Course Detail
Course Description
| Course | Code | Semester | T+P (Hour) | Credit | ECTS |
|---|---|---|---|---|---|
| BIOTECHNOLOGY | BEBY1112981 | Fall Semester | 3+0 | 3 | 8 |
| Course Program | Cuma 13:30-14:15 Cuma 14:30-15:15 Cuma 15:30-16:15 Cuma 16:30-17:15 |
| Prerequisites Courses | |
| Recommended Elective Courses |
| Language of Course | English |
| Course Level | Second Cycle (Master's Degree) |
| Course Type | Elective |
| Course Coordinator | Assist.Prof. Mehmet Hikmet ÜÇIŞIK |
| Name of Lecturer(s) | Assist.Prof. Mehmet Hikmet ÜÇIŞIK |
| Assistant(s) | This course covers the scope of modern biotechnology and the biotech product pipeline; expression hosts, cell culture and cell line development; recombinant DNA technology and synthetic biology; PCR, qPCR and next-generation sequencing; genome editing (CRISPR-Cas, base and prime editing); protein engineering and computational protein design; therapeutic proteins and monoclonal antibodies; upstream and downstream bioprocessing and GMP; characterization and quality of biologics; nucleic acid therapeutics and gene delivery; nanobiotechnology for drug delivery (lipid nanocarriers, extracellular vesicles); cell based therapies and regenerative medicine; molecular diagnostics and biosensors; and patents, licensing, regulation and bioethics. |
| Aim | To provide graduate students with an integrated, application-oriented understanding of modern biotechnology, from molecular tools and expression systems to biomanufacturing, advanced therapies, diagnostics and regulation, and to develop their ability to critically evaluate and design biotechnology-based solutions in biomedical engineering. |
| Course Content | This course contains; Introduction: scope of modern biotechnology, the biotech product pipeline, from rDNA to ATMPs; assignment of term project topics,Cells as factories: expression hosts (E. coli, yeast, CHO, HEK293), cell culture and cell line development,Recombinant DNA technology and synthetic biology: vectors, cloning, DNA assembly,Nucleic acid amplification and analysis: PCR, qPCR, NGS and links to bioinformatics,Genome editing: CRISPR-Cas, base and prime editing, off-target assessment ,Protein engineering: directed evolution, computational and AI-based protein design,Therapeutic proteins and monoclonal antibodies: biosimilars, ADCs, bispecifics ,Bioprocessing: upstream (bioreactors, fermentation), downstream purification, GMP,Characterization and quality of biologics: HPLC, MS, peptide mapping, glycosylation, endotoxin, immunogenicity,Nucleic acid therapeutics and gene delivery: AAV/lentiviral vectors, siRNA/ASO, mRNA-LNP,Nanobiotechnology for drug delivery: lipid nanocarriers, extracellular vesicles ,Cell-based therapies and regenerative medicine: CAR-T, stem cells/iPSC, tissue engineering,Molecular diagnostics and biosensors: liquid biopsy, CRISPR diagnostics, point-of-care,Translation: patents and licensing, regulation (EMA/FDA/TİTCK), bioethics; term project presentations. |
| Course Learning Outcomes | Teaching Methods | Assessment Methods |
| A, D, F |
| Teaching Methods: | |
| Assessment Methods: | A: Traditional Written Exam, D: Oral Exam, F: Project Task |
Course Outline
| Order | Subjects | Preliminary Work |
|---|---|---|
| 1 | Introduction: scope of modern biotechnology, the biotech product pipeline, from rDNA to ATMPs; assignment of term project topics | Godbey: introduction to biotechnology |
| 2 | Cells as factories: expression hosts (E. coli, yeast, CHO, HEK293), cell culture and cell line development | Godbey: cell culture and eukaryotic cells; Glick & Patten: heterologous protein production |
| 3 | Recombinant DNA technology and synthetic biology: vectors, cloning, DNA assembly | Godbey: genetic engineering; Glick & Patten: recombinant DNA technology |
| 4 | Nucleic acid amplification and analysis: PCR, qPCR, NGS and links to bioinformatics | Godbey: PCR; assigned article |
| 5 | Genome editing: CRISPR-Cas, base and prime editing, off-target assessment | Godbey: genome editing; Glick & Patten: CRISPR; assigned article |
| 6 | Protein engineering: directed evolution, computational and AI-based protein design | Glick & Patten: protein engineering; assigned article |
| 7 | Therapeutic proteins and monoclonal antibodies: biosimilars, ADCs, bispecifics | Crommelin: monoclonal antibodies |
| 8 | Bioprocessing: upstream (bioreactors, fermentation), downstream purification, GMP | Godbey: processing and manufacturing; Crommelin: production and downstream processing |
| 9 | Characterization and quality of biologics: HPLC, MS, peptide mapping, glycosylation, endotoxin, immunogenicity | Crommelin: biophysical/biochemical analysis; immunogenicity |
| 10 | Nucleic acid therapeutics and gene delivery: AAV/lentiviral vectors, siRNA/ASO, mRNA-LNP | Godbey: gene delivery, RNAi; Crommelin: oligonucleotides, mRNA, gene therapy |
| 11 | Nanobiotechnology for drug delivery: lipid nanocarriers, extracellular vesicles | Assigned review articles |
| 12 | Cell-based therapies and regenerative medicine: CAR-T, stem cells/iPSC, tissue engineering | Godbey: stem cells, tissue engineering, immunotherapy; Crommelin: cell therapies |
| 13 | Molecular diagnostics and biosensors: liquid biopsy, CRISPR diagnostics, point-of-care | Glick & Patten: molecular diagnostics; assigned article |
| 14 | Translation: patents and licensing, regulation (EMA/FDA/TİTCK), bioethics; term project presentations | Godbey: patents and licenses; project dossier |
| Resources |
| W.T. Godbey, Biotechnology and its Applications: Using Cells to Change the World, 3rd ed., Academic Press (Elsevier), 2026. ISBN 978-0-443-24101-7. If the 3rd edition is not yet available in the library: 2nd ed., 2021, ISBN 978-0-12 817726-6. |
| 1. D.J.A. Crommelin, R.D. Sindelar, B. Meibohm (eds.), Pharmaceutical Biotechnology: Fundamentals and Applications, 6th ed., Springer, 2024. ISBN 978-3-031-30022-6. 2. B.R. Glick, C.L. Patten, Molecular Biotechnology: Principles and Applications of Recombinant DNA, 6th ed., ASM Press / Wiley, 2022. ISBN 978-1-68367-364-4. 3. Weekly review and research articles assigned for the journal club (e.g., Nature Biotechnology, Nature Reviews Drug Discovery, Trends in Biotechnology). |
Course Contribution to Program Qualifications
| Course Contribution to Program Qualifications | |||||||
| No | Program Qualification | Contribution Level | |||||
| 1 | 2 | 3 | 4 | 5 | |||
| 1 | Develop and deepen knowledge in the same or in a different field to the proficiency level based on Bachelor level qualifications. | X | |||||
| 2 | Conceive the interdisciplinary interaction which the field is related with. | X | |||||
| 3 | Use of theoretical and practical knowledge within the field at a proficiency level and solve the problem faced related to the field by using research methods. | X | |||||
| 4 | Interpret the knowledge about the field by integrating the information gathered from different disciplines and formulate new knowledge. | X | |||||
| 5 | Independently conduct studies that require proficiency in the field. | ||||||
| 6 | Take responsibility and develop new strategic solutions as a team member in order to solve unexpected complex problems faced within the applications in the field. | ||||||
| 7 | Evaluate knowledge and skills acquired at proficiency level in the field with a critical approach and direct the learning. | X | |||||
| 8 | Investigate, improve social connections and their conducting norms with a critical view and act to change them when necessary. Communicate with peers by using a foreign language at least at a level of European Language Portfolio B2 General Level. | X | |||||
| 9 | Define the social and environmental aspects of engineering applications. | ||||||
| 10 | Audit the data gathering, interpretation, implementation and announcement stages by taking into consideration the cultural, scientific, and ethic values and teach these values. | ||||||
Assessment Methods
| Contribution Level | Absolute Evaluation | |
| Rate of Midterm Exam to Success | 50 | |
| Rate of Final Exam to Success | 50 | |
| Total | 100 | |
| ECTS / Workload Table | ||||||
| Activities | Number of | Duration(Hour) | Total Workload(Hour) | |||
| Course Hours | 14 | 3 | 42 | |||
| Guided Problem Solving | 0 | 0 | 0 | |||
| Resolution of Homework Problems and Submission as a Report | 1 | 80 | 80 | |||
| Term Project | 14 | 3 | 42 | |||
| Presentation of Project / Seminar | 1 | 20 | 20 | |||
| Quiz | 0 | 0 | 0 | |||
| Midterm Exam | 0 | 0 | 0 | |||
| General Exam | 1 | 40 | 40 | |||
| Performance Task, Maintenance Plan | 0 | 0 | 0 | |||
| Total Workload(Hour) | 224 | |||||
| Dersin AKTS Kredisi = Toplam İş Yükü (Saat)/30*=(224/30) | 7 | |||||
| ECTS of the course: 30 hours of work is counted as 1 ECTS credit. | ||||||
Detail Informations of the Course
Course Description
| Course | Code | Semester | T+P (Hour) | Credit | ECTS |
|---|---|---|---|---|---|
| BIOTECHNOLOGY | BEBY1112981 | Fall Semester | 3+0 | 3 | 8 |
| Course Program | Cuma 13:30-14:15 Cuma 14:30-15:15 Cuma 15:30-16:15 Cuma 16:30-17:15 |
| Prerequisites Courses | |
| Recommended Elective Courses |
| Language of Course | English |
| Course Level | Second Cycle (Master's Degree) |
| Course Type | Elective |
| Course Coordinator | Assist.Prof. Mehmet Hikmet ÜÇIŞIK |
| Name of Lecturer(s) | Assist.Prof. Mehmet Hikmet ÜÇIŞIK |
| Assistant(s) | This course covers the scope of modern biotechnology and the biotech product pipeline; expression hosts, cell culture and cell line development; recombinant DNA technology and synthetic biology; PCR, qPCR and next-generation sequencing; genome editing (CRISPR-Cas, base and prime editing); protein engineering and computational protein design; therapeutic proteins and monoclonal antibodies; upstream and downstream bioprocessing and GMP; characterization and quality of biologics; nucleic acid therapeutics and gene delivery; nanobiotechnology for drug delivery (lipid nanocarriers, extracellular vesicles); cell based therapies and regenerative medicine; molecular diagnostics and biosensors; and patents, licensing, regulation and bioethics. |
| Aim | To provide graduate students with an integrated, application-oriented understanding of modern biotechnology, from molecular tools and expression systems to biomanufacturing, advanced therapies, diagnostics and regulation, and to develop their ability to critically evaluate and design biotechnology-based solutions in biomedical engineering. |
| Course Content | This course contains; Introduction: scope of modern biotechnology, the biotech product pipeline, from rDNA to ATMPs; assignment of term project topics,Cells as factories: expression hosts (E. coli, yeast, CHO, HEK293), cell culture and cell line development,Recombinant DNA technology and synthetic biology: vectors, cloning, DNA assembly,Nucleic acid amplification and analysis: PCR, qPCR, NGS and links to bioinformatics,Genome editing: CRISPR-Cas, base and prime editing, off-target assessment ,Protein engineering: directed evolution, computational and AI-based protein design,Therapeutic proteins and monoclonal antibodies: biosimilars, ADCs, bispecifics ,Bioprocessing: upstream (bioreactors, fermentation), downstream purification, GMP,Characterization and quality of biologics: HPLC, MS, peptide mapping, glycosylation, endotoxin, immunogenicity,Nucleic acid therapeutics and gene delivery: AAV/lentiviral vectors, siRNA/ASO, mRNA-LNP,Nanobiotechnology for drug delivery: lipid nanocarriers, extracellular vesicles ,Cell-based therapies and regenerative medicine: CAR-T, stem cells/iPSC, tissue engineering,Molecular diagnostics and biosensors: liquid biopsy, CRISPR diagnostics, point-of-care,Translation: patents and licensing, regulation (EMA/FDA/TİTCK), bioethics; term project presentations. |
| Course Learning Outcomes | Teaching Methods | Assessment Methods |
| A, D, F |
| Teaching Methods: | |
| Assessment Methods: | A: Traditional Written Exam, D: Oral Exam, F: Project Task |
Course Outline
| Order | Subjects | Preliminary Work |
|---|---|---|
| 1 | Introduction: scope of modern biotechnology, the biotech product pipeline, from rDNA to ATMPs; assignment of term project topics | Godbey: introduction to biotechnology |
| 2 | Cells as factories: expression hosts (E. coli, yeast, CHO, HEK293), cell culture and cell line development | Godbey: cell culture and eukaryotic cells; Glick & Patten: heterologous protein production |
| 3 | Recombinant DNA technology and synthetic biology: vectors, cloning, DNA assembly | Godbey: genetic engineering; Glick & Patten: recombinant DNA technology |
| 4 | Nucleic acid amplification and analysis: PCR, qPCR, NGS and links to bioinformatics | Godbey: PCR; assigned article |
| 5 | Genome editing: CRISPR-Cas, base and prime editing, off-target assessment | Godbey: genome editing; Glick & Patten: CRISPR; assigned article |
| 6 | Protein engineering: directed evolution, computational and AI-based protein design | Glick & Patten: protein engineering; assigned article |
| 7 | Therapeutic proteins and monoclonal antibodies: biosimilars, ADCs, bispecifics | Crommelin: monoclonal antibodies |
| 8 | Bioprocessing: upstream (bioreactors, fermentation), downstream purification, GMP | Godbey: processing and manufacturing; Crommelin: production and downstream processing |
| 9 | Characterization and quality of biologics: HPLC, MS, peptide mapping, glycosylation, endotoxin, immunogenicity | Crommelin: biophysical/biochemical analysis; immunogenicity |
| 10 | Nucleic acid therapeutics and gene delivery: AAV/lentiviral vectors, siRNA/ASO, mRNA-LNP | Godbey: gene delivery, RNAi; Crommelin: oligonucleotides, mRNA, gene therapy |
| 11 | Nanobiotechnology for drug delivery: lipid nanocarriers, extracellular vesicles | Assigned review articles |
| 12 | Cell-based therapies and regenerative medicine: CAR-T, stem cells/iPSC, tissue engineering | Godbey: stem cells, tissue engineering, immunotherapy; Crommelin: cell therapies |
| 13 | Molecular diagnostics and biosensors: liquid biopsy, CRISPR diagnostics, point-of-care | Glick & Patten: molecular diagnostics; assigned article |
| 14 | Translation: patents and licensing, regulation (EMA/FDA/TİTCK), bioethics; term project presentations | Godbey: patents and licenses; project dossier |
| Resources |
| W.T. Godbey, Biotechnology and its Applications: Using Cells to Change the World, 3rd ed., Academic Press (Elsevier), 2026. ISBN 978-0-443-24101-7. If the 3rd edition is not yet available in the library: 2nd ed., 2021, ISBN 978-0-12 817726-6. |
| 1. D.J.A. Crommelin, R.D. Sindelar, B. Meibohm (eds.), Pharmaceutical Biotechnology: Fundamentals and Applications, 6th ed., Springer, 2024. ISBN 978-3-031-30022-6. 2. B.R. Glick, C.L. Patten, Molecular Biotechnology: Principles and Applications of Recombinant DNA, 6th ed., ASM Press / Wiley, 2022. ISBN 978-1-68367-364-4. 3. Weekly review and research articles assigned for the journal club (e.g., Nature Biotechnology, Nature Reviews Drug Discovery, Trends in Biotechnology). |
Course Contribution to Program Qualifications
| Course Contribution to Program Qualifications | |||||||
| No | Program Qualification | Contribution Level | |||||
| 1 | 2 | 3 | 4 | 5 | |||
| 1 | Develop and deepen knowledge in the same or in a different field to the proficiency level based on Bachelor level qualifications. | X | |||||
| 2 | Conceive the interdisciplinary interaction which the field is related with. | X | |||||
| 3 | Use of theoretical and practical knowledge within the field at a proficiency level and solve the problem faced related to the field by using research methods. | X | |||||
| 4 | Interpret the knowledge about the field by integrating the information gathered from different disciplines and formulate new knowledge. | X | |||||
| 5 | Independently conduct studies that require proficiency in the field. | ||||||
| 6 | Take responsibility and develop new strategic solutions as a team member in order to solve unexpected complex problems faced within the applications in the field. | ||||||
| 7 | Evaluate knowledge and skills acquired at proficiency level in the field with a critical approach and direct the learning. | X | |||||
| 8 | Investigate, improve social connections and their conducting norms with a critical view and act to change them when necessary. Communicate with peers by using a foreign language at least at a level of European Language Portfolio B2 General Level. | X | |||||
| 9 | Define the social and environmental aspects of engineering applications. | ||||||
| 10 | Audit the data gathering, interpretation, implementation and announcement stages by taking into consideration the cultural, scientific, and ethic values and teach these values. | ||||||
Assessment Methods
| Contribution Level | Absolute Evaluation | |
| Rate of Midterm Exam to Success | 50 | |
| Rate of Final Exam to Success | 50 | |
| Total | 100 | |