TÜRKÇE
ENGLISH
Information
| 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
(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
Bowman DD. Georgis Parasitology for Veterinarians.10th ed. Elseiver; 2014. p. 326-398.Taylor MA, Coop RL, Wall RL, Veterinary Parasitology. 4th ed. Wiley Blackwell; 2016. Zajac AM, Conboy GA, Veterinary Clinical Parasitology. 8th ed. John Wiley and Sons, Inc; 2012. Freeman S, Herron JC, Evrimsel Analiz. Çıplak, B, Başıbüyük H, Karaytuğ, S, Gündüz, İ. (eds). Palme Yayıncılık, Ankara, 2009. Lemey P, Salemi M, Vandamme AM, The Phylogenetic Handbook, A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Cambridge University Press, 2009. 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 | Students learn to classify the parasites. |
| LO02 | Students know the correct molecular markers used in the classification of the parasites. |
| LO03 | Students can design primers for the amplification of molecular markers. |
| LO04 | Students can edit DNA sequences and compare with the databases. |
| LO05 | Students can select the correct algorithms for multiple sequence alignments and determine the correct substitutions models. |
| LO06 | Students can create phylogenetic trees. |
| LO07 | Students can interpret the phylogenetic trees that they create. |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Develop and deepen the current and advanced knowledge in the field with original thought and / or research at the level of expertise based on the qualifications of the graduate and reach the original definitions that will bring innovation to the field. | 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. | 4 |
| 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. | 3 |
| 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. | 2 |
| 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. | 3 |
| PLO09 | Yetkinlikler - Alana Özgü Yetkinlik | Conducts scientific research in national and international scientific research groups. | 2 |
| PLO10 | Yetkinlikler - Alana Özgü Yetkinlik | Establishes functional interaction by using strategic decision making processes in solving problems encountered in the field. | 2 |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | Big Bang and the evolution of matter | 1. Evrimsel Analiz 2. The Phylogenetic Handbook 3.Bioinformatics and Functional Genomics 4.Essential Bioinformatics | Öğretim Yöntemleri: Soru-Cevap, Tartışma, Anlatım |
| 2 | Structure of parasite cells | Bowman DD. Georgis Parasitology for Veterinarians.10th ed. Elseiver; 2014. p. 326-398. Taylor MA, Coop RL, Wall RL, Veterinary Parasitology. 4th ed. Wiley Blackwell; 2016. | Öğretim Yöntemleri: Soru-Cevap, Anlatım |
| 3 | Classification of parasites | Bowman DD. Georgis Parasitology for Veterinarians.10th ed. Elseiver; 2014. p. 326-398. Taylor MA, Coop RL, Wall RL, Veterinary Parasitology. 4th ed. Wiley Blackwell; 2016. | Öğretim Yöntemleri: Anlatım, Soru-Cevap |
| 4 | The mechanisms of macro and micro evolution | 1. Evrimsel Analiz 2. The Phylogenetic Handbook 3.Bioinformatics and Functional Genomics 4.Essential Bioinformatics | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 5 | Genom structure of parasites, nucleic acids, and DNA replication | 1. Insect Molecular Genetics 2.Moleküler Parazitoloji | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 6 | Transcription, translation, control of gene expression, mechanisms of gene formation and primer design | Freeman S, Herron JC, Evrimsel Analiz. Çıplak, B, Başıbüyük H, Karaytuğ, S, Gündüz, İ. (eds). Palme Yayıncılık, Ankara, 2009. Lemey P, Salemi M, Vandamme AM, The Phylogenetic Handbook, A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Cambridge University Press, 2009. Pevsner J, Bioinformatics and Functional Genomics, Wiley-Blackwell, 2009. Xıong J, Essential Bioinformatics, Cambridge University Press, 2006. | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma |
| 7 | Correcting and interpretation of DNA sequences, genetic databases, BLAST search, understanding the BLAST results | 1.BOLD (Web Sitesi) 2. NCBI (Web Sitesi) 3.CLC MainWorkbench (PC Programı 4.GeniousPrime (PC Programı) 4.MEGAX (PC Programı) | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Alıştırma ve Uygulama, Gösterip Yaptırma |
| 8 | Subject Repeat, with questions and answers | Subject Repeat, with questions and answers | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Alıştırma ve Uygulama, Problem Çözme |
| 9 | Algorithms used in multiple sequence alignment, selection of correct algorithm, computer programs used for multiple sequence alignment | 1. Evrimsel Analiz 2. The Phylogenetic Handbook 3.Bioinformatics and Functional Genomics 4.Essential Bioinformatics 5.BOLD (Web Sitesi) 6. NCBI (Web Sitesi) 7.CLC MainWorkbench (PC Programı 8.GeniousPrime (PC Programı) 9.MEGAX (PC Programı) | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma, Problem Çözme |
| 10 | Choosing the right evolutionary model with using computer software’s | 1. JModel Test (PC Programı) 2. Model Test (PC Programı) 3.MEGAX (PC Programı) 4. CLC MainWorkbench (PC Programı) 5. GeniousPrime (PC Programı) 6. Partition Finder (PC Programı) | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Tartışma, Gösterip Yaptırma, Problem Çözme |
| 11 | Basic concepts of phylogenetics | 1. The Phylogenetic Handbook 2. Bioinformatics and Functional Genomics 3. Essential Bioinformatics | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Alıştırma ve Uygulama, Gösterip Yaptırma |
| 12 | Phylogenetic trees | 1. The Phylogenetic Handbook 2. Bioinformatics and Functional Genomics 3. Essential Bioinformatics | Öğretim Yöntemleri: Anlatım, Alıştırma ve Uygulama, Gösterip Yaptırma, Problem Çözme |
| 13 | Phylogenetic analysis programmes and their use (MEGA, GENIOUS) | 1. JModel Test (PC Programı) 2. Model Test (PC Programı) 3.MEGAX (PC Programı) 4. CLC MainWorkbench (PC Programı) 5. GeniousPrime (PC Programı) 6. Partition Finder (PC Programı) | Öğretim Yöntemleri: Anlatım, Alıştırma ve Uygulama, Gösterip Yaptırma, Problem Çözme |
| 14 | Phylogenetic analysis programmes and their use (CLC mainworkbench, PHYLIP, MRBAYES | 1. JModel Test (PC Programı) 2. Model Test (PC Programı) 3.MEGAX (PC Programı) 4. CLC MainWorkbench (PC Programı) 5. GeniousPrime (PC Programı) 6. Partition Finder (PC Programı) | Öğretim Yöntemleri: Anlatım, Soru-Cevap, Gösterip Yaptırma, Problem Çözme |
| 15 | Mid Term Final Exam | Mid Term Final Exam | Ölçme Yöntemleri: Sözlü Sınav, Ödev, Yazılı Sınav |
| 16 | Mid Term Final Exam | Mid Term Final Exam | Ölçme Yöntemleri: Yazılı Sınav, Sözlü Sınav, Ödev |
| 17 | Mid Term Final Exam | Mid Term Final Exam | Ölçme Yöntemleri: Sözlü Sınav, Yazılı Sınav, Ödev |
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 | 5 | 70 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 0 | 0 | 0 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 5 | 5 |
| Final Exam | 1 | 15 | 15 |
| Total Workload (Hour) | 160 | ||
| Total Workload / 25 (h) | 6,40 | ||
| ECTS | 6 ECTS | ||