GBE 340 | Course Introduction and Application Information - Department of Genetics and Bioengineering

Course Name

Cell Death Mechanisms

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
GBE 340	Fall/Spring	3	0	3	5

Prerequisites	None
Course Language	English
Course Type	Elective
Course Level	First Cycle
Mode of Delivery	-
Teaching Methods and Techniques of the Course	Discussion Group Work Q&A Lecture / Presentation
National Occupation Classification	-
Course Coordinator	Prof. Dr. Zeynep Fırtına Karagonlar
Course Lecturer(s)	Dr. Öğr. Üyesi Gizem AYNA DURAN
Assistant(s)	-

Course Objectives

This course will focus on understanding the basics of conventional as well as unconventional cell death mechanisms and their roles in development, physiology and pathology. It will cover a broad range of topics in cell death field including apoptosis, autophagy, necrosis, necroptosis, lysosome-dependent cell death, entosis, anoikis, ferroptosis, pyroptosis, anastasis, mitotic death and immunogenic cell death.

Learning Outcomes

#	Content	PC Sub	* Contribution Level
#	Content	PC Sub	1	2	3	4	5
1	Be able to explain the basic principles of cell death mechanisms
2	Be able to apply methods used to analyze cell death mechanisms
3	Will be able to evaluate scientific studies in this field in terms of design, hypothesis, and value, and will be able to conduct literature research on a specific subject and share their knowledge about that subject in written and oral form.
4	Explain the interactions between different cell death mechanisms
5	Be able to identify how irregularities in cell death mechanisms can lead to the formation of pathological conditions such as cancer and neurodegenerative diseases.

Course Description

This course covers the description of molecular mechanisms of cell death including apoptosis, autophagy, necrosis, necroptosis, lysosome-dependent cell death, entosis, anoikis, ferroptosis, pyroptosis, anastasis, mitotic death and immunogenic cell death.

Course Category	Core Courses
	Major Area Courses	X
	Supportive Courses
	Media and Management Skills Courses
	Transferable Skill Courses

Week	Subjects	Related Preparation	Learning Outcome
1	Introduction to cell death modalities	Alberts et.al. 6th Edition. Chapter 18.
2	Non-programmed cell death: Necrosis	Alberts et.al. 6th Edition. Chapter 18.
3	Programmed apoptotic cell death: Apoptotic Cell Death and Anoikis	Galluzzi, Lorenzo et al. “Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018” Cell death and differentiation vol. 25,3 (2018): 486-541.
4	Intrinsic and Extrinsic Apoptotic Cell Death	Galluzzi, Lorenzo et al. “Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018” Cell death and differentiation vol. 25,3 (2018): 486-541.
5	Apoptotic Cell Death Detection Methods	Galluzzi, L et al. “Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012” Cell death and differentiation vol. 19,1 (2011): 107-20.
6	Programmed non-apoptotic cell death: Vacuole based
7	Programmed non-apoptotic cell death: Mitochondria and iron based	Kroemer, G et al. “Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009” Cell death and differentiation vol. 16,1 (2008): 3-11.
8	Mid-Term Exam	Kroemer, G et al. “Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009” Cell death and differentiation vol. 16,1 (2008): 3-11.
9	Programmed non-apoptotic cell death: Vacuole based: Immunogenic cell death and others	Galluzzi, Lorenzo et al. “Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018” Cell death and differentiation vol. 25,3 (2018): 486-541.
10	Programmed cell death in prokaryotes	Galluzzi, Lorenzo et al. “Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018” Cell death and differentiation vol. 25,3 (2018): 486-541.
11	Clinical aspects of cell death	Douglas R Green. Means to an End: Apoptosis and Other Cell Death Mechanisms. Cold Spring Harbor Laboratory Press. 2017. Galluzzi, Lorenzo et al. “Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018” Cell death and differentiation vol. 25,3 (2018): 486-541.
12	Non-lethal processes such as anastasis, mitotic destruction and cellular senescence
13	Cell-in-cell death (entosis, cannibalism and imperitosis)	Galluzzi L, Buqué A, Kepp O, Zitvogel L, Kroemer G. Immunogenic cell death in cancer and infectious disease. Nat Rev Immunol. 2017 Feb;17(2):97-111. doi: 10.1038/nri.2016.107. Epub 2016 Oct 17.
14	Semester review
15	Semester review
16	Final exam

Course Notes/Textbooks

Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter. Molecular Biology of the Cell. Sixth Edition. Chapter 18 – Cell Death. Garland Science, 2014: New York and Abingdon, UK.

Douglas R Green. Means to an End: Apoptosis and Other Cell Death Mechanisms. Cold Spring Harbor Laboratory Press. 2017.

Suggested Readings/Materials

Galluzzi, Lorenzo et al. “Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018” Cell death and differentiation vol. 25,3 (2018): 486-541.

Galluzzi, L et al. “Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012” Cell death and differentiation vol. 19,1 (2011): 107-20.

Kroemer, G et al. “Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009” Cell death and differentiation vol. 16,1 (2008): 3-11.

Sun G and Montell DJ. Q&A: Cellular near death experiences-what is anastasis? BMC Biol. 2017 Oct 24;15(1):92. doi: 10.1186/s12915-017-0441-z.

Semester Activities	Number	Weigthing	LO 1	LO 2	LO 3	LO 4	LO 5
Participation
Laboratory / Application
Field Work
Quizzes / Studio Critiques
Portfolio
Homework / Assignments	1	15
Presentation / Jury	1	15
Project
Seminar / Workshop
Oral Exams
Midterm	1	30
Final Exam	1	40
Total

Weighting of Semester Activities on the Final Grade	3	70
Weighting of End-of-Semester Activities on the Final Grade	1	30
Total

Semester Activities	Number	Duration (Hours)	Workload
Theoretical Course Hours (Including exam week: 16 x total hours)	16	3	48
Laboratory / Application Hours (Including exam week: '.16.' x total hours)	16		0
Study Hours Out of Class	16	2	32
Field Work			0
Quizzes / Studio Critiques			0
Portfolio			0
Homework / Assignments	1	10	10
Presentation / Jury	1	20	20
Project			0
Seminar / Workshop			0
Oral Exam			0
Midterms	1	20	20
Final Exam	1	20	20
		Total	150

#	PC Sub	Program Competencies/Outcomes	* Contribution Level
#	PC Sub	Program Competencies/Outcomes	1	2	3	4	5
1	To have adequate knowledge in Mathematics, Science and Genetics and Bioengineering; to be able to use theoretical and applied information in these areas on complex engineering problems.		-	-	-	X	-
2	To be able to identify, define, formulate, and solve complex Genetics and Bioengineering problems; to be able to select and apply proper analysis and modeling methods for this purpose.		-	-	-	X	-
3	To be able to design a complex system, process, device or product under realistic constraints and conditions, in such a way as to meet the requirements; to be able to apply modern design methods for this purpose.		-	-	-	-	-
4	To be able to devise, select, and use modern techniques and tools needed for analysis and solution of complex problems in Genetics and Bioengineering applications; to be able to use information technologies effectively.		-	-	-	-	-
5	To be able to design and conduct experiments, gather data, analyze and interpret results for investigating complex engineering problems or Genetics and Bioengineering research topics.		-	-	-	-	-
6	To be able to work efficiently in Genetics and Bioengineering disciplinary and multi-disciplinary teams; to be able to work individually.		-	-	-	X	-
7	To be able to communicate effectively in Turkish, both orally and in writing; to be able to author and comprehend written reports, to be able to prepare design and implementation reports, to present effectively, to be able to give and receive clear and comprehensible instructions.		-	-	-	-	-
8	To have knowledge about global and social impact of Genetics and Bioengineering practices on health, environment, and safety; to have knowledge about contemporary issues as they pertain to engineering; to be aware of the legal ramifications of Genetics and Bioengineering solutions.		-	-	-	-	-
9	To be aware of ethical behavior, professional and ethical responsibility; to have knowledge about standards utilized in Genetics and Bioengineering applications.		-	-	-	-	-
10	To have knowledge about industrial practices such as project management, risk management, and change management; to have awareness of entrepreneurship and innovation; to have knowledge about sustainable development.		-	-	-	-	-
11	To be able to collect data in the area of Genetics and Bioengineering, and to be able to communicate with colleagues in a foreign language.		-	-	-	-	-
12	To be able to speak a second foreign language at a medium level of fluency efficiently.		-	-	-	-	-
13	To recognize the need for lifelong learning; to be able to access information, to be able to stay current with developments in science and technology; to be able to relate the knowledge accumulated throughout the human history to Genetics and Bioengineering.		-	-	-	-	-