INTERNATIONAL BURCH UNIVERSITY FACULTY OF … · various fundamental courses like chemistry, physics and biology; bioengineering courses: genetics and bioengineering, biotechnology,

INTERNATIONAL BURCH UNIVERSITY

FACULTY OF ENGINEERING AND NATURAL SCIENCES

DEPARTMENT OF GENETICS AND BIOENGINEERING

FIRST CYCLE STUDY PROGRAM SPECIFICATION

SARAJEVO

August, 2019

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TABLE OF CONTENTS

1. 2

1.1. 2

1.2. 3

1.3. 3

1.4. 3

1.5. 3

1.6. 4

1.7. 4

1.8. 5

1.9. 5

1.9.1. ASSESSMENT 4

1.9.2. GRADING 4

1.10. 6

1.11. 6

1.12. 6

1.13. 7

1.14. 7

2. 8

1. PROGRAM DESCRIPTION

1.1. General

Genetics and bioengineering is one of the fastest growing disciplines in science today. The unique

combination of traditional methods and approaches used in genetics combined with the innovative

approaches of bioengineering enable a multidisciplinary approach to solving various biomedical,

forensic, microbiological, engineering, and other related problems. The undergraduate program

lasts three years and enables students to gain a wide overview of the field through the study of

various fundamental courses like chemistry, physics and biology; bioengineering courses: genetics

and bioengineering, biotechnology, molecular biology, etc.; as well as engineering subjects:

programming, calculus etc., which give students the engineering basis necessary for the filed.

The Genetics and Bioengineering Department at International Burch University is located on the

first floor in a separate part of the University facility. In order to avoid possible contamination the

entire department is separated from the rest of the building with a glass door, which can only be

accessed with an ID card. The Department has 4 laboratories: Scientific Research, Cell Biology

and Microbiology, Genetics and Molecular Biology and Chemistry lab in which students pursue

their laboratory exercises.

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The main aim of the genetics and bioengineering undergraduate program at IBU is to prepare

students for their future career through giving them the adequate knowledge, skills, and attitudes

necessary to succeed. Each course is based on the principle that the knowledge gained on the

lectures is followed by the practical application of that knowledge in the laboratory.

This field of study offers a wide range of employment opportunities in Bosnia and Herzegovina as

well as the entire world. The main product of Higher Education Institution International Burch

University, is a skilled and competent graduate ready for the labor market.

1.2. Vision

With the establishment of the Department of Genetics and Bioengineering our goal was to create

a branch that is dynamic, interdisciplinary, ethic, enterprising, open to original concepts,

environmentalist, active in social points, high quality in science, and modern. The aim was to

create a nurturing environment that will enable our students to gain the highest level of knowledge

while creating relationships with faculty and colleagues that would prepare them for careers within

the areas of interest. Program components combine flexibility with rigor, place a priority on

independence and imagination, and emphasize extensive individual faculty-student interactions.

1.3. Mission

The mission of the Department of Genetics and Bioengineering is to train the students to be the

next generation of leaders in the globally competitive fields of life sciences, biotechnology,

industry, academia, and research. The program is developed to meet the increasing demand of

these fields in industry and research, respectively. Our aim is to enable students to become

scientific professionals in fields such as biotechnology, bioinformatics, biomedical engineering,

pharmacy and drug design, nanotechnology, genomic and proteomic research, neuroscience, and

many more.

1.4. Program

The Department of Genetics and Bioengineering offers three degrees: BSc undergraduate (three

years), MSc (either one or two year program), and PhD (three years). Foundational course work

in basic natural sciences, particularly in biology, chemistry, physics, and mathematics, introduces

the students to the fundamentals needed for their future studies of genetics and bioengineering.

Since the entire program is in English during the first year of the bachelor degree students listen

to the course which gives them advanced English reading and writing exercises (in both semesters).

This course enables students to advance their knowledge of the English language which is

necessary throughout the entire program. During the second and third year of the bachelor program

candidates immerse themselves deeper into focused areas by predominantly attending genetic and

bioengineering courses. The curriculum also entails elective courses that are designed to provide

students with opportunities to begin establishing professional skills that are in line with their

interests. Candidates that are enrolled in MSc and PhD programs attend more advanced courses in

agricultural, medical, environmental, and practical biotechnologies while also conducting high

quality research. They are expected to write and defend a thesis/dissertation at the completion of

their studies.

1.5. Program Objectives and Outcomes

The objectives of BSc program are as follows:

● To produce graduates skilled in the fundamental theoretical and practical concepts of future

graduate pursuits should they choose to do so.

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● To prepare graduates to pursue career choices in various genetics and bioengineering or

related interdisciplinary fields that require a strong background in applied sciences or

engineering.

● To equip graduates with problem solving skills, laboratory skills, and design skills

necessary to thrive in technical careers.

● To develop students' abilities to communicate and demonstrate teamwork skills as well as

an ethical demeanor necessary to succeed in their careers.

● To prepare students to continue their professional development through continuing their

educational endeavors and personal development experiences based on their awareness of

database resources and professional societies, journals, and meetings.

Upon completion of this BSc Genetics and Bioengineering program, students should be able to:

● Show a fundamental level of knowledge in the field of genetics and bioengineering as well

as demonstrate knowledge in the fields of basic sciences and electives necessary for the

bioengineering profession.

● Interpret and discuss various different topics related to the field.

● Apply computer programs and programming languages necessary to adequately perform

tasks in the bioengineering field in a scientific manner through the development of

computer literacy.

● Develop a scientific approach to solving various scientific problems and tasks through the

work on various laboratory experiments in the department as well as apply a fundamental

level of skills needed to perform routine laboratory work.

● Master the use of various bioengineering laboratory instruments and machines.

● Collect, analyze and write the results of laboratory experiments and write laboratory

reports.

● Develop habits to work according to laboratory safety procedures and learn various bio-

safety levels.

● Develop team work skills, as well as skills to work in a multidisciplinary environment and

bioethical and public policy awareness.

● Learn to critically analyze laboratory protocols and compare various methodologies.

1.6. Practical Training

Through the entire Bachelor program students have practical or laboratory sessions which follow

the lectures. This enables students to get practical training in various scientific and engineering

fields as well as develop skills necessary for their future career. As mentioned before, Burch

possesses four well-equipped laboratories to meet all of the needs of the program. Students also

gain additional training through visiting various laboratories throughout the course. Besides the

regular laboratory sessions students also have to have an internship practice. This adds significant

workplace experience to a student’s education. It is realized in the collaboration with public and

private institutions based both nationally as well as internationally. With the duration of 30

working days, it enables the student to gain valuable “on the job,” “real-world” work experience

related to a chosen focus in genetics and bioengineering. This practical training also permits

students to establish networks in the areas of work in potential future careers.

1.7. Learning and Teaching

Our learning and teaching methods provide high quality learning opportunities so that

undergraduate and graduate candidates effectively demonstrate achievement in the courses and

modules in their route of study.

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We aim to foster the development of independent study skills, intellectual autonomy as well as a

sense of curiosity while encouraging a commitment to lifelong learning and continuous

professional development. Furthermore, students are urged to be independent in their course of

study by taking on responsibility for their own learning and development. A progressive use of

project learning, integrated assessment, and product/problem-based learning allow students to take

on greater self-direction. Group as well as team work are of particular focus during the scholars’

course of study as they provide personal and enriching interactions that shape students both

socially and intellectually.

Our courses are usually composed of lectures, seminars, tutorials, and practical laboratory

sessions. The use of simulations, role play, case studies, projects, practical work, work-based

learning, workshops, peer tutoring, peer group interaction, self-managed teams, and learner-

managed learning are some of the means by which effective learning is encouraged.

1.8. Teaching/Learning Methods and Strategies

Lectures/classes: Lectures and classes offer information, literature reviews, illustrative

applications and presentations that explore core ideas in the subject matter. Students are expected

to solve problems that are discussed in small class set ups. Attending less than 70% of lectures will

result in failing the course.

Practical sessions: Practical sessions enable students to develop a sense for real life scientific

issues through regular laboratory participation. Each course is accompanied by a minimum of 10

laboratory sessions and attendance is mandatory for all students. Student performance is monitored

and graded through laboratory quizzes and practical exams.

Group project: The group project provides an opportunity for students to solve real genetic,

bioengineering, and biotechnological problems, practice analytic and problem-solving skills, and

work in teams. It is this focus on knowing and doing, on individual achievement as well as

meaningful collaborations that enable our students to reach their intellectual and academic

potential.

Individual project: Individual projects involve literature reviews, problem specification and

experiments/analyses. This enables a student to utilize theoretical techniques they have learned

by applying them in laboratory and library settings.

Expert (guest) lectures and seminars: Guest lectures and seminars provide students with

opportunities to hear internal as well as external visiting speakers. Through this immersion in real-

world science, students are able to broaden their idea and understanding of the field and to

potentially begin visualizing themselves in a science profession.

1.9. Assessment Protocols

The purpose of an outcome-based learning assessment is to improve the quality of learning and

teaching in genetics and bioengineering.

The fundamental principles are:

● A student’s learning is the central focus of the Department‘s efforts.

● Each student is unique and will express and experience learning in a unique way.

● Students must be able to apply their learning beyond the classroom.

● Students should become effective, independent, lifelong learners as a result of their

educational experience.

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1.10. Assessment

Assessment of intellectual skills is done via:

● Written examinations

● Written essay assignments

● Evaluation of practical work

● Group project report and team presentation

● Individual project report and short presentation.

1.11. Grading

The final success of a student after all envisioned forms of testing is evaluated and graded through

the system of comparison ECTS with the scale of grading, as follows:

a) 10 (A) – outstanding performance without errors or with minor errors, carries 95-100

points

b) 9 (B) – above average, with few errors, carries 85-94 points

c) 8 (C) – average, with notable errors, carries 75-84 points

d) 7 (D) – generally good, but with significant shortcomings, carries 65-74 points

e) 6 (E) – meets minimum criteria, carries 55-64 points

f) 5 (F, FX) – performance does not meet minimum criteria, less than 55 points.

1.12. Transferable Skills

By the end of the course, a student will have developed a range of transferable skills including

abilities in:

● Managing their own learning and conducting independent thinking and study

● Problem specification and modeling

● Applying genetic and bioengineering methods to solve real-world problems

● Managing a research project, including planning and time management

● Conducting an engineering-based research-based work, from hypothesis to report writing

● Working in a multi-disciplinary team

● Critical analysis.

1.13. Skills and Other Attributes

● Effective communication of information, arguments, analyses and techniques in a variety

of forms to specialist and non-specialist audiences.

● An ability to undertake further training, develop existing skills, and acquire new

competences that will enable students to assume significant responsibility within

organizations.

1.14. Methods for Evaluating and Improving the Quality and Standards of

Teaching and Learning

● Student focus groups and the annual student survey

● Classroom observation of lecturers

● Instructors possess advanced professional diplomas in teaching and learning in higher

education

● Membership of the higher education academy

● External examiners reports

● Accreditation visits

● Curriculum area review

● Course committees

● Annual and periodic review.

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Indicators of quality and standards:

● Student feedback

● Retention and success rates for each level for each course

● Student module evaluations

● Annual student questionnaires

● First destination statistics

● Professional accreditation

● External examiner reports.

1.15. Criteria for Admission

The Genetics and Bioengineering department at IBU invites applications from candidates whose

breadth of knowledge and curiosity suggest a potential for academic excellence.

In general, only applicants with a distinguished academic record will be considered.

Recommendations as well as a personal statement are carefully weighed as evidence for qualities

we seek in our applicants. Those include evidence of personal skills, communication skills,

literacy, numeracy, study skills, subject and motivation, and work experience as well as

community involvement.

Students whose first language is not English are urged to apply, also. However, mastery of the

English language is tested via standardized means such as IELTS as well as TOEFL.

1.16. Career Prospects

Following completion of a degree, successful graduates, or Bachelors of Genetics and

Bioengineering, work as researchers or administrators in various industries (genetic diagnosis and

medication, chemical, pharmaceutical, food, etc.), spanning across a wide range of disciplines

within biological sciences and biotechnology.

1BOS 101 Bosnian/Croatian/Serbian Language I/ TDE 101 Turkish Language I/ GRM 101 German Language I

2BOS 102 Bosnian/Croatian/Serbian Language II/ TDE 102 Turkish Language II/ GRM 102 German Language II

2. CURRICULUM

First Semester

CODE COURSE NAME T P ECTS

GBE 101 Introduction to Genetics and Bioengineering 2 2 5

GBE 103 General Biology 3 2 6

MTH 107 Survey of Calculus 3 2 6

CEN 111 Programming I 3 2 6

ELT 117 Advanced Reading and Vocabulary I 2 2 5

XXX xxx University Level Elective (Language)1 0 2 2

Total 13 12 30

Second Semester


GBE 102 Cell Biology 2 2 5

GBE 108 General Chemistry 3 2 6

GBE 106 Evolution and Systematics 3 2 6

PHY 104 General Physics 3 2 6

GBE 105 Histology and Embryology 2 2 5

XXX xxx University Level Elective (Language)2 0 2 2

Total 13 12 30

Third Semester


GBE 201 Genetics 2 2 5

GBE 211 Organic Chemistry 3 2 6

GBE 217 Microbiology 2 2 4

GBE 219 Molecular Biology I 2 2 5

GBE 323 Biomedical Instrumentation 2 2 5

GBE xxx Department Level Elective I 2 2 5

Total 13 12 30

Fourth Semester


GBE 202 Biostatistics 2 2 4

GBE 206 Molecular Biology II 2 2 5

GBE 210 Biochemistry 3 2 6

GBE 330 Biosensors 2 2 5

GBE xxx Department Level Elective II 2 2 5

GBE xxx Department Level Elective III 2 2 5

Total 13 12 30

Fifth Semester


GBE 303 Internship 0 4 5

GBE 307 Bioinformatics 2 2 5

GBE 309 Human Genetics 2 2 5

GBE 325 Biomedical Signals and Systems 2 2 5

GBE xxx Department Level Elective IV 2 2 5

GBE xxx Department Level Elective V 2 2 5

Total

10 14 30

Sixth Semester


GBE 392 Genetics and Bioengineering Project 0 4 5

GBE 304 Forensic Genetics 2 2 5

GBE 321 Intelligent Systems 2 2 5

GBE 338 Immunology and Immunogenetics 2 2 5

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GBE xxx Department Level Elective VI 2 2 5

GBE xxx Department Level Elective VII 2 2 5

Total 10 14 30

Department Level Elective Courses


GBE 320 Systems Physiology 2 2 5

GBE 322 Principles of Neurobiology 2 2 5

GBE 324 Biomaterials 2 2 5

GBE 326 Cytogenetics 2 2 5

GBE 327 General Biotechnology and Biosafety 2 2 5

GBE 328 Introduction to Research Methods 2 2 5

GBE 329 Population Genetics 2 2 5

GBE 331 Environmental Biology 2 2 5

GBE 332 Plant Stress Physiology 2 2 5

GBE 333 Plant Physiology and Tissue Culture 2 2 5

GBE 334 Analytical Chemistry 2 2 5

GBE 335 Genomics and Proteomics 2 2 5

GBE 337 Biomechanics 2 2 5

GBE 339 Recombinant DNA Technology 2 2 5

GBE 340 Plant Pathology 2 2 5

GBE 341 Biophysics 2 2 5

GBE 343 Virology 2 2 5

University Level Elective Courses

COURSE

NAME COURSE NAME T P ECTS

BOS 101 Bosnian/Croatian/Serbian Language I 0 2 2

TDE 101 Turkish Language I 0 2 2

GRM 101 German Language I 0 2 2

BOS 102 Bosnian/Croatian/Serbian Language II 0 2 2

TDE 102 Turkish Language II 0 2 2

GRM 102 German Language II 0 2 2

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FIRST SEMESTER

Course Code: GBE 101 Course Name: INTRODUCTION TO GENETICS AND BIOENGINEERING

Level: Undergraduate Year: I Semester: I ECTS Credits: 5

Status: Mandatory Hours/Week: 2+2 Total Hours: 30+30

Course Description

The course covers basic concepts of genetics and bioengineering and their connection with the

spectrum of human activity. It serves as an introduction to the fundamental science and

engineering on which genetics and bioengineering are based upon. Various topics within the

realms of genetics and bioengineering are covered, and it is designed for students who are in their

first year of genetics and bioengineering studies. Upon completion of the course, students will be

familiar with the general history of the field of biotechnology, including a basic knowledge of the

important researchers within the field and their major contributions and discoveries. They will

also be familiar with the basics of classical genetics and will understand the role of DNA in

inheritance. The course is taken concurrently with a laboratory course.

Course Objectives

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

●Giving students general knowledge about the field of bioengineering.

●Introduction to the history and applications of DNA/RNA technology, molecular biology

and bioethics.

●Enabling students to analyze situations or phenomena related to the biological world in a bioethical perspective.

●Teaching students to conduct all experiments in a safe environment by introducing them

to the basics of lab safety.

●Illustrating how to apply bioengineering in the laboratory environment.

●Introduction to experiment designing, result recording and result displaying.

Course Content

(weekly plan)

Week 1: An introduction to genetics (definition and history)

Week 2: Genes and genomes

Week 3: Theory of operon

Week 4: Definitions and levels of genetic engineering

Week 5: Recombinant DNA technology and genomics

Week 6: Basics of biotechnology

Week 7: Microbial, plant, and animal biotechnology

Week 8: MID-TERM EXAM WEEK

Week 9: Bioreactors

Week 10: Definition and usage of various genetic markers

Week 11: Introduction to GMO

Week 12: Introduction to gene therapy

Week 13: Introduction to cloning

Week 14: Introduction to various molecular genetic techniques (DNA extraction, PCR, DNA sequencing,

etc.)

Week 15: Introduction to various molecular genetic techniques (DNA extraction, PCR, DNA sequencing,

etc.)

Week 16: FINAL EXAM WEEK

LABORATORY CONTENT:

Week 1-11: The laboratory exercises will be based on the principle of designing an experiment

and following the results through the entire course. Since the main aim of this course is to

introduce students to genetics and bioengineering, through this lab, students will learn how to

pose a hypothesis, how to create an experiment, measure and report the results, and display them

adequately. This exercise will aid student in learning how to write a laboratory report which they

will encounter through the entire program.

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 %

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Presentation 0 % Final Exam 40 %

Total 100 %

Learning Outcomes

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

1. Recall the basics of genetics and bioengineering

2. Describe and discuss the principles of biotechnology: bacteria, animal and plants

3. Explain genome organization

4. Illustrate the use of genetic markers and gene cloning

5. Differentiate and explain methodologies used in bioengineering

6. Propose how to apply bioengineering in different fields

7. Practice laboratory work in a safe environment

8. Organize and manage an experiment and report on the results

Prerequisite Course(s)

(if any)

None

Language of Instruction English

Mandatory Literature

Nair, A. J. (2010). Introduction to Biotechnology and Genetic Engineering, 1st ed. Sudbury,

MA, USA: Infinity Science Press

Recommended Literature

Brandenberg O., et al. (2011). Introduction to Molecular Biology and Genetic Engineering.

Roma, Italy: FAO

Current scientific literature and recent research papers

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 18 18

Total Workload 129

ECTS Credit (Total Workload / 25) 5

Course Code: GBE 103 Course Name: GENERAL BIOLOGY



Course Description

This course is designed to cover the basics of biology that are needed for future studies of genetics and

bioengineering. Model organisms are usually used to study genetics, which is why students will have an

opportunity to learn about living organisms, as well as how to implement this knowledge in future

studies. The course will begin by introducing the structures of macromolecules, the basic concepts of the

cell, cell organelles, metabolism, cell cycle, inheritance and the flow of genetic information, followed by

binominal classification systems taxonomy as well as basics in ecology. This is taken concurrently with

a laboratory course.

Course Objectives


● Giving students an overview of the living world and the features of life

● Explaining the basic structure and function of cells as the basic units of all living things and as the building blocks of multicellular organisms.

● Teaching students the basics of metabolism, photosynthesis, cell cycle and the basics of inheritance.

● Introduction to the concept of biodiversity and bioethics.

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● Teaching students to use the binominal classification system which is needed throughout the

study.

● Explaining the interactions between organisms and their environments, and the consequences of these interactions in natural populations, communities, and ecosystems.

Course Content

(weekly plan)

Week 1: Introduction to general biology and molecular diversity of life

Week 2: Chemistry of Life: Water and C based molecules. The structure and function of macromolecules

- carbohydrates, proteins, lipids, nucleic acids

Week 3: The cell, cellular organelles and membrane structure

Week 4: Metabolism and Cellular respiration

Week 5: Photosynthesis: Chloroplast structure and function, photosynthetic pigments, photosystems,

excitation of chlorophyll by light, cyclic and noncyclic electron flows

Week 6: Workshop: Scientific Inquiry and scientific writing

Week 7: Cell Cycle, Mitosis and Meiosis


Week 9: Mendel and the gene idea, genotype and phenotype

Week 10: Chromosomal basis of inheritance

Week 11: Molecular basis of inheritance

Week 12: Regulation of Gene expression

Week 13: Workshop: Problem solving tasks: how genetic material can be used for species identification

Week 14: Binominal classification system. Woes and Whittaker classification (visit to the museum of

natural history)

Week 15: Introduction to evolution and introduction to ecology


LABORATORY CONTENT

Week 1: Beginning of classes

Week 2: Lab 1: Making macromolecular models

Week 3: Lab 2: Introduction to Laboratory work, laboratory glassware, safety measures

Week 4: Lab 3: Introduction to Microscopy

Week 5: Lab 4: Distinguishing cell types under the microscope, plant cell

Week 6: Lab 5: Distinguishing cell types under the microscope, animal cell

Week 7: Lab 6: Problem solving tasks: mitosis and meiosis

Week 8:MID-TERM EXAM WEEK

Week 9: Lab 7: Problem solving tasks: Mendelian genetics (autosomal inheritance)

Week 10: Lab 8: Problem solving tasks: Mendelian genetics (sex linked inheritance)

Week 11: Lab 9: Karyotype

Week 12: Lab 10: Problem solving tasks – from DNA to protein

Week 13: Preparation for lab exam

Week 14: Exam from lab course


Teaching Methods

Description

● Interactive lectures and communication with students

● Discussions and group work

● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Discriminate fundaments in the chemistry of life

2. Discriminate the basic concepts of the cell structure

3. Summarize main aspects of anabolism and catabolism

4. Explain the basic concepts of the cell cycle

5. Perform pedigree analysis

6. Use the binominal classification system

7. Summarize main concepts in evolution and ecology

8. Develop basic laboratory techniques appropriate for the field of biology

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(if any)

None


Mandatory Literature Campbell A.N., & Reece J. (2013). Biology, 10th ed. Cambridge, UK: Pearson Publishing

Recommended Literature Starr, C., Taggart, R., Evers, C., & Starr, L. (2008). Biology: The Unity and Diversity of Life, 12th ed.

Andover, Hampshire, UK: Cengage Learning











Total Workload 154


Course Code: MTH 107 Course Name: SURVEY OF CALCULUS



Course Description

Use of calculus is widespread in science, engineering, medicine, business, industry, and

many other fields. Calculus also provides important tools in understanding functions and has

led to the development of new areas of mathematics including real and complex analysis,

topology, and non-Euclidean geometry.

Course Objectives

1-To expand understanding of mathematical topics that may have been previously studied.

2-To introduce and explore topics that possibly have not been part of the student’s

mathematical experience.

3-To develop an appreciation for the development of mathematical thought.

4-To learn the application of mathematics in real life problems and analyzing the results.

Course Content

(weekly plan)

week 1 Linear Equations and Slope, Linear Models, Functions and Their

Properties

week 2 Function Composition; Graphs and Translations, Polynomial

Functions and Quadratic Models, Rational and Exponential Functions

week 3 Inverses and Logarithmic Functions, Applications of Exponential and

Logarithmic Functions

week 4 Introduction to Limits, Evaluating Limits Algebraically, Limits at

Infinity, One-Sided and Unbounded Functions, Continuity

week 5 Continuity and Applications, Rates of Change, Definition of the

Derivative

week 6 Differentiability, Graphical Differentiation, Basic Rules of

Differentiation, Product and Quotient Rules

week 7 The Chain Rule, Implicit Differentiation, Related Rates

week 8 midterm exam

week 9 Derivatives of Exponential Functions, Derivatives of Logarithmic

Functions, Increasing and Decreasing Functions

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week 10 Relative Extrema, Higher Derivatives and Concavity, Curve Sketching

week 11 Second Derivative Test; Absolute Extrema, Applications of Extrema

week 12 Differentials and Linear Approximation, Antiderivatives

week 13 Method of Substitution, Area and the Definite Integral

week 14 The Fundamental Theorem of Calculus

week 15 Area Between Curves

week 16- FINAL exam

Teaching Methods

Description

1-Lectures

2-Recitation

3-Problem solving

4-Exercises

Assessment Methods Description

(%)






Total 100 %

Learning Outcomes

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

01-recognise properties of functions and their inverses

02-recall and use properties of polynomials, rational, exponential, logarithmic, trigonometric

and inverse trigonometric functions

03-understand the terms domain and range

04-sketch graphs, using function, its first derivative, and the second derivative

05-use the algebra of limits, and l’Hôpital’s rule to determine limits of simple expressions

06-apply the procedures of differentiation accurately, including implicit and logarithmic

differentiation

07-apply the differentiation procedures to solve related rates and extreme value problems

08-obtain the linear approximations of functions and to approximate the values of functions

09-perform accurately definite and indefinite integration, using parts, substitution, inverse

substitution

10-understand and apply the procedures for integrating rational functions

11-perform accurately improper integrals 12-calculate the volumes of solid objects, the length of arcs and the surface area

13-perform polar to rectangular and rectangular to polar conversions


(if any)

None


Mandatory Literature Calculus with Applications, Eleventh (or Tenth) Edition by Lial, Greenwell and Ritchey.


Thomas's Calculus, Eleventh Edition, George B. Thomas, Pearson International Edition,

2005

Calculus a Complete Course, Sixth Edition, Robert A. Adams, Pearson Addison Wesley,

2006

Calculus with Analytic Geometry, R.A. Silverman, Prentice Hall, 1985

Calculus, R.A. Adams, Addison Wesley Longman, 2003








15




Total Workload 149


Course code: CEN 111 Course Name: PROGRAMMING I



Course Description

The course provides basic computer literacy and understanding of algorithms and

programming concepts necessary for the realm of engineering. Topics that will be covered

include algorithms, data types, constants, variables, sequences as well as searching and

sorting abstract data types, structures, pointers and strings. Students will perform

exercises in programming languages such as C, and will be graded both on the correctness

of their solutions and the design choices they make in developing their programs.

Course Objectives


✔ To introduce structured programming concept.

✔ To explain programming constructs such as sequential structures, selection

structures, and repetition structures.

✔ To introduce programming with C languages, variables, if-then-else, loop

structures: for/while/do-while, break/ continue/ switch statements, flow chart

solutions, arrays are covered.

✔ To explain the importance and usefulness of programming in genetics and

bioengineering.

✔ To develop a basic understanding of programming concepts and using these

programming concepts in C language.

Course Content

(weekly plan)

Week 1: Introduction

Week 2: Basic computer literacy.

Week 3: Fundamentals of computer programming.

Week 4: Algorithm development and problem solving using flowcharts and

pseudocodes.

Week 5: Data types.

Week 6: Constants.

Week 7: Variables.


Week 9: Basic input/output.

Week 10: Sequences.

Week 11: Selection and repetition structures.

Week 12: Functions and arrays.

Week 13: Searching and sorting, abstract data types, structures, pointers, strings,

input/output and file processing.

Week 14: Searching and sorting, abstract data types, structures, pointers, strings,

input/output and file processing.

Week 15: Preparation for final exam

16


LABORATORY CONTENT

Week 1-11: Exercising the use of programming language C

Teaching Methods

Description



● Consultations

● Laboratory work


(%)






Total 100 %

Learning Outcomes


1. Fundamental aspects of the theories, principles and practice of computing

2. Knowledge of the underlying concepts and principles associated with computing

and supporting technologies, and the ability to evaluate and interpret these

within the context of various areas of application;

3. The necessity of programming in the field of genetics and bioengineering

4. Application of theory, techniques, and relevant tools to the specification,

analysis, design, implementation, and testing of a simple computing product;

5. Evaluation basic theories, processes, and outcomes of computing


(if any)

None


Mandatory Literature Kleinberg, J., Tardos, E. (2005). Algorithm Design. Addison-Wesley: Boston, MA,

USA.

Recommended Literature Deitel, P., Deitel, H. (2012). C: How to Program, 7th ed. Prentice Hall: Upper Saddle

River, NJ, USA.











Total Workload 154


17

Course Code: ELT 117 Course Name: Advanced Reading and Vocabulary I

Level : Undergraduate Year : I Semester : I ECTS Credits : 5

Status : Compulsory Hours/Week : 2+2 Total Hours : 30+30

Course Description This course presents a wide range of authentic reading materials including newspapers, journals,

reviews and academic texts in order to comprehend contrasting viewpoints and to predict and

identify main ideas and to decode hidden clues. It also aims to equip students with intensive and

extensive reading habits. Critical thinking skills such as synthesizing information or analyzing a

problem as well as reacting on the basis of evaluation are fostered. Such sub-skills of reading are

employed by students in their short writings on the topic. Students are expected to improve their

ability to communicate the information and concepts from course reading materials continually

and to improve and expand their vocabulary significantly.

Course Objectives Students will be able to read and comprehend different types of texts. They will have also learned

to acquire new vocabulary on their own and thus to improve their reading and writing skills. In

addition to the integration of reading with writing, research-based instruction will be adopted, so

that students will develop basic research skills including library or internet search.

Course Content

(weekly plan) ● 1st TOPIC Home and the homeless - Home and Travel

● Helping and Hating the Homeless; At home

● 2nd TOPIC: HEALTH Divided Sleep, Long life, Health and medicine

● 3rd TOPIC: History The Robber Barons, The Politics of Progressivism

● Message to Wall Street

● 4th TOPIC: CLOTHING The Necktie; A Young Man and his Kilt

● 5th TOPIC: FILM STUDIES One Hundred Years of Cinema

● Mid-term exam

● A Conversation with Leo Tolstoy on Film; An Interview with James Cameron

● 6th TOPIC: MEDIA STUDY Mind Control and the Internet

● The press and the media; The Use of Social Media in the Arab Spring

● 7th TOPIC: GREAT MINDS The Right-Brain, Left-Brain Controversy

● Artists as Scientists and Entrepreneurs

● 8th TOPIC: THE BRAIN AND MEMORY In Search of Memory

● The Brain and Human Memory Music and the Brain;

● 9TH TOPIC: LEISURE The Art of Paintball

● Final exam Teaching Methods

Description

(list up to 4 methods)

● Reading passages in the classroom.

● Comprehension studies on what is read.

● Vocabulary exercises by topic and short writing assignments on that topic (both in-class and homework assignments).

Assessment Methods

Description (%)






Total 100 %

18

Learning Outcomes

(please write 5-8 outcomes)


1. Read a variety of texts by using a range of strategies, including decoding and guessing

meaning in unfamiliar texts

2. Analyze extensive reading materials with sufficient comprehension to explain and discuss

critical-thinking elements such as author tone, viewpoint, purpose, presumptions and

underlying beliefs, character motivations, text connections to students’ personal lives, and

logical evaluation of text arguments

3. Recognize sentence and paragraph structures

4. Make logical inferences based on materials read and explain them orally and in writing.

5. Acquire sufficient college-level vocabulary to comprehend the texts and use this

vocabulary in student writing and speaking assignments.


(if any)


Mandatory Literature ● Rober F. Cohen and Judy L. Miller. Longman Academic Reading Series 4: Reading Skills for College (LARS). Pearson Education. 2014. (Chapters 1-5)

● Fellag Linda Robinson. From Reading to Writing Level 3. Pearson Education

(FRTW). 2010. (Units 1-4)

● Michael McCarthy and Felicity O’Dell. English Vocabulary in Use. Cambridge University Press (EVIU). 2001

Recommended Literature ● Mikulecky Beatrice S, and Jeffries Linda. Reading Power Series, Pearson ESL, March 2007.










Seminar / Presentation

Total Workload 125


Course Code: BOS 101 Course Name: BOSNIAN/CROATIAN/SERBIAN LANGUAGE I


Status: Elective Hours/Week: 0+2 Total Hours: 0+30

Course Description The purpose of this course is to teach Bosnian language basics at the beginner level.

Course Objectives

Highly personalized course designed to improve knowledge of Bosnian language and

communication and language skills. The objective is to achieve the level of language that

would create confidence to communicate in Bosnian with clients, suppliers and colleagues.

Course Content

(weekly plan)

● Learn how to say „Hello“ and acquaint; the classes of nouns (muški, ženski, srednji rod)

● Personal pronouns (in the first case), introducing oneself: I'm from ...; practicing

personal pronouns by answering the questions Where are you from? Where is

he/she from? Where are they from? Introducing verb to be by questions: Are you

from...? Is he from...?

● Present tense of verb to be (positive, negative and question form); Answering the question „What's your job?“; learning some of names of different jobs and male

and female form for that kind of nouns

● Terminology about the faculty, exercise with cross-words; numbers 1-10 with little

short song about the numbers; first information about plural

● Numbers 11-10.000; speaking exercise about numbers by phone number, prices; demonstrative pronouns

● Introducing the collocations about the speaker's attitude about the contents of

sentence and speaking on the scale from extremely kind to extremely unkind;

declarative, interrogative and exclamatory sentences

19

● Place and sort of accent in Bosnian words; filling out the forms with basic

information (name, surname, date and place of birth...)

● Introducing the question-word (what, where, when...); ordinal numbers and classes of adjectives (muški, ženski, srednji rod)

● Answering on questions What date is...? When it happened? and exercise for

ordinal numbers

● SVO order in Bosnian language, order in declarative and interrogative sentences

Teaching Methods

Description

● Interactive lectures and communications with students

● Discussions and group works

● Presentations


(%)






Total 100 %

Learning Outcomes


1. Speak Bosnian with confidence

2. Interact more confidently when visiting a Bosnian-speaking region or dealing with

Bosnian speakers

3. Build rapport and strengthen relationships with Bosnian-speaking colleagues and

clients through a show of interest in the Bosnian language and culture

4. Demonstrate goodwill and facilitate international communication at both a personal

and organizational level.


(if any)

None

Language of Instruction Bosnian and English

Mandatory Literature Zenaida Karavdić, Bosnian language as a foreign language, IBU, Sarajevo 2010.

Bosanski jezik, Priručnik za strance, Minela Kerla, Nermina Alihodžić-Usejnovski,2013.

Recommended Literature Ronelle Alexander, Ellen Elias-Bursac Bosnian, Croatian, Serbian, a Textbook: With

Exercises and Basic Grammar, University of Wisconsin Press, 2006









1 14 1 14

Seminar / Presentation 1 4 4

Total Workload 50


Course Code: TDE 101 Course Name: TURKISH LANGUAGE I



http://www.amazon.com/exec/obidos/search-handle-url/ref=ntt_athr_dp_sr_2?_encoding=UTF8&search-type=ss&index=books&field-author=Ellen%20Elias-Bursac

20

Course Description

This course is offered to all students entering their first year of genetics and bioengineering

studies. It is taught in Turkish, and it covers basic grammatical rules and focuses on practicing

everyday use of the language. This is the first part of a two-part series that is taught during the

first year. The second part will be taught in the following semester.

Course Objectives


✔ To learn Vocabulary and Grammar.

✔ To use Turkish in everyday life.

✔ To speak, understand, read and write basic Turkish

Teaching Methods

Description

● Interactive lectures and communication with students.

● Discussions and group work.







Total 100 %

Learning Outcomes


1. Basic vocabulary and grammar

2. Communication in Turkish

3. Reading articles in Turkish

4. Writing articles in Turkish

5. Use of Turkish in everyday life situations


(if any)

None

Language of Instruction Turkish

Mandatory Literature Lewis, G. (2001). Turkish Grammar. Oxford University Press: Oxford, UK.

Recommended Literature Dogan, B. O., Wilman, A. (2007). Starting Turkish. Milet Publishing: London, UK.











Total Workload 50


21

Course Code: GRM 101 Course Name: GERMAN LANGUAGE I

Level: Undergraduate Year: 1 Semester: I ECTS Credits: 2


Course Description

Basic communication; structures and vocabulary necessary to comprehend simple daily

conversational dialogues and reading texts, and to engage in daily simple communication; information

about the culture of the target language.

Course Objectives

These courses emphasize the use of the target language for active communication. They have the

following objectives:

● the comprehension of formal and informal spoken language;

● the acquisition of vocabulary and a grasp of language structure to allow for the accurate

reading of newspaper and magazine articles as well as modern literature;

● the ability to compose expository passages;

22

● the ability to express ideas orally with accuracy and fluency. Students will also learn valuable

test-taking strategies and self-evaluative skills.

Course Content

(weekly plan)

All Foreign courses improve grammar, speaking, listening and reading and writing skills. The highly-

trained and experienced staff use a wide range of learning materials and methods, including audio-

visual and ICT. All learners have an initial assessment and interview with a member of staff to

establish their level of that particular foreign language. To ensure maximum progress, this is followed

by an on-course diagnostic assessment to determine more precisely the specific language skills needed

by each learner. The class tutor and learner then agree an individual learning plan to record the

learner’s progress.

Teaching Methods

Description




● Presentations (at least 1 per student per semester)

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


Upon successful completion of the courses in this discipline, the student will have acquired the

following knowledge and skills:

1. Demonstrate the confidence and listening/speaking skills necessary to participate

successfully in spontaneous aural/oral exchanges with native speakers of those particular

languages.

2. Demonstrate reading comprehension of foreign language texts intended for developmental

(or higher level) foreign language courses.

3. Respond appropriately to written or spoken foreign language by writing paragraphs or short

essays that communicate ideas clearly.


(if any) -



● Schritte plus 2 Audio-CD zumArbeitsbuchmitinteraktivenÜbungen, Monika Bovermann,

Daniela Niebisch, Franz Specht, Sylvette Penning-Hiemstra

● Swick, Edward. The Everything Learning German Book: Speak, Write and Understand

Basic German in No Time, Adams Media; 1st edition, 2003.

Recommended Literature /











Total Workload 50

23


SECOND SEMESTER

Course Code: GBE 102 Course Name: CELL BIOLOGY

Level: Undergraduate Year: I Semester: II ECTS Credits: 5


Course Description

The course Cell Biology is designed to give students a general overview of the complexity of the

organism from atom to organisms. Through this course students will comprehend the molecular

basis of life from the chemical composition of the cell and its components to the complexity of

the joining of cells into tissues. The course is focused on the molecular mechanisms witin the cell

and it's ultra structure and function.

Course Objectives


● Making a detailed study on chemical components of cells.

● Introduction to the basics of energy, catalysis, and biosynthesis.

● Illustrating the structure and function of the plasma membrane and cytoskeleton.

● Explaining the structure and function of mitochondrion and chloroplast.

● Studying proteins and DNA.

● Teaching the cell's interaction with its environment and cytoplasmic membrane systems.

● Illustrating basic microscopy of different cell types.

24

Course Content

(weekly plan)

Week 1: Syllabus presentation

Week 2: Cells: the fundamental units of life

Week 3: The use of energy by cells; The shape and structure of proteins

Week 4: DNA and chromosomes

Week 5: DNA replication, repair and recombination

Week 6: From DNA to protein: How cells read the genome

Week 7: Membrane structure


Week 9: Transport across cell membranes

Week 10: Intracellular compartments and protein transport

Week 11: Cytoskeleton

Week 12: Cell division

Week 13: Sexual reproduction and the power of genetics

Week 14: Cell communities

Week 15: Cancer


LABORATORY CONTENT


Week 2, Lab 1: Introduction to the lab course; laboratory rules of conduct

Week 3, Lab 2: Types of living cells (microscopy)

Week 4, Lab 3: Osmosis and diffusion (microscopy)

Week 5, Lab 4: Analysis of plasma membrane stability

Week 6, Lab 5: Isolation of chloroplast

Week 7, Lab 6: Isolation of tyrosinase and enzyme detection


Week 9, Lab 7: Qualitative analysis of biomolecules

Week 10 Lab 8: Human karyotype

Week 11, Lab 9: Barr body (microscopy)

Week 12, Lab 10: Observation of mitosis in onion root tip cells

Week 13, Lab 11: DNA isolation from banana

Week 14: Recap



Teaching Methods

Description



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Show the basic structure of the cell

2. Recognize molecular mechanisms in the cell

3. Interpret cell metabolism

4. Memorize cell cycle, mitosis and meiosis

5. Identify distinction between prokaryotic and eukaryotic cells

6. Illustrate the structure of plant cells in leaf, stem and root

7. Explain the structure of animal cells through the study of human blood cells

8. Describe basic cytogenetics and human karyotype


(if any)

None


25


Alberts, B., Bray, D., Hopkin, K., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P.

(2014). Essential Cell Biology, 5th ed. New York, NY, USA: Garland Science

Recommended Literature Cooper, G.M., & Hausman, R.E. (2009). The Cell: A Molecular Approach, 5th ed. Stamford, CN:

Sinauer Associates, Inc.











Total Workload 127


Course Code: GBE 108 Course Name: GENERAL CHEMISTRY



Course Description

The aim of this course is to introduce the students to basic general chemistry principles and to

prepare them for further advanced chemistry, material science, practical, environmental, and

electronics courses so that they will be able to follow concepts related to the chemistry of

elements, atomic structure, electron configuration and periodicity, ionic and covalent bonding,

molecular geometry and chemical bonding theory, chemical stoichiometry, the gaseous state,

liquids and solids, acids and bases. The course will cover descriptive chemistry, elements and

compounds, basic chemical calculations, mole problems, stoichiometry and solution

concentrations, gas laws, thermochemistry, quantum theory and electronic structure of atoms,

periodic properties of the elements, nuclear chemistry, and chemical bonding. This is taken

concurrently with a laboratory course.

Course Objectives


● Introduction to the basic concepts of chemistry.

● Preparing students for other advanced chemistry courses, material science, practical, environmental, and electronics courses.

● Enabling students to follow subjects related to the chemistry of elements, liquid and solid

state, and spectroscopy.

Course Content

(weekly plan)


Week 2: Basic terms and expressions

Week 3: Metric units in chemistry

Week 4: Atomic and molecular masses

Week 5: Matter and the composition of matter (atoms, elements and PSE, molecules and compounds)

Week 6: Basic calculations in chemistry

Week 7: Appearance of matter (aggregate state and phases, gases, liquids and solutions, solids)


Week 9: Chemical reactions and chemical equilibrium

Week 10: Acids and bases

Week 11: pH

Week 12: Complexes

Week 13: Electrochemistry

Week 14: Thermodynamic considerations

Week 15: Kinetic consideration and stoichiometry

26


LABORATORY CONTENT


Week 2, Lab 1: Lab safety

Week 3, Lab 2: Atomic structure and electron configurations

Week 4, Lab 3: Naming inorganic compounds; Molecular mass calculation and percent composition

Week 5, Lab 4: Amount of substance and concentrations

Week 6, Lab 5: Reactions of Group I and Group II cations; Basic lab equipment

Week 7, Lab 6: Reactions of cations Groups III, IV and V


Week 9, Lab 7: pH value: Calculations and experimental determination

Week 10 Lab 8: Buffer capacity

Week 11, Lab 9: Determining HCl concentration: Acid-base titration

Week 12, Lab 10: Separation of photosynthetic pigments from higher plants by paper chromatography

Week 13, Lab 11: Determination of iron content in green vitriol

Week 14: Preparation for practical exam

Week 15: Practical exam from lab course


Teaching Methods

Description



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Name the units used in chemistry

2. Describe atomic and molecular structures

3. Recall chemical reactions

4. Clarify electrochemistry

5. Describe stoichiometry

6. Grasp skills needed in the chemistry lab

7. Apply basic calculations needed for more advanced courses: preparing molar, percent

solutions, etc.


(if any)

None



Petrucci, R. H., Harwood, W. S., & Herring, F. G. (2007). General Chemistry: Principles and

Modern Applications, 9th ed. Upper Saddle River, NY, USA: Prentice Hall

Recommended Literature Whitten K., Davis R., Peck L., & Stanley G. (2010). General Chemistry, 7th ed. California, USA:

Brooks/Cole.









27



Total Workload 149


Course Code: GBE 106 Course Name: EVOLUTION AND SYSTEMATICS



Course Description

The process of evolution generated the diversity of life on Earth today and in the geological past. The

course gives an overview of evolutionary forces and how they affected life from its beginnings to the

diversity we have today. Further on this course aims to generate a comprehensive review of the

diversity of life on earth through the domains: bacteria, archaea and eukarya. Fortunately, the structure

of this extraordinary diversity, generated by the process of evolution, can be discovered using the

methods of systematics. Systematics, therefore, provides a way to organize the diversity surrounding

us, and make sense of it in an evolutionary framework.

Course Objectives


● Introduction to genomes an their evolution

● Explaining the concept of descendants with modification.

● Providing basic concepts of evolution of populations

● Describing how life began on earth.

● Teaching the tree of life and basics of phylogeny

● Explaining diversity of single cell organisms

● Giving an overview of plant diversity

● Giving an overview of the diversity of invertebrates and vertebrates

● Providing basic information about human evolution

Course Content

(weekly plan)

Week 1: Introduction to the course

Week 2: Genomes and their evolution

Week 3: Descendant with modification

Week 4: The evolution of populations

Week 5: The origin of species

Week 6: History of Life on Earth

Week 7: Workshop


Week 9: Phylogeny and the tree of life

Week 10: Bacteria, Archaea, Protista

Week 11: Plant Diversity

Week 12: Into to Animal diversity

Week 13: Invertebrates

Week 14: Vertebrates

Week 15: Evolution of behavior


LABORATORY CONTENTS:

Lab 1-10 – A series of worksheet and practical exercises designed to understand the fundaments of evolution,

systematics and diversity.

Teaching Methods

Description



● Presentations

Laboratory work


28

Assessment Methods

Description (%)





Total 100 %

Learning Outcomes

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

1. Recall the basics of life on earth beginnings

2. Comprehend the concept of descendant with modifications

3. Identify the basic concepts of evolution

4. Design and set up experiments in a bioethical manner

5. Understand the concept of diversity


(if any)

None


Mandatory Literature Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., & Reece, J. B. (2017). Campbell biology. Pearson Education, Incorporated.












Total Workload 149


Course Code: PHY 104 Course Name: GENERAL PHYSICS



Course Description

This course offers modules of general physics which allows students to acquire practical and

useful basic knowledge in this field. Topics include introduction to thermodynamics, fluids,

kinetic theory of gases, relativity, atoms and etc.. Students will solve problems through example

exercises. This is taken concurrently with a laboratory course.

Course Objectives


● Learn the basic principles in thermodynamics

● Comprehend the basic principles in electromagnetism

● Learn the basic principles in atomic and nuclear physics

● Understand the importance of physics that are necessary for the further courses in the curriculum

Course Content

(weekly plan)

Week 1: Introduction to course

Week 2: Fluids and pressure

Week 3: Temperature and heat

Week 4: The First Law of Thermodynamics

Week 5: The Second Law of Thermodynamics and entropy

29

Week 6: Kinetic Theory of Gasses

Week 7: Preparation for the Midterm Exam (Quiz 1)


Week 9: Coulomb's Law

Week 10: Electric Fields

Week 11: Electrical Circuits

Week 12: Electromagnetic Oscillations and Alternating Current

Week 13: Relativity, Photons, and Matter

Week 14: Atoms and nuclear physics

Week 15: Preparation for the Final Exam (Quiz 2)


LABORATORY CONTENT

Lab 1: Fluids

Lab 2: Pressure

Lab 3: Temperature and heat

Lab 4: The First Law of Thermodynamics

Lab 5: The Second Law of Thermodynamics

Lab 6: Entropy

Lab 7: The Kinetic Theory of Gasses


Lab 9: Coulomb's Law,

Lab 10: Electric Fields

Lab 11: Electrical Circuits

Lab 12: Electrical circuits – Laws

Lab 13: Relativity, Photons, and Matter

Lab 14: Atoms and nuclear physics

Lab 15: Overview


Teaching Methods

Description

● Lectures

● Practical Sessions

● Exercises

● Presentations







Total 100 %

Learning Outcomes


1. Comprehend the basic principles in electromagnetism and thermodynamics

2. Learn the basic principles in atomic and nuclear physics

3. Perceive physics as a crucial filed for the further development of genetics and

bioengineering

4. Understand the basic principle of physics that are crucial for the living organism


(if any)

None


Mandatory Literature Halliday, D., Resnick, R., & Walker, J. (2014). Fundamentals of physics extended, 10th ed. John

Wiley & Sons.


Giancoli, D.C. (2000). Physics for scientist and engineers. New Jersey, NJ, USA: Prentice Hall.

Bueche, F.J. & Hecht, E. (2008). Theory and problems of College Physics, 9th ed. McGraw-Hill

Companies.


30










Total Workload 149


Course Code: GBE 105 Course Name: HISTOLOGY AND EMBRYOLOGY



Course Description

This course provides a broad overview of cellular composition, their integration into tissues, all

tissue type structures, their integration into organs. It provides students an introduction to tissue

and organ structure and function. The first part of the course focuses on main tissue types:

epidermis, connective tissue, muscle and nervous tissue. The second part of the course focus on

major organ systems including: circulatory system, lymphoid system, digestive system,

respiratory system, urogenital system, endocrine system, sensory system. The third part of the

course focuses on the basics of human embryology and the development of a zygote into an

entire organism.

Course Objectives


● Providing a theoretical and applied knowledge in the field of histology and embriology

● Comprehending the cellular components of various tissue types

● Understanding the metabolism of cells within various tissue

● Learning normal normal tissue composition within various organs

● Providing a basis for understanding pathological findings

● Learning to recognize various tissue types and organs on histological slides

● Providing basic embryological knowledge

Course Content

(weekly plan)

Week 1: Introduction to the methods of study in histology

Week 2: Epithilium

Week 3: Connective tissue: general features and adipose tissue

Week 4: Connective tissue: cartilage and bone

Week 5: Muscle tissue

Week 6: Nerve tissue

Week 7: Blood, Hematopoiesis and Immune System


Week 9: Lymphoid system

Week 10: Digestive System

Week 11: Glands associated with the digestive system and Respiratory System

Week 12: Skin and Urinary System

Week 13: Endocrine system

Week 14: Male and female reproductive systems

Week 15: Sensory organs


31

LABORATORY CONTENT

Lab 1: Epithilium

Lab 2: Connective tissue: general features and adipose tissue

Lab 3: Connective tissue: cartilage and bone

Lab 4: Muscle tissue

Lab 5: Nerve tissue Circulatory system, blood, hematopoiesis

Lab 6: Blood, Hematopoiesis and Immune System


Lab 7: Lymphoid system

Lab 8: Digestive System Urinary system

Lab 9: Glands associated with the digestive system and Respiratory System

Lab 10: Skin and Urinary System

Lab 11: Endocrine system

Lab 12: Male and female reproductive systems

Lab 13: Sensory organs


Teaching Methods

Description

● Lectures

● Practical Sessions

● Exercises

● Presentations


Quiz 0% Lab/Practical Exam 20 %





Total 100 %

Learning Outcomes


1. Understand the cellular composition of tissues

2. Distinguish histological slides

3. Know the basic cellular and tissue composition of organs

4. Comprehend basics of embryological development from zygote to organism

5. Learn basic concepts of various cell type functions and metabolism within tissues and organs

6. Understand the integration of cells into tissues, organs and organ systems


(if any)

None


Mandatory Literature Junqueira, L. C., & Carneiro, J. (2005). Basic histology text and atlas, 11th ed. London, UK:

McGraw Hill.

Recommended Literature Sadler, T. W. (2011). Langman's medical embryology, 12th ed. Philadelphia, Pennsylvania, USA:

Lippincott Williams & Wilkins.











32

Total Workload 127


Course Code: BOS 102 Course Name: BOSNIAN/CROATIAN/SERBIAN LANGUAGE II



Course Description

The Bosnian course adopts a multi-level methodology that integrates the skills of reading,

writing, listening, grammar, vocabulary and conversation. These skills are reinforced at all levels

and Bosnian is the only teaching language used in the class, except when it is necessary to

facilitate the explanation of a grammar rule or lexical phrase to a beginner.

Course Objectives

The Bosnian Course seeks to develop in the students the basic linguistic skills, analytical skills,

and cultural and literary knowledge which will enable them to appreciate the uniqueness of other

cultures and to function in Bosnian speaking communities around the world.

Course Content

(weekly plan)

● Three ways of forming present tense in Bosnian language and recognizing what way will

be used with what verb; making simple sentences with verb in present tense

● Collocations to express doubt, uncertainty or ignorance about something

● Collocations to ask about the way and where to find something; adverbs left, right,

straight, back; Genitive and some of its use (with prepositions iz, od, do)

● Collocations about the Post office and Bank; Accusative and some of its use (object in sentence, with prepositions za, na)

● Collocations about the weather; formal/informal communications; present tense of verb

to have

● Conversation in restaurant; meeting with Bosnian meals and names for different kind of food (fruit, vegetable, meat, other); present tense of verb to have

● Present tense and use of verbs to buy, to sit, to tell; future tense compared with present

tense

● Conversation in clothing store; clothes and words related to it (colors, size...); imperative

● Comparison of adjectives, phonetic rule jotovanje

● Conversation about health and parts of body (with four-way cross-words)

Teaching Methods

Description

● Interactive lectures


● Project, Presentations







Total 100 %

Learning Outcomes


1. Understand Bosnian language

2. Communicate in basic Bosnian language

3. Appreciate and know a little about Bosnian culture.


(if any) Bosnian Language I

Language of Instruction Bosnian and English

Mandatory Literature Zenaida Karavdić, Bosnian language as a foreign language, IBU, Sarajevo 2010.

Bosanski jezik, Priručnik za strance, Minela Kerla, Nermina Alihodžić-Usejnovski,2013.

33

Recommended Literature Ronelle Alexander, Ellen Elias-Bursac Bosnian, Croatian, Serbian, a Textbook: With Exercises

and Basic Grammar, University of Wisconsin Press, 2006









Assignment / Homework / Project 14 1 1


Total Workload 50


Course Code: TDE 102 Course Name: TURKISH LANGUAGE II



Course Description

This is the second part of a two-part course series offered at the university. It builds upon the

concepts that students acquired in the previous semester as the course covers basic grammatical

rules and focuses on practicing everyday use of the language. Just like the first part of this series,

this course is also offered to all students.

Course Objectives


✔ After completion of the course students will be able to speak, understand, read and write

more advanced Turkish.

✔ Enable the student to use Turkish in everyday life situations

Teaching Methods

Description

● Interactive lectures and communication

with students







Total 100 %

Learning Outcomes


1. Start using Turkish language

2. Be able to communicate in Turkish

3. Read articles in Turkish

4. Write articles in Turkish

5. Grammar basics


(if any) Turkish Language I

Language of Instruction Turkish

Mandatory Literature Ozturk, T., et al. (2004). Gökkuşağı Türkçe Ders Kitabı 1. Cilt. Dilset Yayınları: Istanbul,

Turkey.

http://www.amazon.com/exec/obidos/search-handle-url/ref=ntt_athr_dp_sr_2?_encoding=UTF8&search-type=ss&index=books&field-author=Ellen%20Elias-Bursac

34

Ozturk, T., et al. (2004). Gökkuşağı Türkçe Çalışma Kitabı 1.Cilt. Dilset Yayınları: Istanbul,

Turkey.

Ozturk, T., et al. (2005). Gökkuşağı Türkçe Dilbigisi Kitabı 1. Cilt. Dilset Yayınları: Istanbul,

Turkey

Ozturk, T., et al. (2005). Gökkuşağı Türkçe Ders Kitabı 2. Cilt. Dilset Yayınları: Istanbul,

Turkey.

Ozturk, T., et al. (2005). Gökkuşağı Türkçe Çalışma Kitabı 2. Cilt. Dilset Yayınları: Istanbul,

Turkey.

Ozturk, T., et al. (2005). Gökkuşağı Türkçe Dilbigisi Kitabı 2. Cilt. Dilset Yayınları: Istanbul,

Turkey.












Total Workload 50


35

Course Code: GRM 102 Course Name: GERMAN LANGUAGE II

Level: Undergraduate Year: 1 Semester: II ECTS Credits: 2


Course Description

This is a continuation of Second Foreign Language I course. Interactive communication; grammatical

structures and vocabulary commonly used in newspapers, magazines, extended dialogues, readings

texts, and short stories; information about the culture of the target language through authentic

materials.

Course Objectives

These courses emphasize the use of the target language for active communication. They have the

following objectives:

● the comprehension of formal and informal spoken language;

● the acquisition of vocabulary and a grasp of language structure to allow for the accurate

reading of newspaper and magazine articles as well as modern literature;

● the ability to compose expository passages;

● the ability to express ideas orally with accuracy and fluency. Students will also learn valuable

test-taking strategies and self-evaluative skills.

Course Content

(weekly plan)

All Foreign courses improve grammar, speaking, listening and reading and writing skills. The highly-

trained and experienced staff use a wide range of learning materials and methods, including audio-

visual and ICT. All learners have an initial assessment and interview with a member of staff to

establish their level of that particular foreign language. To ensure maximum progress, this is followed

by an on-course diagnostic assessment to determine more precisely the specific language skills needed

by each learner. The class tutor and learner then agree an individual learning plan to record the

learner’s progress.

Teaching Methods

Description




● Presentations (at least 1 per student per semester)

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


Upon successful completion of the courses in this discipline, the student will have acquired the

following knowledge and skills:

1. Demonstrate the confidence and listening/speaking skills necessary to participate successfully in

spontaneous aural/oral exchanges with native speakers of those particular languages.

2. Demonstrate reading comprehension of foreign language texts intended for developmental (or

higher level) foreign language courses.

3. Respond appropriately to written or spoken foreign language by writing paragraphs or short

essays that communicate ideas clearly.

Prerequisite Course(s) -

36

(if any)



● Schritte plus 2 Audio-CD zumArbeitsbuchmitinteraktivenÜbungen, Monika Bovermann,

Daniela Niebisch, Franz Specht, Sylvette Penning-Hiemstra

● Swick, Edward. The Everything Learning German Book: Speak, Write and Understand

Basic German in No Time, Adams Media; 1st edition, 2003.


/











Total Workload 50


37

THIRD SEMESTER

Course Code: GBE 201 Course Name: GENETICS

Level: Undergraduate Year: II Semester: III ECTS Credits: 5


Course Description

This course is an overall examination of the basic principles of genetics in prokaryotes and eukaryotes at the

levels of molecules, organelles, cells, as well as multicellular organisms. Topics include Mendelian and non-

Mendelian inheritance, structure and function of chromosomes, biological variation resulting from

recombination and mutation, extranuclear inheritance, cancer genetics, and population genetics. In addition,

the course is covering an introduction to genomics, proteomics and genetic engineering (new technologies).

This is taken concurrently with a laboratory course.

Course Objectives


● Helping students become familiar with the language of genetics.

● Providing students with a strong background in the principles of Mendelian, non-Mendelian, and extranuclear models of inheritance and enabling them to use this knowledge to track alleles through

generations, to categorize and predict genotypes and phenotypes.

● Detailing new technologies of genomics, proteomics and other -omics techniques.

● Explaining the Hardy-Weinberg equilibrium and the requirements for maintaining Hardy-Weinberg equilibrium in a population.

● Connecting genetics with classical science when necessary (e.g., molecular biology and cell biology).

Course Content

(weekly plan)

Week 1: Genes, genomes and genetic analysis

Week 2: DNA structure and genetic variation

Week 3: Transmission genetics, part I

Week 4: Transmission genetics, part II

Week 5: Chromosomes and sex-chromosome inheritance

Week 6: Genetic linkage and mapping

Week 7: Inheritance and mapping practice


Week 9: Human karyotype and chromosome behavior

Week 10: Genetics of bacteria and their viruses

Week 11: Genomics, proteomics and genetic engineering

Week 12: Molecular genetics of the cell cycle and cancer

Week 13: Mitochondrial DNA and extranuclear inheritance

Week 14: Introduction to population genetics

Week 15: Recap


LABORATORY CONTENT


Week 2, Lab 1: Overview of Mendelian genetics – genetic crosses, part I

Week 3, Lab 2: Overview of Mendelian genetics – genetic crosses, part II

Week 4, Lab 3: Non-Mendelian genetics

Week 5, Lab 4: Probability in transmission genetics

Week 6, Lab 5: Probability in the prediction of progeny distributions

Week 7, Lab 6: Genetic linkage and mapping


Week 9, Lab 7: Chi-square test

Week 10 Lab 8: DNA isolation: plasmid from bacterial cells (boiling method)

Week 11, Lab 9: DNA isolation: plant sample (CTAB method)

Week 12, Lab 10: DNA isolation: spider legs (Chelex method)

Week 13, Lab 11: Agarose gel electrophoresis

Week 14: Preparation for lab test

Week 15: Lab test


Teaching Methods

Description



● Presentations

38

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Recall genetics terminology: homozygous, heterozygous, phenotype, genotype, homologous

chromosome pair, etc.

2. Manage Mendelian genetics calculations

3. Assess non-Mendelian genetics

4. Critically discuss extranuclear inheritance

5. Interpret genetic mapping

6. Predict the genotype of bacterial and viral cells in question

7. Explain novel genomic and proteomic techniques, especially in relation to recombinant DNA

technology


(if any) None


Mandatory Literature Hartl, D. L. & Jones, E.W. (2009). Genetics: Analysis of Genes and Genomes, 7th ed. Sudbury, MA: Jones &

Bartlett Publishers.

Recommended

Literature

Hartl, D.L. (2020). Essential Genetics and Genomics, 7th ed. Burlington, MA: Jones & Barlett Learning.










Total Workload 123


Course Code: GBE 211 Course Name: ORGANIC CHEMISTRY



Course Description

Organic chemistry with all different classes of compounds (hydrocarbons, alcohols, amines, carboxylic acids

etc.) is presented through the main chemical reactions of each class of organic compounds. The course

revolves around shared features and unifying concepts and it emphasizes principles that can be repeatedly

applied. Learning on this way, students will see that organic chemistry is integral to biology as well as to

their daily lives.

39

Course Objectives


● To introduce students to organic chemistry.

● To teach about the application to scientific and commercial fields.

● To understand the basics of organic chemistry needed for further studies.

● To learn to use the nomenclature for organic compounds.

● To learn the basic structures of organic molecules.

● To teach about the application to scientific and commercial fields.

● To understand the basics of organic chemistry needed for further studies.

● To learn the basic structures of organic molecules.

Course Content

(weekly plan)


Week 2: Electronic structure and covalent bonding

Week 3: Acids and bases

Week 4: Nomenclature, physical properties and structures of organic compounds

Week 5: Alkenes and alkynes

Week 6: Isomers and physical properties

Week 7: Benzene and its derivatives

Week 8: MIDTERM WEEK

Week 9: Delocalized electrons, UV/Vis Spectroscopy

Week 10: Carbonyl compounds Week 11: The organic chemistry of carbohydrates

Week 12: The organic chemistry of amino acids, peptides, proteins

Week 13: The organic chemistry of enzymes and vitamins

Week 14: The organic chemistry of metabolic pathways

Week 15: The organic chemistry of lipids and nucleic acids


Week 1-15 A series of laboratory and practical exercises

Teaching Methods

Description



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Interpret and use nomenclature of organic compounds

2. Recall chemical reactions in organic chemistry

3. Define and explain basic knowledge on alkanes, alkenes and alkynes

4. Interpret and apply knowledge related to alcohols, ethers, epoxides

5. Recognize the specific properties of benzene and its derivatives

6. Summarize fundamentals of organic chemistry of macromolecules

7. Design and manage a lab experiment in organic chemistry


(if any) None


Mandatory Literature Bruice, P.Y. (2009). Essential organic chemistry, 2nd ed. New York City, NY, USA: Pearson

Education

Recommended Literature McMurry, J. (2012). Organic Chemistry, 8th ed. California, USA: Brooks/Cole.



40









Total Workload 149


Course Code: GBE 217 Course Name: MICROBIOLOGY



Course Description

This course is aimed at providing students with an introduction to microbiology. Students will become

familiar with history and scope, microbial structure and function, nutrition, growth, control of

microorganisms by physical and chemical agents, and the scientific, agronomic, pharmaceutical, and

medical applications of microorganisms. Furthermore, students will gain a sound introduction to diversity

of the microbial world, microbial taxonomy, proteobacteria, high and low GC gram-positives, and archaea.

Furthermore, experimental design and manipulation with microorganisms, their analysis and applications

will be covered. This is taken concurrently with a laboratory course.

Course Objectives


● Introduction to diversity of the microbial world,

● Understand the basics of microbial taxonomy, proteobacteria, archaea.

● Do experimental design and manipulation with microorganisms,

● Conduct microbial analysis and understand their possible application.

Course Content

(weekly plan)


Week 2: History and development of microbiology

Week 3: Functional anatomy of bacteria and bacterial staining techniques

Week 4: Bacterial Metabolism

Week 5: Microbial Growth

Week 6: Control of Microbial Growth and Antibiotics

Week 7: Workshop on using CLSI and EUCAST guidelines for determination of bacterial sensitivity towards

antibiotics

Week 8: MIDTERM EXAM WEEK

Week 9: Genetics of bacteria & biotechnology

Week 10: Bacterial classification

Week 11: Workshop on bacterial identification using biochemical tests and molecular diagnostics

Week 12: Bacterial families– general features of species

Week 13: Bacterial families– general features of species

Week 14: General features of eukaryotes studied in microbiology

Week 15: Basics of Virology


LABORATORY CONTENT

Week 1, Beginning of classes

Week 2, Lab 1: Flow of material in microbiological laboratory, sterilization and disinfection

Week 3, Lab 2: Bacterial Staining Techniques

Week 4, Lab 3: Media Preparation

Week 5, Lab 4: Bacterial Growth Curve

Week 6, Lab 5: Disk diffusion bauer Kirby Method of antibiotic testing

Week 7, Lab 6: MIC determination


Week 9, Lab 7: Species identification in different samples

Week 10 Lab 8: Normal flora testing: thorat and nose swabs

41

Week 11, Lab 9: Enterobacteriaceae, urine analysis

Week 12, Lab 10: Integration of all testing procedures in bacteriology

Week 13, Lab 11: Preparation for practical exam

Week 14, Preparation for practical exam

Week 15, Practical Exam from Lab Course


Teaching Methods

Description



● Presentations

● Guest instructors

● Research projects

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Working knowledge of basic bacterial laboratory techniques, as well as to the foundations of

Microbiology - the concepts of classification, evolution and growth of microorganisms, as well as

a factual and laboratory knowledge of specific microorganism types.

2. Understanding of microbial ecology and practical uses for microorganisms, as well as how they

relate to basic biological concepts.

3. Establish a firm foundation for future Microbiology courses and/or a good appreciation of

concepts needed to make reasoned choices in their everyday lives.

4. In general, they should understand how microorganisms survive where they do, how they are

related, and how they interact with us.

5. In the laboratory they should acquire basic bacteriological skills and should be able to successfully

use them.


(if any) None


Mandatory Literature Tortora, G. J., Funke, B. R., Case, C. L., & Johnson, T. R. (2004). Microbiology: an introduction (Vol. 9).

San Francisco, CA: Benjamin Cummings.


Willey, J., Sherwood L., & Woolverton C. (2008). Microbiology, 7th ed. New York City, NY, USA:

McGraw-Hill Science.Harvey R., Cornelissen C., & Fisher, B. (2012). Microbiology, 3rd ed.

Philadelphia, PA, USA: Lippincott Williams & Wilkins.











Total Workload 100


42

Course Code: GBE 219 Course Name: MOLECULAR BIOLOGY I



Course Description

Molecular Biology I offers students an introduction to the basic principles of DNA, RNA, and

proteins, as well as replication, transcription and translation. The course covers the topics on

small molecules, macromolecules (structure, shape, and information), energy and

biosynthesis, protein function, and basic genetic mechanisms. At the end of the course,

students are expected to understand the central dogma of molecular biology and to know its

specificities in different forms of life: prokaryotes and eukaryotes. This is taken concurrently

with a laboratory course, and it is the first part of the two-part molecular biology lecture series.

Course Objectives


● Making a detailed study on the structure and function of macromolecules.

● Explaining the nature of the genetic material.

● Giving an overview of the passage of information from gene to protein.

● Explaining the processes of DNA replication, repair, recombination and transposition.

● Covering certain techniques of molecular biology.

Course Content

(weekly plan)

Week 1: Cells and genomes

Week 2: Cell chemistry and bioenergetics, part I

Week 3: Cell chemistry and bioenergetics, part II

Week 4: The shape and structure of proteins

Week 5: Protein function

Week 6: DNA and chromosomes

Week 7: The global structure of chromosomes and genome evolution


Week 9: DNA replication and repair

Week 10: Recombination mechanisms

Week 11: Transposable elements

Week 12: How cells read the genome: from DNA to RNA

Week 13: How cells read the genome: from RNA to protein; RNA origins of life

Week 14: Practice problems

Week 15: Recap


LABORATORY CONTENT


Week 2, Lab 1: General laboratory rules of behavior and safety considerations; How to use a

micropipette

Week 3, Lab 2: Introduction to spectrophotometry

Week 4, Lab 3: DNA isolation from buccal swab (salting-out method)

Week 5, Lab 4: DNA isolation from chicken liver (salting-out method)

Week 6, Lab 5: Determining DNA concentration by quantitative spectrophotometric

measurement

Week 7, Lab 6: Agarose gel electrophoresis with Fast Blast stain


Week 9, Lab 7: Restriction endonucleases (theory)

Week 10 Lab 8: Restriction digestion of DNA fragments

Week 11, Lab 9: Agarose gel electrophoresis with SafeView Nucleic Acid stain

Week 12, Lab 10: Restriction mapping

Week 13, Lab 11: Lab test




Teaching Methods

Description



● Laboratory work

Assessment Methods Description (%) Quiz 0 % Lab/Practical Exam 20 %


43




Total 100 %

Learning Outcomes


1. Recall the molecular structure of DNA/RNA and proteins

2. Describe the basis of the central dogma of molecular biology

3. Explain the molecular mechanisms underlying transcription and translation

4. Illustrate the role of genes and proteins in normal functioning of the cell

5. Examine the basic principles of molecular techniques

6. Conduct isolation of DNA from various material

7. Use spectrophotometry to determine the concentration and purity of DNA/RNA

8. Conduct gel electrophoresis


(if any) None


Mandatory Literature Alberts, B., Johnson, A., Lewis, J., Morgan, D., Raff, M., Roberts, K., & Walter, P. (2015).

Molecular Biology of the Cell, 6th ed. New York, NY: Garland Science.


Student handout with practice problems

Sambrook, J., & Russell, D. W. (2006). The condensed protocols from molecular cloning: A

laboratory manual. Cold Spring Harbor, NY, USA: CSHL Press










Total Workload 123


Course Code: GBE 323 Course Name: BIOMEDICAL INSTRUMENTATION



Course Description

This course will introduce the students to basic biomedical engineering technology so that they can

understand and evaluate (and perhaps design) systems and devices that can measure, test, and acquire

biological information. The course will encompass systems of human physiology as well as the bio-

signals they generate. The focus will also be on biosensors, transducers, bio-electrodes used for

acquisition, and amplifiers for measuring bio-potentials. Some bioethics will be discussed as well.

Introduction to fundamentals of biomedical instrumentation, biomedical sensors and physiological

transducers, biomedical recorders, patient monitoring systems, arrhythmia and ambulatory monitoring

instruments, cardiac pacemakers, cardiac defibrillators, MRI and CT systems are the topics covered

within the course.

Course Objectives


● Introduction to basic biomedical instrumentation.

44

● Explaining working principles of biomedical instrumentation.

● Familiarizing students with patients’ security.

● Giving an outline of regulations related to biomedical instrumentation.

Course Content

(weekly plan)

Week 1: Introduction to biomedical instrumentation

Week 2: Biomedical sensors and transducers and bioelectric amplifiers

Week 3: Electrocardiographs

Week 4: Blood pressure measurement and physiological pressure and other cardiovascular

measurements and devices

Week 5: Instrumentation for measurement of brain parameters

Week 6: Biological impedance measurement

Week 7: Respiratory system and its measurement


Week 9: Intensive and coronary care units and pacemakers and defibrillators

Week 10: Electrosurgery

Week 11: Lasers and medical imaging equipment

Week 12: Radiology and nuclear medicine equipment and medical ultrasound

Week 13: Magnetic resonance imaging

Week 14: Computed tomography imaging

Week 15: Patients’ security and law


LABORATORY CONTENT:

Week 1-11: This course is designed so that the students get acquainted with all the instruments

mentioned in the lectures through a series of virtual labs. Through these labs they will learn how to

handle the instruments and, at the same time, interpret the results they obtain.

Teaching Methods

Description




● Consultation

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes



1. Recall basic terminology related to biomedical instrumentation

2. Recognize biomedical instrumentation

3. Practice on a huge area of biomedical instrumentation

4. Interpret principles of work of biomedical instrumentation

5. Evaluate patients' security and law


(if any) None


Mandatory Literature Raden, J.F. (2010). Handbook of Modern Sensors, Physics, Designs and Applications. New York, NY,

USA: Springer-Verlag


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






45






Total Workload 125


FOURTH SEMESTER

Course Code: GBE 202 Course Name: BIOSTATISTICS

Level: Undergraduate Year: II Semester: IV ECTS Credits: 4


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


● 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: Introduction to biostatistics

Week 2: Descriptive statistics

Week 3: Exact test of goodness-of-fit

Week 4: Chi-square test

Week 5: Fisher’s exact test

Week 6: Student’s t-test

Week 7: Paired t-test


Week 9: One-way anova

Week 10: Nested anova

Week 11: Correlation and linear regression

46

Week 12: Spearman rank correlation

Week 13: Kruskal-Wallis test

Week 14: Wilcoxon signed-rank test



LABORATORY CONTENT


Week 2, Lab 1: Descriptive statistics

Week 3, Lab 2: Exact test of goodness-of-fit

Week 4, Lab 3: Chi-square test

Week 5, Lab 4: Fisher’s exact test

Week 6, Lab 5: Student’s t-test

Week 7, Lab 6: Paired t-test


Week 9, Lab 7: One-way anova

Week 10 Lab 8: Nested anova

Week 11, Lab 9: Correlation and linear regression

Week 12, Lab 10: Spearman rank correlation

Week 13, Lab 11: Kruskal-Wallis test

Week 14, Lab 12: Wilcoxon signed-rank test



Teaching Methods

Description



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Deliver an effective presentation of data

2. Perform probability testing

3. Explain the fundamentals of hypothesis testing

4. Make tables and diagrams

5. Operate descriptive statistics in excel

6. Perform the student t test

7. Perform ANOVA

8. Perform regression analysis in excel


(if any) None



McDonald, J. H. (2009). Handbook of biological statistics (Vol. 2, pp. 6-59). Baltimore, MD:

sparky house publishing.

Recommended Literature Bhishma R. (2005). Probability and Statistics for Engineers, 2nd ed. New York City, NY, USA:

Sitech






47






Total Workload 100


Course Code: GBE 206 Course Name: MOLECULAR BIOLOGY II



Course Description

As the second part of a two-part course series in molecular biology, this course covers advanced

topics on gene expression and regulation, protein modifications and ubiquitination, small RNAs

and cell signaling. Current topics, like RNA interference and epigenetics, as well as techniques

in molecular biology are also introduced. This is taken concurrently with a laboratory course.

Course Objectives


● Enabling students to move beyond their introductory textbooks towards a deeper

understanding of modern molecular biology.

● Providing detailed descriptions of cell signaling.

● Providing an insight into the regulation of gene expression at different levels.

● Presenting the most important techniques in molecular biology.

Course Content

(weekly plan)

Week 1: Molecular mechanisms of mutation and DNA repair

Week 2: Molecular mechanisms of gene regulation, part I

Week 3: Molecular mechanisms of gene regulation, part II

Week 4: Post-translational modifications and ubiquitination

Week 5: Cell signaling, part I

Week 6: Cell signaling, part II

Week 7: Cell death


Week 9: Genetic control of development, part I

Week 10: Genetic control of development, part II

Week 11: Stem cells and tissue renewal, part I

Week 12: Analyzing cells, molecules and systems, part I

Week 13: Analyzing cells, molecules and systems, part II

Week 14: Visualizing cells

Week 15: Recap


LABORATORY CONTENT


Week 2, Lab 1: Buffer preparation

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

48

Week 6, Lab 5: Preparation of animal tissue for protein isolation: Chicken muscle

Week 7, Lab 6: Protein isolation from a bacterial culture


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 15: Lab test


Teaching Methods

Description



● Presentations

● Laboratory work





Midterm Exam 25 % Class Deliverables 20%


Total 100 %

Learning Outcomes


1. Deduce gene expression levels and regulation in prokaryotes and eukaryotes 2. Debate molecular mechanisms underlying the processes of gene regulation in different

organisms 3. Understand the most important cell signaling pathways 4. Understand the importance of stem cells in different types of tissues, as well as in tissue

repair and regeneration 5. Perform protein isolation in the laboratory from various samples: animal, plant, bacterial 6. Operate quantification of the isolated proteins in the laboratory 7. Perform SDS-PAGE


(if any) None



Hartl, D.L. (2020). Essential Genetics and Genomics, 7th ed. Burlington, MA: Jones & Barlett

Learning.

Alberts, B., Johnson, A., Lewis, J., Morgan, D., Raff, M., Roberts, K., & Walter, P. (2015).

Molecular Biology of the Cell, 6th ed. New York, NY: Garland Science.


Prabakaran, S., Lippens, G., Steen, H., & Gunawardena, J. (2012). Post‐translational

modification: nature's escape from genetic imprisonment and the basis for dynamic information

encoding. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 4(6), 565-583.










Total Workload 123

49


Course Code: GBE 210 Course Name: BIOCHEMISTRY



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 related

to macromolecule behavior in water solutions. The second part of the course focuses on the metabolism of

carbohydrates, lipids and nitrogen, as well as cellular respiration and hormone metabolism, that is,

metabolism integration. All these cycles are analyzed through a molecular perspective. The course is

accompanied by a practical lab course.

Course Objectives


● Providing a theoretical and applied background in the field of biochemistry.

● Covering the basic chemistry of the most important biological macromolecules, including amino

acids, peptides, lipids and carbohydrates.

● Illustrating the metabolism of carbohydrates, lipids and nitrogen.

● Giving an overview of cellular respiration.

Course Content

(weekly plan)

Week 1: Introduction to biochemistry class

Week 2: Water

Week 3: Amino acids, peptides and proteins

Week 4: Enzymes

Week 5: Carbohydrates and glycobiology

Week 6: Lipids

Week 7: Introduction to metabolism; Glycolysis


Week 9: Gluconeogenesis, the pentose phosphate pathway, and glycogen metabolism

Week 10: The citric acid cycle

Week 11: Electron transport and ATP synthesis

Week 12: Lipid metabolism

Week 13: Amino acid metabolism

Week 14: Nucleotide metabolism

Week 15: Hormonal regulation and integration of mammalian metabolism


LABORATORY CONTENT


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 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


50

Week 15: Lab test


Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Summarize amino acids and proteins

2. Categorize enzymes and explain their kinetics

3. Identify carbohydrates

4. Classify lipids

5. Interpret gluconeogenesis, the pentose phosphate pathway, and glycogen metabolism

6. Illustrate Krebs cycle, electron transport chain and oxidative phosphorylation

7. Explain the basics of metabolism from molecular and medical perspective

8. Use basic laboratory skills and procedures in biochemistry labs


(if any) None



Nelson, D. L, & Cox, M. M. (2017). Lehninger Principles of Biochemistry, 7th ed. Gordonsville, VA:

Macmillan Learning.

Horton, R. A., Moran, L. A., Scrimgeour, G, Perry, M., & Rawn, D. (2006). Principles of Biochemistry, 4th

ed. London, UK: Pearson Education.

Recommended Literature Boyer, R. F. (2006). Concepts in biochemistry, 3rd ed. Hoboken, New Jersey, USA: Wiley.










Total Workload

149


Course Code: GBE 330 Course Name: BIOSENSORS


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

51

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


● 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 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


LABORATORY CONTENT


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 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




Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Describe physical operating principles of biosensors

2. Describe the biology of sensing elements

3. Differentiate a variety of biosensors

4. Recognize limitations of biosensors

5. Predict application areas for different types of biosensors

6. Distinguish measurement accuracy and sources of errors in biosensors

52

7. State technical characteristics of biosensors

8. Discuss measurement standards and sensors network and communication


(if any)

None.





Enderle, J. & Bronzino, J. (2011). Introduction to Biomedical Engineering, 3rd ed. Burlington, MA,

USA: Elsevier Academic Press













Total Workload 125


FIFTH SEMESTER

Course Code: GBE 303 Course Name: INTERNSHIP

Level: Undergraduate Year: III Semester: V ECTS Credits: 5


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.

53

Course Objectives


● 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.







Total 100 %

Learning Outcomes


1. Express the ability to work effectively as part of a team

2. Demonstrate interpersonal, organizational, and problem solving skills within a managed

environment

3. Practice personal responsibility

4. Describe and discuss information in oral, written or graphic forms in order to

communicate effectively with peers and tutors

5. Apply and analyze theory, techniques and relevant tools to the specification, analysis,

design, implementation and testing of samples

6. Judge on the company and/or team performance according to the work experience gained

during internship


(if any) None


Mandatory Literature N/A

Recommended Literature N/A




Defense (1 week) 1 30 30

Internship Notebook Preparation (1 week) 1 20 20


Total Workload 125


54

Course Code: GBE 307 Course Name: BIOINFORMATICS



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 NCBI and Ensembl databases, DNA-, RNA- 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


● 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: Access to sequence data and related information (genomic DNA databases)

Week 3: Access to sequence data and related information (RNA data, protein databases)

55

Week 4: Access to sequence data and related information (genome browsers, individual

genes/proteins, biomedical literature)

Week 5: Pairwise sequence alignment

Week 6: Basic Local Alignment Search Tool (BLAST)

Week 7: Multiple sequence alignment, part I


Week 9: Multiple sequence alignment, part II

Week 10: Advanced database searching, part I

Week 11: Advanced database searching, part II

Week 12: Molecular phylogeny and evolution, part I

Week 13: Molecular phylogeny and evolution, part II

Week 14: Bioinformatic approaches to RNA

Week 15: Recap


LABORATORY CONTENT


Week 2, Lab 1: PubMed

Week 3, Lab 2: NCBI: Nucleotide and Gene databases

Week 4, Lab 3: UniProt

Week 5, Lab 4: UCSC Genome Browser

Week 6, Lab 5: Primer3Plus

Week 7, Lab 6: Pairwise sequence alignment; BLAST


Week 9, Lab 7: Multiple sequence alignment, part 1

Week 10 Lab 8: Multiple sequence alignment, part 2

Week 11, Lab 9: Phylogenetics

Week 12, Lab 10: Protein domain and motif search

Week 13, Lab 11: Recap

Week 14: Preparation for lab exam



Teaching Methods

Description



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Use PubMed for article browsing 2. Employ NCBI for sequence analysis 3. Perform similarity searches 4. Perform multiple sequence alignments 5. Discover different protein databases 6. Create phylogenetic trees


(if any) None


Mandatory Literature Pevsner, J. (2015). Bioinformatics and Functional Genomics, 3rd ed. Hoboken, NJ: John Wiley &

Sons.

Recommended Literature Database information



56









Total Workload 125


Course Code: GBE 309 Course Name: HUMAN GENETICS



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


● 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 2: Introduction to human genetics

Week 3: Meiosis, development and aging

Week 4: Human inheritance

Week 5: Human inheritance continued

Week 6: Genetics of behavior

Week 7: Gene expression and epigenetics


Week 9: Genetic mutations

Week 10: Human chromosomes

Week 11: Introduction to population genetics

Week 12: Genetics of immunity

Week 13: Cancer genetics and genomics

Week 14: Genetic technologies

Week 15: Genetic testing and treatment


57

LABORATORY CONTENT


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 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




Teaching Methods

Description



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Perform pedigree analysis

2. Clarify gene mapping

3. Interpret various human genetic tests

4. Perform DNA isolation

5. Illustrate the molecular mechanism of PCR and perform PCR


(if any) None



Lewis, R. (2009). Human Genetics: Concepts and Applications, 9th ed. New York, NY, USA:

McGraw-Hill


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









58



Total Workload 125


Course Code: GBE 325 Course Name: BIOMEDICAL SIGNALS AND SYSTEMS



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


● 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




● Consultations

● Laboratory work

Assessment Methods

Description (%)




59



Total 100 %

Learning Outcomes



1. Define biomedical system modeling

2. Assess different aspects and methods of applying engineering principles in medicine

3. Review characteristics of biomedical signals

4. Arrange principles of design and implementation of medical devices for physiological signal

processing

5. Interpret results of ECG and EEG signals


(if any) None





Enderle, J. & Bronzino, J. (2011). Introduction to Biomedical Engineering, 3rd ed. Burlington, MA,

USA: Elsevier Academic Press













Total Workload 125


60

SIXTH SEMESTER

Course Code: GBE 392 Course Name: GENETICS AND BIOENGINEERING PROJECT

Level: Undergraduate Year: III Semester: VI ECTS Credits: 5


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


● 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



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Actively participate in courses and begin to take responsibility for learning

2. 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

3. Present information in oral, written or graphic forms in order to communicate

effectively with peers and tutors

4. Apply theory, techniques and relevant tools to the specification, analysis, design,

implementation and testing.

5. Evaluate theories, processes and outcomes within an ambiguous setting


(if any) None


Mandatory Literature N/A





61



Total Workload 125


Course Code: GBE 304 Course Name: FORENSIC GENETICS



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


● 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.

62

● 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 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



LABORATORY CONTENT


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 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




Teaching Methods

Description



● Presentations

● Laboratory work







Total 100 %

Learning Outcomes


1. Apply all sorts of forensic and genetic analysis methods in processing human, animal

and plant biological trace samples

2. Operate forensic samples for forensic analysis

3. Assess the importance of forensic genetics in legal medicine and juridical procedures

4. Conduct DNA isolation

5. Categorize various sequencing methods

6. Explain STR profiling and the use of CODIS

63

7. Employ forensic statistics


(if any) None



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











Total Workload 125


Course Code: GBE 321 Course Name: INTELLIGENT SYSTEMS



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


● 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 9: Perceptrons and Multilayer Perceptrons

Week 10: Neural network Applications

64

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


LABORATORY CONTENTS


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 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



Teaching Methods

Description




● Consultations

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes



1. Designing and applying fuzzy logic system to solve engineering control problems where only

expert linguistic knowledge is available,

2. Designing and applying artificial neural network for solving problems,

3. Different aspects and methods of applying fuzzy logic system and artificial neural network in

Bioengineering,

4. The difference between the classical algorithmic way of solving the problems and the

corresponding learning procedures of artificial neural networks,

5. Technical possibilities, the advantages and the limitations of the fuzzy logic systems, artificial

neural network systems,

6. Usage of available software tools such as Matlab Neural Network Toolbox.

7. Developing Intelligent Expert Systems for solving complex problems in the Bioengineering

area.


(if any) None



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

65

Recommended Literature None











Total Workload 125


Course Code: GBE 338 Course Name: IMMUNOLOGY AND IMMUNOGENETICS



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


✔ 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: Introduction to immunology. Innate immunity

Week 2: Properties and overview of immune responses

Week 3: Cells and tissues of immune system. Major histocompatibility complex molecules

Week 4: Leukocyte migration into tissues

Antigen processing and presentation to T lymphocytes. Antigen receptors and accessory molecules of

T lymphocytes

Week 5: Innate immunity

Week 6: Antibodies and antigens

Week 7: Scientific inquiry


Week 9: MHC

Week 10: Immune receptors and signal transduction

Week 11: Lymphocyte development and antigen receptor gene rearrangement

Week 12: Activation of T lymphocytes Transplantation immunology

Week 13: B Cell activation and antibody production

Week 14: Immunity to microbes & Immunity to tumors

Week 15: Autoimmunity & Hypersensitivity


LABORATORY CONTENTS


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

66

Week 6, Lab 5: Determination of blood type, bleeding and clotting time

Week 7, Lab 6: Osmotic fragility


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)




Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Prepare and interpret blood smears

2. Describe basic organs of the lymph system

3. Perform ABO, MN, Rh blood typing

4. Isolate blood proteins

5. Interpret blood lab results

6. Perform immunological detection of viruses and bacteria


(if any)

None


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











Total Workload 125


67

TECHNICAL ELECTIVE COURSES

Course Code: GBE 320 Course Name: SYSTEMS PHYSIOLOGY

Level: Undergraduate Year: II, III Semester: III, IV, V, VI ECTS Credits: 5


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


● 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 cell physiology, Membranes and movement across the membrane

Week 3: Homeostasis: Mechanisms and signal transduction

Week 4: Endocrine system I

Week 5: Endocrine system II

Week 6: Reproductive system: From sex differentiation to adult reproduction

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


Week 9: Nervous system: Neural communication, mechanisms, and sensory systems

Week 10: Neurophysiology: sensory systems, vision, audition, vestibular system, olfaction, taste

Week 11: Respiratory system: System mechanics, gas transport and control of respiration

Week 12: Urinary system: Kidney, clearance, and the countercurrent mechanism

Week 13: Digestive system: Gastrointestinal motility, secretion, digestion, and absorption

Week 14: Cardiovascular system: Circulation and the design of cardiovascular system

Week 15: Immune system & Integumentary system




Week 2, Lab 1 Introduction to System Physiology; Lab and Safety Rules

Week 3, Lab 2: Osmosis and difussion lab

Week 4, Lab 3: Experimental animals and animal dissection (Salmo truta)

Week 5, Lab 4: Endocrine system - Virtual lab

Week 6, Lab 5: Male and female reproductive system – Virtual lab

68

Week 7, Lab 6: Muscular system - Virtual lab


Week 9, Lab 7: Nervous system – virtual lab

Week 10, Lab 7: Respiratory system – virtual lab and the use of spirometers

Week 11 Lab 8: Urinary system: Urine analysis

Week 12, Lab 9: Digestive system – virtual lab

Week 13, Lab 10: Cardiovascular system – virtual lab

Week 14, Preparation for practical exam

Week 15, Practical exam from lab course


Teaching Methods

Description



● Presentations

Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


6. Recall the basics of physiology of different organ systems

7. Identify the structure and function of various systems

8. Interpret and criticize the concept of experimental animals

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

10. Operate animal dissection safely and efficiently


(if any)

None


Mandatory Literature Linda S. Constanzo (2014), Physiology, Fifth edition, Saunders, Elsevier

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











Total Workload 125


Course Code: GBE 322 Course Name: PRINCIPLES OF NEUROBIOLOGY


69


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


● 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 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 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 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




Teaching Methods

Description




● Presentations

● Laboratory work

Assessment Methods

Description (%)





Presentation 0 % Final Exam 40%

70

Total 100 %

Learning Outcomes



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


(if any)

None


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











Total Workload 125


Course Code: GBE 324 Course Name: BIOMATERIALS



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


● 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.

71

Course Content

(weekly plan)


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 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


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




● Presentations

● Laboratory work

Assessment Methods

Description (%)




Midterm Exam 20 % Class Deliverables 0%


Total 100 %

Learning Outcomes



✔ 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


(if any) None


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









72



Total Workload 125


Course Code: GBE 326 Course Name: CYTOGENETICS



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


● 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 2: DNA, Chromosomes, and Cell Division

Week 3: Human Chromosome Nomenclature: An Overview and Definition of Terms

Week 4: Autosomal Aneuploidy

Week 5: Structural Chromosome Rearrangements

Week 6: Sex Chromosomes, Sex Chromosome Disorders, and Disorders of Sex Development

Week 7: The Cytogenetics of Infertility


73

Week 9: Prenatal Cytogenetics

Week 10: Chromosome Instability

Week 11: The Cytogenetics of Hematologic Neoplasms

Week 12: The Cytogenetics of Solid Tumors

Week 13: Fluorescence in Situ Hybridization (FISH)

Week 14: Microarray-Based Cytogenetics

Week 15: Genomic Imprinting and Uniparental Disomy


LABORATORY CONTENTS


Week 2, Lab 1: Basic Cytogenetics Laboratory Procedures and Instrumentation

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 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




Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


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


(if any)

None


Mandatory Literature Steven L. Gersen, Martha B. Keagle, Editors The Principles of Clinical Cytogenetics, Third edition

(2013), Springer

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






74






Total Workload 125


75

Course Code: GBE 327 Course Name: GENERAL BIOTECHNOLOGY AND BIOSAFETY



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


● 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 2: Recombinant DNA technology

Week 3: Microbial biotechnology

Week 4: Plant biotechnology

Week 5: Bioremediation

Week 6: Animal biotechnology

Week 7: Marine biotechnology


Week 9: Medical biotechnology

Week 10: Biotechnology regulations

Week 11: Ethics in biotechnology

Week 12: Standard methods in molecular biotechnology: Proteins

Week 13: Standard methods in molecular biotechnology: Nucleic acids

Week 14: Use of enzymes in the modification of nucleic acids

Week 15: Other standard methods in molecular biotechnology


LABORATORY CONTENTS

Week 1: Beginning of classes and presentation of seminar assignments

Week 2 – Week 7: Student presentations


Week 9 – 14: Student presentations



Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

76

Learning Outcomes


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


(if any)

None



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











Total Workload 125


77

Course Code: GBE 328 Course Name: INTRODUCTION TO RESEARCH METHODS



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.

The emphasis will be on academic writing and publishing, ethical considerations and safety. 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, as well as preparation of their own

article-style paper and presenting it in front of the class.

Course Objectives


● 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.

● 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.

● Getting deep understanding of academic writing and publishing.

Course Contents

(weekly plan)

Week 1: Introduction to research

Week 2: Experimental design and analysis

Week 3: Communicating scientific information

Week 4: Types of scientific articles

Week 5: Scientific publishing

Week 6: Research ethics

Week 7: Scientific misconduct


Week 9: Writing assignment, introduction

Week 10: Paper presentations

Week 11: Paper presentations

Week 12: Consultations

Week 13: Consultations

Week 14: Presentations of writing assignment

Week 15: Presentations of writing assignment


LABORATORY CONTENTS

Weeks 2-15: The laboratory course is designed so that the students get more in-depth explanation of

scientific research and publishing, especially as related to scientific misconduct, proper scientific

referencing and understanding research articles. Laboratory course will be based on reading and

analyzing chosen articles from relevant fields.

Teaching Methods

Description



● Presentations

● Practice exercises

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Develop a scientific way of reasoning 2. Use various databases necessary for the bioengineering profession 3. Handle different research designs 4. Differentiate the types of academic papers

78

5. Recall the concepts of ethics, plagiarism and scientific misconduct


(if any)

None


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

Recommended Literature Lecture notes

Scientific articles











Total Workload 123


79

Course Code: GBE 329 Course Name: POPULATION GENETICS



Course Description

This course is designed to provide students with a general introduction to population genetics, which

examines the interaction of basic microevolutionary and other related 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


● Teaching students the principles of Hardy-Weinberg equilibrium.

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

● Giving an overview of phylogenetic analyses, their possibilities and limitations, as well as

practical applications.

● Explaining the history of modern humans and 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.

● Giving an overview of quantitative genetics in the context of different populations.

Course Contents

(weekly plan)

Week 1: Background in population genetics

Week 2: Allele and genotype frequencies; Hardy-Weinberg equilibrium and extensions of the principle,

part I

Week 3: Allele and genotype frequencies; Hardy-Weinberg equilibrium and extensions of the principle,

part II

Week 4: Inbreeding

Week 5: Sources of genetic variation (mutation, recombination, transposable elements)

Week 6: Genetic drift

Week 7: Gene flow


Week 9: Natural selection as the driving evolutionary force

Week 10: Case studies of natural selection in human populations

Week 11: Human population structure and history

Week 12: Quantitative genetics and heritability, part I

Week 13: Quantitative genetics and heritability, part II

Week 14: Phylogenetics and speciation

Week 15: Population growth and doubling; Carrying capacity


LABORATORY CONTENTS

Week 1, Beginning of classes

Week 2, Lab 1: Basic statistical models for population genetics

Week 3, Lab 2: Allele and genotype frequencies; Hardy-Weinberg equilibrium

Week 4, Lab 3: Trait inheritance and genetic counseling using HWE

Week 5, Lab 4: Inbreeding

Week 6, Lab 5: Mutation as a source of genetic variation

Week 7, Lab 6: Recombination as a source of genetic variation; Gene mapping


Week 9, Lab 7: Genetic drift

Week 10, Lab 8: Gene flow and FST value

Week 11, Lab 9: Natural selection

Week 12, Lab 10: Population genetics of quantitative traits

Week 13, Lab 11: Analysis of sample articles from the field

Week 14: Preparation for laboratory test

Week 15: Lab test


Teaching Methods

Description



● Mathematical problems

● Sample paper analysis


80

Assessment Methods

Description (%)





Total 100 %

Learning Outcomes


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 microevolutionary driving forces in population genetics

5. Recall basics of phylogenetics

6. Discuss heritability


(if any)

None


Mandatory Literature Relethford, J.H. (2012). Human Population Genetics. Hoboken, NJ: John Wiley & Sons, Inc


Hartl, D.L. & Clark, A.G. (1997). Principles of Population Genetics, 3rd ed. Sunderland, MA: Sinauer

Associates, Inc

Scientific papers

Tutorial handouts











Total Workload 123


81

Course Code: GBE 331 Course Name: ENVIRONMENTAL BIOLOGY


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


● 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 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 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


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



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


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


(if any)

None.

82


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











Total Workload 125


Course Code: GBE 332 Course Name: PLANT STRESS PHYSIOLOGY


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


● Familiarizing students with plant stress physiology.

● Teaching techniques to improve productivity of plants by using some biotechnological

methods.

● Introduction to stress and signal transduction.

83

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 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


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



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


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


(if any)

None


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










84


Total Workload 125


Course Code: GBE 333 Course Name: PLANT PHYSIOLOGY AND TISSUE CULTURE



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


● 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 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


LABORATORY CONTENT



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 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




Teaching Methods

Description



● Presentations

● Laboratory work

85

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


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


(if any)

None.


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











Total Workload 125


Course Code: GBE 334 Course Name: ANALYTICAL CHEMISTRY



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


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

● Explaining titration curves.

● Illustrating steps required to conduct analysis.

● Introduction to potentiometric methods.

86

Course Content

(weekly plan)


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 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


LABORATORY CONTENT


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 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




Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


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


(if any)

None.


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

87

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











Total Workload 125


Course Code: GBE 335 Course Name: GENOMICS AND PROTEOMICS



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 mass spectrometry, SDS-PAGE, and protein sequencing.

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 gene, transcriptome, and protein analysis.

Course Objectives


● 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: Gene expression analysis techniques

Week 3: Protein analysis and proteomics

Week 4: Protein structure

Week 5: Functional and comparative genomics

Week 6: The eukaryotic chromosome, part I

Week 7: The eukaryotic chromosome, part II


Week 9: Genomes across the tree of life

Week 10: Viral genomes

Week 11: Bacterial and archaeal genomes

Week 12: Eukaryotic genomes (fungi)

Week 13: Eukaryotic genomes (from parasites to primates)

Week 14: Human genome

88

Week 15: Human disease


LABORATORY CONTENT


Week 2, Lab 1: NGS applications: Metagenomics (computer project)

Week 3, Lab 2: NGS applications: RNA-Seq (computer project)

Week 4, Lab 3: Prediction of protein 2D and 3D structure (in silico work)

Week 5, Lab 4: Protein-protein interaction networks (in silico work)

Week 6, Lab 5: KEGG database (in silico work)

Week 7, Lab 6: Comparative genomics (in silico work), part I


Week 9, Lab 7: Comparative genomics (in silico work), part II

Week 10 Lab 8: Natural selection analysis (computer project)

Week 11, Lab 9: Epigenomics and pharmacogenomics (paper discussion)

Week 12, Lab 10: OMIM database (in silico work)

Week 13, Lab 11: Recap




Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Develop an understanding of the significant role and essence of genome analysis 2. Describe protein structure and function 3. Compare interactions between proteomes and genomes and various external factors 4. Identify the role that genomics and proteomics play in gene/protein expression analysis


(if any)

None


Mandatory Literature Pevsner, J. (2015). Bioinformatics and Functional Genomics, 3rd ed. Hoboken, NJ: John Wiley & Sons

Recommended Literature Database information











Total Workload 125

89


Course Code: GBE 337 Course Name: BIOMECHANICS



Course Description

This course is combining basics of mechanics with classical topics in biomechanics. The first half of the

semester is offering topics such as movement, force, energy, and work, Newton’s laws, and pendulum.

The second part of the course (after the mid-term exam) is dealing with the application of principles of

mechanics as they refer to the movement of human body. Body systems are discussed from this point of

view, followed by mechanics of upper and lower extremities. This course is taken concurrently with a

lab course.

Course Objectives


● Introduction to the mechanics of rigid bodies and its application to biological systems.

● Explaining physical parameters in mechanics.

● Introduction to biomechanics of biological bodies.

● Giving an outline of new technologies in biomechanics.

Course Content

(weekly plan)

Week 1: Introduction to mechanics

Week 2: Motion in mechanics; straight-line and rotational motion

Week 3: Force and force fields

Week 4: Work, energy, and power

Week 5: Newton’s laws

Week 6: Kinetic and potential energy; impulse, momentum, and angular momentum

Week 7: Fluids. Pendulums


Week 9: Introduction to biomechanics: Application of mechanics to biological bodies

Week 10: Skeletal and muscular systems; Levers and joints

Week 11: Neurological system

Week 12: Mechanics of upper extremities: Shoulder, elbow, and wrist

Week 13: Mechanics of lower extremities: Hip and knee

Week 14: Mechanics of lower extremities: Ankle, foot, and trunk

Week 15: New technology in biomechanics


LABORATORY CONTENT

Week 1-11: The laboratory course is designed so that the students repeat the concepts thought during

the lectures in form of numerical problems in the first part of the semester. The second part of the course

is mainly focused on reading scientific articles related to biomechanics, that is, human movement.

Teaching Methods

Description



● Presentations

● Tutorials

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Describe the mechanics of rigid bodies and its application to biological systems

2. Outline the significance of biomechanics with regards to biological bodies and systems

3. Name new technologies in biomechanics

4. Explain the basic physical parameters in mechanics

5. Assess numerical problems regarding biomechanics

6. Critically discuss scientific articles related to biomechanics and human movement


(if any)

None.

90


Mandatory Literature Beer, F., Johnston, E. R., & Mazurek, D. (2012). Vector mechanics for engineers: Statics, 10th ed. New

York, NY, USA: McGraw-Hill Science

Recommended Literature Chandran, K. B. (1992). Cardiovascular Biomechanics, 1st ed. New York, NY, USA: New York

University Press











Total Workload 125


Course Code: GBE 339 Course Name: RECOMBINANT DNA TECHNOLOGY



Course Description

The course deals with procedures that have been developed to successfully conduct DNA recombination

and produce chimeric DNA, which includes DNA isolation, restriction digestion, DNA ligation,

selection and screening, etc. An important part of the course is ethics related to recombinant DNA

technology. Lab course offers series of experiments that are supposed to show students experimental

workflow in a characteristic DNA recombination protocol.

Course Objectives


✔ Demonstrating practical experience of selected molecular biology techniques.

✔ Demonstrating basic techniques involved in recombinant DNA manipulations including

DNA restriction, ligation, transformation and selection of recombinant plasmid.

91

✔ Demonstrating the principle of PCR and its applications (e.g. Analysis of DNA repeats to

estimate its frequency in the population).

Course Contents

(weekly plan)


Week 2: The basic terminology of recombinant DNA technology

Week 3: Recombination vectors: Plasmids, viruses, competent cells

Week 4: Restriction digestion of DNA samples

Week 5: Chemical synthesis of a DNA sequence

Week 6: DNA ligation

Week 7: Introduction of chimeric DNA into the host organism


Week 9: Expression of recombinant DNA

Week 10: Selection and screening for recombined DNA

Week 11: Recombinant proteins

Week 12: Applications of recombinant DNA technology

Week 13: Ethical considerations in recombinant DNA technology

Week 14: Analysis of scientific articles

Week 15: Student presentations


LABORATORY CONTENTS



Week 3, Lab 2: Ethical considerations in recombinant DNA technology

Week 4, Lab 3: Recombinant DNA technology in bacteria: An overview

Week 5, Lab 4: Preparation of vector DNA: Plasmid isolation

Week 6, Lab 5: Restriction digestion of DNA samples

Week 7, Lab 6: DNA ligation and introduction of novel DNA into the host cell


Week 9, Lab 7: Growing host cells

Week 10 Lab 8: Selection and screening for recombined DNA

Week 11, Lab 9: Usage of recombinant DNA

Week 12, Lab 10: Student presentations

Week 13, Lab 11: Student presentations




Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes

After completion of this course, students should be able to: 1. Categorize molecular mechanisms underlying the PCR reaction

2. Handle molecular cloning

3. Prepare basic tools of engineering: restriction enzymes, ligation, etc.

4. Operate PCR

5. Perform bacterial transformation


(if any)

None


Mandatory Literature Sandhu, S.S. (2010). Recombinant DNA Technology, 1st ed. New Delhi, India: International Publishing

House

92

Recommended Literature Chaudchuri, K. (2013). Recombinant DNA Technology, 1st ed. New Delhi, India: TERI











Total Workload 125


Course Code: GBE 340 Course Name: PLANT PATHOLOGY



Course Description

This course examines disease progression in plants on molecular and morphologic level. Also,

symptoms of plant disease, as well as plant immune system are covered in the first part of the course.

The second part of the course discusses biological agents causing plant diseases, such as bacteria,

viruses, and fungi. Lab course is offering students an opportunity to experimentally examine disease

progression when it is caused by different biological agents and to compare them.

Course Objectives


● Introduction to plant diseases caused by fungi, bacteria, viruses, nematodes and higher

parasitic plants.

● Explaining vectors as means of disease transmission.

● Explaining genetics of plant diseases.

● Giving an outline of plant defense mechanisms.

Course Contents

(weekly plan)

Week 1: Introduction: History of plant pathology and early significant plant diseases

Week 2: Parasitism and disease development. Pathogenesis

Week 3: Genetics of plant disease

Week 4: How pathogens attack plants

Week 5: How plants defend themselves against pathogens

Week 6: Environmental effects on the development of infectious plant disease

Week 7: Plant disease epidemiology


Week 9: Control of plant diseases

Week 10: Plant diseases caused by bacteria and mollicutes

Week 11: Plant diseases caused by viruses

Week 12: Plant diseases caused by fungi

93

Week 13: Plant diseases caused by protozoa

Week 14: Plant diseases caused by nematodes

Week 15: Plant diseases caused by parasitic plants


LABORATORY CONTENTS

Week 1-11: In the lab course, students will get a theoretical introduction into the symptoms and

causative agents of plant diseases. Following that, they will grow plants and infect them with various

causative agents. They will subsequently observe the development of disease symptoms on the plants,

record the results, and discuss them together.

Teaching Methods

Description



● Presentations

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


1. Define pathogenesis

2. Recall the basics of plant disease caused by viruses

3. Classify plant viruses

4. Recall basics of plant diseases caused by fungi

5. Describe transmission of plant viruses through vectors


(if any)

None


Mandatory Literature Schumann, G. L. & D’Arcy, C. J. (2009). Essential plant pathology, 2nd ed. St. Paul, MN, USA:

American Phytopathological Society

Recommended Literature Sambamurty, A.V.S.S. (2005). Textbook of Plant Pathology, 1st ed. New Delhi, India: IK International











Total Workload 125


94

Course Code: GBE 341 Course Name: BIOPHYSICS



Course Description

This course is focused on the application of physical principles in order to: (1) perform a detailed study

of DNA structure and interactions within DNA building blocks, (2) understand the structure and

formation of RNA and proteins, and (3) introduce processes occurring within the basic biological

structures, such as biological membranes.

Course Objectives


● Introduction to physical principles in biophysical processes, biomedical engineering problems.

● Showing the correlation between physics and biological sciences.

● Revising the basics of DNA structure.

● Explaining the impact of physical forces on DNA structure.

● Providing an outline of RNA, protein, molecular and medical biophysics.

Course Contents

(weekly plan)

Week 1: Introduction to biophysics

Week 2: DNA structure

Week 3: Base-pair interactions and DNA melting

Week 4: Mechanics and statistical mechanics of DNA

Week 5: Electrostatics of DNA and DNA-DNA interactions

Week 6: DNA collapse and DNA mesophases

Week 7: DNA organization in chromatin and viruses


Week 9: Biophysics of RNA

Week 10: Biophysics of proteins

Week 11: Molecular biophysics

Week 12: Membrane biophysics

Week 13: Medical biophysics

Week 14: Biomechanics

Week 15: Methods in molecular biophysics

Week 16: FINAL EXAM

LABORATORY CONTENTS

Week 1-11: The laboratory course is designed so that the students prepare oral presentations and

discuss scientific articles on topics covered during the lectures and improve their knowledge in that

way.

Teaching Methods

Description



● Presentations

● Tutorials

Assessment Methods

Description (%)






95

Total 100 %

Learning Outcomes


● Recognize basic physical principles underlying biological processes

● Relate physical principles to biophysical processes

● Apply the knowledge of physical principles on engineering problems

● Make DNA models

● Deliver an effective presentation


(if any)

None


Mandatory Literature Hobbie, R. K. & Roth, B. J. (2009). Intermediate Physics for Medicine and Biology, 4th ed. New York,

NY, USA: Springer


Nelson, P. (2003). Biological Physics: Energy, Information, Life, 1st ed. New York, NY, USA: W. H.

Freeman

Davidovits, P. (2001). Physics in Biology and Medicine. Waltham, MA, USA: Academic Press











Total Workload 125


96

Course Code: GBE 343 Course Name: VIROLOGY



Course Description

This course is aimed at providing students with an introduction to virology. Students will become

familiar with history and scope, virus structure their multiplication and growth in laboratory conditions.

Further on they will be familiarized with the effect of physical and chemical agents on viruses as well

as their ecology. Basics of viral classification will be elaborated as well as some viral families and

genera.

Course Objectives


● Introduction to virus structure

● Understand the basics of viral taxonomy

● Do experimental design and manipulation with viruses,

● Conduct viral analysis and understand their possible application.

Course Contents

(weekly plan)

Week 1: Introducion to the course

Week 2: History and development of virology

Week 3: Virus structure, chemical composition, basic characteristics and classification

Week 4: Viral proliferation and replication

Week 5: Workshop: paper analysis

Week 6: Pathogenesis and cell damage

Week 7: Transformation and pathogenesis

Week 8: MIDTERM EXAM WEEK

Week 9: Vaccines and Chemotherapy

Week 10: Epidemiology and Viral Evolution

Week 11: Laboratory methods for study of viruses and Viral Classification

Week 12: Workshop: discovery of novel viruses and their molecular identification

Week 13: DNA viruses

Week 14: RNA viruses

Week 15: Retroviruses


LABORATORY CONTENTS

Week 1-14 A set of laboratory exercises that cover the topics of cell culture and viral infection.

Teaching Methods

Description



● Presentations

● Guest instructors

● Research projects

● Laboratory work

Assessment Methods

Description (%)






Total 100 %

Learning Outcomes


● Recall and name basic virology laboratory techniques, as well as explain the foundations of virology

● Demonstrate understanding of viral structure and replication cycles

● Translate the knowledge from this course in future virology courses and/or having a good appreciation of concepts needed to make reasoned choices in their everyday lives

● Interpret and explain how viruses survive where they do, how they are related, and how they

interact with us

● Operate with basic microbiological skills and successfully use them in the lab


(if any)

None


97

Mandatory Literature Modrow, S., Falke, D., Truyen, U., & Schätzl, H. (2013). Molecular virology. Berlin: Springer.

Recommended Literature Knipe, D. M., & Howley, P. M. (2001). Fundamental virology (No. Ed. 4). Lippincott Williams &

Wilkins











Total Workload 125


Documents

INTERNATIONAL BURCH UNIVERSITY FACULTY OF … · various fundamental courses like chemistry, physics and biology; bioengineering courses: genetics and bioengineering, biotechnology,