BK034 Molecular Phylogenetic Analysis II

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

Information

Code BK034
Name Molecular Phylogenetic Analysis II
Term 2023-2024 Academic Year
Term Spring
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. SERDAR SATAR
Course Instructor
1


Course Goal / Objective

he necessary sutructure for obtaining phylogenetic data; sampling sizes, cleaning the sequence, allign the sequences, and their analyze by using different programs (FinchTV, Mega 6.0, DnSp, Arlequin, MrBayes, etc.), methods of creating topologies in their own fields, distances between populations-proximity, analyzing important points in determining gene flow are the aim of the course

Course Content

Molecular phylogenetic analyzes performed by comparing DNA and protein sequences reflect all the information from the first ancestors of which the species began to form, and thus, molecular biology, including evolutionary processes, allows the calculation of molecular evolution rates such as the evolutionary relationships of species and helps us understand these processes better. Phylogenetic studies or inferences have become the routine of many studies at the molecular level. Molecular phylogenitic analyzes, where intense knowledge and statistical complexes and different methods are applied, can lead to the development of erroneous evolutionary hypotheses if not properly applied. For these reasons, it is the content of the course to obtain phylogenetic data in the course of Molecular Phylogenetic Analysis.

Course Precondition

To have taken the basic molecular course.

Resources

Internet resources and applications.

Notes

Nothing.


Course Learning Outcomes

Order Course Learning Outcomes
LO01 Allign the DNA and Blast in NCBI
LO02 Learning the programs which are used in molecular genetics
LO03 Rewiev the program results
LO04 Phylogenetic tree drawing


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 1
PLO02 Bilgi - Kuramsal, Olgusal Knows the biology, ecology, systematics and control strategies of diseases, pests and weeds causing yield losses in plants
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. 2
PLO04 Bilgi - Kuramsal, Olgusal Comprehends the plant protection problems, gains the ability to solve the problems via scientific methods 1
PLO05 Beceriler - Bilişsel, Uygulamalı Obtains the skill to use a laboratory, analyzes and evaluates the results and prepares reports. 4
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. 3
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 Introduction the molecular filogenetics Read the course notes and books Öğretim Yöntemleri:
Anlatım
2 Blasting the sequence from NCBI Read the course notes and books Öğretim Yöntemleri:
Anlatım
3 Cleaning the sequence and its allign I Read the course notes and books Öğretim Yöntemleri:
Anlatım
4 Cleaning the sequence and its allign II Read the course notes and books Öğretim Yöntemleri:
Anlatım
5 Cleaning the sequence and its allign III Read the course notes and books Öğretim Yöntemleri:
Anlatım
6 Calculation the population genetics values I Read the course notes and books Öğretim Yöntemleri:
Anlatım
7 Calculation the population genetics values II Read the course notes and books Öğretim Yöntemleri:
Anlatım
8 Mid-Term Exam Read the course notes and books Ölçme Yöntemleri:
Ödev
9 Calculation the population genetics values III Read the course notes and books Öğretim Yöntemleri:
Anlatım
10 AMOVA Analaysis of the molecular variance Arlequin Read the course notes and books Öğretim Yöntemleri:
Anlatım
11 Phylogenetic tree I Read the course notes and books Öğretim Yöntemleri:
Anlatım
12 Phylogenetic tree II Read the course notes and books Öğretim Yöntemleri:
Anlatım
13 Phylogenetic tree III Read the course notes and books Öğretim Yöntemleri:
Anlatım
14 Phylogenetic tree IV Read the course notes and books Öğretim Yöntemleri:
Anlatım
15 Discussion about evolutionary relationships of Phylogenetic tree Read the course notes and books Öğretim Yöntemleri:
Anlatım
16 Term Exams Read the course notes and books Ölçme Yöntemleri:
Sözlü Sınav
17 Term Exams Read the course notes and books Ölçme Yöntemleri:
Sözlü 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: 09.05.2023 11:35