TÜRKÇE
ENGLISH
Information
| Unit | INSTITUTE OF NATURAL AND APPLIED SCIENCES |
| BIOTECHNOLOGY (PhD) (INTERDISCIPLINARY) | |
| Code | BT0135 |
| Name | Phylogenetic Applications in Parasite Systematics |
| Term | 2024-2025 Academic Year |
| Term | Fall |
| Duration (T+A) | 3-2 (T-A) (17 Week) |
| ECTS | 6 ECTS |
| National Credit | 4 National Credit |
| Teaching Language | Türkçe |
| Level | Doktora Dersi |
| Type | Normal |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | |
| Course Instructor |
Prof. Dr. ARMAĞAN ERDEM ÜTÜK
(Güz)
(A Group)
(Ins. in Charge)
|
Course Goal / Objective
The aim of this course is to enable the student to learn the logic of the phylogenetics in the classification of parasites.
Course Content
Molecular marker selection in parasite classification, primer design, obtaining of DNA sequences, correction of dendrograms, multiple sequence alignment, database search, haplotypes analysis, choosing best evolution models, creating, and interpreting the phylogenetic trees are the contents of this course.
Course Precondition
NONE
Resources
Lecture notes and presentations will be used on for the courses
Notes
1. Bowman DD. Georgis Parasitology for Veterinarians.10th ed. Elseiver; 2014. p. 326-398. 2. Taylor MA, Coop RL, Wall RL, Veterinary Parasitology. 4th ed. Wiley Blackwell; 2016. 3. Zajac AM, Conboy GA, Veterinary Clinical Parasitology. 8th ed. John Wiley and Sons, Inc; 2012. 4. Freeman S, Herron JC, Evrimsel Analiz. Çıplak, B, Başıbüyük H, Karaytuğ, S, Gündüz, İ. (eds). Palme Yayıncılık, Ankara, 2009. 5. Lemey P, Salemi M, Vandamme AM, The Phylogenetic Handbook, A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Cambridge University Press, 2009. 6. Pevsner J, Bioinformatics and Functional Genomics, Wiley-Blackwell, 2009. Xıong J, Essential Bioinformatics, Cambridge University Press, 2006.
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | Constructs phylogenetic trees. |
| LO02 | Evaluates the phylogenetic trees they have constructed. |
| LO03 | Selects the appropriate algorithms for multiple sequence analyses and choose the correct substitution models. |
| LO04 | Edits DNA sequences and compare with the databases. |
| LO05 | Designs primers for the amplification of molecular markers. |
| LO06 | Lists the appropriate molecular markers used in the classification of parasites. |
| LO07 | Draws conclusions on the classification of parasites. |
| LO08 | The student discusses the mechanisms of evolutionary change. |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Develops current and advanced knowledge in the field at the level of expertise with original thought and/or research, based on graduate qualifications. | 4 |
| PLO02 | Bilgi - Kuramsal, Olgusal | Understands the interdisciplinary interaction of the field; it achieves original results using knowledge requiring expertise in analysis, synthesis and evaluation of new and complex ideas. | |
| PLO03 | Beceriler - Bilişsel, Uygulamalı | Evaluates, uses and transfers new information in the field with a systematic approach. | 3 |
| PLO04 | Beceriler - Bilişsel, Uygulamalı | Makes critical analysis, synthesis and evaluation of new and complex thoughts. | 3 |
| PLO05 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Makes leadership in environments that require the analysis of original and interdisciplinary problems. | |
| PLO06 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | It extends the limits of knowledge in its field by publishing at least one scientific article in its field in national and / or international refereed journals and / or producing or interpreting an original work. | |
| PLO07 | Yetkinlikler - Öğrenme Yetkinliği | Develops new ideas and methods related to the field by using high level mental processes such as creative and critical thinking, problem solving and decision making. | |
| PLO08 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | He / she defends his / her original opinions in discussing the subjects in his / her field and establishes an effective communication showing his / her competence in the field. | |
| PLO09 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | Establishes functional interaction by using strategic decision making processes in solving problems encountered in the field. | 2 |
| PLO10 | Yetkinlikler - Alana Özgü Yetkinlik | Conducts scientific research in national and international scientific research groups. |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Big Bang and the evolution of matter | No pre-preparation | Öğretim Yöntemleri: Anlatım, Beyin Fırtınası, Gösteri |
| 2 | Structure of parasite cells | Slide review | Öğretim Yöntemleri: Anlatım, Gösteri, Soru-Cevap |
| 3 | Classification of parasites | Slide review | Öğretim Yöntemleri: Anlatım, Soru-Cevap |
| 4 | The mechanisms of macro and micro evolution | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Beyin Fırtınası |
| 5 | Genom structure of parasites, nucleic acids, and DNA replication | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 6 | Transcription, translation, control of gene expression, mechanisms of gene formation and primer design | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 7 | Correcting and interpretation of DNA sequences, genetic databases, BLAST search, understanding the BLAST results | Textbook reading, Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Alıştırma ve Uygulama, Gösterip Yaptırma |
| 8 | Mid-Term Exam | Studying for an exam | Ölçme Yöntemleri: Ödev, Sözlü Sınav |
| 9 | Algorithms used in multiple sequence alignment, selection of correct algorithm, computer programs used for multiple sequence alignment | Slide review | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma, Problem Çözme |
| 10 | Choosing the right evolutionary model with using computer software’s | Slide review | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Gösterip Yaptırma, Problem Çözme |
| 11 | Basic concepts of phylogenetics | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap |
| 12 | Phylogenetic trees | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Beyin Fırtınası |
| 13 | Overview of Phylogenetic Tree Construction Programs | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Gösterip Yaptırma |
| 14 | Access to MEGA, Geneious, CLC Main Workbench, PHYLIP, and MrBayes programs | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma, Alıştırma ve Uygulama |
| 15 | Phylogenetic analysis programmes and their use (MEGA, GENIOUS, CLC mainworkbench, PHYLIP, MRBAYES | Slide review, Conducting internet research | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Alıştırma ve Uygulama, Gösterip Yaptırma |
| 16 | Mid Term Final Exam | Studying for an exam | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev |
| 17 | Mid Term Final Exam | Studying for an exam | Ölçme Yöntemleri: Sözlü Sınav, Yazılı Sınav, Ödev |
Assessment (Exam) Methods and Criteria
| Assessment Type | Midterm / Year Impact | End of Term / End of Year Impact |
|---|---|---|
| 1. Midterm Exam | 100 | 40 |
| General Assessment | ||
| Midterm / Year Total | 100 | 40 |
| 1. Final Exam | - | 60 |
| Grand Total | - | 100 |
Student Workload - ECTS
| Works | Number | Time (Hour) | Workload (Hour) |
|---|---|---|---|
| Course Related Works | |||
| Class Time (Exam weeks are excluded) | 14 | 5 | 70 |
| Out of Class Study (Preliminary Work, Practice) | 14 | 6 | 84 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 1 | 4 | 4 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 1 | 1 |
| Final Exam | 1 | 1 | 1 |
| Total Workload (Hour) | 160 | ||
| Total Workload / 25 (h) | 6,40 | ||
| ECTS | 6 ECTS | ||