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

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FOURTH SEMESTER

 Course Code: GBE 202 Course Name: BIOSTATISTICS Level: Undergraduate Year: II Semester: IV ECTS Credits: 4 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description This is a general introduction to descriptive and inferential statistics. Topics such as techniques and principles for summarizing data, estimation, hypothesis testing, and decision-making will be covered. Students are instructed on the proper use of statistical software to manage, manipulate, and analyze data and to prepare summary reports and graphical displays. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Explaining basic statistical tests. Evaluating the results of statistical tests. Demonstrating modern statistical methods including descriptive and inferential statistics. Showing students that statistics is an important tool in many different disciplines, and is an important research tool. Course Content (weekly plan) Week 1: Fundamentals of statistics Week 2: Presenting data, part 1 Week 3: Presenting data, part 2 Week 4: Descriptive statistics, part 1 Week 5: Descriptive statistics, part 2 Week 6: Probability, part 1 Week 7: Probability, part 2 Week 8: MID-TERM EXAM WEEK Week 9: Probability distributions, part 1 Week 10: Probability distributions, part 2 Week 11: Sampling distributions and confidence intervals, part 1 Week 12: Sampling distributions and confidence intervals, part 2 Week 13: Fundamentals of hypothesis testing, part 1 Week 14: Fundamentals of hypothesis testing, part 2 Week 15: Preparation for final exam Week 16: FINAL EXAM WEEK LABORATORY CONTENT Week 1: Beginning of classes Week 2, Lab 1: Introduction to MS Excel Week 3, Lab 2: Making tables and diagrams in Excel, part 1 Week 4, Lab 3: Making tables and diagrams in Excel, part 2 Week 5, Lab 4: Descriptive statistics in Excel, part 1 Week 6, Lab 5: Descriptive statistics in Excel, part 2 Week 7, Lab 6: Preparation for mid-term Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: Probability Week 10 Lab 8: Chi-square Week 11, Lab 9: ANOVA Week 12, Lab 10: Student’s t-test Week 13, Lab 11: Regression Week 14: Preparation for lab 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: Deliver an effective presentation of data Perform probability testing Explain the fundamentals of hypothesis testing Make tables and diagrams Operate descriptive statistics in excel Perform the student t test Perform ANOVA Perform regression analysis in excel Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature Kreyszig, E. (2001). Advanced Engineering Mathematics, 8th ed. Hoboken, NJ, USA: John Wiley and Sons Recommended Literature Bhishma R. (2005). Probability and Statistics for Engineers, 2nd ed. New York City, NY, USA: Sitech 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 12 12 Preparation for Final Examination 1 16 16 Assignment / Homework / Project 4 4 Seminar / Presentation 4 4 Total Workload 100 ECTS Credit (Total Workload / 25) 4

 Course Code: GBE 206 Course Name: MOLECULAR BIOLOGY II Level: Undergraduate Year: II Semester: IV ECTS Credits: 5 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description As the second part of a two-part course series in Molecular biology, this course covers advanced topics on gene regulation, protein modifications and ubiquitination, DNA and RNA polymerase, and small RNAs. Current topics, like RNA interference and epigenetics, are also introduced. Final part of the course is devoted to the study of genome stability and evolution. This is taken concurrently with a laboratory course. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Enabling students to move beyond their introductory textbooks towards a deeper understanding of modern molecular biology. Providing detailed descriptions of all molecular mechanisms. Introduction to genomics and systematics. Providing an insight into the regulation of gene expression at different levels. Presenting model organisms in molecular biology. Course Content (weekly plan) Week 1: Introduction to the course Week 2: DNA-related proteins Week 3: Polymerase dynamics Week 4: Small RNAs Week 5: Regulation of gene expression by different types of RNA Week 6: RNA silencing pathways Week 7: RNA interference Week 8: MID-TERM EXAM WEEK Week 9: Epigenetics Week 10: Post-translational modifications Week 11: Protein folding and ubiquitination Week 12: Molecular mechanisms of cell differentiation Week 13: The stability of the genome Week 14: Sequence conservation and homology Week 15: Techniques in molecular biology Week 16: FINAL EXAM WEEK LABORATORY CONTENT Week 1: Beginning of classes  Week 2, Lab 1: Introduction to protein analysis Week 3, Lab 2: Protein isolation from kiwi plant Week 4, Lab 3: β-glucosidase isolation from white button mushroom; protein salting-out Week 5, Lab 4: Protein quantification: Bradford method Week 6, Lab 5: Preparation of animal tissue for protein isolation: Chicken muscle Week 7, Lab 6: Protein isolation from a bacterial culture Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: Protein spectrophotometry by Lowry Week 10 Lab 8: PAGE: Introduction and safety considerations Week 11, Lab 9: SDS-PAGE, part I Week 12, Lab 10: SDS-PAGE, part II Week 13, Lab 11: Result analysis 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 % Presentation 0 % Final Exam 40 % Total 100 % Learning Outcomes After completion of this course, students should be able to: Determine comparative genomic studies in prokaryotes and eukaryotes Deduce gene expression levels and regulation in prokaryotes and eukaryotes Debate molecular mechanisms underlying the processes of gene regulation in different organisms Perform protein isolation in the laboratory from various samples: animal, plant, human Operate quantification of the isolated proteins in the laboratory Perform SDS-PAGE Prerequisite Course(s) (if any) Molecular Biology I Language of Instruction English Mandatory Literature Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2007). Molecular biology of the cell, 5th ed. New York, NY, USA: Garland Science Recommended Literature Karp, G. (2013). Cell and molecular biology: Concepts and experiments, 7th ed. Hoboken, NJ, USA: John Wiley Sambrook, J. & Russell, D. W. (2006). The condensed protocol from molecular cloning: A laboratory manual. Cold Spring Harbor, NY, USA: CSHL 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 12 12 Preparation for Final Examination 1 13 13 Assignment / Homework / Project 18 18 Seminar / Presentation 18 18 Total Workload 125 ECTS Credit (Total Workload / 25) 5

 Course Code: GBE 210 Course Name: BIOCHEMISTRY Level: Undergraduate Year: II Semester: IV ECTS Credits: 6 Status: Mandatory Hours/Week: 3+2 Total Hours: 45+30 Course Description This course provides a broad survey of biochemistry from the molecular aspects. It covers the major chemical and biological foundations of biochemistry. The first section of the course focuses on topics related to carbohydrates, proteins, lipids and nucleic acids. Special emphasis is given to the processes of protein synthesis and gene expression. The second part of the course focuses on the metabolism of carbohydrates, lipids and nitrogen. All these cycles are analyzed through a medical and molecular perspective. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Providing a theoretical and applied bacground in the field of biochemistry Defining the molecular components of the cell Illustrating the metabolism of carbohydrates, lipids and nitrogen Illustrating normal biochemical test results Interpreting abnormal results Interpreting biochemical laboratory tests Course Content (weekly plan) Week 1: Introduction to Biochemistry Week 2: Major Components of the body, Molecular Composition of Cells Week 3: Water, Acids, Bases and Buffers Week 4: Aminoacids Week 5: Proteins; Structure Week 6: Protein function Week 7: Enzymes; Enzyme Kinetics Week 8: MID-TERM EXAM WEEK Week 9: Nucleic Acids Week 10: Carbohydrates Week 11: Carbohydrate metabolism Week 12: Lipids Week 13: Lipid metabolism Week 14: Nitrogen metabolism Week 15: Hormones and metabolism integration Week 16: FINAL EXAM WEEK LABORATORY CONTENT Week 1: Beginning of classes Week 2, Lab 1: Basic calculations Week 3, Lab 2: Solution preparation, buffers Week 4, Lab 3: Quantitative estimation of amino acids by ninhydrin Week 5, Lab 4: Separation of amino acids by TLC Week 6, Lab 5: Titration curves of amino acids Week 7, Lab 6: Isoelectric precipitation of proteins Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: Effect of temperature on enzyme kinetics Week 10 Lab 8: Effect of enzyme concentration on enzyme kinetics Week 11, Lab 9: Effect of substrate concentration on enzyme kinetics Week 12, Lab 10: Qualitative analysis of carbohydrates Week 13, Lab 11: Estimation of saponification value of fats and oils 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: Explain molecular basics of organisms Summarize amino-acids and proteins Categorize enzymes Identify carbohydrates Classify lipids Interpret gluconeogenesis, the pentose phosphate pathway, and glycogen metabolism Illustrate Krebs cycle, electron-transport chain Use basic laboratory skills and procedures in biochemistry labs Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature Boyer, R. F. (2006). Concepts in biochemistry, 3rd ed. Hoboken, New Jersey, USA: Wiley. Recommended Literature Lieberman, M., Marks, A. D., Smith, C. M., & Marks, D. B. (2007). Marks' essential medical biochemistry, 1st ed. Philadelphia, Pennsylvania, USA: Lippincott Williams & Wilkins. Garrett, R. H., & Grisham, C. M. (2001). Principles of biochemistry: with a human focus, 1st ed. Salt Lake City, Utah, USA: Thomson Brooks/Cole. ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD) Activities Quantity Duration Workload Lecture (15 weeks x Lecture hours per week) 15 3 45 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 15 15 Preparation for Final Examination 1 15 15 Assignment / Homework / Project 20 20 Seminar / Presentation 20 20 Total Workload 149 ECTS Credit (Total Workload / 25) 6

 Course Code: GBE 330 Course Name: BIOSENSORS Level: Undergraduate Year: II Semester: IV ECTS Credits: 5 Status: Mandatory Hours/Week: 2 + 2 Total Hours: 30 + 30 Course Description Biosensors have emerged as an exciting research area due to the integration of molecular biology with electronics to form devices of modern time. This course will introduce fundamentals of microbiology and biochemistry from engineering prospective and give a comprehensive introduction to the basic features of biosensors. Types of most common biological agents and the ways in which they can be interfaced with a variety of transducers to create a biosensor for biomedical applications will be discussed. Focus will be on optical biosensors, immunobiosensors, and nanobiosensors. New technologies, related research highlights, and main machine interface will also be covered. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Introduction to sensors, especially biosensor-technology to genetics and bioengineering students and the ones who are interested in the subject. Explaining basic concepts in biosensing and bioelectronics. Clarifying typical problems in biosensing and bioelectronics. Course Content (weekly plan) Week 1: Introduction/Overview of the field and applications of biosensors Week 2: Measurement accuracy and sources of errors Week 3: Characteristics and operational modes of sensors Week 4: Static and dynamic characteristics of biosensors Week 5: Measurement standards Week 6: Sensor networks and communication Week 7: Preparation for mid-term exam Week 8: MID-TERM EXAM WEEK Week 9: Biological sensing elements Week 10: Calorimetric biosensors Week 11: Potentiometric biosensors Week 12: Amperometric biosensors Week 13: Optical biosensors Week 14: Piezoelectric biosensors Week 15: Immunobiosensors Week 16: FINAL EXAM WEEK LABORATORY CONTENT Week 1: Beginning of classes Week 2, Lab 1: Introduction/Overview of the field and applications of biosensors Week 3, Lab 2: Measurement accuracy and sources of errors Week 4, Lab 3: Characteristics and operational modes of sensors Week 5, Lab 4: Static and dynamic characteristics of biosensors Week 6, Lab 5: Measurement standards Week 7, Lab 6: Sensor networks and communication Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: Biological sensing elements Week 10 Lab 8: Calorimetric biosensors Week 11, Lab 9: Potentiometric and amperometric biosensors Week 12, Lab 10: Optical biosensors Week 13, Lab 11: Piezoelectric and immunobiosensors 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: Describe physical operating principles of biosensors Describe the biology of sensing elements Differentiate a variety of biosensors Recognize limitations of biosensors Predict application areas for different types of biosensors Distinguish measurement accuracy and sources of errors in biosensors State technical characteristics of biosensors Discuss measurement standards and sensors network and communication Prerequisite Course(s) (if any) None. Language of Instruction English Mandatory Literature Raden, J.F. (2010). Handbook of Modern Sensors, Physics, Designs and Applications. New York, NY, USA: Springer-Verlag Recommended Literature Enderle, J. & Bronzino, J. (2011). Introduction to Biomedical Engineering, 3rd ed. Burlington, MA, USA: Elsevier Academic Press Webster, J.G. & Eren, H. (2014). Measurement, Instrumentation, and Sensors Handbook, 2nd 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 1 18 18 Seminar / Presentation 1 14 14 Total Workload 125 ECTS Credit (Total Workload / 25) 5

FIFTH SEMESTER

 Course Code: GBE 303 Course Name: INTERNSHIP Level: Undergraduate Year: III Semester: V ECTS Credits: 5 Status: Mandatory Hours/Week: 0+4 Total Hours: 0+60 Course Description Students must complete a 30-working-day (6 weeks) practice in a bio-company. Students are expected to learn about a real working environment and get involved in many aspects of genetics and bioengineering development processes. Also, they are expected to start understand what is required for effective day-to-day laboratory maintenance and to develop the sense of responsibility. Internship could be completed either in private or public biology-related sector. Observations from practical training must be documented and presented in the form of a clear and concise technical report (Internship Notebook). Student must also prepare a short portfolio with a MS PowerPoint presentation. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Encouraging students to develop a sense of responsibility. Enabling practical training. Teaching students to prepare reports. Course Content (weekly plan) During this practice, students should be introduced to all types of work and practice that is conducted in the company, institute, or laboratory. Teaching Methods Description Students acquire on-the-job training as they complete their practice. Assessment Methods Description (%) Quiz 0 % Lab/Practical Exam 0 % Homework 0 % Term Paper 0 % Project 0 % Attendance 0 % Midterm Exam 0 % Class Deliverables 50 % Presentation 0 % Final Exam 50 % Total 100 % Learning Outcomes After completion of this course, students should be able to: Express the ability to work effectively as part of a team Demonstrate interpersonal, organizational, and problem solving skills within a managed environment Practice personal responsibility Describe and discuss information in oral, written or graphic forms in order to communicate effectively with peers and tutors Apply and analyze theory, techniques and relevant tools to the specification, analysis, design, implementation and testing of samples Judge on the company and/or team performance according to the work experience gained during internship Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature N/A Recommended Literature N/A ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD) Activities Quantity Duration Workload Laboratory / Practice (15 weeks x Laboratory / Practice hours per week) 15 4 60 Defense (1 week) 1 30 30 Internship Notebook Preparation (1 week) 1 20 20 Seminar / Presentation 1 15 15 Total Workload 125 ECTS Credit (Total Workload / 25) 5

 Course Code: GBE 307 Course Name: BIOINFORMATICS Level: Undergraduate Year: III Semester: V ECTS Credits: 5 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description The aim of the course is to establish a basic background in the significant and more emerging field of bioinformatics. Its main subjects are PubMed and Medline databases, DNA- and protein-based bioinformatics tools, as well as several new and emerging information tools. Students are expected to have a working knowledge of genetics and molecular biology concepts in order to fully benefit from utilization of available information sources. The course is organized concurrently with a laboratory course in which students are applying bioinformatics in practice in order to analyze DNA, RNA, and protein sequences, as well as to study phylogeny. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Showing the importance of bioinformatics as a method to overcome modern biomedical research problems. Enabling skill development in software using, critical evaluation of the results and their interpretation. Illustrating how to work with DNA sequences. Explaining how to work with protein sequences. Illustrating how to construct phylogenetic trees. Course Content (weekly plan) Week 1: Introduction to bioinformatics Week 2: PubMed Week 3: Using nucleotide sequence databases Week 4: Using protein and specialized sequence databases Week 5: Working with a single DNA sequence Week 6: Working with a single nucleotide sequence Week 7: Similarity searches on sequence databases Week 8: MID-TERM EXAM WEEK Week 9: Comparing two sequences Week 10: Building a multiple sequence alignment Week 11: Editing and publishing alignments Week 12: Working with protein 3D structures Week 13: Working with RNA Week 14: Building phylogenetic trees: NJ method Week 15: Building phylogenetic trees: UPGMA method Week 16: FINAL EXAM WEEK LABORATORY CONTENT Week 1: Beginning of classes Week 2, Lab 1: PubMed Week 3, Lab 2: Using nucleotide sequence databases Week 4, Lab 3: Using protein and specialized sequence databases Week 5, Lab 4: Working with a single DNA sequence Week 6, Lab 5: Working with a single nucleotide sequence Week 7, Lab 6: Similarity searches on sequence databases Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: Comparing two sequences Week 10 Lab 8: Building a multiple sequence alignment Week 11, Lab 9: Editing and publishing alignments Week 12, Lab 10: Working with protein 3D structures Week 13, Lab 11: Building phylogenetic trees 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: Use PubMed for article browsing Employ NCBI for sequence analysis Operate single DNA sequences Perform similarity searches Perform multiple sequence alignments Discover different protein databases Create phylogenetic trees Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature Claverie, J. M. & Notredame, C. (2006). Bioinformatics for Dummies, 2nd ed. Hoboken, NJ, USA: Wiley Recommended Literature Campbell, A. M. &Heyer, L. J. (2006). Discovering Genomics, Proteomics, and Bioinformatics, 2nd ed. San Francisco, CA, USA: Benjamin Cummings. 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 15 15 Preparation for Final Examination 1 15 15 Assignment / Homework / Project 13 13 Seminar / Presentation 18 18 Total Workload 125 ECTS Credit (Total Workload / 25) 5

 Course Code: GBE 309 Course Name: HUMAN GENETICS Level: Undergraduate Year: III Semester: V ECTS Credits: 5 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description This course will focus on concepts such as organization, structure, function, and mapping of the human genome; biochemical and molecular basis, screening, prevention, and treatment of various human diseases; genetic variation in humans; gene frequencies in human populations; human developmental genetics, medical genetics, and other aspects of human heredity. This course focuses on the role of genes in human biology. Selected areas of emphasis range from gene structure and identification, inheritance mechanisms (how genes are passed from parent to offspring), and how genes work within the cellular environment, mutations and the consequences of these malfunctions (genetic diseases), to the genetic structure of whole populations, and finally to ethical, legal, and social issues surrounding the application of the new genetic engineering technologies. Basic areas of modern genetics will be covered, with an emphasis primarily on humans. This is taken concurrently with a laboratory course. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Explaining the role of genes in human biology. Providing the basic concepts of molecular genetics. Introduction to population genetics. Illustrating how to analyze human pedigrees and how to perform gene mapping. Course Content (weekly plan) Week 1: Introduction to human genetics Week 2: The basics of human genetics: Structure and function of the human genome Week 3: The mechanisms involved in genetic variation at the level of gene and gene product, mutagenesis and DNA repair, mutations as a cause of genetic disorders Week 4: Human Genome Project Week 5: Pedigree analysis Week 6: Linkage analysis Week 7: Gene mapping Week 8: MID-TERM EXAM WEEK Week 9: The basic principles of inheritance: Mendelian and non-Mendelian genetics (UDP, dynamic mutations, mosaicism, imprinting) Week 10: Multifactorial inheritance: Interaction of genes and environmental factors Week 11: Laboratory methods of DNA (DNA typing/profiling, RFLP, PCR, STR, mtDNA and Y chromosome analysis) and chromosome (karyotyping and FISH) analysis in human genetic practice Week 12: Introduction to gene therapy Week 13: Interpretation and application of various human genetic tests Week 14: Introduction to human population genetics Week 15: Ethical, legal, and social aspects of human genetic testing Week 16: FINAL EXAM WEEK LABORATORY CONTENT Week 1: Beginning of classes  Week 2, Lab 1: Introduction Week 3, Lab 2: Human pedigree analysis Week 4, Lab 3: Human pedigree analysis Week 5, Lab 4: Genetic linkage and mapping Week 6, Lab 5: Mitochondrial DNA isolation from hair (Chelex method) Week 7, Lab 6: Restriction digestion of mtDNA from hair Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: DNA isolation from buccal swab (Chelex method) Week 10 Lab 8: Polymerase chain reaction: Theoretical introduction Week 11, Lab 9: PCR analysis of Rh factor inheritance in humans Week 12, Lab 10: Agarose gel electrophoresis of PCR products Week 13, Lab 11: Agarose gel of PCR products: Results interpretation 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: Perform pedigree analysis Clarify gene mapping Interpret various human genetic tests Perform DNA isolation Illustrate the molecular mechanism of PCR and perform PCR Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature Lewis, R. (2009). Human Genetics: Concepts and Applications, 9th ed. New York, NY, USA: McGraw-Hill Recommended Literature Sudbery, P. & Sudbery, I. (2010). Human and Molecular Genetics, 3rd edition. New York, NY, USA: Pearson Education Ltd Pasternak, J.J. (2005). An Introduction to Human Molecular Genetics: Mechanisms of Inherited Diseases, 2nded. Hoboken, NJ: John Wiley & Sons Cummings, M.R (2014). Human Heredity, 10th ed. Belmont, USA: Brooks/Cole 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 16 16 Seminar / Presentation 1 16 16 Total Workload 125 ECTS Credit (Total Workload / 25) 5

 Course Code: GBE 325 Course Name: BIOMEDICAL SIGNALS AND SYSTEMS Level: Undergraduate Year: III Semester: V ECTS Credits: 5 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description This course will introduce students to medical and biomedical engineering concepts. The focuses are on how signal analysis can clarify the understanding of biomedical signal interpretation and diagnosis. Topics include EEGs, ECGs, EMGs, respiratory and blood pressure (how they are generated and measured), biosignals as random processes, spectral analysis, wavelets, time-frequency functions, and signal processing for pattern recognition. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Introduction to the principles of biomedical signals and systems through ECG, EEG, EMG, NIBP, IBP and respiratory examples. Explaining the importance of engineering in medicine. Giving an outline of characteristics of biomedical signals. Providing basic concepts about the human heart. Providing basic concepts about the respiratory system. Course Content (weekly plan) Week 1: Summary and history of biomedical engineering Week 2: Cell physiology, bio-potentials, membrane, and active potentials Week 3: Bioelectrical phenomena, neurons, synaptic transmission Week 4: Biomedical signals: ECG, EEG, EMG, EOG, respiratory signal, biomedical sensors, biomedical signals processing Week 5: Human heart, cardio-cycle, electrocardiogram, vectocardiogram, electrical field of the heart, methods of ECG signal acquisition Week 6: Methods for acquisition, processing and visualization of ECG signal, heart’s rhythm diagnostic Week 7: ECG waveform and significant segments, ECG interpretation and diagnostics, pacemaker WEEK 8: MID-TERM EXAM WEEK Week 9: Respiratory signal, measurement, extraction from ECG, and measuring respiratory signals Week 10: Blood pressure, invasive and non-invasive measurement methods, biosensors and transducers Week 11: Methods for acquisition, processing and visualization of EEG signal Week 12: Recording and interpretation of EEG, basic concepts and EEG phenomena Week 13: Electrodes for bio-potential measurement, basic electrochemical processes in the cell and tissues, aspects and methods of bioimpedance measurement Week 14: Electrochemical sensors and dialysis: Chemical sensors, separation of the blood components Week 15: Preparation for the final exam WEEK 16: FINAL EXAM WEEK LABORATORY CONTENT: Week 1-11: The laboratory course is designed so that the students go through a series of virtual labs and analyze the studied equipment: their modes of functioning, components, and therapeutic importance in determining diagnosis. Teaching Methods Description (list up to 4 methods) Interactive lectures and communication with students Discussions and group work Consultations 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: Define biomedical system modeling Assess different aspects and methods of applying engineering principles in medicine Review characteristics of biomedical signals Arrange principles of design and implementation of medical devices for physiological signal processing Interpret results of ECG and EEG signals Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature Raden, J.F. (2010). Handbook of Modern Sensors, Physics, Designs and Applications. New York, NY, USA: Springer-Verlag Recommended Literature Enderle, J. & Bronzino, J. (2011). Introduction to Biomedical Engineering, 3rd ed. Burlington, MA, USA: Elsevier Academic Press Webster, J.G. & Eren, H. (2014). Measurement, Instrumentation, and Sensors Handbook, 2nd 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

SIXTH SEMESTER

 Course Code: GBE 392 Course Name: GENETICS AND BIOENGINEERING PROJECT Level: Undergraduate Year: III Semester: VI ECTS Credits: 5 Status: Mandatory Hours/Week: 0+4 Total Hours: 0+60 Course Description This course requires each student to work on a short research project, effectively communicate with their mentors, and apply genetics and bioengineering knowledge in their research work. At the end of research project, each student should submit a hardcopy of the project and defend it with poster presentation in front of a committee containing three juries. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Enabling students to combine theoretical and practical ability for preparation a genetic engineering project and a presentation to the class. Providing material for students to document the research results with a proposal of a design project. Providing students with the experience of conceiving, designing, and implementing a research project proposed. Preparing students to present the implemented project orally. Course Content (weekly plan) Announcement of project proposals by the Department Choosing any of proposed projects, or proposing student’s own project Announcement of the projects assigned to students Mentor-student communication Doing literature review and practical research (if applicable) Submitting all necessary administrative forms Finalizing MS Word version of GBE project Project defense in the form of poster presentation in front of jury members Teaching Methods Description Interactive lectures and communication with students Discussions and group work Presentations Laboratory work Assessment Methods Description (%) Quiz 0 % Lab/Practical Exam 0 % Homework 0 % Term Paper 0 % Project 50 % Attendance 0 % Midterm Exam 0 % Class Deliverables 0 % Presentation 50 % Final Exam 0 % Total 100 % Learning Outcomes After completion of this course, students should be able to: Actively participate in courses and begin to take responsibility for learning Begin to work effectively as par to of a team, developing interpersonal, organizational, and problem solving skills within a managed environment, exercising some personal responsibility Present information in oral, written or graphic forms in order to communicate effectively with peers and tutors Apply theory, techniques and relevant tools to the specification, analysis, design, implementation and testing. Evaluate theories, processes and outcomes within an ambiguous setting Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature N/A Recommended Literature ECTS (ALLOCATED BASED ON STUDENT’S WORKLOAD) Activities Quantity Duration Workload Laboratory / Practice (15 weeks x Laboratory / Practice hours per week) 15 4 60 Assignment / Homework / Project 1 40 40 Seminar / Presentation 1 20 25 Total Workload 125 ECTS Credit (Total Workload / 25) 5

 Course Code: GBE 304 Course Name: FORENSIC GENETICS Level: Undergraduate Year: III Semester: VI ECTS Credits: 5 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description Forensic genetics is the application of science to law and it encompasses various scientific disciplines. This course will introduce various methodologies and applications used in forensic context, as well as the workflow characteristic for forensic investigations. Real forensic cases are used to introduce technique and theory, to demonstrate how case solving requires an interdisciplinary team approach, and to allow students to practice their analytical and logical reasoning skills. Laboratory course is offered concurrently with lectures and is introducing practical research in forensics (such as sample collection, presumptive evidence testing, and DNA analysis and individualization), as well as statistical calculations necessary for presenting evidence in the court. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Introduction to various disciplines and methodologies in forensic genetics. Teaching the roles of numerous scientific disciplines in crime investigations. Explaining the importance of analytical tools in forensic investigation. Explaining the importance of crime scene processing. Introduction to forensic anthropology and odontology. Describing how gender, mitochondrial, and Y-chromosomal DNA analyses are performed. Course Content (weekly plan) Week 1: Presentation of syllabus and course Week 2: Introduction to forensic genetics: Basic principles and historical development, branches of forensic genetics Week 3: Basic genetic, medical, and biochemical principles of forensic DNA testing Week 4: Evaluation of biological traces suitable for DNA analysis: Classification, collection, packaging, labeling, and preservation Week 5: Presumptive and confirmatory testing Week 6: Application of molecular-genetic techniques in forensics (DNA extraction, amplification, qualitative and quantitative characterization) Week 7: Basic parameters and standards of a successful forensic genetics lab Week 8: MID-TERM EXAM WEEK Week 9: Lineage markers Week 10: DNA identification of mass disaster victims Week 11: Application of statistical, population, and medical studies in forensic genetics Week 12: Disputed paternity and maternity testing Week 13: Ethical, legal and, social aspects of DNA testing; Creation of national databases Week 14: Application of DNA analysis results in legal and crime investigations; DNA testing legislation Week 15: Preparation for final exam Week 16: FINAL EXAM WEEK LABORATORY CONTENT Week 1: Beginning of classes Week 2, Lab 1: Types of evidence (DNA and non-DNA), fingerprint analysis Week 3, Lab 2: Evidence collection, labeling, and packaging Week 4, Lab 3: Crime scene (sample collection) Week 5, Lab 4: Presumptive and confirmatory tests Week 6, Lab 5: Kastle-Meyer test and starch-iodine radial diffusion test Week 7, Lab 6: DNA analysis: DNA isolation (Qiagen) Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: DNA analysis: DNA quantification by spectrophotometry Week 10 Lab 8: DNA analysis: RFLP, VNTR, individualization Week 11, Lab 9: RFLP result interpretation Week 12, Lab 10: Paternity testing, paternity index or combined paternity index, probability of paternity, Random Man Not Excluded Week 13, Lab 11: STR profiles 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: Apply all sorts of forensic and genetic analysis methods in processing human, animal and plant biological trace samples Operate forensic samples for forensic analysis Assess the importance of forensic genetics in legal medicine and juridical procedures Conduct DNA isolation Categorize various sequencing methods Explain STR profiling and the use of CODIS Employ forensic statistics Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature Houck, M.M. & Siegel, J. A. (2010). Fundamentals of Forensic Science, 2nd ed. Waltham, MA, USA: Academic Press Recommended Literature Butler, J. M. (2009). Fundamentals of DNA Typing, 1sted. Waltham, MA, USA: Academic 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 16 16 Seminar / Presentation 16 16 Total Workload 125 ECTS Credit (Total Workload / 25) 5

 Course Code: GBE 321 Course Name: INTELLIGENT SYSTEMS Level: Undergraduate Year: III Semester: VI ECTS Credits: 5 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description This course will introduce students to the principles of fuzzy logic systems and artificial neural network systems. The focuses are on using these methods for solving different problems in Bioengineering. Topic include neural networks architectures and fuzzy systems, learning algorithms and application, Matlab software - Neural Network Toolbox and Fuzzy Logic Toolbox. Student will acquire knowledge various neural network and fuzzy systems models. Student is also expected to work effectively as part of a team, to develop interpersonal, organizational, and problem-solving skills within a managed environment and to exercise some personal responsibility. Course Objectives The cognitive, affective and behavioral objectives of this course are following: To provide students with an understanding of the fundamental theory of neural networks, fuzzy logic systems, eule-based systems and expert system development. Course Content (weekly plan) Week 1: Introduction: Characteristics of ANN and Fuzzy Systems, Biological Neuron, Artificial Neuron, Artificial Neural Networks Week 2: Phases in ANN Operation, Network Classification Week 3: Phases in ANN Operation, Network Classification Week 4: Unsupervised Learning: Hebbian Learning, Competitive Learning & Boltzmann Learning Week 5: Unsupervised Learning: Hebbian Learning, Competitive Learning & Boltzmann Learning Week 6: Supervised Learning (Error-Correction learning) and Reinforcement Learning Week 7: Supervised Learning (Error-Correction learning) and Reinforcement Learning Week 8: MID-TERM EXAM WEEK Week 9: Perceptrons and Multilayer Perceptrons Week 10: Neural network Applications Week 11: Neural network Applications Week 12: Fuzzy Sets and Operations Week 13: Fuzzy Representation of Structured Knowledge Week 14: Fuzzy System application and Fuzzy sense in ANN Week 15: Expert systems based on fuzzy logic and artificial neural network Week 16: FINAL EXAM WEEK LABORATORY CONTENTS Week 1: Beginning of classes Week 2, Lab 1: Introduction: Characteristics of ANN and Fuzzy Systems, Biological Neuron, Artificial Neuron, Artificial Neural Networks Week 3, Lab 2: Phases in ANN Operation, Network Classification Week 4, Lab 3: Unsupervised Learning: Hebbian Learning, Competitive Learning & Boltzmann Learning Week 5, Lab 4: Unsupervised Learning: Hebbian Learning, Competitive Learning & Boltzmann Learning Week 6, Lab 5: Supervised Learning (Error-Correction learning) and Reinforcement Learning Week 7, Lab 6: Supervised Learning (Error-Correction learning) and Reinforcement Learning Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: Perceptrons and Multilayer Perceptrons Week 10 Lab 8: Neural network Applications Week 11, Lab 9: Fuzzy Sets and Operations Week 12, Lab 10: Fuzzy Representation of Structured Knowledge Week 13, Lab 11: Fuzzy System application and Fuzzy sense in ANN Week 14, Lab 12: Expert systems based on fuzzy logic and artificial neural network Week 15: 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 Consultations 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: Designing and applying fuzzy logic system to solve engineering control problems where only expert linguistic knowledge is available, Designing and applying artificial neural network for solving problems, Different aspects and methods of applying fuzzy logic system and artificial neural network in Bioengineering, The difference between the classical algorithmic way of solving the problems and the corresponding learning procedures of artificial neural networks, Technical possibilities, the advantages and the limitations of the fuzzy logic systems, artificial neural network systems, Usage of available software tools such as Matlab Neural Network Toolbox. Developing Intelligent Expert Systems for solving complex problems in the Bioengineering area. Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature S. Kumar, “Neural Networks: A Classroom Approach,” McGraw Hill, 2005. J.M. Mendel, “Uncertain Rule-Based Fuzzy Logic Systems”, Prentice-Hall, 2001 Timothy Ross, Fuzzy Logic with Engineering Applications, John Wiley & Sons Inc., 2010. Sandhya Samarasingh, Neural Networks for Applied Sciences and Engineering: From Fundamentals to Complex Pattern Recognition, Auerbach Publications, 2006 S. Haykin, “Neural Networks: A Comprehensive Foundation”, 2nd Ed, Prentice-Hall,1999 L. Fausett, “Fundamentals of Neural Networks: Architectures, Algorithms, and Application s”, Prentice-Hall, 1994 Recommended Literature None 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 338 Course Name: IMMUNOLOGY AND IMMUNOGENETICS Level: Undergraduate Year: III Semester: VI ECTS Credits: 5 Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30 Course Description This course provides a broad survey of modern immunology, covering such topics as molecular concepts of antigenic specificity, chemistry of antibodies and their interactions with antigens and cells, regulation of the immune response, transplantation, autoimmunity, and tumor immunology. The course is taken concurrently with a lab course, which is teaching students basic experimental concepts in immunology, such as differential blood picture, counting blood cells, HLA typing, and hemoglobin analysis. Course Objectives The cognitive, affective and behavioral objectives of this course are following: Providing a theoretical and applied perspective of classical and modern immunology. Teaching students basics of immunogenetics. Explaining HLA typization. Introducing basic Blood tests. Providing basic concepts of allergy. Explaining autoimmunity. Course Contents (weekly plan) Week 1: Properties and overview of immune responses. Innate immunity Week 2: Cells and tissues of immune system Week 3: Antibodies and antigens. Major histocompatibility complex molecules Week 4: Antigen processing and presentation to T lymphocytes. Antigen receptors and accessory molecules of T lymphocytes Week 5: Lymphocyte development and antigen receptor gene rearrangement Week 6: Activation of T lymphocytes Week 7: B cell activation and antibody production Week 8: MID-TERM EXAM WEEK Week 9: Immunological tolerance. Cytokines Week 10: Effector mechanisms of cell-mediated and humoral immunity Week 11: Immunity to microbes Week 12: Transplantation immunology Week 13: Autoimmunity Week 14: Immunity to tumors Week 15: Hypersensitivity Week 16: FINAL EXAM WEEK LABORATORY CONTENTS Week 1: Beginning of classes Week 2, Lab 1: Introduction to lab course Week 3, Lab 2: Blood smear Week 4, Lab 3: Leukocyte count Week 5, Lab 4: RBC count Week 6, Lab 5: Determination of blood type, bleeding and clotting time Week 7, Lab 6: Osmotic fragility Week 8: MID-TERM EXAM WEEK Week 9, Lab 7: Platelet count Week 10 Lab 8: Separation of blood components Week 11, Lab 9: Bacterial antigens Week 12, Lab 10: Precipitation of blood proteins Week 13, Lab 11: ELISA (virtual lab) 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: Prepare and interpret blood smears Describe basic organs of the lymph system Perform ABO, MN, Rh blood typing Isolate blood proteins Interpret blood lab results Perform immunological detection of viruses and bacteria Prerequisite Course(s) (if any) None Language of Instruction English Mandatory Literature Abbas, A. K., Lichtman, A. H. H., & Pillai, S. (2011). Cellular and molecular immunology, 7th ed. Philadelphia, PA, USA: Saunders Recommended Literature Harvey R., Doan T., Melvold R., Viselli S., & Waltenbaugh, C. (2012). Immunology, 2nd ed. Philadelphia, PA, USA: LWW 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