GBE 309 | Course Introduction and Application Information - Department of Genetics and Bioengineering

Course Name

Genetic Engineering Techniques

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
GBE 309	Fall	3	2	4	6

Prerequisites

	GBE 100 To attend the classes (To enrol for the course and get a grade other than NA or W)
and	GBE 206 To attend the classes (To enrol for the course and get a grade other than NA or W)

Course Language

English

Course Type

Required

Course Level

First Cycle

Mode of Delivery

-

Teaching Methods and Techniques of the Course

Discussion
Group Work
Problem Solving
Case Study
Q&A
Application: Experiment / Laboratory / Workshop
Lecture / Presentation

National Occupation Classification

-

Course Coordinator

Dr. Öğr. Üyesi Cihangir Yandım

Course Lecturer(s)

Dr. Öğr. Üyesi Cihangir Yandım

Assistant(s)

Course Objectives

The aim of this course is to teach both the theoretical background and laboratory application principles of the techniques necessary for the processing, modification and artificial transfer of genetic information from cell to cell. In this context, molecular cloning design, use of bacteria and viruses in genetic engineering, expression measurement of artificially transferred genetic material will be taught with modern and conventional techniques.

Learning Outcomes

#	Content	PC Sub	* Contribution Level
#	Content	PC Sub	1	2	3	4	5
1	Define the basic enzyme and plasmid systems required for gene engineering
2	Select the regulatory circuits used in genetic engineering
3	Design plasmids required for recombinant production
4	Describe the purification processes of proteins produced by gene engineering techniques
5	Apply basic molecular cloning and gene expression measurement methods
6	Explain the optional mutation generation methods
7	Explain gene silencing or expression methods with conventional and modern genetic engineering methods
8	Discuss genetic engineering applications from an ethical point of view.

Course Description

This is a course that explains the systems related to the transfer of theoretical knowledge learned in other Genetics and Bioengineering courses into practice. In this context, the necessary materials and processes in laboratory applications will be explained, and students will be able to both design and implement them. The basic plasmid, bacterial and virus systems used in genetic engineering applications, as well as conventional and modern genetic modification techniques will be explained in detail and with their applications. This course includes basic applications so that students can transfer modern applications of basic experimental design and genetic engineering applications from both academic and industrial perspectives.

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	Enzymes used in molecular cloning	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 1. Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017: Chapter-1
2	Plasmids and bacteria used in molecular cloning	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 2. Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017: Chapter-1
3	Plasmid circuit components and their design and isolation	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 2. Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017: Chapter-1 ve 3
4	Gene amplification and cutting techniques for cloning	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 2. Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017: Chapter-2
5	Viral methods in molecular cloning and gene delivery and gene induction	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 2 and 4. Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017: Chapter-4
6	Recombinant protein labeling methods, reporter systems and purification	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 4. Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017: Chapter-6
7	Recombinant protein labeling methods, reporter systems and purification	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 4 / Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017: Chapter 6
8	Midterm
9	Real-time PCR and analysis	Kurnaz, Isil Aksan. Techniques in Genetic Engineering: Chapter 1. Vandesompele, Jo, et al. "Real-time PCR: current technology and applications." Reference gene validation software for improved normalization 2 (2009): 47-64.
10	Mutagenesis	Kurnaz, Isil Aksan. Techniques in Genetic Engineering. Chapter 5
11	Mutagenesis and RNA interference	Kurnaz, Isil Aksan. Techniques in Genetic Engineering. Chapter 5 / Martin, Scott E., and Natasha J. Caplen. "Applications of RNA interference in mammalian systems." Annu. Rev. Genomics Hum. Genet. 8 (2007): 81-108.
12	Conventional gene manipulation	Kurnaz, Isil Aksan. Techniques in Genetic Engineering. Chapter 8. Hoess, R. H., and K. Abremski. "The Cre-lox recombination system." Nucleic Acids and Molecular Biology 4 (1990): 99-109.
13	Gene editing techniques with CRISPR	Kurnaz, Isil Aksan. Techniques in Genetic Engineering. Chapter 8. Ran, F. Ann, et al. "Genome engineering using the CRISPRCas9 system." Nature protocols 8.11 (2013): 2281-2308.
14	Gene editing and ethical discussions	Kurnaz, Isil Aksan. Techniques in Genetic Engineering. Chapter 8. Ran, F. Ann, et al. "Genome engineering using the CRISPRCas9 system." Nature protocols 8.11 (2013): 2281-2308.
15	Semester Review
16	Final exam

Course Notes/Textbooks

Kurnaz, Isil Aksan. Techniques in Genetic Engineering. 1st ed. CRC Press, 2015. Web. 25 Sept. 2021. ISBN 9780367658816

Suggested Readings/Materials

Plasmids 101 – a desktop resource (3rd edition). Addgene, 2017
Vandesompele, Jo, et al. "Real-time PCR: current technologyand applications." Reference gene validation software for improved normalization 2 (2009): 47-64.
Martin, Scott E., and Natasha J. Caplen. "Applications of RNA interference in mammalian systems." Annu. Rev. GenomicsHum. Genet. 8 (2007): 81-108.
Hoess, R. H., and K. Abremski. "The Cre-lox recombination system." Nucleic Acids and Molecular Biology 4 (1990): 99-109.
Ran, F. Ann, et al. "Genome engineering using the CRISPRCas9

Semester Activities	Number	Weigthing	LO 1	LO 2	LO 3	LO 4	LO 5	LO 6	LO 7	LO 8
Participation
Laboratory / Application	1	40
Field Work
Quizzes / Studio Critiques
Portfolio
Homework / Assignments
Presentation / Jury
Project
Seminar / Workshop
Oral Exams
Midterm	1	30
Final Exam	1	30
Total

Weighting of Semester Activities on the Final Grade	2	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	2	32
Study Hours Out of Class	14	2	28
Field Work			0
Quizzes / Studio Critiques			0
Portfolio			0
Homework / Assignments	3	10	30
Presentation / Jury			0
Project			0
Seminar / Workshop			0
Oral Exam			0
Midterms	1	10	10
Final Exam	1	32	32
		Total	180

#	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.		-	-	-	-	-
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.		-	-	-	X	-
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.		-	-	X	-	-
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.		-	-	-	X	-
6	To be able to work efficiently in Genetics and Bioengineering disciplinary and multi-disciplinary teams; to be able to work individually.		-	-	-	-	-
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.		X	-	-	-	-
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.		-	-	-	-	-