Faculty of engineering and natural sciences department of genetics and bioengineering first cycle study program specification



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TECHNICAL ELECTIVE COURSES


Course Code: GBE 320

Course Name: SYSTEMS PHYSIOLOGY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

The course offers an overview of the functioning systems of the human body. The physiology of cells as well as the muscular, nervous, circulatory, respiratory, endocrine, digestive, and urogenital systems is explored. Emphasis is placed on the integration of the individual function of different cells and organ systems into a functional whole, the feedback mechanisms that account for necessary balances, and the consequences of disease. Examples of engineering approaches used to monitor physiological processes and correct physiological deficiencies are included. The course is taken concurrently with laboratory sessions, which are organized as either experiments or virtual labs.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:


  • Introduction to metabolic pathways commonly used by cells and explaining how enzymes function in those pathways.

  • Explaining how neurons communicate with each other and with other cells, such as muscles and glands.

  • Providing basic concepts of blood and how it circulates in the body.

  • Describing how the body defends itself against foreign invaders.

  • Teaching the respiratory system function including breathing and gas exchange in the lungs and body tissues.

  • Explaining how the digestive system mechanically and chemically breaks food down for absorption.

  • Giving an overview of urine formation and its hormonal control.

  • Explaining the difference between reproductive processes that occur in males and those that occur in females.

Course Content

(weekly plan)



Week 1: Introduction to systems physiology

Week 2: Basis of animal function and cell physiology

Week 3: Membranes and movement across the membrane

Week 4: Homeostasis: Mechanisms and signal transduction

Week 5: Endocrine system: Endocrine communication and principles of hormonal systems

Week 6: Nervous system: Neural communication, mechanisms, and sensory systems

Week 7: Muscular system: Muscle contraction and the control of body movement

Week 8: MID-TERM EXAM WEEK

Week 9: Cardiovascular system: Circulation and the design of cardiovascular system

Week 10: Respiratory system: System mechanics, gas transport and control of respiration

Week 11: Urinary system: Kidney, clearance, and the countercurrent mechanism

Week 12: Digestive system: Gastrointestinal motility, secretion, digestion, and absorption

Week 13: Immune system: Integration, temperature, food intake, immunity, and exercise

Week 14: Reproductive system: From sex differentiation to adult reproduction

Week 15: Integumentary system



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS:

Week 1: Beginning of classes

Week 2, Lab 1: Introduction to the lab course; Cell physiology

Week 3, Lab 2: Experimental animals and animal dissection (Lumbricus terrestris)

Week 4, Lab 3: Nervous system – virtual lab

Week 5, Lab 4: Muscular system - virtual lab

Week 6, Lab 5: Cardiovascular system on Salmo trutta fario

Week 7, Lab 6: Isolation of hemolymph from Helix pomatia

Week 8: MID-TERM EXAM WEEK

Week 9, Lab 7: Digestive system – virtual lab

Week 10 Lab 8: Respiratory system – virtual lab and the use of spirometers

Week 11, Lab 9: Urinary system: Urine analysis

Week 12, Lab 10: Endocrine system – virtual lab

Week 13, Lab 11: Male and female reproductive system – virtual lab



Week 14, Preparation for practical exam

Week 15, Practical exam from lab course

Week 16: FINAL EXAM WEEK




Teaching Methods

Description




Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

On successful completion of this course, students should be able to:

  1. Recall the basics of physiology of different organ systems

  2. Identify the structure and function of various systems

  3. Interpret and criticize the concept of experimental animals

  4. Design and set up animal experiments in a bioethical manner

  5. Operate animal dissection safely and efficiently

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Stanfield, C. (2010). Principles of Human Physiology, 4th ed. New York City, NY, USA: Pearson


Recommended Literature

Fox, S. I. (2008). Human physiology, 10th ed. New York City, NY, USA: McGraw Hill

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




16

16

Seminar / Presentation




16

16

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 322

Course Name: PRINCIPLES OF NEUROBIOLOGY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

The course is designed to provide a foundation needed for the eventual understanding of the neural basis of behavior and cognition. This course will consider data and theories of brain-behavior relationships from research in the neurosciences. Progress in neuroscience requires a detailed knowledge of brain function and so cuts across areas such as neurophysiology, neuroanatomy, and neurochemistry. In the first part of the course, a reductionistic approach will be taken and focus will be put on the basic element of nervous systems, the neuron. The objective is to understand the signaling capacities of neurons in terms of cellular mechanisms. In the second part of the course, a more integrative approach will be taken and students will understand how simple sensory, motor, and learning capacities arise from the operations of neural networks. Hormonal and neural elements interaction in producing motivation and emotions will also be discussed.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:


  • Giving an outline of the fundamentals of neurobiology.

  • Explaining basic operating principles of neural tissue.

  • Teaching the molecular basis of neurobiology.

  • Enabling progress to more advanced courses.

Course Content

(weekly plan)



Week 1: Introduction/Overview

Week 2: Ion channels and signaling and structure

Week 3: Resting and action membrane potential

Week 4: Passive membrane properties

Week 5: Synaptic transmission

Week 6: Molecular biology of presynaptic nerve terminals

Week 7: Indirect mechanisms of synaptic transmission

Week 8: MID-TERM EXAM WEEK

Week 9: Mechanosensation

Week 10: Dendrites: Morphology and function

Week 11: Electrical synapses

Week 12: Synaptic plasticity

Week 13: Neural basis of behavior

Week 14: Intrinsic plasticity

Week 15: Cellular mechanisms of learning; Neurodegenerative diseases



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS:

Week 1: Beginning of classes

Week 2, Lab 1: Visualizing the nervous system (worm dissection)

Week 3, Lab 2: Immunocytochemistry of brain sections

Week 4, Lab 3: Exploring the brain: Allen Brain Atlas data portal

Week 5, Lab 4: Exploring brain connectivity: Allen Brain Atlas data portal

Week 6, Lab 5: Human benchmark laboratory (reaction time and memory)

Week 7, Lab 6: Exploratorium: Virtual sheep brain dissections



Week 8: MID-TERM EXAM WEEK

Week 9, Lab 7: Virtual deep brain stimulation surgery

Week 10 Lab 8: Virtual neuroscience lab: Medication study

Week 11, Lab 9: Virtual neuroscience lab: Parkinson's disease study

Week 12, Lab 10: Howard Hughes Medical Institute: Neurophysiology surgery

Week 13, Lab 11: Neuroscience project ideas

Week 14: Preparation for practical exam

Week 15: Practical exam from lab course

Week 16: FINAL EXAM WEEK


Teaching Methods

Description

(list up to 4 methods)




  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40%

Total

100 %

Learning Outcomes

(please write 5-8 outcomes)



On successful completion of this course, students should be able to:

  1. Recall neurobiology terminology

  2. Explain the brain and nervous system

  3. Relate the brain and nervous system to behavior and disease

  4. Assess the importance of molecular biology in neurological processes

  5. Predict the effect of neurological processes on behavior

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Kandel, E., Schwartz, J., & Jessell, T. (2000) Principles of Neural Science, 4th ed. New York City, NY, USA: McGraw Hill Medical

Recommended Literature

Liquin, L. (2015). Principles of Neurobiology, 1st ed. New York City, NY, USA: Garland Science

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 324

Course Name: BIOMATERIALS

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

This course is designed to introduce students to the various classes of biomaterials in use and their application in selected subspecialties of medicine including an understanding of material bulk and surface properties, standard characterization tools, the various biological responses to implanted materials, the clinical context of their use, manufacturing processes, and issues dealing with cost, sterilization, packaging, and design of biomedical devices. It also addresses professional and ethical responsibility encountered in designing medical implants.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:


  • Introduction to the importance of the use of biomaterials and new technologies.

  • Giving and outline of applications of biomaterials in medicine.

  • Explaining terms used in the literature of biomaterials.

  • Teaching the basic characteristics of specific biomaterials.

  • Illustrating the processes and phenomena related to the application of biomaterials.

Course Content

(weekly plan)



Week 1: Introduction to the course

Week 2: Classes of Biomaterials

Week 3: Classes of Biomaterials

Week 4: Applications of biomaterials I

Week 5: Cells and tissues

Week 6: Host reaction to biomaterials

Week 7: Applications of biomaterials II

Week 8: MID-TERM EXAM WEEK

Week 9: Testing of biomaterials

Week 10: WORKSHOP: Analysis of Scientific papers, Nanoparticles as drug delivery systems

Week 11: Applications of biomaterials III

Week 12: WORKSHOP: Analysis of Scientific paper, Detection of microorganisms by nanoparticles

Week 13: Biosensors

Week 14: Workshop: Analysis of Scientific Papers, Biofilms

Week 15: Applications of biomaterials IV



Week 16: FINAL EXAM WEEK
LABORATORY CONTENT:

Week 1-11: The laboratory course is designed so that the students learn about biomaterials through virtual labs. In these sessions, students will get familiar with physical and chemical properties of biomaterials, ways to practically apply them, and their interactions with living systems, that is, cells. Also, students will analyze scientific articles that are utilizing modern techniques in biomaterial processing and application.

Teaching Methods

Description

(list up to 4 methods)




  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0%

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

(please write 5-8 outcomes)



On successful completion of this course, students should be able to:

  • Recognize most of the terms used in the literature of biomaterials

  • Collect basic knowledge of materials that can have biomedical application

  • Discriminate chemical and physical structure of biomaterials

  • Break down mechanical properties and processing of biomaterials

  • Illustrate protein and cell interactions with biomaterials

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Temenoff, J. S. & Mikos, A. G. (2009). Biomaterials: The Intersection of Biology and Materials. International Edition. New York City, NY, USA: Pearson

Recommended Literature

Park J. & Bronzino J. (2002). Biomaterials: Principles and Applications, 1st ed. Boca Raton, FL, USA: CRC Press

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 326

Course Name: CYTOGENETICS

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

This lecture and laboratory course will focus on human chromosome structure and replication, methodology, form and function, identification and techniques for the visualization of chromosome aberrations. The latter part of the semester focuses on evolution and speciation, sex chromosome systems, artificial manipulation of genomes as well as the human karyotype. Chromosome abnormalities will be discussed from the clinical and cytogenetic viewpoint. The course will also cover current topics in cytogenetics, including new methodologies and their use in clinical genetics and research. Laboratory course covers both experimental techniques in cytogenetics, as well as detailed study of human chromosomes through virtual labs and recitations.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to chromosomes, their structure and function.

  • Introduction to the cell cycle.

  • Preparation of chromosomes for observations.

  • Explaining mutations and aberrations.

  • Explaining human karyotype.

Course Contents

(weekly plan)



Week 1: Introduction to cytogenetics

Week 2: Chromosome structure and replication

Week 3: Chromosome form and function

Week 4: Chromosome identification

Week 5: Nuclear division

Week 6: Gene control by position and origin

Week 7: Mutagenesis

Week 8: MID-TERM EXAM WEEK

Week 9: Chromosome mapping

Week 10: Sex chromosome systems

Week 11: Evolution and speciation

Week 12: Artificial manipulation of genomes

Week 13: The human karyotype

Week 14: Chromosomal aberrations and their identification

Week 15: Historical aspects of cytogenetics



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1: Beginning of classes

Week 2, Lab 1: Introduction to lab course

Week 3, Lab 2: Cell Cycle: Interphase, mitosis, and meiosis

Week 4, Lab 3: Techniques of making chromosome slides

Week 5, Lab 4: Chromosome staining techniques, part 1

Week 6, Lab 5: Chromosome staining techniques, part 2

Week 7, Lab 6: Getting and marking cells in prophase or prometaphase



Week 8:MID-TERM EXAM WEEK

Week 9, Lab 7: Study of sex chromatin

Week 10 Lab 8: Microscopic observations and microphotography

Week 11, Lab 9: Nomenclature and chromosome classification

Week 12, Lab 10: Preparing a karyotype

Week 13, Lab 11: Common chromosomal abnormalities



Week 14: Preparation for practical exam

Week 15: Practical exam from lab course

Week 16: FINAL EXAM WEEK

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Analyze the human karyotype

  2. Describe the cell cycle

  3. Classify chromosomal banding and its application

  4. Determine structural and numerical chromosomal aberrations

  5. Explain the nomenclature of chromosomes

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Swanson, C. P., Merz, T., & Young, W. J. (1981). Cytogenetics. The chromosome in division, inheritance and evolution, 2nd ed. Upper Saddle River, NJ, USA: Prentice-Hall

Recommended Literature

Tirunilai, P. (2012). Recent trends in cytogenetic studies, 1st ed. Rijeka, Croatia: InTech

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5




Course Code: GBE 327

Course Name: GENERAL BIOTECHNOLOGY AND BIOSAFETY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

The course deals with the major elements of the global significance of biotechnology, the categories of biotechnology processes and products, and in the context of "traditional" vs. "modern" biotechnology processes. Also, the key developments in the history of biotechnology and the enabling technologies - fermentation, downstream processing; recombinant methods, antibody monoclonals, analysis and automation, genomics, proteomics, metabolomics. Specific aspects of the biotechnology enterprises are highlighted and then the broader issues dealing with biotechnology and society; considerations in the genesis of the typical biotechnology process/product/enterprise: development costs, venture capital, patenting, product safety, legislation and marketing. Case studies on the interdisciplinary nature of biotechnology and factors favoring local/regional development of a biotechnology industry will also be included. We will explore a plethora of technologies used in the fields of genetic engineering, forensics, agriculture, bioremediation and medicine in order to give you a basic but fundamental experimental skill set which can be applied in future secondary and post-secondary laboratory experiences or real-world scenarios.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to basic principles in biotechnology.

  • Designing a gene cloning and fermentation experiment.

  • Discussing scientific papers on the field.

  • Designing and controlling an industrial biotechnological process.

Course Contents

(weekly plan)



Week 1: Introduction to and history of biotechnology – basic definitions, applications in medicine, agriculture and pharmaceutical companies

Week 2: Medical biotechnology – topics in genetics and applications in biotechnology and therapy

Week 3: Medical biotechnology – topics in bioengineering and applications in biotechnology and therapy

Week 4: Xenotransplantation - transfer of genes to bacteria, plants, and animals (vectors, development of vectors, cloning)

Week 5: GMOs I – crop improvement, herbicide resistance, insect resistance, virus resistance, plants as bioreactors

Week 6: GMOs II - the FDA and screening agriculture and transgenic plants, genetically modified foods, application, future applications, and ecological impact of transgenic plants

Week 7: Genetic modification in the food industry: background, history, controversies over risks, application, future directions

Week 8: MID-TERM EXAM WEEK

Week 9: Product pipeline and safety – from molecule to drug

Week 10: Biotechnology and patent law

Week 11: Ethics in biotechnology

Week 12: Principles of laboratory biosafety and biosecurity – facility design and biosafety levels

Week 13: Biological risk assessment – hazardous characteristics and risk assessment

Week 14: Bacterial, fungal and parasitic agents and rickettsial and viral agents and Arboviruses

Week 15: Decontamination and disinfection – environmentally mediated infection transmission, sterilization, spaulding disinfection, decontamination procedures



Week 16: FINAL EXAM WEEK


LABORATORY CONTENTS

Week 1: Beginning of classes and presentation of seminar assignments

Week 2 – Week 7: Student presentations

Week 8: MID-TERM EXAM WEEK

Week 9 – 14: Student presentations



Week 15: Exam from lab course

Week 16: FINAL EXAM WEEK

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Recall the basic concepts of biotechnology and main definitions

  2. Apply knowledge of microbial fermentation in industry

  3. Identify bioreactors and illustrate their mode of operation

  4. Collect knowledge about basic concepts and methods used in plant biotechnology and demonstrate their practical application

  5. Demonstrate sterile techniques required to conduct plant tissue culture

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Thieman, W. J. & Palladino, M. A. (2012). Introduction to Biotechnology, 3rd ed. San Francisco, CA, USA: Benjamin Cummings

Handouts will be compiled and available for purchase in Profi Copy



Recommended Literature

Scientific articles delivered during classes and lab sessions

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5




Course Code: GBE 328

Course Name: INTRODUCTION TO RESEARCH METHODS

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

This course provides an introduction to research methods and designs relevant to biotechnology, genetics, and bioengineering fields. The course will focus on an introduction to various research designs including experimental and non-experimental, as well as quantitative and qualitative research methods. In addition, the course will focus on providing a practical understanding of several statistical tools used in medical and health research. The emphasis will be on knowing when to use various tests, what they measure, and how to interpret results. Finally, students are introduced to different types of scientific articles in genetics and bioengineering and are discussing them in the form of presentation in front of the class.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to the scientific method and its role/importance in biotechnology, genetics and bioengineering.

  • Sharing the process of research and components within the process.

  • Providing an outline of the importance of research questions.

  • Defining key characteristics of a good research questions.

  • Providing an outline of the importance of conducting a review of the literature as part of the empirical process.

  • Introducing students to research tools and search engines that support conducting a literature review.

Course Contents

(weekly plan)



Week 1: Introduction: Research in genetics and bioengineering

Week 2: The scientific method, research ethics

Week 3: Fundamentals of PubMed and the Cochrane Library

Week 4: RefWorks fundamentals

Week 5: How to read the scientific literature

Week 6: Conducting a literature review

Week 7: Preparation for mid-term

Week 8: MID-TERM EXAM WEEK

Week 9: Types of scientific articles

Week 10: Foundations of quantitative research design

Week 11: Statistical methods in health

Week 12: Foundations of qualitative research

Week 13: Introduction to mixed methods

Week 14: Reporting and discussing results

Week 15: Student presentations: Chosen scientific articles



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1-11: The laboratory course is designed so that the students design their own experiment using the studied research methods and analyze and get valid results which they will present to their colleagues.

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Recall the basic concepts of biotechnology and main definitions

  2. Conduct experiments following the scientific method

  3. Develop a scientific way of reasoning

  4. Use various databases necessary for the engineering profession

  5. Describe basic statistic methods

  6. Handle qualitative and quantitative research designs

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Marder, P.M. (2011). Research Methods for Science. Cambridge, UK: Cambridge University Press

Recommended Literature

Lecture notes

Scientific articles



ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




18

18

Seminar / Presentation




14

14

Total Workload

125

ECTS Credit (Total Workload / 25)

5




Course Code: GBE 329

Course Name: POPULATION GENETICS

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30+30

Course Description

This course is designed to provide students with a general introduction to population genetics, which examines the interaction of basic evolutionary processes (including mutation, natural selection, genetic drift, inbreeding, recombination, and gene flow) in determining the genetic composition and evolutionary trajectories of natural populations. Methods of measuring genetic variation in natural populations will also be reviewed and experimental tests of the central concepts derived from population genetics theory will be examined. Empirical examples will involve a broad diversity of organisms, including humans.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Teaching students the principles of Hardy-Weinberg equilibrium.

  • Explaining factors that can affect Hardy-Weinberg equilibrium, such as mutation, inbreeding, migration, and genetic drift.

  • Giving an overview of phylogenetic analyses, their possibilities but also limitations and the evolutionary significance of “short-term” and “long-term” adaptation processes.

  • Explaining basic concepts about the biological, bio-cultural and socio-cultural characteristics of various human groups and their interpopulation variability as an adaptation response to the impact of environmental factors.

  • Providing models of studying contemporary human populations and theoretical evaluations of the impact of genetic and/or ecological factors in terms of phenotype expression of complex features by an array of comparative analyses.

Course Contents

(weekly plan)



Week 1: Introduction to population genetics and the basic principles

Week 2: Allele and genotype frequencies; Hardy-Weinberg equilibrium

Week 3: Genetic variation, sources of genetic variation

Week 4: Genetic drift and mutation

Week 5: Population structure and gene flow

Week 6: Inferring population history and demography

Week 7: Linkage disequilibrium and gene mapping

Week 8: MID-TERM EXAM WEEK

Week 9: Genetic markers in population genetic studies

Week 10: Population genetics of quantitative traits

Week 11: Interaction of genotype and surrounding

Week 12: Heritability: Definition and methods of study

Week 13: Adaptation and speciation

Week 14: Phylogenetic variation

Week 15: Conservation of genetic variation



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1, Beginning of classes

Week 2, Lab 1: Introduction to the lab course

Week 3, Lab 2: Introduction to managing allele frequencies: Mendelian and non-Mendelian inheritance patterns, Human pedigree analysis

Week 4, Lab 3: Allele and genotype frequencies, Hardy-Weinberg principle, part 1

Week 5, Lab 4: Allele and genotype frequencies, Hardy-Weinberg principle, part 2

Week 6, Lab 5: Factors that disturb the genetic equilibrium and their effect: mutation and natural selection

Week 7, Lab 6: Factors that disturb the genetic equilibrium and their effect: genetic drift and inbreeding

Week 8: MIDTERM WEEK

Week 9, Lab 7: Recombination events and genetic mapping

Week 10 Lab 8: Genetic markers in population genetic studies, Statistical calculations of population differentiation

Week 11, Lab 9: Population genetics of quantitative traits: Coalescent theory

Week 12, Lab 10: Phylogenetic studies in evolution

Week 13, Lab 11: Phylogenetic variation in humans: NJ and UPGMA methods



Week 14: Preparation for laboratory exam

Week 15: Exam from lab course

Week 16: FINAL EXAM WEEK

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Explain the basics of population genetics

  2. Calculate the Hardy-Weinberg equilibrium

  3. Find the frequency of alleles and genotypes in a population

  4. Define genetic markers in population genetics

  5. Recall basics of phylogenetics

  6. Discuss heritability

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Nielsen, R. & Slatkin, M. (2013). An Introduction to Population Genetics: Theory and Applications, 1st ed. Sunderland, MA, USA: Sinauer Associates

Recommended Literature

Hamilton, M. (2009). Population genetics, 1sted. Hoboken, NJ, USA: John Wiley & Sons

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




14

14

Seminar / Presentation




18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 331

Course Name: ENVIRONMENTAL BIOLOGY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2 + 2

Total Hours: 30 + 30

Course Description

Environmental biology is dealing with the relationships of living things with themselves and their environments, which are topics covered during this course. Both landscape and marine ecology are briefly presented to the students during the course. Special emphasis is put on population and community ecology as a way of showing the effect of human activity on environment. At the end of semester, students are analyzing ecology-related scientific articles in order to get along with the most recent discoveries in the field. The course is taken concurrently with the lab course, which combines theoretical and in-field classes.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to environmental biology, ecosystems, energy and ecological systems.

  • Explaining biogeochemical cycles, limiting and regulatory factors.

  • Providing basic concepts of population ecology, community ecology and ecosystem development.

  • Giving an overview of landscape ecology, regional ecology and global ecology.

Course Content

(weekly plan)



Week 1: Introduction

Week 2: Scope of ecology

Week 3: Ecosystems

Week 4: Energy and ecological systems

Week 5: Biogeochemical cycles

Week 6: Limiting and regulatory factors

Week 7: Population and community ecology

Week 8: MID-TERM EXAM WEEK

Week 9: Ecosystem development

Week 10: Landscape ecology

Week 11: Marine ecology

Week 12: Regional ecology

Week 13: Biomes

Week 14: Global ecology

Week 15: Student presentations: Analysis of scientific articles on current ecology-related topics



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1-11: The laboratory course is designed so that the students study various aspects of environmental biology and the harmful effect of humans on the environment. The second part of the course is designed so that students go to visit various ecosystems, collect samples from these ecosystems, and analyze them.

Teaching Methods

Description


  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Define the scope of ecology

  2. Enlist and discuss the concepts of ecosystems

  3. Interpret the energy in ecosystem

  4. Analyze the biogeochemical cycles

  5. Distinguish and relate the limiting and regulatory factors in an ecosystem

  6. Enlist and describe the different disciplines of ecology including population ecology, community ecology, ecosystem development, landscape ecology, regional ecology and global ecology

  7. Appraise environmental awareness

  8. Propose environmental problems and design solution approaches

Prerequisite Course(s)

(if any)


None.

Language of Instruction

English

Mandatory Literature

Odum, E. & Barrett, G. W. (2004). Fundamentals of Ecology, 5th ed. Boston, MA, USA: Cengage Learning

Recommended Literature

Verma, P.S. & Agarwal, V.K. (2000). Environmental Biology, 2nd ed. New Delhi, India: S Chand & Co

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project

1

18

18

Seminar / Presentation

1

14

14

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 332

Course Name: PLANT STRESS PHYSIOLOGY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2+2

Total Hours: 30 + 30

Course Description

Any factors that have an impact on external and internal homeostasis of living beings are described as stresses. Plants have many defense systems to avoid negative effects of biotic and/or abiotic stress factors. This course is giving an overview of plant physiology and changes that happen in response to different stresses, such as drought, heat, chilling and freezing, oxygen deficiency, biotic stresses, etc. The final lectures in this course are discussing changes in signal transduction as a response to stress, as well as biotechnological impacts of plant stresses.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Familiarizing students with plant stress physiology.

  • Teaching techniques to improve productivity of plants by using some biotechnological methods.

  • Introduction to stress and signal transduction.

Course Contents

(weekly plan)



Week 1: Introduction to plant physiology

Week 2: Introduction to stress physiology

Week 3: Ecosystems

Week 4: Biotic and abiotic stresses

Week 5: Water deficit and drought stress and tolerance

Week 6: Heat stress and heat shock

Week 7: Chilling and freezing

Week 8: MID-TERM EXAM WEEK

Week 9: Salinity stress

Week 10: Oxygen deficiency

Week 11: Radiation

Week 12: Biotic stresses

Week 13: Secondary stresses

Week 14: Stress and signal transduction

Week 15: Stress and biotechnology



Week 16: FINAL EXAM WEEK
LABORATORY CONTENTS

Week 1-11: The laboratory course will be designed so that in the first part students cultivate their test plants. Through the following weeks, students will expose the plants to different biotic and abiotic stress factors and record the results.

Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Recall the concept of plant physiology

  2. Explain the concept of the stress

  3. Interpret the sensation of stress (signal transduction)

  4. Compare biotic stress and abiotic stress

  5. Integrate tolerance mechanisms in biotechnology

Prerequisite Course(s)

(if any)


None

Language of Instruction

English

Mandatory Literature

Taiz, L. & Zeiger, E. (2010). Plant Physiology, 5th ed. Sunderland, UK: Sinauer Associates Inc

Recommended Literature

Hale, M. G. & Orcutt, D. M. (2000). The physiology of plants under stress, 2nd. Hoboken, NJ, USA: John Wiley & Sons


ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project




18

18

Seminar / Presentation




14

14

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 333

Course Name: PLANT PHYSIOLOGY AND TISSUE CULTURE

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2 + 2

Total Hours: 30 + 30

Course Description

This course is giving an introduction to the basic physical and physiological properties of a plant body. Also, fundamentals of plant metabolism, such as water movement, photosynthesis, respiration, and transpiration, are discussed. This course is mainly focused on contemporary aspects of plant physiology with an emphasis on recent research. Lab course, which is taken concurrently with lectures, is explaining plant morphology and metabolism through practical exercises. Both lectures and lab course are ending with selected topics in plant tissue culture.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to the basic plant structure.

  • Introduction to plant physiology.

  • Explaining molecular mechanisms underlying plant physiological processes.

  • Covering molecular basis of respiration and photosynthesis.

  • Discussing main processes important for the normal functioning of plants.

Course Content

(weekly plan)



Week 1: Introduction to plant physiology and plants as model organisms

Week 2: Introduction to plant cell, tissue and organ morphology, and physiology

Week 3: Fundamentals of plant tissue

Week 4: Plant nucleic acids, gene expression, and signal transduction

Week 5: Water transport and water balance in plants

Week 6: Mineral nutrition

Week 7: Basics of plant development

Week 8: MID-TERM EXAM WEEK

Week 9: Photosynthesis: Light reactions

Week 10: Photosynthesis: Carbon reactions

Week 11: Environmental regulation of photosynthesis  

Week 12: Respiration

Week 13: Lipid metabolism

Week 14: Fundamentals of plant tissue culture

Week 15: Methodologies used in plant tissue culture



Week 16: FINAL EXAM WEEK
LABORATORY CONTENT

Week 1: Beginning of classes

Week 2, Lab 1: Introduction to lab course

Week 3, Lab 2: The plant cell: Microscopy of different plant parts (plant cell – Allium cepa organelles, Aspidistra sp. – chloroplasts, Cucurbita pepo – elements of the vascular system, Helleborus odorus – leaf, stoma)

Week 4, Lab 3: Physiology of the cell: Osmosis

Week 5, Lab 4: Plasmolysis and deplasmolysis

Week 6, Lab 5: Water transport in plants

Week 7, Lab 6: Transpiraton and respiration



Week 8: MID-TERM EXAM WEEK

Week 9, Lab 7: Photosynthesis

Week 10 Lab 8: Enzymes

Week 11, Lab 9: Physiology of plant growth

Week 12, Lab 10: Plant tissue culture: Growing the plants

Week 13, Lab 11: Plant tissue culture: Hormones and media



Week 14: Preparation for practical exam

Week 15: Practical exam from lab course

Week 16: FINAL EXAM WEEK

Teaching Methods

Description


  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Illustrate the basics of plant anatomy necessary to understand plant physiology

  2. Describe molecular mechanisms of photosynthesis

  3. Demonstrate the basics of biochemical cycles that take place in a plant cell

  4. Break down molecular mechanisms of respiration

  5. Perform plant tissue culture

Prerequisite Course(s)

(if any)


None.

Language of Instruction

English

Mandatory Literature

Taiz, L. & Zeiger, E. (2010). Plant physiology, 5th ed. Sunderland, UK: Sinauer Associates, Inc.

Recommended Literature

Pandey, S.N., Sinha, B.K. (2005). Plant physiology, 4th ed. New Delhi, India: Vikas

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project

1

18

18

Seminar / Presentation

1

14

14

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 334

Course Name: ANALYTICAL CHEMISTRY

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2 + 2

Total Hours: 30 + 30

Course Description

This course will address the basic topics in analytical chemistry, such as those related to gravimetric and potentiometric techniques, electrochemistry, as well as precipitation and titration reactions. The second part of the course covers instrumental methods of analysis, like atomic absorption, fluorescence-based techniques, UV/vis, IR, NMR, HPLC, GC, and LCMS. The laboratory component of the course stresses both quantitative and qualitative analyses. The first part of the practical lab course mainly revolves around titration reactions, while the second part of the course teaches students how to apply analytical chemistry principles in food industry and pharmacy.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Providing good understanding of the chemical principles that underpin chemical reactions.

  • Explaining titration curves.

  • Illustrating steps required to conduct analysis.

  • Introduction to potentiometric methods.

Course Content

(weekly plan)



Week 1: Introduction to the course

Week 2: Types of quantitative and qualitative analysis. Steps involved in performing analysis

Week 3: Gravimetric techniques, theory of precipitation, gravimetric factors

Week 4: Introduction to titrimetric analysis, aqueous solution chemistry

Week 5: Titration curves for simple acid/base systems

Week 6: Complex or polyprotic acid-base titrations

Week 7: Precipitation titrations

Week 8: MID-TERM EXAM WEEK

Week 9: Introduction to electrochemistry and redox reactions

Week 10: Potentiometric methods, redox titrations

Week 11: Introduction to spectroscopy: Electromagnetic spectrum, atomic absorption spectroscopy

Week 12: Ultraviolet-visible spectroscopy, fluorescence

Week 13: Nuclear magnetic resonance, infrared spectroscopy, mass spectrometry

Week 14: Affinity separations: Centrifugation, crystallization, extraction, electrophoresis

Week 15: Gas and liquid chromatography



Week 16: FINAL EXAM WEEK
LABORATORY CONTENT

Week 1: Beginning of classes

Week 2, Lab 1: Introduction to analytical chemistry lab

Week 3, Lab 2: Hydrogen ions, pH, and indicators

Week 4, Lab 3: Strong acid vs. strong base and strong acid vs. weak base titration curves using an indicator color reference and pH meter

Week 5, Lab 4: Weak acid vs. strong base and weak acid vs. weak base titration curves using an indicator color reference and pH meter

Week 6, Lab 5: Acid-base titration: Analysis of acid solutions of unknown concentrations

Week 7, Lab 6: Reactions of metal ions



Week 8: MID-TERM EXAM WEEK

Week 9, Lab 7: The formula of a precipitated compound

Week 10 Lab 8: Quantitative analysis of vitamin C contained in foods

Week 11, Lab 9: Water analysis

Week 12, Lab 10: Measurement of the active ingredient in aspirin pills

Week 13, Lab 11: Chemical properties of consumer products



Week 14, Lab 12: Preparation for practical exam

Week 15: Practical exam from lab course

Week 16: FINAL EXAM WEEK

Teaching Methods

Description


  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Describe the differences between quantitative and qualitative analysis

  2. Interpret electrochemistry and redox reactions

  3. Analyze and differentiate potentiometric methods

  4. Operate the range of instrumentation specified in the module safely and efficiently in the chemistry laboratory

  5. Design and perform titrations accurately and safely in the laboratory

Prerequisite Course(s)

(if any)


None.

Language of Instruction

English

Mandatory Literature

Skoog, D. A., West, D. M., Holler, F. J., & Crouch, S. R. (2003). Fundamentals of Analytical Chemistry, 8th ed. Boston, MA, USA: Cengage Learning

Recommended Literature

Christian, G.D. (2003). Analytical Chemistry, 6th ed. Hoboken, NJ, USA: John Wiley & Sons

ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project

1

14

14

Seminar / Presentation

1

18

18

Total Workload

125

ECTS Credit (Total Workload / 25)

5



Course Code: GBE 335

Course Name: GENOMICS AND PROTEOMICS

Level: Undergraduate

Year: II, III

Semester: III, IV, V, VI

ECTS Credits: 5

Status: Elective

Hours/Week: 2 + 2

Total Hours: 30 + 30

Course Description

This course is organized as an integrated presentation of genome organization, genome sequencing and characterization, comparative genomics, and introductory genomic data analysis. It also covers specific applications of genomics in a modern-day industry, in order to give the students an idea about the practical importance of genomics. This course will also cover fundamentals of analytical tools used for protein characterization, some of them being liquid chromatography, mass spectrometry, SDS-PAGE, and 2D and 3D electrophoresis. Additionally, bioinformatics-based approach is discussed on several occasions in order to make students familiar with in silico protein analysis and structure prediction. Lab course is offered and is mostly dealing with bioinformatics tools for protein analysis.

Course Objectives

The cognitive, affective and behavioral objectives of this course are following:

  • Introduction to the structure, organization, function and evolution of the genome.

  • Familiarizing students with the functioning of the genome.

  • Genome sequencing.

  • Introduction to protein and proteomics analysis.

  • Explaining the interactions between genomes and proteins, proteomics methods and procedures as well as software tools.

  • Teaching about the role of proteomics in the analysis of gene/protein expression, the difference in expression profiles in tissues as well as identification of proteins whose expression has been altered as a result of various active processes.

  • Providing basic principles of current proteome analysis and characterization methods as well as their use in biomedical research in protein identification.

Course Content

(weekly plan)



Week 1: Classical DNA sequencing methods: Maxam-Gilbert and Sanger; NGS (next-generation sequencing)

Week 2: SNP genome distribution and mapping; Chromosomal copy number variations (CNVs)

Week 3: Tracing human population migrations using genome variations

Week 4: Genome-wide association studies (GWAS)

Week 5: Studies on chronic myelogenous leukemia (CML)

Week 6: Genomic changes in differentiated somatic tissues; mosaicism

Week 7: Self-reported genome association studies

Week 8: MID-TERM EXAM WEEK

Week 9: Whole-genome sequencing in families exhibiting rare genetic diseases

Week 10: Protein databases: PIR, Swiss-Prot, Pfam, Protein Data Bank

Week 11: Structure proteomics: 3D protein structure development, X-ray crystallography, and NMR spectroscopy

Week 12: Protein sequence analysis: Predicting protein function based on the sequence, analysis of phylogeny

Week 13: Interaction proteomics: Protein-DNA and protein-protein interactions and their role in biology

Week 14: Methods of posttranslational modification: Phosphoproteomics and glycoproteomics

Week 15: Proteomics in clinical use and settings



Week 16: FINAL EXAM WEEK
LABORATORY CONTENT

Week 1: Beginning of classes

Week 2, Lab 1: Introduction to Genomics and Proteomics lab; content presentation

Week 3, Lab 2: Maxam-Gilber and Sanger sequencing (paper discussion)

Week 4, Lab 3: NGS (paper discussion)

Week 5, Lab 4: SNPs and CNVs (paper discussion and in silico analysis)

Week 6, Lab 5: NGC applications: Metagenomics (computer project)

Week 7, Lab 6: NGS applications: RNA-Seq (computer project)



Week 8: MID-TERM EXAM WEEK

Week 9, Lab 7: Natural selection analysis (computer project)

Week 10 Lab 8: The Human Genome Project (paper discussion)

Week 11, Lab 9: Comparative genomics (in silico work)

Week 12, Lab 10: Epigenomics and Pharmacogenomics (paper discussion)

Week 13, Lab 11: Protein analysis: Finding protein motifs and domains; protein-protein interaction networks (in silico work)



Week 14, Lab 12: Preparation for practical exam

Week 15: Practical exam from lab course

Week 16: FINAL EXAM WEEK


Teaching Methods

Description

  • Interactive lectures and communication with students

  • Discussions and group work

  • Presentations

  • Laboratory work

Assessment Methods Description (%)

Quiz

0 %

Lab/Practical Exam

20 %

Homework

0 %

Term Paper

0 %

Project

20 %

Attendance

0 %

Midterm Exam

20 %

Class Deliverables

0 %

Presentation

0 %

Final Exam

40 %

Total

100 %

Learning Outcomes

After completion of this course, students should be able to:

  1. Develop an understanding of the significant role and essence of proteome analysis in current biomedical research

  2. Describe protein structure and function

  3. Compare interactions between proteomes and genomes and various external factors

  4. Identify the role that proteomics plays in gene/protein expression analysis

  5. Apply knowledge of current proteome analysis and characterization methods in biomedical research in protein identification

Prerequisite Course(s)

(if any)


None.

Language of Instruction

English

Mandatory Literature

Liebler, D. C. (2001). Introduction to Proteomics: Tools for the New Biology, 1st ed. Totowa, NJ, USA: Humana Press, Totowa

Recommended Literature

Simson, R. J. (2002). Proteins and Proteomics: A Laboratory Manual. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press

Twyman, R. M. (2004). Principles of Proteomics (Advanced Text Series). Abingdon, Oxford, UK: BIOS Scientific Publishers



ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD)

Activities

Quantity

Duration

Workload

Lecture (15 weeks x Lecture hours per week)

15

2

30

Laboratory / Practice (15 weeks x Laboratory / Practice hours per week)

15

2

30

Midterm Examination (1 week)

1

2

2

Final Examination (1 week)

1

2

2

Preparation for Midterm Examination

1

14

14

Preparation for Final Examination

1

15

15

Assignment / Homework / Project

1

18

18

Seminar / Presentation

1

14

14

Total Workload

125

ECTS Credit (Total Workload / 25)

5
1   2   3   4   5   6


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