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      Department of Genetics and Bioengineering

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      GBE 406 | Course Introduction and Application Information

      Course Name
      Gene Control and Epigenetics
      Code
      Semester
      Theory
      (hour/week)
      Application/Lab
      (hour/week)
      Local Credits
      ECTS
      GBE 406
      FALL
      2
      2
      3
      6

      Prerequisites None
      Course Language English
      Course Type ELECTIVE_COURSE
      Course Level First Cycle
      Mode of Delivery Face-To-Face
      Teaching Methods and Techniques of the Course Discussion
      Group work
      Problem solving
      Case study
      Q&A
      Lecture/Presentation
      National Occupational Classification Code -
      Course Coordinator
      • Doç. Dr. Cihangir Yandım
      Course Lecturer(s)
      • Doç. Dr. Cihangir Yandım
      Assistant(s) -
      Course Objectives The aim of this course is to teach the effects of gene control and epigenetic mechanisms on pluripotency and reprogramming, their role in cell division and cell differentiation, and how errors in these mechanisms lead to diseases. It is also aimed to give techniques related to gene control and measurement of epigenetic mechanisms.
      Learning Outcomes The students who succeeded in this course;
      Name Description PC Sub * Contribution Level
      1 2 3 4 5
      LO1 Will be able to explain the concept of epigenetics and its multi-layered mechanisms, 1.2 X
      LO2 Will be able to discuss epigenetic mechanisms through specific examples, 1.2 X
      LO3 Will be able to explain silencing methods at the transcription level, 4 X
      LO4 Will be able to choose techniques that can analyze the relationship between epigenetics and human diseases, 4 X
      LO5 Will be able to interpret the results of methods measuring epigenetic markers. 5.1 X
      Course Description This course explains the gene control mechanisms that affect development and deteriorate in disease. The course covers epigenetic markers and related techniques to identify differences in gene regulation.
      Related Sustainable Development Goals
      -

       



      Course Category

      Core Courses
      Major Area Courses
      X
      Supportive Courses
      Media and Managment Skills Courses
      Transferable Skill Courses

       

      WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

      Week Subjects Required Materials Learning Outcome
      1 Introduction Epigenetics, Cold Spring Harbor Laboratory Press, 2015 - Chapter 1 LO1
      2 Circuit elements of a gene Molecular Biology of the Cell 6th edition, Garland-Norton, 2015 - Chapter 1 LO1
      3 RNA polymerase and fundamentals of gene control Molecular Biology of the Cell 6th edition, Garland-Norton, 2015. -Chapter 6. Transcription Regulation at the Core: Similarities Among Bacterial, Archaeal, and Eukaryotic RNA Polymerases, Decker and Hinton, Annual Reviews, 2013. LO3
      4 Chromatin and chromsome architecture Molecular Biology of the Cell 6th edition, Garland-Norton, 2015. - Chapter 4. LO1
      5 Histone modifications Epigenetics, Cold Spring Harbor Laboratory Press, 2015.- Chapters 4,5,6. Lateral Thinking: How Histone Modifications Regulate Gene Expression, Lawrence et al., Trends in Genetics, 2016. b844e03f-e191-4b1f-982c-37cd80d63801
      6 Dynamics of chromatin remodeling Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes, Clapier et al. , Nature Reviews, 2017. LO4
      7 Chromatin balance and gene insulation Heterochromatin effects in Friedreich's ataxia and sexual dimorphism. C. Yandım, PhD Thesis, Imperial College London, 2012. Gene Regulation and Epigenetics in Friedreich's ataxia. Yandım et al. J of Neurochem., 2013. LO2
      8 Midterm -
      9 Nuclear architecture Biogenesis and function of nuclear bodies, Mao et al, Trends in Genetics, 2011. LO1
      10 DNA methylation and epigenetic reprogramming Principles of DNA methylation and their implications for biology and medicine, Dor and Cedar., Lancet, 2018. LO4
      11 RNA interference Strategies for silencing human disease using RNA interference, Kim and Rossi, Nature Reviews, 2007. LO3
      12 Epigenetic memory Mechanisms of epigenetic memory, D'Urso and Brickner, Trends in Genetics, 2014. LO5
      13 Induced pluripotency Epigenetics, Cold Spring Harbor Laboratory Press, 2015. - Chapter 28 LO2
      14 Epigenetics and human disease Epigenetics, Cold Spring Harbor Laboratory Press, 2015- Chapter 33. LO5
      15 Review -
      16 Final exam -

       

      Course Notes/Textbooks Human Molecular Genetics by Strachan and Read (2018) Garland Science. ISBN: 0815345895
      Suggested Readings/Materials Chromosome Architecture and Genome Organization by Bernardi (2015) PLoS One
      Heterochromatin effects in Friedrich's ataxia and sexual dimorphism (2012) PhD Thesis by C. Yandım
      Transcription Regulation at the Core: similarities among bacterial archaeal and eukaryotic RNA polymerases by Decker and Hinton (2013) Annual Reviews
      Lateral thinking: how histone modifications regulate gene expression by Lawrence et al. (2016) Trends in Genetics
      Principles of DNA methylation and their implications for biology and medicine by Dor and Cedar (2018) The Lancet
      Molecular mechanisms of RNA interference by Wilson and Doudna (2013) Annual Reviews.

       

      EVALUATION SYSTEM

      Semester Activities Number Weighting LO1 LO2 LO3 LO4 LO5
      Homework / Assignments 4 40 X X X X
      Midterm 1 30 X X X
      Final Exam 1 30 X X X
      Total 6 100

       

      ECTS / WORKLOAD TABLE

      Semester Activities Number Duration (Hours) Workload
      Participation - - -
      Theoretical Course Hours 16 2 32
      Laboratory / Application Hours 16 2 32
      Study Hours Out of Class 14 2 28
      Field Work - - -
      Quizzes / Studio Critiques - - -
      Portfolio - - -
      Homework / Assignments 4 5 20
      Presentation / Jury - - -
      Project - - -
      Seminar / Workshop - - -
      Oral Exams - - -
      Midterms 1 34 34
      Final Exam 1 34 34
          Total 180

       

      COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

      # PC Sub Program Competencies/Outcomes * Contribution Level
      1 2 3 4 5
      1

      Engineering Knowledge: Knowledge of mathematics, science, basic engineering, computation, and related engineering discipline-specific topics; the ability to apply this knowledge to solve complex engineering problems.

      1

      Mathematics

      2

      Science

      LO1 LO2
      3

      Basic Engineering

      4

      Computation

      5

      related engineering discipline-specific topics

      6

      the ability to apply this knowledge to solve complex engineering problems.

      2

      Problem Analysis: Ability to identify, formulate and analyze complex engineering problems using basic knowledge of science, mathematics and engineering, and considering the UN Sustainable Development Goals relevant to the problem being addressed.

      3

      Engineering Design: The ability to devise creative solutions to complex engineering problems; the ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions.

      1

      Ability to design creative solutions to complex engineering problems.

      2

      Ability to design complex systems, processes, devices or products to meet current and future needs, considering realistic constraints and conditions.

      4

      Use of Techniques and Tools: Ability to select and use appropriate tectıniques, resources, and modern engineering and computing tools. including estimation and modeling. far the analysis and solution of complex engineering problems while recognizing their limitations.

      LO3 LO4
      5

      Research and ınvestigation: Ability to use research methods ta investigate complex engineering problems, including literature research, designing and conducting experiments, collecting data, and analyzing and interpreting results.

      1

      Literature research far the study of complex engineering problems

      LO5
      2

      Designing experiments

      3

      Ability to use research methods, including conducting experiments, collecting data. analyzing and interpreting results

      6

      Global lmpact of Engineering Practices: Knowledge of the impacts of engineering practices on s.ociety, health and safety. ttıe economy, sustainability and the environment \ıVlthin the context of the UN Sustainable Development GoaJs; awareness of the legal implications of engineering solutions.

      1

      Knowledge of ttıe impacts of engineering practices on society, health and safety, economy, su.stainability and the environment, within the context of the UN Sustainable Development Goals.

      2

      Awareness of the legal implications of engineering solutions

      7

      Ethical Behavlor: Acting in accordance with the principles of the engineering profession. knowledge about ethical ,esponsibility; awareness of being impartial. without discrimination, and being inclusive of diversity.

      1

      Acting in accordance with engineering professional principles. information about ethical responsibility

      2

      Awareness of being impartial and indusive of diversity, without disaiminating on any subject.

      8

      lndividual and Teamwork: Ability to work effectively individually and as a team member or leader on interdis.ciplinary and multidisciplinary teams (face-to-face, remote or hybrid).

      1

      lndividually and within the discipline

      2

      Ability to work effectivefy as a team member or leader in mutti-disciplinary teams (face-to-face, remote or hybrid)

      9

      Verbal and Written Communication: Taking into account the various differences of the target audience (such as education, language, profession) on technical issues.

      1

      Verbal

      2

      Ability to communicate effectively in writing.

      10

      Project Management: Knowledge of business practices such as project management and economic feasibility analysis; awareness of entrepreneurship and innovation.

      1

      Knowledge of business practices such as project management and economic feasibility analysis;

      2

      Awareness of entrepreneurship and innovation.

      11

      Lifelong Learning: Lifelong learning skills that include being able to learn independently and continuously, adapting to new and developing technologies. and thinking questioningly about tedınological changes

      *1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest


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