BK584 Genom Analyses of Plants and Pathogens

6 ECTS - 2-2 Duration (T+A)- . Semester- 3 National Credit

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

Update Time: 27.06.2024 09:24