Transfers their own ideas and developments in the field, and offers solutions visually and verbally supporting with qualitative and quantitative data. 0 19 Applies ethical principles during study, evaluation and result sharing. 0 * Contribution levels are between 0 (not) and 5 (maximum).   Student Workload - ECTS Works Number Time (Hour) Total Workload (Hour) Course Related Works     Class Time (Exam weeks are excluded) 14 4 56     Out of Class Study (Preliminary Work, Practice) 14 2 28 Assesment Related Works     Homeworks, Projects, Others 1 2 2     Mid-term Exams (Written, Oral, etc.) 1 2 2     Final Exam 1 10 10 Total Workload: 98 Total Workload / 25 (h): 3.92 ECTS Credit: 4