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Information
| Code | BK584 |
| Name | Genom Analyses of Plants and Pathogens |
| Term | 2024-2025 Academic Year |
| Semester | . Semester |
| Duration (T+A) | 2-2 (T-A) (17 Week) |
| ECTS | 6 ECTS |
| National Credit | 3 National Credit |
| Teaching Language | Türkçe |
| Level | Doktora Dersi |
| Type | Normal |
| Mode of study | Yüz Yüze Öğretim |
| Catalog Information Coordinator | Prof. Dr. MUKADDES KAYIM |
Course Goal / Objective
To examine the structure of pathogen-related genes in plants, to classify pathogens according to their nucleotide sequences, to determine protein gene sequences in the development of serological methods to identify pathogens, to construct phylogenetic trees of plants and pathogens
Course Content
Determination of genes related to resistance in plants by bioinformatics analysis, nucleotide sequences of genes, genome organization, genome structures and nucleotide sequences of pathogens, protein motifs, phylogenetic trees according to nucleotide sequences
Course Precondition
No pre requirement
Resources
Phylogenetic Trees Made easy: A How to manual 5. Edition Barry G. Hall 2022
Notes
Courses notes
Course Learning Outcomes
| Order | Course Learning Outcomes |
|---|---|
| LO01 | Learns what is a phylogenetic tree and how to estimate a phylogenetic tree. Learns why a family tree is formed for pathogens. |
| LO02 | Learn how to use the methods and software programs used to align sequences for plant and pathogen's genome. |
| LO03 | Learn to use the major methods to predict phylogenetic tree and how to solve the problems encountered in the formation of phylogenetic trees. |
| LO04 | Learns how to use of database searching for similar genes |
| LO05 | Learns terms used for classifying protein structure and sequences. Learns Available alignments models and database for proteins |
| LO06 | How to compare gene sequences and aminoacids ithe data bank of the world with a specific gene or aminoacids. |
Relation with Program Learning Outcome
| Order | Type | Program Learning Outcomes | Level |
|---|---|---|---|
| PLO01 | Bilgi - Kuramsal, Olgusal | Has knowledge on basic topics about general science, general agricultural engineering and plant production | 2 |
| PLO02 | Bilgi - Kuramsal, Olgusal | Knows the biology, ecology, systematics and control strategies of diseases, pests and weeds causing yield losses in plants | 1 |
| PLO03 | Bilgi - Kuramsal, Olgusal | Knows the identification and the biology of the diseases and how to control diseases,pests and weeds causing yield losses in plants in practice. | 4 |
| PLO04 | Bilgi - Kuramsal, Olgusal | Comprehends the plant protection problems, gains the ability to solve the problems via scientific methods | |
| PLO05 | Beceriler - Bilişsel, Uygulamalı | Obtains the skill to use a laboratory, analyzes and evaluates the results and prepares reports. | 3 |
| PLO06 | Bilgi - Kuramsal, Olgusal | Decides to the most useful control strategy to cope with the plant protection problems and gets them to be used correctly. | |
| PLO07 | Bilgi - Kuramsal, Olgusal | Has necessary knowledge to use the essential technologies, synthesizes them to prepare oral presentations. | 5 |
| PLO08 | Yetkinlikler - Alana Özgü Yetkinlik | Gains the ability to identify problems related to the field and to construct and use high-level scientific research methods in solving them. | |
| PLO09 | Yetkinlikler - Alana Özgü Yetkinlik | Being able to independently carry out a work or project that requires expertise in the field, develop new approaches for solving problems encountered in practice and produce solutions by taking responsibility. | |
| PLO10 | Yetkinlikler - Alana Özgü Yetkinlik | Gains the ability to identify problems related to the field and to construct and use high-level scientific research methods in solving them | |
| PLO11 | Yetkinlikler - Alana Özgü Yetkinlik | Can develop and deepen the knowledge in plant protection in general, in field of expertise in particular, gain the ability to carry out and have studies that will bring innovation to science and reach original results. | |
| PLO12 | Yetkinlikler - İletişim ve Sosyal Yetkinlik | He/she can defend his/her original inventions, opinions, approaches and suggestions in front of experts and discuss them by communicating effectively. | |
| PLO13 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Can associate Plant protection-related subjects with other fields of science, and effectively use the knowledge that requires expertise in the evaluation of new and complex ideas, events, and phenomena. | |
| PLO14 | Yetkinlikler - Bağımsız Çalışabilme ve Sorumluluk Alabilme Yetkinliği | Scientific, technological, social and cultural advances in plant protection; can take active roles in creating an information society, solving problems with scientific methods and making decisions. | |
| PLO15 | Beceriler - Bilişsel, Uygulamalı | Can use the knowledge and experience in the field of Plant Protection to solve the problems encountered in the field of production, takes part in public and private organizations or provides consultancy services. | |
| PLO16 | Yetkinlikler - Alana Özgü Yetkinlik | Gains the ability to transform the results of research and projects into reports/thesis and to present and publish them in international meetings and journals. |
Week Plan
| Week | Topic | Preparation | Methods |
|---|---|---|---|
| 1 | What is Phylogenetic Tree, Why create Phylogenetic Tree | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım |
| 2 | Why create phylogenetic tree for pathogens | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Tartışma |
| 3 | Acquiring the sequences as fasta format | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri |
| 4 | Aligning the sequences | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri |
| 5 | Mojor methods for estimating phylogenetic trees | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri, Tartışma |
| 6 | Neighbor joining trees | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri |
| 7 | Drawing phylogenetic trees | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Alıştırma ve Uygulama |
| 8 | Mid-Term Exam | Study the textbook and presentations for written exam. | Ölçme Yöntemleri: Ödev |
| 9 | Parsimony, Maximum likelihood, Bayesian inference of trees using MrBayes | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri |
| 10 | Reconstructing ancestral sequences | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri |
| 11 | Detecting adaptive evolution | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri, Gösterip Yaptırma |
| 12 | Use of Database searching for similar genes | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri, Gösterip Yaptırma |
| 13 | Terms used for classifying protein structure and sequences | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Tartışma, Soru-Cevap |
| 14 | Available alignments models and database for proteins | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösteri, Gösterip Yaptırma |
| 15 | Creation of phylogenetic trees by sequence samples | Study the textbook and presentations. | Öğretim Yöntemleri: Anlatım, Gösterip Yaptırma |
| 16 | Term Exams | Study the textbook and presentations for written exam. | Ölçme Yöntemleri: Yazılı Sınav, Ödev |
| 17 | Term Exams | Study the textbook and presentations for written exam. | Ölçme Yöntemleri: Yazılı Sınav |
Student Workload - ECTS
| Works | Number | Time (Hour) | Workload (Hour) |
|---|---|---|---|
| Course Related Works | |||
| Class Time (Exam weeks are excluded) | 14 | 4 | 56 |
| Out of Class Study (Preliminary Work, Practice) | 14 | 4 | 56 |
| Assesment Related Works | |||
| Homeworks, Projects, Others | 1 | 2 | 2 |
| Mid-term Exams (Written, Oral, etc.) | 1 | 12 | 12 |
| Final Exam | 1 | 28 | 28 |
| Total Workload (Hour) | 154 | ||
| Total Workload / 25 (h) | 6,16 | ||
| ECTS | 6 ECTS | ||