aim and vision of master course (msc.) program in...

AIM AND VISION OF MASTER COURSE (MSc.) PROGRAM IN BIOTECHNOLOGY:

The Biotechnology program was initiated on September 2011 in the Institute of Science and

Engineering, at Yeditepe University. Through R&D and higher education facilities, the

program aims to train individuals in finding creative solutions to the issues that society faces

in the fields of healthcare, agriculture, food industry and environment, hence providing a

trained workforce in the field of biotechnology.

The vision of the biotechnology program is to work in collaboration with international and

national universities, Techoparks, and R&D Institutes in training and educating professionals,

and to have a voice in the scientific and economical national politics by participating in

industry oriented projects.

ADMISSION TO MASTER’S (M.Sc.) PROGRAM:

To apply for a master's program, a Bachelor's degree must be held or expected to be held

by the end of the term of application and the requirements given below must be met.

- A minimum B.S. cumulative grade point average (CGPA) of 2.00 out of 4.00.

- A minimum score of 55 from ALES or 148 from GRE (Quantitative Reasoning).

- A minimum of 55 from YDS or 66 from TOEFL. Canditates who don’t have aforementioned

scores are required to be successful in the Yeditepe University’s proficiency exam.

- Candidates are required to be successful in the interview held by the department they are

applying for.

GRADUATION REQUIREMENTS FOR BIOTECHNOLOGY MSc. PROGRAM

Students registered with the Biotechnology Master of Science Program should register to

courses with a total of 22 credits / 124 ECTS according to the table below. Courses outside

the Yeditepe University Biotechnology MSc program could only be taken with the approval

of the Advisor and the Chair.

Curriculum for Master of Science Program in Biotechnology

Core Courses

BTEC 501 Basic Biotechnology (4 0 0) 4 / 10 ECTS

BTEC 550 Methods in Scientific Research (0 0 3) 3 / 10 ECTS

BTEC 555 Biostatistics (1 0 4) 3 / 10 ECTS

BTEC 590 Graduate Seminar NC / 2 ECTS

BTEC 600 Thesis in MSc NC / 60 ECTS

Elective Courses

BTEC 504 Pharmaceutical and Medical Biotechnology (3 0 0) 3 / 8 ECTS

BTEC 505 Microbiology (3 0 0) 3 / 8 ECTS

BTEC 506 Plant Biotechnology (3 0 0) 4 / 8 ECTS

BTEC 507 Advanced Biochemistry (3 0 0) 3 / 8 ECTS

BTEC 511 Comparative Physiology (3 0 0) 3 / 8 ECTS

BTEC 512 Ecology (3 0 0) 3 / 8 ECTS

BTEC 513 Introduction to Bioinformatics . (3 0 0) 3 / 8 ECTS

BTEC 514 Cancer Genetics (3 0 0) 3 / 8 ECTS

BTEC 516 Introduction to Nanobiotechnology (3 0 0) 3/ 8 ECTS

BTEC 517 Immunobiology (3 0 0) 3/ 8 ECTS

BTEC 519 Microbiological Aspects of Food Systems (3 0 0) 3 / 8 ECTS

BTEC 521 Gene Expression (3 0 0) 3 / 8 ECTS

BTEC 528 Processing of Bioactive Extracts from Natural Materials (3 0 0) 3/ 8 ECTS

BTEC 532 Drug Delivery Systems and Instruments (3 0 0) 3/ 8 ECTS

BTEC 533 Biomaterials in Tissue Engineering (3 0 0) 3/ 8 ECTS

BTEC 534 Transgenics and Gene Therapy (3 0 0) 3/ 8 ECTS

BTEC 535 Mammalian Tissue Engineering (3 0 0) 3/ 8 ECTS

BTEC 536 Regenerative Biology and Biomedical Applications (3 0 0) 3 / 8 ECTS

BTEC 537 Dosage in Proteins and Peptides (3 0 0) 3/ 8 ECTS

BTEC 538 Nutrigenomics (3 0 0) 3/ 8 ECTS

BTEC 539 Protein Chemistry (3 0 0) 3/ 8 ECTS

BTEC 582 Selected Topics: Signal Transduction Pathways (3 0 0) 3/ 8 ECTS

BTEC 584 Selected Topics: Adult Neurogenesis (3 0 0) 3/ 8 ECTS

BTEC 585 Selected Topics: Microbial Metabolism (3 0 0) 3/ 8 ECTS

BTEC 586 Selected Topics: Applications of Biostatistics in Research (3 0 0) 3/ 8 ECTS

2. YEAR

Thesis Work

COURSE CONTENTS

BTEC 501 Basic Biotechnology (4 0 0) 4

Fermentation technology; basic techniques in biotechnology; biological separation methods

for city and industrial waste water treatment; waste water treatment and bioenergy production

via anaerobic fermentation; malt and beer technology, wine and vinegar technology; lactic

acid fermentation, production of bread yeast.

BTEC 504 Pharmaceutical and Medical Biotechnology (3 0 0) 3

This course includes theoretical background of the application of biotechnology techniques

and applications on therapeutic products, gene therapy, gene application techniques, tissue

engineering, antibody engineering, monoclonal antibodies, vaccines, sera and pharmaceutical

applications.

BTEC 505 Microbiology (3 0 0) 3

This course focuses on the impact of microorganisms on people and the environment. The

growth of microorganisms, their classification, impact on human and plant diseases,

microecology of the water and soil, bacterial genetics, and the applicaiton of microorganisms

in food and industrial technologies, agriculture, pollution and biotechnology will be

investigated. Microbial techniques, human genetics and biotechnology will be discussed.

BTEC 506 Plant Biotechnology (3 0 0) 4

Plant physiology, growth control and hormones, plant tissue engineering techniques,

protoplast cultures, somatic embryogenesis, transformation and regeneration techniques, plant

genetics and A. thaliana modification, transgenic seed studies, improvement of seed

production and quality, improvement of biomass, plant pathogens and improvement of

pathogen resistance, improvement of cold and draught resistance, plant reactors in the

production of proteins, antigens and antibodies.

BTEC 507 Advanced Biochemistry (3 0 0) 3

The life of molecules, structure of carbohydrates and their function, lipids, proteins and

nucleic acids, flow of genetic information, enzymes and enzyme kinetics, membrane

structure, dynamics and function, introduction of bioenergetics, laws of thermodynamics,

ATP and energy, cellular metabolism and fermentation, glycolysis, TCA cycle, oxidative

phosphorylation, photosynthesis, amino acid metabolism, nucleic acid metabolism, fatty acid

metabolism.

BTEC 510 Biotechnology Laboratory Projects (1 0 4) 3

This course involves the thesis project of the master of science candidate, assigned by their

possible thesis advisor. The course is mandatory during the first 2 semesters of the master’s

program.

BTEC 511 Comparative Physiology (3 0 0) 3

Cell physiology, intracellular signaling systems, endocytosis, nervous system and evolution,

muscular, respiratory, circulatory systems and their physiologies, special senses and

hormones.

BTEC 512 Ecology (3 0 0) 3

The interaction of the organisms with their biological and physical environments, concepts of

ecosystem, environmental requirements of organisms, restrictive elements, energy

conversions in the ecosystem, population ecology and community ecology principles, plant

entomology.

BTEC 513 Introduction to Bioinformatics (3 0 0) 3

Biological sequence (DNA, RNA, protein) analysis: alignment, scoring matrices, sequence

similarity and distance, motif search; molecular structure prediction: RNA secondary structure

prediction, protein folding, protein threading, homology modeling; functional genomics and

proteomics: microarray data analysis, transcriptomics, SNP and exon array analysis, high-

throughput protein profiling; pathway analysis: network modeling, graph theory, biochemical

and metabolic pathway simulations; bioinformatic tools: introduction to principles, concepts

and uses of online biological databases and software tools used in the analysis of biological

data.

BTEC 514 Cancer Genetics (3 0 0) 3

Cell proliferation and molecular mechanism, cell cycle and its regulation, oncogenes and

tumor suppressors, diagnostics and therapy. Viral, chemical and physical agents that cause

cancer, tumor types, comparison of embryonic and neoblastic cells, molecular and metabolic

properties of cancer cells, and recent developments in cancer biology.

BTEC 516 Introduction to Nanobiotechnology (3 0 0) 3

This course will cover the biotechnology and biomedicine applications of nanotechnology

world. The methods used for nanotechnology and nanofabrication, medical and

biotechnological applications, future of nanobiotechnology, and its use in diagnostics,

nanofabrication, carbon nanotubes will be covered in addition to molecular production

methods, nano-molecular interactions, molecular transport, self-assembly process, hybrid

species through addition of nanomaterials to biological molecules, nanopower, nano-stroll,

manipulation and control at the nano scale, nano robots and machines, and other recent

applications in the field.

BTEC 517 Immunobiology (3 0 0) 3

Natural and acquired immunity, immunity through transplanted cells, activation and

differentiation of B-lymphocytes, the structure and function of an antibody molecule, antigen-

antibody interactions, differentiation mechanis monoclonal antibodies, the lymphoid system,

MHC restriction, activation and differentiation of the T-lymphocytes, immune tolerance,

immune diseases, sensitivity, fever and allergy, vaccines, autoimmunity, immune deficiencies

and AIDS.

BTEC 519 Microbiological Aspects of Food Systems (3 0 0) 3

National and international impacts of heightened concerns on food safety policy and

regulations affecting the food chain from production to consumption; Physical, metabolic and

genetic characteristics of microorganisms that mediate food fermentations, spoilage or

foodborne illness; Ecology of foods and effects on foodborne microorganisms (fermentative,

spoilage and pathogenic); Microbial injury; Interactions of fermentative microorganisms with

spoilage and/or pathogenic species; The basis for experimental techniques for examining

phenotypic or genetic characteristics of fermentative or pathogenic microorganisms;

Molecular and immunological methods for detecting and identifying foodborne

microorganisms

BTEC 528 Processing of bioactive extracts from natural materials (3 0 0) 3

Bioactive phytochemicals from natural sources: phenolic compounds and polyphenols, major

and minor lipid components, essential oils; their processing, characterization, and

determination of bioactivity. Extraction techniques for their processing: distillation, solvent

extraction, supercritical carbon dioxide extraction, pressurized liquid extraction.

BTEC 532 Drug Delivery Systems and Instruments (3 0 0) 3

Topics in this lecture includes intorduction to drug delivery systems, design of drug delivery

systems, targeted drug delivery systems, polymers etc used in the deisgn of these delivery

systems, transport and pharmacokinetics of drugs, various drug release mechanisms,

pharmaceutical drug delivery systems, and clinical applications.

BTEC 533 Advanced Biomaterials (3 0 0) 3

Properties of materials; Classes of materials used in medicine; Host reactions to biomaterials

and their evaluation; Biological testing of biomaterials; Degradation of materials in the

biological environment; Application of Materials in Medicine, Biology and Artificial Organs

and Biomaterials in Tissue Engineering

BTEC 534 Transgenics and Gene Therapy (3 0 0) 3

Transgenics and animal cloning, biotechnology, transgenic applications in agricultural and

pharmaceutical industries, basic gene therapy techniques, viral vectors and virotherapy, gene

therapy in neurological and immune system disorders and sample cases, cancer gene therapy

and technical problems, human cloning and ethical issues

BTEC 535 Mammalian Tissue Engineering (3 0 0) 3

Introduction to Tissue Engineering; Types and organization of cells, Cellular processes and

Cell-ECM interaction; Cell and Tissue Culture, Bioreactors; Gene expression, Cell

determination; Growth Factors (Cell differentiation); Biomaterials I (Properties, Surface

modifications); Biomaterials II (Biodegradable Polymers); Cell-Biomaterial Interactions

BTEC 537 Dosage in Proteins and Peptides (3 0 0) 3

Design of dosage format in proteins and peptides I: introduction of proteins and peptides,

physical and chemical stability, properties of preformulation and formulation, commercial

preparates and controls, EFB design of dosage format in proteins and peptides II: oral,

parenteral, rectal, nasal, dermal and ocular dosage types, pharmacokinetic properties,

absorption, enzymatic problems, in vivo stability, prodrug approach.

BTEC 538 Nutrigenomics (3 0 0) 3

The effects of diet on molecular physiology, diet-gene and cancer-diet interactions and

complex diseases, individual genetic variations and dietary response, metabolic syndromes,

functional food and nutriceuticals, functional nutrigenomics, transcriptomics and proteomics,

recent advances and applications in nutrigenomics

BTEC 539 Protein Chemistry (3 0 0) 3

Theory and techniques of quantitative analysis of biologically important macromolecules;

thermodynamic and kinetic principles underlying these separation techniques; introduction to

protein structure and function; protein folding and chaperones; protein stability and turnover;

proteasome and protein degradation; ubiquitination and sumoylation; enzyme kinetics and

action; protein-protein interactions; DNA replication; DNA recombination; transcription and

translation.

BTEC 550 Methods in Scientific Research (0 0 3) 3

Article reading and writing, project preparation and presentation, bioethics, biosafety,

statistical methods, use of scientific software specific to the area of research.

BTEC 555 Biostatistics (1 0 4) 3

Fundamentals of biostatistics, various statistical tests (Mann-Whitney, Wilcoxon, Friedman

etc.), ANOVA, Evaluation of high throughput data, Correlation analysis, Basices of

experimental design for biological systems, Power analysis, Statistical methods in sequence

analysis, sampling methods, regression analysis, model based statistical optimization

BTEC 582 Selected Topics: Signal Transduction Pathways (3 0 0) 3

Cell-to-cell communication and signaling mechanisms; signals and receptors, adaptor

proteins, kinase and phosphatases, G protein signaling cascades, small GTP-binding proteins,

phosphatidyl inositol signaling mechanisms- calcium signaling, signaling scaffolds and

signaling between cascades, examples from signaling mechanisms such as Wnt, Notch, BMP

etc; the role of signaling mechanisms in development and disease

BTEC 584 Selected Topics: Adult Neurogenesis (3 0 0) 3

Neural stem cells, neuronal development, neurogenesis in adult olfactory system, adult

hippocampal neurogenesis, neurogenic and non-neurogenic zones, neurogenesis research

methods, regulation and function of neurogenesis, applications of neurogenesis in medicine

BTEC 585 Selected Topics: Microbial Metabolism (3 0 0) 3

Metabolic reactions of microorganisms; microbial energy metabolism (I): glycolysis and TCA

cycle, microbial energy metabolism (II): respiration, fermentation, regulation of microbail

metabolism, nitrogen metabolism, reduction of organic compounds, synthesis of cellular

products and constituents, metabolic engineering and evolutionary engineering

BTEC 586 Selected Topics: Applications of Biostatistics for Research

(3 0 0) 3

Defining appropriate statistical methods for biological and genetics research studies,

hypothesis testing, the inner dynamics of given statistical methods for understanding their

logic, input and output, ANOVA, the difference between the applications of paired and

unpaired t-tests, and other statistical analysis methods such as Kruskal Wallis statistic,

Spearman rank correlation, Wilcoxon signed rank test, Log-rank test, Chi-square test for

analysis of contingency tables, and survival analysis.

BTEC 590 Graduate Seminar NC

Seminars given by faculty members or guest speakers on recent developments in the areas of

genetics, molecular biology, bioengineering, bioinformatics and similar topics, with the

ultimate purpose of expanding the students’ horizons in these areas and on how to make a

presentation in conferences and meetings.

BTEC 600 Thesis in MSc NC

BOLOGNA AND BIOTECHNOLOGY MSc PROGRAM LEARNING OUTCOMES COURSES

PP001 LO001.

Advanced level knowledge of mathematics, statistics, and bioengineering.

BTEC501, BTEC510, BTEC600, BTEC503, BTEC504, BTEC505, BTEC507, BTEC509, BTEC512, BTEC513, BTEC516, BTEC519, BTEC527, BTEC528, BTEC532, BTEC533, BTEC535, BTEC536, BTEC537, BTEC550, BTEC586

PP002 LO002. The ability of designing biological systems, analysis or process in order to meet up with the desired requirements/products.

BTEC510, BTEC504, BTEC506, BTEC513, BTEC516, BTEC527, BTEC528, BTEC532, BTEC533, BTEC534, BTEC537, BTEC550

PP003 LO003. The ability of identification and describing the engineering problems in biotechnology and bioengineering and proposing solution by making use of most up-to-date techniques and instruments.

BTEC510, BTEC550, BTEC502, BTEC504, BTEC507, BTEC509, BTEC513, BTEC527, BTEC532, BTEC537, BTEC539, BTEC585, BTEC582, BTEC586

PP004 LO004. The ability of working efficiently in interdisciplinary teams and being definitive in decision making process by taking responsibilities.

BTEC510, BTEC509, BTEC513, BTEC516, BTEC533, BTEC535, BTEC586

PP005 LO005. The ability of developing efficient communicating skills in the field of biotechnology and presenting oneself efficiently in social and scientific arena/platforms.

BTEC550, BTEC600

PP006 LO006. The ability to have occupational ethics and social responsibilities, intellectual conscious in areas of professional conversations, declarations, and applications.

BTEC501, BTEC550, BTEC590, BTEC600, BTEC502, BTEC505, BTEC506, BTEC512, BTEC514, BTEC515, BTEC518, BTEC534, BTEC536, BTEC538, BTEC584,

PP007 LO007. The ability of perceiving occupational ethics and their implications on the society at legal and economic level.

BTEC550, BTEC504, BTEC511, BTEC513, BTEC516, BTEC527, BTEC528, BTEC532,

BTEC533, BTEC534, BTEC535, BTEC586

PP008 LO008.

The ability of retaining the necessity of lifelong education, learning, and improvement and gain the skills to achieve this.

BTEC501, BTEC503, BTEC505, BTEC506, BTEC507, BTEC512, BTEC513, BTEC516, BTEC517, BTEC534, BTEC535, BTEC536, BTEC539, BTEC550, BTEC585

PP009 LO009.

The ability of perceiving the impact of bioengineering, genetics, and biotechnology products and solutions at the environmental, global and social levels.

BTEC501, BTEC550, BTEC590, BTEC600, BTEC502, BTEC505, BTEC506, BTEC512, BTEC514, BTEC515, BTEC518, BTEC534, BTEC536, BTEC538, BTEC584,

PP010 LO010 The ability to express oneself in English orally and in writing at global platform.

BTEC550, BTEC590, BTEC600

PROGRAM PROFICIENCY

PP001: Equipped with advanced level theoretical and practical knowledge and skills in mathematical, scientific, and engineering (especially in bioengineering) fields, which are required in academic or industrial life.

PP002: Provides efficient solution with scientific methods and analytical techniques to the questions and issues, by having the theoretical and practical fundamental biotechnology and molecular biological knowledge and the skills to design and operate the experiments related to the genetics and bioengineering.

PP003: Equipped with skills in the collection, analysis, and interpretation of experiment/investigation/ research results and/or data in the filed of Biotechnology using classical methods (i.e. classical genetics calculations) and as well as computerized technology (i.e. bioinformatics tools).

PP004: Participates in decision-making process by taking role in planning and time management with analytical thinking ability and literature mining by accessing to the databases and other information sources, as an individual or as a member of interdisciplinary team collaborations in studies in biotechnology fields

PP005:. Equipped with skills in presenting scientific studies in the field of biotechnology systematically and clearly at national and international platforms.

PP006: The ability to have clear communication skills, in oral and written forms, on current topics of biotechonology using information and communication technology, and to involve in teamwork and interdisciplinary studies by developing responsible, innovative, self-confident and competitive personal skills.

PP007: Provides consciousness about the impact of bioengineering and biotechnology at the global and social levels, and produce and announce novel and innovative solutions (that can improve international competitiveness) to the problems in the field through projects and events organizations.

PP008: Critically evaluates the gained knowledge and skills in biotechnology field by closely following the advances in science and technology and sustains a professional progress in the light of lifelong education, learning, self-improvement notions.

PP009: Possesses the awareness of occupational ethics and social responsibilities, states declarations and applications convenient to social and cultural values, avoid any kind of statement or activity of endangering the environmental and human health, and self-concious about the legal issues surrounding the biotechnological applications.

PP010: The ability to use written and oral English in national and international publications according to the B2 level of the Common European Framework of Reference for Language.

COURSE INFORMATON

Course Title Code Semester T+U Hour

Credits ECTS

FUNDEMENTALS OF

BIOTECHNOLOGY BTEC 501

1-2 3 + 0 3 10

Prerequisites NONE

Language of Instruction

English

Course Level MSc

Course Type Compulsory

Course Coordinator

Assoc.Prof.Dr. Fatma Neşe Kök

Instructors Assoc.Prof.Dr. Fatma Neşe Kök

Assistants NONE

Internship NONE

Goals To understand the importance of biomaterials in Medicine and provide background information about the usage area of biomaterials

Content

Basis of fermentation technology; fundamentals of enzyme engineering; purification of biomolecules; classification of bioreactors; utilization of genetically modified microorganisms; transgenic plants and animals; environmental biotechnology; medical biotechnology; sustainability

Course Learning Outcomes Program Learning

Outcomes

Teaching Methods

Assessment Methods

1) Learns about the different areas of biotechnology

1,4,8,9 1,2 A,C

2) Learns fermentation technology, types of bioreactors and their applications

1 1,2 A

3) Learns the usage of different organisms and cells in the production

1 1,2 A

4) Understands the effect of protein 1,7,8 1,2 A,C

engineering and recombinant DNA technology on biotechnology

Teaching Methods:

1: Lecture, 2: Question-Answer, 3: Laboratory, 4: Case-study

Assessment Methods:

A: Testing, B: Laboratory, C: Homework, D: Project

COURSE CONTENT

Week Topics Study Materials

1 Introduction; Biotechnology as an interdisciplinary area Textbook and Add.

Sources

2 Fermentation technology and bioreactors-1 Textbook

3 Fermentation technology and bioreactors-2 Textbook

4 Purification of biomolecules Textbook

5 Industrial enzymes Textbook and Add.

Sources

6 Protein engineering Textbook and Add.

Sources

7 Sustainability Textbook and Add.

Sources

8 Midterm Textbook

9 Environmental biotechnology Textbook and Add.

Sources

10 Transgenic plats and animals Textbook

11 Medical biotechnology-1 Textbook and Add.

Sources

12 Medical biotechnology-2 Textbook and Add.

Sources

13 Presentations Add. Sources

14 Presentations Add. Sources

RECOMMENDED SOURCES

Textbook

Introduction to Biotechnology, 2nd edition, William J. Thieman and Michael A. Palladino, Pearson Int. Ed., 2009 Introduction to Biotechnology, W. J. Thieman ve M. A. Palladino, Benjamin Cummings; 2008, ISBN-10: 0321491459

Additional Resources Recent papers

MATERIAL SHARING

Documents Lecture notes are given to students

Assignments Presentations from recent papers will be prepared

Exams 1 Midterm, 1 Project Presentation and 1 Final

ASSESSMENT

IN-TERM STUDIES NUMBER PERCENTAGE

Mid-terms 1 50

Assignment 1 50

Total 100

CONTRIBUTION OF FINAL EXAMINATION TO OVERALL GRADE

40

CONTRIBUTION OF IN-TERM STUDIES TO OVERALL GRADE

60

Total 100

COURSE CATEGORY Expertise

COURSE'S CONTRIBUTION TO PROGRAM

No Program Learning Outcomes

Contribution Level

1 2 3 4 5

1 Advanced level knowledge of mathematics, statistics, and bioengineering.

X

2 The ability of designing biological systems, analysis or process in order to meet up with the desired requirements/products.

X

3

The ability of identification and describing the engineering problems in biotechnology and bioengineering and proposing solution by making use of most up-to-date techniques and instruments.

4 The ability of working efficiently in interdisciplinary teams and being definitive in decision making process by taking responsibilities.

X

5 The ability of developing efficient communicating skills in the field of biotechnology and presenting oneself efficiently in social and scientific arena/platforms.

6 The ability to have occupational ethics and social responsibilities, intellectual conscious in areas of professional conversations, declarations, and applications.

7 The ability of perceiving occupational ethics and their implications on the society at legal and economic level.

X

8 The ability of retaining the necessity of lifelong education, learning, and improvement and gain the skills to achieve this.

X

9 The ability of perceiving the impact of bioengineering, genetics, and biotechnology products and solutions at the environmental, global and social levels.

X

10 The ability to express oneself in English orally and in writing at global platform.

ECTS ALLOCATED BASED ON STUDENT WORKLOAD BY THE COURSE DESCRIPTION

Activities Quantity Duration (Hour)

Total Workload

(Hour)

Course Duration (Excluding the exam weeks: 14x Total course hours)

14 3 42

Hours for off-the-classroom study (Pre-study, practice)

14 8 112

Mid-term examination 1 15 15

Laboratory - - -

Homework 1 40 40

Project - - -

Final examination 1 30 30

Total Work Load 239

Total Work Load / 25 (h) 9.56

ECTS Credit of the Course 10

COURSE INFORMATON


Credits ECTS

PHARMACEUTICAL AND MEDICAL BIOTECHNOLOGY

BTEC 504

1-2 3 + 0 3 8

Prerequisites NONE


English

Course Level MSc and PhD Degrees

Course Type Elective

Course Coordinator

Prof. Dr.Recep Serdar Alpan

Instructors Prof. Dr.Recep Serdar Alpan Prof. Dr. Ece Genç

Assistants NONE

Internship NONE

Goals

To understand theoretical background of the application of biotechnology techniques and applications on therapeutic products, gene therapy, gene application techniques, tissue engineering, antibody engineering, monoclonal antibodies, vaccines, sera and pharmaceutical applications.

Content

Introduction to Medical Biotechnology; Protein isolation and expression technics in Medical Biotechnology; Biotechnology in Pharmaceutical Production; Tissue Engineering; Monoclonal antibodies and cellular targeted immunologic therapeutic applications; Drug development with Recombinant DNA Technology; Gene Therapy Applications in Medicine siRNA, Micro-RNA Drugs; Recombinant Vaccines; Drugs that reverse Drug Resistance


Outcomes

Teaching Methods

Assessment Methods

1) Understands theoretical background of the application of biotechnology techniques and applications on therapeutic products

2,4,9 1,2 A,C,D

2) Learns types of cells used in Tissue Engineering and Recombinant technology

2,3,4,7 1,2 A,C,D

3) Learns Gene Therapy and effect on ethics

2,3,4,7 1,2 A,C,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to Medical Biotechnology Textbook and

Current Literature

2 Protein isolation and expression technics in Medical Biotechnology

Textbook and Current Literature

3 Biotechnology in Pharmaceutical Production Textbook and

Current Literature

4 Tissue Engineering Textbook and

Current Literature

5 Monoclonal antibodies and cellular targeted immunologic therapeutic applications


6 Drug development with Recombinant DNA Technology I


7 Drug development with Recombinant DNA Technology II


8 Mid-term Textbook and

Current Literature

9 Gene Therapy Applications in Medicine I Textbook and

Current Literature

10 Gene Therapy Applications in Medicine I Textbook and

Current Literature

11 siRNA, Micro-RNA Drugs Textbook and

Current Literature

12 Recombinant Vaccines I Textbook and

Current Literature

13 Recombinant Vaccines II Textbook and

Current Literature

14 Drugs that reverse Drug Resistance Textbook and

Current Literature

RECOMMENDED SOURCES

Textbook Pongracz & Keen, Medical Biotechnology, Churchill Livingston, Elsevier

Additional Resources Current Literatures about Medical Biotechnolgy

MATERIAL SHARING


Assignments Project assignment sheet containing project subjects and directions about how to prepare presentation is given to students


ASSESSMENT


Mid-terms 1 50

Term Project 1 50

Total 100


40


60

Total 100

COURSE CATEGORY Field Courses


No Program Learning Outcomes Contribution

Level

1 2 3 4 5


2

The ability of designing biological systems, analysis or process in order to meet up with the desired requirements/products.

X

3


X

4

The ability of working efficiently in interdisciplinary teams and being definitive in decision making process by taking responsibilities.

X

5

The ability of developing efficient communicating skills in the field of biotechnology and presenting oneself efficiently in social and scientific arena/platforms.

6

The ability to have occupational ethics and social responsibilities, intellectual conscious in areas of professional conversations, declarations, and applications.


X



X




Total Workload

(Hour)


14 3 42

Hours for off-the-classroom study (Pre-study, 12 9 108

practice)


Laboratory - - -

Homework - - -

Project 1 30 30


Total Work Load 186



COURSE INFORMATON

Course Title Code Semester T+U Hour Credits ECTS

MICROBIOLOGY BTEC 505 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Assist Prof. Dr. May Korachi

Instructors Assist Prof. Dr. May Korachi

Assistants NONE

Internship NONE

Goals

This course integrates an introduction to microbiology with an emphasis on the important skills of: 1) critical thinking; 2) scientific writing; and 3) public presentation. This course seeks to provide students with an understanding of important scientific concepts, an ability to think critically, and an understanding of the importance of microbiology to society in general. Additionally, this course seeks to provide an appreciation of the importance of the natural world.The study of the taxonomy, morphology, and physiology of microorganisms, emphasizing: 1) their relation to medicine, industry, agriculture and use in biotechnology

Content

Although the specific focus is on microorganisms, the course

incorporates a thorough review of important subjects (e.g.,

cellular respiration, enzyme activity, basic genetics, use of

microbes in genetic study and biotechnology). Microbes used

in genetic studies, for industrial purposes, and for medical

research.


Outcomes

Teaching Methods

Assessment Methods

1) Develops a sufficient background for those students who wish to study more advanced topics related to microbes

5,8,9 1,2 A,C,D

2) Provides familiarity with basic microbes in medicine, food and agriculture

5,8,9,10 1,2 A,C,D

3) Provides an understanding of the role of microbes in disease transmission and prevention

5,8,9,10 1,2 A,C,D

4) Aids the development of the ability to think scientifically and to evaluate information critically through case studies and presentations.

4,5,8,9,10 1,2,4 A,C,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Anaerobic, aerobic and microaerophilic microorganisms Textbook

2 Microbes in food and dairy Textbook

3 Microbes in agriculture Textbook

4 Oral microbes Textbook

5 Medical microbes in disease Textbook

6 Microbial diversity and Extremophiles

Textbook

7 Environmental Microbial Technology

Textbook

8 Environmental Microbial Technology

Textbook

9 Midterm Textbook

10 Bioprocess Engineering and Technology

Textbook

11 Recombinant DNA Technology Textbook

12 Enzyme Technology Textbook

13 Fermentation Technology Textbook

14 Recent trends in Virology and microbiology Textbook

RECOMMENDED SOURCES

Textbook Microbiology. L.M. Prescott, J.P. Harley, and D.A. Klein. Fifth edition. WCB/McGraw-Hill Press, Boston, MA 2002.

Additional Resources Lecture slides and handouts

MATERIAL SHARING


Assignments Case studies and group assignments with presentations.

Exams 1 Midterm, 1 case studyhomework & presentation and 1 Final

ASSESSMENT


Mid-terms 1 50

Assignment (case study) 1 50

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5



3


4


X

5


X

6




X


X


X



Total Workload

(Hour)


14 3 42


14 4 56


Laboratory - - -

Homework 2 20 40

Project (case study) 1 40 40


Total Work Load 189



COURSE INFORMATON


PLANT BIOTECHNOLOGY BTEC 506 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Asst.Prof.Dr. Andrew Harvey

Instructors Asst.Prof.Dr. Andrew Harvey

Assistants NONE

Internship NONE

Goals To understand the basic principles involved in

Content

Plant physiology, growth control and hormones, plant tissue engineering techniques, protoplast cultures, somatic embryogenesis, transformation and regeneration techniques, plant genetics and A. thaliana modification, transgenic seed studies, improvement of seed production and quality, improvement of biomass, plant pathogens and improvement of pathogen resistance, improvement of cold and drought resistance, plant reactors in the production of proteins, antigens and antibodies.


Outcomes

Teaching Methods

Assessment Methods

1) Understands the basic concepts of plant genetics and inheritance.

1,8 1,2 A,C

2) Understands basic plant biology and physiology and their application in plant tissue culture

1,8 1,2 A,C

3) Interprets and explains plant DNA vector construction and the methods and goals of plant transformation.

1,4 1,2 A,C

4) Explains and evaluates the analysis of transgenic plants.

1,4,7 1,2 A,C

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to Genetic Modification of Plants Textbook

2 Flavr Savr Tomatoes Textbook

3 Bt Gene Technology; Roundup Ready Technology Textbook

4 Golden Rice Technology Textbook

5 Midterm 1 Textbook

6 Functional Genomics Technologies I Textbook

7 Functional Genomics Technologies II Textbook

8 Abiotic Stress Resistance Textbook

9 Food Industry Technologies Textbook

10 Assignment week Textbook

11 Plant Cell Wall Technologies I Textbook

12 Plant Cell Wall Technologies II Textbook

13 Plant Cell Walls and Nutrition Textbook

14 Biofuels Technology Textbook

RECOMMENDED SOURCES

Textbook “Plant Biotechnology: The genetic manipulation of plants” 2nd Ed., Slater A., Scott N.W., Fowler M.R., Oxford University Press

Additional Resources Any recent textbook on advanced plant biotechnology will be of use.

MATERIAL SHARING


Assignments Report/essay on a current/emerging plant biotechnology topic.


ASSESSMENT


Mid-terms 1 50

Assignment 1 15

Term Project 1 35

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


X

2


3


4


X

5


6 The ability to have occupational ethics and social

responsibilities, intellectual conscious in areas of professional conversations, declarations, and applications.


X


X





Total Workload

(Hour)


14 3 42


14 6 84


Laboratory - - -

Homework 1 20 20

Project 1 30 30


Total Work Load 185



COURSE INFORMATON

Course Title Code Semester L+P Hour Credits ECTS

ADVANCED BIOCHEMISTRY BTEC 507 3 3 + 0 3 8

Prerequisites NONE


English

Course Level MS or PhD


Course Coordinator

Prof. Dr. Mustafa Çulha

Instructors Prof. Dr. Mustafa Çulha

Assistants NONE

Internship NONE

Goals This course is designed to help the students understand the concepts and importance of biochemistry and the fundamental biochemical processes behind living processes.

Content

The life of molecules, structure of carbohydrates and their function, lipids, proteins and nucleic acids, flow of genetic information, enzymes and enzyme kinetics, membrane structure, dynamics and function, introduction of bioenergetics, laws of thermodynamics, ATP and energy, cellular metabolism and fermentation, glycolysis, TCA cycle, oxidative phosphorylation, photosynthesis, amino acid metabolism, nucleic acid metabolism, fatty acid metabolism.


Outcomes

Teaching Methods

Assessment Methods

1) Understand the structure of carbohydrates and their function, lipids, proteins and nucleic acids, flow of genetic information, ,

1,2,4 1,2 A,C

2) Understands enzymes and enzyme kinetics, membrane structure, dynamics and function, introduction of bioenergetics, laws of thermodynamics

1,2,4 1,2 A,C

3) Understands ATP and energy, cellular metabolism and fermentation, glycolysis,

1,2,4 1,2 A,C

TCA cycle, oxidative phosphorylation, photosynthesis, amino acid metabolism, nucleic acid metabolism, fatty acid metabolism

Teaching Methods:


Assessment Methods:


COURSE CONTENT

Week Topics Study

Materials

1 The life of molecules, structure of carbohydrates and their function, and fermentation,

Textbook

2 Lipids, proteins Textbook

3 Nucleic acids Textbook

4 Flow of genetic information Textbook

5 Enzymes and enzyme kinetics, Textbook

6 Membrane structure dynamics and function,

Textbook

7 MIDTERM EXAM I Textbook

8 Introduction of bioenergetics, Textbook

9 Laws of thermodynamics, Textbook

10 Glycolysis, TCA cycle Textbook

11 Oxidative phosphorylation Textbook

12 Photosynthesis Textbook

13 Amino acid metabolism Textbook

14 MIDTERM EXAM II Textbook

15 Nucleic acid metabolism Textbook

16 Fatty acid metabolism Textbook

RECOMMENDED SOURCES

Textbook Biochemistry, Matthews, Van Holde, Ahern, 4th Ed. (International Edition) or similar

Additional Resources Literature

MATERIAL SHARING

Documents Lecture notes are emailed to students as pdf.

Assignments

Exams 2 midterms and 1 final.

ASSESSMENT


Mid-terms 2 55

Assignment 1 45

Total 100


45


55

Total 100




Contribution Level

1 2 3 4 5

1 Advanced level knowledge of mathematics, science, and bioengineering.

X

2

The ability of identification and describing the engineering problems in genetics and bioengineering and proposing solution by making use of most up-to-date techniques and instruments.

X

3

To have the ability of the implementation in genetics and bioengineering topics, designing experiments independently, performing experiments, collecting data, analysis of the data and interpretation of the results.

4 The ability of designing a biological system, operation, and process by making use of modern techniques in order to meet up with the desired requirements/products.

X


6 The ability of producing new, original, and innovative proposals and projects by inquiring investigative, productive, and enterprising capability.

7 The awareness in social, legal, and economical topics with consciousness in professional and ethical responsibilities.

8 The ability of communicating in contemporary and present oneself efficiently in national and international social and scientific arena/platforms.





Total Workload

(Hour)


14 3 42


14 8 112


Laboratory - - -

Homework 4 5 20

Project - - -


Total Work Load 183

Total Work Load / 25 (h) 7,32


COURSE INFORMATON


Credits ECTS

BIOTECHNOLOGY LABORATORY PROJECTS

BTEC 510

1-2 1 + 0 3 10

Prerequisites NONE


English

Course Level MSc

Course Type Core Course

Course Coordinator

Supervisor of candidate

Instructors Supervisor of candidate

Assistants NONE

Internship NONE

Goals To gain experience about current research areas in Biotechonolgy, Genetics and Bioengineering

Content Experiment topics are given by supervisor of candidate that is already enrolled one of the programme and selected research topic.


Outcomes

Teaching Methods

Assessment Methods

Gains experience about in Biotechnology and Genetic applications .

3,4,8 1,2 B

Teaching Methods:

1: Lecture, 2: Question-Answer, 3: Discussion, 4: Case-study

Assessment Methods:


COURSE CONTENT


1-14 Candidate performs experiment in Laboratory. Latest published

article

RECOMMENDED SOURCES

Textbook -

Additional Resources Latest published articles

MATERIAL SHARING

Documents Reference article is given to candiate by its supervisor

Assignments -

Exams -

ASSESSMENT


Laboratory 1 100

Total 100


-


100

Total 100

COURSE CATEGORY Expertise Courses



Contribution Level

1 2 3 4 5



3


X


X





X





Total Workload

(Hour)


14 1 14


14 1 14

Mid-term examination - - -

Experiment 14 15 210

Homework - - -

Project - - -

Final examination - - -

Total Work Load 238



COURSE INFORMATON


COMPARATIVE PHYSIOLOGY

BTEC511 2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Prof.Dr.Bayram Yılmaz

Instructors Prof.Dr.BayramYılmaz

Assistants NONE

Internship NONE

Goals To understand the basic physiological principles of the human body and the differences between physiological needs of different organisms.

Content

Introduction to physiology and homeostasis concept; General characteristics of blood and its elements; Cardiovascular system and microcirculation; Respiratory system (Ventilation and perfusion) and Gase exchange (Transportation of O2 and CO2); Renal functions, glomerular filtration, reabsorption and secretion; Acid-base balance in the body; Body Fluids and mechanisms of transportation in the cell membrane level; Membrane action potential and functions of neurons; Muscle physiology (skeletal and smooth); Cardiac cycle and regulation of blood pressure; Blood clotting and hemostasis; Endocrine system


Outcomes

Teaching Methods

Assessment Methods

1) Understands the homeostasis concept

2,8,10 1,2 A,C,D

2) Learns physiological systems 2,8,10 1,2 A,C,D

3) Understands the regulation of physiological systems

2,8 1,2 A,C,D

4) Understands the membrane action potential and its physiological importance

2,4 1,2 A,C,D

Teaching Methods:


Assessment Methods:

A: Testing, B: Experiment, C: Homework, D: Project

COURSE CONTENT


1 Introduction and Explanation of Presentation Topics Textbook

2 Definiton of physiology and homeostasis Textbook

3 General aspects of blood and erythrocytes Textbook

4 Cardiovascular system and microcirculation Textbook

5 Respiratory system (Ventilation and perfusion) and Gase exchange (Transportation of O2 and CO2)

Textbook

6 Renal functions, glomerular filtration, reabsorption and secretion

Textbook

7 Acid-base balance in the body Textbook

8 Body Fluids and mechanisms of transportation in the cell membrane level

Textbook

9 Midterm Textbook

10 Membrane action potential and functions of neurons Textbook

11 Muscle physiology (skeletal and smooth) Textbook

12 Cardiac cycle and regulation of blood pressure Textbook

13 Blood clotting and hemostasis Textbook

14 Endocrine system Textbook

RECOMMENDED SOURCES

Textbook Textbook of medical physiology by Arthur C. Guyton, John E. Hall.

Additional Resources Human Physiology by Stuart Ira Fox.

MATERIAL SHARING

Documents Lecture and presentation notes are given to students

Assignments

Exams 1 Midterm, 2 Presentations (for each student), 1 Final

ASSESSMENT


Mid-terms 1 50

Assignment 2 50

Total 100


40


60

Total 60




Contribution Level

1 2 3 4 5

1 Advanced level knowledge of mathematics, statistics, and bioengineering


X

3



X





X



X



Total Workload

(Hour)


14 2 28


14 8 112


Experiment - - -

Homework 2 20 40

Project - - -


Total Work Load 188



COURSE INFORMATON


ECOLOGY BTEC 512 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Prof. Dr. Metin TURAN

Instructors Prof. Dr. Metin TURAN

Assistants NONE

Internship NONE

Goals

Concepts and theories of ecology (habitat, population, ecosystem) to learn ensure the protection of ecology, sustainable sense, to determine the difference between natural ecosystems and agro-eco system, environmental factors (climatic, edaphic factors, biological and topographical factors) is aimed to teach the impact on the balance.

Content

Physical and biological interactions of organisms with their environment, ecosystem concepts, organisms, environmental requirements, limiting factors, energy cycles, ecosystems, biogeochemical cycles, population and community ecology principles of ecology, plant entomology


Outcomes

Teaching Methods

Assessment Methods

1) Learns the basic principles of ecology and ecological factors

2 1,2 A,C, D

2) Learns the definition of ecology, learning of ecosystem and concepts.

4 1,2, A,B, D

3) Understands the physical and biological interactions of organisms with their environment ecology

3 1,2 A,C,D

4) Understands the biogeochemical cycles of ecosystems with energy cycles

5, 9 1,2,3 A,B, D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction and presentation issues Textbook

2 Definition of ecology, the basic principles Textbook

3 Concepts of ecosystem Textbook

4 Physical and biological interactions of organisms with their environment

Textbook

5 Determination of the mutual effects of the organisms with the environment (application)

Laboratory

6 Environmental requirements of organisms Textbook

7 The limiting factors for life and a variety of vital activity of organisms

Textbook

8 Energy cycles, ecosystems, biogeochemical cycles Textbook

9 Midterm

10 Biogeochemical cycles (application) Greenhouse

11 Ecology of population Textbook

12 Ecology of community Textbook

13 Plant entomology Textbook

14 Presentations

RECOMMENDED SOURCES

Textbook Prof. Dr. Metin TURAN, 2006. Agriculturae of Ecological textbook.

Additional Resources

Prof. Dr. Nicolas Lampkin, 1990. Organic FarmingPublished by Farming Pres Books and Videos Wharfedale Road Ipswich IP1 4LG, United Kingdom

Prof. Dr. Sücaatin KIRIMHAN, 2005. Organik Tarım Sistemleri ve Çevre 1. Baskı 350.s Tuhan Kitabevi, Ofset Matbaacılık Tesisleri, Ankara

Hürriyet Taşbaşlı, Bilal Zeytin, 2003. Organik Tarımın Temel İlkeleri Tarım ve Köy İşleri Banklığı, Araştıram

ve Planlama Koordinasyon Kurulu Başkanlığı Anakara.

Prasanthrajan, M. and Mahendran, Agrotech, P.P., 2008. A Text Book on Ecology and Environmental Science.

Basu, R.N., and Naya Udyog, 2004. A Compendium of Terms in Ecology and Environment.

Pandey, B.N. and Jyoti, M.K. 2012. Ecology and Environment.

Bhatia, S.C. 2008. Ecology and Sustainable Development, Vols. I and II Atlantic.

Purohit, S.S. and Rajiv Ranjan, 2003. Ecology, Environment and Pollution, Agrobios.

MATERIAL SHARING



Exams 1 Midterm, 1 homework, 1 Project Presentation and 1 Final

ASSESSMENT


Mid-terms 1 50

Laboratory 1 10

Assignment 2 20

Term Project 1 20

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


2


X

3


X

4


X

5


x

6





x




Total Workload

(Hour)


14 3 42


14 5 70


Laboratory 1 5 5

Homework 2 20 40

Project 1 40 40


Total Work Load 211



COURSE INFORMATON


Credits ECTS

INTRODUCTION TO BIOINFORMATICS

BTEC 513 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Prof.Dr.Işıl Aksan Kurnaz

Instructors Yard. Doç. Işıl Aksan Kurnaz

Assistants NONE

Internship NONE

Goals To obtain an advance understanding of signal transduction pathways and their impact on normal development and disease

Content

Biological sequence (DNA, RNA, protein) analysis: alignment,

scoring matrices, sequence similarity and distance, motif

search; molecular structure prediction: RNA secondary

structure prediction, protein folding, protein threading,

homology modeling; functional genomics and proteomics:

microarray data analysis, transcriptomics, SNP and exon

array analysis, high-throughput protein profiling; pathway

analysis: network modeling, graph theory, biochemical and

metabolic pathway simulations; bioinformatic tools:

introduction to principles, concepts and uses of online

biological databases and software tools used in the analysis

of biological data.

Course Learning Outcomes Program Teaching Assessment

Learning Outcomes

Methods Methods

1) Awareness about basic principles of bioinformatics

1,3,5,8,9,10 1,3,4 A,C

2) Skills to employ basic bioinformatic tools

1,3,5,8,9,10 1,3,4 A,C

3) Awareness about applications of bioinformatics

1,3,5,8,9,10 1,3,4 A,C

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to the course and short history Lecture materials and handouts

2

Biological sequence analysis, alignment tools, basic alignment algorithms (Needleman-Wunsch, Smith-Waterman, etc)

Lecture materials and handouts

3 scoring matrices, sequence similarity and distance, motif search


4 molecular structure prediction: RNA secondary structure prediction


5 molecular structure prediction: protein folding, protein threading,


6 molecular structure prediction: homology modeling Lecture materials and handouts

7 functional genomics and proteomics: microarray data analysis, transcriptomics


8 SNP and exon array analysis, Lecture materials and handouts

9 high-throughput protein profiling Lecture materials and handouts

10 pathway analysis: network modeling, graph theory, biochemical and metabolic pathway simulations


11

bioinformatic tools: introduction to principles, concepts and uses of online biological databases and software tools used in the analysis of biological data (e.g. MINT, DIP, HPRD, GRID, MIPS, KEGG).


12 Student presentations Lecture materials and handouts

13 Student presentations Lecture materials

and handouts

14 FINAL EXAM Lecture materials and handouts

RECOMMENDED SOURCES

Textbook Research articles; lecture notes; powerpoint presentations

Additional Resources none

MATERIAL SHARING

Documents Exam results are posted on the Exam Results Board, and exam papers are shown to all those students who want to see them.

Assignments

In the second half of the semester, students are each assigned a different contemporary research article to be presented during class. They are also expected tp write a review article following the format of Trends in Genetics.

Exams Student Presentations and 1 Final

ASSESSMENT


Assignment 1 50

Term Project 1 50

Total 100


50


50

Total 100

COURSE CATEGORY Expertise/Field Courses



Contribution Level

1 2 3 4 5


X

2


3


X

4


5


X

6




X


X


X



Total Workload

(Hour)


14 4 56


14 4 56


Laboratory - - -

Homework 2 20 40

Project 1 40 40


Total Work Load 207



COURSE INFORMATON


CANCER GENETICS BTEC 514 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Assoc.Prof.Dr. Dilek Telci

Instructors Assoc.Prof.Dr. Dilek Telci

Assistants NONE

Internship NONE

Goals

To ensure that students gain knowledge about the development and biology of cancer with specific emphasis on molecular pathways involved in cancer cell transformation. To discuss the targeted cancer therapies developed for each molecular pathway.

Content

Introduction to molecular biology of cancer with special emphasis

placed on its etiology, development, genetics, treatments and

preventions. Nature of the disease; epidemiology; causes of cancer

(heredity, chemical, radiation, viral and environmental factors);

genetic changes in cancer; oncogenes and tumor suppressor

genes; apoptosis and metastasis. Viral vectors that cause cancer

development.


Outcomes

Teaching Methods

Assessment Methods

1) Comprehends the basic principles of cancer transformation and formation.

8,9 1,2 A,C

2) Understands the importance of oncegenes and tumor supressor genes in cancer development with a mechanistic approach

8 1,2,3 A,C

3) Understand the importance of apoptotic and survival signaling cascades

8 1,2,3 A,C

in cancer development.

4) Comprehend the role of metastasis and stem cells in cancer development

8 1,2,3 A,C

5) Learns the cancer immunolgy and the causative microbial agents.

8,9 1,2 A,C

6) Explains the use of classic traditional chemotherapeutic versus targeted drug therapy in cancer treament.

7,8,10 1,2 A,C

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to cancer biology; the life of a cancer Textbook

2 DNA structure and stability; mutations vs. repair Textbook

3 Regulation of gene expression Textbook

4 Growth factor signalling and oncogenes, Cell Cycle Textbook

5 Growth Inhibition and tumour suppressor genes Textbook

6 Assignment subject submission; discussion on essay writing

Textbook

7 Midterm 1 Textbook

8 Apoptosis Textbook

9 Paper Discussion (students will talk about the progress in their written assignments)

Textbook

10 Stem cells and differentiation Textbook

11 Metastasis Textbook

12 Infections and inflammation Textbook

13 The cancer industry: drug development and clinical trial design

Textbook

14 The cancer industry: drug development and clinical trial design

Textbook

RECOMMENDED SOURCES

Textbook Molecular Biology of the Cell, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,

Peter Walter, 5th edition.

Additional Resources Review Papers

MATERIAL SHARING

Documents Lecture notes

Assignments Subject of homework must be chosen by the student

Exams 1 Midterm and 1 Final

ASSESSMENT


Mid-terms 1 40

Assignment 1 60

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5



3 The ability of identification and describing the engineering problems in biotechnology and bioengineering and proposing solution by making use of most up-to-date

techniques and instruments.

4


5


6



X


X


X


X



Total Workload

(Hour)


14 3 42


14 7 98


Laboratory - - -

Homework 1 45 45

Project - - -


Total Work Load 191

Total Work Load / 25 (h) 7,64

COURSE INFORMATON


Credits ECTS

INTRODUCTION TO

NANOBIOTECHNOLOGY BTEC 516

1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Prof.Dr.Mustafa Çulha

Instructors Prof.Dr.Mustafa Çulha

Assistants NONE

Internship NONE

Goals Students taking this course realize the importance of nanotechnology and nanobiotechnology concept and the impact of this emerging field on human life.

Content

This course will cover the biotechnology and biomedicine applications of nanotechnology world. The methods used for nanotechnology and nanofabrication, medical and biotechnological applications, future of nanobiotechnology, and its use in diagnostics, nanofabrication, and nanostructures such as gold, silver and carbon nanotubes will be covered in addition to molecular production methods, nano-molecular interactions, molecular transport, self-assembly process, hybrid species through addition of nanomaterials to biological molecules, nanopower, nano-stroll, manipulation and control at the nano scale, nano robots and machines, and other recent applications in the field.


Outcomes

Teaching Methods

Assessment Methods

1) Understands classes and usage area of biomaterials used in medicine

1,2,3,4 1,2 A,C

2) Learns properties of biomaterials 1,2,3,4 1,2 A,C

3) Explains host reactions to biomaterials and their evaluation

1,2,3,4 1,2 A,C

4) Understands Tissue Engineering 1,2,3,4 1,2 A,C

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Nanotechnology/nanobiotechnology concept and a brief history

Various Sources

2 What are the limits to smallness? How small can we make?

Various Sources

3 Some Nanoparticles/Structures: Gold, silver, carbon nanotubes, nanoshells, etc.

Various Sources

4 Nanoparticle Preparation/Production and Chracterization Techniques

Various Sources

5 Imaging Techniques for Nanoworld: SEM, TEM, SPMs:AFM, STM, etc

Various Sources

6 Components of a Living Cell Various Sources

7 Cellular Imaging and Biomedical Imaging Various Sources

8 Nanomedicine Various Sources

9 Nanobiosensing Various Sources

10 Assembly of Nanoparticles on Surfaces and into High Ordered Structures

Various Sources

11 Biological nanomechines Various Sources

12 Behavior of nanomaterials in living systems Various Sources

13 Student Presentations Various Sources

14 Student Presentations Various Sources

RECOMMENDED SOURCES

Textbook Literature and any text book related to the subsjects

Additional Resources Literature

MATERIAL SHARING



Exams 1 Midterm, 1 Presentation, 1 Term Paper and 1 Final

ASSESSMENT


Mid-terms 1 40

Assignment 2 60

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


X

2


X

3


X


X









Total Workload

(Hour)


14 3 42


14 5 70


Laboratory - - -

Homework 3 20 60

Project - - -


Total Work Load 183



COURSE INFORMATON


IMMUNOBIOLOGY BTEC 517 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Asisst. Prof. Dr. May Korachi

Instructors Asisst. Prof. Dr. May Korachi

Assistants NONE

Internship NONE

Goals

To gain a basic understanding of the cells of the immune system in both the innate and adaptive immune system. The process of inflammation and how cells interact during disease.

Content

Natural and acquired immunity, immunity through

transplanted cells, activation and differentiation of B-

lymphocytes, the structure and function of an antibody

molecule, antigen-antibody interactions, differentiation

mechanis monoclonal antibodies, the lymphoid system, MHC

restriction, activation and differentiation of the T-lymphocytes,

immune tolerance, immune diseases, sensitivity, fever and

allergy, vaccines, autoimmunity, immune deficiencies and

AIDS.


Outcomes

Teaching Methods

Assessment Methods

1) Develops a sufficient background in the immunology for those students who wish to study more advanced topics

5,8,9,10 1,2 A,C,D

2) Provides familiarity with basic cells of the immune system

5,8,9,10 1,2 A,C,D

3) Provides an understanding of the role of the innate and adaptive immune system

5,8,9,10 1,2 A,C,D

4) Gains an understanding of the inflammatory pathway and role of major cytokines.

5,8,9,10 1,2,4 A,C,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to Immunology Slides and handouts

2 The mechanical and chemical defenses of the immune system

Slides and handouts

3 The innate immune system Slides and handouts

4 B cells and antibodies Slides and handouts

5 Miderm I Case study I Slides and handouts

6 The magic of antigen presentation Slides and handouts

7 T cells and cytokines Slides and handouts

8 Lymphoid organs and lymphocyte trafficking Slides and handouts

9 Midterm II Slides and handouts

10 Immunopathology Slides and handouts

11 Cancer and the immune system Slides and handouts

12 Latest research in İmmunogenetics Slides and handouts

13 Important cytokines and pathways presentations Slides and handouts

14 Important cytokines and pathways presentations Slides and handouts

RECOMMENDED SOURCES

Textbook Janeway et al. Immunobiology The Immune System in Health and Disease, 6th edition, 2005.

Additional Resources Lecture slides and handouts

MATERIAL SHARING


Assignments Case studies and group assignments with presentations.

Exams 1 Midterm, 1 case studyhomework & presentation and 1 Final

ASSESSMENT


Mid-terms 1 50

Assignment (case study) 1 50

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


2


3


4


5


X

6




X


X


X



Total Workload

(Hour)


14 3 42


14 4 56


Laboratory - - -

Homework 2 20 40

Project (case study) 1 40 40


Total Work Load 189



COURSE INFORMATON


Credits ECTS

MICROBIOLOGICAL ASPECTS OF FOOD SYSTEMS

BTEC 519

1-2 3 + 0 3 8

Prerequisites NONE


English

Course Level MSc


Course Coordinator

Assoc. Prof. F. Yeşim Ekinci

Instructors Assoc. Prof. F. Yeşim Ekinci

Assistants NONE

Internship NONE

Goals

To provide graduate students in Food Technology, Animal and Food Industries, Microbiology, Biotecnology and related programs with increased understanding of microorganisms that are responsible for foodborne illness, food spoilage and food fermentations and how they impact public health and the food industry

Content

Discuss national and international impacts of heightened food safety concerns on policy and regulations affecting the food chain from production to consumption ;physical, metabolic and genetic characteristics of microorganisms that mediate food fermentations, spoilage or foodborne illness; Apply information gained to real-life problems


Outcomes

Teaching Methods

Assessment Methods

1) Ensures that the graduate students gain basic food microbiology background at a theoretical level and undestand role of microorganisms in food systems

3,9 1,2,4 A,D

2) Understands role of fermentation microorganisms in Food Industry

3,9 1,2,4 A,D

3) Identifies microbial problems during food processing and to determine critical control points, and to solve them using the most up-to-date techniques and tools

3,9 1,2,4 A,D

4) Identifies food spoilage and pathogens organisms and to solve the problem using the most up-to-date techniques and tools

3,9 1,2,4 A,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction: review of syllabus, course objectives, semester assignments. Food safety issues/legislation

Lecture Notes

2 Review of intrinsic and extrinsic parameters; injury, preservation, inactivation

Lecture Notes

3

Gram-negative foodborne pathogens – issues, syndromes, control, prevention: Escherichia coli O157:H7 and characteristics that make it a successful pathogen; Salmonella, Campylobacter, foodborne vibrios

Lecture Notes

4 Risk assessment; production food safety issues Lecture Notes

5 Gram-positive foodborne pathogens - syndromes,

control, prevention: Listeria monocytogenes, clostridia, etc.

Lecture Notes

6 Non-bacterial foodborne illnesses: Viruses (hepatitis A, Norwalk, rotaviruses); fungal foodborne illness; parasitic: cryptosporidiosis, cyclosporiasis, amebiasis, giardiasis

Lecture Notes

7 Other foodborne illnesses: scombroid, ciguatera, paralytic shellfish poisoning, bovine spongiform encephalopathy (nv Creutzsfeldt-Jakobs disease and prions).

Lecture Notes

8 Rapid detection or identification methodology including immunological and molecular methods

Lecture Notes

9 Other food safety issues: Agricultural biotechnology food products; food allergies

Lecture Notes

10

Control and inactivation technology: Chemical, thermal,

irradiation, hydrostatic pressure, ozonation, high intensity

electric fields, other methods.

Lecture Notes

11 Review of food fermentation principles, fermentative bacteria in foods (emphasizing lactic acid bacteria and propionibacteria)

Lecture Notes

12

Food fermentations: Cucumber fermentation, cheese manufacture or other dairy fermentations, sourdough bread. Traditional fermented products. Starter cultures. Food fermentation problems and solutions. Biological control of foodborne pathogens and spoilage organisms

Lecture Notes

13 Bacteriocins of lactic and propionic acid bacteria; discovery, purification, genetics, applications.

Lecture Notes

14 Current and future food microbiology issues Lecture Notes

RECOMMENDED SOURCES

Textbook Lecture notes

Additional Resources Readings from web sites, Federal Register, and current literature

MATERIAL SHARING

Documents Readings from web sites, Federal Register, and current literature

Assignments

Exams

ASSESSMENT


Mid-terms 2 40

Assignenment (Presentations) 5 60

Total 100


30


70

Total 100




Contribution Level

1 2 3 4 5



3


x







x




Total Workload

(Hour)


14 3 42


14 4 56


Laboratory - - -

Homework (Presentation) 5 10 50

Project - - -


Total Work Load 190



COURSE INFORMATON


GENE EXPRESSION BTEC 521 1-2 3 + 0 3 8

Prerequisites None


English



Course Coordinator

Assoc. Prof. Dr. Ahmet ARMAN

Instructors Assoc. Prof. Dr. Ahmet ARMAN

Assistants NONE

Internship NONE

Goals

To understand genetic code, transcription, traslation and

role of RNA polymerase and transcription factors on

regulation of gene expression in Prokaryotic systems

Content

Genetic code, Transcription ans translation in Prokaryotes

and example of gene regulation in prokaryotes

Course Learning Outcomes

Program Learning Outcome

s

Teaching Methods

Assessment Methods

1) Understands Genetic code 1,8,10 1,2 A,C,D

2) Learns transcription and

translation in prokaryotes 1,2,4,8,10 1,2 A,C,D

3) Learns function of RNA

polymerase and trasncription

factors in gene regulation in

prokaryotic system

1,8,10 1,2 A,C,D

4) Learns gene regulation in

different systems in prokaryotes 1,8,10 1,2 A,C,D

Teaching 1: Lecture, 2: Question-Answer, 3: Laboratory, 4: Case-study

Methods:

Assessment Methods:


COURSE CONTENT


1 Genetic code Textbook

2 Transcription in Prokaryotes Textbook

3 Protein Synthesis in prokaryotes Textbook

4 Mutations Textbook

5 Suppressor mutations in prokaryotes Textbook

6 RNA polmerase in Gene regulations Textbook

7 Transcription factors Textbook

8 Promoter analysis in prokaryotes Textbook

9 Midterm Textbook

10 DNA-Protein interactions Textbook

11 Tecniques for determining of gene expression Textbook

12 Example of gene regulation in prokaryotes Textbook

13 Presentation Textbook

14 Presentation

15 Presentation

16 Presentation

RECOMMENDED SOURCES

Textbook Gene Expression and Regulation, Jun MA


MATERIAL SHARING


Assignments Project assignment sheet containing project subjects and

http://www.slic2.wsu.edu:82/hurlbert/micro101/pages/Chap1.html

directions about how to prepare presentation is given to students


ASSESSMENT


Mid-terms 1 50

Term Project 1 50

Total 100


40


60

Total 100



No Program Learning Outcomes Contribution Level

1 2 3 4 5


x


X

3



X

5


6 The ability to have occupational ethics and social responsibilities, intellectual conscious in areas of professional conversations, declarations, and

applications.



X

9

The ability of perceiving the impact of bioengineering, genetics, and biotechnology products and solutions at the environmental, global and social levels.


X



Total Workload

(Hour)


14 4 56


14 4 56


Laboratory - - -

Homework 2 20 40

Project 1 40 40


Total Work Load 203



COURSE INFORMATON


Credits ECTS

PROCESSING OF BIOACTIVE COMPOUNDS FROM NATURAL MATERIALS

BTEC 528

1-2 3 + 0 3 8

Prerequisites NONE


English

Course Level MSc Degrees


Course Coordinator

Assist. Prof. Özlem Güçlü Üstündağ

Instructors Assist. Prof. Özlem Güçlü Üstündağ

Assistants NONE

Internship NONE

Goals

To provide knowledge on the bioactive compounds in natural materials: their chemistry, characterization, and biological activity To enable understanding of the fundamentals of the extraction techniques used in the processing of bioactive compounds To develop an understanding of the application of these techniques to the processing of bioactive compounds focusing on process design

Content

Bioactive phytochemicals from natural sources: phenolic compounds and polyphenols, major and minor lipid components, essential oils; their processing, characterization, and determination of bioactivity. Extraction techniques for their processing: distillation, solvent extraction, supercritical carbon dioxide extraction, pressurized liquid extraction.


Outcomes

Teaching Methods

Assessment Methods

1) Learns on bioactive compounds in natural materials

1 1,2 A,C

2) Learns on the extraction techniques used in their processing

1,2,3 1,2 A,C

3) Gets ability to select the suitable extraction technique(s) considering the process objectives, target compounds and available resources

1,3,5,10 1,2 A,C

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to bioactive compounds and health effects Lecture notes,

required readings

2 Chemistry of bioactive compounds: phenolics, lipid components, essential oils

Lecture notes, required readings

3 Chemistry of bioactive compounds: phenolics, lipid components, essential oils


4 Chemistry of bioactive compounds: phenolics, lipid components, essential oils Presentations


5 Characterization and biological activity Midterm 1


6 Characterization and biological activity Presentations


7 Characterization and biological activity Extraction techniques and their fundamentals


8 Extraction techniques and their fundamentals Lecture notes,

required readings

9 Extraction techniques and their fundamentals Lecture notes,

required readings

10 Processing of bioactive compounds: Applications and process design Midterm 2


11 Processing of bioactive compounds: Applications and process design, Presentations


12 Processing of bioactive compounds: Applications and process design, Presentations


13 Processing of bioactive compounds: Applications and process design


14 Processing of bioactive compounds: Applications and process design


RECOMMENDED SOURCES

Textbook Lecture notes prepared by the instructor.

Additional Resources Selected readings from current literature as required reading material for the course

MATERIAL SHARING

Documents Lecture notes, required reading material

Assignments Information and instructions on presentations and assignments are given to students

Exams Midterms (2) Presentation (1) Final (1)

ASSESSMENT


Midterms 2 30

Assignments 7 70

Total 100


30


70

Total 100




Contribution Level

1 2 3 4 5


X

2 The ability of designing biological systems, analysis or X

process in order to meet up with the desired requirements/products.

3


X

4


5


X

6






X



Total Workload

(Hour)


14 3 42


14 4 56


Assignments 7 5 35

Final 1 30 30

Total Work Load 193

COURSE INFORMATON


Credits ECTS

DRUG DELIVERY SYSTEMS AND INSTRUMENTS

BTEC 532

1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Assist.Prof.Dr. Gülengül DUMAN

Instructors Assist.Prof.Dr. Gülengül DUMAN

Assistants NONE

Internship NONE

Goals The aim of this course is to gain students the carriers of novel ‘Drug Delivery Systems (DDS)’.

Content

Introduction to materials and biomaterials as carriers of novel and modern ‘Drug Delivery Systems ‘(DDS). Discuss to design of New Drug Delivery System: Micro-particle system, Composition of Liposomes, Transdermal Drug Delivery Systems, Iontophoresis Applications. Peptide Protein Gene and Drug Delivery Systems. Infusion Pumps and Implantable Drug Delivery systems. Inhaler Drug Delivery Systems. Micro-needle and Microchip Technology.


Outcomes

Teaching Methods

Assessment Methods

1) Learns biomaterials as carriers of novel ‘Drug Delivery Systems (DDS)’.

1,2,8,10 1,2,4 A,C,D

2) Learns inhaler Devices and Infusion Pumps Micro-particles, Liposomes, Micro-needle and Microchip technology. Implants and inserts. Protein Drug Delivery

1,2,4,10 1,2,4

A,C,D

3) Learns to use theoretical and applied information to understand the

1,2,4,5,10 1,2,4 A,C,D

applications of DDS.

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to ‘New Drug Delivery Systems’ benefits, mechanism and materials

Textbook, Course notes, Videos

2 Classification of ‘ New Drug Delivery Systems’ Textbook, Course notes, Videos

3 Ocular Drug Delivery systems Textbook, Course notes, Videos

4 Transdermal Drug Delivery Systems Textbook, Course notes, Videos

5 Iontophoresis Applications


6 Micro-needle Technology, Microchip application Textbook, Course notes, Videos

7 Oral Administration Novel systems: Osmotic Pump etc


8 Implants: Gliadel Wafer, Duros etc. Textbook, Course notes, Videos

9 Vaginal Administration Route: Intrauterine devices Textbook, Course notes, Videos

10 Nano Technology, Textbook, Course notes, Videos

11 Liposomes, Stealth Liposomes, Textbook, Course notes, Videos

12 Infusion Pumps Textbook, Course notes, Videos

13 Biotechnological Products Overview Textbook, Course notes, Videos

14 Protein Drug Delivery Textbook, Course notes, Videos

RECOMMENDED SOURCES

Textbook Ansel, H.C., Pharmaceutical dosage forms and drug delivery systems. Lea and Febiger, Philadelphia

Additional Resources Video, Notes

MATERIAL SHARING



Exams 1 Project Presentation and 1 Final

ASSESSMENT


Mid-terms - -

Laboratory - -

Assignment 1 30

Term Project 1 30

Final 1 40

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


X


X

3 The ability of identification and describing the engineering problems in biotechnology and bioengineering and

proposing solution by making use of most up-to-date techniques and instruments.


X


X




X



X



Total Workload

(Hour)


14 4 56


14 4 56


Laboratory - - -

Homework 1 20 30

Project 1 20 30


Total Work Load 192



COURSE INFORMATON


ADVANCED BIOMATERIALS BTEC 533 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Prof.Dr.Gamze Torun Köse

Instructors Prof.Dr.Gamze Torun Köse

Assistants NONE

Internship NONE

Goals To understand the importance of biomaterials in Medicine and provide background information about the usage area of biomaterials

Content

Mechanical and Surface Properties of materials, Surface characterization, Classes of materials used in medicine, Host reactions to biomaterials and their evaluation, Tissue Engineering


Outcomes

Teaching Methods

Assessment Methods

1) Understands classes and usage area of biomaterials used in medicine

2,4 1,2 A,D

2) Learns properties of biomaterials 2,4 1,2 A,D

3) Explains Host reactions to biomaterials and their evaluation

2 1,2 A,D

4) Understands Tissue Engineering 1,2,4,7 1,2 A,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT



2 Properties of biomaterials I Textbook

3 Properties of biomaterials II Textbook

4 Classes of materials used in medicine I Textbook

5 Classes of materials used in medicine II Textbook

6 Host reactions to biomaterials and their evaluation Textbook

7 Biological testing of biomaterials Textbook

8 Degradation of biomaterials in the biological environment Textbook

9 Application of materials in Medicine, Biology and Artificial Organs

Textbook

10 MIDTERM Textbook

11 Tissue Engineering Textbook

12 Presentations Textbook



RECOMMENDED SOURCES

Textbook Biomaterials Science – Ratner, Hoffman, Schoen, Lemons

Additional Resources Biomaterials: Principles and Applications – J.B.Park and J.D.Bronzino

MATERIAL SHARING




ASSESSMENT


Mid-terms 1 50

Term Project 1 50

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


X

2


X

3


4


X

5


6 The ability to have occupational ethics and social responsibilities, intellectual conscious in areas of

professional conversations, declarations, and applications.


X






Total Workload

(Hour)


14 3 42


14 4 56


Laboratory - - -

Homework 2 20 40

Project 1 40 40


Total Work Load 189



COURSE INFORMATON


TRANSGENICS AND GENE THERAPY

BTEC 534 1-2 3 + 0 3 8

Prerequisites NONE


English

Course Level MSc Degree


Course Coordinator

Assist. Prof. Dr. Hüseyin Çimen

Instructors Assist. Prof. Dr. Hüseyin Çimen

Assistants NONE

Internship NONE

Goals To gain knowledge about gene therapy applications by understanding transgene technology and to ensure the discussin of related ethical issues.

Content

Transgenics and animal cloning, biotechnology, transgenic applications in agricultural and pharmaceutical industries, basic gene therapy techniques, viral vectors and virotherapy, gene therapy in neurological and immune system disorders and sample cases, cancer gene therapy and technical problems, human cloning and ethical issues


Outcomes

Teaching Methods

Assessment Methods

1) Learns the recombinant DNA technology and its applications.

2, 8 1, 2 A, D

2) Perceives the gene cloning and its application in gene therapy

2, 8 1, 2 A, D

3) Learns and discusses the production of transgenic organism and related ethical issues

2, 6, 8, 9 1, 2, 3 A, D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction and determination of presentation topics

2 Recombinant DNA technology Textbook

3 Transgenics and use in biotechnology Textbook

4 Gene cloning in animals Textbook

5 Gene cloning in plants Textbook

6 Genetically modified organisms I Textbook

7 Genetically modified organisms II Textbook

8 Genetically modified organisms: Discussion Textbook

9 Midterm Textbook

10 Gene therapy and application examples Textbook

11 Ethics in gene therapy: Discussion Textbook




RECOMMENDED SOURCES

Textbook Anthony J.F. Griffiths v.d., An Introduction to Genetic Analysis, 7th ed., W. H. Freeman and Company


MATERIAL SHARING


Assignments


ASSESSMENT


Mid-terms 1 50

Term Project 1 50

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


2


X

3


4


5


6


X



X


X




Total Workload

(Hour)


14 3 42


14 6 84


Laboratory - - -

Homework - - -

Project 1 40 40


Total Work Load 186



COURSE INFORMATON


Credits ECTS

MAMMALIAN TISSUE ENGINEERING

BTEC 535

1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Prof.Dr.Gamze Torun Köse

Instructors Prof.Dr.Gamze Torun Köse

Assistants NONE

Internship NONE

Goals

To understand the basic principles involved in development and fabrication of artificial cellular materials for the replacement of defective tissue

Content

Introduction to Tissue Engineering; Types and organization of cells, Cellular processes and Cell-ECM interaction; Cell and Tissue Culture, Bioreactors; Gene expression, Cell determination; Growth Factors (Cell differentiation); Biomaterials I (Properties, Surface modifications); Biomaterials II (Biodegradable Polymers); Cell-Biomaterial Interactions


Outcomes

Teaching Methods

Assessment Methods

1) Understands biomaterials used in Tissue Engineering

2,4 1,2 A,C,D

2) Learns types of cells used in Tissue Engineering

2,4 1,2 A,C,D

3) Understands the effects of growth factors

2,4 1,2 A,C,D

4) Understands industrial aspects of Tissue Engineering

1,2,4,7 1,2 A,C,D


Methods:

Assessment Methods:


COURSE CONTENT



2 Organization of cells Textbook

3 Cellular processes and Cell-ECM interaction Textbook

4 Gene expression, cell determination and differentiation Textbook

5 Cell and tissue culture Textbook

6 Tailoring of biomaterials for tissue engineering Textbook

7 Growth factors Textbook

8 Integration with host tissue Textbook

9 Midterm Textbook

10 Scaling up for ex vivo cultivation Textbook

11 Industrial aspects of tissue engineering Textbook




RECOMMENDED SOURCES

Textbook Lanza R.P., Langer R., Chick W.L., Principles of Tissue Engineering, Academic Press


Yaszemski M.J. etal., Tissue Engineering and Novel Delivery Systems, Marcel Dekker Shi D., Biomaterials and Tissue Engineering, Springer

MATERIAL SHARING




ASSESSMENT


Mid-terms 1 50

Term Project 1 50

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


X

2


X

3


4


X

5


6



X






Total Workload

(Hour)


14 3 42


14 4 56


Laboratory - - -

Homework 2 20 40

Project 1 40 40


Total Work Load 189



COURSE INFORMATON


Regenerative Biology and Biomedical Applications

BTEC 536

1-2 3 + 0 3 8

Prerequisites None


English



Course Coordinator

Assist. Prof. Dr. Fatih Kocabaş

Instructors Assist. Prof. Dr. Fatih Kocabaş

Assistants NONE

Internship NONE

Goals An introduction to stem cell technologies

Content

The course will cover topics in the basic biology of embryonic,

fetal and adult stem cells; the tools, methods and

experimental protocols needed to study and characterize

stem cells; as well as the application of stem cells to treat

specific human diseases. The course is intended for master’s

degree students in the Biotechnology Program of Yeditepe

University. Students are expected to acquire knowledge and

understanding of the basic biology of embryonic and tissue

specific stem cells, the potential application of stem cell for

the treatment of human diseases and different experimental

approaches used to study and characterize stem cells.


Outcomes

Teaching Methods

Assessment Methods

Students define the basic principles of regeneration

2,3 1,2 A,D

Students interpret on the effect of age, extend of injury, tissue type, species difference on the extent of regeneration

4,8 1,2 A,D

Student explain the methods of analysis of extend of regeneration and cell types involved

2,3 1,2 A,D

Student describe different animals models of use in regeneration

3 1,2,3 A,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 An Overview of stem cell biology Class notes/text

book

2 Overview of basic and translational research of stem cells

Class notes/text book

3 Human embryonic stem cells Class notes/text

book

4 Generation of pluripotent stem cells Class notes/text

book

5 Origin of primordial germ cells and embryonic germ cells, Trophoblast stem cells, Extraembryonic endoderm stem cells.


6 Neural stem cells, Hematopoietic stem cells, retinal stem cells, hair follicle stem cells


7 Vascular progenitors, skeletal muscle stem cells, cardiac stem cells, kidney stem cells


8 Mesenchymal stem cells Class notes/text

book

9 Stem cells in the liver, pancreas, intestine, and teeth Class notes/text

book

10 Tissue engineering with mesenchymal stem cells,Therapeutic potential of neural stem cells


11 Preclinical studies using stem cells to treat heart disease, β-cell replacement therapy, Embryonic stem cells in tissue engineering


12

Stem cells for the treatment of muscular dystrophy, Regeneration of epidermis from adult keratinocyte stem cells, Application of stem cells to bone regeneration


13 Stem cell gene therapy, Viral and non-viral vectors, Genetically corrected stem cells and their use for gene therapy


14 Ethics of stem cell research Class notes/text

book

RECOMMENDED SOURCES

Textbook Essentials of Stem Cell Biology, Robert Lanza and Anthony Altala, 2nd Edition.

Additional Resources Class notes, internet resources

MATERIAL SHARING

Documents Lecture notes are shared with the students

Assignments 1 term paper with presentation

Exams 1 midterm and 1 final

ASSESSMENT


Mid-terms 1 60

Laboratory

Assignment

Project 1 40

Total 100


50


50

Total 100




Contribution Level

1 2 3 4 5


2


X

3


X

4


5


X

6


X


X


X


X




Total Workload

(Hour)


14 3 52


14 6 84


Laboratory

Homework

Project 1 20 20


Total Work Load 181

COURSE INFORMATON


Credits ECTS

PROTEIN AND PEPTIDE DOSAGE FORMS

BTEC 537

1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Assist. Prof. Dr. Gülengül DUMAN

Instructors Assist. Prof. Dr. Gülengül DUMAN

Assistants NONE

Internship NONE

Goals To understand the basic principles involved in amino acids, peptide and proteins for the development of peptide and proteins drug delivery sytems

Content

Introduction to basic structural principles of amino acids, peptide and proteins and their functions; Protein stability and peptide and proteins drug delivery sytems using different polymers or biomaterials.


Outcomes

Teaching Methods

Assessment Methods

1) Understands basic structural principles of amino acids, peptide and proteins

1,2 1,2,4 A,C,D

2) Learns functions of amino acids, peptide and proteins and their functions;

1,2,4 1,2,4 A,C,D

3) Explains the stability and formulation of Protein stability and peptide and proteins drug delivery sytems

2,4,5,6 1,2,4 A,C,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT

Week Topics Study

Materials

1 Introduction to basic principles involved in amino acids, peptide and proteins


2 The basic structural principles of amino acids, peptide and proteins


3 The amino acids, peptide and proteins and their functions Textbook, Course notes, Videos

4 The stability of peptide and proteins


5 The stability of peptide and proteins


6 The proteins drug delivery systems using different polymers or biomaterials


7 The proteins drug delivery systems using different polymers or biomaterials.


8 The peptide and proteins drug delivery systems


9 The peptide and proteins drug delivery systems


10 The peptide and proteins drug delivery systems and device


11 Presentations Textbook, Course notes, Videos

12 Presentations Textbook, Course notes, Videos

13 Presentations Textbook,

Course notes, Videos

14 Presentations


RECOMMENDED SOURCES

Textbook Ansel, H.C., Pharmaceutical dosage forms and drug delivery systems. Lea and Febiger, Philadelphia

Additional Resources Carl Branden John Tooze’ Introduction to Protein Structure’ ,Garland Publishing , London UK.

MATERIAL SHARING



Exams 1 Project Presentation and 1 Final

ASSESSMENT


Assignment 1 50

Term Project 1 50

Total 100


60


40

Total 100




Contribution Level

1 2 3 4 5


X

2


X

3


4


X

5


X

6


X







Total Workload

(Hour)


14 4 56


14 4 56

Mid-term examinations - - -

Laboratory - - -

Homework 1 20 30

Project 1 20 30


Total Work Load 192



COURSE INFORMATON


NUTRIGENOMICS BTEC 538 1-2 3 + 0 3 8

Prerequisites NONE


English

Course Level MSc


Course Coordinator

Assoc. Prof. F. Yeşim Ekinci

Instructors Assoc. Prof. F. Yeşim Ekinci

Assistants NONE

Internship NONE

Goals

To provide understanding to graduate students in nutrigenomics, or nutritional genomics area which is a multidisciplinary science that combines information from genetics, nutrition, physiology, pathology, molecular biology, bioinformatics, biocomputation, sociology, ethics, and other disciplines.

Content

The effects of diet on molecular physiology, diet-gene and cancer-diet interactions and complex diseases, individual genetic variations and dietary response, metabolic syndromes, functional food and nutriceuticals, functional nutrigenomics, transcriptomics and proteomics, recent advances and applications in nutrigenomics


Outcomes

Teaching Methods

Assessment Methods

1) Understands the basics of genetics, genomics and gene regulation with relation to diet

1,7 1,2,4 A,D

2) Have good understanding of the concepts of molecular nutrition research (signals and signaling pathways, dietary sensors (nuclear receptors), organ sensing, use of animal models)

1,7 1,2,4 A,D

3) Have some understanding of the concepts of Nutrigenetics (genetic susceptibility, SNPs, polygenic (complex) diseases, "personalized" diet);

1,7 1,2,4 A,D

4) Extracts relevant data/information from internet for molecular nutrition research

1,7 1,2,4 A,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1-2

Characteristics of studies in nutrigenomics. Omic technologies. Methodological characteristics, their potential and limitations. Applications. Other useful methodologies

Lecture Notes

3 Microarrays. DNA arrays. Types and preparation. Strategies of experimental design: Hybridisation and processing. Data analysis. Other molecular arrays.

Lecture Notes

4-5 Methods of genomic study. SNPs. Nutrigenetics. Genetic screening tests. Cardiochip, lipochip. Nutritional epigenetics

Lecture Notes

6

Methods of transcriptomic study. General characteristics. Techniques to determine absolute and relative expression. Serial Analysis of Gene Expression (SAGE). Methods based on interference RNAs

Lecture Notes

7 Technical aspects of proteomics. Protein separation methods. Detection methods. Sequence identification methods. Databases

Lecture Notes

8-9

Applications of proteomics. Characteristics of studies in proteomics. Types of proteomics. Techniques for the study of differential gene expression profile. Techniques for the study of post-translational modifications. Techniques for the identification of protein interaction (test with yeast hybrids). Protein arrays.

Lecture Notes

10 Approach to metabonome study. Sample characteristics. Detection, separation and identification techniques. Data analysis. Integration and the concept of systems biology.

Lecture Notes

11-12

Therapeutic applications. Health and illness biomarkers. Characteristics of biomarkers. Analysis of predisposition to nutritional diseases. Personalised medicine. Gene correction. Gene silencing strategies. Hijack of transcription factors

Lecture Notes

13-14 Applications to foods. Functional foods. Pathogen detection. Authentication of foods. Detection of genetically modified organisms

Lecture Notes

RECOMMENDED SOURCES

Textbook Lecture notes

Additional Resources Readings from web sites, Federal Register, and current literature

MATERIAL SHARING



Exams 2 Midterms, 5 Homeworks and 1 Final

ASSESSMENT


Mid-terms 2 40

Assignenment (Presentations) 5 60

Total 100


30


70

Total 100




Contribution Level

1 2 3 4 5


x


3






x






Total Workload

(Hour)


14 3 42


14 4 56


Laboratory - - -

Homework (Presentation) 5 10 50

Project - - -


Total Work Load 190



COURSE INFORMATON


PROTEIN CHEMISTRY BTEC 539 1-2 3 + 0 3 8

Prerequisites NONE


English

Course Level MSc Degree


Course Coordinator

Assist. Prof. Dr. Hüseyin Çimen

Instructors Assist. Prof. Dr. Hüseyin Çimen

Assistants NONE

Internship NONE

Goals To gain knowledge about the synthesis of proteins and their roles in the biomolecular mechanisms, protein engineering techniques and its use in biotechnology.

Content

Theory and techniques of quantitative analysis of biologically important macromolecules; thermodynamic and kinetic principles underlying these separation techniques; introduction to protein structure and function; protein folding and chaperones; protein stability and turnover; proteasome and protein degradation; ubiquitination and sumoylation; enzyme kinetics and action; protein-protein interactions; DNA replication; DNA recombination; transcription and translation.


Outcomes

Teaching Methods

Assessment Methods

1) Learns the general principles in protein synthesis.

8 1, 2 A, D

2) Perceives the techniques used to study protein structure and function.

3, 8 1, 2 A, D

3) Learns and discusses the use of protein engineering tools in molecular medicine

3, 8 1, 2, 3 A, D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction and determination of presentation topics

2 Protein structure and function Textbook

3 Protein synthesis and kinetics Textbook

4 Protein processing and turnover Textbook

5 Protein expression in organisms Textbook

6 Protein purification Textbook

7 Protein characterization Textbook

8 Methods to determine protein structure Textbook

9 Midterm Textbook

10 Protein engineering in molecular medicine Textbook

11 Protein engineering in molecular medicine: Discussion Textbook




RECOMMENDED SOURCES

Textbook David Whitford, Proteins: Structure and Function, Wiley


MATERIAL SHARING


Assignments


ASSESSMENT


Mid-terms 1 50

Term Project 1 50

Total 100


40


60

Total 100

COURSE CATEGORY Expertise/Field Courses



Contribution Level

1 2 3 4 5


2


3


X

4


5


6 The ability to have occupational ethics and social

responsibilities, intellectual conscious in areas of professional conversations, declarations, and applications.



X





Total Workload

(Hour)


14 3 42


14 6 84


Laboratory - - -

Homework - - -

Project 1 40 40


Total Work Load 186



COURSE INFORMATON

Course Title Code Semester L+P Hour

Credits ECTS

METHODS IN SCIENTIFIC RESEARCH

BTEC 550

1-2 3 + 0 3 8

Prerequisites NONE


English


Course Type Compulsory

Course Coordinator

Asst. Prof. Mayur Tamhane

Instructors Asst. Prof. Mayur Tamhane

Assistants NONE

Internship NONE

Goals

The course trains participants with the knowledge and skills of Methods used to address Scientific Research and representation of scientific contribution towards revealing real world phenomena.

Content

Scientific Research Methodology, Elements of Scientific Research, History of Scientific Philosophy, Guidelines for Empirical Research, Pseudoscience and Authentic Science, Steps of Scientific Method – Research, Problem, Hypothesis, Experiment, Results, Discussion and Conclusion, Writing a Research Paper – Guide, Structure of Research Paper – Title, Abstract, Introduction, Methodology, Results, Discussion, Conclusion, References, Types of Research Study Design – Experimental, Observational, Qualitative, Quantitative, Opinion-based, Semi-experimental, Descriptive, Correlational Studies, Literature Review and its significance, Data Analysis - Statistical Interpretation of raw data, Grants and Research Proposal – accessing database and submission process review


Outcomes

Teaching Methods

Assessment Methods

1) Acquires the principles of Scientific Philosophy

7,8 1 A

2) Understands structure of Research Hypothesis generation and evaluation

2,6 1,2 A

3) Knows how to conduct ethical research techniques and analysis so as to contribute to scientific knowledge including educational purpose

7,9 1,2 A,C

4) Learns the process of setting up independant research programmes through grantsmanship skills

2,3 1,2,4 A,C,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT

Week Topics Study

Materials

1 Scientific Research Methodology Textbook

2 Elements of Scientific Research Textbook

3 History of Scientific Philosophy Textbook

4 Guidelines for Empirical Research Textbook

5 Pseudoscience and Authentic Science Textbook

6 Steps of Scientific Method – Research, Problem, Hypothesis, Experiment, Results, Discussion and Conclusion - I

Textbook

7 Steps of Scientific Method – Research, Problem, Hypothesis, Experiment, Results, Discussion and Conclusion - II

Textbook

8 Writing a Research Paper – Guide, Structure of Research Paper – Title, Abstract, Introduction, Methodology, Results, Discussion, Conclusion, References - I

Textbook

9 Writing a Research Paper – Guide, Structure of Research Paper – Title, Abstract, Introduction, Methodology, Results, Discussion, Conclusion, References - II

Textbook

10 Types of Research Study Design – Experimental, Observational, Qualitative, Quantitative, Opinion-based, Semi-experimental, Descriptive, Correlational Studies

Textbook

11 Literature Review and its significance Textbook

12 Data Analysis - Statistical Interpretation of raw data Textbook

13 Grants and Research Proposal – accessing database and submission process review - I

Textbook

14 Grants and Research Proposal – accessing database and Textbook

submission process review - II

15 SEMINAR PRESENTATION

16 FINAL EXAM Textbook

RECOMMENDED SOURCES

Textbook 1. How to Write a Research Paper – Year 2011 Shuttleworth M,

Experiment-Resources

Additional Resources 2. Explorable website – www.explorable.com

MATERIAL SHARING

Documents Lecture notes are emailed to students as pdf

Assignments Assignment reports are collected every other week

Exams 1 Final

ASSESSMENT


Assignment 6 20

Term Project 1 80

Total 100


50

CONTRIBUTION OF IN-TERM TRAINING TO OVERALL GRADE

50

Total 100




Contribution Level

1 2 3 4 5

1 Advanced level knowledge of mathematics, science, and bioengineering.

2

The ability of identification and describing the engineering problems in genetics and bioengineering and proposing solution by making use of most up-to-date techniques and instruments.

X

3

To have the ability of the implementation in genetics and bioengineering topics, designing experiments independently, performing experiments, collecting data, analysis of the data and interpretation of the results.

X

4 The ability of designing a biological system, operation, and process by making use of modern techniques in order to meet up with the desired requirements/products.


6 The ability of producing new, original, and innovative proposals and projects by inquiring investigative, productive, and enterprising capability.

X

7 The awareness in social, legal, and economical topics with consciousness in professional and ethical responsibilities.

X

8 The ability of communicating in contemporary and present oneself efficiently in national and international social and scientific arena/platforms.

X


X




Total Workload

(Hour)


14 3 42


14 5 70


Laboratory - - -

Homework 6 7 42

Project 1 40 40


Total Work Load 197



COURSE INFORMATON


Credits ECTS

SPECIAL TOPICS: SIGNAL TRANSDUCTION PATHWAYS

BTEC 582 (formerly offered as BTEC 522)

1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator


Instructors Prof.Dr. Işıl Aksan Kurnaz

Assistants NONE

Internship NONE

Goals To obtain an advance understanding of signal transduction pathways and their impact on normal development and disease

Content

Cell-to-cell communication and signaling mechanisms;

signals and receptors, adaptor proteins, kinase and

phosphatases, G protein signaling cascades, small GTP-

binding proteins, phosphatidyl inositol signaling mechanisms-

calcium signaling, signaling scaffolds and signaling between

cascades, examples from signaling mechanisms such as

Wnt, Notch, BMP etc; the role of signaling mechanisms in

development and disease


Outcomes

Teaching Methods

Assessment Methods

1) Understands basic types of signals, receptors and signal transduction

1,3,5,8,9,10 1,2,4 A,C

pathways

2) Appreciates the importance of signaling in normal development

1,3,5,8,9,10 1,2,4 A,C

3) Puts into context signalling and disease

1,3,5,8,9,10 1,2,4 A,C

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction to the course; cell-cell communication and signalling mechanisms


2 Signals and receptors Lecture materials and handouts

3 Adaptor proteins


4 Kinases and phosphatases; protein kinase A


5 G-protein signal cascade; small GTP-binding proteins


6 Phosphatidyl inositol signal cascades; calcium signaling


7 Lipid signals and nuclear receptors


8 Signaling Scaffolds; crosstalk between cascades Student presentations


9 Downstream effectors of signaling pathways Student presentations


10 Wnt signaling; Notch signaling Student presentations


11 BMP signaling Student presentations


12 Growth Factor signaling Student presentations


13 Signaling in development and disease Student presentations



RECOMMENDED SOURCES

Textbook Research articles; lecture notes; powerpoint presentations


MATERIAL SHARING


Assignments



ASSESSMENT


Mid-terms - -

Laboratory - -

Assignment 1 25

Project 1 25

Final 1 50

Total 100


50


50

Total 100




Contribution Level

1 2 3 4 5


X


3


X



X




X


X


X



Total Workload

(Hour)


14 4 56


14 4 56


Laboratory - - -

Homework 2 20 40

Project 1 40 40


Total Work Load 207



COURSE INFORMATON


Credits ECTS

SPECIAL TOPICS: ADULT NEUROGENESIS

BTEC 584 (formerly

offered as BTEC 524)

1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator


Instructors Prof.Dr. Işıl Aksan Kurnaz

Assistants NONE

Internship NONE

Goals To obtain an advance understanding of neurogenesis in the adults

Content

Neural stem cells, neuronal development, neurogenesis in

adult olfactory system, adult hippocampal neurogenesis,

neurogenic and non-neurogenic zones, neurogenesis

research methods, regulation and function of neurogenesis,

applications of neurogenesis in medicine


Outcomes

Teaching Methods

Assessment Methods

1) Understands adult neurogenesis, neural stem cells, regeneration

1,3,5,8,9,10 1,2,4 A,C

2) Follows recent techniques in the study of neurogenesis

1,3,5,8,9,10 1,2,4 A,C

3) Puts into context neurogenesis and medical applications

1,3,5,8,9,10 1,2,4 A,C


Methods:

Assessment Methods:


COURSE CONTENT


1 Adult Neurogenesis: Introduction Lecture materials

and handouts

2 Neural Stem Cells Lecture materials and handouts

3 Neuronal Development Lecture materials and handouts

4 Neurogenesis in the adult olfactory system


5 Adult hippocampal neurogenesis


6 Technical notes Lecture materials and handouts

7 Neurogenic and non-neurogenic regions


8 Regulation Lecture materials and handouts

9 Function Lecture materials and handouts

10 Medicine Lecture materials and handouts





RECOMMENDED SOURCES

Textbook

1. Research articles; lecture notes; powerpoint presentations; 2. Adult Neurogenesis; G. Kempermann, OUP; ISBN: 978-0-19-517971-2


MATERIAL SHARING


Assignments



ASSESSMENT


Assignment 1 50

Term Project 1 50

Total 100


50


50

Total 100




Contribution Level

1 2 3 4 5


X

2


3


X

4


5


X

6




X


X


X



Total Workload

(Hour)


14 4 56


14 4 56


Laboratory - - -

Homework 2 20 40

Project 1 40 40


Total Work Load 207

COURSE INFORMATON


MICROBIAL METABOLISM BTEC 585 1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Prof. Dr. Zeynep Petek ÇAKAR

Instructors Prof. Dr. Zeynep Petek ÇAKAR

Assistants NONE

Internship NONE

Goals

To understand the basic principles of microbial metabolism and gain insight into systems biology applications of microbial metabolism, such as metabolic engineering and evolutionary engineering

Content

Metabolic reactions of microorganisms; microbial energy

metabolism (I): glycolysis and TCA cycle, microbial energy

metabolism (II): respiration, fermentation, regulation of

microbial metabolism, nitrogen metabolism, degradation of

organic compounds, synthesis of cellular products and

constituents, metabolic engineering and evolutionary

engineering


Outcomes

Teaching Methods

Assessment Methods

1) Learns basic principles of microbial metabolism and its applications in metabolic and evolutionary engineering

1,2,3,6,7,8,9 1,2 A,D

2) Learns how to present a scientific research article on microbial metabolism

1,5,10 1,2 C,D

3) Makes a detailed literature survey on a microbial metabolism/metabolic engineering topic of interest

1,2,3,8 1,2 C,D

4) Writes a review article in a scientific format and present it in class

1,2,3,5,6,7,10 1,2 A,C,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Metabolic reactions of microorganisms Textbook

2 Microbial energy metabolism (I): Glycolysis and TCA cycle

Textbook, journal articles

3 Microbial energy metabolism (II): respiration, fermentation

Textbook, journal articles

4 Regulation of microbial metabolism Textbook, journal

articles

5 Nitrogen metabolism Textbook, journal

articles

6 Degradation of organic compounds Textbook, journal

articles

7 Synthesis of cellular constituents and products Textbook, journal

articles

8 Metabolic engineering (I) Textbook, journal

articles

9 Metabolic engineering (II) Textbook, journal

articles

10 Evolutionary engineering (I) Textbook, journal

articles

11 Evolutionary engineering (II) Textbook, journal

articles

12 Review Paper Presentations (I) Textbook, journal

articles

13 Review Paper Presentations (II) Textbook, journal

articles

14 Review Paper Presentations (III) Textbook, journal

articles

RECOMMENDED SOURCES

Textbook

Brock Biology of Microorganisms, thirteenth edition, 2011, M.T. Madigan, J.M.Martinko, Pearson

An introduction to metabolic and cellular engineering, second edition, 2012, S. Cortassa, M.A. Aon, A.A. Iglesias, J.C. Aon, D. Lloyd, World Scientific Any biochemistry textbook (e.g. by Stryer, Zubay, Lehninger etc.)

Additional Resources recent scientific research articles published in a SCI-cited biotechnology journal.

MATERIAL SHARING

Documents Lecture notes are provided to students.

Assignments

1 research article presentation in class, a review paper (written) assignment on a microbial metabolism/metabolic engineering topic of interest, presentation of that review paper in class at the end of the term.

Exams 1 midterm exam and 1 Final exam

ASSESSMENT


Mid-terms 1 25

Assignment 1 25

Term Project 1 50

Total 100


40


60

Total 100




Contribution Level

1 2 3 4 5


x

2


x

3


x

4


5


x

6


x


x


x


x


x



Total Workload

(Hour)


14 3 42


14 4 56


Laboratory - - -

Homework 1 30 30

Project 1 50 50


Total Work Load 189



COURSE INFORMATON


Credits ECTS

SELECTED TOPICS: APPLICATIONS OF BIOSTATISTICS FOR RESEARCH

BTEC 586

1-2 3 + 0 3 8

Prerequisites NONE


English



Course Coordinator

Asst. Prof. Dr. Esin Öztürk Işık

Instructors Asst. Prof. Dr. Esin Öztürk Işık

Assistants NONE

Internship NONE

Goals To understand the basic principles of biostatistics, statistical procedures for different kinds of hypothesis testing, and their applications for research in biotechnology

Content

Defining appropriate statistical methods for biological and genetics research studies, hypothesis testing, the inner dynamics of given statistical methods for understanding their logic, input and output, ANOVA, the difference between the applications of paired and unpaired t-tests, and other statistical analysis methods such as Kruskal Wallis statistic, Spearman rank correlation, Wilcoxon signed rank test, Log-rank test, Chi-square test for analysis of contingency tables, and survival analysis.


Outcomes

Teaching Methods

Assessment Methods

1) Learns about different biostatistical analysis methods

1 1,2,3 A,C

2) Solves homework questions 1 1,2,3 A,D

3) Understands ethical responsibilities of biotechnology employees in

6,7 1,2,3 A

healthcare

4) Awares of importance of biostatistics in healthcare

9 1,2,3 A,C

5) Prepares project and to make presentation

1,5,8,10 1,2,3 A,D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1 Introduction, Sampling, Experimentation, Measurement Textbook & Power

point slides

2 Descriptive Statistics Textbook & Power

point slides

3 Analysis of Variance Textbook & Power

point slides

4 t-test Textbook & Power

point slides

5 Multiple Comparisons Textbook & Power

point slides

6 Rates and Proportions (z-test, Chi-square test) Textbook & Power

point slides

7 Power and Sample Size Textbook & Power

point slides

8 Regression and Correlation Textbook & Power

point slides

9 Repeated Measures(paired t-test) Textbook & Power

point slides

10 Repeated measures (Repeated measures ANOVA) Textbook & Power

point slides

11 Nonparametric Methods Textbook & Power

point slides

12 Survival Analysis Textbook & Power

point slides

13 Project Presentations -

14 Project Presentations -

RECOMMENDED SOURCES

Textbook Primer of Biostatistics (6th ed.) By Stanton A. Glantz (McGraw-Hill)- 2005

Additional Resources -

MATERIAL SHARING

Documents Lecture notes

Assignments -

Exams -

ASSESSMENT


Mid-terms 1 40

Assignment 10 40

Term Project 1 20

Total 100


30


70

Total 100




Contribution Level

1 2 3 4 5


X

2


3


4


5


X

6


X


X


X


X


X



Total Workload

(Hour)

Course Duration (Including the exam week: 14x Total course hours)

14 3 42


14 2 28


Laboratory - - -

Homework 10 5 50


Project 1 40 40

Total Work Load 190

COURSE INFORMATON


MSc SEMINAR BTEC 590 1-2 1 + 0 1 1

Prerequisites NONE


English

Course Level MSc


Course Coordinator

Assoc.Prof.Dilek Telci

Instructors Assoc.Prof.Dilek Telci

Assistants NONE

Internship NONE

Goals To gain knowledge about current research areas in Biotechonolgy and R&D topics in Industrial biotechnology.

Content

Seminars given by faculty members or guest speakers on recent developments in the areas of genetics, molecular biology, bioengineering, bioinformatics, as well as by students on their own research topics, with the ultimate purpose of expanding the students’ horizons in these areas as well as providing them with theoretical and practical skills on how to make a presentation in conferences and meetings.


Outcomes

Teaching Methods

Assessment Methods

Gains information about current research topics in Biotechnology and learns about the recent R&D subjects in Industrial biotechnology. .

7,8,9 1,2 C

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1-14 Researchers or R&D scientist from Industrial Biotechnology are invited to give one-hour presentations.

Textbook

RECOMMENDED SOURCES

Textbook -

Additional Resources Notes taken by students in one-hour presentations given by researchers or R&D scientist from Industrial Biotechnology.

MATERIAL SHARING

Documents Notes taken by students in one-hour presentations given by researchers or R&D scientist from Industrial Biotechnology.

Assignments Studenst are asked to prepare an assigments on a presenation subject which they have found interesting.

Exams

ASSESSMENT


Assignment 1 100

Total 100


-


100

Total 100




Contribution Level

1 2 3 4 5


2


3


4


5


6



X


X


X




Total Workload

(Hour)


14 1 14


14 2 28


Experiment - - -

Homework 1 3 3

Project - - -

Final examination - - -

Total Work Load 45



COURSE INFORMATON


MSc. Thesis BTEC 600 3-4 1 + 0 0 30

Prerequisites


English

Course Level PhD


Course Coordinator

Prof. Dr. Fikrettin Şahin

Instructors Thesis advisor

Assistants NONE

Internship NONE

Goals To accomplish the new and novel study in biotechnology area in

whole perspective. To realize the necessities of the study and learn

the knowledge of the theme.

Content

To review the updated articles, interpret them, to decide the

appropriate route of study and perform the necessary experiments

to gather all data and lastly make decision and comment about

results.


Outcomes

Teaching Methods

Assessment Methods

To gain knowledge and experience via experiments and interpret the data during thesis study

1,2,3,4,5,6,7,8,9 2, 3 B, D

Teaching Methods:


Assessment Methods:


COURSE CONTENT


1-14 To use the knowledge from interpretation of experiments in thesis study

Books, Review and Research articles

RECOMMENDED SOURCES

Textbook -

Additional Resources -

MATERIAL SHARING

Documents

Assignments

Exams

ASSESSMENT


Mid-terms

Experiment 14 50

Assignment

Project 1 50

Total 100


100


0

Total 100



No Program Learning Outcomes Contribution Level

1 2 3 4 5


X


X

3


X

4


X

5


X

6


X


X


X


X


X



Total Workload

(Hour)


14 53 742


Mid-term examination

Experiment

Homework

Project


Total Work Load 745



Assesment Of Courses According To The Learning Outcomes For Biotechnology MSc Program

BTEC PO 1 PO 2 PO 3 PO 4 PO 5 PO 6 PO 7 PO 8 PO 9 PO 10

501 4 2

4

4 2 5 504

5 4 5

5

5

505

4 5

5 4 4

506 4

5

5 5 507 5 5

5

510

5 5

5 511

3

5

5

2

512

4 4 3

5 5 513 5

3

5

5 5 5

514

5 5 5 5

516 3 5 5 5 517

5

5 4 4

519

4

4 521 5 4

4

5

4

528 4 5 5

5

5

532 3 5

4 5

4

4

533 4 2

5

4 534

4

3

3 5

535 4 5

5

5 536 0 5 5 0 4 3 2 5 3 0

537 5 4

5 4 4 538 5

4

539

5

3 550

5 5

5 5 5 4

582 5

3

5

5 5 5

584 5

3

5

5 5 5

585 2 3 5

5 5 5 5 5 5

586 5

4 3 3 4 4 4

590

5 5 5 600 5 5 3 3 4 5 5 5 5 4