BYF716 - OPTO-BIOPHYSICAL METHODS II

Course Name Code Semester Theory
(hours/week)		 Application
(hours/week)		 Credit ECTS
OPTO-BIOPHYSICAL METHODS II BYF716 Spring 2 2 3 9
PrequisitesNone
Course languageTurkish
Course typeElective 
Mode of DeliveryFace-to-Face 
Learning and teaching strategiesLecture
Demonstration
Experiment
 
Instructor (s)Prof. Dr. Nuhan Puralı 
Course objectiveTo supply the students with some essential information and experience new generation optical imaging systems and analysis methods, used in defining the cellular structure and function. 
Learning outcomes
  1. To improve the knowledge and experience of the graduate students in new generation super resolution microscopes, functional imaging, molecular labeling and image analysis.
Course ContentIn reference to a general opinion microscope is perhaps the best device in having its function already defined in its name, the device used to observe objects in the micro scale. Further, microscope is the most common laboratory devices. Thus, it is very frequently used in medical research as well as in the other branches. Though, various types of microscopes have been invented for studying structure and the function of the biological samples light microscpes are superior to the others due to the noninvassive property of the light. However, until very near history use of the light miscopes have been limited by two boundry conditions; resolution limit imposed by the diffraction and the diffuculty in scanning in large samples. The limits has largely been broken by the recent technological developments in the field. The super resolution fluorescent microscopes has reached to nano scale resolution and CLARITY and light sheet methods enebled to image the whole brain connectome at a microsco 
References1.Hücre elektrofizyolojisi ve Görüntülemenin Temelleri. Nuhan Puralı, Veri Medikal İstanbul 2008.
2.Fluorescence microscopy. Herman B. Springer-Verlag, 1998.
3.Confocal microscopy. Conn PM. In Methods in enzymology. Volume 307. 1999.
4. Optical Imaging Techniques in Cell Biology. Guy Cox. 2007.
5. Super resolution microscoy. Naure Collection. May 2018.
6.Superresolution imaging using single-molecule localization. Patterson, G. Davidson, M., Manley, S. and Lippincott-Schwartz, J. Annual Review of Physical Chemistry 61:345-367 (2010).
7. A guide to super-resolution fluorescence microscopy. Schermelleh, L., Heintzmann, R. and Leonhardt, H. Journal of Cell Biology 190: 165-175 (2010).
8. Molecules and methods for super-resolution imaging. Thompson, R. E., Biteen, J. S., Lord, S. J., Conley, N. R. and Moerner, W. E.Methods in Enzymology 475: 27-59 (2010).
 

Course outline weekly

WeeksTopics
Week 1Light microscope, general principles and conventional methods.
Week 2Fluorescent principle, fluorescent microscope
Week 3Resolution problem
Week 4Near field microscopy
Week 5STED microscope
Week 6PALM methods
Week 7Examination
Week 8Problem in scanning large samples
Week 9Multiphoton method
Week 10CLARITY method
Week 11Light sheet microscope
Week 12Reflected light method
Week 13Optogenetics
Week 14Cryo-EM
Week 15Discussion
Week 16Final examination

Assesment methods

Course activitiesNumberPercentage
Attendance145
Laboratory145
Application00
Field activities00
Specific practical training00
Assignments120
Presentation00
Project00
Seminar00
Midterms130
Final exam140
Total100
Percentage of semester activities contributing grade succes3060
Percentage of final exam contributing grade succes140
Total100

WORKLOAD AND ECTS CALCULATION

Activities Number Duration (hour) Total Work Load
Course Duration (x14) 14 2 28
Laboratory 14 2 28
Application000
Specific practical training000
Field activities000
Study Hours Out of Class (Preliminary work, reinforcement, ect)14684
Presentation / Seminar Preparation000
Project000
Homework assignment13030
Midterms (Study duration)12020
Final Exam (Study duration) 14040
Total Workload45100230

Matrix Of The Course Learning Outcomes Versus Program Outcomes

D.9. Key Learning OutcomesContrubition level*
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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    X
4. Awaring of the fact that biophysics is a multidisciplinary field, follows the developments in other branches of the Medical&Basic Sciences     
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    X
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