Ä°MM618 - FROM GENOME TO DISEASE IN PRIMARY IMMUNODEFICIENCIES: CELLULAR and MOLECULAR FEATURES

Course Name Code Semester Theory
(hours/week)		 Application
(hours/week)		 Credit ECTS
FROM GENOME TO DISEASE IN PRIMARY IMMUNODEFICIENCIES: CELLULAR and MOLECULAR FEATURES Ä°MM618 2nd Semester 2 2 3 6
PrequisitesTo graduate from department of biology, molecular biology and genetics and faculty of pharmacy, dentistry and medicine
Course languageTurkish
Course typeElective 
Mode of DeliveryFace-to-Face 
Learning and teaching strategiesOther  
Instructor (s)Instructor, Dr. Sevil Oskay Halaçlı 
Course objectiveThe aim of the course is to provide with theoretically and practically the objective functional studies and experimental methods related to cellular and molecular mechanisms in diseases 
Learning outcomes
  1. Theoretical knowledge about cellular studies in primary immunodeficiencies.
  2. To plan targeted molecular studies related to underlying the molecular mechanisms disease in primary immunodeficiencies.
Course ContentI.Cellular biology and molecular biology in primary immunodeficiencies
II. Mutation types and their characterization in primary immunodeficiencies
III. Effect of mutations on mRNA expression in primary immunodeficiencies
IV. Effect of mutations on protein expression in primary immunodeficiencies
V. Detection of protein expression by flow cytometry in primary immunodeficiencies (LRBA, STK4 deficiency etc).
VI.Detection of protein function by flow cytometry in primary immunodeficiencies (detection of STAT3, STAT1 phosphorylations etc).
VII. Detection of cellular functions in primary immunodeficiencies (Analysis of proliferative responses in combined immunodefiencies etc).
VIII. Gen-protein interactions and their detection methods in primary immunodeficiencies (STAT3, STAT1 deficiency etc).
IX. Protein-protein interactions and their detection methods in primary immunodeficiencies 
References? Oskay Halacli S, Deniz Cagdas Ayvaz, Cagman Tan, Elif Uz, Ä°lhan Tezcan, S. Ozden Sanal, STK4 gene deficiency in two siblings. Clin Immunol. 2015 Dec;161(2):316-23.
? Ahmad Fahim Ismail, Sevil Oskay Halacli, Nouf Babteen, Mario De Piano, Tracey A. Martin, Wen G. Jiang, Muhammad Shamim Khan, Prokar Dasgupta, Claire M. Wells, PAK5 mediates cell: cell adhesion integrity via interaction with E-cadherin in bladder cancer cells, Biochemical Journal Mar 24, 2017, 474 (8) 1333-1346.
? Oskay Halacli S. FOXP1 enhances tumor cell migration by repression of NFAT1 transcriptional activity in MDA-MB-231 cells. Cell Biol Int. 2017 Jan;41(1):102-110. 

Course outline weekly

WeeksTopics
Week 1Cellular biology and molecular biology in primary immunodeficiencies
Week 2The cause of mutations and types of mutations in primary immunodeficiencies
Week 3Determination methods of mutations and their characterization in primary immunodeficiencies
Week 4Effect of mutations on mRNA expression and mRNA surveillance mechanisms in primary immunodeficiencies
Week 5Detection of mRNA expressions by RT-PCR in primary immunodeficiencies
Week 6Effect of mutations on protein expression and protein surveillance mechanisms in primary immunodeficiencies
Week 7Evaluation of protein expression by flow cytometry in primary immunodeficiencies
Week 8Detection of protein function by flow cytometry in primary immunodeficiencies
Week 9Analysis methods
Week 10Detection of cellular functions in primary immunodeficiencies
Week 11Gen-protein interactions and their detection methods in primary immunodeficiencies
Week 12Protein-protein interactions and their detection methods in primary immunodeficiencies
Week 13Fundamental signaling mechanisms in primary immunodeficiencies
Week 14Student seminars
Week 15Final Exam

Assesment methods

Course activitiesNumberPercentage
Attendance1410
Laboratory610
Application00
Field activities00
Specific practical training00
Assignments00
Presentation00
Project120
Seminar130
Midterms00
Final exam130
Total100
Percentage of semester activities contributing grade succes2360
Percentage of final exam contributing grade succes2240
Total100

WORKLOAD AND ECTS CALCULATION

Activities Number Duration (hour) Total Work Load
Course Duration (x14) 14 2 28
Laboratory 0 0 0
Application14228
Specific practical training000
Field activities000
Study Hours Out of Class (Preliminary work, reinforcement, ect)14570
Presentation / Seminar Preparation000
Project000
Homework assignment14456
Midterms (Study duration)2918
Final Exam (Study duration) 11010
Total Workload5932210

Matrix Of The Course Learning Outcomes Versus Program Outcomes

D.9. Key Learning OutcomesContrubition level*
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1. Accesses medical literature on basic and clinical immunology and -related fields and evaluates them.   X  
2. Gains the necessary theoretical knowledge for their research and formulates hypotheses. Conducts research on immune system components and molecular structures, plans the appropriate methodology.    X 
3. Investigates gene structures from molecular literature studies, demonstrates them through sequence analysis, interprets the data, reaches conclusions, and publishes these findings.    X 
4. Demonstrates comprehensive and systematic knowledge on basic immunology, including understanding immunological mechanisms, immune system components, and their functions, also possesses knowledge in molecular genetics and biology.   X  
5. Utilizes current statistical approach to evaluate the obtained data. Presents research at national and international conferences and publishes findings under mentorship.   X  
6. Upon completion of the basic immunology master's program, the student, under the guidance of their consultant, drafts a research proposal adhering to ethical guidelines, determines the budget, provides feedback on projects authored by other researchers, participates in collaborative projects from the planning stage, offers insights, suggests changes, and presents alternative solutions.  X  

*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest