COURSE UNIT TITLE

: MOLECULAR AND CELL BIOLOGY TECHIQUES I

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
TBG 6100 MOLECULAR AND CELL BIOLOGY TECHIQUES I ELECTIVE 2 2 0 9

Offered By

Medical Biology and Genetics

Level of Course Unit

Third Cycle Programmes (Doctorate Degree)

Course Coordinator

PROFESSOR DOCTOR HAKKI OGÜN SERCAN

Offered to

Audiology
Laboratory Animal Science
Anatomy
Molecular Pathology
Toxicology
Exercise Physiology
Biochemistry
Biomechanics
Biophysics
Medical Biology and Genetics
Histology and Embryology
Physiology
Translational Oncology
Medical Parasitology
Microbiology
Pharmacology
Basic Neuroscience
Molecular Medicine
Molecular Medicine
Translational Oncology

Course Objective

1- To acquire the knowledge and skills on basic methods for nucleic acid research.
2- To acquire advance knowledge on the nucleic acid quantification and to acquire the skills to perform relative and absolute quantification of RNA levels using PCR.
3- To acquire the skills for detecting DNA methylation by PCR based methods (MS-PCR, bisulfide PCR, COBRA)

Learning Outcomes of the Course Unit

1   Discusses PCR dynamics and compares different methods of quantification.
2   Explains in detail DNA structure, methyl-DNA structure and methylation mechanisms
3   Explains different methodology used for the detection of methylated DNA.
4   Uses his/her knowledge of methodology to design primers for MS-PCR and bisulfide PCR
5   Has acquired the skills to perform DNA and RNA isolation, cDNA synthesis and agarose gel electrophoresis
6   Optimizes target and reference gene PCR s for quantification
7   Can perform relative quantitative PCR both by conventional methods and is capable of analyzing the results correctly.
8   Can perform relative quantitative PCR both by using a real-time instrument and is capable of analyzing the results correctly.
9   Can perform bisulfide modification of genomic DNA, purify samples, perform MS-PCR and/or bisulfide PCR reactions and analyze the results both manually and by using commercial kits.
10   Is able to estimate the methylation level by COBRA analysis
11   Is able to determine gene expression levels by analyzing protein levels by western blot and immunostaining protocols.

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 Genomic DNA: organization, isolation and quantification
2 Genomic DNA: analysis methods (agarose gel electrophoresis, Southern Blot, mauation analysis: SSCP, PCR, sequencing).
3 RNA regulation;
4 RNA isolation;
5 RNA analysis methods (agarose gel electrophoresis, Northern Blot, RACE).
6 Gene expression
7 cDNA (synthesis, semi-quantitative PCR, qPCR)
8 Regulation of gene expression (EMSA, ChIP).
9 Recombinant DNA technology
10 vector types, cloning plasmids (restriction enzyme analysis)
11 expression vectors (bacterial, yeast, mammalian)
12 recombinant plasmid production (RE digestion, ligation, plasmid transformation, plasmid isolation, characterization)
13 recombinant protein production (bacterial, yeast, insect)
14 recombinant protein purification (HIs-tag, GST-tag, purification methods)
15 Western blot

Recomended or Required Reading

Main textbook
Current Protocols in Molecular Biology, Wiley, Online ISBN: 9780471142720

References
- Methods In Molecular Biology Vol 200 - DNA Methylation Protocols - Humana Press.2002
- Methods In Molecular Biology - Volume 226 - PCR Protocols, Second Edition - Humana Press 2003.
- Methods in Molecular Biology Vol 193 RT-PCR Protocols Humana Press -2002
- Recent Publications

Planned Learning Activities and Teaching Methods

Lectures: Basic theoretical concepts will be explained during lectures
Laboratory Work: Each student will perform the experiment and applications given by the course coordinator during the course. Every observation and data is expected to be recorded in his/her laboratory notebook; which will be handed in at the end of the course.

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA
1 PRF PERFORMANCE
2 FIN FINAL EXAM
3 FCG FINAL COURSE GRADE PRF * 0.40 + FIN*0.60
4 RST RESIT
5 FCGR FINAL COURSE GRADE (RESIT) PRF * 0.40 + FCGR*0.60


Further Notes About Assessment Methods

None

Assessment Criteria

To be announced.

Language of Instruction

Turkish

Course Policies and Rules

The maximum number of student is limited to 4.
It is obligatory to have taken the SBE course with the code TBG5039 (Basic Molecular Biological Methods 1) and to be successful.

Contact Details for the Lecturer(s)

(232) 412 65 54, hani.alotaibi@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours)
Lectures 15 2 30
Preparations before/after weekly lectures 15 3 45
Preparation for final exam 1 10 10
Preparation for midterm exam 1 10 10
Preparing Individual Assignments 5 10 50
Manuscript Preparation 5 10 50
Preparation of the Concept Map 3 8 24
Final 1 3 3
Midterm 1 3 3
TOTAL WORKLOAD (hours) 225

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8PO.9PO.10PO.11PO.12
LO.1555
LO.2555
LO.3555
LO.4555
LO.5555
LO.6555
LO.7555
LO.8555
LO.9555
LO.10555
LO.11555

CONTACT INFORMATION
Dokuz Eylül Üniversitesi Cumhuriyet Bulvarı No: 144 35210 Alsancak / İZMİR
Phone: +90(232) 412 12 12 - Fax: +90 (232) 464 81 35

Copyright 2015 DEÜ. BİD

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