GBE 411 | Course Introduction and Application Information - Department of Genetics and Bioengineering

Course Name

Design and Analysis in Bioengineering

Code	Semester	Theory (hour/week)	Application/Lab (hour/week)	Local Credits	ECTS
GBE 411	Fall/Spring	2	2	3	5

Prerequisites	None
Course Language	English
Course Type	Elective
Course Level	First Cycle
Mode of Delivery	-
Teaching Methods and Techniques of the Course	-
National Occupation Classification	-
Course Coordinator	Dr. Öğr. Üyesi Cihangir Yandım
Course Lecturer(s)	Dr. Öğr. Üyesi Cihangir Yandım Dr. Öğr. Üyesi Mine Güngörmüşler
Assistant(s)	Araş. Gör. Hüseyin Saygın Portakal

Course Objectives

The aim of this course is to teach design and analysis strategies of bioengineered molecular diagnostics and medicinal biomolecules together with their bioprocess production pipeline.

Learning Outcomes

#	Content	PC Sub	* Contribution Level
#	Content	PC Sub	1	2	3	4	5
1	Design a bioengineered molecular diagnostic tool and analyse its efficiency.
2	Discuss the limitations of a molecular diagnostic tool.
3	Explain the principles in the design and analysis in multiplex diagnostics.
4	Design a bioengineered drug using simulation modelling.
5	Determine an experimental optimization pipeline in bioprocess production.
6	Explain the principles of bioreactor design.
7	Discuss the strategies in the design and analysis of downstream processing.
8	Analyse the feasibility of a bioprocess design.

Course Description

Design and analysis of bioengineered molecular diagnostics and medicinal biomolecules as well as their production pipeline with a computational and simulation-based approach will be given. Following detailed explanations on molecular diagnostics design and drug simulation modelling with relevant examples, final steps of biological drug and diagnostics production in a factory setting will be covered. A platform where students will be able to use their knowledge and skills will be introduced via project homeworks.

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	Design and analysis of a diagnostic test	• Chapter 4 and 5. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (6th edition). Rifai, Horvath, Wittwer. Elsevier, 2018 • How to evaluate a diagnostic test. Leeflang and Allerberger. Clin Microbiol Infect. 2019;25(1):54-59 • Designing studies for diagnostic tests. Bakke. Clin Respir J. 2008;2 Suppl 1:72-5. • Characteristics of good diagnostic studies. Mol et al. Semin Reprod Med. 2003;21(1):17-25.
2	Design, limitations and applications of Biosensors	• Blueprints for biosensors: Designs,Limitations and Applications. Carpenter et al. Genes (Basel). 2018; 9(8): 375.
3	Design and analysis of immunoassays	• Chapter 23. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (6th edition). Rifai, Horvath, Wittwer. Elsevier, 2018 • Designing paper-based immunoassays for biomedical applications. Hristov et al. Sensors (Basel). 2019; 19(3): 554.
4	Design and analysis of nucleic acid tests	• Guidance on the development and validation of diagnostic tests that depend on nucleic acid amplification and detection. Saunders et al. J Clin Virol. 2013; 56(3):260-70.
5	System miniaturization	• Chapter 24. Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (6th edition). Rifai, Horvath, Wittwer. Elsevier, 2018 • Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: a review. Ahmad and Hashsham. Anal Chim Acta. 2012 Jul 6;733:1-15. • Miniaturized immunoassays: moving beyond the microplate. Vercht and Bakhtiar. Bioanalysis. 2012 Jan;4(2):177-88. • Bioengineering methods for analysis of cells in vitro. Underhill et al. Annu Rev Cell Dev Biol. 2012;28:385-410.
6	Designing biodrugs with molecular docking	• Chapter 3. Computational Drug Discovery and Design. Springer Protocols, Humana Press, 2018. Gore and Jagtap. • Molecular Docking and structure-based drug design strategies. Ferreira et al. Molecules. 2015; 22;20(7):13384-421.
7	Simulation of biomolecular dynamics	• Chapter 6 and 13. Computational Drug Discovery and Design. Springer Protocols, Humana Press, 2018. Gore and Jagtap. • Bridging molecular docking to molecular dynamics in Exploring ligand-protein recognition process: An overview. Salmaso and Moro. Front Pharmacol. 2018 Aug 22;9:923
8	Review and Midterm Exam
9	Bioprocess optimization and experimental design	• Experimental design methods for bioengineering applications. Gundogdu et al. Crit Rev Biotechnol. 2016;36(2):368-88. • Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012
10	Bioprocess optimization and experimental design	• Model-assisted design of experiments as a concept for knowledge-based bioprocess development. Moller et al. Bioprocess Biosyst Eng. 2019 May;42(5):867-882. • Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012
11	Bioreactor design	• Chapter 14. Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012
12	Bioreactor design	• Chapter 14. Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012
13	Downstream processing design and analysis	• Downstream Processing Technologies/Capturing and Final Purification : Opportunities for Innovation, Change, and Improvement. A Review of Downstream Processing Developments in Protein Purification. Singh and Herzer. Adv Biochem Eng Biotechnol. 2018;165:115-178.
14	Feasibility Analysis	• Integrated continuous bioprocessing: Economic, operational, and environmental feasibility for clinical and commercial antibody manufacture. Pollock et al. Biotechnol Prog. 2017 ; 33(4): 854–866.
15	Review of the semester
16	Final Exam

Course Notes/Textbooks

Tietz Textbook of Clinical Chemistry and Molecular Diagnostics (6^th edition). Rifai, Horvath, Wittwer. Elsevier, 2018 ISBN: 978-0-323-35921-4
Computational Drug Discovery and Design. Springer Protocols, Humana Press, 2018. Gore and Jagtap. ISBN 978-1-4939-7755-0
Bioprocess Engineering Principles (2nd Edition),Doran P, Academic Press, 2012. ISBN: 978-0122208515

Suggested Readings/Materials

• How to evaluate a diagnostic test. Leeflang and Allerberger. Clin Microbiol Infect. 2019;25(1):54-59

• Designing studies for diagnostic tests. Bakke. Clin Respir J. 2008;2 Suppl 1:72-5.

• Characteristics of good diagnostic studies. Mol et al. Semin Reprod Med. 2003;21(1):17-25.

• Blueprints for biosensors: Designs,Limitations and Applications. Carpenter et al. Genes (Basel). 2018; 9(8): 375.

• Designing paper-based immunoassays for biomedical applications. Hristov et al. Sensors (Basel). 2019; 19(3): 554.

• Guidance on the development and validation of diagnostic tests that depend on nucleic acid amplification and detection. Saunders et al. J Clin Virol. 2013; 56(3):260-70.

• Miniaturized nucleic acid amplification systems for rapid and point-of-care diagnostics: a review. Ahmad and Hashsham. Anal Chim Acta. 2012 Jul 6;733:1-15.

• Miniaturized immunoassays: moving beyond the microplate. Vercht and Bakhtiar. Bioanalysis. 2012 Jan;4(2):177-88.

• Bioengineering methods for analysis of cells in vitro. Underhill et al. Annu Rev Cell Dev Biol. 2012;28:385-410..

• Molecular Docking and structure-based drug design strategies. Ferreira et al. Molecules. 2015; 22;20(7):13384-421.

• Bridging molecular docking to molecular dynamics in Exploring ligand-protein recognition process: An overview. Salmaso and Moro. Front Pharmacol. 2018

• Experimental design methods for bioengineering applications. Gundogdu et al. Crit Rev Biotechnol. 2016;36(2):368-88.

• Model-assisted design of experiments as a concept for knowledge-based bioprocess development. Moller et al. Bioprocess Biosyst Eng. 2019 May;42(5):867-882.

• Downstream Processing Technologies/Capturing and Final Purification : Opportunities for Innovation, Change, and Improvement. A Review of Downstream Processing Developments in Protein Purification. Singh and Herzer. Adv Biochem Eng Biotechnol. 2018;165:115-178.

• Integrated continuous bioprocessing: Economic, operational, and environmental feasibility for clinical and commercial antibody manufacture. Pollock et al. Biotechnol Prog. 2017 ; 33(4): 854–866.

• Heller et al. Annu Rev Anal Chem (Palo Alto Calif). 2018; 12;11(1):79-100.

Semester Activities	Number	Weighting	LO 1	LO 2	LO 3	LO 4	LO 5	LO 6	LO 7	LO 8
Participation
Laboratory / Application
Field Work
Quizzes / Studio Critiques
Portfolio
Homework / Assignments
Presentation / Jury	2	20
Project	2	40
Seminar / Workshop
Oral Exams
Midterm	1	15
Final Exam	1	25
Total

Weighting of Semester Activities on the Final Grade	5	75
Weighting of End-of-Semester Activities on the Final Grade	1	25
Total

Semester Activities	Number	Duration (Hours)	Workload
Theoretical Course Hours (Including exam week: 16 x total hours)	16	2	32
Laboratory / Application Hours (Including exam week: '.16.' x total hours)	16	2	32
Study Hours Out of Class	16	1	16
Field Work			0
Quizzes / Studio Critiques			0
Portfolio			0
Homework / Assignments			0
Presentation / Jury	2	3	6
Project	2	14	28
Seminar / Workshop			0
Oral Exam			0
Midterms	1	16	16
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.		-	-	-	-	-
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.		-	-	-	-	-
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.		-	-	-	-	-
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.		-	-	X	-	-
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.		-	-	-	-	-