Biotechnology

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.

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.

WEEKLY PLAN

1. WEEK 1

   Introduction: scope of modern biotechnology, the biotech product pipeline, from rDNA to ATMPs; assignment of term project topics

   Preparation: Godbey: introduction to biotechnology

2. WEEK 2

   Cells as factories: expression hosts (E. coli, yeast, CHO, HEK293), cell culture and cell line development

   Preparation: Godbey: cell culture and eukaryotic cells; Glick & Patten: heterologous protein production

3. WEEK 3

   Recombinant DNA technology and synthetic biology: vectors, cloning, DNA assembly

   Preparation: Godbey: genetic engineering; Glick & Patten: recombinant DNA technology

4. WEEK 4

   Nucleic acid amplification and analysis: PCR, qPCR, NGS and links to bioinformatics

   Preparation: Godbey: PCR; assigned article

5. WEEK 5

   Genome editing: CRISPR-Cas, base and prime editing, off-target assessment

   Preparation: Godbey: genome editing; Glick & Patten: CRISPR; assigned article

6. WEEK 6

   Protein engineering: directed evolution, computational and AI-based protein design

   Preparation: Glick & Patten: protein engineering; assigned article

7. WEEK 7

   Therapeutic proteins and monoclonal antibodies: biosimilars, ADCs, bispecifics

   Preparation: Crommelin: monoclonal antibodies

8. WEEK 8

   Bioprocessing: upstream (bioreactors, fermentation), downstream purification, GMP

   Preparation: Godbey: processing and manufacturing; Crommelin: production and downstream processing

9. WEEK 9

   Characterization and quality of biologics: HPLC, MS, peptide mapping, glycosylation, endotoxin, immunogenicity

   Preparation: Crommelin: biophysical/biochemical analysis; immunogenicity

10. WEEK 10

    Nucleic acid therapeutics and gene delivery: AAV/lentiviral vectors, siRNA/ASO, mRNA-LNP

    Preparation: Godbey: gene delivery, RNAi; Crommelin: oligonucleotides, mRNA, gene therapy

11. WEEK 11

    Nanobiotechnology for drug delivery: lipid nanocarriers, extracellular vesicles

    Preparation: Assigned review articles

12. WEEK 12

    Cell-based therapies and regenerative medicine: CAR-T, stem cells/iPSC, tissue engineering

    Preparation: Godbey: stem cells, tissue engineering, immunotherapy; Crommelin: cell therapies

13. WEEK 13

    Molecular diagnostics and biosensors: liquid biopsy, CRISPR diagnostics, point-of-care

    Preparation: Glick & Patten: molecular diagnostics; assigned article

14. WEEK 14

    Translation: patents and licensing, regulation (EMA/FDA/TİTCK), bioethics; term project presentations

    Preparation: Godbey: patents and licenses; project dossier

ASSESSMENT

• Rate of Midterm Exam to Success50%
• Rate of Final Exam to Success50%

WORKLOAD

READING

• 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).

TEACHING STAFF

• Assist.Prof. Mehmet Hikmet ÜÇIŞIKCOORDINATOR
• Assist.Prof. Mehmet Hikmet ÜÇIŞIK