TÜRKÇE
ENGLISH
Information
| Unit | INSTITUTE OF MEDICAL SCIENCES |
| TRANSLATIONAL MEDICINE (PhD) (ENGLISH) (INTERDISCIPLINARY) | |
| Code | Trans634 |
| Name | 3D Organoid Techniques |
| Term | 2025-2026 Academic Year |
| Term | Fall and Spring |
| Duration (T+A) | 1-6 (T-A) (17 Week) |
| ECTS | 8 ECTS |
| National Credit | 4 National Credit |
| Teaching Language | İngilizce |
| Level | Doktora Dersi |
| Type | Normal |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | Doç. Dr. Yasemin SAYGIDEĞER |
| Course Instructor |
Dr. Öğr. Üyesi ÖZGECAN KAYALAR
(Bahar)
(A Group)
(Ins. in Charge)
|
Course Goal / Objective
The objective of this course is to provide students with a comprehensive understanding of the theoretical foundations and practical applications of 3D organoid systems. The course aims to cover the mechanisms of stem cell self-organization, bioengineering methodologies, and the critical role of these models in disease modeling and personalized medicine.
Course Content
The course content covers the history of cell culture, comparison of 2D and 3D systems, pluripotent and adult stem cell biology, extracellular matrix (ECM) interactions, biomaterials engineering, microfluidic systems (Organ-on-a-chip), tissue-specific organoid protocols (brain, gut, liver, etc.), advanced imaging and the other techniques.
Course Precondition
Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture
Resources
Current publications, websites, current books, current literature related to the topic.
Notes
Current publications
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | Analyze the biological and mechanical differences between 2D and 3D cell culture systems |
| LO02 | Explain the self-organization processes of stem cells during organoid formation |
| LO03 | Identify specialized 3D culture protocols and growth factor requirements for various organ systems |
| LO04 | Evaluate the impact of biomaterials and bioreactors on organoid maturation |
| LO05 | Comprehend the application methods of organoid technology in drug development and toxicity testing |
| LO06 | Apply advanced imaging and analysis methods to organoid data |
| LO07 | Critically discuss the ethical dimensions of organoid research (consciousness, donor rights, etc.) |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Develops and deepens the current and advanced level knowledge of translational medicine via unique thoughts or researches at a level of proficiency, find out original definitions that will bring innovation in the field of translational medicine. | 1 |
| PLO02 | Bilgi - Kuramsal, Olgusal | Conceives the interdisciplinary interactions related to translational medicine; analyzes synthesizes and evaluates original and new thoughts. | |
| PLO03 | Bilgi - Kuramsal, Olgusal | Explains the usage of tool, devices and instruments requiered for knowledge and technologies about translational medicine and its related disciplines. | |
| PLO04 | Bilgi - Kuramsal, Olgusal | Defines frequently used statistical methods in translational medicine and related disciplines, uses statistical softwares effectively. | |
| PLO05 | Beceriler - Bilişsel, Uygulamalı | Uses both theoretical and practical knowledge at an advanced level in the studies related to translational medicine. | |
| PLO06 | Beceriler - Bilişsel, Uygulamalı | Develops a new thoughts, method and designment/application which brings innovation in translational medicine or implements a known thoughts, method and designment/application in different fields, investigates, comprehends, designs, adapts, implements an original topic. | |
| PLO07 | Beceriler - Bilişsel, Uygulamalı | Writes the report of his/her research which he/she participated, | |
| PLO08 | Beceriler - Bilişsel, Uygulamalı | Makes necessary investigations by using tool, devices and instrument required for knowledge and technologies about translational medicine and related disciplines at an advanced level, develops a new and creative solution (device, method, treatment, drug) for the problems. | |
| PLO09 | Beceriler - Bilişsel, Uygulamalı | Uses statistical software in the field of Translational Medicine effectively, chooses statistical methods correctly, calculates and interprets correctly. | |
| PLO10 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Maintains the organization of Translational Medicine laboratories and develops solutions in case of encountering unforeseen complex situations during laboratory working hours. | 4 |
| PLO11 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Conducts scientific studies in translational medicine and related fields independently or as a team member. | 4 |
| PLO12 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Writes the report of his/her research in which he/she participated, publishes in a national or international reputed journal (indexing in SCI, SCI-Expanded, SSCI, or AHCI), and presents it at scientific meetings. | |
| PLO13 | Yetkinlikler - Öğrenme Yetkinliği | Follows evidence-based practices and conducts research on professional practices that will create evidence in their field. | 3 |
| PLO14 | Yetkinlikler - Öğrenme Yetkinliği | Applies the principles of advanced professional development and lifelong learning in the field of Translational Medicine. | 2 |
| PLO15 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | Communicate current developments and studies within the field to both professional and non-professional groups systematically using written, oral and visual techniques by supporting with quantitative and qualitative data. | |
| PLO16 | Bilgi - Kuramsal, Olgusal | Learns how to teach a concept, subject, phenomenon or case related to Translational Medicine. | 2 |
| PLO17 | Belirsiz | Communicate and discuss orally, in written and visually with peers by using a foreign language at least at a level of European Language Portfolio B2 General Level. | |
| PLO18 | Yetkinlikler - Alana Özgü Yetkinlik | Audit the data gathering, interpretation, implementation and announcement stages by taking into consideration the cultural, scientific, and ethic values and uses these issues for social strategy, implementation plans and frame of quality processes. | |
| PLO19 | Yetkinlikler - Alana Özgü Yetkinlik | Knows the importance of ethical principles and ethical committees for the individual and society, acts ethically. | |
| PLO20 | Yetkinlikler - Alana Özgü Yetkinlik | Increases the awareness of society about translational medicine. |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Evolution of Cell Culture: From 2D Monolayers to 3D Systems. | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 2 | Stem Cell Biology: Cellular Sources of Organoids | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 3 | Mechanisms of Self-Organization and Morphogenesis Principles | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 4 | Extracellular Matrix (ECM) and Hydrogels | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 5 | 3D Culture Techniques: Hanging Drop, Low-Adhesive Plates, In-Support Material, and Bioreactors | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Deney / Laboratuvar, Alıştırma ve Uygulama |
| 6 | Integration with Biomimic Interfaces, Microfluidic Systems, and Organ-on-a-Chip Technologies | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Alıştırma ve Uygulama, Deney / Laboratuvar |
| 7 | Cell viability, cell cytotoxicity, forskolin-induced swelling test, cilia function, and epithelial barrier function analyses in organoids | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Alıştırma ve Uygulama |
| 8 | Mid-Term Exam | General Review | Ölçme Yöntemleri: Sözlü Sınav, Performans Değerlendirmesi, Ödev |
| 9 | Organoid Imaging and Analysis Techniques | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Alıştırma ve Uygulama |
| 10 | Epithelial Organoids: Lung Epithelial Organoids, Apical-Inward and Apical-Outward Organoids | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Alıştırma ve Uygulama |
| 11 | Cancer Organoids - Tumoroids | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Alıştırma ve Uygulama, Tartışma |
| 12 | Neural Organoids and Neurological 3D Disease Models | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Alıştırma ve Uygulama |
| 13 | Modeling of Intestinal Organoids and Development of Clonal Organoids | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 14 | Stomach and Pancreas Organoids and 3D Disease Models | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Soru-Cevap, Anlatım, Tartışma, Alıştırma ve Uygulama |
| 15 | Ovarian Organoids and 3D Disease Models | Having taken a course in cell culture techniques or possessing demonstrable knowledge and competence related to cell culture | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Alıştırma ve Uygulama |
| 16 | Term Exams | General Review | Ölçme Yöntemleri: Sözlü Sınav, Yazılı Sınav, Ödev, Performans Değerlendirmesi |
| 17 | Term Exams | Oral/Writing Exam | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev, Performans Değerlendirmesi |
Student Workload - ECTS
| Works | Number | Time (Hour) | Workload (Hour) |
|---|---|---|---|
| Course Related Works | |||
| Class Time (Exam weeks are excluded) | 14 | 6 | 84 |
| Out of Class Study (Preliminary Work, Practice) | 14 | 6 | 84 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 1 | 6 | 6 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 6 | 6 |
| Final Exam | 1 | 14 | 14 |
| Total Workload (Hour) | 194 | ||
| Total Workload / 25 (h) | 7,76 | ||
| ECTS | 8 ECTS | ||