COURSE UNIT TITLE

: USE OF MOLECULAR TOOLS IN BIOTECHNOLOGY

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
ELECTIVE

Offered By

Graduate School of Natural and Applied Sciences

Level of Course Unit

Second Cycle Programmes (Master's Degree)

Course Coordinator

ASSOCIATE PROFESSOR ERGIN ŞAHIN

Offered to

Ph.D. in Biology
Biology

Course Objective

To learn biotechnology and its usage areas

Learning Outcomes of the Course Unit

1   1. Learns the importance, definition and usage of biotechnology.
2   2. Knows the recombinant DNA technologies and genetic methods used in biotechnology.
3   3. Learns the vector systems, hosts and cloning strategies in gene cloning.
4   4. Associates biotechnology with genomics and proteomics.
5   5. Attains knowledge about the novel dimensions gained by gene engineering to biotechnology.
6   6. Attains knowledge about the usage potential and ethics of biotechnology.

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 Definition of scientific terms: Biotechnology, Genetic Engineering, Molecular Biology and Recombinant DNA technology, Model organisms used in Recombinant DNA technology, Introduction to methods based on the gene manipulations by genetic engineering, Restriction modification systems, their types and usage potentials, Cloning hosts and vector systems
2 1st generation Plasmid vectors (PBR322), New generation Plasmid vectors (Puc18), Ti plasmid vector, Replacement vectors of Lamda bacteriophage (Charon 4A and 16), Faj M13 vector (M13mp18), Kosmids (pJB8)
3 Artificial Bacterial Chromosomes (pBAC 108L), Artificial Yeast Chromosomes (pYAC3), Shuttle vectors, Fusion vectors, Expression vectors (pse420, pet)
4 Retroviral vectors (MLV and SAX), Adenoviral vectors and Baculovirus expression vector system (BEVS), Comparison of vector systems, Gene transfer to mammals and plant host cells
5 Finding the right clone by using Reporter genes, DNA sequencing, hybridization, gen chips, PCR and Southern Blotting techniques, transfer mechanisms in Prokaryotes (conjugation, transduction, transformation, transposition and electroporation methods), Competent E. coli preparation before transformation
6 Separation of DNA and protein molecules by polyacrylamide and agarose gel electrophoresis, Formation of a restriction map of a gene by restriction digestion
7 Chemical synthesis of DNA by solid phase method for the production of probe and primer
8 DNA sequencing analysis by Sanger dideoxy nucleotide method, Gene cloning, Cloning strategies by Lambda phage or plasmid vectors and their applications
9 cDNA synthesis by reverse transcription, Genomic libraries and calculating the number of clones that could carry a whole genome, Chromosome and cDNA libraries, Gene chips and their applications by transcriptome and cDNA, DNA sequencing and bioinformatics
10 Determination of evolutionary distances of genes by phylogenetic analyses, Whole Genom sequencing approaches (Clone-clone and shotgun methods), Genome, Proteome, Transcriptome, Bioinformatics, Genomic (Structural, functional and comparative genomic), Proteomic (2-D gel electrophoresis and Maldi-Toff analyses)
11 Gene therapy studies and new viral vectors for potential usage applications in gene therapy, Biotechnological approaches in the diagnosis of diseases and the determination of mutant genotypes, Recombinant drugs and insulin synthesis, Recombinant vaccines, DNA vaccines, Eatable vaccines
12 CRISPR genome editing tools and their uses in bioengineering, medicine, veterinary and agriculture
13 Gene cloning in zygotes in mammals and the first clone sheep Dolly, Living beings with GMO (Genetically Modified Organisms), Transgenic animals, pharming animals
14 Gene cloning to plants and frog embryos, Transgenic plants, Gene cloning via Tip-plasmid, Agricultural plants with GMO, Discoveries in plant biotechnology, Applications in biotechnology and its ethics

Recomended or Required Reading

"Biyoloji Campbell ve Reece. 9. baskıdan Türkçe çeviri. 2013. Palme yayıncılık.
- Brock, Biology of Microorganisms, 2009. Madigan M.T., Martinko J. M., Dunlap P. V., and Clark D. P. Twelfth Edition, Pearson International Edition, 1301 Sansome Street, San
- Genetik Kavramlar, Klug, W. S., Cumming, M. R. and Spencer, C.A. 2009. Sekizinci baskıdan çeviri, Çeviri Editörü: Prof. Dr. Cihan Öner, Palme Yayınevi, Ankara.
- Lehninger Principles of Biochemistry, Fourth Edition, David L. Nelson and Michael M. Cox ,Copyright 2004 by W. H. Freeman & Company
- Life: The Science of Biology. David Sadava, David M. Hillis, H. Craig Heller, and May R. Berenbaum, 2012-10th edition
- Musunuru, K. (2021). Genome editing: a practical guide to research and clinical applications. Academic Press.

Planned Learning Activities and Teaching Methods

The course will consist of lectures, class discussions, and presentations.

Assessment Methods

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


Further Notes About Assessment Methods

None

Assessment Criteria

mid-term and final exams

Language of Instruction

Turkish

Course Policies and Rules

Attendance to at least 70% for the lectures is an essential requirement of this course and is the responsibility of the student. It is necessary that attendance to the lecture delivery must be on time. Any unethical behavior that occurs either in presentations or in exams will be dealt with as outlined in school policy. You can find the undergraduate policy at http://web.deu.edu.tr/fen

Contact Details for the Lecturer(s)

e-mail: ergin.sahin@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours)
Lectures 14 2 28
Tutorials 14 2 28
Preparations before/after weekly lectures 13 4 52
Preparation for midterm exam 1 6 6
Preparation for final exam 1 10 10
Final 1 3 3
Midterm 1 2 2
TOTAL WORKLOAD (hours) 129

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8PO.9PO.10PO.11PO.12
LO.1544
LO.2445
LO.3544
LO.4455
LO.5455
LO.6445

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

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