MEB707 - METHODS IN GENOME ANALYSIS

Course Name Code Semester Theory
(hours/week)		 Application
(hours/week)		 Credit ECTS
METHODS IN GENOME ANALYSIS MEB707 Fall 3 2 4 10
PrequisitesLimited to a quota of 5 students
Course languageTurkish
Course typeElective 
Mode of DeliveryFace-to-Face 
Learning and teaching strategiesLecture
Discussion
Demonstration
Experiment
 
Instructor (s)Prof. Çetin KOCAEFE, Prof. Didem DAYANGAÇ-ERDEN 
Course objectiveThe aim of this course is to teach laboratory methods about genomics and functional investigations of genes and nucleic acid fragments.  
Learning outcomes
  1. Students will; Knows the various aims, methodology and pitfalls of PCR applications. Can define the principal framework of primer design and employ PCR techniques according to the scientific question.
  2. Knows principles and limitations of RFLP and DNA sequence analysis methods which are used in order to analyze PCR products.
  3. Employs cloning techniques for in-vivo amplification.
  4. Gains information about the application principles of Real Time PCR technique, becomes capable of answering questions related the principles of probe design and quantitative expression profiling.
  5. Knows the fundemental principles of protein analysis techniques.
  6. Gains the ability to choose the appropriate technique to solve a problem in the field of genomics.
  7. Interpretes and discusses scientific data.
Course ContentIn this course; in vivo and in vitro cloning methods, gene expression analysis at the RNA and protein level, high throughput technologies and their application areas will be discussed.  
References1. Molecular Cloning: A laboratory manual. Ed. Michael R. Green, Joseph Sambrook. CSHL Press.
2. Real time PCR Ed. T. Dorak. Taylor & Francis.
3. Current Protocols in Molecular Biology, Wiley Interscience. 

Course outline weekly

WeeksTopics
Week 1The use of genomics tools and application principles in the diagnosis of inherited disorders and identification of the molecular basis of disease.
Week 2Amplification of DNA-I: Polymerase Chain Reaction (PCR), principles and practical applications (Laboratory)
Week 3Amplification of DNA-II: Analysis of PCR products (Laboratory) a. Electrophoretic techniques. b. Fragment analysis (RFLP) c. Sequence analysis
Week 4Nucleic acid hybridization techniques: Blotting, probe preparation and labeling approaches, applications of hybridization methods
Week 5Cell based cloning methods-I: Plasmid vectors; cloning and gene expression vectors, gene transfer techniques
Week 6Cell based cloning methods-II: (Laboratory) a. Plasmid transformation b. Colony picking and expansion c. Plasmid isolation and analysis
Week 7Laboratory
Week 8Mammalian gene transfer: Viral and non-viral vector systems and fundamentals of gene replacement therapy
Week 9Gene expression analysis-I: Northern Blot, semi-quantitative RT-PCR and quantitative real-time PCR methods and fields of application
Week 10Gene expression analysis-II (Laboratory) a. RNA isolation b. cDNA synthesis c. Real-time PCR
Week 11Protein analysis-I: Protein analysis methods in functional genomics (western blotting, immunostaining, elisa)
Week 12Protein analysis-II: (Laboratory) a. Western blotting b. Immunostaining
Week 13Laboratory
Week 14Applications of high-throughput genomics technologies: Parallel sequencing and microarray systems (gene expression analysis and SNP analysis)
Week 15Preparation for the final exam
Week 16Final exam

Assesment methods

Course activitiesNumberPercentage
Attendance00
Laboratory740
Application00
Field activities00
Specific practical training00
Assignments00
Presentation00
Project00
Seminar00
Midterms00
Final exam160
Total100
Percentage of semester activities contributing grade succes740
Percentage of final exam contributing grade succes160
Total100

WORKLOAD AND ECTS CALCULATION

Activities Number Duration (hour) Total Work Load
Course Duration (x14) 14 3 42
Laboratory 7 15 105
Application000
Specific practical training000
Field activities000
Study Hours Out of Class (Preliminary work, reinforcement, ect)149126
Presentation / Seminar Preparation000
Project000
Homework assignment000
Midterms (Study duration)000
Final Exam (Study duration) 11515
Total Workload3642288

Matrix Of The Course Learning Outcomes Versus Program Outcomes

D.9. Key Learning OutcomesContrubition level*
12345
1. Graduates have knowledge related to the biophysical principles underlying all processes of life at the level of cell/tissue/organ/system    X
2. Has an ability use his/her higher intellectual processes such as critical thinking, problem solving decision development during his/her education period     
3. Can take part in some research activities to contribute to the solution of a problem in the field of biophysics     
4. Awaring of the fact that biophysics is a multidisciplinary field, follows the developments in other branches of the Medical&Basic Sciences    X
5. Can use computer software and laboratory equipment to produce appropriate stimulus, acquire the biological signals under the ideal conditions, quantitatively analyse the raw data     
6. Acquired knowledge at an expertise level in statistical methods. Can choose the most suitable method for his/her research     
7. Is aware of the importance of the ethical rules and regulations and perform laboratory research as defined by the GLP, Bio-Safety principles     
8. Has the capacity of successfully preparing and presenting the report of the research work he/she takes part in, publishing at least one manuscript     
9. Follows the activities of the national&international organizations related to his/her expertise and takes part in them     
10. Shares the knowledge he/she acquired from biophysics with partners from all parts of the society; contributes to the formation of the knowledge-based society     

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