Department of Biomedical Engineering

GBE 340 | Course Introduction and Application Information

Course Name

Cell Death Mechanisms

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

Prerequisites	None
Course Language	English
Course Type	ELECTIVE_COURSE
Course Level	First Cycle
Mode of Delivery	Face to Face
Teaching Methods and Techniques of the Course	Discussion Group Work Q&A Lecture / Presentation
National Occupational Classification Code	-
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

The students who succeeded in this course;

Name	Description	PC Sub	* Contribution Level
Name	Description	PC Sub	1	2	3	4	5
LO1	Explain the basic principles of cell death mechanisms and apply these principles to solve current problems in the field	1.2			X
LO2	Explain the methods used to analyse cell death mechanisms	5.1			X
LO3	Model cell death mechanisms, and will be able to report this model individually and present it orally	8.1			X
LO4	Explain the role of cell death mechanisms in embryonic development and how dysregulation of these mechanisms can lead to pathological conditions such as cancer and neurodegenerative diseases	1.5			X

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.

Related Sustainable Development Goals

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

WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

Week	Subjects	Required Materials	Learning Outcome
1	Introduction to cell death modalities	Alberts et.al. 6th Edition. Chapter 18.	LO1
2	Non-programmed cell death: Necrosis	Alberts et.al. 6th Edition. Chapter 18.	LO1
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.	LO1
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.	LO2
5	Apoptotic Cell Death Detection Methods	Hugh J. M. Brady. Apoptosis Methods and Protocols. Humana Press 2004. https://doi.org/10.1385/1592598129	LO2
6	Programmed non-apoptotic cell death: Vacuole based	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.	LO2
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.	LO2
8	Midterm		-
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.	LO3
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.	LO3
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.	LO4
12	Non-lethal processes such as anastasis, mitotic destruction and cellular senescence	Hochman A. Programmed cell death in prokaryotes. Crit Rev Microbiol. 1997;23(3):207-14.	LO4
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.	LO4
14	Review of the semester		-
15	Review of the semester		-
16	Final		-

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	-

EVALUATION SYSTEM

Semester Activities	Number	Weighting	LO1	LO2	LO3	LO4
Homework / Assignments	1	25			X	X
Presentation / Jury	1	25		X	X
Midterm	1	20	X	X
Final Exam	1	30	X	X		X
Total	4	100

ECTS / WORKLOAD TABLE

Semester Activities	Number	Duration (Hours)	Workload
Participation	-	-	-
Theoretical Course Hours	16	3	48
Laboratory / Application Hours	-	-	-
Study Hours Out of Class	16	2	32
Field Work	-	-	-
Quizzes / Studio Critiques	-	-	-
Portfolio	-	-	-
Homework / Assignments	1	10	10
Presentation / Jury	1	20	20
Project	-	-	-
Seminar / Workshop	-	-	-
Oral Exams	-	-	-
Midterms	1	20	20
Final Exam	1	20	20
		Total	150

COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

#	PC Sub	Program Competencies/Outcomes	* Contribution Level
#	PC Sub	Program Competencies/Outcomes	1	2	3	4	5
1	Engineering Knowledge: Knowledge of mathematics, science, basic engineering, computation, and related engineering discipline-specific topics; the ability to apply this knowledge to solve complex engineering problems.
	1	Mathematics
	2	Science			LO1
	3	Basic Engineering
	4	Computation
	5	Related engineering discipline-specific topics			LO4
	6	The ability to apply this knowledge to solve complex engineering problems
2	Problem Analysis: Ability to identify, formulate and analyze complex engineering problems using basic knowledge of science, mathematics and engineering, and considering the UN Sustainable Development Goals relevant to the problem being addressed.
3	Engineering Design: The ability to devise creative solutions to complex engineering problems; the ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions.
	1	Ability to design creative solutions to complex engineering problems
	2	Ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions
4	Use of Techniques and Tools: Ability to select and use appropriate techniques, resources, and modern engineering and computing tools, including estimation and modeling, for the analysis and solution of complex engineering problems, while recognizing their limitations.
5	Research and Investigation: Ability to use research methods to investigate complex engineering problems, including literature research, designing and conducting experiments, collecting data, and analyzing and interpreting results.
	1	Literature research for the study of complex engineering problems			LO2
	2	Designing experiments
	3	Ability to use research methods, including conducting experiments, collecting data. analyzing and interpreting results
6	Global Impact of Engineering Practices: Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals; awareness of the legal implications of engineering solutions.
	1	Knowledge of the impacts of engineering practices on society, health and safety, economy, sustainability, and the environment, within the context of the UN Sustainable Development Goals
	2	Awareness of the legal implications of engineering solutions
7	Ethical Behavior: Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility; awareness of being impartial, without discrimination, and being inclusive of diversity.
	1	Acting in accordance with the principles of the engineering profession, knowledge about ethical responsibility ethical responsibility
	2	Awareness of being impartial and inclusive of diversity, without discriminating on any subject
8	Individual and Teamwork: Ability to work effectively, individually and as a team member or leader on interdisciplinary and multidisciplinary teams (face-to-face, remote or hybrid).
	1	Ability to work individually and within the discipline			LO3
	2	Ability to work effectively as a team member or leader in multidisciplinary teams (face-to-face, remote or hybrid)
9	Verbal and Written Communication: Taking into account the various differences of the target audience (such as education, language, profession) on technical issues.
	1	Ability to communicate verbally
	2	Ability to communicate effectively in writing
10	Project Management: Knowledge of business practices such as project management and economic feasibility analysis; awareness of entrepreneurship and innovation.
	1	Knowledge of business practices such as project management and economic feasibility analysis
	2	Awareness of entrepreneurship and innovation
11	Lifelong Learning: Lifelong learning skills that include being able to learn independently and continuously, adapting to new and developing technologies, and thinking questioningly about technological changes.