BIO645 Advanced Plant Biotechnology
Syllabus | International University of Sarajevo - Last Update on Oct 10, 2026
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Genetics and Bioengineering
Mohamed Ibrahim
Course Lecturer
Course Objectives
1. Evaluate the current and emerging applications of plant biotechnology in agriculture, research and bioproduction. 2. Define, integrate and critically evaluate advanced concepts in plant molecular biology, genetics and biotechnology. 3. Understand and select appropriate research methodologies for plant genome engineering and functional genomics. 4. Develop competence in interpreting genomic, transcriptomic, proteomic and other omics datasets. 5. Apply CRISPR-based genome editing, synthetic biology and bioinformatics concepts to plant research problems. 6. Develop awareness of rapidly changing technologies and continuous professional learning. 7. Evaluate biosafety, ethical, regulatory and societal dimensions of advanced plant biotechnology.
Learning Outcomes
After successful completion of the course, the student will be able to:
Course Materials
Required Textbook
• Slater, A., Scott, N. & Fowler, M. Plant Biotechnology: The Genetic Manipulation of Plants. Oxford University Press. (Foundational reference; supplemented extensively by current literature.) • Alberts et al. Molecular Biology of the Cell. Current edition. Garland Science. (Selected molecular-biology background.) • Current review and primary research articles supplied by the lecturer through the IUS learning platform.
Additional Literature
- Additional selected articles in the field of Plant Biotechnology. 1. Tuncel A. et al. (2025). CRISPR–Cas applications in agriculture and plant research. Nature Reviews Molecular Cell Biology, 26, 419–441. 2. Gilbertson L., Puchta H. & Slotkin R.K. (2025). The future of genome editing in plants. Nature Plants, 11, 680–685. 3. Zhao Y. et al. (2025). Advances and prospects of large DNA fragment editing in plants. Nature Plants, 11, 2461–2475. 4. Vats S. et al. (2024). Prime editing in plants: prospects and challenges. Journal of Experimental Botany, 75, 5344–5356. 5. Zhao et al. (2025). The evolving landscape of precise DNA insertion in plants. Nature Communications. 6. James J.S. et al. (2025). The design and engineering of synthetic genomes. Nature Reviews Genetics, 26, 298–319. 7. Lan T. et al. (2025). Genome synthesis in plants. Nature Reviews Bioengineering, 3, 875–889. 8. Borowsky A.T. & Bailey-Serres J. (2024). Rewiring gene circuitry for plant improvement. Nature Genetics, 56, 1574–1582. 9. Ragland C.J., Shih K.Y. & Dinneny J.R. (2024). Choreographing root architecture and rhizosphere interactions through synthetic biology. Nature Communications, 15, 1370. 10. Gulati G.S. et al. (2025). Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nature Reviews Molecular Cell Biology, 26, 11–31.Teaching Methods
Presentations and Research article analysis
Class discussions with examples
Team assigments
Team presentation that involve real data, summary, interpretation and reporting and Field visits
Weekly Topics
| Week | Topic | Readings / References |
|---|---|---|
| 1 | Advanced Plant Genomics: genome organization, gene regulation, pangenomes and crop diversity | Chapter 1 |
| 2 | Selected topics in Plant biotechnology | |
| 3 📍 | Plant Transformation and Genome-Engineering Delivery: Agrobacterium, biolistics, protoplasts, viral and emerging delivery systems | Chapter 5 |
| 4 | The genetic manipulation of herbicide tolerance | Chapter 5 |
| 5 | 1st progress report | |
| 6 | Plant Transformation and Genome-Engineering Delivery: Agrobacterium, biolistics, protoplasts, viral and emerging delivery systems | Chapter6 |
| 7 | CRISPR/Cas Genome Editing in Plants: Cas9/Cas12, guide design, NHEJ/HDR, multiplexing and validation | Chapter 7 |
| 8 | Midterm Research Workshop: Critical analysis of advanced plant-biotechnology papers and student presentations | Chapter 7 |
| 9 | 2nd progress report | |
| 10 | Plant Proteomics and Protein Interactomics: LC-MS/MS, MALDI-TOF, quantitative proteomics, PTMs and PPI networks | Chapter 9 |
| 11 | Plant Stress Biotechnology: drought, salinity, heat, oxidative stress, immunity and multi-omics responses | Chapter 10 |
| 12 | Plant Synthetic Biology and Metabolic Engineering: genetic circuits, promoters, pathway engineering and plant–microbe interactions | Chapter 10 |
| 13 | Molecular Farming and Plant-Based Bioproduction: vaccines, antibodies, recombinant proteins, chloroplast/transient systems | Chapter 11 |
| 14 | 3rd and final progress report | |
| 15 | Revision |
Course Schedule (All Sections)
| Section | Type | Day 1 | Venue 1 | Day 2 | Venue 2 |
|---|---|---|---|---|---|
| BIO645.1 | Course | Wednesday 17:00 - 19:50 | B F1.17 | - | - |
Office Hours & Room
| Day | Time | Office | Notes |
|---|---|---|---|
| Monday | 12:00 - 15:00 | A F1.14 | |
| Tuesday | 10:00 - 12:00 | A F1.14 | |
| Wednesday | 10:00 - 12:00 | A F1.14 | |
| Thursday | 10:00 - 12:00 | A F1.14 | |
| Friday | 10:00 - 12:00 | A F1.14 |
Assessment Methods and Criteria
Assessment Components
Final Exam
AI: Not AllowedAlignment with Learning Outcomes : 1 2 3 4 5
Term project and presentation
AI: Not AllowedAlignment with Learning Outcomes : 1 2 3 4 5
midterm
AI: Not AllowedAlignment with Learning Outcomes : 1 2 4 5
paper analysis
AI: Not AllowedAlignment with Learning Outcomes : 1 2 3 4 5
IUS Grading System
| Grading Scale | IUS Grading System | IUS Coeff. | Letter (B&H) | Numerical (B&H) |
|---|---|---|---|---|
| 0 - 44 | F | 0 | F | 5 |
| 45 - 54 | E | 1 | ||
| 55 - 64 | C | 2 | E | 6 |
| 65 - 69 | C+ | 2.3 | D | 7 |
| 70 -74 | B- | 2.7 | ||
| 75 - 79 | B | 3 | C | 8 |
| 80 - 84 | B+ | 3.3 | ||
| 85 - 94 | A- | 3.7 | B | 9 |
| 95 - 100 | A | 4 | A | 10 |
Late Work Policy
Information about late submission policies will be shared during class and posted in this section. Please check back for official guidelines.
ECTS Credit Calculation
📚 Student Workload
This 6 ECTS credit course corresponds to 150 hours of total student workload, distributed as follows:
Lectures
45 hours ⏳ (15 week × 3 h)
Assignments
10 hours ⏳ (5 week × 2 h)
homework
10 hours ⏳ (2 week × 5 h)
Final Exam study
20 hours ⏳ (1 week × 20 h)
Term Project/presentation
20 hours ⏳ (4 week × 5 h)
Home study
45 hours ⏳ (15 week × 3 h)
150 Total Workload Hours
6 ECTS Credits
Course Policies
Academic Integrity
All work submitted must be your own. Plagiarism, cheating, or any form of academic dishonesty will result in disciplinary action according to university policies. When in doubt about citation practices, consult the instructor.
Attendance Policy
Students are expected to adhere to the attendance requirements as outlined in the International University of Sarajevo Study Rules and Regulations. Excessive absences, whether excused or unexcused, may impact academic performance and eligibility for assessment. Mandatory sessions (e.g., labs, workshops) require attendance unless formally exempted. For detailed policies on absences, documentation, and penalties, please refer to the official university regulations.
Technology & AI Policy
Laptops/tablets may be used for note-taking only during lectures. Phones should be silenced and put away during all class sessions. Audio/video recording requires prior permission from the instructor.
Artificial Intelligence (AI) Usage: The use of AI tools (e.g., ChatGPT, Copilot, Gemini) varies by assessment component. Please refer to the AI usage indicator next to each assessment item in the Assessment Methods and Criteria section above. Submitting AI-generated content as your own work, where AI is not explicitly allowed, constitutes an academic integrity violation.
Communication Policy
All course-related communication should occur through official university channels (institutional email or SIS). Emails should include [BIO645] in the subject line.
Academic Quality Assurance Policy
Course Academic Quality Assurance is achieved through Semester Student Survey. At the end of each academic year, the institution of higher education is obliged to evaluate work of the academic staff, or the success of realization of the curricula.
Learning Tips
Be prepared to contribute thoughtfully during class discussions, labs, or collaborative work. Active participation deepens understanding and encourages critical thinking.
Complete assigned readings or prep materials before class. Take notes, highlight key ideas, and jot down questions. Aim to grasp core concepts and their applications—not just facts.
Use course frameworks or methodologies to analyze problems, case studies, or projects. Begin early to allow time for reflection and refinement. Seek feedback to improve your work.
Don’t hesitate to reach out when something is unclear. Use office hours, discussion boards, or peer networks to clarify concepts and stay on track.
Syllabus Last Updated on Oct 10, 2026 | International University of Sarajevo
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Referencing Curricula Print this page
| Course Code | Course Title | Weekly Hours* | ECTS | Weekly Class Schedule | ||||||
| T | P | |||||||||
| BIO645 | Advanced Plant Biotechnology | 3 | 0 | 6 | Thursday 17:00 - 19:50 | |||||
| Prerequisite | None | It is a prerequisite to | - | |||||||
| Lecturer | Mohamed Ibrahim | Office Hours / Room / Phone | Monday: 12:00-15:00 Tuesday: 10:00-12:00 Wednesday: 10:00-12:00 Thursday: 10:00-12:00 Friday: 10:00-12:00 |
|||||||
| mragab@ius.edu.ba | ||||||||||
| Assistant | Assistant E-mail | |||||||||
| Course Objectives | 1. Evaluate the current and emerging applications of plant biotechnology in agriculture, research and bioproduction. 2. Define, integrate and critically evaluate advanced concepts in plant molecular biology, genetics and biotechnology. 3. Understand and select appropriate research methodologies for plant genome engineering and functional genomics. 4. Develop competence in interpreting genomic, transcriptomic, proteomic and other omics datasets. 5. Apply CRISPR-based genome editing, synthetic biology and bioinformatics concepts to plant research problems. 6. Develop awareness of rapidly changing technologies and continuous professional learning. 7. Evaluate biosafety, ethical, regulatory and societal dimensions of advanced plant biotechnology. |
|||||||||
| Textbook | • Slater, A., Scott, N. & Fowler, M. Plant Biotechnology: The Genetic Manipulation of Plants. Oxford University Press. (Foundational reference; supplemented extensively by current literature.) • Alberts et al. Molecular Biology of the Cell. Current edition. Garland Science. (Selected molecular-biology background.) • Current review and primary research articles supplied by the lecturer through the IUS learning platform. | |||||||||
| Additional Literature |
|
|||||||||
| Learning Outcomes | After successful completion of the course, the student will be able to: | |||||||||
| Teaching Methods | Presentations and Research article analysis. Class discussions with examples. Team assigments. Team presentation that involve real data, summary, interpretation and reporting and Field visits. | |||||||||
| Teaching Method Delivery | Face-to-face | Teaching Method Delivery Notes | ||||||||
| WEEK | TOPIC | REFERENCE | ||||||||
| Week 1 | Advanced Plant Genomics: genome organization, gene regulation, pangenomes and crop diversity | Chapter 1 | ||||||||
| Week 2 | Selected topics in Plant biotechnology | |||||||||
| Week 3 | Plant Transformation and Genome-Engineering Delivery: Agrobacterium, biolistics, protoplasts, viral and emerging delivery systems | Chapter 5 | ||||||||
| Week 4 | The genetic manipulation of herbicide tolerance | Chapter 5 | ||||||||
| Week 5 | 1st progress report | |||||||||
| Week 6 | Plant Transformation and Genome-Engineering Delivery: Agrobacterium, biolistics, protoplasts, viral and emerging delivery systems | Chapter6 | ||||||||
| Week 7 | CRISPR/Cas Genome Editing in Plants: Cas9/Cas12, guide design, NHEJ/HDR, multiplexing and validation | Chapter 7 | ||||||||
| Week 8 | Midterm Research Workshop: Critical analysis of advanced plant-biotechnology papers and student presentations | Chapter 7 | ||||||||
| Week 9 | 2nd progress report | |||||||||
| Week 10 | Plant Proteomics and Protein Interactomics: LC-MS/MS, MALDI-TOF, quantitative proteomics, PTMs and PPI networks | Chapter 9 | ||||||||
| Week 11 | Plant Stress Biotechnology: drought, salinity, heat, oxidative stress, immunity and multi-omics responses | Chapter 10 | ||||||||
| Week 12 | Plant Synthetic Biology and Metabolic Engineering: genetic circuits, promoters, pathway engineering and plant–microbe interactions | Chapter 10 | ||||||||
| Week 13 | Molecular Farming and Plant-Based Bioproduction: vaccines, antibodies, recombinant proteins, chloroplast/transient systems | Chapter 11 | ||||||||
| Week 14 | 3rd and final progress report | |||||||||
| Week 15 | Revision | |||||||||
| Assessment Methods and Criteria | Evaluation Tool | Quantity | Weight | Alignment with LOs | AI Usage |
| Final Exam | 1 | 40 | 1,2,3,4,5 | Not Allowed | |
| Semester Evaluation Components | |||||
| Term project and presentation | 5 | 25 | 1,2,3,4,5 | Not Allowed | |
| midterm | 5 | 25 | 1,2,4,5 | Not Allowed | |
| paper analysis | 3 | 10 | 1,2,3,4,5 | Not Allowed | |
| *** ECTS Credit Calculation *** | |||||
| Activity | Hours | Weeks | Student Workload Hours | Activity | Hours | Weeks | Student Workload Hours | |||
| Lectures | 3 | 15 | 45 | Assignments | 2 | 5 | 10 | |||
| homework | 5 | 2 | 10 | Final Exam study | 20 | 1 | 20 | |||
| Term Project/presentation | 5 | 4 | 20 | Home study | 3 | 15 | 45 | |||
| Total Workload Hours = | 150 | |||||||||
| *T= Teaching, P= Practice | ECTS Credit = | 6 | ||||||||
| Course Academic Quality Assurance: Semester Student Survey | Last Update Date: 01/10/2026 | |||||||||